diff --git a/doc/Eqs/compute_dpd.jpg b/doc/Eqs/compute_dpd.jpg new file mode 100644 index 0000000000..42ed03db15 Binary files /dev/null and b/doc/Eqs/compute_dpd.jpg differ diff --git a/doc/Eqs/compute_dpd.tex b/doc/Eqs/compute_dpd.tex new file mode 100644 index 0000000000..3d4338db08 --- /dev/null +++ b/doc/Eqs/compute_dpd.tex @@ -0,0 +1,12 @@ +\documentstyle[12pt]{article} +\pagestyle{empty} +\begin{document} + +\begin{eqnarray*} + U^{cond} = \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ + U^{mech} = \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\ + U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech}) \\ + \theta_{avg} = (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\ +\end{eqnarray*} + +\end{document} diff --git a/doc/Eqs/fix_eos-cv.jpg b/doc/Eqs/fix_eos-cv.jpg new file mode 100644 index 0000000000..37eeac8e2d Binary files /dev/null and b/doc/Eqs/fix_eos-cv.jpg differ diff --git a/doc/Eqs/fix_eos-cv.tex b/doc/Eqs/fix_eos-cv.tex new file mode 100644 index 0000000000..e084bac9bc --- /dev/null +++ b/doc/Eqs/fix_eos-cv.tex @@ -0,0 +1,9 @@ +\documentstyle[12pt]{article} +\pagestyle{empty} +\begin{document} + +$$ + u_{i} = u^{mech}_{i} + u^{cond}_{i} = C_{V} \theta_{i} +$$ + +\end{document} diff --git a/doc/Eqs/pair_dpd_conservative.jpg b/doc/Eqs/pair_dpd_conservative.jpg new file mode 100644 index 0000000000..aa0006caa2 Binary files /dev/null and b/doc/Eqs/pair_dpd_conservative.jpg differ diff --git a/doc/Eqs/pair_dpd_conservative.tex b/doc/Eqs/pair_dpd_conservative.tex new file mode 100644 index 0000000000..db89b987aa --- /dev/null +++ b/doc/Eqs/pair_dpd_conservative.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} +\pagestyle{empty} +\begin{document} + +$$ +F^C = A \omega_{ij} \qquad \qquad r_{ij} < r_c +$$ + +\end{document} diff --git a/doc/Eqs/pair_dpd_omega.jpg b/doc/Eqs/pair_dpd_omega.jpg new file mode 100644 index 0000000000..fd25f00f19 Binary files /dev/null and b/doc/Eqs/pair_dpd_omega.jpg differ diff --git a/doc/Eqs/pair_dpd_omega.tex b/doc/Eqs/pair_dpd_omega.tex new file mode 100644 index 0000000000..fbd533abfa --- /dev/null +++ b/doc/Eqs/pair_dpd_omega.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} +\pagestyle{empty} +\begin{document} + +$$ + \omega_{ij} = 1 - \frac{r_{ij}}{r_{c}} +$$ + +\end{document} diff --git a/doc/Manual.html b/doc/Manual.html index e9c8d09569..eb68cfcaf1 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -135,7 +135,7 @@

LAMMPS-ICMS Documentation

-

29 Jan 2016 version

+

3 Feb 2016 version

Version info:

@@ -253,23 +253,24 @@ it gives quick access to documentation for all LAMMPS commands.

  • 4.17. USER-COLVARS package
  • 4.18. USER-CUDA package
  • 4.19. USER-DIFFRACTION package
    • -
  • 4.20. USER-DRUDE package
    • -
  • 4.21. USER-EFF package
    • -
  • 4.22. USER-FEP package
    • -
  • 4.23. USER-H5MD package
    • -
  • 4.24. USER-INTEL package
    • -
  • 4.25. USER-LB package
    • -
  • 4.26. USER-MGPT package
    • -
  • 4.27. USER-MISC package
    • -
  • 4.28. USER-MOLFILE package
    • -
  • 4.29. USER-OMP package
    • -
  • 4.30. USER-PHONON package
    • -
  • 4.31. USER-QMMM package
    • -
  • 4.32. USER-QTB package
    • -
  • 4.33. USER-REAXC package
    • -
  • 4.34. USER-SMD package
    • -
  • 4.35. USER-SMTBQ package
    • -
  • 4.36. USER-SPH package
    • +
  • 4.20. USER-DPD package
    • +
  • 4.21. USER-DRUDE package
    • +
  • 4.22. USER-EFF package
    • +
  • 4.23. USER-FEP package
    • +
  • 4.24. USER-H5MD package
    • +
  • 4.25. USER-INTEL package
    • +
  • 4.26. USER-LB package
    • +
  • 4.27. USER-MGPT package
    • +
  • 4.28. USER-MISC package
    • +
  • 4.29. USER-MOLFILE package
    • +
  • 4.30. USER-OMP package
    • +
  • 4.31. USER-PHONON package
    • +
  • 4.32. USER-QMMM package
    • +
  • 4.33. USER-QTB package
    • +
  • 4.34. USER-REAXC package
    • +
  • 4.35. USER-SMD package
    • +
  • 4.36. USER-SMTBQ package
    • +
  • 4.37. USER-SPH package
  • 5. Accelerating LAMMPS performance
      diff --git a/doc/Manual.txt b/doc/Manual.txt index 8a37bd2a91..8d5bcada1e 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS-ICMS Users Manual - + @@ -21,7 +21,7 @@

      LAMMPS-ICMS Documentation :c,h3 -29 Jan 2016 version :c,h4 +3 Feb 2016 version :c,h4 Version info: :h4 diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 56406c28d3..dd0dc11e0e 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -758,12 +758,12 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

      LAMMPS is built with the appropriate package.

      ---+++ @@ -771,56 +771,63 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

      - - - - - - - - + + + + + + + + + + - - - + + + - - - + + + - - - + + + - - - + + + + - + + - - + - + + + + +
      adapt/fep atc ave/correlate/long ave/spatial/spheredrude
      drude/transform/directdrude/transform/reverse colvarsgleimdipi
      langevin/drude
      drudedrude/transform/directdrude/transform/reverseeos/cveos/tablegle
      imdipilangevin/drude langevin/eff lb/fluid lb/momentumlb/pclb/rigid/pc/sphere
      lb/viscous
      lb/pclb/rigid/pc/spherelb/viscous meso meso/stationary nph/effnpt/effnve/eff
      nvt/eff
      npt/effnve/effnvt/eff nvt/sllod/eff phonon pimdqbmsstqeq/reax
      qmmm
      qbmsstqeq/reaxqmmm qtb reax/c/bonds reax/c/speciessaed/vtksmd
      smd/adjust/dt
      saed/vtkshardlowsmdsmd/adjust/dt smd/integrate/tlsph smd/integrate/ulsphsmd/move/triangulated/surface
      smd/move/triangulated/surface smd/setvel smd/tlsph/reference/configuration
      smd/wall/surfacesmd/wall/surface temp/rescale/eff ti/rsti/spring
      ti/spring ttm/mod     
      @@ -934,62 +941,62 @@ KOKKOS, o = USER-OMP, t = OPT.

      used if LAMMPS is built with the appropriate package.

      ++-- + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - - - + + + - -
      ackland/atom basal/atomdpddpd/atom fep force/tallyheat/flux/tallyke/eff
      ke/atom/eff
      heat/flux/tallyke/effke/atom/eff meso/e/atom meso/rho/atom meso/t/atompe/tallysaed
      smd/contact/radius
      pe/tallysaedsmd/contact/radius smd/damage smd/hourglass/error smd/internal/energysmd/plastic/strainsmd/plastic/strain/rate
      smd/rho
      smd/plastic/strainsmd/plastic/strain/ratesmd/rho smd/tlsph/defgrad smd/tlsph/dt smd/tlsph/num/neighssmd/tlsph/shapesmd/tlsph/strain
      smd/tlsph/strain/rate
      smd/tlsph/shapesmd/tlsph/strainsmd/tlsph/strain/rate smd/tlsph/stress smd/triangle/mesh/vertices smd/ulsph/num/neighssmd/ulsph/strainsmd/ulsph/strain/rate
      smd/ulsph/stress
      smd/ulsph/strainsmd/ulsph/strain/ratesmd/ulsph/stress smd/vol stress/tally temp/drudetemp/efftemp/deform/eff
      temp/region/eff
      temp/efftemp/deform/efftemp/region/eff temp/rotate xrd    
      @@ -1157,9 +1164,9 @@ KOKKOS, o = USER-OMP, t = OPT.

      if LAMMPS is built with the appropriate package.

      ---+++ @@ -1169,52 +1176,57 @@ if LAMMPS - + + + + + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 2cc0d5994f..12749a7528 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -604,10 +604,12 @@ package"_Section_start.html#start_3. "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, "ave/spatial/sphere"_fix_ave_spatial_sphere.html, +"colvars"_fix_colvars.html, "drude"_fix_drude.html, "drude/transform/direct"_fix_drude_transform.html, "drude/transform/reverse"_fix_drude_transform.html, -"colvars"_fix_colvars.html, +"eos/cv"_fix_eos_vs.html, +"eos/table"_fix_eos_table.html, "gle"_fix_gle.html, "imd"_fix_imd.html, "ipi"_fix_ipi.html, @@ -634,6 +636,7 @@ package"_Section_start.html#start_3. "reax/c/bonds"_fix_reaxc_bonds.html, "reax/c/species"_fix_reaxc_species.html, "saed/vtk"_fix_saed_vtk.html, +"shardlow"_fix_shardlow.html, "smd"_fix_smd.html, "smd/adjust/dt"_fix_smd_adjust_dt.html, "smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, @@ -734,6 +737,8 @@ package"_Section_start.html#start_3. "ackland/atom"_compute_ackland_atom.html, "basal/atom"_compute_basal_atom.html, +"dpd"_compute_dpd.html, +"dpd/atom"_compute_dpd_atom.html, "fep"_compute_fep.html, "force/tally"_compute_tally.html, "heat/flux/tally"_compute_tally.html, @@ -903,6 +908,9 @@ package"_Section_start.html#start_3. "coul/cut/soft (o)"_pair_lj_soft.html, "coul/diel (o)"_pair_coul_diel.html, "coul/long/soft (o)"_pair_lj_soft.html, +"dpd/conservative"_pair_dpd_conservative.html, +"dpd/fdt"_pair_dpd_fdt.html, +"dpd/fdt/energy"_pair_dpd_fdt.html, "eam/cd (o)"_pair_eam.html, "edip (o)"_pair_edip.html, "eff/cut"_pair_eff.html, diff --git a/doc/Section_packages.html b/doc/Section_packages.html index cdb1bb033d..62cfaab8dd 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -97,23 +97,24 @@
    • 4.17. USER-COLVARS package
    • 4.18. USER-CUDA package
    • 4.19. USER-DIFFRACTION package
      • -
    • 4.20. USER-DRUDE package
      • -
    • 4.21. USER-EFF package
      • -
    • 4.22. USER-FEP package
      • -
    • 4.23. USER-H5MD package
      • -
    • 4.24. USER-INTEL package
      • -
    • 4.25. USER-LB package
      • -
    • 4.26. USER-MGPT package
      • -
    • 4.27. USER-MISC package
      • -
    • 4.28. USER-MOLFILE package
      • -
    • 4.29. USER-OMP package
      • -
    • 4.30. USER-PHONON package
      • -
    • 4.31. USER-QMMM package
      • -
    • 4.32. USER-QTB package
      • -
    • 4.33. USER-REAXC package
      • -
    • 4.34. USER-SMD package
      • -
    • 4.35. USER-SMTBQ package
      • -
    • 4.36. USER-SPH package
      • +
    • 4.20. USER-DPD package
      • +
    • 4.21. USER-DRUDE package
      • +
    • 4.22. USER-EFF package
      • +
    • 4.23. USER-FEP package
      • +
    • 4.24. USER-H5MD package
      • +
    • 4.25. USER-INTEL package
      • +
    • 4.26. USER-LB package
      • +
    • 4.27. USER-MGPT package
      • +
    • 4.28. USER-MISC package
      • +
    • 4.29. USER-MOLFILE package
      • +
    • 4.30. USER-OMP package
      • +
    • 4.31. USER-PHONON package
      • +
    • 4.32. USER-QMMM package
      • +
    • 4.33. USER-QTB package
      • +
    • 4.34. USER-REAXC package
      • +
    • 4.35. USER-SMD package
      • +
    • 4.36. USER-SMTBQ package
      • +
    • 4.37. USER-SPH package
    • 5. Accelerating LAMMPS performance
      • @@ -741,7 +742,21 @@ serial.

      - + + + + + + + + + @@ -755,7 +770,7 @@ serial.

      - + @@ -766,7 +781,7 @@ serial.

      - + @@ -780,7 +795,7 @@ serial.

      - + @@ -794,7 +809,7 @@ serial.

      - + - + @@ -825,7 +840,7 @@ serial.

      - + @@ -839,7 +854,7 @@ serial.

      - + @@ -856,7 +871,7 @@ serial.

      - + @@ -870,7 +885,7 @@ serial.

      - + @@ -887,7 +902,7 @@ serial.

      - + @@ -901,7 +916,7 @@ serial.

      - + @@ -912,7 +927,7 @@ serial.

      - + @@ -926,7 +941,7 @@ serial.

      - + @@ -937,7 +952,7 @@ serial.

      - + @@ -951,7 +966,7 @@ serial.

      - + @@ -965,7 +980,7 @@ serial.

      - + @@ -979,7 +994,7 @@ serial.

      - + @@ -990,7 +1005,7 @@ serial.

      - + @@ -1004,7 +1019,7 @@ serial.

      - + @@ -1026,6 +1041,8 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua (U Blaise Pascal).

      (4) The SMTBQ package was created by Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS, France).

      +

      (4) The USER-DPD package was created by James Larentzos, Timothy +Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp).

      If the Library is not listed as lib/package, then it is a third-party library not included in the LAMMPS distribution. See the src/package/Makefile.lammps file for info on where to download the @@ -1200,8 +1217,32 @@ theory.

      Arkansas. Contact him directly if you have questions.

      +
      +

      4.20. USER-DPD package

      +

      This package implements the dissipative particle dynamics (DPD) method +under isothermal, isoenergetic, isobaric and isenthalpic conditions. +The DPD equations of motion are integrated efficiently through the +Shardlow splitting algorithm.

      +

      See these doc pages and their related commands to get started:

      + +

      There are example scripts for using this package in examples/USER/dpd.

      +

      The people who created this package are James Larentzos +(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at +engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil). +Contact them directly if you have questions.

      +
      +
      -

      4.20. USER-DRUDE package

      +

      4.21. USER-DRUDE package

      This package implements methods for simulating polarizable systems in LAMMPS using thermalized Drude oscillators.

      See these doc pages and their related commands to get started:

      @@ -1221,7 +1262,7 @@ Agilio Padua.

      -

      4.21. USER-EFF package

      +

      4.22. USER-EFF package

      This package contains a LAMMPS implementation of the electron Force Field (eFF) currently under development at Caltech, as described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, @@ -1255,7 +1296,7 @@ have questions.

      -

      4.22. USER-FEP package

      +

      4.23. USER-FEP package

      This package provides methods for performing free energy perturbation simulations with soft-core pair potentials in LAMMPS.

      See these doc pages and their related commands to get started:

      @@ -1270,7 +1311,7 @@ Contact him directly if you have questions.

      -

      4.23. USER-H5MD package

      +

      4.24. USER-H5MD package

      This package contains a dump h5md command for performing a dump of atom properties in HDF5 format. HDF5 files are binary, portable and self-describing and can be examined and used by a variety of auxiliary tools. The output HDF5 @@ -1284,7 +1325,7 @@ directly if you have questions.

      -

      4.24. USER-INTEL package

      +

      4.25. USER-INTEL package

      This package provides options for performing neighbor list and non-bonded force calculations in single, mixed, or double precision and also a capability for accelerating calculations with an @@ -1296,7 +1337,7 @@ Intel(R) Xeon Phi(TM) coprocessor.

      -

      4.25. USER-LB package

      +

      4.26. USER-LB package

      This package contains a LAMMPS implementation of a background Lattice-Boltzmann fluid, which can be used to model MD particles influenced by hydrodynamic forces.

      @@ -1308,7 +1349,7 @@ Western Ontario. Contact them directly if you have questions.

      -

      4.26. USER-MGPT package

      +

      4.27. USER-MGPT package

      This package contains a fast implementation for LAMMPS of quantum-based MGPT multi-ion potentials. The MGPT or model GPT method derives from first-principles DFT-based generalized pseudopotential @@ -1331,7 +1372,7 @@ Contact them directly if you have any questions.

      -

      4.27. USER-MISC package

      +

      4.28. USER-MISC package

      The files in this package are a potpourri of (mostly) unrelated features contributed to LAMMPS by users. Each feature is a single pair of files (*.cpp and *.h).

      @@ -1348,7 +1389,7 @@ about the feature or its coding.

      -

      4.28. USER-MOLFILE package

      +

      4.29. USER-MOLFILE package

      This package contains a dump molfile command which uses molfile plugins that are bundled with the VMD molecular visualization and @@ -1367,7 +1408,7 @@ application itself.

      -

      4.29. USER-OMP package

      +

      4.30. USER-OMP package

      This package provides OpenMP multi-threading support and other optimizations of various LAMMPS pair styles, dihedral styles, and fix styles.

      @@ -1378,7 +1419,7 @@ styles, and fix styles.

      -

      4.30. USER-PHONON package

      +

      4.31. USER-PHONON package

      This package contains a fix phonon command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations.

      @@ -1390,7 +1431,7 @@ if you have questions.

      -

      4.31. USER-QMMM package

      +

      4.32. USER-QMMM package

      This package provides a fix qmmm command which allows LAMMPS to be used in a QM/MM simulation, currently only in combination with pw.x code from the Quantum ESPRESSO package.

      @@ -1407,7 +1448,7 @@ without changes to LAMMPS itself.

      -

      4.32. USER-QTB package

      +

      4.33. USER-QTB package

      This package provides a self-consistent quantum treatment of the vibrational modes in a classical molecular dynamics simulation. By coupling the MD simulation to a colored thermostat, it introduces zero @@ -1429,7 +1470,7 @@ have questions.

      -

      4.33. USER-REAXC package

      +

      4.34. USER-REAXC package

      This package contains a implementation for LAMMPS of the ReaxFF force field. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential @@ -1457,7 +1498,7 @@ questions.

      -

      4.34. USER-SMD package

      +

      4.35. USER-SMD package

      This package implements smoothed Mach dynamics (SMD) in LAMMPS. Currently, the package has the following features:

        @@ -1481,7 +1522,7 @@ you have questions.

      -

      4.35. USER-SMTBQ package

      +

      4.36. USER-SMTBQ package

      This package implements the Second Moment Tight Binding - QEq (SMTB-Q) potential for the description of ionocovalent bonds in oxides.

      There are example scripts for using this package in @@ -1495,7 +1536,7 @@ them directly if you have any questions.

      -

      4.36. USER-SPH package

      +

      4.37. USER-SPH package

      This package implements smoothed particle hydrodynamics (SPH) in LAMMPS. Currently, the package has the following features:

        diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index f56fdbce00..9c97e14d24 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -200,6 +200,7 @@ USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sd USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, - +USER-DPD, dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, - USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, - USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, - USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, - @@ -244,6 +245,9 @@ Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua (4) The SMTBQ package was created by Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS, France). +(4) The USER-DPD package was created by James Larentzos, Timothy +Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp). + If the Library is not listed as lib/package, then it is a third-party library not included in the LAMMPS distribution. See the src/package/Makefile.lammps file for info on where to download the @@ -454,6 +458,33 @@ Arkansas. Contact him directly if you have questions. :line +USER-DPD package :h4 + +This package implements the dissipative particle dynamics (DPD) method +under isothermal, isoenergetic, isobaric and isenthalpic conditions. +The DPD equations of motion are integrated efficiently through the +Shardlow splitting algorithm. + +See these doc pages and their related commands to get started: + +"compute dpd"_compute_dpd.html +"compute dpd/atom"_compute_dpd_atom.html +"fix_eos/cv"_fix_eos_table.html +"fix_eos/table"_fix_eos_table.html +"fix_shardlow"_fix_shardlow.html +"pair_dpd/conservative"_pair_dpd_conservative.html +"pair_dpd/fdt"_pair_dpd_fdt.html +"pair_dpd/fdt/energy"_pair_dpd_fdt.html :ul + +There are example scripts for using this package in examples/USER/dpd. + +The people who created this package are James Larentzos +(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at +engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil). +Contact them directly if you have questions. + +:line + USER-DRUDE package :h4 This package implements methods for simulating polarizable systems diff --git a/doc/Section_start.html b/doc/Section_start.html index 80e0fc84b9..10c092176e 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -436,8 +436,8 @@ performance.

        files for doing particle dumps in XTC format. This is only necessary if your platform does have its own XDR files available. See the Restrictions section of the dump command for details.

        -

        Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D- -DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These +

        Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, +-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These settings refer to use of 4-byte (small) vs 8-byte (big) integers within LAMMPS, as specified in src/lmptype.h. The only reason to use the BIGBIG setting is to enable simulation of huge molecular systems @@ -1288,7 +1288,7 @@ use this executable to run on a single processor by typing something like: “lmp_win_mpi -in in.lj”.

      -

      The screen output from LAMMPS is described in the next section. As it +

      The screen output from LAMMPS is described in a section below. As it runs, LAMMPS also writes a log.lammps file with the same information.

      Note that this sequence of commands copies the LAMMPS executable (lmp_linux) to the directory with the input files. This may not be diff --git a/doc/Section_start.txt b/doc/Section_start.txt index f811a22475..41708dc402 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -311,8 +311,8 @@ files for doing particle dumps in XTC format. This is only necessary if your platform does have its own XDR files available. See the Restrictions section of the "dump"_dump.html command for details. -Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, -D- -DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These +Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, +-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These settings refer to use of 4-byte (small) vs 8-byte (big) integers within LAMMPS, as specified in src/lmptype.h. The only reason to use the BIGBIG setting is to enable simulation of huge molecular systems @@ -1266,7 +1266,7 @@ like: "lmp_win_mpi -in in.lj". :l,ule :line -The screen output from LAMMPS is described in the next section. As it +The screen output from LAMMPS is described in a section below. As it runs, LAMMPS also writes a log.lammps file with the same information. Note that this sequence of commands copies the LAMMPS executable diff --git a/doc/_sources/Manual.txt b/doc/_sources/Manual.txt new file mode 100644 index 0000000000..62a89d1c8e --- /dev/null +++ b/doc/_sources/Manual.txt @@ -0,0 +1,104 @@ +.. raw:: html + +

      + +LAMMPS Documentation +==================== + +29 Jan 2016 version +------------------- + +Version info: +------------- + +The LAMMPS "version" is the date when it was released, such as 1 May +2010. LAMMPS is updated continuously. Whenever we fix a bug or add a +feature, we release it immediately, and post a notice on `this page of the WWW site `_. Each dated copy of LAMMPS contains all the +features and bug-fixes up to and including that version date. The +version date is printed to the screen and logfile every time you run +LAMMPS. It is also in the file src/version.h and in the LAMMPS +directory name created when you unpack a tarball, and at the top of +the first page of the manual (this page). + +* If you browse the HTML doc pages on the LAMMPS WWW site, they always + describe the most current version of LAMMPS. +* If you browse the HTML doc pages included in your tarball, they + describe the version you have. +* The `PDF file `_ on the WWW site or in the tarball is updated + about once per month. This is because it is large, and we don't want + it to be part of every patch. +* There is also a `Developer.pdf `_ file in the doc + directory, which describes the internal structure and algorithms of + LAMMPS. +LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel +Simulator. + +LAMMPS is a classical molecular dynamics simulation code designed to +run efficiently on parallel computers. It was developed at Sandia +National Laboratories, a US Department of Energy facility, with +funding from the DOE. It is an open-source code, distributed freely +under the terms of the GNU Public License (GPL). + +The primary developers of LAMMPS are `Steve Plimpton `_, Aidan +Thompson, and Paul Crozier who can be contacted at +sjplimp,athomps,pscrozi at sandia.gov. The `LAMMPS WWW Site `_ at +http://lammps.sandia.gov has more information about the code and its +uses. + +.. _bug: http://lammps.sandia.gov/bug.html + + + +.. _sjp: http://www.sandia.gov/~sjplimp + + + + +---------- + + +The LAMMPS documentation is organized into the following sections. If +you find errors or omissions in this manual or have suggestions for +useful information to add, please send an email to the developers so +we can improve the LAMMPS documentation. + +Once you are familiar with LAMMPS, you may want to bookmark :ref:`this page ` at Section_commands.html#comm since +it gives quick access to documentation for all LAMMPS commands. + +`PDF file `_ of the entire manual, generated by +`htmldoc `_ + + +.. toctree:: + :maxdepth: 2 + :numbered: + + Section_intro + Section_start + Section_commands + Section_packages + Section_accelerate + Section_howto + Section_example + Section_perf + Section_tools + Section_modify + Section_python + Section_errors + Section_history + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`search` + +.. raw:: html + + + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_accelerate.txt b/doc/_sources/Section_accelerate.txt new file mode 100644 index 0000000000..eaa5e34e9d --- /dev/null +++ b/doc/_sources/Section_accelerate.txt @@ -0,0 +1,430 @@ +Accelerating LAMMPS performance +=============================== + +This section describes various methods for improving LAMMPS +performance for different classes of problems running on different +kinds of machines. + +There are two thrusts to the discussion that follows. The +first is using code options that implement alternate algorithms +that can speed-up a simulation. The second is to use one +of the several accelerator packages provided with LAMMPS that +contain code optimized for certain kinds of hardware, including +multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors. + +* 5.1 :ref:`Measuring performance ` +* 5.2 :ref:`Algorithms and code options to boost performace ` +* 5.3 :ref:`Accelerator packages with optimized styles ` +* 5.3.1 :doc:`USER-CUDA package ` +* 5.3.2 :doc:`GPU package ` +* 5.3.3 :doc:`USER-INTEL package ` +* 5.3.4 :doc:`KOKKOS package ` +* 5.3.5 :doc:`USER-OMP package ` +* 5.3.6 :doc:`OPT package ` +* 5.4 :ref:`Comparison of various accelerator packages ` +The `Benchmark page `_ of the LAMMPS +web site gives performance results for the various accelerator +packages discussed in Section 5.2, for several of the standard LAMMPS +benchmark problems, as a function of problem size and number of +compute nodes, on different hardware platforms. + + + + + +.. _acc_1: + +Measuring performance +--------------------------------- + +Before trying to make your simulation run faster, you should +understand how it currently performs and where the bottlenecks are. + +The best way to do this is run the your system (actual number of +atoms) for a modest number of timesteps (say 100 steps) on several +different processor counts, including a single processor if possible. +Do this for an equilibrium version of your system, so that the +100-step timings are representative of a much longer run. There is +typically no need to run for 1000s of timesteps to get accurate +timings; you can simply extrapolate from short runs. + +For the set of runs, look at the timing data printed to the screen and +log file at the end of each LAMMPS run. :ref:`This section ` of the manual has an overview. + +Running on one (or a few processors) should give a good estimate of +the serial performance and what portions of the timestep are taking +the most time. Running the same problem on a few different processor +counts should give an estimate of parallel scalability. I.e. if the +simulation runs 16x faster on 16 processors, its 100% parallel +efficient; if it runs 8x faster on 16 processors, it's 50% efficient. + +The most important data to look at in the timing info is the timing +breakdown and relative percentages. For example, trying different +options for speeding up the long-range solvers will have little impact +if they only consume 10% of the run time. If the pairwise time is +dominating, you may want to look at GPU or OMP versions of the pair +style, as discussed below. Comparing how the percentages change as +you increase the processor count gives you a sense of how different +operations within the timestep are scaling. Note that if you are +running with a Kspace solver, there is additional output on the +breakdown of the Kspace time. For PPPM, this includes the fraction +spent on FFTs, which can be communication intensive. + +Another important detail in the timing info are the histograms of +atoms counts and neighbor counts. If these vary widely across +processors, you have a load-imbalance issue. This often results in +inaccurate relative timing data, because processors have to wait when +communication occurs for other processors to catch up. Thus the +reported times for "Communication" or "Other" may be higher than they +really are, due to load-imbalance. If this is an issue, you can +uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile +LAMMPS, to obtain synchronized timings. + + +---------- + + +.. _acc_2: + +General strategies +------------------------------ + +.. note:: + + this section 5.2 is still a work in progress + +Here is a list of general ideas for improving simulation performance. +Most of them are only applicable to certain models and certain +bottlenecks in the current performance, so let the timing data you +generate be your guide. It is hard, if not impossible, to predict how +much difference these options will make, since it is a function of +problem size, number of processors used, and your machine. There is +no substitute for identifying performance bottlenecks, and trying out +various options. + +* rRESPA +* 2-FFT PPPM +* Staggered PPPM +* single vs double PPPM +* partial charge PPPM +* verlet/split run style +* processor command for proc layout and numa layout +* load-balancing: balance and fix balance + +2-FFT PPPM, also called *analytic differentiation* or *ad* PPPM, uses +2 FFTs instead of the 4 FFTs used by the default *ik differentiation* +PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to +achieve the same accuracy as 4-FFT PPPM. For problems where the FFT +cost is the performance bottleneck (typically large problems running +on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. + +Staggered PPPM performs calculations using two different meshes, one +shifted slightly with respect to the other. This can reduce force +aliasing errors and increase the accuracy of the method, but also +doubles the amount of work required. For high relative accuracy, using +staggered PPPM allows one to half the mesh size in each dimension as +compared to regular PPPM, which can give around a 4x speedup in the +kspace time. However, for low relative accuracy, using staggered PPPM +gives little benefit and can be up to 2x slower in the kspace +time. For example, the rhodopsin benchmark was run on a single +processor, and results for kspace time vs. relative accuracy for the +different methods are shown in the figure below. For this system, +staggered PPPM (using ik differentiation) becomes useful when using a +relative accuracy of slightly greater than 1e-5 and above. + +.. image:: JPG/rhodo_staggered.jpg + :align: center + +.. note:: + + Using staggered PPPM may not give the same increase in accuracy + of energy and pressure as it does in forces, so some caution must be + used if energy and/or pressure are quantities of interest, such as + when using a barostat. + + +---------- + + +.. _acc_3: + +Packages with optimized styles +------------------------------------------ + +Accelerated versions of various :doc:`pair_style `, +:doc:`fixes `, :doc:`computes `, and other commands have +been added to LAMMPS, which will typically run faster than the +standard non-accelerated versions. Some require appropriate hardware +to be present on your system, e.g. GPUs or Intel Xeon Phi +coprocessors. + +All of these commands are in packages provided with LAMMPS. An +overview of packages is give in :doc:`Section packages `. + +These are the accelerator packages +currently in LAMMPS, either as standard or user packages: + ++--------------------------------------+------------------------------------------------+ +| :doc:`USER-CUDA ` | for NVIDIA GPUs | ++--------------------------------------+------------------------------------------------+ +| :doc:`GPU ` | for NVIDIA GPUs as well as OpenCL support | ++--------------------------------------+------------------------------------------------+ +| :doc:`USER-INTEL ` | for Intel CPUs and Intel Xeon Phi | ++--------------------------------------+------------------------------------------------+ +| :doc:`KOKKOS ` | for GPUs, Intel Xeon Phi, and OpenMP threading | ++--------------------------------------+------------------------------------------------+ +| :doc:`USER-OMP ` | for OpenMP threading | ++--------------------------------------+------------------------------------------------+ +| :doc:`OPT ` | generic CPU optimizations | ++--------------------------------------+------------------------------------------------+ + +Inverting this list, LAMMPS currently has acceleration support for +three kinds of hardware, via the listed packages: + ++----------------+-------------------------------------------------------------------------------------------------------------------------------------------------+ +| Many-core CPUs | :doc:`USER-INTEL `, :doc:`KOKKOS `, :doc:`USER-OMP `, :doc:`OPT ` packages | ++----------------+-------------------------------------------------------------------------------------------------------------------------------------------------+ +| NVIDIA GPUs | :doc:`USER-CUDA `, :doc:`GPU `, :doc:`KOKKOS ` packages | ++----------------+-------------------------------------------------------------------------------------------------------------------------------------------------+ +| Intel Phi | :doc:`USER-INTEL `, :doc:`KOKKOS ` packages | ++----------------+-------------------------------------------------------------------------------------------------------------------------------------------------+ + +Which package is fastest for your hardware may depend on the size +problem you are running and what commands (accelerated and +non-accelerated) are invoked by your input script. While these doc +pages include performance guidelines, there is no substitute for +trying out the different packages appropriate to your hardware. + +Any accelerated style has the same name as the corresponding standard +style, except that a suffix is appended. Otherwise, the syntax for +the command that uses the style is identical, their functionality is +the same, and the numerical results it produces should also be the +same, except for precision and round-off effects. + +For example, all of these styles are accelerated variants of the +Lennard-Jones :doc:`pair_style lj/cut `: + +* :doc:`pair_style lj/cut/cuda ` +* :doc:`pair_style lj/cut/gpu ` +* :doc:`pair_style lj/cut/intel ` +* :doc:`pair_style lj/cut/kk ` +* :doc:`pair_style lj/cut/omp ` +* :doc:`pair_style lj/cut/opt ` + +To see what accelerate styles are currently available, see +:ref:`Section_commands 5 ` of the manual. The +doc pages for individual commands (e.g. :doc:`pair lj/cut ` or +:doc:`fix nve `) also list any accelerated variants available +for that style. + +To use an accelerator package in LAMMPS, and one or more of the styles +it provides, follow these general steps. Details vary from package to +package and are explained in the individual accelerator doc pages, +listed above: + ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ +| build the accelerator library | only for USER-CUDA and GPU packages | ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ +| install the accelerator package | make yes-opt, make yes-user-intel, etc | ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ +| add compile/link flags to Makefile.machine | in src/MAKE,
      + only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ +| re-build LAMMPS | make machine | ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ +| run a LAMMPS simulation | lmp_machine < in.script
      + mpirun -np 32 lmp_machine -in in.script | ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ +| enable the accelerator package | via "-c on" and "-k on" :ref:`command-line switches `,
      + only for USER-CUDA and KOKKOS packages | ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ +| set any needed options for the package | via "-pk" :ref:`command-line switch ` or + :doc:`package ` command,
      + only if defaults need to be changed | ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ +| use accelerated styles in your input script | via "-sf" :ref:`command-line switch ` or + :doc:`suffix ` command | ++---------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------+ + +Note that the first 4 steps can be done as a single command, using the +src/Make.py tool. This tool is discussed in :ref:`Section 2.4 ` of the manual, and its use is +illustrated in the individual accelerator sections. Typically these +steps only need to be done once, to create an executable that uses one +or more accelerator packages. + +The last 4 steps can all be done from the command-line when LAMMPS is +launched, without changing your input script, as illustrated in the +individual accelerator sections. Or you can add +:doc:`package ` and :doc:`suffix ` commands to your input +script. + +.. note:: + + With a few exceptions, you can build a single LAMMPS executable + with all its accelerator packages installed. Note however that the + USER-INTEL and KOKKOS packages require you to choose one of their + hardware options when building for a specific platform. I.e. CPU or + Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi + option for the KOKKOS package. + +These are the exceptions. You cannot build a single executable with: + +* both the USER-INTEL Phi and KOKKOS Phi options +* the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages + +See the examples/accelerate/README and make.list files for sample +Make.py commands that build LAMMPS with any or all of the accelerator +packages. As an example, here is a command that builds with all the +GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda), +including settings to build the needed auxiliary USER-CUDA and GPU +libraries for Kepler GPUs: + +.. parsed-literal:: + + Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi -cuda mode=double arch=35 -gpu mode=double arch=35 \ -kokkos cuda arch=35 lib-all file mpi + +The examples/accelerate directory also has input scripts that can be +used with all of the accelerator packages. See its README file for +details. + +Likewise, the bench directory has FERMI and KEPLER and PHI +sub-directories with Make.py commands and input scripts for using all +the accelerator packages on various machines. See the README files in +those dirs. + +As mentioned above, the `Benchmark page `_ of the LAMMPS web site gives +performance results for the various accelerator packages for several +of the standard LAMMPS benchmark problems, as a function of problem +size and number of compute nodes, on different hardware platforms. + +Here is a brief summary of what the various packages provide. Details +are in the individual accelerator sections. + +* Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU + packages, and can be run on NVIDIA GPUs. The speed-up on a GPU + depends on a variety of factors, discussed in the accelerator + sections. +* Styles with an "intel" suffix are part of the USER-INTEL + package. These styles support vectorized single and mixed precision + calculations, in addition to full double precision. In extreme cases, + this can provide speedups over 3.5x on CPUs. The package also + supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) + coprocessors. This can result in additional speedup over 2x depending + on the hardware configuration. +* Styles with a "kk" suffix are part of the KOKKOS package, and can be + run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel + Xeon Phi in "native" mode. The speed-up depends on a variety of + factors, as discussed on the KOKKOS accelerator page. +* Styles with an "omp" suffix are part of the USER-OMP package and allow + a pair-style to be run in multi-threaded mode using OpenMP. This can + be useful on nodes with high-core counts when using less MPI processes + than cores is advantageous, e.g. when running with PPPM so that FFTs + are run on fewer MPI processors or when the many MPI tasks would + overload the available bandwidth for communication. +* Styles with an "opt" suffix are part of the OPT package and typically + speed-up the pairwise calculations of your simulation by 5-25% on a + CPU. +The individual accelerator package doc pages explain: + +* what hardware and software the accelerated package requires +* how to build LAMMPS with the accelerated package +* how to run with the accelerated package either via command-line switches or modifying the input script +* speed-ups to expect +* guidelines for best performance +* restrictions + + +---------- + + +.. _acc_4: + +Comparison of various accelerator packages +------------------------------------------------------ + +.. note:: + + this section still needs to be re-worked with additional KOKKOS + and USER-INTEL information. + +The next section compares and contrasts the various accelerator +options, since there are multiple ways to perform OpenMP threading, +run on GPUs, and run on Intel Xeon Phi coprocessors. + +All 3 of these packages accelerate a LAMMPS calculation using NVIDIA +hardware, but they do it in different ways. + +As a consequence, for a particular simulation on specific hardware, +one package may be faster than the other. We give guidelines below, +but the best way to determine which package is faster for your input +script is to try both of them on your machine. See the benchmarking +section below for examples where this has been done. + +**Guidelines for using each package optimally:** + +* The GPU package allows you to assign multiple CPUs (cores) to a single + GPU (a common configuration for "hybrid" nodes that contain multicore + CPU(s) and GPU(s)) and works effectively in this mode. The USER-CUDA + package does not allow this; you can only use one CPU per GPU. +* The GPU package moves per-atom data (coordinates, forces) + back-and-forth between the CPU and GPU every timestep. The USER-CUDA + package only does this on timesteps when a CPU calculation is required + (e.g. to invoke a fix or compute that is non-GPU-ized). Hence, if you + can formulate your input script to only use GPU-ized fixes and + computes, and avoid doing I/O too often (thermo output, dump file + snapshots, restart files), then the data transfer cost of the + USER-CUDA package can be very low, causing it to run faster than the + GPU package. +* The GPU package is often faster than the USER-CUDA package, if the + number of atoms per GPU is smaller. The crossover point, in terms of + atoms/GPU at which the USER-CUDA package becomes faster depends + strongly on the pair style. For example, for a simple Lennard Jones + system the crossover (in single precision) is often about 50K-100K + atoms per GPU. When performing double precision calculations the + crossover point can be significantly smaller. +* Both packages compute bonded interactions (bonds, angles, etc) on the + CPU. This means a model with bonds will force the USER-CUDA package + to transfer per-atom data back-and-forth between the CPU and GPU every + timestep. If the GPU package is running with several MPI processes + assigned to one GPU, the cost of computing the bonded interactions is + spread across more CPUs and hence the GPU package can run faster. +* When using the GPU package with multiple CPUs assigned to one GPU, its + performance depends to some extent on high bandwidth between the CPUs + and the GPU. Hence its performance is affected if full 16 PCIe lanes + are not available for each GPU. In HPC environments this can be the + case if S2050/70 servers are used, where two devices generally share + one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide + full 16 lanes to each of the PCIe 2.0 16x slots. +**Differences between the two packages:** + +* The GPU package accelerates only pair force, neighbor list, and PPPM + calculations. The USER-CUDA package currently supports a wider range + of pair styles and can also accelerate many fix styles and some + compute styles, as well as neighbor list and PPPM calculations. +* The USER-CUDA package does not support acceleration for minimization. +* The USER-CUDA package does not support hybrid pair styles. +* The USER-CUDA package can order atoms in the neighbor list differently + from run to run resulting in a different order for force accumulation. +* The USER-CUDA package has a limit on the number of atom types that can be + used in a simulation. +* The GPU package requires neighbor lists to be built on the CPU when using + exclusion lists or a triclinic simulation box. +* The GPU package uses more GPU memory than the USER-CUDA package. This + is generally not a problem since typical runs are computation-limited + rather than memory-limited. +Examples +"""""""" + +The LAMMPS distribution has two directories with sample input scripts +for the GPU and USER-CUDA packages. + +* lammps/examples/gpu = GPU package files +* lammps/examples/USER/cuda = USER-CUDA package files + +These contain input scripts for identical systems, so they can be used +to benchmark the performance of both packages on your system. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_commands.txt b/doc/_sources/Section_commands.txt new file mode 100644 index 0000000000..7025e5797a --- /dev/null +++ b/doc/_sources/Section_commands.txt @@ -0,0 +1,814 @@ +Commands +======== + +This section describes how a LAMMPS input script is formatted and the +input script commands used to define a LAMMPS simulation. + +| 3.1 :ref:`LAMMPS input script ` +| 3.2 :ref:`Parsing rules ` +| 3.3 :ref:`Input script structure ` +| 3.4 :ref:`Commands listed by category ` +| 3.5 :ref:`Commands listed alphabetically ` +| + + + + + +.. _cmd_1: + +LAMMPS input script +------------------- + +LAMMPS executes by reading commands from a input script (text file), +one line at a time. When the input script ends, LAMMPS exits. Each +command causes LAMMPS to take some action. It may set an internal +variable, read in a file, or run a simulation. Most commands have +default settings, which means you only need to use the command if you +wish to change the default. + +In many cases, the ordering of commands in an input script is not +important. However the following rules apply: + +(1) LAMMPS does not read your entire input script and then perform a +simulation with all the settings. Rather, the input script is read +one line at a time and each command takes effect when it is read. +Thus this sequence of commands: + +.. parsed-literal:: + + timestep 0.5 + run 100 + run 100 + +does something different than this sequence: + +.. parsed-literal:: + + run 100 + timestep 0.5 + run 100 + +In the first case, the specified timestep (0.5 fmsec) is used for two +simulations of 100 timesteps each. In the 2nd case, the default +timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5 +fmsec timestep is used for the 2nd one. + +(2) Some commands are only valid when they follow other commands. For +example you cannot set the temperature of a group of atoms until atoms +have been defined and a group command is used to define which atoms +belong to the group. + +(3) Sometimes command B will use values that can be set by command A. +This means command A must precede command B in the input script if it +is to have the desired effect. For example, the +:doc:`read_data ` command initializes the system by setting +up the simulation box and assigning atoms to processors. If default +values are not desired, the :doc:`processors ` and +:doc:`boundary ` commands need to be used before read_data to +tell LAMMPS how to map processors to the simulation box. + +Many input script errors are detected by LAMMPS and an ERROR or +WARNING message is printed. :doc:`This section ` gives +more information on what errors mean. The documentation for each +command lists restrictions on how the command can be used. + + +---------- + + +.. _cmd_2: + +Parsing rules +------------- + +Each non-blank line in the input script is treated as a command. +LAMMPS commands are case sensitive. Command names are lower-case, as +are specified command arguments. Upper case letters may be used in +file names or user-chosen ID strings. + +Here is how each line in the input script is parsed by LAMMPS: + +(1) If the last printable character on the line is a "&" character, +the command is assumed to continue on the next line. The next line is +concatenated to the previous line by removing the "&" character and +line break. This allows long commands to be continued across two or +more lines. See the discussion of triple quotes in (6) for how to +continue a command across multiple line without using "&" characters. + +(2) All characters from the first "#" character onward are treated as +comment and discarded. See an exception in (6). Note that a +comment after a trailing "&" character will prevent the command from +continuing on the next line. Also note that for multi-line commands a +single leading "#" will comment out the entire command. + +(3) The line is searched repeatedly for $ characters, which indicate +variables that are replaced with a text string. See an exception in +(6). + +If the $ is followed by curly brackets, then the variable name is the +text inside the curly brackets. If no curly brackets follow the $, +then the variable name is the single character immediately following +the $. Thus ${myTemp} and $x refer to variable names "myTemp" and +"x". + +How the variable is converted to a text string depends on what style +of variable it is; see the `variable `_ doc page for details. +It can be a variable that stores multiple text strings, and return one +of them. The returned text string can be multiple "words" (space +separated) which will then be interpreted as multiple arguments in the +input command. The variable can also store a numeric formula which +will be evaluated and its numeric result returned as a string. + +As a special case, if the $ is followed by parenthesis, then the text +inside the parenthesis is treated as an "immediate" variable and +evaluated as an :doc:`equal-style variable `. This is a way +to use numeric formulas in an input script without having to assign +them to variable names. For example, these 3 input script lines: + +.. parsed-literal:: + + variable X equal (xlo+xhi)/2+sqrt(v_area) + region 1 block $X 2 INF INF EDGE EDGE + variable X delete + +can be replaced by + +.. parsed-literal:: + + region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE + +so that you do not have to define (or discard) a temporary variable X. + +Note that neither the curly-bracket or immediate form of variables can +contain nested $ characters for other variables to substitute for. +Thus you cannot do this: + +.. parsed-literal:: + + variable a equal 2 + variable b2 equal 4 + print "B2 = ${b$a}" + +Nor can you specify this $($x-1.0) for an immediate variable, but +you could use $(v_x-1.0), since the latter is valid syntax for an +:doc:`equal-style variable `. + +See the :doc:`variable ` command for more details of how +strings are assigned to variables and evaluated, and how they can be +used in input script commands. + +(4) The line is broken into "words" separated by whitespace (tabs, +spaces). Note that words can thus contain letters, digits, +underscores, or punctuation characters. + +(5) The first word is the command name. All successive words in the +line are arguments. + +(6) If you want text with spaces to be treated as a single argument, +it can be enclosed in either single or double or triple quotes. A +long single argument enclosed in single or double quotes can span +multiple lines if the "&" character is used, as described above. When +the lines are concatenated together (and the "&" characters and line +breaks removed), the text will become a single line. If you want +multiple lines of an argument to retain their line breaks, the text +can be enclosed in triple quotes, in which case "&" characters are not +needed. For example: + +.. parsed-literal:: + + print "Volume = $v" + print 'Volume = $v' + if "${steps} > 1000" then quit + variable a string "red green blue & + purple orange cyan" + print """ + System volume = $v + System temperature = $t + """ + +In each case, the single, double, or triple quotes are removed when +the single argument they enclose is stored internally. + +See the :doc:`dump modify format `, :doc:`print `, +:doc:`if `, and :doc:`python ` commands for examples. + +A "#" or "$" character that is between quotes will not be treated as a +comment indicator in (2) or substituted for as a variable in (3). + +.. note:: + + If the argument is itself a command that requires a quoted + argument (e.g. using a :doc:`print ` command as part of an + :doc:`if ` or :doc:`run every ` command), then single, double, or + triple quotes can be nested in the usual manner. See the doc pages + for those commands for examples. Only one of level of nesting is + allowed, but that should be sufficient for most use cases. + + +---------- + + +.. _cmd_3: + +Input script structure +---------------------------------- + +This section describes the structure of a typical LAMMPS input script. +The "examples" directory in the LAMMPS distribution contains many +sample input scripts; the corresponding problems are discussed in +:doc:`Section_example `, and animated on the `LAMMPS WWW Site `_. + +A LAMMPS input script typically has 4 parts: + +1. Initialization +2. Atom definition +3. Settings +4. Run a simulation + +The last 2 parts can be repeated as many times as desired. I.e. run a +simulation, change some settings, run some more, etc. Each of the 4 +parts is now described in more detail. Remember that almost all the +commands need only be used if a non-default value is desired. + +(1) Initialization + +Set parameters that need to be defined before atoms are created or +read-in from a file. + +The relevant commands are :doc:`units `, +:doc:`dimension `, :doc:`newton `, +:doc:`processors `, :doc:`boundary `, +:doc:`atom_style `, :doc:`atom_modify `. + +If force-field parameters appear in the files that will be read, these +commands tell LAMMPS what kinds of force fields are being used: +:doc:`pair_style `, :doc:`bond_style `, +:doc:`angle_style `, :doc:`dihedral_style `, +:doc:`improper_style `. + +(2) Atom definition + +There are 3 ways to define atoms in LAMMPS. Read them in from a data +or restart file via the :doc:`read_data ` or +:doc:`read_restart ` commands. These files can contain +molecular topology information. Or create atoms on a lattice (with no +molecular topology), using these commands: :doc:`lattice `, +:doc:`region `, :doc:`create_box `, +:doc:`create_atoms `. The entire set of atoms can be +duplicated to make a larger simulation using the +:doc:`replicate ` command. + +(3) Settings + +Once atoms and molecular topology are defined, a variety of settings +can be specified: force field coefficients, simulation parameters, +output options, etc. + +Force field coefficients are set by these commands (they can also be +set in the read-in files): :doc:`pair_coeff `, +:doc:`bond_coeff `, :doc:`angle_coeff `, +:doc:`dihedral_coeff `, +:doc:`improper_coeff `, +:doc:`kspace_style `, :doc:`dielectric `, +:doc:`special_bonds `. + +Various simulation parameters are set by these commands: +:doc:`neighbor `, :doc:`neigh_modify `, +:doc:`group `, :doc:`timestep `, +:doc:`reset_timestep `, :doc:`run_style `, +:doc:`min_style `, :doc:`min_modify `. + +Fixes impose a variety of boundary conditions, time integration, and +diagnostic options. The :doc:`fix ` command comes in many flavors. + +Various computations can be specified for execution during a +simulation using the :doc:`compute `, +:doc:`compute_modify `, and :doc:`variable ` +commands. + +Output options are set by the :doc:`thermo `, :doc:`dump `, +and :doc:`restart ` commands. + +(4) Run a simulation + +A molecular dynamics simulation is run using the :doc:`run ` +command. Energy minimization (molecular statics) is performed using +the :doc:`minimize ` command. A parallel tempering +(replica-exchange) simulation can be run using the +:doc:`temper ` command. + + +---------- + + +.. _cmd_4: + +Commands listed by category +--------------------------- + +This section lists all LAMMPS commands, grouped by category. The +:ref:`next section ` lists the same commands alphabetically. Note +that some style options for some commands are part of specific LAMMPS +packages, which means they cannot be used unless the package was +included when LAMMPS was built. Not all packages are included in a +default LAMMPS build. These dependencies are listed as Restrictions +in the command's documentation. + +Initialization: + +:doc:`atom_modify `, :doc:`atom_style `, +:doc:`boundary `, :doc:`dimension `, +:doc:`newton `, :doc:`processors `, :doc:`units ` + +Atom definition: + +:doc:`create_atoms `, :doc:`create_box `, +:doc:`lattice `, :doc:`read_data `, +:doc:`read_dump `, :doc:`read_restart `, +:doc:`region `, :doc:`replicate ` + +Force fields: + +:doc:`angle_coeff `, :doc:`angle_style `, +:doc:`bond_coeff `, :doc:`bond_style `, +:doc:`dielectric `, :doc:`dihedral_coeff `, +:doc:`dihedral_style `, +:doc:`improper_coeff `, +:doc:`improper_style `, +:doc:`kspace_modify `, :doc:`kspace_style `, +:doc:`pair_coeff `, :doc:`pair_modify `, +:doc:`pair_style `, :doc:`pair_write `, +:doc:`special_bonds ` + +Settings: + +:doc:`comm_style `, :doc:`group `, :doc:`mass `, +:doc:`min_modify `, :doc:`min_style `, +:doc:`neigh_modify `, :doc:`neighbor `, +:doc:`reset_timestep `, :doc:`run_style `, +:doc:`set `, :doc:`timestep `, :doc:`velocity ` + +Fixes: + +:doc:`fix `, :doc:`fix_modify `, :doc:`unfix ` + +Computes: + +:doc:`compute `, :doc:`compute_modify `, +:doc:`uncompute ` + +Output: + +:doc:`dump `, :doc:`dump image `, +:doc:`dump_modify `, :doc:`dump movie `, +:doc:`restart `, :doc:`thermo `, +:doc:`thermo_modify `, :doc:`thermo_style `, +:doc:`undump `, :doc:`write_data `, +:doc:`write_dump `, :doc:`write_restart ` + +Actions: + +:doc:`delete_atoms `, :doc:`delete_bonds `, +:doc:`displace_atoms `, :doc:`change_box `, +:doc:`minimize `, :doc:`neb ` :doc:`prd `, +:doc:`rerun `, :doc:`run `, :doc:`temper ` + +Miscellaneous: + +:doc:`clear `, :doc:`echo `, :doc:`if `, +:doc:`include `, :doc:`jump `, :doc:`label
      coul/diel (o)
      coul/long/soft (o)eam/cd (o)dpd/conservativedpd/fdtdpd/fdt/energy
      eam/cd (o) edip (o) eff/cutgauss/cut
      gauss/cutlennard/mdf
      lennard/mdf list lj/charmm/coul/long/soft (o)lj/cut/coul/cut/soft (o)
      lj/cut/coul/cut/soft (o)lj/cut/coul/long/soft (o)
      lj/cut/coul/long/soft (o) lj/cut/dipole/sf (go) lj/cut/soft (o)lj/cut/tip4p/long/soft (o)
      lj/cut/tip4p/long/soft (o)lj/mdf
      lj/mdf lj/sdk (gko) lj/sdk/coul/long (go)lj/sdk/coul/msm (o)
      lj/sdk/coul/msm (o)lj/sf (o)
      lj/sf (o) meam/spline meam/sw/splinemgpt
      mgptquip
      quip reax/c smd/hertzsmd/tlsph
      smd/tlsphsmd/triangulated/surface
      smd/triangulated/surface smd/ulsph smtbqsph/heatconduction
      sph/heatconductionsph/idealgas
      sph/idealgas sph/lj sph/rhosumsph/taitwater
      sph/taitwatersph/taitwater/morris
      sph/taitwater/morris srp tersoff/table (o)thole
      tholetip4p/long/soft (o)
      tip4p/long/soft (o)     
      USER-DRUDE
      USER-DPDdissipative particle dynamics (DPD)Larentzos & Mattox & Brennan (5)src/USER-DPD/READMEUSER/dpd
        +
      • +
      +
        +
      • +
      +
      USER-DRUDE Drude oscillators Dequidt & Devemy & Padua (3) tutorial
      USER-EFF
      USER-EFF electron force field Andres Jaramillo-Botero (Caltech) pair_style eff/cut
      USER-FEP
      USER-FEP free energy perturbation Agilio Padua (U Blaise Pascal Clermont-Ferrand) compute fep
      USER-H5MD
      USER-H5MD dump output via HDF5 Pierre de Buyl (KU Leuven) dump h5md lib/h5md
      USER-INTEL
      USER-INTEL Vectorized CPU and Intel(R) coprocessor styles
      1. Michael Brown (Intel)
        2. @@ -811,7 +826,7 @@ serial.
      USER-LB
      USER-LB Lattice Boltzmann fluid Colin Denniston (U Western Ontario) fix lb/fluid
      USER-MGPT
      USER-MGPT fast MGPT multi-ion potentials Tomas Oppelstrup & John Moriarty (LLNL) pair_style mgpt
      USER-MISC
      USER-MISC single-file contributions USER-MISC/README USER-MISC/README
      USER-MOLFILE
      USER-MOLFILE VMD molfile plug-ins Axel Kohlmeyer (Temple U) dump molfile VMD-MOLFILE
      USER-OMP
      USER-OMP OpenMP threaded styles Axel Kohlmeyer (Temple U) Section accelerate
      USER-PHONON
      USER-PHONON phonon dynamical matrix Ling-Ti Kong (Shanghai Jiao Tong U) fix phonon
      USER-QMMM
      USER-QMMM QM/MM coupling Axel Kohlmeyer (Temple U) fix qmmm lib/qmmm
      USER-QTB
      USER-QTB quantum nuclear effects Yuan Shen (Stanford) fix qtb fix_qbmsst
      USER-QUIP
      USER-QUIP QUIP/libatoms interface Albert Bartok-Partay (U Cambridge) pair_style quip lib/quip
      USER-REAXC
      USER-REAXC C version of ReaxFF Metin Aktulga (LBNL) pair_style reaxc
      USER-SMD
      USER-SMD smoothed Mach dynamics Georg Ganzenmuller (EMI) userguide.pdf
      USER-SMTBQ
      USER-SMTBQ Second Moment Tight Binding - QEq potential Salles & Maras & Politano & Tetot (4) pair_style smtbq
      USER-SPH
      USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI) userguide.pdf
      USER-TALLY
      USER-TALLY Pairwise tallied computes Axel Kohlmeyer (Temple U) compute
       
             
      ` + +.. _global: + +Global/per-atom/local data +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Various output-related commands work with three different styles of +data: global, per-atom, or local. A global datum is one or more +system-wide values, e.g. the temperature of the system. A per-atom +datum is one or more values per atom, e.g. the kinetic energy of each +atom. Local datums are calculated by each processor based on the +atoms it owns, but there may be zero or more per atom, e.g. a list of +bond distances. + +.. _scalar: + +Scalar/vector/array data +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Global, per-atom, and local datums can each come in three kinds: a +single scalar value, a vector of values, or a 2d array of values. The +doc page for a "compute" or "fix" or "variable" that generates data +will specify both the style and kind of data it produces, e.g. a +per-atom vector. + +When a quantity is accessed, as in many of the output commands +discussed below, it can be referenced via the following bracket +notation, where ID in this case is the ID of a compute. The leading +"c_" would be replaced by "f_" for a fix, or "v_" for a variable: + ++------------+--------------------------------------------+ +| c_ID | entire scalar, vector, or array | ++------------+--------------------------------------------+ +| c_ID[I] | one element of vector, one column of array | ++------------+--------------------------------------------+ +| c_ID[I][J] | one element of array | ++------------+--------------------------------------------+ + +In other words, using one bracket reduces the dimension of the data +once (vector -> scalar, array -> vector). Using two brackets reduces +the dimension twice (array -> scalar). Thus a command that uses +scalar values as input can typically also process elements of a vector +or array. + +.. _thermo: + +Thermodynamic output +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The frequency and format of thermodynamic output is set by the +:doc:`thermo `, :doc:`thermo_style `, and +:doc:`thermo_modify ` commands. The +:doc:`thermo_style ` command also specifies what values +are calculated and written out. Pre-defined keywords can be specified +(e.g. press, etotal, etc). Three additional kinds of keywords can +also be specified (c_ID, f_ID, v_name), where a :doc:`compute ` +or :doc:`fix ` or :doc:`variable ` provides the value to be +output. In each case, the compute, fix, or variable must generate +global values for input to the :doc:`thermo_style custom ` +command. + +Note that thermodynamic output values can be "extensive" or +"intensive". The former scale with the number of atoms in the system +(e.g. total energy), the latter do not (e.g. temperature). The +setting for :doc:`thermo_modify norm ` determines whether +extensive quantities are normalized or not. Computes and fixes +produce either extensive or intensive values; see their individual doc +pages for details. :doc:`Equal-style variables ` produce only +intensive values; you can include a division by "natoms" in the +formula if desired, to make an extensive calculation produce an +intensive result. + +.. _dump: + +Dump file output +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Dump file output is specified by the :doc:`dump ` and +:doc:`dump_modify ` commands. There are several +pre-defined formats (dump atom, dump xtc, etc). + +There is also a :doc:`dump custom ` format where the user +specifies what values are output with each atom. Pre-defined atom +attributes can be specified (id, x, fx, etc). Three additional kinds +of keywords can also be specified (c_ID, f_ID, v_name), where a +:doc:`compute ` or :doc:`fix ` or :doc:`variable ` +provides the values to be output. In each case, the compute, fix, or +variable must generate per-atom values for input to the :doc:`dump custom ` command. + +There is also a :doc:`dump local ` format where the user specifies +what local values to output. A pre-defined index keyword can be +specified to enumuerate the local values. Two additional kinds of +keywords can also be specified (c_ID, f_ID), where a +:doc:`compute ` or :doc:`fix ` or :doc:`variable ` +provides the values to be output. In each case, the compute or fix +must generate local values for input to the :doc:`dump local ` +command. + +.. _fixoutput: + +Fixes that write output files +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Several fixes take various quantities as input and can write output +files: :doc:`fix ave/time `, :doc:`fix ave/spatial `, :doc:`fix ave/histo `, +:doc:`fix ave/correlate `, and :doc:`fix print `. + +The :doc:`fix ave/time ` command enables direct output to +a file and/or time-averaging of global scalars or vectors. The user +specifies one or more quantities as input. These can be global +:doc:`compute ` values, global :doc:`fix ` values, or +:doc:`variables ` of any style except the atom style which +produces per-atom values. Since a variable can refer to keywords used +by the :doc:`thermo_style custom ` command (like temp or +press) and individual per-atom values, a wide variety of quantities +can be time averaged and/or output in this way. If the inputs are one +or more scalar values, then the fix generate a global scalar or vector +of output. If the inputs are one or more vector values, then the fix +generates a global vector or array of output. The time-averaged +output of this fix can also be used as input to other output commands. + +The :doc:`fix ave/spatial ` command enables direct +output to a file of spatial-averaged per-atom quantities like those +output in dump files, within 1d layers of the simulation box. The +per-atom quantities can be atom density (mass or number) or atom +attributes such as position, velocity, force. They can also be +per-atom quantities calculated by a :doc:`compute `, by a +:doc:`fix `, or by an atom-style :doc:`variable `. The +spatial-averaged output of this fix can also be used as input to other +output commands. + +The :doc:`fix ave/histo ` command enables direct output +to a file of histogrammed quantities, which can be global or per-atom +or local quantities. The histogram output of this fix can also be +used as input to other output commands. + +The :doc:`fix ave/correlate ` command enables direct +output to a file of time-correlated quantities, which can be global +scalars. The correlation matrix output of this fix can also be used +as input to other output commands. + +The :doc:`fix print ` command can generate a line of output +written to the screen and log file or to a separate file, periodically +during a running simulation. The line can contain one or more +:doc:`variable ` values for any style variable except the atom +style). As explained above, variables themselves can contain +references to global values generated by :doc:`thermodynamic keywords `, :doc:`computes `, +:doc:`fixes `, or other :doc:`variables `, or to per-atom +values for a specific atom. Thus the :doc:`fix print ` +command is a means to output a wide variety of quantities separate +from normal thermodynamic or dump file output. + +.. _computeoutput: + +Computes that process output quantities +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The :doc:`compute reduce ` and :doc:`compute reduce/region ` commands take one or more per-atom +or local vector quantities as inputs and "reduce" them (sum, min, max, +ave) to scalar quantities. These are produced as output values which +can be used as input to other output commands. + +The :doc:`compute slice ` command take one or more global +vector or array quantities as inputs and extracts a subset of their +values to create a new vector or array. These are produced as output +values which can be used as input to other output commands. + +The :doc:`compute property/atom ` command takes a +list of one or more pre-defined atom attributes (id, x, fx, etc) and +stores the values in a per-atom vector or array. These are produced +as output values which can be used as input to other output commands. +The list of atom attributes is the same as for the :doc:`dump custom ` command. + +The :doc:`compute property/local ` command takes +a list of one or more pre-defined local attributes (bond info, angle +info, etc) and stores the values in a local vector or array. These +are produced as output values which can be used as input to other +output commands. + +.. _fixoutput: + +Fixes that process output quantities +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The :doc:`fix vector ` command can create global vectors as +output from global scalars as input, accumulating them one element at +a time. + +The :doc:`fix ave/atom ` command performs time-averaging +of per-atom vectors. The per-atom quantities can be atom attributes +such as position, velocity, force. They can also be per-atom +quantities calculated by a :doc:`compute `, by a +:doc:`fix `, or by an atom-style :doc:`variable `. The +time-averaged per-atom output of this fix can be used as input to +other output commands. + +The :doc:`fix store/state ` command can archive one or +more per-atom attributes at a particular time, so that the old values +can be used in a future calculation or output. The list of atom +attributes is the same as for the :doc:`dump custom ` command, +including per-atom quantities calculated by a :doc:`compute `, +by a :doc:`fix `, or by an atom-style :doc:`variable `. +The output of this fix can be used as input to other output commands. + +.. _compute: + +Computes that generate values to output +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Every :doc:`compute ` in LAMMPS produces either global or +per-atom or local values. The values can be scalars or vectors or +arrays of data. These values can be output using the other commands +described in this section. The doc page for each compute command +describes what it produces. Computes that produce per-atom or local +values have the word "atom" or "local" in their style name. Computes +without the word "atom" or "local" produce global values. + +.. _fix: + +Fixes that generate values to output +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Some :doc:`fixes ` in LAMMPS produces either global or per-atom or +local values which can be accessed by other commands. The values can +be scalars or vectors or arrays of data. These values can be output +using the other commands described in this section. The doc page for +each fix command tells whether it produces any output quantities and +describes them. + +.. _variable: + +Variables that generate values to output +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Every :doc:`variables ` defined in an input script generates +either a global scalar value or a per-atom vector (only atom-style +variables) when it is accessed. The formulas used to define equal- +and atom-style variables can contain references to the thermodynamic +keywords and to global and per-atom data generated by computes, fixes, +and other variables. The values generated by variables can be output +using the other commands described in this section. + +.. _table: + +Summary table of output options and data flow between commands +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +This table summarizes the various commands that can be used for +generating output from LAMMPS. Each command produces output data of +some kind and/or writes data to a file. Most of the commands can take +data from other commands as input. Thus you can link many of these +commands together in pipeline form, where data produced by one command +is used as input to another command and eventually written to the +screen or to a file. Note that to hook two commands together the +output and input data types must match, e.g. global/per-atom/local +data and scalar/vector/array data. + +Also note that, as described above, when a command takes a scalar as +input, that could be an element of a vector or array. Likewise a +vector input could be a column of an array. + ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| Command | Input | Output | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`thermo_style custom ` | global scalars | screen, log file | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`dump custom ` | per-atom vectors | dump file | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`dump local ` | local vectors | dump file | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fix print ` | global scalar from variable | screen, file | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`print ` | global scalar from variable | screen | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`computes ` | N/A | global/per-atom/local scalar/vector/array | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fixes ` | N/A | global/per-atom/local scalar/vector/array | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`variables ` | global scalars, per-atom vectors | global scalar, per-atom vector | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`compute reduce ` | per-atom/local vectors | global scalar/vector | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`compute slice ` | global vectors/arrays | global vector/array | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`compute property/atom ` | per-atom vectors | per-atom vector/array | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`compute property/local ` | local vectors | local vector/array | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fix vector ` | global scalars | global vector | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fix ave/atom ` | per-atom vectors | per-atom vector/array | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fix ave/time ` | global scalars/vectors | global scalar/vector/array, file | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fix ave/spatial ` | per-atom vectors | global array, file | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fix ave/histo ` | global/per-atom/local scalars and vectors | global array, file | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fix ave/correlate ` | global scalars | global array, file | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| :doc:`fix store/state ` | per-atom vectors | per-atom vector/array | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ +| | | | | ++--------------------------------------------------------+-------------------------------------------+-------------------------------------------+--+ + + +---------- + + +.. _howto_16: + +Thermostatting, barostatting, and computing temperature +------------------------------------------------------- + +Thermostatting means controlling the temperature of particles in an MD +simulation. Barostatting means controlling the pressure. Since the +pressure includes a kinetic component due to particle velocities, both +these operations require calculation of the temperature. Typically a +target temperature (T) and/or pressure (P) is specified by the user, +and the thermostat or barostat attempts to equilibrate the system to +the requested T and/or P. + +Temperature is computed as kinetic energy divided by some number of +degrees of freedom (and the Boltzmann constant). Since kinetic energy +is a function of particle velocity, there is often a need to +distinguish between a particle's advection velocity (due to some +aggregate motiion of particles) and its thermal velocity. The sum of +the two is the particle's total velocity, but the latter is often what +is wanted to compute a temperature. + +LAMMPS has several options for computing temperatures, any of which +can be used in thermostatting and barostatting. These :doc:`compute commands ` calculate temperature, and the :doc:`compute pressure ` command calculates pressure. + +* :doc:`compute temp ` +* :doc:`compute temp/sphere ` +* :doc:`compute temp/asphere ` +* :doc:`compute temp/com ` +* :doc:`compute temp/deform ` +* :doc:`compute temp/partial ` +* :doc:`compute temp/profile ` +* :doc:`compute temp/ramp ` +* :doc:`compute temp/region ` + +All but the first 3 calculate velocity biases directly (e.g. advection +velocities) that are removed when computing the thermal temperature. +:doc:`Compute temp/sphere ` and :doc:`compute temp/asphere ` compute kinetic energy for +finite-size particles that includes rotational degrees of freedom. +They both allow for velocity biases indirectly, via an optional extra +argument, another temperature compute that subtracts a velocity bias. +This allows the translational velocity of spherical or aspherical +particles to be adjusted in prescribed ways. + +Thermostatting in LAMMPS is performed by :doc:`fixes `, or in one +case by a pair style. Several thermostatting fixes are available: +Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling +(temp/rescale). Dissipative particle dynamics (DPD) thermostatting +can be invoked via the *dpd/tstat* pair style: + +* :doc:`fix nvt ` +* :doc:`fix nvt/sphere ` +* :doc:`fix nvt/asphere ` +* :doc:`fix nvt/sllod ` +* :doc:`fix temp/berendsen ` +* :doc:`fix temp/csvr ` +* :doc:`fix langevin ` +* :doc:`fix temp/rescale ` +* :doc:`pair_style dpd/tstat ` + +:doc:`Fix nvt ` only thermostats the translational velocity of +particles. :doc:`Fix nvt/sllod ` also does this, except +that it subtracts out a velocity bias due to a deforming box and +integrates the SLLOD equations of motion. See the :ref:`NEMD simulations ` section of this page for further details. :doc:`Fix nvt/sphere ` and :doc:`fix nvt/asphere ` thermostat not only translation +velocities but also rotational velocities for spherical and aspherical +particles. + +DPD thermostatting alters pairwise interactions in a manner analagous +to the per-particle thermostatting of :doc:`fix langevin `. + +Any of the thermostatting fixes can use temperature computes that +remove bias which has two effects. First, the current calculated +temperature, which is compared to the requested target temperature, is +caluclated with the velocity bias removed. Second, the thermostat +adjusts only the thermal temperature component of the particle's +velocities, which are the velocities with the bias removed. The +removed bias is then added back to the adjusted velocities. See the +doc pages for the individual fixes and for the +:doc:`fix_modify ` command for instructions on how to assign +a temperature compute to a thermostatting fix. For example, you can +apply a thermostat to only the x and z components of velocity by using +it in conjunction with :doc:`compute temp/partial `. Of you could thermostat only +the thermal temperature of a streaming flow of particles without +affecting the streaming velocity, by using :doc:`compute temp/profile `. + +.. note:: + + Only the nvt fixes perform time integration, meaning they update + the velocities and positions of particles due to forces and velocities + respectively. The other thermostat fixes only adjust velocities; they + do NOT perform time integration updates. Thus they should be used in + conjunction with a constant NVE integration fix such as these: + +* :doc:`fix nve ` +* :doc:`fix nve/sphere ` +* :doc:`fix nve/asphere ` + +Barostatting in LAMMPS is also performed by :doc:`fixes `. Two +barosttating methods are currently available: Nose-Hoover (npt and +nph) and Berendsen: + +* :doc:`fix npt ` +* :doc:`fix npt/sphere ` +* :doc:`fix npt/asphere ` +* :doc:`fix nph ` +* :doc:`fix press/berendsen ` + +The :doc:`fix npt ` commands include a Nose-Hoover thermostat +and barostat. :doc:`Fix nph ` is just a Nose/Hoover barostat; +it does no thermostatting. Both :doc:`fix nph ` and :doc:`fix press/bernendsen ` can be used in conjunction +with any of the thermostatting fixes. + +As with the thermostats, :doc:`fix npt ` and :doc:`fix nph ` only use translational motion of the particles in +computing T and P and performing thermo/barostatting. :doc:`Fix npt/sphere ` and :doc:`fix npt/asphere ` thermo/barostat using not only +translation velocities but also rotational velocities for spherical +and aspherical particles. + +All of the barostatting fixes use the :doc:`compute pressure ` compute to calculate a current +pressure. By default, this compute is created with a simple :doc:`compute temp ` (see the last argument of the :doc:`compute pressure ` command), which is used to calculated +the kinetic componenet of the pressure. The barostatting fixes can +also use temperature computes that remove bias for the purpose of +computing the kinetic componenet which contributes to the current +pressure. See the doc pages for the individual fixes and for the +:doc:`fix_modify ` command for instructions on how to assign +a temperature or pressure compute to a barostatting fix. + +.. note:: + + As with the thermostats, the Nose/Hoover methods (:doc:`fix npt ` and :doc:`fix nph `) perform time integration. + :doc:`Fix press/berendsen ` does NOT, so it should + be used with one of the constant NVE fixes or with one of the NVT + fixes. + +Finally, thermodynamic output, which can be setup via the +:doc:`thermo_style ` command, often includes temperature +and pressure values. As explained on the doc page for the +:doc:`thermo_style ` command, the default T and P are +setup by the thermo command itself. They are NOT the ones associated +with any thermostatting or barostatting fix you have defined or with +any compute that calculates a temperature or pressure. Thus if you +want to view these values of T and P, you need to specify them +explicitly via a :doc:`thermo_style custom ` command. Or +you can use the :doc:`thermo_modify ` command to +re-define what temperature or pressure compute is used for default +thermodynamic output. + + +---------- + + +.. _howto_17: + +Walls +----- + +Walls in an MD simulation are typically used to bound particle motion, +i.e. to serve as a boundary condition. + +Walls in LAMMPS can be of rough (made of particles) or idealized +surfaces. Ideal walls can be smooth, generating forces only in the +normal direction, or frictional, generating forces also in the +tangential direction. + +Rough walls, built of particles, can be created in various ways. The +particles themselves can be generated like any other particle, via the +:doc:`lattice ` and :doc:`create_atoms ` commands, +or read in via the :doc:`read_data ` command. + +Their motion can be constrained by many different commands, so that +they do not move at all, move together as a group at constant velocity +or in response to a net force acting on them, move in a prescribed +fashion (e.g. rotate around a point), etc. Note that if a time +integration fix like :doc:`fix nve ` or :doc:`fix nvt ` +is not used with the group that contains wall particles, their +positions and velocities will not be updated. + +* :doc:`fix aveforce ` - set force on particles to average value, so they move together +* :doc:`fix setforce ` - set force on particles to a value, e.g. 0.0 +* :doc:`fix freeze ` - freeze particles for use as granular walls +* :doc:`fix nve/noforce ` - advect particles by their velocity, but without force +* :doc:`fix move ` - prescribe motion of particles by a linear velocity, oscillation, rotation, variable + +The :doc:`fix move ` command offers the most generality, since +the motion of individual particles can be specified with +:doc:`variable ` formula which depends on time and/or the +particle position. + +For rough walls, it may be useful to turn off pairwise interactions +between wall particles via the :doc:`neigh_modify exclude ` command. + +Rough walls can also be created by specifying frozen particles that do +not move and do not interact with mobile particles, and then tethering +other particles to the fixed particles, via a :doc:`bond `. +The bonded particles do interact with other mobile particles. + +Idealized walls can be specified via several fix commands. :doc:`Fix wall/gran ` creates frictional walls for use with +granular particles; all the other commands create smooth walls. + +* :doc:`fix wall/reflect ` - reflective flat walls +* :doc:`fix wall/lj93 ` - flat walls, with Lennard-Jones 9/3 potential +* :doc:`fix wall/lj126 ` - flat walls, with Lennard-Jones 12/6 potential +* :doc:`fix wall/colloid ` - flat walls, with :doc:`pair_style colloid ` potential +* :doc:`fix wall/harmonic ` - flat walls, with repulsive harmonic spring potential +* :doc:`fix wall/region ` - use region surface as wall +* :doc:`fix wall/gran ` - flat or curved walls with :doc:`pair_style granular ` potential + +The *lj93*, *lj126*, *colloid*, and *harmonic* styles all allow the +flat walls to move with a constant velocity, or oscillate in time. +The :doc:`fix wall/region ` command offers the most +generality, since the region surface is treated as a wall, and the +geometry of the region can be a simple primitive volume (e.g. a +sphere, or cube, or plane), or a complex volume made from the union +and intersection of primitive volumes. :doc:`Regions ` can also +specify a volume "interior" or "exterior" to the specified primitive +shape or *union* or *intersection*. :doc:`Regions ` can also be +"dynamic" meaning they move with constant velocity, oscillate, or +rotate. + +The only frictional idealized walls currently in LAMMPS are flat or +curved surfaces specified by the :doc:`fix wall/gran ` +command. At some point we plan to allow regoin surfaces to be used as +frictional walls, as well as triangulated surfaces. + + +---------- + + +.. _howto_18: + +Elastic constants +----------------- + +Elastic constants characterize the stiffness of a material. The formal +definition is provided by the linear relation that holds between the +stress and strain tensors in the limit of infinitesimal deformation. +In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where +the repeated indices imply summation. s_ij are the elements of the +symmetric stress tensor. e_kl are the elements of the symmetric strain +tensor. C_ijkl are the elements of the fourth rank tensor of elastic +constants. In three dimensions, this tensor has 3^4=81 elements. Using +Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij +is now the derivative of s_i w.r.t. e_j. Because s_i is itself a +derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at +most 7*6/2 = 21 distinct elements. + +At zero temperature, it is easy to estimate these derivatives by +deforming the simulation box in one of the six directions using the +:doc:`change_box ` command and measuring the change in the +stress tensor. A general-purpose script that does this is given in the +examples/elastic directory described in :doc:`this section `. + +Calculating elastic constants at finite temperature is more +challenging, because it is necessary to run a simulation that perfoms +time averages of differential properties. One way to do this is to +measure the change in average stress tensor in an NVT simulations when +the cell volume undergoes a finite deformation. In order to balance +the systematic and statistical errors in this method, the magnitude of +the deformation must be chosen judiciously, and care must be taken to +fully equilibrate the deformed cell before sampling the stress +tensor. Another approach is to sample the triclinic cell fluctuations +that occur in an NPT simulation. This method can also be slow to +converge and requires careful post-processing :ref:`(Shinoda) ` + + +---------- + + +.. _howto_19: + +Library interface to LAMMPS +--------------------------- + +As described in :ref:`Section_start 5 `, LAMMPS +can be built as a library, so that it can be called by another code, +used in a :ref:`coupled manner ` with other +codes, or driven through a :doc:`Python interface `. + +All of these methodologies use a C-style interface to LAMMPS that is +provided in the files src/library.cpp and src/library.h. The +functions therein have a C-style argument list, but contain C++ code +you could write yourself in a C++ application that was invoking LAMMPS +directly. The C++ code in the functions illustrates how to invoke +internal LAMMPS operations. Note that LAMMPS classes are defined +within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ +application. + +Library.cpp contains these 5 basic functions: + +.. parsed-literal:: + + void lammps_open(int, char **, MPI_Comm, void **) + void lammps_close(void *) + int lammps_version(void *) + void lammps_file(void *, char *) + char *lammps_command(void *, char *) + +The lammps_open() function is used to initialize LAMMPS, passing in a +list of strings as if they were :ref:`command-line arguments ` when LAMMPS is run in +stand-alone mode from the command line, and a MPI communicator for +LAMMPS to run under. It returns a ptr to the LAMMPS object that is +created, and which is used in subsequent library calls. The +lammps_open() function can be called multiple times, to create +multiple instances of LAMMPS. + +LAMMPS will run on the set of processors in the communicator. This +means the calling code can run LAMMPS on all or a subset of +processors. For example, a wrapper script might decide to alternate +between LAMMPS and another code, allowing them both to run on all the +processors. Or it might allocate half the processors to LAMMPS and +half to the other code and run both codes simultaneously before +syncing them up periodically. Or it might instantiate multiple +instances of LAMMPS to perform different calculations. + +The lammps_close() function is used to shut down an instance of LAMMPS +and free all its memory. + +The lammps_version() function can be used to determined the specific +version of the underlying LAMMPS code. This is particularly useful +when loading LAMMPS as a shared library via dlopen(). The code using +the library interface can than use this information to adapt to +changes to the LAMMPS command syntax between versions. The returned +LAMMPS version code is an integer (e.g. 2 Sep 2015 results in +20150902) that grows with every new LAMMPS version. + +The lammps_file() and lammps_command() functions are used to pass a +file or string to LAMMPS as if it were an input script or single +command in an input script. Thus the calling code can read or +generate a series of LAMMPS commands one line at a time and pass it +thru the library interface to setup a problem and then run it, +interleaving the lammps_command() calls with other calls to extract +information from LAMMPS, perform its own operations, or call another +code's library. + +Other useful functions are also included in library.cpp. For example: + +.. parsed-literal:: + + void *lammps_extract_global(void *, char *) + void *lammps_extract_atom(void *, char *) + void *lammps_extract_compute(void *, char *, int, int) + void *lammps_extract_fix(void *, char *, int, int, int, int) + void *lammps_extract_variable(void *, char *, char *) + int lammps_set_variable(void *, char *, char *) + int lammps_get_natoms(void *) + void lammps_get_coords(void *, double *) + void lammps_put_coords(void *, double *) + +These can extract various global or per-atom quantities from LAMMPS as +well as values calculated by a compute, fix, or variable. The +"set_variable" function can set an existing string-style variable to a +new value, so that subsequent LAMMPS commands can access the variable. +The "get" and "put" operations can retrieve and reset atom +coordinates. See the library.cpp file and its associated header file +library.h for details. + +The key idea of the library interface is that you can write any +functions you wish to define how your code talks to LAMMPS and add +them to src/library.cpp and src/library.h, as well as to the :doc:`Python interface `. The routines you add can access or +change any LAMMPS data you wish. The examples/COUPLE and python +directories have example C++ and C and Python codes which show how a +driver code can link to LAMMPS as a library, run LAMMPS on a subset of +processors, grab data from LAMMPS, change it, and put it back into +LAMMPS. + + +---------- + + +.. _howto_20: + +Calculating thermal conductivity +-------------------------------- + +The thermal conductivity kappa of a material can be measured in at +least 4 ways using various options in LAMMPS. See the examples/KAPPA +directory for scripts that implement the 4 methods discussed here for +a simple Lennard-Jones fluid model. Also, see :ref:`this section ` of the manual for an analogous +discussion for viscosity. + +The thermal conducitivity tensor kappa is a measure of the propensity +of a material to transmit heat energy in a diffusive manner as given +by Fourier's law + +J = -kappa grad(T) + +where J is the heat flux in units of energy per area per time and +grad(T) is the spatial gradient of temperature. The thermal +conductivity thus has units of energy per distance per time per degree +K and is often approximated as an isotropic quantity, i.e. as a +scalar. + +The first method is to setup two thermostatted regions at opposite +ends of a simulation box, or one in the middle and one at the end of a +periodic box. By holding the two regions at different temperatures +with a :ref:`thermostatting fix `, the energy +added to the hot region should equal the energy subtracted from the +cold region and be proportional to the heat flux moving between the +regions. See the paper by :ref:`Ikeshoji and Hafskjold ` for +details of this idea. Note that thermostatting fixes such as :doc:`fix nvt `, :doc:`fix langevin `, and :doc:`fix temp/rescale ` store the cumulative energy they +add/subtract. + +Alternatively, as a second method, the :doc:`fix heat ` +command can used in place of thermostats on each of two regions to +add/subtract specified amounts of energy to both regions. In both +cases, the resulting temperatures of the two regions can be monitored +with the "compute temp/region" command and the temperature profile of +the intermediate region can be monitored with the :doc:`fix ave/spatial ` and :doc:`compute ke/atom ` commands. + +The third method is to perform a reverse non-equilibrium MD simulation +using the :doc:`fix thermal/conductivity ` +command which implements the rNEMD algorithm of Muller-Plathe. +Kinetic energy is swapped between atoms in two different layers of the +simulation box. This induces a temperature gradient between the two +layers which can be monitored with the :doc:`fix ave/spatial ` and :doc:`compute ke/atom ` commands. The fix tallies the +cumulative energy transfer that it performs. See the :doc:`fix thermal/conductivity ` command for +details. + +The fourth method is based on the Green-Kubo (GK) formula which +relates the ensemble average of the auto-correlation of the heat flux +to kappa. The heat flux can be calculated from the fluctuations of +per-atom potential and kinetic energies and per-atom stress tensor in +a steady-state equilibrated simulation. This is in contrast to the +two preceding non-equilibrium methods, where energy flows continuously +between hot and cold regions of the simulation box. + +The :doc:`compute heat/flux ` command can calculate +the needed heat flux and describes how to implement the Green_Kubo +formalism using additional LAMMPS commands, such as the :doc:`fix ave/correlate ` command to calculate the needed +auto-correlation. See the doc page for the :doc:`compute heat/flux ` command for an example input script +that calculates the thermal conductivity of solid Ar via the GK +formalism. + + +---------- + + +.. _howto_21: + +Calculating viscosity +--------------------- + +The shear viscosity eta of a fluid can be measured in at least 4 ways +using various options in LAMMPS. See the examples/VISCOSITY directory +for scripts that implement the 4 methods discussed here for a simple +Lennard-Jones fluid model. Also, see :ref:`this section ` of the manual for an analogous +discussion for thermal conductivity. + +Eta is a measure of the propensity of a fluid to transmit momentum in +a direction perpendicular to the direction of velocity or momentum +flow. Alternatively it is the resistance the fluid has to being +sheared. It is given by + +J = -eta grad(Vstream) + +where J is the momentum flux in units of momentum per area per time. +and grad(Vstream) is the spatial gradient of the velocity of the fluid +moving in another direction, normal to the area through which the +momentum flows. Viscosity thus has units of pressure-time. + +The first method is to perform a non-equlibrium MD (NEMD) simulation +by shearing the simulation box via the :doc:`fix deform ` +command, and using the :doc:`fix nvt/sllod ` command to +thermostat the fluid via the SLLOD equations of motion. +Alternatively, as a second method, one or more moving walls can be +used to shear the fluid in between them, again with some kind of +thermostat that modifies only the thermal (non-shearing) components of +velocity to prevent the fluid from heating up. + +In both cases, the velocity profile setup in the fluid by this +procedure can be monitored by the :doc:`fix ave/spatial ` command, which determines +grad(Vstream) in the equation above. E.g. the derivative in the +y-direction of the Vx component of fluid motion or grad(Vstream) = +dVx/dy. The Pxy off-diagonal component of the pressure or stress +tensor, as calculated by the :doc:`compute pressure ` +command, can also be monitored, which is the J term in the equation +above. See :ref:`this section ` of the manual +for details on NEMD simulations. + +The third method is to perform a reverse non-equilibrium MD simulation +using the :doc:`fix viscosity ` command which implements +the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is +swapped between atoms in two different layers of the simulation box in +a different dimension. This induces a velocity gradient which can be +monitored with the :doc:`fix ave/spatial ` command. +The fix tallies the cummulative momentum transfer that it performs. +See the :doc:`fix viscosity ` command for details. + +The fourth method is based on the Green-Kubo (GK) formula which +relates the ensemble average of the auto-correlation of the +stress/pressure tensor to eta. This can be done in a steady-state +equilibrated simulation which is in contrast to the two preceding +non-equilibrium methods, where momentum flows continuously through the +simulation box. + +Here is an example input script that calculates the viscosity of +liquid Ar via the GK formalism: + +.. parsed-literal:: + + # Sample LAMMPS input script for viscosity of liquid Ar + +.. parsed-literal:: + + units real + variable T equal 86.4956 + variable V equal vol + variable dt equal 4.0 + variable p equal 400 # correlation length + variable s equal 5 # sample interval + variable d equal $p*$s # dump interval + +.. parsed-literal:: + + # convert from LAMMPS real units to SI + +.. parsed-literal:: + + variable kB equal 1.3806504e-23 # [J/K/** Boltzmann + variable atm2Pa equal 101325.0 + variable A2m equal 1.0e-10 + variable fs2s equal 1.0e-15 + variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m} + +.. parsed-literal:: + + # setup problem + +.. parsed-literal:: + + dimension 3 + boundary p p p + lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 + region box block 0 4 0 4 0 4 + create_box 1 box + create_atoms 1 box + mass 1 39.948 + pair_style lj/cut 13.0 + pair_coeff * * 0.2381 3.405 + timestep ${dt} + thermo $d + +.. parsed-literal:: + + # equilibration and thermalization + +.. parsed-literal:: + + velocity all create $T 102486 mom yes rot yes dist gaussian + fix NVT all nvt temp $T $T 10 drag 0.2 + run 8000 + +.. parsed-literal:: + + # viscosity calculation, switch to NVE if desired + +.. parsed-literal:: + + #unfix NVT + #fix NVE all nve + +.. parsed-literal:: + + reset_timestep 0 + variable pxy equal pxy + variable pxz equal pxz + variable pyz equal pyz + fix SS all ave/correlate $s $p $d & + v_pxy v_pxz v_pyz type auto file S0St.dat ave running + variable scale equal ${convert}/(${kB}*$T)*$V*$s*${dt} + variable v11 equal trap(f_SS[3])*${scale} + variable v22 equal trap(f_SS[4])*${scale} + variable v33 equal trap(f_SS[5])*${scale} + thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 + run 100000 + variable v equal (v_v11+v_v22+v_v33)/3.0 + variable ndens equal count(all)/vol + print "average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3" + + +---------- + + +.. _howto_22: + +Calculating a diffusion coefficient +----------------------------------- + +The diffusion coefficient D of a material can be measured in at least +2 ways using various options in LAMMPS. See the examples/DIFFUSE +directory for scripts that implement the 2 methods discussed here for +a simple Lennard-Jones fluid model. + +The first method is to measure the mean-squared displacement (MSD) of +the system, via the :doc:`compute msd ` command. The slope +of the MSD versus time is proportional to the diffusion coefficient. +The instantaneous MSD values can be accumulated in a vector via the +:doc:`fix vector ` command, and a line fit to the vector to +compute its slope via the :doc:`variable slope ` function, and +thus extract D. + +The second method is to measure the velocity auto-correlation function +(VACF) of the system, via the :doc:`compute vacf ` +command. The time-integral of the VACF is proportional to the +diffusion coefficient. The instantaneous VACF values can be +accumulated in a vector via the :doc:`fix vector ` command, +and time integrated via the :doc:`variable trap ` function, +and thus extract D. + + +---------- + + +.. _howto_23: + +Using chunks to calculate system properties +------------------------------------------- + +In LAMMS, "chunks" are collections of atoms, as defined by the +:doc:`compute chunk/atom ` command, which assigns +each atom to a chunk ID (or to no chunk at all). The number of chunks +and the assignment of chunk IDs to atoms can be static or change over +time. Examples of "chunks" are molecules or spatial bins or atoms +with similar values (e.g. coordination number or potential energy). + +The per-atom chunk IDs can be used as input to two other kinds of +commands, to calculate various properties of a system: + +* :doc:`fix ave/chunk ` +* any of the :doc:`compute */chunk ` commands + +Here, each of the 3 kinds of chunk-related commands is briefly +overviewed. Then some examples are given of how to compute different +properties with chunk commands. + +Compute chunk/atom command: +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +This compute can assign atoms to chunks of various styles. Only atoms +in the specified group and optional specified region are assigned to a +chunk. Here are some possible chunk definitions: + ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ +| atoms in same molecule | chunk ID = molecule ID | ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ +| atoms of same atom type | chunk ID = atom type | ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ +| all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom | ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ +| atoms in same cluster | chunk ID = output of :doc:`compute cluster/atom ` command | ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ +| atoms in same spatial bin | chunk ID = bin ID | ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ +| atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies | ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ +| atoms with similar potential energy | chunk ID = output of :doc:`compute pe/atom ` | ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ +| atoms with same local defect structure | chunk ID = output of :doc:`compute centro/atom ` or :doc:`compute coord/atom ` command | ++---------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------+ + +Note that chunk IDs are integer values, so for atom properties or +computes that produce a floating point value, they will be truncated +to an integer. You could also use the compute in a variable that +scales the floating point value to spread it across multiple intergers. + +Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = +pencils, 3d bins = boxes, spherical bins, cylindrical bins. + +This compute also calculates the number of chunks *Nchunk*, which is +used by other commands to tally per-chunk data. *Nchunk* can be a +static value or change over time (e.g. the number of clusters). The +chunk ID for an individual atom can also be static (e.g. a molecule +ID), or dynamic (e.g. what spatial bin an atom is in as it moves). + +Note that this compute allows the per-atom output of other +:doc:`computes `, :doc:`fixes `, and +:doc:`variables ` to be used to define chunk IDs for each +atom. This means you can write your own compute or fix to output a +per-atom quantity to use as chunk ID. See +:doc:`Section_modify ` of the documentation for how to +do this. You can also define a :doc:`per-atom variable ` in +the input script that uses a formula to generate a chunk ID for each +atom. + +Fix ave/chunk command: +^^^^^^^^^^^^^^^^^^^^^^ + +This fix takes the ID of a :doc:`compute chunk/atom ` command as input. For each chunk, +it then sums one or more specified per-atom values over the atoms in +each chunk. The per-atom values can be any atom property, such as +velocity, force, charge, potential energy, kinetic energy, stress, +etc. Additional keywords are defined for per-chunk properties like +density and temperature. More generally any per-atom value generated +by other :doc:`computes `, :doc:`fixes `, and :doc:`per-atom variables `, can be summed over atoms in each chunk. + +Similar to other averaging fixes, this fix allows the summed per-chunk +values to be time-averaged in various ways, and output to a file. The +fix produces a global array as output with one row of values per +chunk. + +Compute */chunk commands: +^^^^^^^^^^^^^^^^^^^^^^^^^ + +Currently the following computes operate on chunks of atoms to produce +per-chunk values. + +* :doc:`compute com/chunk ` +* :doc:`compute gyration/chunk ` +* :doc:`compute inertia/chunk ` +* :doc:`compute msd/chunk ` +* :doc:`compute property/chunk ` +* :doc:`compute temp/chunk ` +* :doc:`compute torque/chunk ` +* :doc:`compute vcm/chunk ` + +They each take the ID of a :doc:`compute chunk/atom ` command as input. As their names +indicate, they calculate the center-of-mass, radius of gyration, +moments of inertia, mean-squared displacement, temperature, torque, +and velocity of center-of-mass for each chunk of atoms. The :doc:`compute property/chunk ` command can tally the +count of atoms in each chunk and extract other per-chunk properties. + +The reason these various calculations are not part of the :doc:`fix ave/chunk command `, is that each requires a more +complicated operation than simply summing and averaging over per-atom +values in each chunk. For example, many of them require calculation +of a center of mass, which requires summing mass*position over the +atoms and then dividing by summed mass. + +All of these computes produce a global vector or global array as +output, wih one or more values per chunk. They can be used +in various ways: + +* As input to the :doc:`fix ave/time ` command, which can + write the values to a file and optionally time average them. +* As input to the :doc:`fix ave/histo ` command to + histogram values across chunks. E.g. a histogram of cluster sizes or + molecule diffusion rates. +* As input to special functions of :doc:`equal-style variables `, like sum() and max(). E.g. to find the + largest cluster or fastest diffusing molecule. +Example calculations with chunks +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Here are eaxmples using chunk commands to calculate various +properties: + +(1) Average velocity in each of 1000 2d spatial bins: + +.. parsed-literal:: + + compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced + fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out + +(2) Temperature in each spatial bin, after subtracting a flow +velocity: + +.. parsed-literal:: + + compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced + compute vbias all temp/profile 1 0 0 y 10 + fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out + +(3) Center of mass of each molecule: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all com/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +(4) Total force on each molecule and ave/max across all molecules: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out + variable xave equal ave(f_1**2**) + variable xmax equal max(f_1**2**) + thermo 1000 + thermo_style custom step temp v_xave v_xmax + +(5) Histogram of cluster sizes: + +.. parsed-literal:: + + compute cluster all cluster/atom 1.0 + compute cc1 all chunk/atom c_cluster compress yes + compute size all property/chunk cc1 count + fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo + + +---------- + + +.. _howto_24: + +Setting parameters for the :doc:`kspace_style pppm/disp ` command +------------------------------------------------------------------------------- + +The PPPM method computes interactions by splitting the pair potential +into two parts, one of which is computed in a normal pairwise fashion, +the so-called real-space part, and one of which is computed using the +Fourier transform, the so called reciprocal-space or kspace part. For +both parts, the potential is not computed exactly but is approximated. +Thus, there is an error in both parts of the computation, the +real-space and the kspace error. The just mentioned facts are true +both for the PPPM for Coulomb as well as dispersion interactions. The +deciding difference - and also the reason why the parameters for +pppm/disp have to be selected with more care - is the impact of the +errors on the results: The kspace error of the PPPM for Coulomb and +dispersion interaction and the real-space error of the PPPM for +Coulomb interaction have the character of noise. In contrast, the +real-space error of the PPPM for dispersion has a clear physical +interpretation: the underprediction of cohesion. As a consequence, the +real-space error has a much stronger effect than the kspace error on +simulation results for pppm/disp. Parameters must thus be chosen in a +way that this error is much smaller than the kspace error. + +When using pppm/disp and not making any specifications on the PPPM +parameters via the kspace modify command, parameters will be tuned +such that the real-space error and the kspace error are equal. This +will result in simulations that are either inaccurate or slow, both of +which is not desirable. For selecting parameters for the pppm/disp +that provide fast and accurate simulations, there are two approaches, +which both have their up- and downsides. + +The first approach is to set desired real-space an kspace accuracies +via the *kspace_modify force/disp/real* and *kspace_modify +force/disp/kspace* commands. Note that the accuracies have to be +specified in force units and are thus dependend on the chosen unit +settings. For real units, 0.0001 and 0.002 seem to provide reasonable +accurate and efficient computations for the real-space and kspace +accuracies. 0.002 and 0.05 work well for most systems using lj +units. PPPM parameters will be generated based on the desired +accuracies. The upside of this approach is that it usually provides a +good set of parameters and will work for both the *kspace_modify diff +ad* and *kspace_modify diff ik* options. The downside of the method +is that setting the PPPM parameters will take some time during the +initialization of the simulation. + +The second approach is to set the parameters for the pppm/disp +explicitly using the *kspace_modify mesh/disp*, *kspace_modify +order/disp*, and *kspace_modify gewald/disp* commands. This approach +requires a more experienced user who understands well the impact of +the choice of parameters on the simulation accuracy and +performance. This approach provides a fast initialization of the +simulation. However, it is sensitive to errors: A combination of +parameters that will perform well for one system might result in +far-from-optimal conditions for other simulations. For example, +parametes that provide accurate and fast computations for +all-atomistic force fields can provide insufficient accuracy or +united-atomistic force fields (which is related to that the latter +typically have larger dispersion coefficients). + +To avoid inaccurate or inefficient simulations, the pppm/disp stops +simulations with an error message if no action is taken to control the +PPPM parameters. If the automatic parameter generation is desired and +real-space and kspace accuracies are desired to be equal, this error +message can be suppressed using the *kspace_modify disp/auto yes* +command. + +A reasonable approach that combines the upsides of both methods is to +make the first run using the *kspace_modify force/disp/real* and +*kspace_modify force/disp/kspace* commands, write down the PPPM +parameters from the outut, and specify these parameters using the +second approach in subsequent runs (which have the same composition, +force field, and approximately the same volume). + +Concerning the performance of the pppm/disp there are two more things +to consider. The first is that when using the pppm/disp, the cutoff +parameter does no longer affect the accuracy of the simulation +(subject to that gewald/disp is adjusted when changing the cutoff). +The performance can thus be increased by examining different values +for the cutoff parameter. A lower bound for the cutoff is only set by +the truncation error of the repulsive term of pair potentials. + +The second is that the mixing rule of the pair style has an impact on +the computation time when using the pppm/disp. Fastest computations +are achieved when using the geometric mixing rule. Using the +arithmetic mixing rule substantially increases the computational cost. +The computational overhead can be reduced using the *kspace_modify +mix/disp geom* and *kspace_modify splittol* commands. The first +command simply enforces geometric mixing of the dispersion +coeffiecients in kspace computations. This introduces some error in +the computations but will also significantly speed-up the +simulations. The second keyword sets the accuracy with which the +dispersion coefficients are approximated using a matrix factorization +approach. This may result in better accuracy then using the first +command, but will usually also not provide an equally good increase of +efficiency. + +Finally, pppm/disp can also be used when no mixing rules apply. +This can be achieved using the *kspace_modify mix/disp none* command. +Note that the code does not check automatically whether any mixing +rule is fulfilled. If mixing rules do not apply, the user will have +to specify this command explicitly. + + +---------- + + +.. _howto_25: + +Polarizable models +------------------ + +In polarizable force fields the charge distributions in molecules and +materials respond to their electrostatic environements. Polarizable +systems can be simulated in LAMMPS using three methods: + +* the fluctuating charge method, implemented in the :doc:`QEQ ` + package, +* the adiabatic core-shell method, implemented in the + :ref:`CORESHELL ` package, +* the thermalized Drude dipole method, implemented in the + :ref:`USER-DRUDE ` package. +The fluctuating charge method calculates instantaneous charges on +interacting atoms based on the electronegativity equalization +principle. It is implemented in the :doc:`fix qeq ` which is +available in several variants. It is a relatively efficient technique +since no additional particles are introduced. This method allows for +charge transfer between molecules or atom groups. However, because the +charges are located at the interaction sites, off-plane components of +polarization cannot be represented in planar molecules or atom groups. + +The two other methods share the same basic idea: polarizable atoms are +split into one core atom and one satellite particle (called shell or +Drude particle) attached to it by a harmonic spring. Both atoms bear +a charge and they represent collectively an induced electric dipole. +These techniques are computationally more expensive than the QEq +method because of additional particles and bonds. These two +charge-on-spring methods differ in certain features, with the +core-shell model being normally used for ionic/crystalline materials, +whereas the so-called Drude model is normally used for molecular +systems and fluid states. + +The core-shell model is applicable to crystalline materials where the +high symmetry around each site leads to stable trajectories of the +core-shell pairs. However, bonded atoms in molecules can be so close +that a core would interact too strongly or even capture the Drude +particle of a neighbor. The Drude dipole model is relatively more +complex in order to remediate this and other issues. Specifically, the +Drude model includes specific thermostating of the core-Drude pairs +and short-range damping of the induced dipoles. + +The three polarization methods can be implemented through a +self-consistent calculation of charges or induced dipoles at each +timestep. In the fluctuating charge scheme this is done by the matrix +inversion method in :doc:`fix qeq/point `, but for core-shell +or Drude-dipoles the relaxed-dipoles technique would require an slow +iterative procedure. These self-consistent solutions yield accurate +trajectories since the additional degrees of freedom representing +polarization are massless. An alternative is to attribute a mass to +the additional degrees of freedom and perform time integration using +an extended Lagrangian technique. For the fluctuating charge scheme +this is done by :doc:`fix qeq/dynamic `, and for the +charge-on-spring models by the methods outlined in the next two +sections. The assignment of masses to the additional degrees of +freedom can lead to unphysical trajectories if care is not exerted in +choosing the parameters of the poarizable models and the simulation +conditions. + +In the core-shell model the vibration of the shells is kept faster +than the ionic vibrations to mimic the fast response of the +polarizable electrons. But in molecular systems thermalizing the +core-Drude pairs at temperatures comparable to the rest of the +simulation leads to several problems (kinetic energy transfer, too +short a timestep, etc.) In order to avoid these problems the relative +motion of the Drude particles with respect to their cores is kept +"cold" so the vibration of the core-Drude pairs is very slow, +approaching the self-consistent regime. In both models the +temperature is regulated using the velocities of the center of mass of +core+shell (or Drude) pairs, but in the Drude model the actual +relative core-Drude particle motion is thermostated separately as +well. + + +---------- + + +.. _howto_26: + +Adiabatic core/shell model +-------------------------- + +The adiabatic core-shell model by :ref:`Mitchell and Finchham ` is a simple method for adding +polarizability to a system. In order to mimic the electron shell of +an ion, a satellite particle is attached to it. This way the ions are +split into a core and a shell where the latter is meant to react to +the electrostatic environment inducing polarizability. + +Technically, shells are attached to the cores by a spring force f = +k*r where k is a parametrized spring constant and r is the distance +between the core and the shell. The charges of the core and the shell +add up to the ion charge, thus q(ion) = q(core) + q(shell). This +setup introduces the ion polarizability (alpha) given by +alpha = q(shell)^2 / k. In a +similar fashion the mass of the ion is distributed on the core and the +shell with the core having the larger mass. + +To run this model in LAMMPS, :doc:`atom_style ` *full* can +be used since atom charge and bonds are needed. Each kind of +core/shell pair requires two atom types and a bond type. The core and +shell of a core/shell pair should be bonded to each other with a +harmonic bond that provides the spring force. For example, a data file +for NaCl, as found in examples/coreshell, has this format: + +.. parsed-literal:: + + 432 atoms # core and shell atoms + 216 bonds # number of core/shell springs + +.. parsed-literal:: + + 4 atom types # 2 cores and 2 shells for Na and Cl + 2 bond types + +.. parsed-literal:: + + 0.0 24.09597 xlo xhi + 0.0 24.09597 ylo yhi + 0.0 24.09597 zlo zhi + +.. parsed-literal:: + + Masses # core/shell mass ratio = 0.1 + +.. parsed-literal:: + + 1 20.690784 # Na core + 2 31.90500 # Cl core + 3 2.298976 # Na shell + 4 3.54500 # Cl shell + +.. parsed-literal:: + + Atoms + +.. parsed-literal:: + + 1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1 + 2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1 + 3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2 + 4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2 + (...) + +.. parsed-literal:: + + Bonds # Bond topology for spring forces + +.. parsed-literal:: + + 1 2 1 2 # spring for core/shell pair 1 + 2 2 3 4 # spring for core/shell pair 2 + (...) + +Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only +defined between the shells. Coulombic interactions are defined +between all cores and shells. If desired, additional bonds can be +specified between cores. + +The :doc:`special_bonds ` command should be used to +turn-off the Coulombic interaction within core/shell pairs, since that +interaction is set by the bond spring. This is done using the +:doc:`special_bonds ` command with a 1-2 weight = 0.0, +which is the default value. It needs to be considered whether one has +to adjust the :doc:`special_bonds ` weighting according +to the molecular topology since the interactions of the shells are +bypassed over an extra bond. + +Note that this core/shell implementation does not require all ions to +be polarized. One can mix core/shell pairs and ions without a +satellite particle if desired. + +Since the core/shell model permits distances of r = 0.0 between the +core and shell, a pair style with a "cs" suffix needs to be used to +implement a valid long-range Coulombic correction. Several such pair +styles are provided in the CORESHELL package. See :doc:`this doc page ` for details. All of the core/shell enabled pair +styles require the use of a long-range Coulombic solver, as specified +by the :doc:`kspace_style ` command. Either the PPPM or +Ewald solvers can be used. + +For the NaCL example problem, these pair style and bond style settings +are used: + +.. parsed-literal:: + + pair_style born/coul/long/cs 20.0 20.0 + pair_coeff * * 0.0 1.000 0.00 0.00 0.00 + pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na + pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl + pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl + +.. parsed-literal:: + + bond_style harmonic + bond_coeff 1 63.014 0.0 + bond_coeff 2 25.724 0.0 + +When running dynamics with the adiabatic core/shell model, the +following issues should be considered. Since the relative motion of +the core and shell particles corresponds to the polarization, typical +thermostats can alter the polarization behaviour, meaning the shell +will not react freely to its electrostatic environment. This is +critical during the equilibration of the system. Therefore +it's typically desirable to decouple the relative motion of the +core/shell pair, which is an imaginary degree of freedom, from the +real physical system. To do that, the :doc:`compute temp/cs ` command can be used, in conjunction with +any of the thermostat fixes, such as :doc:`fix nvt ` or `fix langevin `_. This compute uses the center-of-mass velocity +of the core/shell pairs to calculate a temperature, and insures that +velocity is what is rescaled for thermostatting purposes. This +compute also works for a system with both core/shell pairs and +non-polarized ions (ions without an attached satellite particle). The +:doc:`compute temp/cs ` command requires input of two +groups, one for the core atoms, another for the shell atoms. +Non-polarized ions which might also be included in the treated system +should not be included into either of these groups, they are taken +into account by the *group-ID* (2nd argument) of the compute. The +groups can be defined using the :doc:`group *type* ` command. +Note that to perform thermostatting using this definition of +temperature, the :doc:`fix modify temp ` command should be +used to assign the compute to the thermostat fix. Likewise the +:doc:`thermo_modify temp ` command can be used to make +this temperature be output for the overall system. + +For the NaCl example, this can be done as follows: + +.. parsed-literal:: + + group cores type 1 2 + group shells type 3 4 + compute CSequ all temp/cs cores shells + fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system + fix thermostatequ all nve # integrator as needed for the berendsen thermostat + fix_modify thermoberendsen temp CSequ + thermo_modify temp CSequ # output of center-of-mass derived temperature + +If :doc:`compute temp/cs ` is used, the decoupled +relative motion of the core and the shell should in theory be +stable. However numerical fluctuation can introduce a small +momentum to the system, which is noticable over long trajectories. +Therefore it is recomendable to use the :doc:`fix momentum ` command in combination with :doc:`compute temp/cs ` when equilibrating the system to +prevent any drift. + +When intializing the velocities of a system with core/shell pairs, it +is also desirable to not introduce energy into the relative motion of +the core/shell particles, but only assign a center-of-mass velocity to +the pairs. This can be done by using the *bias* keyword of the +:doc:`velocity create ` command and assigning the :doc:`compute temp/cs ` command to the *temp* keyword of the +:doc:`velocity ` commmand, e.g. + +.. parsed-literal:: + + velocity all create 1427 134 bias yes temp CSequ + velocity all scale 1427 temp CSequ + +It is important to note that the polarizability of the core/shell +pairs is based on their relative motion. Therefore the choice of +spring force and mass ratio need to ensure much faster relative motion +of the 2 atoms within the core/shell pair than their center-of-mass +velocity. This allow the shells to effectively react instantaneously +to the electrostatic environment. This fast movement also limits the +timestep size that can be used. + +The primary literature of the adiabatic core/shell model suggests that +the fast relative motion of the core/shell pairs only allows negligible +energy transfer to the environment. Therefore it is not intended to +decouple the core/shell degree of freedom from the physical system +during production runs. In other words, the :doc:`compute temp/cs ` command should not be used during +production runs and is only required during equilibration. This way one +is consistent with literature (based on the code packages DL_POLY or +GULP for instance). + +The mentioned energy transfer will typically lead to a a small drift +in total energy over time. This internal energy can be monitored +using the :doc:`compute chunk/atom ` and :doc:`compute temp/chunk ` commands. The internal kinetic +energies of each core/shell pair can then be summed using the sum() +special function of the :doc:`variable ` command. Or they can +be time/averaged and output using the :doc:`fix ave/time ` +command. To use these commands, each core/shell pair must be defined +as a "chunk". If each core/shell pair is defined as its own molecule, +the molecule ID can be used to define the chunks. If cores are bonded +to each other to form larger molecules, the chunks can be identified +by the :doc:`fix property/atom ` via assigning a +core/shell ID to each atom using a special field in the data file read +by the :doc:`read_data ` command. This field can then be +accessed by the :doc:`compute property/atom ` +command, to use as input to the :doc:`compute chunk/atom ` command to define the core/shell +pairs as chunks. + +For example, + +.. parsed-literal:: + + fix csinfo all property/atom i_CSID # property/atom command + read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file + compute prop all property/atom i_CSID + compute cs_chunk all chunk/atom c_prop + compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs + fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector + +The additional section in the date file would be formatted like this: + +.. parsed-literal:: + + CS-Info # header of additional section + +.. parsed-literal:: + + 1 1 # column 1 = atom ID, column 2 = core/shell ID + 2 1 + 3 2 + 4 2 + 5 3 + 6 3 + 7 4 + 8 4 + (...) + + +---------- + + +.. _howto_27: + +Drude induced dipoles +--------------------- + +The thermalized Drude model, similarly to the :ref:`core-shell ` +model, representes induced dipoles by a pair of charges (the core atom +and the Drude particle) connected by a harmonic spring. The Drude +model has a number of features aimed at its use in molecular systems +(:ref:`Lamoureux and Roux `): + +* Thermostating of the additional degrees of freedom associated with the + induced dipoles at very low temperature, in terms of the reduced + coordinates of the Drude particles with respect to their cores. This + makes the trajectory close to that of relaxed induced dipoles. +* Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle + pair represents a single (polarizable) atom, so the special screening + factors in a covalent structure should be the same for the core and + the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4 + special neighbor relations from their respective cores. +* Stabilization of the interactions between induced dipoles. Drude + dipoles on covalently bonded atoms interact too strongly due to the + short distances, so an atom may capture the Drude particle of a + neighbor, or the induced dipoles within the same molecule may align + too much. To avoid this, damping at short range can be done by Thole + functions (for which there are physical grounds). This Thole damping + is applied to the point charges composing the induced dipole (the + charge of the Drude particle and the opposite charge on the core, not + to the total charge of the core atom). +A detailed tutorial covering the usage of Drude induced dipoles in +LAMMPS is :doc:`available here `. + +As with the core-shell model, the cores and Drude particles should +appear in the data file as standard atoms. The same holds for the +springs between them, which are described by standard harmonic bonds. +The nature of the atoms (core, Drude particle or non-polarizable) is +specified via the :doc:`fix drude ` command. The special +list of neighbors is automatically refactored to account for the +equivalence of core and Drude particles as regards special 1-2 to 1-4 +screening. It may be necessary to use the *extra* keyword of the +:doc:`special_bonds ` command. If using :doc:`fix shake `, make sure no Drude particle is in this fix +group. + +There are two ways to thermostat the Drude particles at a low +temperature: use either :doc:`fix langevin/drude ` +for a Langevin thermostat, or :doc:`fix drude/transform/* ` for a Nose-Hoover +thermostat. The former requires use of the command :doc:`comm_modify vel yes `. The latter requires two separate integration +fixes like *nvt* or *npt*. The correct temperatures of the reduced +degrees of freedom can be calculated using the :doc:`compute temp/drude `. This requires also to use the +command *comm_modify vel yes*. + +Short-range damping of the induced dipole interactions can be achieved +using Thole functions through the the :doc:`pair style thole ` in :doc:`pair_style hybrid/overlay ` +with a Coulomb pair style. It may be useful to use *coul/long/cs* or +similar from the CORESHELL package if the core and Drude particle come +too close, which can cause numerical issues. + + + + + +.. _Berendsen: + + + +**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, +6269-6271 (1987). + +.. _Cornell: + + + +**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, +Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). + +.. _Horn: + + + +**(Horn)** Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon, +J Chem Phys, 120, 9665 (2004). + +.. _Ikeshoji: + + + +**(Ikeshoji)** Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 +(1994). + +.. _MacKerell: + + + +**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, +Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). + +.. _Mayo: + + + +**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). + +.. _Jorgensen: + + + +**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem +Phys, 79, 926 (1983). + +.. _Price: + + + +**(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004). + +.. _Shinoda: + + + +**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). + +.. _MitchellFinchham: + + + +**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter, +5, 1031-1038 (1993). + +.. _Lamoureux: + + + +**(Lamoureux and Roux)** G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_intro.txt b/doc/_sources/Section_intro.txt new file mode 100644 index 0000000000..e91563b587 --- /dev/null +++ b/doc/_sources/Section_intro.txt @@ -0,0 +1,593 @@ +Introduction +============ + +This section provides an overview of what LAMMPS can and can't do, +describes what it means for LAMMPS to be an open-source code, and +acknowledges the funding and people who have contributed to LAMMPS +over the years. + +| 1.1 :ref:`What is LAMMPS ` +| 1.2 :ref:`LAMMPS features ` +| 1.3 :ref:`LAMMPS non-features ` +| 1.4 :ref:`Open source distribution ` +| 1.5 :ref:`Acknowledgments and citations ` +| + + + + + +.. _intro_1: + +What is LAMMPS +-------------- + +LAMMPS is a classical molecular dynamics code that models an ensemble +of particles in a liquid, solid, or gaseous state. It can model +atomic, polymeric, biological, metallic, granular, and coarse-grained +systems using a variety of force fields and boundary conditions. + +For examples of LAMMPS simulations, see the Publications page of the +`LAMMPS WWW Site `_. + +LAMMPS runs efficiently on single-processor desktop or laptop +machines, but is designed for parallel computers. It will run on any +parallel machine that compiles C++ and supports the `MPI `_ +message-passing library. This includes distributed- or shared-memory +parallel machines and Beowulf-style clusters. + +.. _mpi: http://www-unix.mcs.anl.gov/mpi + + + +LAMMPS can model systems with only a few particles up to millions or +billions. See :doc:`Section_perf ` for information on +LAMMPS performance and scalability, or the Benchmarks section of the +`LAMMPS WWW Site `_. + +LAMMPS is a freely-available open-source code, distributed under the +terms of the `GNU Public License `_, which means you can use or +modify the code however you wish. See :ref:`this section ` for a +brief discussion of the open-source philosophy. + +.. _gnu: http://www.gnu.org/copyleft/gpl.html + + + +LAMMPS is designed to be easy to modify or extend with new +capabilities, such as new force fields, atom types, boundary +conditions, or diagnostics. See :doc:`Section_modify ` +for more details. + +The current version of LAMMPS is written in C++. Earlier versions +were written in F77 and F90. See +:doc:`Section_history ` for more information on +different versions. All versions can be downloaded from the `LAMMPS WWW Site `_. + +LAMMPS was originally developed under a US Department of Energy CRADA +(Cooperative Research and Development Agreement) between two DOE labs +and 3 companies. It is distributed by `Sandia National Labs `_. +See :ref:`this section ` for more information on LAMMPS funding and +individuals who have contributed to LAMMPS. + +.. _snl: http://www.sandia.gov + + + +In the most general sense, LAMMPS integrates Newton's equations of +motion for collections of atoms, molecules, or macroscopic particles +that interact via short- or long-range forces with a variety of +initial and/or boundary conditions. For computational efficiency +LAMMPS uses neighbor lists to keep track of nearby particles. The +lists are optimized for systems with particles that are repulsive at +short distances, so that the local density of particles never becomes +too large. On parallel machines, LAMMPS uses spatial-decomposition +techniques to partition the simulation domain into small 3d +sub-domains, one of which is assigned to each processor. Processors +communicate and store "ghost" atom information for atoms that border +their sub-domain. LAMMPS is most efficient (in a parallel sense) for +systems whose particles fill a 3d rectangular box with roughly uniform +density. Papers with technical details of the algorithms used in +LAMMPS are listed in :ref:`this section `. + + +---------- + + +.. _intro_2: + +LAMMPS features +--------------- + +This section highlights LAMMPS features, with pointers to specific +commands which give more details. If LAMMPS doesn't have your +favorite interatomic potential, boundary condition, or atom type, see +:doc:`Section_modify `, which describes how you can add +it to LAMMPS. + +General features +^^^^^^^^^^^^^^^^ + +* runs on a single processor or in parallel +* distributed-memory message-passing parallelism (MPI) +* spatial-decomposition of simulation domain for parallelism +* open-source distribution +* highly portable C++ +* optional libraries used: MPI and single-processor FFT +* GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features +* easy to extend with new features and functionality +* runs from an input script +* syntax for defining and using variables and formulas +* syntax for looping over runs and breaking out of loops +* run one or multiple simulations simultaneously (in parallel) from one script +* build as library, invoke LAMMPS thru library interface or provided Python wrapper +* couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both + +Particle and model types +^^^^^^^^^^^^^^^^^^^^^^^^ + +(:doc:`atom style ` command) + +* atoms +* coarse-grained particles (e.g. bead-spring polymers) +* united-atom polymers or organic molecules +* all-atom polymers, organic molecules, proteins, DNA +* metals +* granular materials +* coarse-grained mesoscale models +* finite-size spherical and ellipsoidal particles +* finite-size line segment (2d) and triangle (3d) particles +* point dipole particles +* rigid collections of particles +* hybrid combinations of these + +Force fields +^^^^^^^^^^^^ + +(:doc:`pair style `, :doc:`bond style `, +:doc:`angle style `, :doc:`dihedral style `, +:doc:`improper style `, :doc:`kspace style ` +commands) + +* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated +* charged pairwise potentials: Coulombic, point-dipole +* manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic +* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald) +* polarization models: :doc:`QEq `, :ref:`core/shell model `, :ref:`Drude dipole model ` +* charge equilibration (QEq via dynamic, point, shielded, Slater methods) +* coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO +* mesoscopic potentials: granular, Peridynamics, SPH +* electron force field (eFF, AWPMD) +* bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable) +* angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS) +* dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS +* improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS) +* polymer potentials: all-atom, united-atom, bead-spring, breakable +* water potentials: TIP3P, TIP4P, SPC +* implicit solvent potentials: hydrodynamic lubrication, Debye +* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options +* access to `KIM archive `_ of potentials via :doc:`pair kim ` +* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation +* overlaid potentials: superposition of multiple pair potentials + +Atom creation +^^^^^^^^^^^^^ + +(:doc:`read_data `, :doc:`lattice `, +:doc:`create_atoms `, :doc:`delete_atoms `, +:doc:`displace_atoms `, :doc:`replicate ` commands) + +* read in atom coords from files +* create atoms on one or more lattices (e.g. grain boundaries) +* delete geometric or logical groups of atoms (e.g. voids) +* replicate existing atoms multiple times +* displace atoms + +Ensembles, constraints, and boundary conditions +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +(:doc:`fix ` command) + +* 2d or 3d systems +* orthogonal or non-orthogonal (triclinic symmetry) simulation domains +* constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators +* thermostatting options for groups and geometric regions of atoms +* pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions +* simulation box deformation (tensile and shear) +* harmonic (umbrella) constraint forces +* rigid body constraints +* SHAKE bond and angle constraints +* Monte Carlo bond breaking, formation, swapping +* atom/molecule insertion and deletion +* walls of various kinds +* non-equilibrium molecular dynamics (NEMD) +* variety of additional boundary conditions and constraints + +Integrators +^^^^^^^^^^^ + +(:doc:`run `, :doc:`run_style `, :doc:`minimize ` commands) + +* velocity-Verlet integrator +* Brownian dynamics +* rigid body integration +* energy minimization via conjugate gradient or steepest descent relaxation +* rRESPA hierarchical timestepping +* rerun command for post-processing of dump files + +Diagnostics +^^^^^^^^^^^ + +* see the various flavors of the :doc:`fix ` and :doc:`compute ` commands + +Output +^^^^^^ + +(:doc:`dump `, :doc:`restart ` commands) + +* log file of thermodynamic info +* text dump files of atom coords, velocities, other per-atom quantities +* binary restart files +* parallel I/O of dump and restart files +* per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc) +* user-defined system-wide (log file) or per-atom (dump file) calculations +* spatial and time averaging of per-atom quantities +* time averaging of system-wide quantities +* atom snapshots in native, XYZ, XTC, DCD, CFG formats + +Multi-replica models +^^^^^^^^^^^^^^^^^^^^ + +:doc:`nudged elastic band ` +:doc:`parallel replica dynamics ` +:doc:`temperature accelerated dynamics ` +:doc:`parallel tempering ` + +Pre- and post-processing +^^^^^^^^^^^^^^^^^^^^^^^^ + +* Various pre- and post-processing serial tools are packaged + with LAMMPS; see these :doc:`doc pages `. +* Our group has also written and released a separate toolkit called + `Pizza.py `_ which provides tools for doing setup, analysis, + plotting, and visualization for LAMMPS simulations. Pizza.py is + written in `Python `_ and is available for download from `the Pizza.py WWW site `_. +.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html + + + +.. _python: http://www.python.org + + + +Specialized features +^^^^^^^^^^^^^^^^^^^^ + +These are LAMMPS capabilities which you may not think of as typical +molecular dynamics options: + +* :doc:`static ` and :doc:`dynamic load-balancing ` +* :doc:`generalized aspherical particles ` +* :doc:`stochastic rotation dynamics (SRD) ` +* :doc:`real-time visualization and interactive MD ` +* calculate :doc:`virtual diffraction patterns ` +* :doc:`atom-to-continuum coupling ` with finite elements +* coupled rigid body integration via the :doc:`POEMS ` library +* :doc:`QM/MM coupling ` +* :doc:`path-integral molecular dynamics (PIMD) ` and :doc:`this as well ` +* Monte Carlo via :doc:`GCMC ` and :doc:`tfMC ` and :doc:`atom swapping ` +* :doc:`Direct Simulation Monte Carlo ` for low-density fluids +* :doc:`Peridynamics mesoscale modeling ` +* :doc:`Lattice Boltzmann fluid ` +* :doc:`targeted ` and :doc:`steered ` molecular dynamics +* :doc:`two-temperature electron model ` + + +---------- + + +.. _intro_3: + +LAMMPS non-features +------------------- + +LAMMPS is designed to efficiently compute Newton's equations of motion +for a system of interacting particles. Many of the tools needed to +pre- and post-process the data for such simulations are not included +in the LAMMPS kernel for several reasons: + +* the desire to keep LAMMPS simple +* they are not parallel operations +* other codes already do them +* limited development resources + +Specifically, LAMMPS itself does not: + +* run thru a GUI +* build molecular systems +* assign force-field coefficients automagically +* perform sophisticated analyses of your MD simulation +* visualize your MD simulation +* plot your output data + +A few tools for pre- and post-processing tasks are provided as part of +the LAMMPS package; they are described in :doc:`this section `. However, many people use other codes or +write their own tools for these tasks. + +As noted above, our group has also written and released a separate +toolkit called `Pizza.py `_ which addresses some of the listed +bullets. It provides tools for doing setup, analysis, plotting, and +visualization for LAMMPS simulations. Pizza.py is written in +`Python `_ and is available for download from `the Pizza.py WWW site `_. + +LAMMPS requires as input a list of initial atom coordinates and types, +molecular topology information, and force-field coefficients assigned +to all atoms and bonds. LAMMPS will not build molecular systems and +assign force-field parameters for you. + +For atomic systems LAMMPS provides a :doc:`create_atoms ` +command which places atoms on solid-state lattices (fcc, bcc, +user-defined, etc). Assigning small numbers of force field +coefficients can be done via the :doc:`pair coeff `, :doc:`bond coeff `, :doc:`angle coeff `, etc commands. +For molecular systems or more complicated simulation geometries, users +typically use another code as a builder and convert its output to +LAMMPS input format, or write their own code to generate atom +coordinate and molecular topology for LAMMPS to read in. + +For complicated molecular systems (e.g. a protein), a multitude of +topology information and hundreds of force-field coefficients must +typically be specified. We suggest you use a program like +`CHARMM `_ or `AMBER `_ or other molecular builders to setup +such problems and dump its information to a file. You can then +reformat the file as LAMMPS input. Some of the tools in :doc:`this section ` can assist in this process. + +Similarly, LAMMPS creates output files in a simple format. Most users +post-process these files with their own analysis tools or re-format +them for input into other programs, including visualization packages. +If you are convinced you need to compute something on-the-fly as +LAMMPS runs, see :doc:`Section_modify ` for a discussion +of how you can use the :doc:`dump ` and :doc:`compute ` and +:doc:`fix ` commands to print out data of your choosing. Keep in +mind that complicated computations can slow down the molecular +dynamics timestepping, particularly if the computations are not +parallel, so it is often better to leave such analysis to +post-processing codes. + +A very simple (yet fast) visualizer is provided with the LAMMPS +package - see the :ref:`xmovie ` tool in :doc:`this section `. It creates xyz projection views of +atomic coordinates and animates them. We find it very useful for +debugging purposes. For high-quality visualization we recommend the +following packages: + +* `VMD `_ +* `AtomEye `_ +* `PyMol `_ +* `Raster3d `_ +* `RasMol `_ + +Other features that LAMMPS does not yet (and may never) support are +discussed in :doc:`Section_history `. + +Finally, these are freely-available molecular dynamics codes, most of +them parallel, which may be well-suited to the problems you want to +model. They can also be used in conjunction with LAMMPS to perform +complementary modeling tasks. + +* `CHARMM `_ +* `AMBER `_ +* `NAMD `_ +* `NWCHEM `_ +* `DL_POLY `_ +* `Tinker `_ + +.. _charmm: http://www.scripps.edu/brooks + + + +.. _amber: http://amber.scripps.edu + + + +.. _namd: http://www.ks.uiuc.edu/Research/namd/ + + + +.. _nwchem: http://www.emsl.pnl.gov/docs/nwchem/nwchem.html + + + +.. _dlpoly: http://www.cse.clrc.ac.uk/msi/software/DL_POLY + + + +.. _tinker: http://dasher.wustl.edu/tinker + + + +CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for +modeling biological molecules. CHARMM and AMBER use +atom-decomposition (replicated-data) strategies for parallelism; NAMD +and NWCHEM use spatial-decomposition approaches, similar to LAMMPS. +Tinker is a serial code. DL_POLY includes potentials for a variety of +biological and non-biological materials; both a replicated-data and +spatial-decomposition version exist. + + +---------- + + +.. _intro_4: + +Open source distribution +------------------------ + +LAMMPS comes with no warranty of any kind. As each source file states +in its header, it is a copyrighted code that is distributed free-of- +charge, under the terms of the `GNU Public License `_ (GPL). This +is often referred to as open-source distribution - see +`www.gnu.org `_ or `www.opensource.org `_ for more +details. The legal text of the GPL is in the LICENSE file that is +included in the LAMMPS distribution. + +.. _gnuorg: http://www.gnu.org + + + +.. _opensource: http://www.opensource.org + + + +Here is a summary of what the GPL means for LAMMPS users: + +(1) Anyone is free to use, modify, or extend LAMMPS in any way they +choose, including for commercial purposes. + +(2) If you distribute a modified version of LAMMPS, it must remain +open-source, meaning you distribute it under the terms of the GPL. +You should clearly annotate such a code as a derivative version of +LAMMPS. + +(3) If you release any code that includes LAMMPS source code, then it +must also be open-sourced, meaning you distribute it under the terms +of the GPL. + +(4) If you give LAMMPS files to someone else, the GPL LICENSE file and +source file headers (including the copyright and GPL notices) should +remain part of the code. + +In the spirit of an open-source code, these are various ways you can +contribute to making LAMMPS better. You can send email to the +`developers `_ on any of these +items. + +* Point prospective users to the `LAMMPS WWW Site `_. Mention it in + talks or link to it from your WWW site. +* If you find an error or omission in this manual or on the `LAMMPS WWW Site `_, or have a suggestion for something to clarify or include, + send an email to the + `developers `_. +* If you find a bug, :ref:`Section_errors 2 ` + describes how to report it. +* If you publish a paper using LAMMPS results, send the citation (and + any cool pictures or movies if you like) to add to the Publications, + Pictures, and Movies pages of the `LAMMPS WWW Site `_, with links + and attributions back to you. +* Create a new Makefile.machine that can be added to the src/MAKE + directory. +* The tools sub-directory of the LAMMPS distribution has various + stand-alone codes for pre- and post-processing of LAMMPS data. More + details are given in :doc:`Section_tools `. If you write + a new tool that users will find useful, it can be added to the LAMMPS + distribution. +* LAMMPS is designed to be easy to extend with new code for features + like potentials, boundary conditions, diagnostic computations, etc. + :doc:`This section ` gives details. If you add a + feature of general interest, it can be added to the LAMMPS + distribution. +* The Benchmark page of the `LAMMPS WWW Site `_ lists LAMMPS + performance on various platforms. The files needed to run the + benchmarks are part of the LAMMPS distribution. If your machine is + sufficiently different from those listed, your timing data can be + added to the page. +* You can send feedback for the User Comments page of the `LAMMPS WWW Site `_. It might be added to the page. No promises. +* Cash. Small denominations, unmarked bills preferred. Paper sack OK. + Leave on desk. VISA also accepted. Chocolate chip cookies + encouraged. + +---------- + + +.. _intro_5: + +Acknowledgments and citations +------------------------------------------- + +LAMMPS development has been funded by the `US Department of Energy `_ (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life +programs and its `OASCR `_ and `OBER `_ offices. + +Specifically, work on the latest version was funded in part by the US +Department of Energy's Genomics:GTL program +(`www.doegenomestolife.org `_) under the `project `_, "Carbon +Sequestration in Synechococcus Sp.: From Molecular Machines to +Hierarchical Modeling". + +.. _doe: http://www.doe.gov + + + +.. _gtl: http://www.doegenomestolife.org + + + +.. _ourgtl: http://www.genomes2life.org + + + +.. _oascr: http://www.sc.doe.gov/ascr/home.html + + + +.. _ober: http://www.er.doe.gov/production/ober/ober_top.html + + + +The following paper describe the basic parallel algorithms used in +LAMMPS. If you use LAMMPS results in your published work, please cite +this paper and include a pointer to the `LAMMPS WWW Site `_ +(http://lammps.sandia.gov): + +S. J. Plimpton, **Fast Parallel Algorithms for Short-Range Molecular +Dynamics**, J Comp Phys, 117, 1-19 (1995). + +Other papers describing specific algorithms used in LAMMPS are listed +under the `Citing LAMMPS link `_ of +the LAMMPS WWW page. + +The `Publications link `_ on the +LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is +not listed there for some reason, feel free to send us the info. If +the simulations in your paper produced cool pictures or animations, +we'll be pleased to add them to the +`Pictures `_ or +`Movies `_ pages of the LAMMPS WWW +site. + +The core group of LAMMPS developers is at Sandia National Labs: + +* Steve Plimpton, sjplimp at sandia.gov +* Aidan Thompson, athomps at sandia.gov +* Paul Crozier, pscrozi at sandia.gov + +The following folks are responsible for significant contributions to +the code, or other aspects of the LAMMPS development effort. Many of +the packages they have written are somewhat unique to LAMMPS and the +code would not be as general-purpose as it is without their expertise +and efforts. + +* Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages +* Roy Pollock (LLNL), Ewald and PPPM solvers +* Mike Brown (ORNL), brownw at ornl.gov, GPU package +* Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential +* Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics +* Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion +* Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling +* Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD +* Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package +* Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field +* Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling +* Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF +* Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package + +As discussed in :doc:`Section_history `, LAMMPS +originated as a cooperative project between DOE labs and industrial +partners. Folks involved in the design and testing of the original +version of LAMMPS were the following: + +* John Carpenter (Mayo Clinic, formerly at Cray Research) +* Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) +* Steve Lustig (Dupont) +* Jim Belak (LLNL) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_modify.txt b/doc/_sources/Section_modify.txt new file mode 100644 index 0000000000..5fcdfeb83e --- /dev/null +++ b/doc/_sources/Section_modify.txt @@ -0,0 +1,984 @@ +Modifying & extending LAMMPS +============================ + +This section describes how to customize LAMMPS by modifying +and extending its source code. + +| 10.1 :ref:`Atom styles ` +| 10.2 :ref:`Bond, angle, dihedral, improper potentials ` +| 10.3 :ref:`Compute styles ` +| 10.4 :ref:`Dump styles ` +| 10.5 :ref:`Dump custom output options ` +| 10.6 :ref:`Fix styles ` which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc +| 10.7 :ref:`Input script commands ` +| 10.8 :ref:`Kspace computations ` +| 10.9 :ref:`Minimization styles ` +| 10.10 :ref:`Pairwise potentials ` +| 10.11 :ref:`Region styles ` +| 10.12 :ref:`Body styles ` +| 10.13 :ref:`Thermodynamic output options ` +| 10.14 :ref:`Variable options ` +| 10.15 :ref:`Submitting new features for inclusion in LAMMPS ` +| + +LAMMPS is designed in a modular fashion so as to be easy to modify and +extend with new functionality. In fact, about 75% of its source code +is files added in this fashion. + +In this section, changes and additions users can make are listed along +with minimal instructions. If you add a new feature to LAMMPS and +think it will be of interest to general users, we encourage you to +submit it to the developers for inclusion in the released version of +LAMMPS. Information about how to do this is provided +:ref:`below `. + +The best way to add a new feature is to find a similar feature in +LAMMPS and look at the corresponding source and header files to figure +out what it does. You will need some knowledge of C++ to be able to +understand the hi-level structure of LAMMPS and its class +organization, but functions (class methods) that do actual +computations are written in vanilla C-style code and operate on simple +C-style data structures (vectors and arrays). + +Most of the new features described in this section require you to +write a new C++ derived class (except for exceptions described below, +where you can make small edits to existing files). Creating a new +class requires 2 files, a source code file (*.cpp) and a header file +(*.h). The derived class must provide certain methods to work as a +new option. Depending on how different your new feature is compared +to existing features, you can either derive from the base class +itself, or from a derived class that already exists. Enabling LAMMPS +to invoke the new class is as simple as putting the two source +files in the src dir and re-building LAMMPS. + +The advantage of C++ and its object-orientation is that all the code +and variables needed to define the new feature are in the 2 files you +write, and thus shouldn't make the rest of LAMMPS more complex or +cause side-effect bugs. + +Here is a concrete example. Suppose you write 2 files pair_foo.cpp +and pair_foo.h that define a new class PairFoo that computes pairwise +potentials described in the classic 1997 :ref:`paper ` by Foo, et al. +If you wish to invoke those potentials in a LAMMPS input script with a +command like + +.. parsed-literal:: + + pair_style foo 0.1 3.5 + +then your pair_foo.h file should be structured as follows: + +.. parsed-literal:: + + #ifdef PAIR_CLASS + PairStyle(foo,PairFoo) + #else + ... + (class definition for PairFoo) + ... + #endif + +where "foo" is the style keyword in the pair_style command, and +PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h +files. + +When you re-build LAMMPS, your new pairwise potential becomes part of +the executable and can be invoked with a pair_style command like the +example above. Arguments like 0.1 and 3.5 can be defined and +processed by your new class. + +As illustrated by this pairwise example, many kinds of options are +referred to in the LAMMPS documentation as the "style" of a particular +command. + +The instructions below give the header file for the base class that +these styles are derived from. Public variables in that file are ones +used and set by the derived classes which are also used by the base +class. Sometimes they are also used by the rest of LAMMPS. Virtual +functions in the base class header file which are set = 0 are ones you +must define in your new derived class to give it the functionality +LAMMPS expects. Virtual functions that are not set to 0 are functions +you can optionally define. + +Additionally, new output options can be added directly to the +thermo.cpp, dump_custom.cpp, and variable.cpp files as explained +below. + +Here are additional guidelines for modifying LAMMPS and adding new +functionality: + +* Think about whether what you want to do would be better as a pre- or + post-processing step. Many computations are more easily and more + quickly done that way. +* Don't do anything within the timestepping of a run that isn't + parallel. E.g. don't accumulate a bunch of data on a single processor + and analyze it. You run the risk of seriously degrading the parallel + efficiency. +* If your new feature reads arguments or writes output, make sure you + follow the unit conventions discussed by the :doc:`units ` + command. +* If you add something you think is truly useful and doesn't impact + LAMMPS performance when it isn't used, send an email to the + `developers `_. We might be + interested in adding it to the LAMMPS distribution. See further + details on this at the bottom of this page. + + + + +.. _mod_1: + +Atom styles +----------- + +Classes that define an :doc:`atom style ` are derived from +the AtomVec class and managed by the Atom class. The atom style +determines what attributes are associated with an atom. A new atom +style can be created if one of the existing atom styles does not +define all the attributes you need to store and communicate with +atoms. + +Atom_vec_atomic.cpp is a simple example of an atom style. + +Here is a brief description of methods you define in your new derived +class. See atom_vec.h for details. + ++-----------------------+--------------------------------------------------------------------------------+ +| init | one time setup (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| grow | re-allocate atom arrays to longer lengths (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| grow_reset | make array pointers in Atom and AtomVec classes consistent (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| copy | copy info for one atom to another atom's array locations (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_comm | store an atom's info in a buffer communicated every timestep (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_comm_vel | add velocity info to communication buffer (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_comm_hybrid | store extra info unique to this atom style (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_comm | retrieve an atom's info from the buffer (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_comm_vel | also retrieve velocity info (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_comm_hybrid | retreive extra info unique to this atom style (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_reverse | store an atom's info in a buffer communicating partial forces (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_reverse_hybrid | store extra info unique to this atom style (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_reverse | retrieve an atom's info from the buffer (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_reverse_hybrid | retreive extra info unique to this atom style (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_border | store an atom's info in a buffer communicated on neighbor re-builds (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_border_vel | add velocity info to buffer (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_border_hybrid | store extra info unique to this atom style (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_border | retrieve an atom's info from the buffer (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_border_vel | also retrieve velocity info (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_border_hybrid | retreive extra info unique to this atom style (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_exchange | store all an atom's info to migrate to another processor (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_exchange | retrieve an atom's info from the buffer (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| size_restart | number of restart quantities associated with proc's atoms (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| pack_restart | pack atom quantities into a buffer (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| unpack_restart | unpack atom quantities from a buffer (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| create_atom | create an individual atom of this style (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| data_atom | parse an atom line from the data file (required) | ++-----------------------+--------------------------------------------------------------------------------+ +| data_atom_hybrid | parse additional atom info unique to this atom style (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| data_vel | parse one line of velocity information from data file (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| data_vel_hybrid | parse additional velocity data unique to this atom style (optional) | ++-----------------------+--------------------------------------------------------------------------------+ +| memory_usage | tally memory allocated by atom arrays (required) | ++-----------------------+--------------------------------------------------------------------------------+ + +The constructor of the derived class sets values for several variables +that you must set when defining a new atom style, which are documented +in atom_vec.h. New atom arrays are defined in atom.cpp. Search for +the word "customize" and you will find locations you will need to +modify. + +.. note:: + + It is possible to add some attributes, such as a molecule ID, to + atom styles that do not have them via the :doc:`fix property/atom ` command. This command also + allows new custom attributes consisting of extra integer or + floating-point values to be added to atoms. See the :doc:`fix property/atom ` doc page for examples of cases + where this is useful and details on how to initialize, access, and + output the custom values. + +New :doc:`pair styles `, :doc:`fixes `, or +:doc:`computes ` can be added to LAMMPS, as discussed below. +The code for these classes can use the per-atom properties defined by +fix property/atom. The Atom class has a find_custom() method that is +useful in this context: + +.. parsed-literal:: + + int index = atom->find_custom(char *name, int &flag); + +The "name" of a custom attribute, as specified in the :doc:`fix property/atom ` command, is checked to verify +that it exists and its index is returned. The method also sets flag = +0/1 depending on whether it is an integer or floating-point attribute. +The vector of values associated with the attribute can then be +accessed using the returned index as + +.. parsed-literal:: + + int *ivector = atom->ivector[index]; + double *dvector = atom->dvector[index]; + +Ivector or dvector are vectors of length Nlocal = # of owned atoms, +which store the attributes of individual atoms. + + +---------- + + +.. _mod_2: + +Bond, angle, dihedral, improper potentials +------------------------------------------ + +Classes that compute molecular interactions are derived from the Bond, +Angle, Dihedral, and Improper classes. New styles can be created to +add new potentials to LAMMPS. + +Bond_harmonic.cpp is the simplest example of a bond style. Ditto for +the harmonic forms of the angle, dihedral, and improper style +commands. + +Here is a brief description of common methods you define in your +new derived class. See bond.h, angle.h, dihedral.h, and improper.h +for details and specific additional methods. + ++----------------------+---------------------------------------------------------------------------+ +| init | check if all coefficients are set, calls *init_style* (optional) | ++----------------------+---------------------------------------------------------------------------+ +| init_style | check if style specific conditions are met (optional) | ++----------------------+---------------------------------------------------------------------------+ +| compute | compute the molecular interactions (required) | ++----------------------+---------------------------------------------------------------------------+ +| settings | apply global settings for all types (optional) | ++----------------------+---------------------------------------------------------------------------+ +| coeff | set coefficients for one type (required) | ++----------------------+---------------------------------------------------------------------------+ +| equilibrium_distance | length of bond, used by SHAKE (required, bond only) | ++----------------------+---------------------------------------------------------------------------+ +| equilibrium_angle | opening of angle, used by SHAKE (required, angle only) | ++----------------------+---------------------------------------------------------------------------+ +| write & read_restart | writes/reads coeffs to restart files (required) | ++----------------------+---------------------------------------------------------------------------+ +| single | force and energy of a single bond or angle (required, bond or angle only) | ++----------------------+---------------------------------------------------------------------------+ +| memory_usage | tally memory allocated by the style (optional) | ++----------------------+---------------------------------------------------------------------------+ + + +---------- + + +.. _mod_3: + +Compute styles +-------------- + +Classes that compute scalar and vector quantities like temperature +and the pressure tensor, as well as classes that compute per-atom +quantities like kinetic energy and the centro-symmetry parameter +are derived from the Compute class. New styles can be created +to add new calculations to LAMMPS. + +Compute_temp.cpp is a simple example of computing a scalar +temperature. Compute_ke_atom.cpp is a simple example of computing +per-atom kinetic energy. + +Here is a brief description of methods you define in your new derived +class. See compute.h for details. + ++---------------------+-----------------------------------------------------------------+ +| init | perform one time setup (required) | ++---------------------+-----------------------------------------------------------------+ +| init_list | neighbor list setup, if needed (optional) | ++---------------------+-----------------------------------------------------------------+ +| compute_scalar | compute a scalar quantity (optional) | ++---------------------+-----------------------------------------------------------------+ +| compute_vector | compute a vector of quantities (optional) | ++---------------------+-----------------------------------------------------------------+ +| compute_peratom | compute one or more quantities per atom (optional) | ++---------------------+-----------------------------------------------------------------+ +| compute_local | compute one or more quantities per processor (optional) | ++---------------------+-----------------------------------------------------------------+ +| pack_comm | pack a buffer with items to communicate (optional) | ++---------------------+-----------------------------------------------------------------+ +| unpack_comm | unpack the buffer (optional) | ++---------------------+-----------------------------------------------------------------+ +| pack_reverse | pack a buffer with items to reverse communicate (optional) | ++---------------------+-----------------------------------------------------------------+ +| unpack_reverse | unpack the buffer (optional) | ++---------------------+-----------------------------------------------------------------+ +| remove_bias | remove velocity bias from one atom (optional) | ++---------------------+-----------------------------------------------------------------+ +| remove_bias_all | remove velocity bias from all atoms in group (optional) | ++---------------------+-----------------------------------------------------------------+ +| restore_bias | restore velocity bias for one atom after remove_bias (optional) | ++---------------------+-----------------------------------------------------------------+ +| restore_bias_all | same as before, but for all atoms in group (optional) | ++---------------------+-----------------------------------------------------------------+ +| pair_tally_callback | callback function for *tally*-style computes (optional). | ++---------------------+-----------------------------------------------------------------+ +| memory_usage | tally memory usage (optional) | ++---------------------+-----------------------------------------------------------------+ + +Tally-style computes are a special case, as their computation is done +in two stages: the callback function is registered with the pair style +and then called from the Pair::ev_tally() function, which is called for +each pair after force and energy has been computed for this pair. Then +the tallied values are retrieved with the standard compute_scalar or +compute_vector or compute_peratom methods. The USER-TALLY package +provides *examples*_compute_tally.html for utilizing this mechanism. + + +---------- + + +.. _mod_4: + +Dump styles +----------- + +.. _mod_5: + +Dump custom output options +-------------------------- + +Classes that dump per-atom info to files are derived from the Dump +class. To dump new quantities or in a new format, a new derived dump +class can be added, but it is typically simpler to modify the +DumpCustom class contained in the dump_custom.cpp file. + +Dump_atom.cpp is a simple example of a derived dump class. + +Here is a brief description of methods you define in your new derived +class. See dump.h for details. + ++--------------+---------------------------------------------------+ +| write_header | write the header section of a snapshot of atoms | ++--------------+---------------------------------------------------+ +| count | count the number of lines a processor will output | ++--------------+---------------------------------------------------+ +| pack | pack a proc's output data into a buffer | ++--------------+---------------------------------------------------+ +| write_data | write a proc's data to a file | ++--------------+---------------------------------------------------+ + +See the :doc:`dump ` command and its *custom* style for a list of +keywords for atom information that can already be dumped by +DumpCustom. It includes options to dump per-atom info from Compute +classes, so adding a new derived Compute class is one way to calculate +new quantities to dump. + +Alternatively, you can add new keywords to the dump custom command. +Search for the word "customize" in dump_custom.cpp to see the +half-dozen or so locations where code will need to be added. + + +---------- + + +.. _mod_6: + +Fix styles +---------- + +In LAMMPS, a "fix" is any operation that is computed during +timestepping that alters some property of the system. Essentially +everything that happens during a simulation besides force computation, +neighbor list construction, and output, is a "fix". This includes +time integration (update of coordinates and velocities), force +constraints or boundary conditions (SHAKE or walls), and diagnostics +(compute a diffusion coefficient). New styles can be created to add +new options to LAMMPS. + +Fix_setforce.cpp is a simple example of setting forces on atoms to +prescribed values. There are dozens of fix options already in LAMMPS; +choose one as a template that is similar to what you want to +implement. + +Here is a brief description of methods you can define in your new +derived class. See fix.h for details. + ++-------------------------+-------------------------------------------------------------------------------------------+ +| setmask | determines when the fix is called during the timestep (required) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| init | initialization before a run (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| setup_pre_exchange | called before atom exchange in setup (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| setup_pre_force | called before force computation in setup (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| setup | called immediately before the 1st timestep and after forces are computed (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_setup_pre_force | like setup_pre_force, but for minimizations instead of MD runs (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_setup | like setup, but for minimizations instead of MD runs (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| initial_integrate | called at very beginning of each timestep (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| pre_exchange | called before atom exchange on re-neighboring steps (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| pre_neighbor | called before neighbor list build (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| pre_force | called before pair & molecular forces are computed (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| post_force | called after pair & molecular forces are computed and communicated (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| final_integrate | called at end of each timestep (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| end_of_step | called at very end of timestep (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| write_restart | dumps fix info to restart file (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| restart | uses info from restart file to re-initialize the fix (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| grow_arrays | allocate memory for atom-based arrays used by fix (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| copy_arrays | copy atom info when an atom migrates to a new processor (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| pack_exchange | store atom's data in a buffer (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| unpack_exchange | retrieve atom's data from a buffer (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| pack_restart | store atom's data for writing to restart file (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| unpack_restart | retrieve atom's data from a restart file buffer (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| size_restart | size of atom's data (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| maxsize_restart | max size of atom's data (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| setup_pre_force_respa | same as setup_pre_force, but for rRESPA (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| initial_integrate_respa | same as initial_integrate, but for rRESPA (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| post_integrate_respa | called after the first half integration step is done in rRESPA (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| pre_force_respa | same as pre_force, but for rRESPA (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| post_force_respa | same as post_force, but for rRESPA (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| final_integrate_respa | same as final_integrate, but for rRESPA (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_pre_force | called after pair & molecular forces are computed in minimizer (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_post_force | called after pair & molecular forces are computed and communicated in minmizer (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_store | store extra data for linesearch based minimization on a LIFO stack (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_pushstore | push the minimization LIFO stack one element down (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_popstore | pop the minimization LIFO stack one element up (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_clearstore | clear minimization LIFO stack (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_step | reset or move forward on line search minimization (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| min_dof | report number of degrees of freedom *added* by this fix in minimization (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| max_alpha | report maximum allowed step size during linesearch minimization (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| pack_comm | pack a buffer to communicate a per-atom quantity (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| unpack_comm | unpack a buffer to communicate a per-atom quantity (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| pack_reverse_comm | pack a buffer to reverse communicate a per-atom quantity (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| unpack_reverse_comm | unpack a buffer to reverse communicate a per-atom quantity (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| dof | report number of degrees of freedom *removed* by this fix during MD (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| compute_scalar | return a global scalar property that the fix computes (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| compute_vector | return a component of a vector property that the fix computes (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| compute_array | return a component of an array property that the fix computes (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| deform | called when the box size is changed (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| reset_target | called when a change of the target temperature is requested during a run (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| reset_dt | is called when a change of the time step is requested during a run (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| modify_param | called when a fix_modify request is executed (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| memory_usage | report memory used by fix (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ +| thermo | compute quantities for thermodynamic output (optional) | ++-------------------------+-------------------------------------------------------------------------------------------+ + +Typically, only a small fraction of these methods are defined for a +particular fix. Setmask is mandatory, as it determines when the fix +will be invoked during the timestep. Fixes that perform time +integration (*nve*, *nvt*, *npt*) implement initial_integrate() and +final_integrate() to perform velocity Verlet updates. Fixes that +constrain forces implement post_force(). + +Fixes that perform diagnostics typically implement end_of_step(). For +an end_of_step fix, one of your fix arguments must be the variable +"nevery" which is used to determine when to call the fix and you must +set this variable in the constructor of your fix. By convention, this +is the first argument the fix defines (after the ID, group-ID, style). + +If the fix needs to store information for each atom that persists from +timestep to timestep, it can manage that memory and migrate the info +with the atoms as they move from processors to processor by +implementing the grow_arrays, copy_arrays, pack_exchange, and +unpack_exchange methods. Similarly, the pack_restart and +unpack_restart methods can be implemented to store information about +the fix in restart files. If you wish an integrator or force +constraint fix to work with rRESPA (see the :doc:`run_style ` +command), the initial_integrate, post_force_integrate, and +final_integrate_respa methods can be implemented. The thermo method +enables a fix to contribute values to thermodynamic output, as printed +quantities and/or to be summed to the potential energy of the system. + + +---------- + + +.. _mod_7: + +Input script commands +--------------------- + +New commands can be added to LAMMPS input scripts by adding new +classes that have a "command" method. For example, the create_atoms, +read_data, velocity, and run commands are all implemented in this +fashion. When such a command is encountered in the LAMMPS input +script, LAMMPS simply creates a class with the corresponding name, +invokes the "command" method of the class, and passes it the arguments +from the input script. The command method can perform whatever +operations it wishes on LAMMPS data structures. + +The single method your new class must define is as follows: + ++---------+-----------------------------------------+ +| command | operations performed by the new command | ++---------+-----------------------------------------+ + +Of course, the new class can define other methods and variables as +needed. + + +---------- + + +.. _mod_8: + +Kspace computations +------------------- + +Classes that compute long-range Coulombic interactions via K-space +representations (Ewald, PPPM) are derived from the KSpace class. New +styles can be created to add new K-space options to LAMMPS. + +Ewald.cpp is an example of computing K-space interactions. + +Here is a brief description of methods you define in your new derived +class. See kspace.h for details. + ++--------------+----------------------------------------------+ +| init | initialize the calculation before a run | ++--------------+----------------------------------------------+ +| setup | computation before the 1st timestep of a run | ++--------------+----------------------------------------------+ +| compute | every-timestep computation | ++--------------+----------------------------------------------+ +| memory_usage | tally of memory usage | ++--------------+----------------------------------------------+ + + +---------- + + +.. _mod_9: + +Minimization styles +------------------- + +Classes that perform energy minimization derived from the Min class. +New styles can be created to add new minimization algorithms to +LAMMPS. + +Min_cg.cpp is an example of conjugate gradient minimization. + +Here is a brief description of methods you define in your new derived +class. See min.h for details. + ++--------------+------------------------------------------+ +| init | initialize the minimization before a run | ++--------------+------------------------------------------+ +| run | perform the minimization | ++--------------+------------------------------------------+ +| memory_usage | tally of memory usage | ++--------------+------------------------------------------+ + + +---------- + + +.. _mod_10: + +Pairwise potentials +------------------- + +Classes that compute pairwise interactions are derived from the Pair +class. In LAMMPS, pairwise calculation include manybody potentials +such as EAM or Tersoff where particles interact without a static bond +topology. New styles can be created to add new pair potentials to +LAMMPS. + +Pair_lj_cut.cpp is a simple example of a Pair class, though it +includes some optional methods to enable its use with rRESPA. + +Here is a brief description of the class methods in pair.h: + ++-------------------------------+-------------------------------------------------------------------+ +| compute | workhorse routine that computes pairwise interactions | ++-------------------------------+-------------------------------------------------------------------+ +| settings | reads the input script line with arguments you define | ++-------------------------------+-------------------------------------------------------------------+ +| coeff | set coefficients for one i,j type pair | ++-------------------------------+-------------------------------------------------------------------+ +| init_one | perform initialization for one i,j type pair | ++-------------------------------+-------------------------------------------------------------------+ +| init_style | initialization specific to this pair style | ++-------------------------------+-------------------------------------------------------------------+ +| write & read_restart | write/read i,j pair coeffs to restart files | ++-------------------------------+-------------------------------------------------------------------+ +| write & read_restart_settings | write/read global settings to restart files | ++-------------------------------+-------------------------------------------------------------------+ +| single | force and energy of a single pairwise interaction between 2 atoms | ++-------------------------------+-------------------------------------------------------------------+ +| compute_inner/middle/outer | versions of compute used by rRESPA | ++-------------------------------+-------------------------------------------------------------------+ + +The inner/middle/outer routines are optional. + + +---------- + + +.. _mod_11: + +Region styles +------------- + +Classes that define geometric regions are derived from the Region +class. Regions are used elsewhere in LAMMPS to group atoms, delete +atoms to create a void, insert atoms in a specified region, etc. New +styles can be created to add new region shapes to LAMMPS. + +Region_sphere.cpp is an example of a spherical region. + +Here is a brief description of methods you define in your new derived +class. See region.h for details. + ++-------+--------------------------------------------+ +| match | determine whether a point is in the region | ++-------+--------------------------------------------+ + + +---------- + + +.. _mod_12: + +Body styles +----------- + +Classes that define body particles are derived from the Body class. +Body particles can represent complex entities, such as surface meshes +of discrete points, collections of sub-particles, deformable objects, +etc. + +See :ref:`Section_howto 14 ` of the manual for +an overview of using body particles and the :doc:`body ` doc page +for details on the various body styles LAMMPS supports. New styles +can be created to add new kinds of body particles to LAMMPS. + +Body_nparticle.cpp is an example of a body particle that is treated as +a rigid body containing N sub-particles. + +Here is a brief description of methods you define in your new derived +class. See body.h for details. + ++--------------------+-----------------------------------------------------------+ +| data_body | process a line from the Bodies section of a data file | ++--------------------+-----------------------------------------------------------+ +| noutrow | number of sub-particles output is generated for | ++--------------------+-----------------------------------------------------------+ +| noutcol | number of values per-sub-particle output is generated for | ++--------------------+-----------------------------------------------------------+ +| output | output values for the Mth sub-particle | ++--------------------+-----------------------------------------------------------+ +| pack_comm_body | body attributes to communicate every timestep | ++--------------------+-----------------------------------------------------------+ +| unpack_comm_body | unpacking of those attributes | ++--------------------+-----------------------------------------------------------+ +| pack_border_body | body attributes to communicate when reneighboring is done | ++--------------------+-----------------------------------------------------------+ +| unpack_border_body | unpacking of those attributes | ++--------------------+-----------------------------------------------------------+ + + +---------- + + +.. _mod_13: + +Thermodynamic output options +---------------------------- + +There is one class that computes and prints thermodynamic information +to the screen and log file; see the file thermo.cpp. + +There are two styles defined in thermo.cpp: "one" and "multi". There +is also a flexible "custom" style which allows the user to explicitly +list keywords for quantities to print when thermodynamic info is +output. See the :doc:`thermo_style ` command for a list +of defined quantities. + +The thermo styles (one, multi, etc) are simply lists of keywords. +Adding a new style thus only requires defining a new list of keywords. +Search for the word "customize" with references to "thermo style" in +thermo.cpp to see the two locations where code will need to be added. + +New keywords can also be added to thermo.cpp to compute new quantities +for output. Search for the word "customize" with references to +"keyword" in thermo.cpp to see the several locations where code will +need to be added. + +Note that the :doc:`thermo_style custom ` command already allows +for thermo output of quantities calculated by :doc:`fixes `, +:doc:`computes `, and :doc:`variables `. Thus, it may +be simpler to compute what you wish via one of those constructs, than +by adding a new keyword to the thermo command. + + +---------- + + +.. _mod_14: + +Variable options +---------------- + +There is one class that computes and stores :doc:`variable ` +information in LAMMPS; see the file variable.cpp. The value +associated with a variable can be periodically printed to the screen +via the :doc:`print `, :doc:`fix print `, or +:doc:`thermo_style custom ` commands. Variables of style +"equal" can compute complex equations that involve the following types +of arguments: + +.. parsed-literal:: + + thermo keywords = ke, vol, atoms, ... + other variables = v_a, v_myvar, ... + math functions = div(x,y), mult(x,y), add(x,y), ... + group functions = mass(group), xcm(group,x), ... + atom values = x[123], y[3], vx[34], ... + compute values = c_mytemp[0], c_thermo_press[3], ... + +Adding keywords for the :doc:`thermo_style custom ` command +(which can then be accessed by variables) was discussed +:ref:`here ` on this page. + +Adding a new math function of one or two arguments can be done by +editing one section of the Variable::evaulate() method. Search for +the word "customize" to find the appropriate location. + +Adding a new group function can be done by editing one section of the +Variable::evaulate() method. Search for the word "customize" to find +the appropriate location. You may need to add a new method to the +Group class as well (see the group.cpp file). + +Accessing a new atom-based vector can be done by editing one section +of the Variable::evaulate() method. Search for the word "customize" +to find the appropriate location. + +Adding new :doc:`compute styles ` (whose calculated values can +then be accessed by variables) was discussed +:ref:`here ` on this page. + + + + + +.. _mod_15: + +Submitting new features for inclusion in LAMMPS +----------------------------------------------- + +We encourage users to submit new features to `the developers `_ that they add to +LAMMPS, especially if you think they will be of interest to other +users. If they are broadly useful we may add them as core files to +LAMMPS or as part of a :ref:`standard package `. +Else we will add them as a user-contributed file or package. Examples +of user packages are in src sub-directories that start with USER. The +USER-MISC package is simply a collection of (mostly) unrelated single +files, which is the simplest way to have your contribution quickly +added to the LAMMPS distribution. You can see a list of the both +standard and user packages by typing "make package" in the LAMMPS src +directory. + +Note that by providing us the files to release, you are agreeing to +make them open-source, i.e. we can release them under the terms of the +GPL, used as a license for the rest of LAMMPS. See :ref:`Section 1.4 ` for details. + +With user packages and files, all we are really providing (aside from +the fame and fortune that accompanies having your name in the source +code and on the `Authors page `_ +of the `LAMMPS WWW site `_), is a means for you to distribute your +work to the LAMMPS user community, and a mechanism for others to +easily try out your new feature. This may help you find bugs or make +contact with new collaborators. Note that you're also implicitly +agreeing to support your code which means answer questions, fix bugs, +and maintain it if LAMMPS changes in some way that breaks it (an +unusual event). + +.. note:: + + If you prefer to actively develop and support your add-on + feature yourself, then you may wish to make it available for download + from your own website, as a user package that LAMMPS users can add to + their copy of LAMMPS. See the `Offsite LAMMPS packages and tools `_ page of the LAMMPS web + site for examples of groups that do this. We are happy to advertise + your package and web site from that page. Simply email the + `developers `_ with info about + your package and we will post it there. + +The previous sections of this doc page describe how to add new "style" +files of various kinds to LAMMPS. Packages are simply collections of +one or more new class files which are invoked as a new style within a +LAMMPS input script. If designed correctly, these additions typically +do not require changes to the main core of LAMMPS; they are simply +add-on files. If you think your new feature requires non-trivial +changes in core LAMMPS files, you'll need to `communicate with the developers `_, since we may or may +not want to make those changes. An example of a trivial change is +making a parent-class method "virtual" when you derive a new child +class from it. + +Here are the steps you need to follow to submit a single file or user +package for our consideration. Following these steps will save both +you and us time. See existing files in packages in the src dir for +examples. + +* All source files you provide must compile with the most current + version of LAMMPS. +* If you want your file(s) to be added to main LAMMPS or one of its + standard packages, then it needs to be written in a style compatible + with other LAMMPS source files. This is so the developers can + understand it and hopefully maintain it. This basically means that + the code accesses data structures, performs its operations, and is + formatted similar to other LAMMPS source files, including the use of + the error class for error and warning messages. +* If you want your contribution to be added as a user-contributed + feature, and it's a single file (actually a *.cpp and *.h file) it can + rapidly be added to the USER-MISC directory. Send us the one-line + entry to add to the USER-MISC/README file in that dir, along with the + 2 source files. You can do this multiple times if you wish to + contribute several individual features. +* If you want your contribution to be added as a user-contribution and + it is several related featues, it is probably best to make it a user + package directory with a name like USER-FOO. In addition to your new + files, the directory should contain a README text file. The README + should contain your name and contact information and a brief + description of what your new package does. If your files depend on + other LAMMPS style files also being installed (e.g. because your file + is a derived class from the other LAMMPS class), then an Install.sh + file is also needed to check for those dependencies. See other README + and Install.sh files in other USER directories as examples. Send us a + tarball of this USER-FOO directory. +* Your new source files need to have the LAMMPS copyright, GPL notice, + and your name and email address at the top, like other + user-contributed LAMMPS source files. They need to create a class + that is inside the LAMMPS namespace. If the file is for one of the + USER packages, including USER-MISC, then we are not as picky about the + coding style (see above). I.e. the files do not need to be in the + same stylistic format and syntax as other LAMMPS files, though that + would be nice for developers as well as users who try to read your + code. +* You must also create a documentation file for each new command or + style you are adding to LAMMPS. This will be one file for a + single-file feature. For a package, it might be several files. These + are simple text files which we auto-convert to HTML. Thus they must + be in the same format as other *.txt files in the lammps/doc directory + for similar commands and styles; use one or more of them as a starting + point. As appropriate, the text files can include links to equations + (see doc/Eqs/*.tex for examples, we auto-create the associated JPG + files), or figures (see doc/JPG for examples), or even additional PDF + files with further details (see doc/PDF for examples). The doc page + should also include literature citations as appropriate; see the + bottom of doc/fix_nh.txt for examples and the earlier part of the same + file for how to format the cite itself. The "Restrictions" section of + the doc page should indicate that your command is only available if + LAMMPS is built with the appropriate USER-MISC or USER-FOO package. + See other user package doc files for examples of how to do this. The + txt2html tool we use to convert to HTML can be downloaded from `this site `_, so you can perform + the HTML conversion yourself to proofread your doc page. +* For a new package (or even a single command) you can include one or + more example scripts. These should run in no more than 1 minute, even + on a single processor, and not require large data files as input. See + directories under examples/USER for examples of input scripts other + users provided for their packages. +* If there is a paper of yours describing your feature (either the + algorithm/science behind the feature itself, or its initial usage, or + its implementation in LAMMPS), you can add the citation to the *.cpp + source file. See src/USER-EFF/atom_vec_electron.cpp for an example. + A LaTeX citation is stored in a variable at the top of the file and a + single line of code that references the variable is added to the + constructor of the class. Whenever a user invokes your feature from + their input script, this will cause LAMMPS to output the citation to a + log.cite file and prompt the user to examine the file. Note that you + should only use this for a paper you or your group authored. + E.g. adding a cite in the code for a paper by Nose and Hoover if you + write a fix that implements their integrator is not the intended + usage. That kind of citation should just be in the doc page you + provide. +Finally, as a general rule-of-thumb, the more clear and +self-explanatory you make your doc and README files, and the easier +you make it for people to get started, e.g. by providing example +scripts, the more likely it is that users will try out your new +feature. + + + + + +.. _Foo: + + + +**(Foo)** Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_packages.txt b/doc/_sources/Section_packages.txt new file mode 100644 index 0000000000..dee6c8632d --- /dev/null +++ b/doc/_sources/Section_packages.txt @@ -0,0 +1,1052 @@ +Packages +======== + +This section gives a quick overview of the add-on packages that extend +LAMMPS functionality. + +| 4.1 :ref:`Standard packages ` +| 4.2 :ref:`User packages ` +| + +LAMMPS includes many optional packages, which are groups of files that +enable a specific set of features. For example, force fields for +molecular systems or granular systems are in packages. You can see +the list of all packages by typing "make package" from within the src +directory of the LAMMPS distribution. + +See :ref:`Section_start 3 ` of the manual for +details on how to include/exclude specific packages as part of the +LAMMPS build process, and for more details about the differences +between standard packages and user packages. + +Unless otherwise noted below, every package is independent of all the +others. I.e. any package can be included or excluded in a LAMMPS +build, independent of all other packages. However, note that some +packages include commands derived from commands in other packages. If +the other package is not installed, the derived command from the new +package will also not be installed when you include the new one. +E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package +will not be installed as part of the USER-OMP package if the KSPACE +package is not also installed, since it contains the pair +lj/cut/coul/long command. If you later install the KSPACE pacakge and +the USER-OMP package is already installed, both the pair +lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed. + +The two tables below list currently available packages in LAMMPS, with +a one-line descriptions of each. The sections below give a few more +details, including instructions for building LAMMPS with the package, +either via the make command or the Make.py tool described in :ref:`Section 2.4 `. + + + + + +.. _pkg_1: + +Standard packages +----------------------------- + +The current list of standard packages is as follows. + ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| Package | Description | Author(s) | Doc page | Example | Library | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| ASPHERE | aspherical particles | - | :ref:`Section_howto 6.14 ` | ellipse | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| BODY | body-style particles | - | :doc:`body ` | body | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| CLASS2 | class 2 force fields | - | :doc:`pair_style lj/class2 ` | - | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| COLLOID | colloidal particles | - | :doc:`atom_style colloid ` | colloid | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| COMPRESS | I/O compression | Axel Kohlmeyer (Temple U) | :doc:`dump */gz ` | - | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| CORESHELL | adiabatic core/shell model | Hendrik Heenen (Technical U of Munich) | :ref:`Section_howto 6.25 ` | coreshell | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| DIPOLE | point dipole particles | - | :doc:`pair_style dipole/cut ` | dipole | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| FLD | Fast Lubrication Dynamics | Kumar & Bybee & Higdon (1) | :doc:`pair_style lubricateU ` | - | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| GPU | GPU-enabled styles | Mike Brown (ORNL) | :doc:`Section accelerate ` | gpu | lib/gpu | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| GRANULAR | granular systems | - | :ref:`Section_howto 6.6 ` | pour | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| KIM | openKIM potentials | Smirichinski & Elliot & Tadmor (3) | :doc:`pair_style kim ` | kim | KIM | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| KOKKOS | Kokkos-enabled styles | Trott & Edwards (4) | :doc:`Section_accelerate ` | kokkos | lib/kokkos | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| KSPACE | long-range Coulombic solvers | - | :doc:`kspace_style ` | peptide | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| MANYBODY | many-body potentials | - | :doc:`pair_style tersoff ` | shear | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| MEAM | modified EAM potential | Greg Wagner (Sandia) | :doc:`pair_style meam ` | meam | lib/meam | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| MC | Monte Carlo options | - | :doc:`fix gcmc ` | - | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| MOLECULE | molecular system force fields | - | :ref:`Section_howto 6.3 ` | peptide | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| OPT | optimized pair styles | Fischer & Richie & Natoli (2) | :doc:`Section accelerate ` | - | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| PERI | Peridynamics models | Mike Parks (Sandia) | :doc:`pair_style peri ` | peri | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| POEMS | coupled rigid body motion | Rudra Mukherjee (JPL) | :doc:`fix poems ` | rigid | lib/poems | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| PYTHON | embed Python code in an input script | - | :doc:`python ` | python | lib/python | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| REAX | ReaxFF potential | Aidan Thompson (Sandia) | :doc:`pair_style reax ` | reax | lib/reax | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| REPLICA | multi-replica methods | - | :ref:`Section_howto 6.5 ` | tad | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| RIGID | rigid bodies | - | :doc:`fix rigid ` | rigid | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| SHOCK | shock loading methods | - | :doc:`fix msst ` | - | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| SNAP | quantum-fit potential | Aidan Thompson (Sandia) | :doc:`pair snap ` | snap | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| SRD | stochastic rotation dynamics | - | :doc:`fix srd ` | srd | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| VORONOI | Voronoi tesselations | Daniel Schwen (LANL) | :doc:`compute voronoi/atom ` | - | Voro++ | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| XTC | dumps in XTC format | - | :doc:`dump ` | - | - | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ +| | | | | | | ++-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+ + +The "Authors" column lists a name(s) if a specific person is +responible for creating and maintaining the package. +More details on +multiple authors are give below. + +(1) The FLD package was created by Amit Kumar and Michael Bybee from +Jonathan Higdon's group at UIUC. + +(2) The OPT package was created by James Fischer (High Performance +Technologies), David Richie, and Vincent Natoli (Stone Ridge +Technolgy). + +(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott, +and Ellad Tadmor (U Minn). + +(4) The KOKKOS package was created primarily by Christian Trott +(Sandia). It uses the Kokkos library which was developed by Carter +Edwards, Christian, and collaborators at Sandia. + +The "Doc page" column links to either a portion of the +:doc:`Section_howto ` of the manual, or an input script +command implemented as part of the package. + +The "Example" column is a sub-directory in the examples directory of +the distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory. + +The "Library" column lists an external library which must be built +first and which LAMMPS links to when it is built. If it is listed as +lib/package, then the code for the library is under the lib directory +of the LAMMPS distribution. See the lib/package/README file for info +on how to build the library. If it is not listed as lib/package, then +it is a third-party library not included in the LAMMPS distribution. +See the src/package/README or src/package/Makefile.lammps file for +info on where to download the library. :ref:`Section start ` of the manual also gives details +on how to build LAMMPS with both kinds of auxiliary libraries. + +Except where explained below, all of these packages can be installed, +and LAMMPS re-built, by issuing these commands from the src dir. + +.. parsed-literal:: + + make yes-package + make machine + or + Make.py -p package -a machine + +To un-install the package and re-build LAMMPS without it: + +.. parsed-literal:: + + make no-package + make machine + or + Make.py -p ^package -a machine + +"Package" is the name of the package in lower-case letters, +e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or +serial. + + + + + +Build instructions for COMPRESS package +----------------------------- + + +Build instructions for GPU package +------------------------ + + +Build instructions for KIM package +------------------------ + + +Build instructions for KOKKOS package +--------------------------- + + +Build instructions for KSPACE package +--------------------------- + + +Build instructions for MEAM package +------------------------- + + +Build instructions for POEMS package +-------------------------- + + +Build instructions for PYTHON package +--------------------------- + + +Build instructions for REAX package +------------------------- + + +Build instructions for VORONOI package +---------------------------- + + +Build instructions for XTC package +------------------------ + + + +---------- + + +.. _pkg_2: + +User packages +------------------------- + +The current list of user-contributed packages is as follows: + ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| Package | Description | Author(s) | Doc page | Example | Pic/movie | Library | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-ATC | atom-to-continuum coupling | Jones & Templeton & Zimmerman (1) | :doc:`fix atc ` | USER/atc | `atc `_ | lib/atc | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-AWPMD | wave-packet MD | Ilya Valuev (JIHT) | :doc:`pair_style awpmd/cut ` | USER/awpmd | - | lib/awpmd | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-CG-CMM | coarse-graining model | Axel Kohlmeyer (Temple U) | :doc:`pair_style lj/sdk ` | USER/cg-cmm | `cg `_ | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-COLVARS | collective variables | Fiorin & Henin & Kohlmeyer (2) | :doc:`fix colvars ` | USER/colvars | `colvars `_ | lib/colvars | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-CUDA | NVIDIA GPU styles | Christian Trott (U Tech Ilmenau) | :doc:`Section accelerate ` | USER/cuda | - | lib/cuda | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-DIFFRACTION | virutal x-ray and electron diffraction | Shawn Coleman (ARL) | :doc:`compute xrd ` | USER/diffraction | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-DPD | dissipative particle dynamics (DPD) | Larentzos & Mattox & Brennan (5) | src/USER-DPD/README | USER/dpd | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-DRUDE | Drude oscillators | Dequidt & Devemy & Padua (3) | :doc:`tutorial ` | USER/drude | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-EFF | electron force field | Andres Jaramillo-Botero (Caltech) | :doc:`pair_style eff/cut ` | USER/eff | `eff `_ | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-FEP | free energy perturbation | Agilio Padua (U Blaise Pascal Clermont-Ferrand) | :doc:`compute fep ` | USER/fep | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-H5MD | dump output via HDF5 | Pierre de Buyl (KU Leuven) | :doc:`dump h5md ` | - | - | lib/h5md | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-INTEL | Vectorized CPU and Intel(R) coprocessor styles | W. Michael Brown (Intel) | :doc:`Section accelerate ` | examples/intel | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-LB | Lattice Boltzmann fluid | Colin Denniston (U Western Ontario) | :doc:`fix lb/fluid ` | USER/lb | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-MGPT | fast MGPT multi-ion potentials | Tomas Oppelstrup & John Moriarty (LLNL) | :doc:`pair_style mgpt ` | USER/mgpt | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-MISC | single-file contributions | USER-MISC/README | USER-MISC/README | - | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-MOLFILE | `VMD `_ molfile plug-ins | Axel Kohlmeyer (Temple U) | :doc:`dump molfile ` | - | - | VMD-MOLFILE | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-OMP | OpenMP threaded styles | Axel Kohlmeyer (Temple U) | :doc:`Section accelerate ` | - | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-PHONON | phonon dynamical matrix | Ling-Ti Kong (Shanghai Jiao Tong U) | :doc:`fix phonon ` | USER/phonon | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-QMMM | QM/MM coupling | Axel Kohlmeyer (Temple U) | :doc:`fix qmmm ` | USER/qmmm | - | lib/qmmm | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-QTB | quantum nuclear effects | Yuan Shen (Stanford) | :doc:`fix qtb ` :doc:`fix_qbmsst ` | qtb | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-QUIP | QUIP/libatoms interface | Albert Bartok-Partay (U Cambridge) | :doc:`pair_style quip ` | USER/quip | - | lib/quip | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-REAXC | C version of ReaxFF | Metin Aktulga (LBNL) | :doc:`pair_style reaxc ` | reax | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-SMD | smoothed Mach dynamics | Georg Ganzenmuller (EMI) | `userguide.pdf `_ | USER/smd | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-SMTBQ | Second Moment Tight Binding - QEq potential | Salles & Maras & Politano & Tetot (4) | :doc:`pair_style smtbq ` | USER/smtbq | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-SPH | smoothed particle hydrodynamics | Georg Ganzenmuller (EMI) | `userguide.pdf `_ | USER/sph | `sph `_ | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| USER-TALLY | Pairwise tallied computes | Axel Kohlmeyer (Temple U) | :doc:`compute <...>/tally ` | USER/tally | - | - | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ +| | | | | | | | ++------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+ + +.. _atc: http://lammps.sandia.gov/pictures.html#atc + + + +.. _cg: http://lammps.sandia.gov/pictures.html#cg + + + +.. _eff: http://lammps.sandia.gov/movies.html#eff + + + +.. _sph: http://lammps.sandia.gov/movies.html#sph + + + +.. _VMD: http://www.ks.uiuc.edu/Research/vmd + + + +The "Authors" column lists a name(s) if a specific person is +responible for creating and maintaining the package. + +(1) The ATC package was created by Reese Jones, Jeremy Templeton, and +Jon Zimmerman (Sandia). + +(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using +the colvars module library written by Giacomo Fiorin (Temple U) and +Jerome Henin (LISM, Marseille, France). + +(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal +Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua +(U Blaise Pascal). + +(4) The SMTBQ package was created by Nicolas Salles, Emile Maras, +Olivier Politano, and Robert Tetot (LAAS-CNRS, France). + +(4) The USER-DPD package was created by James Larentzos, Timothy +Mattox, and John Brennan (Army Research Lab (ARL) and Engility Corp). + +If the Library is not listed as lib/package, then it is a third-party +library not included in the LAMMPS distribution. See the +src/package/Makefile.lammps file for info on where to download the +library from. + +The "Doc page" column links to either a portion of the +:doc:`Section_howto ` of the manual, or an input script +command implemented as part of the package, or to additional +documentation provided within the package. + +The "Example" column is a sub-directory in the examples directory of +the distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory. USER/cuda +refers to the examples/USER/cuda directory. + +The "Library" column lists an external library which must be built +first and which LAMMPS links to when it is built. If it is listed as +lib/package, then the code for the library is under the lib directory +of the LAMMPS distribution. See the lib/package/README file for info +on how to build the library. If it is not listed as lib/package, then +it is a third-party library not included in the LAMMPS distribution. +See the src/package/Makefile.lammps file for info on where to download +the library. :ref:`Section start ` of the +manual also gives details on how to build LAMMPS with both kinds of +auxiliary libraries. + +Except where explained below, all of these packages can be installed, +and LAMMPS re-built, by issuing these commands from the src dir. + +.. parsed-literal:: + + make yes-user-package + make machine + or + Make.py -p package -a machine + +To un-install the package and re-build LAMMPS without it: + +.. parsed-literal:: + + make no-user-package + make machine + or + Make.py -p ^package -a machine + +"Package" is the name of the package (in this case without the user +prefix) in lower-case letters, e.g. drude or phonon, and "machine" is +the build target, e.g. mpi or serial. + + + + + +USER-ATC package +---------------- + +This package implements a "fix atc" command which can be used in a +LAMMPS input script. This fix can be employed to either do concurrent +coupling of MD with FE-based physics surrogates or on-the-fly +post-processing of atomic information to continuum fields. + +See the doc page for the fix atc command to get started. At the +bottom of the doc page are many links to additional documentation +contained in the doc/USER/atc directory. + +There are example scripts for using this package in examples/USER/atc. + +This package uses an external library in lib/atc which must be +compiled before making LAMMPS. See the lib/atc/README file and the +LAMMPS manual for information on building LAMMPS with external +libraries. + +The primary people who created this package are Reese Jones (rjones at +sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon +Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if +you have questions. + + +---------- + + +USER-AWPMD package +------------------ + +This package contains a LAMMPS implementation of the Antisymmetrized +Wave Packet Molecular Dynamics (AWPMD) method. + +See the doc page for the pair_style awpmd/cut command to get started. + +There are example scripts for using this package in examples/USER/awpmd. + +This package uses an external library in lib/awpmd which must be +compiled before making LAMMPS. See the lib/awpmd/README file and the +LAMMPS manual for information on building LAMMPS with external +libraries. + +The person who created this package is Ilya Valuev at the JIHT in +Russia (valuev at physik.hu-berlin.de). Contact him directly if you +have questions. + + +---------- + + +USER-CG-CMM package +------------------- + +This package implements 3 commands which can be used in a LAMMPS input +script: + +* pair_style lj/sdk +* pair_style lj/sdk/coul/long +* angle_style sdk + +These styles allow coarse grained MD simulations with the +parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) +(SDK), with extensions to simulate ionic liquids, electrolytes, lipids +and charged amino acids. + +See the doc pages for these commands for details. + +There are example scripts for using this package in +examples/USER/cg-cmm. + +This is the second generation implementation reducing the the clutter +of the previous version. For many systems with electrostatics, it will +be faster to use pair_style hybrid/overlay with lj/sdk and coul/long +instead of the combined lj/sdk/coul/long style. since the number of +charged atom types is usually small. For any other coulomb +interactions this is now required. To exploit this property, the use +of the kspace_style pppm/cg is recommended over regular pppm. For all +new styles, input file backward compatibility is provided. The old +implementation is still available through appending the /old +suffix. These will be discontinued and removed after the new +implementation has been fully validated. + +The current version of this package should be considered beta +quality. The CG potentials work correctly for "normal" situations, but +have not been testing with all kinds of potential parameters and +simulation systems. + +The person who created this package is Axel Kohlmeyer at Temple U +(akohlmey at gmail.com). Contact him directly if you have questions. + + +---------- + + +USER-COLVARS package +-------------------- + +This package implements the "fix colvars" command which can be +used in a LAMMPS input script. + +This fix allows to use "collective variables" to implement +Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella +Sampling and Restraints. This code consists of two parts: + +* A portable collective variable module library written and maintained +* by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and +* Jerome Henin (LISM, CNRS, Marseille, France). This code is located in +* the directory lib/colvars and needs to be compiled first. The colvars +* fix and an interface layer, exchanges information between LAMMPS and +* the collective variable module. + +See the doc page of :doc:`fix colvars ` for more details. + +There are example scripts for using this package in +examples/USER/colvars + +This is a very new interface that does not yet support all +features in the module and will see future optimizations +and improvements. The colvars module library is also available +in NAMD has been thoroughly used and tested there. Bugs and +problems are likely due to the interface layers code. +Thus the current version of this package should be considered +beta quality. + +The person who created this package is Axel Kohlmeyer at Temple U +(akohlmey at gmail.com). Contact him directly if you have questions. + + +---------- + + +USER-CUDA package +----------------- + +This package provides acceleration of various LAMMPS pair styles, fix +styles, compute styles, and long-range Coulombics via PPPM for NVIDIA +GPUs. + +See this section of the manual to get started: + +:ref:`Section_accelerate ` + +There are example scripts for using this package in +examples/USER/cuda. + +This package uses an external library in lib/cuda which must be +compiled before making LAMMPS. See the lib/cuda/README file and the +LAMMPS manual for information on building LAMMPS with external +libraries. + +The person who created this package is Christian Trott at the +University of Technology Ilmenau, Germany (christian.trott at +tu-ilmenau.de). Contact him directly if you have questions. + + +---------- + + +USER-DIFFRACTION package +------------------------ + +This package contains the commands neeed to calculate x-ray and +electron diffraction intensities based on kinematic diffraction +theory. + +See these doc pages and their related commands to get started: + +* :doc:`compute xrd ` +* :doc:`compute saed ` +* :doc:`fix saed/vtk ` + +The person who created this package is Shawn P. Coleman +(shawn.p.coleman8.ctr at mail.mil) while at the University of +Arkansas. Contact him directly if you have questions. + + +---------- + + +USER-DPD package +---------------- + +This package implements the dissipative particle dynamics (DPD) method +under isothermal, isoenergetic, isobaric and isenthalpic conditions. +The DPD equations of motion are integrated efficiently through the +Shardlow splitting algorithm. + +See these doc pages and their related commands to get started: + +* :doc:`compute dpd ` +* :doc:`compute dpd/atom ` +* :doc:`fix_eos/cv ` +* :doc:`fix_eos/table ` +* :doc:`fix_shardlow ` +* :doc:`pair_dpd/conservative ` +* :doc:`pair_dpd/fdt ` +* :doc:`pair_dpd/fdt/energy ` + +There are example scripts for using this package in examples/USER/dpd. + +The people who created this package are James Larentzos +(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at +engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil). +Contact them directly if you have questions. + + +---------- + + +USER-DRUDE package +------------------ + +This package implements methods for simulating polarizable systems +in LAMMPS using thermalized Drude oscillators. + +See these doc pages and their related commands to get started: + +* :doc:`Drude tutorial ` +* :doc:`fix drude ` +* :doc:`compute temp/drude ` +* :doc:`fix langevin/drude ` +* :doc:`fix drude/transform/... ` +* :doc:`pair thole ` + +There are auxiliary tools for using this package in tools/drude. + +The person who created this package is Alain Dequidt at Universite +Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr) +Contact him directly if you have questions. Co-authors: Julien Devemy, +Agilio Padua. + + +---------- + + +USER-EFF package +---------------- + +This package contains a LAMMPS implementation of the electron Force +Field (eFF) currently under development at Caltech, as described in +A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, +2010. The eFF potential was first introduced by Su and Goddard, in +2007. + +eFF can be viewed as an approximation to QM wave packet dynamics and +Fermionic molecular dynamics, combining the ability of electronic +structure methods to describe atomic structure, bonding, and chemistry +in materials, and of plasma methods to describe nonequilibrium +dynamics of large systems with a large number of highly excited +electrons. We classify it as a mixed QM-classical approach rather than +a conventional force field method, which introduces QM-based terms (a +spin-dependent repulsion term to account for the Pauli exclusion +principle and the electron wavefunction kinetic energy associated with +the Heisenberg principle) that reduce, along with classical +electrostatic terms between nuclei and electrons, to the sum of a set +of effective pairwise potentials. This makes eFF uniquely suited to +simulate materials over a wide range of temperatures and pressures +where electronically excited and ionized states of matter can occur +and coexist. + +The necessary customizations to the LAMMPS core are in place to +enable the correct handling of explicit electron properties during +minimization and dynamics. + +See the doc page for the pair_style eff/cut command to get started. + +There are example scripts for using this package in +examples/USER/eff. + +There are auxiliary tools for using this package in tools/eff. + +The person who created this package is Andres Jaramillo-Botero at +CalTech (ajaramil at wag.caltech.edu). Contact him directly if you +have questions. + + +---------- + + +USER-FEP package +---------------- + +This package provides methods for performing free energy perturbation +simulations with soft-core pair potentials in LAMMPS. + +See these doc pages and their related commands to get started: + +* :doc:`fix adapt/fep ` +* :doc:`compute fep ` +* :doc:`soft pair styles ` + +The person who created this package is Agilio Padua at Universite +Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr) +Contact him directly if you have questions. + + +---------- + + +USER-H5MD package +----------------- + +This package contains a :doc:`dump h5md ` command for +performing a dump of atom properties in HDF5 format. `HDF5 files `_ are binary, portable and self-describing and can be +examined and used by a variety of auxiliary tools. The output HDF5 +files are structured in a format called H5MD, which was designed to +store molecular data, and can be used and produced by various MD and +MD-related codes. The :doc:`dump h5md ` command gives a +citation to a paper describing the format. + +.. _HDF5: http://www.hdfgroup.org/HDF5/ + + + +The person who created this package and the underlying H5MD format is +Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him +directly if you have questions. + + +---------- + + +USER-INTEL package +------------------ + +This package provides options for performing neighbor list and +non-bonded force calculations in single, mixed, or double precision +and also a capability for accelerating calculations with an +Intel(R) Xeon Phi(TM) coprocessor. + +See this section of the manual to get started: + +:ref:`Section_accelerate ` + +The person who created this package is W. Michael Brown at Intel +(michael.w.brown at intel.com). Contact him directly if you have questions. + + +---------- + + +USER-LB package +--------------- + +This package contains a LAMMPS implementation of a background +Lattice-Boltzmann fluid, which can be used to model MD particles +influenced by hydrodynamic forces. + +See this doc page and its related commands to get started: + +:doc:`fix lb/fluid ` + +The people who created this package are Frances Mackay (fmackay at +uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of +Western Ontario. Contact them directly if you have questions. + + +---------- + + +USER-MGPT package +----------------- + +This package contains a fast implementation for LAMMPS of +quantum-based MGPT multi-ion potentials. The MGPT or model GPT method +derives from first-principles DFT-based generalized pseudopotential +theory (GPT) through a series of systematic approximations valid for +mid-period transition metals with nearly half-filled d bands. The +MGPT method was originally developed by John Moriarty at Lawrence +Livermore National Lab (LLNL). + +In the general matrix representation of MGPT, which can also be +applied to f-band actinide metals, the multi-ion potentials are +evaluated on the fly during a simulation through d- or f-state matrix +multiplication, and the forces that move the ions are determined +analytically. The *mgpt* pair style in this package calculates forces +and energies using an optimized matrix-MGPT algorithm due to Tomas +Oppelstrup at LLNL. + +See this doc page to get started: + +:doc:`pair_style mgpt ` + +The persons who created the USER-MGPT package are Tomas Oppelstrup +(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) +Contact them directly if you have any questions. + + +---------- + + +USER-MISC package +----------------- + +The files in this package are a potpourri of (mostly) unrelated +features contributed to LAMMPS by users. Each feature is a single +pair of files (*.cpp and *.h). + +More information about each feature can be found by reading its doc +page in the LAMMPS doc directory. The doc page which lists all LAMMPS +input script commands is as follows: + +:ref:`Section_commands ` + +User-contributed features are listed at the bottom of the fix, +compute, pair, etc sections. + +The list of features and author of each is given in the +src/USER-MISC/README file. + +You should contact the author directly if you have specific questions +about the feature or its coding. + + +---------- + + +USER-MOLFILE package +-------------------- + +This package contains a dump molfile command which uses molfile +plugins that are bundled with the +`VMD `_ molecular visualization and +analysis program, to enable LAMMPS to dump its information in formats +compatible with various molecular simulation tools. + +The package only provides the interface code, not the plugins. These +can be obtained from a VMD installation which has to match the +platform that you are using to compile LAMMPS for. By adding plugins +to VMD, support for new file formats can be added to LAMMPS (or VMD or +other programs that use them) without having to recompile the +application itself. + +See this doc page to get started: + +:ref:`dump molfile ` + +The person who created this package is Axel Kohlmeyer at Temple U +(akohlmey at gmail.com). Contact him directly if you have questions. + + +---------- + + +USER-OMP package +---------------- + +This package provides OpenMP multi-threading support and +other optimizations of various LAMMPS pair styles, dihedral +styles, and fix styles. + +See this section of the manual to get started: + +:ref:`Section_accelerate ` + +The person who created this package is Axel Kohlmeyer at Temple U +(akohlmey at gmail.com). Contact him directly if you have questions. + + +---------- + + +USER-PHONON package +------------------- + +This package contains a fix phonon command that calculates dynamical +matrices, which can then be used to compute phonon dispersion +relations, directly from molecular dynamics simulations. + +See this doc page to get started: + +:doc:`fix phonon ` + +The person who created this package is Ling-Ti Kong (konglt at +sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly +if you have questions. + + +---------- + + +USER-QMMM package +----------------- + +This package provides a fix qmmm command which allows LAMMPS to be +used in a QM/MM simulation, currently only in combination with pw.x +code from the `Quantum ESPRESSO `_ package. + +.. _espresso: http://www.quantum-espresso.org + + + +The current implementation only supports an ONIOM style mechanical +coupling to the Quantum ESPRESSO plane wave DFT package. +Electrostatic coupling is in preparation and the interface has been +written in a manner that coupling to other QM codes should be possible +without changes to LAMMPS itself. + +See this doc page to get started: + +:doc:`fix qmmm ` + +as well as the lib/qmmm/README file. + +The person who created this package is Axel Kohlmeyer at Temple U +(akohlmey at gmail.com). Contact him directly if you have questions. + + +---------- + + +USER-QTB package +---------------- + +This package provides a self-consistent quantum treatment of the +vibrational modes in a classical molecular dynamics simulation. By +coupling the MD simulation to a colored thermostat, it introduces zero +point energy into the system, alter the energy power spectrum and the +heat capacity towards their quantum nature. This package could be of +interest if one wants to model systems at temperatures lower than +their classical limits or when temperatures ramp up across the +classical limits in the simulation. + +See these two doc pages to get started: + +:doc:`fix qtb ` provides quantum nulcear correction through a +colored thermostat and can be used with other time integration schemes +like :doc:`fix nve ` or :doc:`fix nph `. + +:doc:`fix qbmsst ` enables quantum nuclear correction of a +multi-scale shock technique simulation by coupling the quantum thermal +bath with the shocked system. + +The person who created this package is Yuan Shen (sy0302 at +stanford.edu) at Stanford University. Contact him directly if you +have questions. + + +---------- + + +USER-REAXC package +------------------ + +This package contains a implementation for LAMMPS of the ReaxFF force +field. ReaxFF uses distance-dependent bond-order functions to +represent the contributions of chemical bonding to the potential +energy. It was originally developed by Adri van Duin and the Goddard +group at CalTech. + +The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in +C, should give identical or very similar results to pair_style reax, +which is a ReaxFF implementation on top of a Fortran library, a +version of which library was originally authored by Adri van Duin. + +The reax/c version should be somewhat faster and more scalable, +particularly with respect to the charge equilibration calculation. It +should also be easier to build and use since there are no complicating +issues with Fortran memory allocation or linking to a Fortran library. + +For technical details about this implemention of ReaxFF, see +this paper: + +Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods +and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty, +S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011). + +See the doc page for the pair_style reax/c command for details +of how to use it in LAMMPS. + +The person who created this package is Hasan Metin Aktulga (hmaktulga +at lbl.gov), while at Purdue University. Contact him directly, or +Aidan Thompson at Sandia (athomps at sandia.gov), if you have +questions. + + +---------- + + +USER-SMD package +---------------- + +This package implements smoothed Mach dynamics (SMD) in +LAMMPS. Currently, the package has the following features: + +* Does liquids via traditional Smooth Particle Hydrodynamics (SPH) + +* Also solves solids mechanics problems via a state of the art + stabilized meshless method with hourglass control. + +* Can specify hydrostatic interactions independently from material + strength models, i.e. pressure and deviatoric stresses are separated. + +* Many material models available (Johnson-Cook, plasticity with + hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new + material models. + +* Rigid boundary conditions (walls) can be loaded as surface geometries + from *.STL files. + +See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started. + +There are example scripts for using this package in examples/USER/smd. + +The person who created this package is Georg Ganzenmuller at the +Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in +Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if +you have questions. + + +---------- + + +USER-SMTBQ package +------------------ + +This package implements the Second Moment Tight Binding - QEq (SMTB-Q) +potential for the description of ionocovalent bonds in oxides. + +There are example scripts for using this package in +examples/USER/smtbq. + +See this doc page to get started: + +:doc:`pair_style smtbq ` + +The persons who created the USER-SMTBQ package are Nicolas Salles, +Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at +these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact +them directly if you have any questions. + + +---------- + + +USER-SPH package +---------------- + +This package implements smoothed particle hydrodynamics (SPH) in +LAMMPS. Currently, the package has the following features: + +* Tait, ideal gas, Lennard-Jones equation of states, full support for + complete (i.e. internal-energy dependent) equations of state + +* Plain or Monaghans XSPH integration of the equations of motion + +* Density continuity or density summation to propagate the density field + +* Commands to set internal energy and density of particles from the + input script + +* Output commands to access internal energy and density for dumping and + thermo output + +See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started. + +There are example scripts for using this package in examples/USER/sph. + +The person who created this package is Georg Ganzenmuller at the +Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in +Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if +you have questions. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_perf.txt b/doc/_sources/Section_perf.txt new file mode 100644 index 0000000000..65f761c120 --- /dev/null +++ b/doc/_sources/Section_perf.txt @@ -0,0 +1,74 @@ +Performance & scalability +========================= + +LAMMPS performance on several prototypical benchmarks and machines is +discussed on the Benchmarks page of the `LAMMPS WWW Site `_ where +CPU timings and parallel efficiencies are listed. Here, the +benchmarks are described briefly and some useful rules of thumb about +their performance are highlighted. + +These are the 5 benchmark problems: + +#. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 + neighbors per atom), NVE integration +#. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ + pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per + atom), NVE integration +#. EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45 + neighbors per atom), NVE integration +#. Chute = granular chute flow, frictional history potential with 1.1 + sigma cutoff (7 neighbors per atom), NVE integration +#. Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force + field with a 10 Angstrom LJ cutoff (440 neighbors per atom), + particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT + integration +The input files for running the benchmarks are included in the LAMMPS +distribution, as are sample output files. Each of the 5 problems has +32,000 atoms and runs for 100 timesteps. Each can be run as a serial +benchmarks (on one processor) or in parallel. In parallel, each +benchmark can be run as a fixed-size or scaled-size problem. For +fixed-size benchmarking, the same 32K atom problem is run on various +numbers of processors. For scaled-size benchmarking, the model size +is increased with the number of processors. E.g. on 8 processors, a +256K-atom problem is run; on 1024 processors, a 32-million atom +problem is run, etc. + +A useful metric from the benchmarks is the CPU cost per atom per +timestep. Since LAMMPS performance scales roughly linearly with +problem size and timesteps, the run time of any problem using the same +model (atom style, force field, cutoff, etc) can then be estimated. +For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler +under Red Hat Linux), the CPU run-time in seconds/atom/timestep for +the 5 problems is + ++----------------+---------+---------+---------+---------+-----------+ +| Problem: | LJ | Chain | EAM | Chute | Rhodopsin | ++----------------+---------+---------+---------+---------+-----------+ +| CPU/atom/step: | 4.55E-6 | 2.18E-6 | 9.38E-6 | 2.18E-6 | 1.11E-4 | ++----------------+---------+---------+---------+---------+-----------+ +| Ratio to LJ: | 1.0 | 0.48 | 2.06 | 0.48 | 24.5 | ++----------------+---------+---------+---------+---------+-----------+ + +The ratios mean that if the atomic LJ system has a normalized cost of +1.0, the bead-spring chains and granular systems run 2x faster, while +the EAM metal and solvated protein models run 2x and 25x slower +respectively. The bulk of these cost differences is due to the +expense of computing a particular pairwise force field for a given +number of neighbors per atom. + +Performance on a parallel machine can also be predicted from the +one-processor timings if the parallel efficiency can be estimated. +The communication bandwidth and latency of a particular parallel +machine affects the efficiency. On most machines LAMMPS will give +fixed-size parallel efficiencies on these benchmarks above 50% so long +as the atoms/processor count is a few 100 or greater - i.e. on 64 to +128 processors. Likewise, scaled-size parallel efficiencies will +typically be 80% or greater up to very large processor counts. The +benchmark data on the `LAMMPS WWW Site `_ gives specific examples on +some different machines, including a run of 3/4 of a billion LJ atoms +on 1500 processors that ran at 85% parallel efficiency. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_python.txt b/doc/_sources/Section_python.txt new file mode 100644 index 0000000000..966370ebcd --- /dev/null +++ b/doc/_sources/Section_python.txt @@ -0,0 +1,1009 @@ +Python interface to LAMMPS +========================== + +LAMMPS can work together with Python in two ways. First, Python can +wrap LAMMPS through the :ref:`LAMMPS library interface `, so that a Python script can +create one or more instances of LAMMPS and launch one or more +simulations. In Python lingo, this is "extending" Python with LAMMPS. + +Second, LAMMPS can use the Python interpreter, so that a LAMMPS input +script can invoke Python code, and pass information back-and-forth +between the input script and Python functions you write. The Python +code can also callback to LAMMPS to query or change its attributes. +In Python lingo, this is "embedding" Python in LAMMPS. + +This section describes how to do both. + +* 11.1 :ref:`Overview of running LAMMPS from Python ` +* 11.2 :ref:`Overview of using Python from a LAMMPS script ` +* 11.3 :ref:`Building LAMMPS as a shared library ` +* 11.4 :ref:`Installing the Python wrapper into Python ` +* 11.5 :ref:`Extending Python with MPI to run in parallel ` +* 11.6 :ref:`Testing the Python-LAMMPS interface ` +* 11.7 :ref:`Using LAMMPS from Python ` +* 11.8 :ref:`Example Python scripts that use LAMMPS ` + +If you are not familiar with it, `Python `_ is a +powerful scripting and programming language which can essentially do +anything that faster, lower-level languages like C or C++ can do, but +typically with much fewer lines of code. When used in embedded mode, +Python can perform operations that the simplistic LAMMPS input script +syntax cannot. Python can be also be used as a "glue" language to +drive a program through its library interface, or to hook multiple +pieces of software together, such as a simulation package plus a +visualization package, or to run a coupled multiscale or multiphysics +model. + +See :ref:`Section_howto 10 ` of the manual and +the couple directory of the distribution for more ideas about coupling +LAMMPS to other codes. See :ref:`Section_howto 19 ` for a description of the LAMMPS +library interface provided in src/library.cpp and src/library.h, and +how to extend it for your needs. As described below, that interface +is what is exposed to Python either when calling LAMMPS from Python or +when calling Python from a LAMMPS input script and then calling back +to LAMMPS from Python code. The library interface is designed to be +easy to add functions to. Thus the Python interface to LAMMPS is also +easy to extend as well. + +If you create interesting Python scripts that run LAMMPS or +interesting Python functions that can be called from a LAMMPS input +script, that you think would be useful to other users, please `email them to the developers `_. We can +include them in the LAMMPS distribution. + + + + + +.. _py_1: + +Overview of running LAMMPS from Python +-------------------------------------- + +The LAMMPS distribution includes a python directory with all you need +to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS +library interface, with one wrapper function per LAMMPS library +function. This file makes it is possible to do the following either +from a Python script, or interactively from a Python prompt: create +one or more instances of LAMMPS, invoke LAMMPS commands or give it an +input script, run LAMMPS incrementally, extract LAMMPS results, an +modify internal LAMMPS variables. From a Python script you can do +this in serial or parallel. Running Python interactively in parallel +does not generally work, unless you have a version of Python that +extends standard Python to enable multiple instances of Python to read +what you type. + +To do all of this, you must first build LAMMPS as a shared library, +then insure that your Python can find the python/lammps.py file and +the shared library. These steps are explained in subsequent sections +11.3 and 11.4. Sections 11.5 and 11.6 discuss using MPI from a +parallel Python program and how to test that you are ready to use +LAMMPS from Python. Section 11.7 lists all the functions in the +current LAMMPS library interface and how to call them from Python. + +Section 11.8 gives some examples of coupling LAMMPS to other tools via +Python. For example, LAMMPS can easily be coupled to a GUI or other +visualization tools that display graphs or animations in real time as +LAMMPS runs. Examples of such scripts are inlcluded in the python +directory. + +Two advantages of using Python to run LAMMPS are how concise the +language is, and that it can be run interactively, enabling rapid +development and debugging of programs. If you use it to mostly invoke +costly operations within LAMMPS, such as running a simulation for a +reasonable number of timesteps, then the overhead cost of invoking +LAMMPS thru Python will be negligible. + +The Python wrapper for LAMMPS uses the amazing and magical (to me) +"ctypes" package in Python, which auto-generates the interface code +needed between Python and a set of C interface routines for a library. +Ctypes is part of standard Python for versions 2.5 and later. You can +check which version of Python you have installed, by simply typing +"python" at a shell prompt. + + +---------- + + +.. _py_2: + +Overview of using Python from a LAMMPS script +--------------------------------------------- + +.. note:: + + It is not currently possible to use the :doc:`python ` + command described in this section with Python 3, only with Python 2. + The C API changed from Python 2 to 3 and the LAMMPS code is not + compatible with both. + +LAMMPS has a :doc:`python ` command which can be used in an +input script to define and execute a Python function that you write +the code for. The Python function can also be assigned to a LAMMPS +python-style variable via the :doc:`variable ` command. Each +time the variable is evaluated, either in the LAMMPS input script +itself, or by another LAMMPS command that uses the variable, this will +trigger the Python function to be invoked. + +The Python code for the function can be included directly in the input +script or in an auxiliary file. The function can have arguments which +are mapped to LAMMPS variables (also defined in the input script) and +it can return a value to a LAMMPS variable. This is thus a mechanism +for your input script to pass information to a piece of Python code, +ask Python to execute the code, and return information to your input +script. + +Note that a Python function can be arbitrarily complex. It can import +other Python modules, instantiate Python classes, call other Python +functions, etc. The Python code that you provide can contain more +code than the single function. It can contain other functions or +Python classes, as well as global variables or other mechanisms for +storing state between calls from LAMMPS to the function. + +The Python function you provide can consist of "pure" Python code that +only performs operations provided by standard Python. However, the +Python function can also "call back" to LAMMPS through its +Python-wrapped library interface, in the manner described in the +previous section 11.1. This means it can issue LAMMPS input script +commands or query and set internal LAMMPS state. As an example, this +can be useful in an input script to create a more complex loop with +branching logic, than can be created using the simple looping and +brancing logic enabled by the :doc:`next ` and :doc:`if ` +commands. + +See the :doc:`python ` doc page and the :doc:`variable ` +doc page for its python-style variables for more info, including +examples of Python code you can write for both pure Python operations +and callbacks to LAMMPS. + +To run pure Python code from LAMMPS, you only need to build LAMMPS +with the PYTHON package installed: + +make yes-python +make machine + +Note that this will link LAMMPS with the Python library on your +system, which typically requires several auxiliary system libraries to +also be linked. The list of these libraries and the paths to find +them are specified in the lib/python/Makefile.lammps file. You need +to insure that file contains the correct information for your version +of Python and your machine to successfully build LAMMPS. See the +lib/python/README file for more info. + +If you want to write Python code with callbacks to LAMMPS, then you +must also follow the steps overviewed in the preceeding section (11.1) +for running LAMMPS from Python. I.e. you must build LAMMPS as a +shared library and insure that Python can find the python/lammps.py +file and the shared library. + + +---------- + + +.. _py_3: + +Building LAMMPS as a shared library +----------------------------------- + +Instructions on how to build LAMMPS as a shared library are given in +:ref:`Section_start 5 `. A shared library is one +that is dynamically loadable, which is what Python requires to wrap +LAMMPS. On Linux this is a library file that ends in ".so", not ".a". + +>From the src directory, type + +.. parsed-literal:: + + make foo mode=shlib + +where foo is the machine target name, such as linux or g++ or serial. +This should create the file liblammps_foo.so in the src directory, as +well as a soft link liblammps.so, which is what the Python wrapper will +load by default. Note that if you are building multiple machine +versions of the shared library, the soft link is always set to the +most recently built version. + +If this fails, see :ref:`Section_start 5 ` for +more details, especially if your LAMMPS build uses auxiliary libraries +like MPI or FFTW which may not be built as shared libraries on your +system. + + +---------- + + +.. _py_4: + +Installing the Python wrapper into Python +----------------------------------------- + +For Python to invoke LAMMPS, there are 2 files it needs to know about: + +* python/lammps.py +* src/liblammps.so + +Lammps.py is the Python wrapper on the LAMMPS library interface. +Liblammps.so is the shared LAMMPS library that Python loads, as +described above. + +You can insure Python can find these files in one of two ways: + +* set two environment variables +* run the python/install.py script + +If you set the paths to these files as environment variables, you only +have to do it once. For the csh or tcsh shells, add something like +this to your ~/.cshrc file, one line for each of the two files: + +.. parsed-literal:: + + setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python + setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src + +If you use the python/install.py script, you need to invoke it every +time you rebuild LAMMPS (as a shared library) or make changes to the +python/lammps.py file. + +You can invoke install.py from the python directory as + +.. parsed-literal:: + + % python install.py [libdir] [pydir] + +The optional libdir is where to copy the LAMMPS shared library to; the +default is /usr/local/lib. The optional pydir is where to copy the +lammps.py file to; the default is the site-packages directory of the +version of Python that is running the install script. + +Note that libdir must be a location that is in your default +LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a +location that Python looks in by default for imported modules, like +its site-packages dir. If you want to copy these files to +non-standard locations, such as within your own user space, you will +need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables +accordingly, as above. + +If the install.py script does not allow you to copy files into system +directories, prefix the python command with "sudo". If you do this, +make sure that the Python that root runs is the same as the Python you +run. E.g. you may need to do something like + +.. parsed-literal:: + + % sudo /usr/local/bin/python install.py [libdir] [pydir] + +You can also invoke install.py from the make command in the src +directory as + +.. parsed-literal:: + + % make install-python + +In this mode you cannot append optional arguments. Again, you may +need to prefix this with "sudo". In this mode you cannot control +which Python is invoked by root. + +Note that if you want Python to be able to load different versions of +the LAMMPS shared library (see :ref:`this section ` below), you will +need to manually copy files like liblammps_g++.so into the appropriate +system directory. This is not needed if you set the LD_LIBRARY_PATH +environment variable as described above. + + +---------- + + +.. _py_5: + +Extending Python with MPI to run in parallel +-------------------------------------------- + +If you wish to run LAMMPS in parallel from Python, you need to extend +your Python with an interface to MPI. This also allows you to +make MPI calls directly from Python in your script, if you desire. + +There are several Python packages available that purport to wrap MPI +as a library and allow MPI functions to be called from Python. + +These include + +* `pyMPI `_ +* `maroonmpi `_ +* `mpi4py `_ +* `myMPI `_ +* `Pypar `_ + +All of these except pyMPI work by wrapping the MPI library and +exposing (some portion of) its interface to your Python script. This +means Python cannot be used interactively in parallel, since they do +not address the issue of interactive input to multiple instances of +Python running on different processors. The one exception is pyMPI, +which alters the Python interpreter to address this issue, and (I +believe) creates a new alternate executable (in place of "python" +itself) as a result. + +In principle any of these Python/MPI packages should work to invoke +LAMMPS in parallel and to make MPI calls themselves from a Python +script which is itself running in parallel. However, when I +downloaded and looked at a few of them, their documentation was +incomplete and I had trouble with their installation. It's not clear +if some of the packages are still being actively developed and +supported. + +The packages Pypar and mpi4py have both been successfully tested with +LAMMPS. Pypar is simpler and easy to set up and use, but supports +only a subset of MPI. Mpi4py is more MPI-feature complete, but also a +bit more complex to use. As of version 2.0.0, mpi4py is the only +python MPI wrapper that allows passing a custom MPI communicator to +the LAMMPS constructor, which means one can easily run one or more +LAMMPS instances on subsets of the total MPI ranks. + + +---------- + + +Pypar requires the ubiquitous `Numpy package `_ +be installed in your Python. After launching Python, type + +.. parsed-literal:: + + import numpy + +to see if it is installed. If not, here is how to install it (version +1.3.0b1 as of April 2009). Unpack the numpy tarball and from its +top-level directory, type + +.. parsed-literal:: + + python setup.py build + sudo python setup.py install + +The "sudo" is only needed if required to copy Numpy files into your +Python distribution's site-packages directory. + +To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it +and from its "source" directory, type + +.. parsed-literal:: + + python setup.py build + sudo python setup.py install + +Again, the "sudo" is only needed if required to copy Pypar files into +your Python distribution's site-packages directory. + +If you have successully installed Pypar, you should be able to run +Python and type + +.. parsed-literal:: + + import pypar + +without error. You should also be able to run python in parallel +on a simple test script + +.. parsed-literal:: + + % mpirun -np 4 python test.py + +where test.py contains the lines + +.. parsed-literal:: + + import pypar + print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) + +and see one line of output for each processor you run on. + +.. note:: + + To use Pypar and LAMMPS in parallel from Python, you must insure + both are using the same version of MPI. If you only have one MPI + installed on your system, this is not an issue, but it can be if you + have multiple MPIs. Your LAMMPS build is explicit about which MPI it + is using, since you specify the details in your lo-level + src/MAKE/Makefile.foo file. Pypar uses the "mpicc" command to find + information about the MPI it uses to build against. And it tries to + load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find + the MPI library that LAMMPS is using. If you have problems running + both Pypar and LAMMPS together, this is an issue you may need to + address, e.g. by moving other MPI installations so that Pypar finds + the right one. + + +---------- + + +To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it +and from its main directory, type + +.. parsed-literal:: + + python setup.py build + sudo python setup.py install + +Again, the "sudo" is only needed if required to copy mpi4py files into +your Python distribution's site-packages directory. To install with +user privilege into the user local directory type + +.. parsed-literal:: + + python setup.py install --user + +If you have successully installed mpi4py, you should be able to run +Python and type + +.. parsed-literal:: + + from mpi4py import MPI + +without error. You should also be able to run python in parallel +on a simple test script + +.. parsed-literal:: + + % mpirun -np 4 python test.py + +where test.py contains the lines + +.. parsed-literal:: + + from mpi4py import MPI + comm = MPI.COMM_WORLD + print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) + +and see one line of output for each processor you run on. + +.. note:: + + To use mpi4py and LAMMPS in parallel from Python, you must + insure both are using the same version of MPI. If you only have one + MPI installed on your system, this is not an issue, but it can be if + you have multiple MPIs. Your LAMMPS build is explicit about which MPI + it is using, since you specify the details in your lo-level + src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find + information about the MPI it uses to build against. And it tries to + load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find + the MPI library that LAMMPS is using. If you have problems running + both mpi4py and LAMMPS together, this is an issue you may need to + address, e.g. by moving other MPI installations so that mpi4py finds + the right one. + + +---------- + + +.. _py_6: + +Testing the Python-LAMMPS interface +----------------------------------- + +To test if LAMMPS is callable from Python, launch Python interactively +and type: + +.. parsed-literal:: + + >>> from lammps import lammps + >>> lmp = lammps() + +If you get no errors, you're ready to use LAMMPS from Python. If the +2nd command fails, the most common error to see is + +.. parsed-literal:: + + OSError: Could not load LAMMPS dynamic library + +which means Python was unable to load the LAMMPS shared library. This +typically occurs if the system can't find the LAMMPS shared library or +one of the auxiliary shared libraries it depends on, or if something +about the library is incompatible with your Python. The error message +should give you an indication of what went wrong. + +You can also test the load directly in Python as follows, without +first importing from the lammps.py file: + +.. parsed-literal:: + + >>> from ctypes import CDLL + >>> CDLL("liblammps.so") + +If an error occurs, carefully go thru the steps in :ref:`Section_start 5 ` and above about building a shared +library and about insuring Python can find the necessary two files +it needs. + +**Test LAMMPS and Python in serial:** +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +To run a LAMMPS test in serial, type these lines into Python +interactively from the bench directory: + +.. parsed-literal:: + + >>> from lammps import lammps + >>> lmp = lammps() + >>> lmp.file("in.lj") + +Or put the same lines in the file test.py and run it as + +.. parsed-literal:: + + % python test.py + +Either way, you should see the results of running the in.lj benchmark +on a single processor appear on the screen, the same as if you had +typed something like: + +.. parsed-literal:: + + lmp_g++ -in in.lj + +**Test LAMMPS and Python in parallel:** +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +To run LAMMPS in parallel, assuming you have installed the +`Pypar `_ package as discussed above, create a test.py file +containing these lines: + +.. parsed-literal:: + + import pypar + from lammps import lammps + lmp = lammps() + lmp.file("in.lj") + print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp + pypar.finalize() + +To run LAMMPS in parallel, assuming you have installed the +`mpi4py `_ package as discussed above, create a test.py file +containing these lines: + +.. parsed-literal:: + + from mpi4py import MPI + from lammps import lammps + lmp = lammps() + lmp.file("in.lj") + me = MPI.COMM_WORLD.Get_rank() + nprocs = MPI.COMM_WORLD.Get_size() + print "Proc %d out of %d procs has" % (me,nprocs),lmp + MPI.Finalize() + +You can either script in parallel as: + +.. parsed-literal:: + + % mpirun -np 4 python test.py + +and you should see the same output as if you had typed + +.. parsed-literal:: + + % mpirun -np 4 lmp_g++ -in in.lj + +Note that if you leave out the 3 lines from test.py that specify Pypar +commands you will instantiate and run LAMMPS independently on each of +the P processors specified in the mpirun command. In this case you +should get 4 sets of output, each showing that a LAMMPS run was made +on a single processor, instead of one set of output showing that +LAMMPS ran on 4 processors. If the 1-processor outputs occur, it +means that Pypar is not working correctly. + +Also note that once you import the PyPar module, Pypar initializes MPI +for you, and you can use MPI calls directly in your Python script, as +described in the Pypar documentation. The last line of your Python +script should be pypar.finalize(), to insure MPI is shut down +correctly. + +**Running Python scripts:** +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Note that any Python script (not just for LAMMPS) can be invoked in +one of several ways: + +.. parsed-literal:: + + % python foo.script + % python -i foo.script + % foo.script + +The last command requires that the first line of the script be +something like this: + +.. parsed-literal:: + + #!/usr/local/bin/python + #!/usr/local/bin/python -i + +where the path points to where you have Python installed, and that you +have made the script file executable: + +.. parsed-literal:: + + % chmod +x foo.script + +Without the "-i" flag, Python will exit when the script finishes. +With the "-i" flag, you will be left in the Python interpreter when +the script finishes, so you can type subsequent commands. As +mentioned above, you can only run Python interactively when running +Python on a single processor, not in parallel. + + + + + +.. _py_7: + +Using LAMMPS from Python +------------------------ + +As described above, the Python interface to LAMMPS consists of a +Python "lammps" module, the source code for which is in +python/lammps.py, which creates a "lammps" object, with a set of +methods that can be invoked on that object. The sample Python code +below assumes you have first imported the "lammps" module in your +Python script, as follows: + +.. parsed-literal:: + + from lammps import lammps + +These are the methods defined by the lammps module. If you look at +the files src/library.cpp and src/library.h you will see that they +correspond one-to-one with calls you can make to the LAMMPS library +from a C++ or C or Fortran program. + +.. parsed-literal:: + + lmp = lammps() # create a LAMMPS object using the default liblammps.so library + 4 optional args are allowed: name, cmdargs, ptr, comm + lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object + lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later + lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library + lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = ["-echo","screen"] + +.. parsed-literal:: + + lmp.close() # destroy a LAMMPS object + +version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 + +.. parsed-literal:: + + lmp.file(file) # run an entire input script, file = "in.lj" + lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" + +.. parsed-literal:: + + xlo = lmp.extract_global(name,type) # extract a global quantity + # name = "boxxlo", "nlocal", etc + # type = 0 = int + # 1 = double + +.. parsed-literal:: + + coords = lmp.extract_atom(name,type) # extract a per-atom quantity + # name = "x", "type", etc + # type = 0 = vector of ints + # 1 = array of ints + # 2 = vector of doubles + # 3 = array of doubles + +.. parsed-literal:: + + eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute + v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix + # id = ID of compute or fix + # style = 0 = global data + # 1 = per-atom data + # 2 = local data + # type = 0 = scalar + # 1 = vector + # 2 = array + # i,j = indices of value in global vector or array + +.. parsed-literal:: + + var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable + # name = name of variable + # group = group ID (ignored for equal-style variables) + # flag = 0 = equal-style variable + # 1 = atom-style variable + +.. parsed-literal:: + + flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful + natoms = lmp.get_natoms() # total # of atoms as int + data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID + # name = "x", "charge", "type", etc + # count = # of per-atom values, 1 or 3, etc + lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID + # name = "x", "charge", "type", etc + # count = # of per-atom values, 1 or 3, etc + + +---------- + + +.. note:: + + Currently, the creation of a LAMMPS object from within lammps.py + does not take an MPI communicator as an argument. There should be a + way to do this, so that the LAMMPS instance runs on a subset of + processors if desired, but I don't know how to do it from Pypar. So + for now, it runs with MPI_COMM_WORLD, which is all the processors. If + someone figures out how to do this with one or more of the Python + wrappers for MPI, like Pypar, please let us know and we will amend + these doc pages. + +The lines + +.. parsed-literal:: + + from lammps import lammps + lmp = lammps() + +create an instance of LAMMPS, wrapped in a Python class by the lammps +Python module, and return an instance of the Python class as lmp. It +is used to make all subequent calls to the LAMMPS library. + +Additional arguments can be used to tell Python the name of the shared +library to load or to pass arguments to the LAMMPS instance, the same +as if LAMMPS were launched from a command-line prompt. + +If the ptr argument is set like this: + +.. parsed-literal:: + + lmp = lammps(ptr=lmpptr) + +then lmpptr must be an argument passed to Python via the LAMMPS +:doc:`python ` command, when it is used to define a Python +function that is invoked by the LAMMPS input script. This mode of +using Python with LAMMPS is described above in 11.2. The variable +lmpptr refers to the instance of LAMMPS that called the embedded +Python interpreter. Using it as an argument to lammps() allows the +returned Python class instance "lmp" to make calls to that instance of +LAMMPS. See the :doc:`python ` command doc page for examples +using this syntax. + +Note that you can create multiple LAMMPS objects in your Python +script, and coordinate and run multiple simulations, e.g. + +.. parsed-literal:: + + from lammps import lammps + lmp1 = lammps() + lmp2 = lammps() + lmp1.file("in.file1") + lmp2.file("in.file2") + +The file() and command() methods allow an input script or single +commands to be invoked. + +The extract_global(), extract_atom(), extract_compute(), +extract_fix(), and extract_variable() methods return values or +pointers to data structures internal to LAMMPS. + +For extract_global() see the src/library.cpp file for the list of +valid names. New names could easily be added. A double or integer is +returned. You need to specify the appropriate data type via the type +argument. + +For extract_atom(), a pointer to internal LAMMPS atom-based data is +returned, which you can use via normal Python subscripting. See the +extract() method in the src/atom.cpp file for a list of valid names. +Again, new names could easily be added. A pointer to a vector of +doubles or integers, or a pointer to an array of doubles (double **) +or integers (int **) is returned. You need to specify the appropriate +data type via the type argument. + +For extract_compute() and extract_fix(), the global, per-atom, or +local data calulated by the compute or fix can be accessed. What is +returned depends on whether the compute or fix calculates a scalar or +vector or array. For a scalar, a single double value is returned. If +the compute or fix calculates a vector or array, a pointer to the +internal LAMMPS data is returned, which you can use via normal Python +subscripting. The one exception is that for a fix that calculates a +global vector or array, a single double value from the vector or array +is returned, indexed by I (vector) or I and J (array). I,J are +zero-based indices. The I,J arguments can be left out if not needed. +See :ref:`Section_howto 15 ` of the manual for a +discussion of global, per-atom, and local data, and of scalar, vector, +and array data types. See the doc pages for individual +:doc:`computes ` and :doc:`fixes ` for a description of what +they calculate and store. + +For extract_variable(), an :doc:`equal-style or atom-style variable ` is evaluated and its result returned. + +For equal-style variables a single double value is returned and the +group argument is ignored. For atom-style variables, a vector of +doubles is returned, one value per atom, which you can use via normal +Python subscripting. The values will be zero for atoms not in the +specified group. + +The get_natoms() method returns the total number of atoms in the +simulation, as an int. + +The gather_atoms() method returns a ctypes vector of ints or doubles +as specified by type, of length count*natoms, for the property of all +the atoms in the simulation specified by name, ordered by count and +then by atom ID. The vector can be used via normal Python +subscripting. If atom IDs are not consecutively ordered within +LAMMPS, a None is returned as indication of an error. + +Note that the data structure gather_atoms("x") returns is different +from the data structure returned by extract_atom("x") in four ways. +(1) Gather_atoms() returns a vector which you index as x[i]; +extract_atom() returns an array which you index as x[i][j]. (2) +Gather_atoms() orders the atoms by atom ID while extract_atom() does +not. (3) Gathert_atoms() returns a list of all atoms in the +simulation; extract_atoms() returns just the atoms local to each +processor. (4) Finally, the gather_atoms() data structure is a copy +of the atom coords stored internally in LAMMPS, whereas extract_atom() +returns an array that effectively points directly to the internal +data. This means you can change values inside LAMMPS from Python by +assigning a new values to the extract_atom() array. To do this with +the gather_atoms() vector, you need to change values in the vector, +then invoke the scatter_atoms() method. + +The scatter_atoms() method takes a vector of ints or doubles as +specified by type, of length count*natoms, for the property of all the +atoms in the simulation specified by name, ordered by bount and then +by atom ID. It uses the vector of data to overwrite the corresponding +properties for each atom inside LAMMPS. This requires LAMMPS to have +its "map" option enabled; see the :doc:`atom_modify ` +command for details. If it is not, or if atom IDs are not +consecutively ordered, no coordinates are reset. + +The array of coordinates passed to scatter_atoms() must be a ctypes +vector of ints or doubles, allocated and initialized something like +this: + +.. parsed-literal:: + + from ctypes import * + natoms = lmp.get_natoms() + n3 = 3*natoms + x = (n3*c_double)() + x[0] = x coord of atom with ID 1 + x[1] = y coord of atom with ID 1 + x[2] = z coord of atom with ID 1 + x[3] = x coord of atom with ID 2 + ... + x[n3-1] = z coord of atom with ID natoms + lmp.scatter_coords("x",1,3,x) + +Alternatively, you can just change values in the vector returned by +gather_atoms("x",1,3), since it is a ctypes vector of doubles. + + +---------- + + +As noted above, these Python class methods correspond one-to-one with +the functions in the LAMMPS library interface in src/library.cpp and +library.h. This means you can extend the Python wrapper via the +following steps: + +* Add a new interface function to src/library.cpp and + src/library.h. +* Rebuild LAMMPS as a shared library. +* Add a wrapper method to python/lammps.py for this interface + function. +* You should now be able to invoke the new interface function from a + Python script. Isn't ctypes amazing? + + + + +.. _py_8: + +Example Python scripts that use LAMMPS +-------------------------------------- + +These are the Python scripts included as demos in the python/examples +directory of the LAMMPS distribution, to illustrate the kinds of +things that are possible when Python wraps LAMMPS. If you create your +own scripts, send them to us and we can include them in the LAMMPS +distribution. + ++----------------------------------------------------------------+--------------------------------------------------+ +| trivial.py | read/run a LAMMPS input script thru Python | ++----------------------------------------------------------------+--------------------------------------------------+ +| demo.py | invoke various LAMMPS library interface routines | ++----------------------------------------------------------------+--------------------------------------------------+ +| simple.py | run in parallel | ++----------------------------------------------------------------+--------------------------------------------------+ +| similar to examples/COUPLE/simple/simple.cpp | split.py | ++----------------------------------------------------------------+--------------------------------------------------+ +| same as simple.py but running in parallel on a subset of procs | gui.py | ++----------------------------------------------------------------+--------------------------------------------------+ +| GUI go/stop/temperature-slider to control LAMMPS | plot.py | ++----------------------------------------------------------------+--------------------------------------------------+ +| real-time temeperature plot with GnuPlot via Pizza.py | viz_tool.py | ++----------------------------------------------------------------+--------------------------------------------------+ +| real-time viz via some viz package | vizplotgui_tool.py | ++----------------------------------------------------------------+--------------------------------------------------+ +| combination of viz_tool.py and plot.py and gui.py | | ++----------------------------------------------------------------+--------------------------------------------------+ + + +---------- + + +For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" +with "gl" or "atomeye" or "pymol" or "vmd", depending on what +visualization package you have installed. + +Note that for GL, you need to be able to run the Pizza.py GL tool, +which is included in the pizza sub-directory. See the `Pizza.py doc pages `_ for more info: + +.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html + + + +Note that for AtomEye, you need version 3, and there is a line in the +scripts that specifies the path and name of the executable. See the +AtomEye WWW pages `here `_ or `here `_ for more details: + +.. parsed-literal:: + + http://mt.seas.upenn.edu/Archive/Graphics/A + http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html + +.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A + + + +.. _atomeye3: http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html + + + +The latter link is to AtomEye 3 which has the scriping +capability needed by these Python scripts. + +Note that for PyMol, you need to have built and installed the +open-source version of PyMol in your Python, so that you can import it +from a Python script. See the PyMol WWW pages `here `_ or +`here `_ for more details: + +.. parsed-literal:: + + http://www.pymol.org + http://sourceforge.net/scm/?type=svn&group_id=4546 + +.. _pymol: http://www.pymol.org + + + +.. _pymolopen: http://sourceforge.net/scm/?type=svn&group_id=4546 + + + +The latter link is to the open-source version. + +Note that for VMD, you need a fairly current version (1.8.7 works for +me) and there are some lines in the pizza/vmd.py script for 4 PIZZA +variables that have to match the VMD installation on your system. + + +---------- + + +See the python/README file for instructions on how to run them and the +source code for individual scripts for comments about what they do. + +Here are screenshots of the vizplotgui_tool.py script in action for +different visualization package options. Click to see larger images: + +.. thumbnail:: JPG/screenshot_gl.jpg + +.. thumbnail:: JPG/screenshot_atomeye.jpg + +.. thumbnail:: JPG/screenshot_pymol.jpg + +.. thumbnail:: JPG/screenshot_vmd.jpg + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_start.txt b/doc/_sources/Section_start.txt new file mode 100644 index 0000000000..0e08548e4c --- /dev/null +++ b/doc/_sources/Section_start.txt @@ -0,0 +1,2154 @@ +Getting Started +=============== + +This section describes how to build and run LAMMPS, for both new and +experienced users. + +| 2.1 :ref:`What's in the LAMMPS distribution ` +| 2.2 :ref:`Making LAMMPS ` +| 2.3 :ref:`Making LAMMPS with optional packages ` +| 2.4 :ref:`Building LAMMPS via the Make.py script ` +| 2.5 :ref:`Building LAMMPS as a library ` +| 2.6 :ref:`Running LAMMPS ` +| 2.7 :ref:`Command-line options ` +| 2.8 :ref:`Screen output ` +| 2.9 :ref:`Tips for users of previous versions ` +| + + + + + +.. _start_1: + +What's in the LAMMPS distribution +----------------------------------------------- + +When you download a LAMMPS tarball you will need to unzip and untar +the downloaded file with the following commands, after placing the +tarball in an appropriate directory. + +.. parsed-literal:: + + gunzip lammps*.tar.gz + tar xvf lammps*.tar + +This will create a LAMMPS directory containing two files and several +sub-directories: + ++------------+--------------------------------------------+ +| README | text file | ++------------+--------------------------------------------+ +| LICENSE | the GNU General Public License (GPL) | ++------------+--------------------------------------------+ +| bench | benchmark problems | ++------------+--------------------------------------------+ +| doc | documentation | ++------------+--------------------------------------------+ +| examples | simple test problems | ++------------+--------------------------------------------+ +| potentials | embedded atom method (EAM) potential files | ++------------+--------------------------------------------+ +| src | source files | ++------------+--------------------------------------------+ +| tools | pre- and post-processing tools | ++------------+--------------------------------------------+ + +Note that the `download page `_ also has links to download +Windows exectubles and installers, as well as pre-built executables +for a few specific Linux distributions. It also has instructions for +how to download/install LAMMPS for Macs (via Homebrew), and to +download and update LAMMPS from SVN and Git repositories, which gives +you the same files that are in the download tarball. + +.. _download: http://lammps.sandia.gov/download.html + + + +The Windows and Linux executables for serial or parallel only include +certain packages and bug-fixes/upgrades listed on `this page `_ up to a certain date, as +stated on the download page. If you want an executable with +non-included packages or that is more current, then you'll need to +build LAMMPS yourself, as discussed in the next section. + +Skip to the :ref:`Running LAMMPS ` sections for info on how to +launch a LAMMPS Windows executable on a Windows box. + + +---------- + + +.. _start_2: + +Making LAMMPS +--------------------------- + +This section has the following sub-sections: + +* :ref:`Read this first ` +* :ref:`Steps to build a LAMMPS executable ` +* :ref:`Common errors that can occur when making LAMMPS ` +* :ref:`Additional build tips ` +* :ref:`Building for a Mac ` +* :ref:`Building for Windows ` + + +---------- + + +.. _start_2_1: + +***Read this first:*** + +If you want to avoid building LAMMPS yourself, read the preceeding +section about options available for downloading and installing +executables. Details are discussed on the `download `_ page. + +Building LAMMPS can be simple or not-so-simple. If all you need are +the default packages installed in LAMMPS, and MPI is already installed +on your machine, or you just want to run LAMMPS in serial, then you +can typically use the Makefile.mpi or Makefile.serial files in +src/MAKE by typing one of these lines (from the src dir): + +.. parsed-literal:: + + make mpi + make serial + +Note that on a facility supercomputer, there are often "modules" +loaded in your environment that provide the compilers and MPI you +should use. In this case, the "mpicxx" compile/link command in +Makefile.mpi should just work by accessing those modules. + +It may be the case that one of the other Makefile.machine files in the +src/MAKE sub-directories is a better match to your system (type "make" +to see a list), you can use it as-is by typing (for example): + +.. parsed-literal:: + + make stampede + +If any of these builds (with an existing Makefile.machine) works on +your system, then you're done! + +If you want to do one of the following: + +* use optional LAMMPS features that require additional libraries +* use optional packages that require additional libraries +* use optional accelerator packages that require special compiler/linker settings +* run on a specialized platform that has its own compilers, settings, or other libs to use + +then building LAMMPS is more complicated. You may need to find where +auxiliary libraries exist on your machine or install them if they +don't. You may need to build additional libraries that are part of +the LAMMPS package, before building LAMMPS. You may need to edit a +Makefile.machine file to make it compatible with your system. + +Note that there is a Make.py tool in the src directory that automates +several of these steps, but you still have to know what you are doing. +:ref:`Section 2.4 ` below describes the tool. It is a convenient +way to work with installing/un-installing various packages, the +Makefile.machine changes required by some packages, and the auxiliary +libraries some of them use. + +Please read the following sections carefully. If you are not +comfortable with makefiles, or building codes on a Unix platform, or +running an MPI job on your machine, please find a local expert to help +you. Many compilation, linking, and run problems that users have are +often not really LAMMPS issues - they are peculiar to the user's +system, compilers, libraries, etc. Such questions are better answered +by a local expert. + +If you have a build problem that you are convinced is a LAMMPS issue +(e.g. the compiler complains about a line of LAMMPS source code), then +please post the issue to the `LAMMPS mail list `_. + +If you succeed in building LAMMPS on a new kind of machine, for which +there isn't a similar machine Makefile included in the +src/MAKE/MACHINES directory, then send it to the developers and we can +include it in the LAMMPS distribution. + + +---------- + + +.. _start_2_2: + +***Steps to build a LAMMPS executable:*** + +**Step 0** + +The src directory contains the C++ source and header files for LAMMPS. +It also contains a top-level Makefile and a MAKE sub-directory with +low-level Makefile.* files for many systems and machines. See the +src/MAKE/README file for a quick overview of what files are available +and what sub-directories they are in. + +The src/MAKE dir has a few files that should work as-is on many +platforms. The src/MAKE/OPTIONS dir has more that invoke additional +compiler, MPI, and other setting options commonly used by LAMMPS, to +illustrate their syntax. The src/MAKE/MACHINES dir has many more that +have been tweaked or optimized for specific machines. These files are +all good starting points if you find you need to change them for your +machine. Put any file you edit into the src/MAKE/MINE directory and +it will be never be touched by any LAMMPS updates. + +>From within the src directory, type "make" or "gmake". You should see +a list of available choices from src/MAKE and all of its +sub-directories. If one of those has the options you want or is the +machine you want, you can type a command like: + +.. parsed-literal:: + + make mpi + or + make serial_icc + or + gmake mac + +Note that the corresponding Makefile.machine can exist in src/MAKE or +any of its sub-directories. If a file with the same name appears in +multiple places (not a good idea), the order they are used is as +follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. +This gives preference to a file you have created/edited and put in +src/MAKE/MINE. + +Note that on a multi-processor or multi-core platform you can launch a +parallel make, by using the "-j" switch with the make command, which +will build LAMMPS more quickly. + +If you get no errors and an executable like lmp_mpi or lmp_g++_serial +or lmp_mac is produced, then you're done; it's your lucky day. + +Note that by default only a few of LAMMPS optional packages are +installed. To build LAMMPS with optional packages, see :ref:`this section ` below. + +**Step 1** + +If Step 0 did not work, you will need to create a low-level Makefile +for your machine, like Makefile.foo. You should make a copy of an +existing Makefile.* in src/MAKE or one of its sub-directories as a +starting point. The only portions of the file you need to edit are +the first line, the "compiler/linker settings" section, and the +"LAMMPS-specific settings" section. When it works, put the edited +file in src/MAKE/MINE and it will not be altered by any future LAMMPS +updates. + +**Step 2** + +Change the first line of Makefile.foo to list the word "foo" after the +"#", and whatever other options it will set. This is the line you +will see if you just type "make". + +**Step 3** + +The "compiler/linker settings" section lists compiler and linker +settings for your C++ compiler, including optimization flags. You can +use g++, the open-source GNU compiler, which is available on all Unix +systems. You can also use mpicxx which will typically be available if +MPI is installed on your system, though you should check which actual +compiler it wraps. Vendor compilers often produce faster code. On +boxes with Intel CPUs, we suggest using the Intel icc compiler, which +can be downloaded from `Intel's compiler site `_. + +.. _intel: http://www.intel.com/software/products/noncom + + + +If building a C++ code on your machine requires additional libraries, +then you should list them as part of the LIB variable. You should +not need to do this if you use mpicxx. + +The DEPFLAGS setting is what triggers the C++ compiler to create a +dependency list for a source file. This speeds re-compilation when +source (*.cpp) or header (*.h) files are edited. Some compilers do +not support dependency file creation, or may use a different switch +than -D. GNU g++ and Intel icc works with -D. If your compiler can't +create dependency files, then you'll need to create a Makefile.foo +patterned after Makefile.storm, which uses different rules that do not +involve dependency files. Note that when you build LAMMPS for the +first time on a new platform, a long list of *.d files will be printed +out rapidly. This is not an error; it is the Makefile doing its +normal creation of dependencies. + +**Step 4** + +The "system-specific settings" section has several parts. Note that +if you change any -D setting in this section, you should do a full +re-compile, after typing "make clean" (which will describe different +clean options). + +The LMP_INC variable is used to include options that turn on ifdefs +within the LAMMPS code. The options that are currently recogized are: + +* -DLAMMPS_GZIP +* -DLAMMPS_JPEG +* -DLAMMPS_PNG +* -DLAMMPS_FFMPEG +* -DLAMMPS_MEMALIGN +* -DLAMMPS_XDR +* -DLAMMPS_SMALLBIG +* -DLAMMPS_BIGBIG +* -DLAMMPS_SMALLSMALL +* -DLAMMPS_LONGLONG_TO_LONG +* -DPACK_ARRAY +* -DPACK_POINTER +* -DPACK_MEMCPY + +The read_data and dump commands will read/write gzipped files if you +compile with -DLAMMPS_GZIP. It requires that your machine supports +the "popen()" function in the standard runtime library and that a gzip +executable can be found by LAMMPS during a run. + +.. note:: + + on some clusters with high-speed networks, using the fork() + library calls (required by popen()) can interfere with the fast + communication library and lead to simulations using compressed output + or input to hang or crash. For selected operations, compressed file + I/O is also available using a compression library instead, which are + provided in the COMPRESS package. From more details about compiling + LAMMPS with packages, please see below. + +If you use -DLAMMPS_JPEG, the :doc:`dump image ` command +will be able to write out JPEG image files. For JPEG files, you must +also link LAMMPS with a JPEG library, as described below. If you use +-DLAMMPS_PNG, the :doc:`dump image ` command will be able to write +out PNG image files. For PNG files, you must also link LAMMPS with a +PNG library, as described below. If neither of those two defines are +used, LAMMPS will only be able to write out uncompressed PPM image +files. + +If you use -DLAMMPS_FFMPEG, the :doc:`dump movie ` command +will be available to support on-the-fly generation of rendered movies +the need to store intermediate image files. It requires that your +machines supports the "popen" function in the standard runtime library +and that an FFmpeg executable can be found by LAMMPS during the run. + +.. note:: + + Similar to the note above, this option can conflict with + high-speed networks, because it uses popen(). + +Using -DLAMMPS_MEMALIGN= enables the use of the +posix_memalign() call instead of malloc() when large chunks or memory +are allocated by LAMMPS. This can help to make more efficient use of +vector instructions of modern CPUS, since dynamically allocated memory +has to be aligned on larger than default byte boundaries (e.g. 16 +bytes instead of 8 bytes on x86 type platforms) for optimal +performance. + +If you use -DLAMMPS_XDR, the build will include XDR compatibility +files for doing particle dumps in XTC format. This is only necessary +if your platform does have its own XDR files available. See the +Restrictions section of the :doc:`dump ` command for details. + +Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG, +-DLAMMPS_SMALLSMALL settings. The default is -DLAMMPS_SMALLBIG. These +settings refer to use of 4-byte (small) vs 8-byte (big) integers +within LAMMPS, as specified in src/lmptype.h. The only reason to use +the BIGBIG setting is to enable simulation of huge molecular systems +(which store bond topology info) with more than 2 billion atoms, or to +track the image flags of moving atoms that wrap around a periodic box +more than 512 times. Normally, the only reason to use SMALLSMALL is +if your machine does not support 64-bit integers, though you can use +SMALLSMALL setting if you are running in serial or on a desktop +machine or small cluster where you will never run large systems or for +long time (more than 2 billion atoms, more than 2 billion timesteps). +See the :ref:`Additional build tips ` section below for more +details on these settings. + +Note that two packages, USER-ATC and USER-CUDA are not currently +compatible with -DLAMMPS_BIGBIG. Also the GPU package requires the +lib/gpu library to be compiled with the same setting, or the link will +fail. + +The -DLAMMPS_LONGLONG_TO_LONG setting may be needed if your system or +MPI version does not recognize "long long" data types. In this case a +"long" data type is likely already 64-bits, in which case this setting +will convert to that data type. + +Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY +options can make for faster parallel FFTs (in the PPPM solver) on some +platforms. The -DPACK_ARRAY setting is the default. See the +:doc:`kspace_style ` command for info about PPPM. See +Step 6 below for info about building LAMMPS with an FFT library. + +**Step 5** + +The 3 MPI variables are used to specify an MPI library to build LAMMPS +with. Note that you do not need to set these if you use the MPI +compiler mpicxx for your CC and LINK setting in the section above. +The MPI wrapper knows where to find the needed files. + +If you want LAMMPS to run in parallel, you must have an MPI library +installed on your platform. If MPI is installed on your system in the +usual place (under /usr/local), you also may not need to specify these +3 variables, assuming /usr/local is in your path. On some large +parallel machines which use "modules" for their compile/link +environements, you may simply need to include the correct module in +your build environment, before building LAMMPS. Or the parallel +machine may have a vendor-provided MPI which the compiler has no +trouble finding. + +Failing this, these 3 variables can be used to specify where the mpi.h +file (MPI_INC) and the MPI library file (MPI_PATH) are found and the +name of the library file (MPI_LIB). + +If you are installing MPI yourself, we recommend Argonne's MPICH2 +or OpenMPI. MPICH can be downloaded from the `Argonne MPI site `_. OpenMPI can +be downloaded from the `OpenMPI site `_. +Other MPI packages should also work. If you are running on a big +parallel platform, your system people or the vendor should have +already installed a version of MPI, which is likely to be faster +than a self-installed MPICH or OpenMPI, so find out how to build +and link with it. If you use MPICH or OpenMPI, you will have to +configure and build it for your platform. The MPI configure script +should have compiler options to enable you to use the same compiler +you are using for the LAMMPS build, which can avoid problems that can +arise when linking LAMMPS to the MPI library. + +If you just want to run LAMMPS on a single processor, you can use the +dummy MPI library provided in src/STUBS, since you don't need a true +MPI library installed on your system. See src/MAKE/Makefile.serial +for how to specify the 3 MPI variables in this case. You will also +need to build the STUBS library for your platform before making LAMMPS +itself. Note that if you are building with src/MAKE/Makefile.serial, +e.g. by typing "make serial", then the STUBS library is built for you. + +To build the STUBS library from the src directory, type "make +mpi-stubs", or from the src/STUBS dir, type "make". This should +create a libmpi_stubs.a file suitable for linking to LAMMPS. If the +build fails, you will need to edit the STUBS/Makefile for your +platform. + +The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime() +that calls gettimeofday() . If your system doesn't support +gettimeofday() , you'll need to insert code to call another timer. +Note that the ANSI-standard function clock() rolls over after an hour +or so, and is therefore insufficient for timing long LAMMPS +simulations. + +**Step 6** + +The 3 FFT variables allow you to specify an FFT library which LAMMPS +uses (for performing 1d FFTs) when running the particle-particle +particle-mesh (PPPM) option for long-range Coulombics via the +:doc:`kspace_style ` command. + +LAMMPS supports various open-source or vendor-supplied FFT libraries +for this purpose. If you leave these 3 variables blank, LAMMPS will +use the open-source `KISS FFT library `_, which is +included in the LAMMPS distribution. This library is portable to all +platforms and for typical LAMMPS simulations is almost as fast as FFTW +or vendor optimized libraries. If you are not including the KSPACE +package in your build, you can also leave the 3 variables blank. + +Otherwise, select which kinds of FFTs to use as part of the FFT_INC +setting by a switch of the form -DFFT_XXX. Recommended values for XXX +are: MKL, SCSL, FFTW2, and FFTW3. Legacy options are: INTEL, SGI, +ACML, and T3E. For backward compatability, using -DFFT_FFTW will use +the FFTW2 library. Using -DFFT_NONE will use the KISS library +described above. + +You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, +so the compiler and linker can find the needed FFT header and library +files. Note that on some large parallel machines which use "modules" +for their compile/link environements, you may simply need to include +the correct module in your build environment. Or the parallel machine +may have a vendor-provided FFT library which the compiler has no +trouble finding. + +FFTW is a fast, portable library that should also work on any +platform. You can download it from +`www.fftw.org `_. Both the legacy version 2.1.X and +the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3. +Building FFTW for your box should be as simple as ./configure; make. +Note that on some platforms FFTW2 has been pre-installed, and uses +renamed files indicating the precision it was compiled with, +e.g. sfftw.h, or dfftw.h instead of fftw.h. In this case, you can +specify an additional define variable for FFT_INC called -DFFTW_SIZE, +which will select the correct include file. In this case, for FFT_LIB +you must also manually specify the correct library, namely -lsfftw or +-ldfftw. + +The FFT_INC variable also allows for a -DFFT_SINGLE setting that will +use single-precision FFTs with PPPM, which can speed-up long-range +calulations, particularly in parallel or on GPUs. Fourier transform +and related PPPM operations are somewhat insensitive to floating point +truncation errors and thus do not always need to be performed in +double precision. Using the -DFFT_SINGLE setting trades off a little +accuracy for reduced memory use and parallel communication costs for +transposing 3d FFT data. Note that single precision FFTs have only +been tested with the FFTW3, FFTW2, MKL, and KISS FFT options. + +**Step 7** + +The 3 JPG variables allow you to specify a JPEG and/or PNG library +which LAMMPS uses when writing out JPEG or PNG files via the :doc:`dump image ` command. These can be left blank if you do not +use the -DLAMMPS_JPEG or -DLAMMPS_PNG switches discussed above in Step +4, since in that case JPEG/PNG output will be disabled. + +A standard JPEG library usually goes by the name libjpeg.a or +libjpeg.so and has an associated header file jpeglib.h. Whichever +JPEG library you have on your platform, you'll need to set the +appropriate JPG_INC, JPG_PATH, and JPG_LIB variables, so that the +compiler and linker can find it. + +A standard PNG library usually goes by the name libpng.a or libpng.so +and has an associated header file png.h. Whichever PNG library you +have on your platform, you'll need to set the appropriate JPG_INC, +JPG_PATH, and JPG_LIB variables, so that the compiler and linker can +find it. + +As before, if these header and library files are in the usual place on +your machine, you may not need to set these variables. + +**Step 8** + +Note that by default only a few of LAMMPS optional packages are +installed. To build LAMMPS with optional packages, see :ref:`this section ` below, before proceeding to Step 9. + +**Step 9** + +That's it. Once you have a correct Makefile.foo, and you have +pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need +to do from the src directory is type something like this: + +.. parsed-literal:: + + make foo + or + gmake foo + +You should get the executable lmp_foo when the build is complete. + + +---------- + + +.. _start_2_3: + +***Errors that can occur when making LAMMPS:*** + +.. note:: + + If an error occurs when building LAMMPS, the compiler or linker + will state very explicitly what the problem is. The error message + should give you a hint as to which of the steps above has failed, and + what you need to do in order to fix it. Building a code with a + Makefile is a very logical process. The compiler and linker need to + find the appropriate files and those files need to be compatible with + LAMMPS source files. When a make fails, there is usually a very + simple reason, which you or a local expert will need to fix. + +Here are two non-obvious errors that can occur: + +(1) If the make command breaks immediately with errors that indicate +it can't find files with a "*" in their names, this can be because +your machine's native make doesn't support wildcard expansion in a +makefile. Try gmake instead of make. If that doesn't work, try using +a -f switch with your make command to use a pre-generated +Makefile.list which explicitly lists all the needed files, e.g. + +.. parsed-literal:: + + make makelist + make -f Makefile.list linux + gmake -f Makefile.list mac + +The first "make" command will create a current Makefile.list with all +the file names in your src dir. The 2nd "make" command (make or +gmake) will use it to build LAMMPS. Note that you should +include/exclude any desired optional packages before using the "make +makelist" command. + +(2) If you get an error that says something like 'identifier "atoll" +is undefined', then your machine does not support "long long" +integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described +above in Step 4. + + +---------- + + +.. _start_2_4: + +***Additional build tips:*** + +(1) Building LAMMPS for multiple platforms. + +You can make LAMMPS for multiple platforms from the same src +directory. Each target creates its own object sub-directory called +Obj_target where it stores the system-specific *.o files. + +(2) Cleaning up. + +Typing "make clean-all" or "make clean-machine" will delete *.o object +files created when LAMMPS is built, for either all builds or for a +particular machine. + +(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or +-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL + +As explained above, any of these 3 settings can be specified on the +LMP_INC line in your low-level src/MAKE/Makefile.foo. + +The default is -DLAMMPS_SMALLBIG which allows for systems with up to +2^63 atoms and 2^63 timesteps (about 9e18). The atom limit is for +atomic systems which do not store bond topology info and thus do not +require atom IDs. If you use atom IDs for atomic systems (which is +the default) or if you use a molecular model, which stores bond +topology info and thus requires atom IDs, the limit is 2^31 atoms +(about 2 billion). This is because the IDs are stored in 32-bit +integers. + +Likewise, with this setting, the 3 image flags for each atom (see the +:doc:`dump ` doc page for a discussion) are stored in a 32-bit +integer, which means the atoms can only wrap around a periodic box (in +each dimension) at most 512 times. If atoms move through the periodic +box more than this many times, the image flags will "roll over", +e.g. from 511 to -512, which can cause diagnostics like the +mean-squared displacement, as calculated by the :doc:`compute msd ` command, to be faulty. + +To allow for larger atomic systems with atom IDs or larger molecular +systems or larger image flags, compile with -DLAMMPS_BIGBIG. This +stores atom IDs and image flags in 64-bit integers. This enables +atomic or molecular systems with atom IDS of up to 2^63 atoms (about +9e18). And image flags will not "roll over" until they reach 2^20 = +1048576. + +If your system does not support 8-byte integers, you will need to +compile with the -DLAMMPS_SMALLSMALL setting. This will restrict the +total number of atoms (for atomic or molecular systems) and timesteps +to 2^31 (about 2 billion). Image flags will roll over at 2^9 = 512. + +Note that in src/lmptype.h there are definitions of all these data +types as well as the MPI data types associated with them. The MPI +types need to be consistent with the associated C data types, or else +LAMMPS will generate a run-time error. As far as we know, the +settings defined in src/lmptype.h are portable and work on every +current system. + +In all cases, the size of problem that can be run on a per-processor +basis is limited by 4-byte integer storage to 2^31 atoms per processor +(about 2 billion). This should not normally be a limitation since such +a problem would have a huge per-processor memory footprint due to +neighbor lists and would run very slowly in terms of CPU secs/timestep. + + +---------- + + +.. _start_2_5: + +***Building for a Mac:*** + +OS X is BSD Unix, so it should just work. See the +src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files. + + +---------- + + +.. _start_2_6: + +***Building for Windows:*** + +The LAMMPS download page has an option to download both a serial and +parallel pre-built Windows executable. See the :ref:`Running LAMMPS ` section for instructions on running these executables +on a Windows box. + +The pre-built executables hosted on the `LAMMPS download page `_ are built with a subset +of the available packages; see the download page for the list. These +are single executable files. No examples or documentation in +included. You will need to download the full source code package to +obtain those. + +As an alternative, you can download "daily builds" (and some older +versions) of the installer packages from +`rpm.lammps.org/windows.html `_. +These executables are built with most optional packages and the +download includes documentation, some tools and most examples. + +If you want a Windows version with specific packages included and +excluded, you can build it yourself. + +One way to do this is install and use cygwin to build LAMMPS with a +standard unix style make program, just as you would on a Linux box; +see src/MAKE/MACHINES/Makefile.cygwin. + + +---------- + + +.. _start_3: + +Making LAMMPS with optional packages +-------------------------------------------------- + +This section has the following sub-sections: + +* :ref:`Package basics ` +* :ref:`Including/excluding packages ` +* :ref:`Packages that require extra libraries ` +* :ref:`Packages that require Makefile.machine settings ` + +Note that the following :ref:`Section 2.4 ` describes the Make.py +tool which can be used to install/un-install packages and build the +auxiliary libraries which some of them use. It can also auto-edit a +Makefile.machine to add settings needed by some packages. + + +---------- + + +.. _start_3_1: + +***Package basics:*** + +The source code for LAMMPS is structured as a set of core files which +are always included, plus optional packages. Packages are groups of +files that enable a specific set of features. For example, force +fields for molecular systems or granular systems are in packages. + +You can see the list of all packages by typing "make package" from +within the src directory of the LAMMPS distribution. This also lists +various make commands that can be used to manipulate packages. + +If you use a command in a LAMMPS input script that is specific to a +particular package, you must have built LAMMPS with that package, else +you will get an error that the style is invalid or the command is +unknown. Every command's doc page specfies if it is part of a +package. You can also type + +.. parsed-literal:: + + lmp_machine -h + +to run your executable with the optional :ref:`-h command-line switch ` for "help", which will simply list the styles and +commands known to your executable, and immediately exit. + +There are two kinds of packages in LAMMPS, standard and user packages. +More information about the contents of standard and user packages is +given in :doc:`Section_packages ` of the manual. The +difference between standard and user packages is as follows: + +Standard packages, such as molecule or kspace, are supported by the +LAMMPS developers and are written in a syntax and style consistent +with the rest of LAMMPS. This means we will answer questions about +them, debug and fix them if necessary, and keep them compatible with +future changes to LAMMPS. + +User packages, such as user-atc or user-omp, have been contributed by +users, and always begin with the user prefix. If they are a single +command (single file), they are typically in the user-misc package. +Otherwise, they are a a set of files grouped together which add a +specific functionality to the code. + +User packages don't necessarily meet the requirements of the standard +packages. If you have problems using a feature provided in a user +package, you may need to contact the contributor directly to get help. +Information on how to submit additions you make to LAMMPS as single +files or either a standard or user-contributed package are given in +:ref:`this section ` of the documentation. + +Some packages (both standard and user) require additional auxiliary +libraries when building LAMMPS. See more details below. + + +---------- + + +.. _start_3_2: + +***Including/excluding packages:*** + +To use (or not use) a package you must include it (or exclude it) +before building LAMMPS. From the src directory, this is typically as +simple as: + +.. parsed-literal:: + + make yes-colloid + make g++ + +or + +.. parsed-literal:: + + make no-manybody + make g++ + +.. note:: + + You should NOT include/exclude packages and build LAMMPS in a + single make command using multiple targets, e.g. make yes-colloid g++. + This is because the make procedure creates a list of source files that + will be out-of-date for the build if the package configuration changes + within the same command. + +Some packages have individual files that depend on other packages +being included. LAMMPS checks for this and does the right thing. +I.e. individual files are only included if their dependencies are +already included. Likewise, if a package is excluded, other files +dependent on that package are also excluded. + +If you will never run simulations that use the features in a +particular packages, there is no reason to include it in your build. +For some packages, this will keep you from having to build auxiliary +libraries (see below), and will also produce a smaller executable +which may run a bit faster. + +When you download a LAMMPS tarball, these packages are pre-installed +in the src directory: KSPACE, MANYBODY,MOLECULE. When you download +LAMMPS source files from the SVN or Git repositories, no packages are +pre-installed. + +Packages are included or excluded by typing "make yes-name" or "make +no-name", where "name" is the name of the package in lower-case, e.g. +name = kspace for the KSPACE package or name = user-atc for the +USER-ATC package. You can also type "make yes-standard", "make +no-standard", "make yes-std", "make no-std", "make yes-user", "make +no-user", "make yes-all" or "make no-all" to include/exclude various +sets of packages. Type "make package" to see the all of the +package-related make options. + +.. note:: + + Inclusion/exclusion of a package works by simply moving files + back and forth between the main src directory and sub-directories with + the package name (e.g. src/KSPACE, src/USER-ATC), so that the files + are seen or not seen when LAMMPS is built. After you have included or + excluded a package, you must re-build LAMMPS. + +Additional package-related make options exist to help manage LAMMPS +files that exist in both the src directory and in package +sub-directories. You do not normally need to use these commands +unless you are editing LAMMPS files or have downloaded a patch from +the LAMMPS WWW site. + +Typing "make package-update" or "make pu" will overwrite src files +with files from the package sub-directories if the package has been +included. It should be used after a patch is installed, since patches +only update the files in the package sub-directory, but not the src +files. Typing "make package-overwrite" will overwrite files in the +package sub-directories with src files. + +Typing "make package-status" or "make ps" will show which packages are +currently included. Of those that are included, it will list files +that are different in the src directory and package sub-directory. +Typing "make package-diff" lists all differences between these files. +Again, type "make package" to see all of the package-related make +options. + + +---------- + + +.. _start_3_3: + +***Packages that require extra libraries:*** + +A few of the standard and user packages require additional auxiliary +libraries. Many of them are provided with LAMMPS, in which case they +must be compiled first, before LAMMPS is built, if you wish to include +that package. If you get a LAMMPS build error about a missing +library, this is likely the reason. See the +:doc:`Section_packages ` doc page for a list of +packages that have these kinds of auxiliary libraries. + +The lib directory in the distribution has sub-directories with package +names that correspond to the needed auxiliary libs, e.g. lib/gpu. +Each sub-directory has a README file that gives more details. Code +for most of the auxiliary libraries is included in that directory. +Examples are the USER-ATC and MEAM packages. + +A few of the lib sub-directories do not include code, but do include +instructions (and sometimes scripts) that automate the process of +downloading the auxiliary library and installing it so LAMMPS can link +to it. Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD +packages. + +The lib/python directory (for the PYTHON package) contains only a +choice of Makefile.lammps.* files. This is because no auxiliary code +or libraries are needed, only the Python library and other system libs +that should already available on your system. However, the +Makefile.lammps file is needed to tell LAMMPS which libs to use and +where to find them. + +For libraries with provided code, the sub-directory README file +(e.g. lib/atc/README) has instructions on how to build that library. +Typically this is done by typing something like: + +.. parsed-literal:: + + make -f Makefile.g++ + +If one of the provided Makefiles is not appropriate for your system +you will need to edit or add one. Note that all the Makefiles have a +setting for EXTRAMAKE at the top that specifies a Makefile.lammps.* +file. + +If the library build is successful, it will produce 2 files in the lib +directory: + +.. parsed-literal:: + + libpackage.a + Makefile.lammps + +The Makefile.lammps file will be a copy of the EXTRAMAKE file setting +specified in the library Makefile.* you used. + +Note that you must insure that the settings in Makefile.lammps are +appropriate for your system. If they are not, the LAMMPS build will +fail. + +As explained in the lib/package/README files, the settings in +Makefile.lammps are used to specify additional system libraries and +their locations so that LAMMPS can build with the auxiliary library. +For example, if the MEAM package is used, the auxiliary library +consists of F90 code, built with a Fortran complier. To link that +library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is +built with, typically requires additional Fortran-to-C libraries be +included in the link. Another example are the BLAS and LAPACK +libraries needed to use the USER-ATC or USER-AWPMD packages. + +For libraries without provided code, the sub-directory README file has +information on where to download the library and how to build it, +e.g. lib/voronoi/README and lib/smd/README. The README files also +describe how you must either (a) create soft links, via the "ln" +command, in those directories to point to where you built or installed +the packages, or (b) check or edit the Makefile.lammps file in the +same directory to provide that information. + +Some of the sub-directories, e.g. lib/voronoi, also have an install.py +script which can be used to automate the process of +downloading/building/installing the auxiliary library, and setting the +needed soft links. Type "python install.py" for further instructions. + +As with the sub-directories containing library code, if the soft links +or settings in the lib/package/Makefile.lammps files are not correct, +the LAMMPS build will typically fail. + + +---------- + + +.. _start_3_4: + +***Packages that require Makefile.machine settings*** + +A few packages require specific settings in Makefile.machine, to +either build or use the package effectively. These are the +USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what +flags to add or what variables to define are given on the doc pages +that describe each of these accelerator packages in detail: + +* :doc:`USER-INTEL package ` +* :doc:`KOKKOS package ` +* :doc:`USER-OMP package ` +* :doc:`OPT package ` + +Here is a brief summary of what Makefile.machine changes are needed. +Note that the Make.py tool, described in the next :ref:`Section 2.4 ` can automatically add the needed info to an existing +machine Makefile, using simple command-line arguments. + +In src/MAKE/OPTIONS see the following Makefiles for examples of the +changes described below: + +* Makefile.intel_cpu +* Makefile.intel_phi +* Makefile.kokkos_omp +* Makefile.kokkos_cuda +* Makefile.kokkos_phi +* Makefile.omp + +For the USER-INTEL package, you have 2 choices when building. You can +build with CPU or Phi support. The latter uses Xeon Phi chips in +"offload" mode. Each of these modes requires additional settings in +your Makefile.machine for CCFLAGS and LINKFLAGS. + +For CPU mode (if using an Intel compiler): + +* CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits +* LINKFLAGS: add -fopenmp + +For Phi mode add the following in addition to the CPU mode flags: + +* CCFLAGS: add -DLMP_INTEL_OFFLOAD and +* LINKFLAGS: add -offload + +And also add this to CCFLAGS: + +.. parsed-literal:: + + -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" + +For the KOKKOS package, you have 3 choices when building. You can +build with OMP or Cuda or Phi support. Phi support uses Xeon Phi +chips in "native" mode. This can be done by setting the following +variables in your Makefile.machine: + +* for OMP support, set OMP = yes +* for Cuda support, set OMP = yes and CUDA = yes +* for Phi support, set OMP = yes and MIC = yes + +These can also be set as additional arguments to the make command, e.g. + +.. parsed-literal:: + + make g++ OMP=yes MIC=yes + +Building the KOKKOS package with CUDA support requires a Makefile +machine that uses the NVIDIA "nvcc" compiler, as well as an +appropriate "arch" setting appropriate to the GPU hardware and NVIDIA +software you have on your machine. See +src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine +Makefile. + +For the USER-OMP package, your Makefile.machine needs additional +settings for CCFLAGS and LINKFLAGS. + +* CCFLAGS: add -fopenmp and -restrict +* LINKFLAGS: add -fopenmp + +For the OPT package, your Makefile.machine needs an additional +settings for CCFLAGS. + +* CCFLAGS: add -restrict + + +---------- + + +.. _start_4: + +Building LAMMPS via the Make.py tool +-------------------------------------------------- + +The src directory includes a Make.py script, written in Python, which +can be used to automate various steps of the build process. It is +particularly useful for working with the accelerator packages, as well +as other packages which require auxiliary libraries to be built. + +The goal of the Make.py tool is to allow any complex multi-step LAMMPS +build to be performed as a single Make.py command. And you can +archive the commands, so they can be re-invoked later via the -r +(redo) switch. If you find some LAMMPS build procedure that can't be +done in a single Make.py command, let the developers know, and we'll +see if we can augment the tool. + +You can run Make.py from the src directory by typing either: + +.. parsed-literal:: + + Make.py -h + python Make.py -h + +which will give you help info about the tool. For the former to work, +you may need to edit the first line of Make.py to point to your local +Python. And you may need to insure the script is executable: + +.. parsed-literal:: + + chmod +x Make.py + +Here are examples of build tasks you can perform with Make.py: + ++--------------------------------------------------------------------------------+---------------------------------------------------------+ +| Install/uninstall packages | Make.py -p no-lib kokkos omp intel | ++--------------------------------------------------------------------------------+---------------------------------------------------------+ +| Build specific auxiliary libs | Make.py -a lib-atc lib-meam | ++--------------------------------------------------------------------------------+---------------------------------------------------------+ +| Build libs for all installed packages | Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all | ++--------------------------------------------------------------------------------+---------------------------------------------------------+ +| Create a Makefile from scratch with compiler and MPI settings | Make.py -m none -cc g++ -mpi mpich -a file | ++--------------------------------------------------------------------------------+---------------------------------------------------------+ +| Augment Makefile.serial with settings for installed packages | Make.py -p intel -intel cpu -m serial -a file | ++--------------------------------------------------------------------------------+---------------------------------------------------------+ +| Add JPG and FFTW support to Makefile.mpi | Make.py -m mpi -jpg -fft fftw -a file | ++--------------------------------------------------------------------------------+---------------------------------------------------------+ +| Build LAMMPS with a parallel make using Makefile.mpi | Make.py -j 16 -m mpi -a exe | ++--------------------------------------------------------------------------------+---------------------------------------------------------+ +| Build LAMMPS and libs it needs using Makefile.serial with accelerator settings | Make.py -p gpu intel -intel cpu -a lib-all file serial | ++--------------------------------------------------------------------------------+---------------------------------------------------------+ + +The bench and examples directories give Make.py commands that can be +used to build LAMMPS with the various packages and options needed to +run all the benchmark and example input scripts. See these files for +more details: + +* bench/README +* bench/FERMI/README +* bench/KEPLER/README +* bench/PHI/README +* examples/README +* examples/accelerate/README +* examples/accelerate/make.list + +All of the Make.py options and syntax help can be accessed by using +the "-h" switch. + +E.g. typing "Make.py -h" gives + +.. parsed-literal:: + + Syntax: Make.py switch args ... + switches can be listed in any order + help switch: + -h prints help and syntax for all other specified switches + switch for actions: + -a lib-all, lib-dir, clean, file, exe or machine + list one or more actions, in any order + machine is a Makefile.machine suffix, must be last if used + one-letter switches: + -d (dir), -j (jmake), -m (makefile), -o (output), + -p (packages), -r (redo), -s (settings), -v (verbose) + switches for libs: + -atc, -awpmd, -colvars, -cuda + -gpu, -meam, -poems, -qmmm, -reax + switches for build and makefile options: + -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png + +Using the "-h" switch with other switches and actions gives additional +info on all the other specified switches or actions. The "-h" can be +anywhere in the command-line and the other switches do not need their +arguments. E.g. type "Make.py -h -d -atc -intel" will print: + +.. parsed-literal:: + + -d dir + dir = LAMMPS home dir + if -d not specified, working dir must be lammps/src + +.. parsed-literal:: + + -atc make=suffix lammps=suffix2 + all args are optional and can be in any order + make = use Makefile.suffix (def = g++) + lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile) + +.. parsed-literal:: + + -intel mode + mode = cpu or phi (def = cpu) + build Intel package for CPU or Xeon Phi + +Note that Make.py never overwrites an existing Makefile.machine. +Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or +rename if desired. Likewise it creates an executable named +src/lmp_auto, which you can rename using the -o switch if desired. + +The most recently executed Make.py commmand is saved in +src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke +the last command, or you can save a sequence of one or more Make.py +commands to a file and invoke the file of commands using "-r". You +can also label the commands in the file and invoke one or more of them +by name. + +A typical use of Make.py is to start with a valid Makefile.machine for +your system, that works for a vanilla LAMMPS build, i.e. when optional +packages are not installed. You can then use Make.py to add various +settings (FFT, JPG, PNG) to the Makefile.machine as well as change its +compiler and MPI options. You can also add additional packages to the +build, as well as build the needed supporting libraries. + +You can also use Make.py to create a new Makefile.machine from +scratch, using the "-m none" switch, if you also specify what compiler +and MPI options to use, via the "-cc" and "-mpi" switches. + + +---------- + + +.. _start_5: + +Building LAMMPS as a library +------------------------------------------ + +LAMMPS can be built as either a static or shared library, which can +then be called from another application or a scripting language. See +:ref:`this section ` for more info on coupling +LAMMPS to other codes. See :doc:`this section ` for +more info on wrapping and running LAMMPS from Python. + +**Static library:** +^^^^^^^^^^^^^^^^^^^ + +To build LAMMPS as a static library (*.a file on Linux), type + +.. parsed-literal:: + + make foo mode=lib + +where foo is the machine name. This kind of library is typically used +to statically link a driver application to LAMMPS, so that you can +insure all dependencies are satisfied at compile time. This will use +the ARCHIVE and ARFLAGS settings in src/MAKE/Makefile.foo. The build +will create the file liblammps_foo.a which another application can +link to. It will also create a soft link liblammps.a, which will +point to the most recently built static library. + +**Shared library:** +^^^^^^^^^^^^^^^^^^^ + +To build LAMMPS as a shared library (*.so file on Linux), which can be +dynamically loaded, e.g. from Python, type + +.. parsed-literal:: + + make foo mode=shlib + +where foo is the machine name. This kind of library is required when +wrapping LAMMPS with Python; see :doc:`Section_python ` +for details. This will use the SHFLAGS and SHLIBFLAGS settings in +src/MAKE/Makefile.foo and perform the build in the directory +Obj_shared_foo. This is so that each file can be compiled with the +-fPIC flag which is required for inclusion in a shared library. The +build will create the file liblammps_foo.so which another application +can link to dyamically. It will also create a soft link liblammps.so, +which will point to the most recently built shared library. This is +the file the Python wrapper loads by default. + +Note that for a shared library to be usable by a calling program, all +the auxiliary libraries it depends on must also exist as shared +libraries. This will be the case for libraries included with LAMMPS, +such as the dummy MPI library in src/STUBS or any package libraries in +lib/packages, since they are always built as shared libraries using +the -fPIC switch. However, if a library like MPI or FFTW does not +exist as a shared library, the shared library build will generate an +error. This means you will need to install a shared library version +of the auxiliary library. The build instructions for the library +should tell you how to do this. + +Here is an example of such errors when the system FFTW or provided +lib/colvars library have not been built as shared libraries: + +.. parsed-literal:: + + /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation + R_X86_64_32 against `.rodata' can not be used when making a shared + object; recompile with -fPIC + /usr/local/lib/libfftw3.a: could not read symbols: Bad value + +.. parsed-literal:: + + /usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o): + relocation R_X86_64_32 against `__pthread_key_create' can not be used + when making a shared object; recompile with -fPIC + ../../lib/colvars/libcolvars.a: error adding symbols: Bad value + +As an example, here is how to build and install the `MPICH library `_, a popular open-source version of MPI, distributed by +Argonne National Labs, as a shared library in the default +/usr/local/lib location: + +.. _mpich: http://www-unix.mcs.anl.gov/mpi + + + +.. parsed-literal:: + + ./configure --enable-shared + make + make install + +You may need to use "sudo make install" in place of the last line if +you do not have write privileges for /usr/local/lib. The end result +should be the file /usr/local/lib/libmpich.so. + +**Additional requirement for using a shared library:** +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The operating system finds shared libraries to load at run-time using +the environment variable LD_LIBRARY_PATH. So you may wish to copy the +file src/liblammps.so or src/liblammps_g++.so (for example) to a place +the system can find it by default, such as /usr/local/lib, or you may +wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the +current version of the shared library is always available to programs +that use it. + +For the csh or tcsh shells, you would add something like this to your +~/.cshrc file: + +.. parsed-literal:: + + setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src + +**Calling the LAMMPS library:** +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Either flavor of library (static or shared) allows one or more LAMMPS +objects to be instantiated from the calling program. + +When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS +namespace; you can safely use any of its classes and methods from +within the calling code, as needed. + +When used from a C or Fortran program or a scripting language like +Python, the library has a simple function-style interface, provided in +src/library.cpp and src/library.h. + +See the sample codes in examples/COUPLE/simple for examples of C++ and +C and Fortran codes that invoke LAMMPS thru its library interface. +There are other examples as well in the COUPLE directory which are +discussed in :ref:`Section_howto 10 ` of the +manual. See :doc:`Section_python ` of the manual for a +description of the Python wrapper provided with LAMMPS that operates +through the LAMMPS library interface. + +The files src/library.cpp and library.h define the C-style API for +using LAMMPS as a library. See :ref:`Section_howto 19 ` of the manual for a description of the +interface and how to extend it for your needs. + + +---------- + + +.. _start_6: + +Running LAMMPS +---------------------------- + +By default, LAMMPS runs by reading commands from standard input. Thus +if you run the LAMMPS executable by itself, e.g. + +.. parsed-literal:: + + lmp_linux + +it will simply wait, expecting commands from the keyboard. Typically +you should put commands in an input script and use I/O redirection, +e.g. + +.. parsed-literal:: + + lmp_linux < in.file + +For parallel environments this should also work. If it does not, use +the '-in' command-line switch, e.g. + +.. parsed-literal:: + + lmp_linux -in in.file + +:doc:`This section ` describes how input scripts are +structured and what commands they contain. + +You can test LAMMPS on any of the sample inputs provided in the +examples or bench directory. Input scripts are named in.* and sample +outputs are named log.*.name.P where name is a machine and P is the +number of processors it was run on. + +Here is how you might run a standard Lennard-Jones benchmark on a +Linux box, using mpirun to launch a parallel job: + +.. parsed-literal:: + + cd src + make linux + cp lmp_linux ../bench + cd ../bench + mpirun -np 4 lmp_linux -in in.lj + +See `this page `_ for timings for this and the other benchmarks on +various platforms. Note that some of the example scripts require +LAMMPS to be built with one or more of its optional packages. + +.. _bench: http://lammps.sandia.gov/bench.html + + + + +---------- + + +On a Windows box, you can skip making LAMMPS and simply download an +executable, as described above, though the pre-packaged executables +include only certain packages. + +To run a LAMMPS executable on a Windows machine, first decide whether +you want to download the non-MPI (serial) or the MPI (parallel) +version of the executable. Download and save the version you have +chosen. + +For the non-MPI version, follow these steps: + +* Get a command prompt by going to Start->Run... , + then typing "cmd". +* Move to the directory where you have saved lmp_win_no-mpi.exe + (e.g. by typing: cd "Documents"). +* At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj + with the name of your LAMMPS input script. +For the MPI version, which allows you to run LAMMPS under Windows on +multiple processors, follow these steps: + +* Download and install + `MPICH2 `_ + for Windows. +* You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2 + package. Put them in same directory (or path) as the LAMMPS Windows + executable. +* Get a command prompt by going to Start->Run... , + then typing "cmd". +* Move to the directory where you have saved lmp_win_mpi.exe + (e.g. by typing: cd "Documents"). +* Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in + in.lj", replacing in.lj with the name of your LAMMPS input script. +* Note that you may need to provide smpd with a passphrase (it doesn't + matter what you type). +* In this mode, output may not immediately show up on the screen, so if + your input script takes a long time to execute, you may need to be + patient before the output shows up. :l Alternatively, you can still + use this executable to run on a single processor by typing something + like: "lmp_win_mpi -in in.lj". + +---------- + + +The screen output from LAMMPS is described in a section below. As it +runs, LAMMPS also writes a log.lammps file with the same information. + +Note that this sequence of commands copies the LAMMPS executable +(lmp_linux) to the directory with the input files. This may not be +necessary, but some versions of MPI reset the working directory to +where the executable is, rather than leave it as the directory where +you launch mpirun from (if you launch lmp_linux on its own and not +under mpirun). If that happens, LAMMPS will look for additional input +files and write its output files to the executable directory, rather +than your working directory, which is probably not what you want. + +If LAMMPS encounters errors in the input script or while running a +simulation it will print an ERROR message and stop or a WARNING +message and continue. See :doc:`Section_errors ` for a +discussion of the various kinds of errors LAMMPS can or can't detect, +a list of all ERROR and WARNING messages, and what to do about them. + +LAMMPS can run a problem on any number of processors, including a +single processor. In theory you should get identical answers on any +number of processors and on any machine. In practice, numerical +round-off can cause slight differences and eventual divergence of +molecular dynamics phase space trajectories. + +LAMMPS can run as large a problem as will fit in the physical memory +of one or more processors. If you run out of memory, you must run on +more processors or setup a smaller problem. + + +---------- + + +.. _start_7: + +Command-line options +---------------------------------- + +At run time, LAMMPS recognizes several optional command-line switches +which may be used in any order. Either the full word or a one-or-two +letter abbreviation can be used: + +* -c or -cuda +* -e or -echo +* -h or -help +* -i or -in +* -k or -kokkos +* -l or -log +* -nc or -nocite +* -pk or -package +* -p or -partition +* -pl or -plog +* -ps or -pscreen +* -r or -restart +* -ro or -reorder +* -sc or -screen +* -sf or -suffix +* -v or -var + +For example, lmp_ibm might be launched as follows: + +.. parsed-literal:: + + mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy + mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy + +Here are the details on the options: + +.. parsed-literal:: + + -cuda on/off + +Explicitly enable or disable CUDA support, as provided by the +USER-CUDA package. Even if LAMMPS is built with this package, as +described above in :ref:`Section 2.3 `, this switch must be set to +enable running with the CUDA-enabled styles the package provides. If +the switch is not set (the default), LAMMPS will operate as if the +USER-CUDA package were not installed; i.e. you can run standard LAMMPS +or with the GPU package, for testing or benchmarking purposes. + +.. parsed-literal:: + + -echo style + +Set the style of command echoing. The style can be *none* or *screen* +or *log* or *both*. Depending on the style, each command read from +the input script will be echoed to the screen and/or logfile. This +can be useful to figure out which line of your script is causing an +input error. The default value is *log*. The echo style can also be +set by using the :doc:`echo ` command in the input script itself. + +.. parsed-literal:: + + -help + +Print a brief help summary and a list of options compiled into this +executable for each LAMMPS style (atom_style, fix, compute, +pair_style, bond_style, etc). This can tell you if the command you +want to use was included via the appropriate package at compile time. +LAMMPS will print the info and immediately exit if this switch is +used. + +.. parsed-literal:: + + -in file + +Specify a file to use as an input script. This is an optional switch +when running LAMMPS in one-partition mode. If it is not specified, +LAMMPS reads its script from standard input, typically from a script +via I/O redirection; e.g. lmp_linux < in.run. I/O redirection should +also work in parallel, but if it does not (in the unlikely case that +an MPI implementation does not support it), then use the -in flag. +Note that this is a required switch when running LAMMPS in +multi-partition mode, since multiple processors cannot all read from +stdin. + +.. parsed-literal:: + + -kokkos on/off keyword/value ... + +Explicitly enable or disable KOKKOS support, as provided by the KOKKOS +package. Even if LAMMPS is built with this package, as described +above in :ref:`Section 2.3 `, this switch must be set to enable +running with the KOKKOS-enabled styles the package provides. If the +switch is not set (the default), LAMMPS will operate as if the KOKKOS +package were not installed; i.e. you can run standard LAMMPS or with +the GPU or USER-CUDA or USER-OMP packages, for testing or benchmarking +purposes. + +Additional optional keyword/value pairs can be specified which +determine how Kokkos will use the underlying hardware on your +platform. These settings apply to each MPI task you launch via the +"mpirun" or "mpiexec" command. You may choose to run one or more MPI +tasks per physical node. Note that if you are running on a desktop +machine, you typically have one physical node. On a cluster or +supercomputer there may be dozens or 1000s of physical nodes. + +Either the full word or an abbreviation can be used for the keywords. +Note that the keywords do not use a leading minus sign. I.e. the +keyword is "t", not "-t". Also note that each of the keywords has a +default setting. Example of when to use these options and what +settings to use on different platforms is given in :ref:`Section 5.8 `. + +* d or device +* g or gpus +* t or threads +* n or numa + +.. parsed-literal:: + + device Nd + +This option is only relevant if you built LAMMPS with CUDA=yes, you +have more than one GPU per node, and if you are running with only one +MPI task per node. The Nd setting is the ID of the GPU on the node to +run on. By default Nd = 0. If you have multiple GPUs per node, they +have consecutive IDs numbered as 0,1,2,etc. This setting allows you +to launch multiple independent jobs on the node, each with a single +MPI task per node, and assign each job to run on a different GPU. + +.. parsed-literal:: + + gpus Ng Ns + +This option is only relevant if you built LAMMPS with CUDA=yes, you +have more than one GPU per node, and you are running with multiple MPI +tasks per node (up to one per GPU). The Ng setting is how many GPUs +you will use. The Ns setting is optional. If set, it is the ID of a +GPU to skip when assigning MPI tasks to GPUs. This may be useful if +your desktop system reserves one GPU to drive the screen and the rest +are intended for computational work like running LAMMPS. By default +Ng = 1 and Ns is not set. + +Depending on which flavor of MPI you are running, LAMMPS will look for +one of these 3 environment variables + +.. parsed-literal:: + + SLURM_LOCALID (various MPI variants compiled with SLURM support) + MV2_COMM_WORLD_LOCAL_RANK (Mvapich) + OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI) + +which are initialized by the "srun", "mpirun" or "mpiexec" commands. +The environment variable setting for each MPI rank is used to assign a +unique GPU ID to the MPI task. + +.. parsed-literal:: + + threads Nt + +This option assigns Nt number of threads to each MPI task for +performing work when Kokkos is executing in OpenMP or pthreads mode. +The default is Nt = 1, which essentially runs in MPI-only mode. If +there are Np MPI tasks per physical node, you generally want Np*Nt = +the number of physical cores per node, to use your available hardware +optimally. This also sets the number of threads used by the host when +LAMMPS is compiled with CUDA=yes. + +.. parsed-literal:: + + numa Nm + +This option is only relevant when using pthreads with hwloc support. +In this case Nm defines the number of NUMA regions (typicaly sockets) +on a node which will be utilizied by a single MPI rank. By default Nm += 1. If this option is used the total number of worker-threads per +MPI rank is threads*numa. Currently it is always almost better to +assign at least one MPI rank per NUMA region, and leave numa set to +its default value of 1. This is because letting a single process span +multiple NUMA regions induces a significant amount of cross NUMA data +traffic which is slow. + +.. parsed-literal:: + + -log file + +Specify a log file for LAMMPS to write status information to. In +one-partition mode, if the switch is not used, LAMMPS writes to the +file log.lammps. If this switch is used, LAMMPS writes to the +specified file. In multi-partition mode, if the switch is not used, a +log.lammps file is created with hi-level status information. Each +partition also writes to a log.lammps.N file where N is the partition +ID. If the switch is specified in multi-partition mode, the hi-level +logfile is named "file" and each partition also logs information to a +file.N. For both one-partition and multi-partition mode, if the +specified file is "none", then no log files are created. Using a +:doc:`log ` command in the input script will override this setting. +Option -plog will override the name of the partition log files file.N. + +.. parsed-literal:: + + -nocite + +Disable writing the log.cite file which is normally written to list +references for specific cite-able features used during a LAMMPS run. +See the `citation page `_ for more +details. + +.. parsed-literal:: + + -package style args .... + +Invoke the :doc:`package ` command with style and args. The +syntax is the same as if the command appeared at the top of the input +script. For example "-package gpu 2" or "-pk gpu 2" is the same as +:doc:`package gpu 2 ` in the input script. The possible styles +and args are documented on the :doc:`package ` doc page. This +switch can be used multiple times, e.g. to set options for the +USER-INTEL and USER-OMP packages which can be used together. + +Along with the "-suffix" command-line switch, this is a convenient +mechanism for invoking accelerator packages and their options without +having to edit an input script. + +.. parsed-literal:: + + -partition 8x2 4 5 ... + +Invoke LAMMPS in multi-partition mode. When LAMMPS is run on P +processors and this switch is not used, LAMMPS runs in one partition, +i.e. all P processors run a single simulation. If this switch is +used, the P processors are split into separate partitions and each +partition runs its own simulation. The arguments to the switch +specify the number of processors in each partition. Arguments of the +form MxN mean M partitions, each with N processors. Arguments of the +form N mean a single partition with N processors. The sum of +processors in all partitions must equal P. Thus the command +"-partition 8x2 4 5" has 10 partitions and runs on a total of 25 +processors. + +Running with multiple partitions can e useful for running +:ref:`multi-replica simulations `, where each +replica runs on on one or a few processors. Note that with MPI +installed on a machine (e.g. your desktop), you can run on more +(virtual) processors than you have physical processors. + +To run multiple independent simulatoins from one input script, using +multiple partitions, see :ref:`Section_howto 4 ` +of the manual. World- and universe-style :doc:`variables ` +are useful in this context. + +.. parsed-literal:: + + -plog file + +Specify the base name for the partition log files, so partition N +writes log information to file.N. If file is none, then no partition +log files are created. This overrides the filename specified in the +-log command-line option. This option is useful when working with +large numbers of partitions, allowing the partition log files to be +suppressed (-plog none) or placed in a sub-directory (-plog +replica_files/log.lammps) If this option is not used the log file for +partition N is log.lammps.N or whatever is specified by the -log +command-line option. + +.. parsed-literal:: + + -pscreen file + +Specify the base name for the partition screen file, so partition N +writes screen information to file.N. If file is none, then no +partition screen files are created. This overrides the filename +specified in the -screen command-line option. This option is useful +when working with large numbers of partitions, allowing the partition +screen files to be suppressed (-pscreen none) or placed in a +sub-directory (-pscreen replica_files/screen). If this option is not +used the screen file for partition N is screen.N or whatever is +specified by the -screen command-line option. + +.. parsed-literal:: + + -restart restartfile *remap* datafile keyword value ... + +Convert the restart file into a data file and immediately exit. This +is the same operation as if the following 2-line input script were +run: + +.. parsed-literal:: + + read_restart restartfile *remap* + write_data datafile keyword value ... + +Note that the specified restartfile and datafile can have wild-card +characters ("*",%") as described by the +:doc:`read_restart ` and :doc:`write_data ` +commands. But a filename such as file.* will need to be enclosed in +quotes to avoid shell expansion of the "*" character. + +Note that following restartfile, the optional flag *remap* can be +used. This has the same effect as adding it to the +:doc:`read_restart ` command, as explained on its doc +page. This is only useful if the reading of the restart file triggers +an error that atoms have been lost. In that case, use of the remap +flag should allow the data file to still be produced. + +Also note that following datafile, the same optional keyword/value +pairs can be listed as used by the :doc:`write_data ` +command. + +.. parsed-literal:: + + -reorder nth N + -reorder custom filename + +Reorder the processors in the MPI communicator used to instantiate +LAMMPS, in one of several ways. The original MPI communicator ranks +all P processors from 0 to P-1. The mapping of these ranks to +physical processors is done by MPI before LAMMPS begins. It may be +useful in some cases to alter the rank order. E.g. to insure that +cores within each node are ranked in a desired order. Or when using +the :doc:`run_style verlet/split ` command with 2 partitions +to insure that a specific Kspace processor (in the 2nd partition) is +matched up with a specific set of processors in the 1st partition. +See the :doc:`Section_accelerate ` doc pages for +more details. + +If the keyword *nth* is used with a setting *N*, then it means every +Nth processor will be moved to the end of the ranking. This is useful +when using the :doc:`run_style verlet/split ` command with 2 +partitions via the -partition command-line switch. The first set of +processors will be in the first partition, the 2nd set in the 2nd +partition. The -reorder command-line switch can alter this so that +the 1st N procs in the 1st partition and one proc in the 2nd partition +will be ordered consecutively, e.g. as the cores on one physical node. +This can boost performance. For example, if you use "-reorder nth 4" +and "-partition 9 3" and you are running on 12 processors, the +processors will be reordered from + +.. parsed-literal:: + + 0 1 2 3 4 5 6 7 8 9 10 11 + +to + +.. parsed-literal:: + + 0 1 2 4 5 6 8 9 10 3 7 11 + +so that the processors in each partition will be + +.. parsed-literal:: + + 0 1 2 4 5 6 8 9 10 + 3 7 11 + +See the "processors" command for how to insure processors from each +partition could then be grouped optimally for quad-core nodes. + +If the keyword is *custom*, then a file that specifies a permutation +of the processor ranks is also specified. The format of the reorder +file is as follows. Any number of initial blank or comment lines +(starting with a "#" character) can be present. These should be +followed by P lines of the form: + +.. parsed-literal:: + + I J + +where P is the number of processors LAMMPS was launched with. Note +that if running in multi-partition mode (see the -partition switch +above) P is the total number of processors in all partitions. The I +and J values describe a permutation of the P processors. Every I and +J should be values from 0 to P-1 inclusive. In the set of P I values, +every proc ID should appear exactly once. Ditto for the set of P J +values. A single I,J pairing means that the physical processor with +rank I in the original MPI communicator will have rank J in the +reordered communicator. + +Note that rank ordering can also be specified by many MPI +implementations, either by environment variables that specify how to +order physical processors, or by config files that specify what +physical processors to assign to each MPI rank. The -reorder switch +simply gives you a portable way to do this without relying on MPI +itself. See the `processors out `_ command for how to output +info on the final assignment of physical processors to the LAMMPS +simulation domain. + +.. parsed-literal:: + + -screen file + +Specify a file for LAMMPS to write its screen information to. In +one-partition mode, if the switch is not used, LAMMPS writes to the +screen. If this switch is used, LAMMPS writes to the specified file +instead and you will see no screen output. In multi-partition mode, +if the switch is not used, hi-level status information is written to +the screen. Each partition also writes to a screen.N file where N is +the partition ID. If the switch is specified in multi-partition mode, +the hi-level screen dump is named "file" and each partition also +writes screen information to a file.N. For both one-partition and +multi-partition mode, if the specified file is "none", then no screen +output is performed. Option -pscreen will override the name of the +partition screen files file.N. + +.. parsed-literal:: + + -suffix style args + +Use variants of various styles if they exist. The specified style can +be *cuda*, *gpu*, *intel*, *kk*, *omp*, *opt*, or *hybrid*. These refer +to optional packages that LAMMPS can be built with, as described above in +:ref:`Section 2.3 `. The "cuda" style corresponds to the USER-CUDA +package, the "gpu" style to the GPU package, the "intel" style to the +USER-INTEL package, the "kk" style to the KOKKOS package, the "opt" +style to the OPT package, and the "omp" style to the USER-OMP package. The +hybrid style is the only style that accepts arguments. It allows for two +packages to be specified. The first package specified is the default and +will be used if it is available. If no style is available for the first +package, the style for the second package will be used if available. For +example, "-suffix hybrid intel omp" will use styles from the USER-INTEL +package if they are installed and available, but styles for the USER-OMP +package otherwise. + +Along with the "-package" command-line switch, this is a convenient +mechanism for invoking accelerator packages and their options without +having to edit an input script. + +As an example, all of the packages provide a :doc:`pair_style lj/cut ` variant, with style names lj/cut/cuda, +lj/cut/gpu, lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A +variant style can be specified explicitly in your input script, +e.g. pair_style lj/cut/gpu. If the -suffix switch is used the +specified suffix (cuda,gpu,intel,kk,omp,opt) is automatically appended +whenever your input script command creates a new +:doc:`atom `, :doc:`pair `, :doc:`fix `, +:doc:`compute `, or :doc:`run ` style. If the variant +version does not exist, the standard version is created. + +For the GPU package, using this command-line switch also invokes the +default GPU settings, as if the command "package gpu 1" were used at +the top of your input script. These settings can be changed by using +the "-package gpu" command-line switch or the :doc:`package gpu ` command in your script. + +For the USER-INTEL package, using this command-line switch also +invokes the default USER-INTEL settings, as if the command "package +intel 1" were used at the top of your input script. These settings +can be changed by using the "-package intel" command-line switch or +the :doc:`package intel ` command in your script. If the +USER-OMP package is also installed, the hybrid style with "intel omp" +arguments can be used to make the omp suffix a second choice, if a +requested style is not available in the USER-INTEL package. It will +also invoke the default USER-OMP settings, as if the command "package +omp 0" were used at the top of your input script. These settings can +be changed by using the "-package omp" command-line switch or the +:doc:`package omp ` command in your script. + +For the KOKKOS package, using this command-line switch also invokes +the default KOKKOS settings, as if the command "package kokkos" were +used at the top of your input script. These settings can be changed +by using the "-package kokkos" command-line switch or the :doc:`package kokkos ` command in your script. + +For the OMP package, using this command-line switch also invokes the +default OMP settings, as if the command "package omp 0" were used at +the top of your input script. These settings can be changed by using +the "-package omp" command-line switch or the :doc:`package omp ` command in your script. + +The :doc:`suffix ` command can also be used within an input +script to set a suffix, or to turn off or back on any suffix setting +made via the command line. + +.. parsed-literal:: + + -var name value1 value2 ... + +Specify a variable that will be defined for substitution purposes when +the input script is read. This switch can be used multiple times to +define multiple variables. "Name" is the variable name which can be a +single character (referenced as $x in the input script) or a full +string (referenced as ${abc}). An :doc:`index-style variable ` will be created and populated with the +subsequent values, e.g. a set of filenames. Using this command-line +option is equivalent to putting the line "variable name index value1 +value2 ..." at the beginning of the input script. Defining an index +variable as a command-line argument overrides any setting for the same +index variable in the input script, since index variables cannot be +re-defined. See the :doc:`variable ` command for more info on +defining index and other kinds of variables and :ref:`this section ` for more info on using variables +in input scripts. + +.. note:: + + Currently, the command-line parser looks for arguments that + start with "-" to indicate new switches. Thus you cannot specify + multiple variable values if any of they start with a "-", e.g. a + negative numeric value. It is OK if the first value1 starts with a + "-", since it is automatically skipped. + + +---------- + + +.. _start_8: + +LAMMPS screen output +---------------------------------- + +As LAMMPS reads an input script, it prints information to both the +screen and a log file about significant actions it takes to setup a +simulation. When the simulation is ready to begin, LAMMPS performs +various initializations and prints the amount of memory (in MBytes per +processor) that the simulation requires. It also prints details of +the initial thermodynamic state of the system. During the run itself, +thermodynamic information is printed periodically, every few +timesteps. When the run concludes, LAMMPS prints the final +thermodynamic state and a total run time for the simulation. It then +appends statistics about the CPU time and storage requirements for the +simulation. An example set of statistics is shown here: + +Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms + +.. parsed-literal:: + + Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s + 97.0% CPU use with 4 MPI tasks x no OpenMP threads + +.. parsed-literal:: + + MPI task timings breakdown: + Section | min time | avg time | max time |%varavg| %total + --------------------------------------------------------------- + Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60 + Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21 + Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97 + Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12 + Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74 + Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02 + Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08 + Other | | 0.007178 | | | 0.26 + +.. parsed-literal:: + + Nlocal: 501 ave 508 max 490 min + Histogram: 1 0 0 0 0 0 1 1 0 1 + Nghost: 6586.25 ave 6628 max 6548 min + Histogram: 1 0 1 0 0 0 1 0 0 1 + Neighs: 177007 ave 180562 max 170212 min + Histogram: 1 0 0 0 0 0 0 1 1 1 + +.. parsed-literal:: + + Total # of neighbors = 708028 + Ave neighs/atom = 353.307 + Ave special neighs/atom = 2.34032 + Neighbor list builds = 26 + Dangerous builds = 0 + +The first section provides a global loop timing summary. The loop time +is the total wall time for the section. The *Performance* line is +provided for convenience to help predicting the number of loop +continuations required and for comparing performance with other +similar MD codes. The CPU use line provides the CPU utilzation per +MPI task; it should be close to 100% times the number of OpenMP +threads (or 1). Lower numbers correspond to delays due to file I/O or +insufficient thread utilization. + +The MPI task section gives the breakdown of the CPU run time (in +seconds) into major categories: + +* *Pair* stands for all non-bonded force computation +* *Bond* stands for bonded interactions: bonds, angles, dihedrals, impropers +* *Kspace* stands for reciprocal space interactions: Ewald, PPPM, MSM +* *Neigh* stands for neighbor list construction +* *Comm* stands for communicating atoms and their properties +* *Output* stands for writing dumps and thermo output +* *Modify* stands for fixes and computes called by them +* *Other* is the remaining time + +For each category, there is a breakdown of the least, average and most +amount of wall time a processor spent on this section. Also you have the +variation from the average time. Together these numbers allow to gauge +the amount of load imbalance in this segment of the calculation. Ideally +the difference between minimum, maximum and average is small and thus +the variation from the average close to zero. The final column shows +the percentage of the total loop time is spent in this section. + +When using the :doc:`timer full ` setting, an additional column +is present that also prints the CPU utilization in percent. In +addition, when using *timer full* and the :doc:`package omp ` +command are active, a similar timing summary of time spent in threaded +regions to monitor thread utilization and load balance is provided. A +new entry is the *Reduce* section, which lists the time spend in +reducing the per-thread data elements to the storage for non-threaded +computation. These thread timings are taking from the first MPI rank +only and and thus, as the breakdown for MPI tasks can change from MPI +rank to MPI rank, this breakdown can be very different for individual +ranks. Here is an example output for this section: + +Thread timings breakdown (MPI rank 0): +Total threaded time 0.6846 / 90.6% +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18 +Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68 +Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89 +Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70 +Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55 + +The third section lists the number of owned atoms (Nlocal), ghost atoms +(Nghost), and pair-wise neighbors stored per processor. The max and min +values give the spread of these values across processors with a 10-bin +histogram showing the distribution. The total number of histogram counts +is equal to the number of processors. + +The last section gives aggregate statistics for pair-wise neighbors +and special neighbors that LAMMPS keeps track of (see the +:doc:`special_bonds ` command). The number of times +neighbor lists were rebuilt during the run is given as well as the +number of potentially "dangerous" rebuilds. If atom movement +triggered neighbor list rebuilding (see the +:doc:`neigh_modify ` command), then dangerous +reneighborings are those that were triggered on the first timestep +atom movement was checked for. If this count is non-zero you may wish +to reduce the delay factor to insure no force interactions are missed +by atoms moving beyond the neighbor skin distance before a rebuild +takes place. + +If an energy minimization was performed via the +:doc:`minimize ` command, additional information is printed, +e.g. + +.. parsed-literal:: + + Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + -6372.3765206 -8328.46998942 -8328.46998942 + Force two-norm initial, final = 1059.36 5.36874 + Force max component initial, final = 58.6026 1.46872 + Final line search alpha, max atom move = 2.7842e-10 4.0892e-10 + Iterations, force evaluations = 701 1516 + +The first line prints the criterion that determined the minimization +to be completed. The third line lists the initial and final energy, +as well as the energy on the next-to-last iteration. The next 2 lines +give a measure of the gradient of the energy (force on all atoms). +The 2-norm is the "length" of this force vector; the inf-norm is the +largest component. Then some information about the line search and +statistics on how many iterations and force-evaluations the minimizer +required. Multiple force evaluations are typically done at each +iteration to perform a 1d line minimization in the search direction. + +If a :doc:`kspace_style ` long-range Coulombics solve was +performed during the run (PPPM, Ewald), then additional information is +printed, e.g. + +.. parsed-literal:: + + FFT time (% of Kspce) = 0.200313 (8.34477) + FFT Gflps 3d 1d-only = 2.31074 9.19989 + +The first line gives the time spent doing 3d FFTs (4 per timestep) and +the fraction it represents of the total KSpace time (listed above). +Each 3d FFT requires computation (3 sets of 1d FFTs) and communication +(transposes). The total flops performed is 5Nlog_2(N), where N is the +number of points in the 3d grid. The FFTs are timed with and without +the communication and a Gflop rate is computed. The 3d rate is with +communication; the 1d rate is without (just the 1d FFTs). Thus you +can estimate what fraction of your FFT time was spent in +communication, roughly 75% in the example above. + + +---------- + + +.. _start_9: + +Tips for users of previous LAMMPS versions +-------------------------------------------------------- + +The current C++ began with a complete rewrite of LAMMPS 2001, which +was written in F90. Features of earlier versions of LAMMPS are listed +in :doc:`Section_history `. The F90 and F77 versions +(2001 and 99) are also freely distributed as open-source codes; check +the `LAMMPS WWW Site `_ for distribution information if you prefer +those versions. The 99 and 2001 versions are no longer under active +development; they do not have all the features of C++ LAMMPS. + +If you are a previous user of LAMMPS 2001, these are the most +significant changes you will notice in C++ LAMMPS: + +(1) The names and arguments of many input script commands have +changed. All commands are now a single word (e.g. read_data instead +of read data). + +(2) All the functionality of LAMMPS 2001 is included in C++ LAMMPS, +but you may need to specify the relevant commands in different ways. + +(3) The format of the data file can be streamlined for some problems. +See the :doc:`read_data ` command for details. The data file +section "Nonbond Coeff" has been renamed to "Pair Coeff" in C++ LAMMPS. + +(4) Binary restart files written by LAMMPS 2001 cannot be read by C++ +LAMMPS with a :doc:`read_restart ` command. This is +because they were output by F90 which writes in a different binary +format than C or C++ writes or reads. Use the *restart2data* tool +provided with LAMMPS 2001 to convert the 2001 restart file to a text +data file. Then edit the data file as necessary before using the C++ +LAMMPS :doc:`read_data ` command to read it in. + +(5) There are numerous small numerical changes in C++ LAMMPS that mean +you will not get identical answers when comparing to a 2001 run. +However, your initial thermodynamic energy and MD trajectory should be +close if you have setup the problem for both codes the same. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/Section_tools.txt b/doc/_sources/Section_tools.txt new file mode 100644 index 0000000000..7d96e007f2 --- /dev/null +++ b/doc/_sources/Section_tools.txt @@ -0,0 +1,737 @@ +Additional tools +================ + +LAMMPS is designed to be a computational kernel for performing +molecular dynamics computations. Additional pre- and post-processing +steps are often necessary to setup and analyze a simulation. A few +additional tools are provided with the LAMMPS distribution and are +described in this section. + +Our group has also written and released a separate toolkit called +`Pizza.py `_ which provides tools for doing setup, analysis, +plotting, and visualization for LAMMPS simulations. Pizza.py is +written in `Python `_ and is available for download from `the Pizza.py WWW site `_. + +.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html + + + +.. _python: http://www.python.org + + + +Note that many users write their own setup or analysis tools or use +other existing codes and convert their output to a LAMMPS input format +or vice versa. The tools listed here are included in the LAMMPS +distribution as examples of auxiliary tools. Some of them are not +actively supported by Sandia, as they were contributed by LAMMPS +users. If you have problems using them, we can direct you to the +authors. + +The source code for each of these codes is in the tools sub-directory +of the LAMMPS distribution. There is a Makefile (which you may need +to edit for your platform) which will build several of the tools which +reside in that directory. Some of them are larger packages in their +own sub-directories with their own Makefiles. + +* :ref:`amber2lmp ` +* :ref:`binary2txt ` +* :ref:`ch2lmp ` +* :ref:`chain ` +* :ref:`colvars ` +* :ref:`createatoms ` +* :ref:`data2xmovie ` +* :ref:`eam database ` +* :ref:`eam generate ` +* :ref:`eff ` +* :ref:`emacs ` +* :ref:`fep ` +* :ref:`i-pi ` +* :ref:`ipp ` +* :ref:`kate ` +* :ref:`lmp2arc ` +* :ref:`lmp2cfg ` +* :ref:`lmp2vmd ` +* :ref:`matlab ` +* :ref:`micelle2d ` +* :ref:`moltemplate ` +* :ref:`msi2lmp ` +* :ref:`phonon ` +* :ref:`polymer bonding ` +* :ref:`pymol_asphere ` +* :ref:`python ` +* :ref:`reax ` +* :ref:`restart2data ` +* :ref:`vim ` +* :ref:`xmgrace ` +* :ref:`xmovie ` + + +---------- + + +.. _amber: + +amber2lmp tool +-------------------------- + +The amber2lmp sub-directory contains two Python scripts for converting +files back-and-forth between the AMBER MD code and LAMMPS. See the +README file in amber2lmp for more information. + +These tools were written by Keir Novik while he was at Queen Mary +University of London. Keir is no longer there and cannot support +these tools which are out-of-date with respect to the current LAMMPS +version (and maybe with respect to AMBER as well). Since we don't use +these tools at Sandia, you'll need to experiment with them and make +necessary modifications yourself. + + +---------- + + +.. _binary: + +binary2txt tool +---------------------------- + +The file binary2txt.cpp converts one or more binary LAMMPS dump file +into ASCII text files. The syntax for running the tool is + +.. parsed-literal:: + + binary2txt file1 file2 ... + +which creates file1.txt, file2.txt, etc. This tool must be compiled +on a platform that can read the binary file created by a LAMMPS run, +since binary files are not compatible across all platforms. + + +---------- + + +.. _charmm: + +ch2lmp tool +------------------------ + +The ch2lmp sub-directory contains tools for converting files +back-and-forth between the CHARMM MD code and LAMMPS. + +They are intended to make it easy to use CHARMM as a builder and as a +post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an +ensemble built in CHARMM into its LAMMPS equivalent. Using +lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files. + +See the README file in the ch2lmp sub-directory for more information. + +These tools were created by Pieter in't Veld (pjintve at sandia.gov) +and Paul Crozier (pscrozi at sandia.gov) at Sandia. + + +---------- + + +.. _chain: + +chain tool +---------------------- + +The file chain.f creates a LAMMPS data file containing bead-spring +polymer chains and/or monomer solvent atoms. It uses a text file +containing chain definition parameters as an input. The created +chains and solvent atoms can strongly overlap, so LAMMPS needs to run +the system initially with a "soft" pair potential to un-overlap it. +The syntax for running the tool is + +.. parsed-literal:: + + chain < def.chain > data.file + +See the def.chain or def.chain.ab files in the tools directory for +examples of definition files. This tool was used to create the +system for the :doc:`chain benchmark `. + + +---------- + + +.. _colvars: + +colvars tools +--------------------------- + +The colvars directory contains a collection of tools for postprocessing +data produced by the colvars collective variable library. +To compile the tools, edit the makefile for your system and run "make". + +Please report problems and issues the colvars library and its tools +at: https://github.com/colvars/colvars/issues + +abf_integrate: + +MC-based integration of multidimensional free energy gradient +Version 20110511 + +.. parsed-literal:: + + Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >] + +The LAMMPS interface to the colvars collective variable library, as +well as these tools, were created by Axel Kohlmeyer (akohlmey at +gmail.com) at ICTP, Italy. + + +---------- + + +.. _create: + +createatoms tool +----------------------------- + +The tools/createatoms directory contains a Fortran program called +createAtoms.f which can generate a variety of interesting crystal +structures and geometries and output the resulting list of atom +coordinates in LAMMPS or other formats. + +See the included Manual.pdf for details. + +The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. + + +---------- + + +.. _data: + +data2xmovie tool +--------------------------- + +The file data2xmovie.c converts a LAMMPS data file into a snapshot +suitable for visualizing with the :ref:`xmovie ` tool, as if it had +been output with a dump command from LAMMPS itself. The syntax for +running the tool is + +.. parsed-literal:: + + data2xmovie [options] < infile > outfile + +See the top of the data2xmovie.c file for a discussion of the options. + + +---------- + + +.. _eamdb: + +eam database tool +----------------------------- + +The tools/eam_database directory contains a Fortran program that will +generate EAM alloy setfl potential files for any combination of 16 +elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, +Zr. The files can then be used with the :doc:`pair_style eam/alloy ` command. + +The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, +and is based on his paper: + +X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, +144113 (2004). + + +---------- + + +.. _eamgn: + +eam generate tool +----------------------------- + +The tools/eam_generate directory contains several one-file C programs +that convert an analytic formula into a tabulated :doc:`embedded atom method (EAM) ` setfl potential file. The potentials they +produce are in the potentials directory, and can be used with the +:doc:`pair_style eam/alloy ` command. + +The source files and potentials were provided by Gerolf Ziegenhain +(gerolf at ziegenhain.com). + + +---------- + + +.. _eff: + +eff tool +------------------ + +The tools/eff directory contains various scripts for generating +structures and post-processing output for simulations using the +electron force field (eFF). + +These tools were provided by Andres Jaramillo-Botero at CalTech +(ajaramil at wag.caltech.edu). + + +---------- + + +.. _emacs: + +emacs tool +---------------------- + +The tools/emacs directory contains a Lips add-on file for Emacs that +enables a lammps-mode for editing of input scripts when using Emacs, +with various highlighting options setup. + +These tools were provided by Aidan Thompson at Sandia +(athomps at sandia.gov). + + +---------- + + +.. _fep: + +fep tool +------------------ + +The tools/fep directory contains Python scripts useful for +post-processing results from performing free-energy perturbation +simulations using the USER-FEP package. + +The scripts were contributed by Agilio Padua (Universite Blaise +Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr. + +See README file in the tools/fep directory. + + +---------- + + +.. _ipi: + +i-pi tool +------------------- + +The tools/i-pi directory contains a version of the i-PI package, with +all the LAMMPS-unrelated files removed. It is provided so that it can +be used with the :doc:`fix ipi ` command to perform +path-integral molecular dynamics (PIMD). + +The i-PI package was created and is maintained by Michele Ceriotti, +michele.ceriotti at gmail.com, to interface to a variety of molecular +dynamics codes. + +See the tools/i-pi/manual.pdf file for an overview of i-PI, and the +:doc:`fix ipi ` doc page for further details on running PIMD +calculations with LAMMPS. + + +---------- + + +.. _ipp: + +ipp tool +------------------ + +The tools/ipp directory contains a Perl script ipp which can be used +to facilitate the creation of a complicated file (say, a lammps input +script or tools/createatoms input file) using a template file. + +ipp was created and is maintained by Reese Jones (Sandia), rjones at +sandia.gov. + +See two examples in the tools/ipp directory. One of them is for the +tools/createatoms tool's input file. + + +---------- + + +.. _kate: + +kate tool +-------------------- + +The file in the tools/kate directory is an add-on to the Kate editor +in the KDE suite that allow syntax highlighting of LAMMPS input +scripts. See the README.txt file for details. + +The file was provided by Alessandro Luigi Sellerio +(alessandro.sellerio at ieni.cnr.it). + + +---------- + + +.. _arc: + +lmp2arc tool +---------------------- + +The lmp2arc sub-directory contains a tool for converting LAMMPS output +files to the format for Accelrys' Insight MD code (formerly +MSI/Biosym and its Discover MD code). See the README file for more +information. + +This tool was written by John Carpenter (Cray), Michael Peachey +(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic +(jec at mayo.edu), but still fields questions about the tool. + +This tool was updated for the current LAMMPS C++ version by Jeff +Greathouse at Sandia (jagreat at sandia.gov). + + +---------- + + +.. _cfg: + +lmp2cfg tool +---------------------- + +The lmp2cfg sub-directory contains a tool for converting LAMMPS output +files into a series of *.cfg files which can be read into the +`AtomEye `_ visualizer. See +the README file for more information. + +This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). + + +---------- + + +.. _vmd: + +lmp2vmd tool +---------------------- + +The lmp2vmd sub-directory contains a README.txt file that describes +details of scripts and plugin support within the `VMD package `_ for visualizing LAMMPS +dump files. + +The VMD plugins and other supporting scripts were written by Axel +Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn. + + +---------- + + +.. _matlab: + +matlab tool +------------------------ + +The matlab sub-directory contains several :ref:`MATLAB ` scripts for +post-processing LAMMPS output. The scripts include readers for log +and dump files, a reader for EAM potential files, and a converter that +reads LAMMPS dump files and produces CFG files that can be visualized +with the `AtomEye `_ +visualizer. + +See the README.pdf file for more information. + +These scripts were written by Arun Subramaniyan at Purdue Univ +(asubrama at purdue.edu). + +.. _matlab: http://www.mathworks.com + + + + +---------- + + +.. _micelle: + +micelle2d tool +---------------------------- + +The file micelle2d.f creates a LAMMPS data file containing short lipid +chains in a monomer solution. It uses a text file containing lipid +definition parameters as an input. The created molecules and solvent +atoms can strongly overlap, so LAMMPS needs to run the system +initially with a "soft" pair potential to un-overlap it. The syntax +for running the tool is + +.. parsed-literal:: + + micelle2d < def.micelle2d > data.file + +See the def.micelle2d file in the tools directory for an example of a +definition file. This tool was used to create the system for the +:doc:`micelle example `. + + +---------- + + +.. _moltemplate: + +moltemplate tool +---------------------------------- + +The moltemplate sub-directory contains a Python-based tool for +building molecular systems based on a text-file description, and +creating LAMMPS data files that encode their molecular topology as +lists of bonds, angles, dihedrals, etc. See the README.TXT file for +more information. + +This tool was written by Andrew Jewett (jewett.aij at gmail.com), who +supports it. It has its own WWW page at +`http://moltemplate.org `_. + + +---------- + + +.. _msi: + +msi2lmp tool +---------------------- + +The msi2lmp sub-directory contains a tool for creating LAMMPS input +data files from Accelrys' Insight MD code (formerly MSI/Biosym and +its Discover MD code). See the README file for more information. + +This tool was written by John Carpenter (Cray), Michael Peachey +(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic +(jec at mayo.edu), but still fields questions about the tool. + +This tool may be out-of-date with respect to the current LAMMPS and +Insight versions. Since we don't use it at Sandia, you'll need to +experiment with it yourself. + + +---------- + + +.. _phonon: + +phonon tool +------------------------ + +The phonon sub-directory contains a post-processing tool useful for +analyzing the output of the :doc:`fix phonon ` command in +the USER-PHONON package. + +See the README file for instruction on building the tool and what +library it needs. And see the examples/USER/phonon directory +for example problems that can be post-processed with this tool. + +This tool was written by Ling-Ti Kong at Shanghai Jiao Tong +University. + + +---------- + + +.. _polybond: + +polymer bonding tool +----------------------------------- + +The polybond sub-directory contains a Python-based tool useful for +performing "programmable polymer bonding". The Python file +lmpsdata.py provides a "Lmpsdata" class with various methods which can +be invoked by a user-written Python script to create data files with +complex bonding topologies. + +See the Manual.pdf for details and example scripts. + +This tool was written by Zachary Kraus at Georgia Tech. + + +---------- + + +.. _pymol: + +pymol_asphere tool +------------------------------ + +The pymol_asphere sub-directory contains a tool for converting a +LAMMPS dump file that contains orientation info for ellipsoidal +particles into an input file for the :ref:`PyMol visualization package `. + +.. _pymol: http://pymol.sourceforge.net + + + +Specifically, the tool triangulates the ellipsoids so they can be +viewed as true ellipsoidal particles within PyMol. See the README and +examples directory within pymol_asphere for more information. + +This tool was written by Mike Brown at Sandia. + + +---------- + + +.. _pythontools: + +python tool +----------------------------- + +The python sub-directory contains several Python scripts +that perform common LAMMPS post-processing tasks, such as: + +* extract thermodynamic info from a log file as columns of numbers +* plot two columns of thermodynamic info from a log file using GnuPlot +* sort the snapshots in a dump file by atom ID +* convert multiple :doc:`NEB ` dump files into one dump file for viz +* convert dump files into XYZ, CFG, or PDB format for viz by other packages + +These are simple scripts built on `Pizza.py `_ modules. See the +README for more info on Pizza.py and how to use these scripts. + + +---------- + + +.. _reax: + +reax tool +-------------------- + +The reax sub-directory contains stand-alond codes that can +post-process the output of the :doc:`fix reax/bonds ` +command from a LAMMPS simulation using :doc:`ReaxFF `. See +the README.txt file for more info. + +These tools were written by Aidan Thompson at Sandia. + + +---------- + + +.. _restart: + +restart2data tool +------------------------------- + +.. note:: + + This tool is now obsolete and is not included in the current + LAMMPS distribution. This is becaues there is now a + :doc:`write_data ` command, which can create a data file + from within an input script. Running LAMMPS with the "-r" + :ref:`command-line switch ` as follows: + +lmp_g++ -r restartfile datafile + +is the same as running a 2-line input script: + +read_restart restartfile +write_data datafile + +which will produce the same data file that the restart2data tool used +to create. The following information is included in case you have an +older version of LAMMPS which still includes the restart2data tool. + +The file restart2data.cpp converts a binary LAMMPS restart file into +an ASCII data file. The syntax for running the tool is + +.. parsed-literal:: + + restart2data restart-file data-file (input-file) + +Input-file is optional and if specified will contain LAMMPS input +commands for the masses and force field parameters, instead of putting +those in the data-file. Only a few force field styles currently +support this option. + +This tool must be compiled on a platform that can read the binary file +created by a LAMMPS run, since binary files are not compatible across +all platforms. + +Note that a text data file has less precision than a binary restart +file. Hence, continuing a run from a converted data file will +typically not conform as closely to a previous run as will restarting +from a binary restart file. + +If a "%" appears in the specified restart-file, the tool expects a set +of multiple files to exist. See the :doc:`restart ` and +:doc:`write_restart ` commands for info on how such sets +of files are written by LAMMPS, and how the files are named. + + +---------- + + +.. _vim: + +vim tool +------------------ + +The files in the tools/vim directory are add-ons to the VIM editor +that allow easier editing of LAMMPS input scripts. See the README.txt +file for details. + +These files were provided by Gerolf Ziegenhain (gerolf at +ziegenhain.com) + + +---------- + + +.. _xmgrace: + +xmgrace tool +-------------------------- + +The files in the tools/xmgrace directory can be used to plot the +thermodynamic data in LAMMPS log files via the xmgrace plotting +package. There are several tools in the directory that can be used in +post-processing mode. The lammpsplot.cpp file can be compiled and +used to create plots from the current state of a running LAMMPS +simulation. + +See the README file for details. + +These files were provided by Vikas Varshney (vv0210 at gmail.com) + + +---------- + + +.. _xmovie: + +xmovie tool +------------------------ + +The xmovie tool is an X-based visualization package that can read +LAMMPS dump files and animate them. It is in its own sub-directory +with the tools directory. You may need to modify its Makefile so that +it can find the appropriate X libraries to link against. + +The syntax for running xmovie is + +.. parsed-literal:: + + xmovie [options] dump.file1 dump.file2 ... + +If you just type "xmovie" you will see a list of options. Note that +by default, LAMMPS dump files are in scaled coordinates, so you +typically need to use the -scale option with xmovie. When xmovie runs +it opens a visualization window and a control window. The control +options are straightforward to use. + +Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he +spent a summer at Sandia. It displays 2d projections of a 3d domain. +While simple in design, it is an amazingly fast program that can +render large numbers of atoms very quickly. It's a useful tool for +debugging LAMMPS input and output and making sure your simulation is +doing what you think it should. The animations on the Examples page +of the `LAMMPS WWW site `_ were created with xmovie. + +I've lost contact with Mike, so I hope he's comfortable with us +distributing his great tool! + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/accelerate_cuda.txt b/doc/_sources/accelerate_cuda.txt new file mode 100644 index 0000000000..857bd04496 --- /dev/null +++ b/doc/_sources/accelerate_cuda.txt @@ -0,0 +1,223 @@ +:doc:`Return to Section accelerate overview ` + +5.USER-CUDA package +------------------- + +The USER-CUDA package was developed by Christian Trott (Sandia) while +at U Technology Ilmenau in Germany. It provides NVIDIA GPU versions +of many pair styles, many fixes, a few computes, and for long-range +Coulombics via the PPPM command. It has the following general +features: + +* The package is designed to allow an entire LAMMPS calculation, for + many timesteps, to run entirely on the GPU (except for inter-processor + MPI communication), so that atom-based data (e.g. coordinates, forces) + do not have to move back-and-forth between the CPU and GPU. +* The speed-up advantage of this approach is typically better when the + number of atoms per GPU is large +* Data will stay on the GPU until a timestep where a non-USER-CUDA fix + or compute is invoked. Whenever a non-GPU operation occurs (fix, + compute, output), data automatically moves back to the CPU as needed. + This may incur a performance penalty, but should otherwise work + transparently. +* Neighbor lists are constructed on the GPU. +* The package only supports use of a single MPI task, running on a + single CPU (core), assigned to each GPU. +Here is a quick overview of how to use the USER-CUDA package: + +* build the library in lib/cuda for your GPU hardware with desired precision +* include the USER-CUDA package and build LAMMPS +* use the mpirun command to specify 1 MPI task per GPU (on each node) +* enable the USER-CUDA package via the "-c on" command-line switch +* specify the # of GPUs per node +* use USER-CUDA styles in your input script + +The latter two steps can be done using the "-pk cuda" and "-sf cuda" +:ref:`command-line switches ` respectively. Or +the effect of the "-pk" or "-sf" switches can be duplicated by adding +the :doc:`package cuda ` or :doc:`suffix cuda ` commands +respectively to your input script. + +**Required hardware/software:** + +To use this package, you need to have one or more NVIDIA GPUs and +install the NVIDIA Cuda software on your system: + +Your NVIDIA GPU needs to support Compute Capability 1.3. This list may +help you to find out the Compute Capability of your card: + +http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units + +Install the Nvidia Cuda Toolkit (version 3.2 or higher) and the +corresponding GPU drivers. The Nvidia Cuda SDK is not required, but +we recommend it also be installed. You can then make sure its sample +projects can be compiled without problems. + +**Building LAMMPS with the USER-CUDA package:** + +This requires two steps (a,b): build the USER-CUDA library, then build +LAMMPS with the USER-CUDA package. + +You can do both these steps in one line, using the src/Make.py script, +described in :ref:`Section 2.4 ` of the manual. +Type "Make.py -h" for help. If run from the src directory, this +command will create src/lmp_cuda using src/MAKE/Makefile.mpi as the +starting Makefile.machine: + +.. parsed-literal:: + + Make.py -p cuda -cuda mode=single arch=20 -o cuda -a lib-cuda file mpi + +Or you can follow these two (a,b) steps: + +(a) Build the USER-CUDA library + +The USER-CUDA library is in lammps/lib/cuda. If your *CUDA* toolkit +is not installed in the default system directoy */usr/local/cuda* edit +the file *lib/cuda/Makefile.common* accordingly. + +To build the library with the settings in lib/cuda/Makefile.default, +simply type: + +.. parsed-literal:: + + make + +To set options when the library is built, type "make OPTIONS", where +*OPTIONS* are one or more of the following. The settings will be +written to the *lib/cuda/Makefile.defaults* before the build. + +.. parsed-literal:: + + *precision=N* to set the precision level + N = 1 for single precision (default) + N = 2 for double precision + N = 3 for positions in double precision + N = 4 for positions and velocities in double precision + *arch=M* to set GPU compute capability + M = 35 for Kepler GPUs + M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470) (default) + M = 21 for CC2.1 (GF104/114, e.g. GTX560, GTX460, GTX450) + M = 13 for CC1.3 (GF200, e.g. C1060, GTX285) + *prec_timer=0/1* to use hi-precision timers + 0 = do not use them (default) + 1 = use them + this is usually only useful for Mac machines + *dbg=0/1* to activate debug mode + 0 = no debug mode (default) + 1 = yes debug mode + this is only useful for developers + *cufft=1* for use of the CUDA FFT library + 0 = no CUFFT support (default) + in the future other CUDA-enabled FFT libraries might be supported + +If the build is successful, it will produce the files liblammpscuda.a and +Makefile.lammps. + +Note that if you change any of the options (like precision), you need +to re-build the entire library. Do a "make clean" first, followed by +"make". + +(b) Build LAMMPS with the USER-CUDA package + +.. parsed-literal:: + + cd lammps/src + make yes-user-cuda + make machine + +No additional compile/link flags are needed in Makefile.machine. + +Note that if you change the USER-CUDA library precision (discussed +above) and rebuild the USER-CUDA library, then you also need to +re-install the USER-CUDA package and re-build LAMMPS, so that all +affected files are re-compiled and linked to the new USER-CUDA +library. + +**Run with the USER-CUDA package from the command line:** + +The mpirun or mpiexec command sets the total number of MPI tasks used +by LAMMPS (one or multiple per compute node) and the number of MPI +tasks used per node. E.g. the mpirun command in MPICH does this via +its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. + +When using the USER-CUDA package, you must use exactly one MPI task +per physical GPU. + +You must use the "-c on" :ref:`command-line switch ` to enable the USER-CUDA package. +The "-c on" switch also issues a default :doc:`package cuda 1 ` +command which sets various USER-CUDA options to default values, as +discussed on the :doc:`package ` command doc page. + +Use the "-sf cuda" :ref:`command-line switch `, +which will automatically append "cuda" to styles that support it. Use +the "-pk cuda Ng" :ref:`command-line switch ` to +set Ng = # of GPUs per node to a different value than the default set +by the "-c on" switch (1 GPU) or change other :doc:`package cuda ` options. + +.. parsed-literal:: + + lmp_machine -c on -sf cuda -pk cuda 1 -in in.script # 1 MPI task uses 1 GPU + mpirun -np 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script # 2 MPI tasks use 2 GPUs on a single 16-core (or whatever) node + mpirun -np 24 -ppn 2 lmp_machine -c on -sf cuda -pk cuda 2 -in in.script # ditto on 12 16-core nodes + +The syntax for the "-pk" switch is the same as same as the "package +cuda" command. See the :doc:`package ` command doc page for +details, including the default values used for all its options if it +is not specified. + +Note that the default for the :doc:`package cuda ` command is +to set the Newton flag to "off" for both pairwise and bonded +interactions. This typically gives fastest performance. If the +:doc:`newton ` command is used in the input script, it can +override these defaults. + +**Or run with the USER-CUDA package by editing an input script:** + +The discussion above for the mpirun/mpiexec command and the requirement +of one MPI task per GPU is the same. + +You must still use the "-c on" :ref:`command-line switch ` to enable the USER-CUDA package. + +Use the :doc:`suffix cuda ` command, or you can explicitly add a +"cuda" suffix to individual styles in your input script, e.g. + +.. parsed-literal:: + + pair_style lj/cut/cuda 2.5 + +You only need to use the :doc:`package cuda ` command if you +wish to change any of its option defaults, including the number of +GPUs/node (default = 1), as set by the "-c on" :ref:`command-line switch `. + +**Speed-ups to expect:** + +The performance of a GPU versus a multi-core CPU is a function of your +hardware, which pair style is used, the number of atoms/GPU, and the +precision used on the GPU (double, single, mixed). + +See the `Benchmark page `_ of the +LAMMPS web site for performance of the USER-CUDA package on different +hardware. + +**Guidelines for best performance:** + +* The USER-CUDA package offers more speed-up relative to CPU performance + when the number of atoms per GPU is large, e.g. on the order of tens + or hundreds of 1000s. +* As noted above, this package will continue to run a simulation + entirely on the GPU(s) (except for inter-processor MPI communication), + for multiple timesteps, until a CPU calculation is required, either by + a fix or compute that is non-GPU-ized, or until output is performed + (thermo or dump snapshot or restart file). The less often this + occurs, the faster your simulation will run. +Restrictions +"""""""""""" + + +None. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/accelerate_gpu.txt b/doc/_sources/accelerate_gpu.txt new file mode 100644 index 0000000000..924768ce5f --- /dev/null +++ b/doc/_sources/accelerate_gpu.txt @@ -0,0 +1,249 @@ +:doc:`Return to Section accelerate overview ` + +5.GPU package +------------- + +The GPU package was developed by Mike Brown at ORNL and his +collaborators, particularly Trung Nguyen (ORNL). It provides GPU +versions of many pair styles, including the 3-body Stillinger-Weber +pair style, and for :doc:`kspace_style pppm ` for +long-range Coulombics. It has the following general features: + +* It is designed to exploit common GPU hardware configurations where one + or more GPUs are coupled to many cores of one or more multi-core CPUs, + e.g. within a node of a parallel machine. +* Atom-based data (e.g. coordinates, forces) moves back-and-forth + between the CPU(s) and GPU every timestep. +* Neighbor lists can be built on the CPU or on the GPU +* The charge assignement and force interpolation portions of PPPM can be + run on the GPU. The FFT portion, which requires MPI communication + between processors, runs on the CPU. +* Asynchronous force computations can be performed simultaneously on the + CPU(s) and GPU. +* It allows for GPU computations to be performed in single or double + precision, or in mixed-mode precision, where pairwise forces are + computed in single precision, but accumulated into double-precision + force vectors. +* LAMMPS-specific code is in the GPU package. It makes calls to a + generic GPU library in the lib/gpu directory. This library provides + NVIDIA support as well as more general OpenCL support, so that the + same functionality can eventually be supported on a variety of GPU + hardware. +Here is a quick overview of how to use the GPU package: + +* build the library in lib/gpu for your GPU hardware wity desired precision +* include the GPU package and build LAMMPS +* use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU +* specify the # of GPUs per node +* use GPU styles in your input script + +The latter two steps can be done using the "-pk gpu" and "-sf gpu" +:ref:`command-line switches ` respectively. Or +the effect of the "-pk" or "-sf" switches can be duplicated by adding +the :doc:`package gpu ` or :doc:`suffix gpu ` commands +respectively to your input script. + +**Required hardware/software:** + +To use this package, you currently need to have an NVIDIA GPU and +install the NVIDIA Cuda software on your system: + +* Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information +* Go to http://www.nvidia.com/object/cuda_get.html +* Install a driver and toolkit appropriate for your system (SDK is not necessary) +* Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to list supported devices and properties + +**Building LAMMPS with the GPU package:** + +This requires two steps (a,b): build the GPU library, then build +LAMMPS with the GPU package. + +You can do both these steps in one line, using the src/Make.py script, +described in :ref:`Section 2.4 ` of the manual. +Type "Make.py -h" for help. If run from the src directory, this +command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the +starting Makefile.machine: + +.. parsed-literal:: + + Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi + +Or you can follow these two (a,b) steps: + +(a) Build the GPU library + +The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in +lib/gpu) appropriate for your system. You should pay special +attention to 3 settings in this makefile. + +* CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system +* CUDA_ARCH = needs to be appropriate to your GPUs +* CUDA_PREC = precision (double, mixed, single) you desire + +See lib/gpu/Makefile.linux.double for examples of the ARCH settings +for different GPU choices, e.g. Fermi vs Kepler. It also lists the +possible precision settings: + +.. parsed-literal:: + + CUDA_PREC = -D_SINGLE_SINGLE # single precision for all calculations + CUDA_PREC = -D_DOUBLE_DOUBLE # double precision for all calculations + CUDA_PREC = -D_SINGLE_DOUBLE # accumulation of forces, etc, in double + +The last setting is the mixed mode referred to above. Note that your +GPU must support double precision to use either the 2nd or 3rd of +these settings. + +To build the library, type: + +.. parsed-literal:: + + make -f Makefile.machine + +If successful, it will produce the files libgpu.a and Makefile.lammps. + +The latter file has 3 settings that need to be appropriate for the +paths and settings for the CUDA system software on your machine. +Makefile.lammps is a copy of the file specified by the EXTRAMAKE +setting in Makefile.machine. You can change EXTRAMAKE or create your +own Makefile.lammps.machine if needed. + +Note that to change the precision of the GPU library, you need to +re-build the entire library. Do a "clean" first, e.g. "make -f +Makefile.linux clean", followed by the make command above. + +(b) Build LAMMPS with the GPU package + +.. parsed-literal:: + + cd lammps/src + make yes-gpu + make machine + +No additional compile/link flags are needed in Makefile.machine. + +Note that if you change the GPU library precision (discussed above) +and rebuild the GPU library, then you also need to re-install the GPU +package and re-build LAMMPS, so that all affected files are +re-compiled and linked to the new GPU library. + +**Run with the GPU package from the command line:** + +The mpirun or mpiexec command sets the total number of MPI tasks used +by LAMMPS (one or multiple per compute node) and the number of MPI +tasks used per node. E.g. the mpirun command in MPICH does this via +its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. + +When using the GPU package, you cannot assign more than one GPU to a +single MPI task. However multiple MPI tasks can share the same GPU, +and in many cases it will be more efficient to run this way. Likewise +it may be more efficient to use less MPI tasks/node than the available +# of CPU cores. Assignment of multiple MPI tasks to a GPU will happen +automatically if you create more MPI tasks/node than there are +GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be +shared by 4 MPI tasks. + +Use the "-sf gpu" :ref:`command-line switch `, +which will automatically append "gpu" to styles that support it. Use +the "-pk gpu Ng" :ref:`command-line switch ` to +set Ng = # of GPUs/node to use. + +.. parsed-literal:: + + lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU + mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node + mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes + +Note that if the "-sf gpu" switch is used, it also issues a default +:doc:`package gpu 1 ` command, which sets the number of +GPUs/node to 1. + +Using the "-pk" switch explicitly allows for setting of the number of +GPUs/node to use and additional options. Its syntax is the same as +same as the "package gpu" command. See the :doc:`package ` +command doc page for details, including the default values used for +all its options if it is not specified. + +Note that the default for the :doc:`package gpu ` command is to +set the Newton flag to "off" pairwise interactions. It does not +affect the setting for bonded interactions (LAMMPS default is "on"). +The "off" setting for pairwise interaction is currently required for +GPU package pair styles. + +**Or run with the GPU package by editing an input script:** + +The discussion above for the mpirun/mpiexec command, MPI tasks/node, +and use of multiple MPI tasks/GPU is the same. + +Use the :doc:`suffix gpu ` command, or you can explicitly add an +"gpu" suffix to individual styles in your input script, e.g. + +.. parsed-literal:: + + pair_style lj/cut/gpu 2.5 + +You must also use the :doc:`package gpu ` command to enable the +GPU package, unless the "-sf gpu" or "-pk gpu" :ref:`command-line switches ` were used. It specifies the +number of GPUs/node to use, as well as other options. + +**Speed-ups to expect:** + +The performance of a GPU versus a multi-core CPU is a function of your +hardware, which pair style is used, the number of atoms/GPU, and the +precision used on the GPU (double, single, mixed). + +See the `Benchmark page `_ of the +LAMMPS web site for performance of the GPU package on various +hardware, including the Titan HPC platform at ORNL. + +You should also experiment with how many MPI tasks per GPU to use to +give the best performance for your problem and machine. This is also +a function of the problem size and the pair style being using. +Likewise, you should experiment with the precision setting for the GPU +library to see if single or mixed precision will give accurate +results, since they will typically be faster. + +**Guidelines for best performance:** + +* Using multiple MPI tasks per GPU will often give the best performance, + as allowed my most multi-core CPU/GPU configurations. +* If the number of particles per MPI task is small (e.g. 100s of + particles), it can be more efficient to run with fewer MPI tasks per + GPU, even if you do not use all the cores on the compute node. +* The :doc:`package gpu ` command has several options for tuning + performance. Neighbor lists can be built on the GPU or CPU. Force + calculations can be dynamically balanced across the CPU cores and + GPUs. GPU-specific settings can be made which can be optimized + for different hardware. See the :doc:`packakge ` command + doc page for details. +* As described by the :doc:`package gpu ` command, GPU + accelerated pair styles can perform computations asynchronously with + CPU computations. The "Pair" time reported by LAMMPS will be the + maximum of the time required to complete the CPU pair style + computations and the time required to complete the GPU pair style + computations. Any time spent for GPU-enabled pair styles for + computations that run simultaneously with :doc:`bond `, + :doc:`angle `, :doc:`dihedral `, + :doc:`improper `, and :doc:`long-range ` + calculations will not be included in the "Pair" time. +* When the *mode* setting for the package gpu command is force/neigh, + the time for neighbor list calculations on the GPU will be added into + the "Pair" time, not the "Neigh" time. An additional breakdown of the + times required for various tasks on the GPU (data copy, neighbor + calculations, force computations, etc) are output only with the LAMMPS + screen output (not in the log file) at the end of each run. These + timings represent total time spent on the GPU for each routine, + regardless of asynchronous CPU calculations. +* The output section "GPU Time Info (average)" reports "Max Mem / Proc". + This is the maximum memory used at one time on the GPU for data + storage by a single MPI process. +Restrictions +"""""""""""" + + +None. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/accelerate_intel.txt b/doc/_sources/accelerate_intel.txt new file mode 100644 index 0000000000..680a1a4e92 --- /dev/null +++ b/doc/_sources/accelerate_intel.txt @@ -0,0 +1,317 @@ +:doc:`Return to Section accelerate overview ` + +5.USER-INTEL package +-------------------- + +The USER-INTEL package was developed by Mike Brown at Intel +Corporation. It provides two methods for accelerating simulations, +depending on the hardware you have. The first is acceleration on +Intel(R) CPUs by running in single, mixed, or double precision with +vectorization. The second is acceleration on Intel(R) Xeon Phi(TM) +coprocessors via offloading neighbor list and non-bonded force +calculations to the Phi. The same C++ code is used in both cases. +When offloading to a coprocessor from a CPU, the same routine is run +twice, once on the CPU and once with an offload flag. + +Note that the USER-INTEL package supports use of the Phi in "offload" +mode, not "native" mode like the :doc:`KOKKOS package `. + +Also note that the USER-INTEL package can be used in tandem with the +:doc:`USER-OMP package `. This is useful when +offloading pair style computations to the Phi, so that other styles +not supported by the USER-INTEL package, e.g. bond, angle, dihedral, +improper, and long-range electrostatics, can run simultaneously in +threaded mode on the CPU cores. Since less MPI tasks than CPU cores +will typically be invoked when running with coprocessors, this enables +the extra CPU cores to be used for useful computation. + +As illustrated below, if LAMMPS is built with both the USER-INTEL and +USER-OMP packages, this dual mode of operation is made easier to use, +via the "-suffix hybrid intel omp" :ref:`command-line switch ` or the :doc:`suffix hybrid intel omp ` command. Both set a second-choice suffix to "omp" so +that styles from the USER-INTEL package will be used if available, +with styles from the USER-OMP package as a second choice. + +Here is a quick overview of how to use the USER-INTEL package for CPU +acceleration, assuming one or more 16-core nodes. More details +follow. + +.. parsed-literal:: + + use an Intel compiler + use these CCFLAGS settings in Makefile.machine: -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits + use these LINKFLAGS settings in Makefile.machine: -fopenmp, -xHost + make yes-user-intel yes-user-omp # including user-omp is optional + make mpi # build with the USER-INTEL package, if settings (including compiler) added to Makefile.mpi + make intel_cpu # or Makefile.intel_cpu already has settings, uses Intel MPI wrapper + Make.py -v -p intel omp -intel cpu -a file mpich_icc # or one-line build via Make.py for MPICH + Make.py -v -p intel omp -intel cpu -a file ompi_icc # or for OpenMPI + Make.py -v -p intel omp -intel cpu -a file intel_cpu # or for Intel MPI wrapper + +.. parsed-literal:: + + lmp_machine -sf intel -pk intel 0 omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, no USER-OMP + mpirun -np 32 lmp_machine -sf intel -in in.script # 2 nodess, 16 MPI tasks/node, no threads, no USER-OMP + lmp_machine -sf hybrid intel omp -pk intel 0 omp 16 -pk omp 16 -in in.script # 1 node, 1 MPI task/node, 16 threads/task, with USER-OMP + mpirun -np 32 -ppn 4 lmp_machine -sf hybrid intel omp -pk omp 4 -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task, with USER-OMP + +Here is a quick overview of how to use the USER-INTEL package for the +same CPUs as above (16 cores/node), with an additional Xeon Phi(TM) +coprocessor per node. More details follow. + +.. parsed-literal:: + + Same as above for building, with these additions/changes: + add the flag -DLMP_INTEL_OFFLOAD to CCFLAGS in Makefile.machine + add the flag -offload to LINKFLAGS in Makefile.machine + for Make.py change "-intel cpu" to "-intel phi", and "file intel_cpu" to "file intel_phi" + +.. parsed-literal:: + + mpirun -np 32 lmp_machine -sf intel -pk intel 1 -in in.script # 2 nodes, 16 MPI tasks/node, 240 total threads on coprocessor, no USER-OMP + mpirun -np 16 -ppn 8 lmp_machine -sf intel -pk intel 1 omp 2 -in in.script # 2 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, no USER-OMP + mpirun -np 32 -ppn 8 lmp_machine -sf hybrid intel omp -pk intel 1 omp 2 -pk omp 2 -in in.script # 4 nodes, 8 MPI tasks/node, 2 threads/task, 240 total threads on coprocessor, with USER-OMP + +**Required hardware/software:** + +Your compiler must support the OpenMP interface. Use of an Intel(R) +C++ compiler is recommended, but not required. However, g++ will not +recognize some of the settings listed above, so they cannot be used. +Optimizations for vectorization have only been tested with the +Intel(R) compiler. Use of other compilers may not result in +vectorization, or give poor performance. + +The recommended version of the Intel(R) compiler is 14.0.1.106. +Versions 15.0.1.133 and later are also supported. If using Intel(R) +MPI, versions 15.0.2.044 and later are recommended. + +To use the offload option, you must have one or more Intel(R) Xeon +Phi(TM) coprocessors and use an Intel(R) C++ compiler. + +**Building LAMMPS with the USER-INTEL package:** + +The lines above illustrate how to include/build with the USER-INTEL +package, for either CPU or Phi support, in two steps, using the "make" +command. Or how to do it with one command via the src/Make.py script, +described in :ref:`Section 2.4 ` of the manual. +Type "Make.py -h" for help. Because the mechanism for specifing what +compiler to use (Intel in this case) is different for different MPI +wrappers, 3 versions of the Make.py command are shown. + +Note that if you build with support for a Phi coprocessor, the same +binary can be used on nodes with or without coprocessors installed. +However, if you do not have coprocessors on your system, building +without offload support will produce a smaller binary. + +If you also build with the USER-OMP package, you can use styles from +both packages, as described below. + +Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must +include "-fopenmp". Likewise, if you use an Intel compiler, the +CCFLAGS setting must include "-restrict". For Phi support, the +"-DLMP_INTEL_OFFLOAD" (CCFLAGS) and "-offload" (LINKFLAGS) settings +are required. The other settings listed above are optional, but will +typically improve performance. The Make.py command will add all of +these automatically. + +If you are compiling on the same architecture that will be used for +the runs, adding the flag *-xHost* to CCFLAGS enables vectorization +with the Intel(R) compiler. Otherwise, you must provide the correct +compute node architecture to the -x option (e.g. -xAVX). + +Example machines makefiles Makefile.intel_cpu and Makefile.intel_phi +are included in the src/MAKE/OPTIONS directory with settings that +perform well with the Intel(R) compiler. The latter has support for +offload to Phi coprocessors; the former does not. + +**Run with the USER-INTEL package from the command line:** + +The mpirun or mpiexec command sets the total number of MPI tasks used +by LAMMPS (one or multiple per compute node) and the number of MPI +tasks used per node. E.g. the mpirun command in MPICH does this via +its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. + +If you compute (any portion of) pairwise interactions using USER-INTEL +pair styles on the CPU, or use USER-OMP styles on the CPU, you need to +choose how many OpenMP threads per MPI task to use. If both packages +are used, it must be done for both packages, and the same thread count +value should be used for both. Note that the product of MPI tasks * +threads/task should not exceed the physical number of cores (on a +node), otherwise performance will suffer. + +When using the USER-INTEL package for the Phi, you also need to +specify the number of coprocessor/node and optionally the number of +coprocessor threads per MPI task to use. Note that coprocessor +threads (which run on the coprocessor) are totally independent from +OpenMP threads (which run on the CPU). The default values for the +settings that affect coprocessor threads are typically fine, as +discussed below. + +As in the lines above, use the "-sf intel" or "-sf hybrid intel omp" +:ref:`command-line switch `, which will +automatically append "intel" to styles that support it. In the second +case, "omp" will be appended if an "intel" style does not exist. + +Note that if either switch is used, it also invokes a default command: +:doc:`package intel 1 `. If the "-sf hybrid intel omp" switch +is used, the default USER-OMP command :doc:`package omp 0 ` is +also invoked (if LAMMPS was built with USER-OMP). Both set the number +of OpenMP threads per MPI task via the OMP_NUM_THREADS environment +variable. The first command sets the number of Xeon Phi(TM) +coprocessors/node to 1 (ignored if USER-INTEL is built for CPU-only), +and the precision mode to "mixed" (default value). + +You can also use the "-pk intel Nphi" :ref:`command-line switch ` to explicitly set Nphi = # of Xeon +Phi(TM) coprocessors/node, as well as additional options. Nphi should +be >= 1 if LAMMPS was built with coprocessor support, otherswise Nphi += 0 for a CPU-only build. All the available coprocessor threads on +each Phi will be divided among MPI tasks, unless the *tptask* option +of the "-pk intel" :ref:`command-line switch ` is +used to limit the coprocessor threads per MPI task. See the :doc:`package intel ` command for details, including the default values +used for all its options if not specified, and how to set the number +of OpenMP threads via the OMP_NUM_THREADS environment variable if +desired. + +If LAMMPS was built with the USER-OMP package, you can also use the +"-pk omp Nt" :ref:`command-line switch ` to +explicitly set Nt = # of OpenMP threads per MPI task to use, as well +as additional options. Nt should be the same threads per MPI task as +set for the USER-INTEL package, e.g. via the "-pk intel Nphi omp Nt" +command. Again, see the :doc:`package omp ` command for +details, including the default values used for all its options if not +specified, and how to set the number of OpenMP threads via the +OMP_NUM_THREADS environment variable if desired. + +**Or run with the USER-INTEL package by editing an input script:** + +The discussion above for the mpirun/mpiexec command, MPI tasks/node, +OpenMP threads per MPI task, and coprocessor threads per MPI task is +the same. + +Use the :doc:`suffix intel ` or :doc:`suffix hybrid intel omp ` commands, or you can explicitly add an "intel" or +"omp" suffix to individual styles in your input script, e.g. + +.. parsed-literal:: + + pair_style lj/cut/intel 2.5 + +You must also use the :doc:`package intel ` command, unless the +"-sf intel" or "-pk intel" :ref:`command-line switches ` were used. It specifies how many +coprocessors/node to use, as well as other OpenMP threading and +coprocessor options. The :doc:`package ` doc page explains how +to set the number of OpenMP threads via an environment variable if +desired. + +If LAMMPS was also built with the USER-OMP package, you must also use +the :doc:`package omp ` command to enable that package, unless +the "-sf hybrid intel omp" or "-pk omp" :ref:`command-line switches ` were used. It specifies how many +OpenMP threads per MPI task to use (should be same as the setting for +the USER-INTEL package), as well as other options. Its doc page +explains how to set the number of OpenMP threads via an environment +variable if desired. + +**Speed-ups to expect:** + +If LAMMPS was not built with coprocessor support (CPU only) when +including the USER-INTEL package, then acclerated styles will run on +the CPU using vectorization optimizations and the specified precision. +This may give a substantial speed-up for a pair style, particularly if +mixed or single precision is used. + +If LAMMPS was built with coproccesor support, the pair styles will run +on one or more Intel(R) Xeon Phi(TM) coprocessors (per node). The +performance of a Xeon Phi versus a multi-core CPU is a function of +your hardware, which pair style is used, the number of +atoms/coprocessor, and the precision used on the coprocessor (double, +single, mixed). + +See the `Benchmark page `_ of the +LAMMPS web site for performance of the USER-INTEL package on different +hardware. + +.. note:: + + Setting core affinity is often used to pin MPI tasks and OpenMP + threads to a core or group of cores so that memory access can be + uniform. Unless disabled at build time, affinity for MPI tasks and + OpenMP threads on the host (CPU) will be set by default on the host + when using offload to a coprocessor. In this case, it is unnecessary + to use other methods to control affinity (e.g. taskset, numactl, + I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script with + the *no_affinity* option to the :doc:`package intel ` command + or by disabling the option at build time (by adding + -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile). + Disabling this option is not recommended, especially when running on a + machine with hyperthreading disabled. + +**Guidelines for best performance on an Intel(R) Xeon Phi(TM) +coprocessor:** + +* The default for the :doc:`package intel ` command is to have + all the MPI tasks on a given compute node use a single Xeon Phi(TM) + coprocessor. In general, running with a large number of MPI tasks on + each node will perform best with offload. Each MPI task will + automatically get affinity to a subset of the hardware threads + available on the coprocessor. For example, if your card has 61 cores, + with 60 cores available for offload and 4 hardware threads per core + (240 total threads), running with 24 MPI tasks per node will cause + each MPI task to use a subset of 10 threads on the coprocessor. Fine + tuning of the number of threads to use per MPI task or the number of + threads to use per core can be accomplished with keyword settings of + the :doc:`package intel ` command. +* If desired, only a fraction of the pair style computation can be + offloaded to the coprocessors. This is accomplished by using the + *balance* keyword in the :doc:`package intel ` command. A + balance of 0 runs all calculations on the CPU. A balance of 1 runs + all calculations on the coprocessor. A balance of 0.5 runs half of + the calculations on the coprocessor. Setting the balance to -1 (the + default) will enable dynamic load balancing that continously adjusts + the fraction of offloaded work throughout the simulation. This option + typically produces results within 5 to 10 percent of the optimal fixed + balance. +* When using offload with CPU hyperthreading disabled, it may help + performance to use fewer MPI tasks and OpenMP threads than available + cores. This is due to the fact that additional threads are generated + internally to handle the asynchronous offload tasks. +* If running short benchmark runs with dynamic load balancing, adding a + short warm-up run (10-20 steps) will allow the load-balancer to find a + near-optimal setting that will carry over to additional runs. +* If pair computations are being offloaded to an Intel(R) Xeon Phi(TM) + coprocessor, a diagnostic line is printed to the screen (not to the + log file), during the setup phase of a run, indicating that offload + mode is being used and indicating the number of coprocessor threads + per MPI task. Additionally, an offload timing summary is printed at + the end of each run. When offloading, the frequency for :doc:`atom sorting ` is changed to 1 so that the per-atom data is + effectively sorted at every rebuild of the neighbor lists. +* For simulations with long-range electrostatics or bond, angle, + dihedral, improper calculations, computation and data transfer to the + coprocessor will run concurrently with computations and MPI + communications for these calculations on the host CPU. The USER-INTEL + package has two modes for deciding which atoms will be handled by the + coprocessor. This choice is controlled with the *ghost* keyword of + the :doc:`package intel ` command. When set to 0, ghost atoms + (atoms at the borders between MPI tasks) are not offloaded to the + card. This allows for overlap of MPI communication of forces with + computation on the coprocessor when the :doc:`newton ` setting + is "on". The default is dependent on the style being used, however, + better performance may be achieved by setting this option + explictly. +Restrictions +"""""""""""" + + +When offloading to a coprocessor, :doc:`hybrid ` styles +that require skip lists for neighbor builds cannot be offloaded. +Using :doc:`hybrid/overlay ` is allowed. Only one intel +accelerated style may be used with hybrid styles. +:doc:`Special_bonds ` exclusion lists are not currently +supported with offload, however, the same effect can often be +accomplished by setting cutoffs for excluded atom types to 0. None of +the pair styles in the USER-INTEL package currently support the +"inner", "middle", "outer" options for rRESPA integration via the +:doc:`run_style respa ` command; only the "pair" option is +supported. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/accelerate_kokkos.txt b/doc/_sources/accelerate_kokkos.txt new file mode 100644 index 0000000000..7f137b42ab --- /dev/null +++ b/doc/_sources/accelerate_kokkos.txt @@ -0,0 +1,527 @@ +:doc:`Return to Section accelerate overview ` + +5.KOKKOS package +---------------- + +The KOKKOS package was developed primarily by Christian Trott (Sandia) +with contributions of various styles by others, including Sikandar +Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia). The +underlying Kokkos library was written primarily by Carter Edwards, +Christian Trott, and Dan Sunderland (all Sandia). + +The KOKKOS package contains versions of pair, fix, and atom styles +that use data structures and macros provided by the Kokkos library, +which is included with LAMMPS in lib/kokkos. + +The Kokkos library is part of +`Trilinos `_ and can also be +downloaded from `Github `_. Kokkos is a +templated C++ library that provides two key abstractions for an +application like LAMMPS. First, it allows a single implementation of +an application kernel (e.g. a pair style) to run efficiently on +different kinds of hardware, such as a GPU, Intel Phi, or many-core +CPU. + +The Kokkos library also provides data abstractions to adjust (at +compile time) the memory layout of basic data structures like 2d and +3d arrays and allow the transparent utilization of special hardware +load and store operations. Such data structures are used in LAMMPS to +store atom coordinates or forces or neighbor lists. The layout is +chosen to optimize performance on different platforms. Again this +functionality is hidden from the developer, and does not affect how +the kernel is coded. + +These abstractions are set at build time, when LAMMPS is compiled with +the KOKKOS package installed. All Kokkos operations occur within the +context of an individual MPI task running on a single node of the +machine. The total number of MPI tasks used by LAMMPS (one or +multiple per compute node) is set in the usual manner via the mpirun +or mpiexec commands, and is independent of Kokkos. + +Kokkos currently provides support for 3 modes of execution (per MPI +task). These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs), +and OpenMP (for Intel Phi). Note that the KOKKOS package supports +running on the Phi in native mode, not offload mode like the +USER-INTEL package supports. You choose the mode at build time to +produce an executable compatible with specific hardware. + +Here is a quick overview of how to use the KOKKOS package +for CPU acceleration, assuming one or more 16-core nodes. +More details follow. + +use a C++11 compatible compiler +make yes-kokkos +make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package +make kokkos_omp # or Makefile.kokkos_omp already has variable set +Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py + +.. parsed-literal:: + + mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads + mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task + mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task + mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task + +* specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support +* include the KOKKOS package and build LAMMPS +* enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script + +Here is a quick overview of how to use the KOKKOS package for GPUs, +assuming one or more nodes, each with 16 cores and a GPU. More +details follow. + +discuss use of NVCC, which Makefiles to examine + +use a C++11 compatible compiler +KOKKOS_DEVICES = Cuda, OpenMP +KOKKOS_ARCH = Kepler35 +make yes-kokkos +make machine +Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda + +.. parsed-literal:: + + mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU + mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes + +.. parsed-literal:: + + mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU + mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes + +Here is a quick overview of how to use the KOKKOS package +for the Intel Phi: + +.. parsed-literal:: + + use a C++11 compatible compiler + KOKKOS_DEVICES = OpenMP + KOKKOS_ARCH = KNC + make yes-kokkos + make machine + Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi + +host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading): +mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240 +mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240 +mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240 +mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis + +**Required hardware/software:** + +Kokkos support within LAMMPS must be built with a C++11 compatible +compiler. If using gcc, version 4.8.1 or later is required. + +To build with Kokkos support for CPUs, your compiler must support the +OpenMP interface. You should have one or more multi-core CPUs so that +multiple threads can be launched by each MPI task running on a CPU. + +To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software +version 6.5 or later must be installed on your system. See the +discussion for the :doc:`USER-CUDA ` and +:doc:`GPU ` packages for details of how to check and do +this. + +.. note:: + + For good performance of the KOKKOS package on GPUs, you must + have Kepler generation GPUs (or later). The Kokkos library exploits + texture cache options not supported by Telsa generation GPUs (or + older). + +To build with Kokkos support for Intel Xeon Phi coprocessors, your +sysmte must be configured to use them in "native" mode, not "offload" +mode like the USER-INTEL package supports. + +**Building LAMMPS with the KOKKOS package:** + +You must choose at build time whether to build for CPUs (OpenMP), +GPUs, or Phi. + +You can do any of these in one line, using the src/Make.py script, +described in :ref:`Section 2.4 ` of the manual. +Type "Make.py -h" for help. If run from the src directory, these +commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and +lmp_kokkos_phi. Note that the OMP and PHI options use +src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA +option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda. + +The latter two steps can be done using the "-k on", "-pk kokkos" and +"-sf kk" :ref:`command-line switches ` +respectively. Or the effect of the "-pk" or "-sf" switches can be +duplicated by adding the :doc:`package kokkos ` or :doc:`suffix kk ` commands respectively to your input script. + +Or you can follow these steps: + +CPU-only (run all-MPI or with OpenMP threading): + +.. parsed-literal:: + + cd lammps/src + make yes-kokkos + make g++ KOKKOS_DEVICES=OpenMP + +Intel Xeon Phi: + +.. parsed-literal:: + + cd lammps/src + make yes-kokkos + make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC + +CPUs and GPUs: + +.. parsed-literal:: + + cd lammps/src + make yes-kokkos + make cuda KOKKOS_DEVICES=Cuda + +These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the +make command line which requires a GNU-compatible make command. Try +"gmake" if your system's standard make complains. + +.. note:: + + If you build using make line variables and re-build LAMMPS twice + with different KOKKOS options and the *same* target, e.g. g++ in the + first two examples above, then you *must* perform a "make clean-all" + or "make clean-machine" before each build. This is to force all the + KOKKOS-dependent files to be re-compiled with the new options. + +You can also hardwire these make variables in the specified machine +makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above, +with a line like: + +.. parsed-literal:: + + KOKKOS_ARCH = KNC + +Note that if you build LAMMPS multiple times in this manner, using +different KOKKOS options (defined in different machine makefiles), you +do not have to worry about doing a "clean" in between. This is +because the targets will be different. + +.. note:: + + The 3rd example above for a GPU, uses a different machine + makefile, in this case src/MAKE/Makefile.cuda, which is included in + the LAMMPS distribution. To build the KOKKOS package for a GPU, this + makefile must use the NVIDA "nvcc" compiler. And it must have a + KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and + installed software. Typical values for KOKKOS_ARCH are given below, + as well as other settings that must be included in the machine + makefile, if you create your own. + +.. note:: + + Currently, there are no precision options with the KOKKOS + package. All compilation and computation is performed in double + precision. + +There are other allowed options when building with the KOKKOS package. +As above, they can be set either as variables on the make command line +or in Makefile.machine. This is the full list of options, including +those discussed above, Each takes a value shown below. The +default value is listed, which is set in the +lib/kokkos/Makefile.kokkos file. + +#Default settings specific options +#Options: force_uvm,use_ldg,rdc + +* KOKKOS_DEVICES, values = *OpenMP*, *Serial*, *Pthreads*, *Cuda*, default = *OpenMP* +* KOKKOS_ARCH, values = *KNC*, *SNB*, *HSW*, *Kepler*, *Kepler30*, *Kepler32*, *Kepler35*, *Kepler37*, *Maxwell*, *Maxwell50*, *Maxwell52*, *Maxwell53*, *ARMv8*, *BGQ*, *Power7*, *Power8*, default = *none* +* KOKKOS_DEBUG, values = *yes*, *no*, default = *no* +* KOKKOS_USE_TPLS, values = *hwloc*, *librt*, default = *none* +* KOKKOS_CUDA_OPTIONS, values = *force_uvm*, *use_ldg*, *rdc* + +KOKKOS_DEVICE sets the parallelization method used for Kokkos code +(within LAMMPS). KOKKOS_DEVICES=OpenMP means that OpenMP will be +used. KOKKOS_DEVICES=Pthreads means that pthreads will be used. +KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used. + +If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE +directory must use "nvcc" as its compiler, via its CC setting. For +best performance its CCFLAGS setting should use -O3 and have a +KOKKOS_ARCH setting that matches the compute capability of your NVIDIA +hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note +the minimal required compute capability is 2.0, but this will give +signicantly reduced performance compared to Kepler generation GPUs +with compute capability 3.x. For the LINK setting, "nvcc" should not +be used; instead use g++ or another compiler suitable for linking C++ +applications. Often you will want to use your MPI compiler wrapper +for this setting (i.e. mpicxx). Finally, the lo-level Makefile must +also have a "Compilation rule" for creating *.o files from *.cu files. +See src/Makefile.cuda for an example of a lo-level Makefile with all +of these settings. + +KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not +migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be +used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not +necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP +provides alternative methods via environment variables for binding +threads to hardware cores. More info on binding threads to cores is +given in :ref:`this section `. + +KOKKOS_ARCH=KNC enables compiler switches needed when compling for an +Intel Phi processor. + +KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism +on most Unix platforms. This library is not available on all +platforms. + +KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style +within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time +debugging information that can be useful. It also enables runtime +bounds checking on Kokkos data structures. + +KOKKOS_CUDA_OPTIONS are additional options for CUDA. + +For more information on Kokkos see the Kokkos programmers' guide here: +/lib/kokkos/doc/Kokkos_PG.pdf. + +**Run with the KOKKOS package from the command line:** + +The mpirun or mpiexec command sets the total number of MPI tasks used +by LAMMPS (one or multiple per compute node) and the number of MPI +tasks used per node. E.g. the mpirun command in MPICH does this via +its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. + +When using KOKKOS built with host=OMP, you need to choose how many +OpenMP threads per MPI task will be used (via the "-k" command-line +switch discussed below). Note that the product of MPI tasks * OpenMP +threads/task should not exceed the physical number of cores (on a +node), otherwise performance will suffer. + +When using the KOKKOS package built with device=CUDA, you must use +exactly one MPI task per physical GPU. + +When using the KOKKOS package built with host=MIC for Intel Xeon Phi +coprocessor support you need to insure there are one or more MPI tasks +per coprocessor, and choose the number of coprocessor threads to use +per MPI task (via the "-k" command-line switch discussed below). The +product of MPI tasks * coprocessor threads/task should not exceed the +maximum number of threads the coproprocessor is designed to run, +otherwise performance will suffer. This value is 240 for current +generation Xeon Phi(TM) chips, which is 60 physical cores * 4 +threads/core. Note that with the KOKKOS package you do not need to +specify how many Phi coprocessors there are per node; each +coprocessors is simply treated as running some number of MPI tasks. + +You must use the "-k on" :ref:`command-line switch ` to enable the KOKKOS package. It +takes additional arguments for hardware settings appropriate to your +system. Those arguments are :ref:`documented here `. The two most commonly used +options are: + +.. parsed-literal:: + + -k on t Nt g Ng + +The "t Nt" option applies to host=OMP (even if device=CUDA) and +host=MIC. For host=OMP, it specifies how many OpenMP threads per MPI +task to use with a node. For host=MIC, it specifies how many Xeon Phi +threads per MPI task to use within a node. The default is Nt = 1. +Note that for host=OMP this is effectively MPI-only mode which may be +fine. But for host=MIC you will typically end up using far less than +all the 240 available threads, which could give very poor performance. + +The "g Ng" option applies to device=CUDA. It specifies how many GPUs +per compute node to use. The default is 1, so this only needs to be +specified is you have 2 or more GPUs per compute node. + +The "-k on" switch also issues a "package kokkos" command (with no +additional arguments) which sets various KOKKOS options to default +values, as discussed on the :doc:`package ` command doc page. + +Use the "-sf kk" :ref:`command-line switch `, +which will automatically append "kk" to styles that support it. Use +the "-pk kokkos" :ref:`command-line switch ` if +you wish to change any of the default :doc:`package kokkos ` +optionns set by the "-k on" :ref:`command-line switch `. + +Note that the default for the :doc:`package kokkos ` command is +to use "full" neighbor lists and set the Newton flag to "off" for both +pairwise and bonded interactions. This typically gives fastest +performance. If the :doc:`newton ` command is used in the input +script, it can override the Newton flag defaults. + +However, when running in MPI-only mode with 1 thread per MPI task, it +will typically be faster to use "half" neighbor lists and set the +Newton flag to "on", just as is the case for non-accelerated pair +styles. You can do this with the "-pk" :ref:`command-line switch `. + +**Or run with the KOKKOS package by editing an input script:** + +The discussion above for the mpirun/mpiexec command and setting +appropriate thread and GPU values for host=OMP or host=MIC or +device=CUDA are the same. + +You must still use the "-k on" :ref:`command-line switch ` to enable the KOKKOS package, and +specify its additional arguments for hardware options appopriate to +your system, as documented above. + +Use the :doc:`suffix kk ` command, or you can explicitly add a +"kk" suffix to individual styles in your input script, e.g. + +.. parsed-literal:: + + pair_style lj/cut/kk 2.5 + +You only need to use the :doc:`package kokkos ` command if you +wish to change any of its option defaults, as set by the "-k on" +:ref:`command-line switch `. + +**Speed-ups to expect:** + +The performance of KOKKOS running in different modes is a function of +your hardware, which KOKKOS-enable styles are used, and the problem +size. + +Generally speaking, the following rules of thumb apply: + +* When running on CPUs only, with a single thread per MPI task, + performance of a KOKKOS style is somewhere between the standard + (un-accelerated) styles (MPI-only mode), and those provided by the + USER-OMP package. However the difference between all 3 is small (less + than 20%). +* When running on CPUs only, with multiple threads per MPI task, + performance of a KOKKOS style is a bit slower than the USER-OMP + package. +* When running on GPUs, KOKKOS is typically faster than the USER-CUDA + and GPU packages. +* When running on Intel Xeon Phi, KOKKOS is not as fast as + the USER-INTEL package, which is optimized for that hardware. +See the `Benchmark page `_ of the +LAMMPS web site for performance of the KOKKOS package on different +hardware. + +**Guidelines for best performance:** + +Here are guidline for using the KOKKOS package on the different +hardware configurations listed above. + +Many of the guidelines use the :doc:`package kokkos ` command +See its doc page for details and default settings. Experimenting with +its options can provide a speed-up for specific calculations. + +**Running on a multi-core CPU:** + +If N is the number of physical cores/node, then the number of MPI +tasks/node * number of threads/task should not exceed N, and should +typically equal N. Note that the default threads/task is 1, as set by +the "t" keyword of the "-k" :ref:`command-line switch `. If you do not change this, no +additional parallelism (beyond MPI) will be invoked on the host +CPU(s). + +You can compare the performance running in different modes: + +* run with 1 MPI task/node and N threads/task +* run with N MPI tasks/node and 1 thread/task +* run with settings in between these extremes + +Examples of mpirun commands in these modes are shown above. + +When using KOKKOS to perform multi-threading, it is important for +performance to bind both MPI tasks to physical cores, and threads to +physical cores, so they do not migrate during a simulation. + +If you are not certain MPI tasks are being bound (check the defaults +for your MPI installation), binding can be forced with these flags: + +.. parsed-literal:: + + OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ... + Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ... + +For binding threads with the KOKKOS OMP option, use thread affinity +environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or +later, intel 12 or later) setting the environment variable +OMP_PROC_BIND=true should be sufficient. For binding threads with the +KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option, as +discussed in :ref:`Section 2.3.4 ` of the +manual. + +**Running on GPUs:** + +Insure the -arch setting in the machine makefile you are using, +e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software +(see :ref:`this section ` of the manual for +details). + +The -np setting of the mpirun command should set the number of MPI +tasks/node to be equal to the # of physical GPUs on the node. + +Use the "-k" :ref:`command-line switch ` to +specify the number of GPUs per node, and the number of threads per MPI +task. As above for multi-core CPUs (and no GPU), if N is the number +of physical cores/node, then the number of MPI tasks/node * number of +threads/task should not exceed N. With one GPU (and one MPI task) it +may be faster to use less than all the available cores, by setting +threads/task to a smaller value. This is because using all the cores +on a dual-socket node will incur extra cost to copy memory from the +2nd socket to the GPU. + +Examples of mpirun commands that follow these rules are shown above. + +.. note:: + + When using a GPU, you will achieve the best performance if your + input script does not use any fix or compute styles which are not yet + Kokkos-enabled. This allows data to stay on the GPU for multiple + timesteps, without being copied back to the host CPU. Invoking a + non-Kokkos fix or compute, or performing I/O for + :doc:`thermo ` or :doc:`dump ` output will cause data + to be copied back to the CPU. + +You cannot yet assign multiple MPI tasks to the same GPU with the +KOKKOS package. We plan to support this in the future, similar to the +GPU package in LAMMPS. + +You cannot yet use both the host (multi-threaded) and device (GPU) +together to compute pairwise interactions with the KOKKOS package. We +hope to support this in the future, similar to the GPU package in +LAMMPS. + +**Running on an Intel Phi:** + +Kokkos only uses Intel Phi processors in their "native" mode, i.e. +not hosted by a CPU. + +As illustrated above, build LAMMPS with OMP=yes (the default) and +MIC=yes. The latter insures code is correctly compiled for the Intel +Phi. The OMP setting means OpenMP will be used for parallelization on +the Phi, which is currently the best option within Kokkos. In the +future, other options may be added. + +Current-generation Intel Phi chips have either 61 or 57 cores. One +core should be excluded for running the OS, leaving 60 or 56 cores. +Each core is hyperthreaded, so there are effectively N = 240 (4*60) or +N = 224 (4*56) cores to run on. + +The -np setting of the mpirun command sets the number of MPI +tasks/node. The "-k on t Nt" command-line switch sets the number of +threads/task as Nt. The product of these 2 values should be N, i.e. +240 or 224. Also, the number of threads/task should be a multiple of +4 so that logical threads from more than one MPI task do not run on +the same physical core. + +Examples of mpirun commands that follow these rules are shown above. + +Restrictions +"""""""""""" + + +As noted above, if using GPUs, the number of MPI tasks per compute +node should equal to the number of GPUs per compute node. In the +future Kokkos will support assigning multiple MPI tasks to a single +GPU. + +Currently Kokkos does not support AMD GPUs due to limits in the +available backend programming models. Specifically, Kokkos requires +extensive C++ support from the Kernel language. This is expected to +change in the future. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/accelerate_omp.txt b/doc/_sources/accelerate_omp.txt new file mode 100644 index 0000000000..252b10b027 --- /dev/null +++ b/doc/_sources/accelerate_omp.txt @@ -0,0 +1,178 @@ +:doc:`Return to Section accelerate overview ` + +5.USER-OMP package +------------------ + +The USER-OMP package was developed by Axel Kohlmeyer at Temple +University. It provides multi-threaded versions of most pair styles, +nearly all bonded styles (bond, angle, dihedral, improper), several +Kspace styles, and a few fix styles. The package currently uses the +OpenMP interface for multi-threading. + +Here is a quick overview of how to use the USER-OMP package, assuming +one or more 16-core nodes. More details follow. + +.. parsed-literal:: + + use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine + make yes-user-omp + make mpi # build with USER-OMP package, if settings added to Makefile.mpi + make omp # or Makefile.omp already has settings + Make.py -v -p omp -o mpi -a file mpi # or one-line build via Make.py + +.. parsed-literal:: + + lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads + mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task + mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task + +**Required hardware/software:** + +Your compiler must support the OpenMP interface. You should have one +or more multi-core CPUs so that multiple threads can be launched by +each MPI task running on a CPU. + +**Building LAMMPS with the USER-OMP package:** + +The lines above illustrate how to include/build with the USER-OMP +package in two steps, using the "make" command. Or how to do it with +one command via the src/Make.py script, described in :ref:`Section 2.4 ` of the manual. Type "Make.py -h" for +help. + +Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must +include "-fopenmp". Likewise, if you use an Intel compiler, the +CCFLAGS setting must include "-restrict". The Make.py command will +add these automatically. + +**Run with the USER-OMP package from the command line:** + +The mpirun or mpiexec command sets the total number of MPI tasks used +by LAMMPS (one or multiple per compute node) and the number of MPI +tasks used per node. E.g. the mpirun command in MPICH does this via +its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode. + +You need to choose how many OpenMP threads per MPI task will be used +by the USER-OMP package. Note that the product of MPI tasks * +threads/task should not exceed the physical number of cores (on a +node), otherwise performance will suffer. + +As in the lines above, use the "-sf omp" :ref:`command-line switch `, which will automatically append +"omp" to styles that support it. The "-sf omp" switch also issues a +default :doc:`package omp 0 ` command, which will set the +number of threads per MPI task via the OMP_NUM_THREADS environment +variable. + +You can also use the "-pk omp Nt" :ref:`command-line switch `, to explicitly set Nt = # of OpenMP +threads per MPI task to use, as well as additional options. Its +syntax is the same as the :doc:`package omp ` command whose doc +page gives details, including the default values used if it is not +specified. It also gives more details on how to set the number of +threads via the OMP_NUM_THREADS environment variable. + +**Or run with the USER-OMP package by editing an input script:** + +The discussion above for the mpirun/mpiexec command, MPI tasks/node, +and threads/MPI task is the same. + +Use the :doc:`suffix omp ` command, or you can explicitly add an +"omp" suffix to individual styles in your input script, e.g. + +.. parsed-literal:: + + pair_style lj/cut/omp 2.5 + +You must also use the :doc:`package omp ` command to enable the +USER-OMP package. When you do this you also specify how many threads +per MPI task to use. The command doc page explains other options and +how to set the number of threads via the OMP_NUM_THREADS environment +variable. + +**Speed-ups to expect:** + +Depending on which styles are accelerated, you should look for a +reduction in the "Pair time", "Bond time", "KSpace time", and "Loop +time" values printed at the end of a run. + +You may see a small performance advantage (5 to 20%) when running a +USER-OMP style (in serial or parallel) with a single thread per MPI +task, versus running standard LAMMPS with its standard un-accelerated +styles (in serial or all-MPI parallelization with 1 task/core). This +is because many of the USER-OMP styles contain similar optimizations +to those used in the OPT package, described in :doc:`Section accelerate 5.3.6 `. + +With multiple threads/task, the optimal choice of number of MPI +tasks/node and OpenMP threads/task can vary a lot and should always be +tested via benchmark runs for a specific simulation running on a +specific machine, paying attention to guidelines discussed in the next +sub-section. + +A description of the multi-threading strategy used in the USER-OMP +package and some performance examples are `presented here `_ + +**Guidelines for best performance:** + +For many problems on current generation CPUs, running the USER-OMP +package with a single thread/task is faster than running with multiple +threads/task. This is because the MPI parallelization in LAMMPS is +often more efficient than multi-threading as implemented in the +USER-OMP package. The parallel efficiency (in a threaded sense) also +varies for different USER-OMP styles. + +Using multiple threads/task can be more effective under the following +circumstances: + +* Individual compute nodes have a significant number of CPU cores but + the CPU itself has limited memory bandwidth, e.g. for Intel Xeon 53xx + (Clovertown) and 54xx (Harpertown) quad-core processors. Running one + MPI task per CPU core will result in significant performance + degradation, so that running with 4 or even only 2 MPI tasks per node + is faster. Running in hybrid MPI+OpenMP mode will reduce the + inter-node communication bandwidth contention in the same way, but + offers an additional speedup by utilizing the otherwise idle CPU + cores. +* The interconnect used for MPI communication does not provide + sufficient bandwidth for a large number of MPI tasks per node. For + example, this applies to running over gigabit ethernet or on Cray XT4 + or XT5 series supercomputers. As in the aforementioned case, this + effect worsens when using an increasing number of nodes. +* The system has a spatially inhomogeneous particle density which does + not map well to the :doc:`domain decomposition scheme ` or + :doc:`load-balancing ` options that LAMMPS provides. This is + because multi-threading achives parallelism over the number of + particles, not via their distribution in space. +* A machine is being used in "capability mode", i.e. near the point + where MPI parallelism is maxed out. For example, this can happen when + using the :doc:`PPPM solver ` for long-range + electrostatics on large numbers of nodes. The scaling of the KSpace + calculation (see the :doc:`kspace_style ` command) becomes + the performance-limiting factor. Using multi-threading allows less + MPI tasks to be invoked and can speed-up the long-range solver, while + increasing overall performance by parallelizing the pairwise and + bonded calculations via OpenMP. Likewise additional speedup can be + sometimes be achived by increasing the length of the Coulombic cutoff + and thus reducing the work done by the long-range solver. Using the + :doc:`run_style verlet/split ` command, which is compatible + with the USER-OMP package, is an alternative way to reduce the number + of MPI tasks assigned to the KSpace calculation. +Additional performance tips are as follows: + +* The best parallel efficiency from *omp* styles is typically achieved + when there is at least one MPI task per physical CPU chip, i.e. socket + or die. +* It is usually most efficient to restrict threading to a single + socket, i.e. use one or more MPI task per socket. +* NOTE: By default, several current MPI implementations use a processor + affinity setting that restricts each MPI task to a single CPU core. + Using multi-threading in this mode will force all threads to share the + one core and thus is likely to be counterproductive. Instead, binding + MPI tasks to a (multi-core) socket, should solve this issue. +Restrictions +"""""""""""" + + +None. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/accelerate_opt.txt b/doc/_sources/accelerate_opt.txt new file mode 100644 index 0000000000..24355b7aa5 --- /dev/null +++ b/doc/_sources/accelerate_opt.txt @@ -0,0 +1,74 @@ +:doc:`Return to Section accelerate overview ` + +5.OPT package +------------- + +The OPT package was developed by James Fischer (High Performance +Technologies), David Richie, and Vincent Natoli (Stone Ridge +Technologies). It contains a handful of pair styles whose compute() +methods were rewritten in C++ templated form to reduce the overhead +due to if tests and other conditional code. + +Here is a quick overview of how to use the OPT package. More details +follow. + +.. parsed-literal:: + + make yes-opt + make mpi # build with the OPT pacakge + Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py + +.. parsed-literal:: + + lmp_mpi -sf opt -in in.script # run in serial + mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel + +**Required hardware/software:** + +None. + +**Building LAMMPS with the OPT package:** + +The lines above illustrate how to build LAMMPS with the OPT package in +two steps, using the "make" command. Or how to do it with one command +via the src/Make.py script, described in :ref:`Section 2.4 ` of the manual. Type "Make.py -h" for +help. + +Note that if you use an Intel compiler to build with the OPT package, +the CCFLAGS setting in your Makefile.machine must include "-restrict". +The Make.py command will add this automatically. + +**Run with the OPT package from the command line:** + +As in the lines above, use the "-sf opt" :ref:`command-line switch `, which will automatically append +"opt" to styles that support it. + +**Or run with the OPT package by editing an input script:** + +Use the :doc:`suffix opt ` command, or you can explicitly add an +"opt" suffix to individual styles in your input script, e.g. + +.. parsed-literal:: + + pair_style lj/cut/opt 2.5 + +**Speed-ups to expect:** + +You should see a reduction in the "Pair time" value printed at the end +of a run. On most machines for reasonable problem sizes, it will be a +5 to 20% savings. + +**Guidelines for best performance:** + +Just try out an OPT pair style to see how it performs. + +Restrictions +"""""""""""" + + +None. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_charmm.txt b/doc/_sources/angle_charmm.txt new file mode 100644 index 0000000000..b4384a91dc --- /dev/null +++ b/doc/_sources/angle_charmm.txt @@ -0,0 +1,113 @@ +.. index:: angle_style charmm + +angle_style charmm command +========================== + +angle_style charmm/intel command +================================ + +angle_style charmm/kk command +============================= + +angle_style charmm/omp command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style charmm + +Examples +"""""""" + +.. parsed-literal:: + + angle_style charmm + angle_coeff 1 300.0 107.0 50.0 3.0 + +Description +""""""""""" + +The *charmm* angle style uses the potential + +.. image:: Eqs/angle_charmm.jpg + :align: center + +with an additional Urey_Bradley term based on the distance *r* between +the 1st and 3rd atoms in the angle. K, theta0, Kub, and Rub are +coefficients defined for each angle type. + +See :ref:`(MacKerell) ` for a description of the CHARMM force +field. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy/radian^2) +* theta0 (degrees) +* K_ub (energy/distance^2) +* r_ub (distance) + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +---------- + + +.. _MacKerell: + + + +**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, +Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_class2.txt b/doc/_sources/angle_class2.txt new file mode 100644 index 0000000000..7615433281 --- /dev/null +++ b/doc/_sources/angle_class2.txt @@ -0,0 +1,139 @@ +.. index:: angle_style class2 + +angle_style class2 command +========================== + +angle_style class2/omp command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style class2 + +Examples +"""""""" + +.. parsed-literal:: + + angle_style class2 + angle_coeff * 75.0 + angle_coeff 1 bb 10.5872 1.0119 1.5228 + angle_coeff * ba 3.6551 24.895 1.0119 1.5228 + +Description +""""""""""" + +The *class2* angle style uses the potential + +.. image:: Eqs/angle_class2.jpg + :align: center + +where Ea is the angle term, Ebb is a bond-bond term, and Eba is a +bond-angle term. Theta0 is the equilibrium angle and r1 and r2 are +the equilibrium bond lengths. + +See :ref:`(Sun) ` for a description of the COMPASS class2 force field. + +Coefficients for the Ea, Ebb, and Eba formulas must be defined for +each angle type via the :doc:`angle_coeff ` command as in +the example above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands. + +These are the 4 coefficients for the Ea formula: + +* theta0 (degrees) +* K2 (energy/radian^2) +* K3 (energy/radian^3) +* K4 (energy/radian^4) + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of the various K are in per-radian. + +For the Ebb formula, each line in a :doc:`angle_coeff ` +command in the input script lists 4 coefficients, the first of which +is "bb" to indicate they are BondBond coefficients. In a data file, +these coefficients should be listed under a "BondBond Coeffs" heading +and you must leave out the "bb", i.e. only list 3 coefficients after +the angle type. + +* bb +* M (energy/distance^2) +* r1 (distance) +* r2 (distance) + +For the Eba formula, each line in a :doc:`angle_coeff ` +command in the input script lists 5 coefficients, the first of which +is "ba" to indicate they are BondAngle coefficients. In a data file, +these coefficients should be listed under a "BondAngle Coeffs" heading +and you must leave out the "ba", i.e. only list 4 coefficients after +the angle type. + +* ba +* N1 (energy/distance^2) +* N2 (energy/distance^2) +* r1 (distance) +* r2 (distance) + +The theta0 value in the Eba formula is not specified, since it is the +same value from the Ea formula. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the CLASS2 +package. See the :ref:`Making LAMMPS ` section +for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +---------- + + +.. _Sun: + + + +**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_coeff.txt b/doc/_sources/angle_coeff.txt new file mode 100644 index 0000000000..8a619c14e4 --- /dev/null +++ b/doc/_sources/angle_coeff.txt @@ -0,0 +1,116 @@ +.. index:: angle_coeff + +angle_coeff command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_coeff N args + +* N = angle type (see asterisk form below) +* args = coefficients for one or more angle types + +Examples +"""""""" + +.. parsed-literal:: + + angle_coeff 1 300.0 107.0 + angle_coeff * 5.0 + angle_coeff 2*10 5.0 + +Description +""""""""""" + +Specify the angle force field coefficients for one or more angle types. +The number and meaning of the coefficients depends on the angle style. +Angle coefficients can also be set in the data file read by the +:doc:`read_data ` command or in a restart file. + +N can be specified in one of two ways. An explicit numeric value can +be used, as in the 1st example above. Or a wild-card asterisk can be +used to set the coefficients for multiple angle types. This takes the +form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, +then an asterisk with no numeric values means all types from 1 to N. A +leading asterisk means all types from 1 to n (inclusive). A trailing +asterisk means all types from n to N (inclusive). A middle asterisk +means all types from m to n (inclusive). + +Note that using an angle_coeff command can override a previous setting +for the same angle type. For example, these commands set the coeffs +for all angle types, then overwrite the coeffs for just angle type 2: + +.. parsed-literal:: + + angle_coeff * 200.0 107.0 1.2 + angle_coeff 2 50.0 107.0 + +A line in a data file that specifies angle coefficients uses the exact +same format as the arguments of the angle_coeff command in an input +script, except that wild-card asterisks should not be used since +coefficients for all N types must be listed in the file. For example, +under the "Angle Coeffs" section of a data file, the line that +corresponds to the 1st example above would be listed as + +.. parsed-literal:: + + 1 300.0 107.0 + +The :doc:`angle_style class2 ` is an exception to this +rule, in that an additional argument is used in the input script to +allow specification of the cross-term coefficients. See its +doc page for details. + + +---------- + + +Here is an alphabetic list of angle styles defined in LAMMPS. Click on +the style to display the formula it computes and coefficients +specified by the associated :doc:`angle_coeff ` command. + +Note that there are also additional angle styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the angle section of :ref:`this page `. + +* :doc:`angle_style none ` - turn off angle interactions +* :doc:`angle_style hybrid ` - define multiple styles of angle interactions + +* :doc:`angle_style charmm ` - CHARMM angle +* :doc:`angle_style class2 ` - COMPASS (class 2) angle +* :doc:`angle_style cosine ` - cosine angle potential +* :doc:`angle_style cosine/delta ` - difference of cosines angle potential +* :doc:`angle_style cosine/periodic ` - DREIDING angle +* :doc:`angle_style cosine/squared ` - cosine squared angle potential +* :doc:`angle_style harmonic ` - harmonic angle +* :doc:`angle_style table ` - tabulated by angle + + +---------- + + +Restrictions +"""""""""""" + + +This command must come after the simulation box is defined by a +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. + +An angle style must be defined before any angle coefficients are +set, either in the input script or in a data file. + +Related commands +"""""""""""""""" + +:doc:`angle_style ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_cosine.txt b/doc/_sources/angle_cosine.txt new file mode 100644 index 0000000000..ef925b8d37 --- /dev/null +++ b/doc/_sources/angle_cosine.txt @@ -0,0 +1,85 @@ +.. index:: angle_style cosine + +angle_style cosine command +========================== + +angle_style cosine/omp command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style cosine + +Examples +"""""""" + +.. parsed-literal:: + + angle_style cosine + angle_coeff * 75.0 + +Description +""""""""""" + +The *cosine* angle style uses the potential + +.. image:: Eqs/angle_cosine.jpg + :align: center + +where K is defined for each angle type. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_cosine_delta.txt b/doc/_sources/angle_cosine_delta.txt new file mode 100644 index 0000000000..7329ffff1f --- /dev/null +++ b/doc/_sources/angle_cosine_delta.txt @@ -0,0 +1,90 @@ +.. index:: angle_style cosine/delta + +angle_style cosine/delta command +================================ + +angle_style cosine/delta/omp command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style cosine/delta + +Examples +"""""""" + +.. parsed-literal:: + + angle_style cosine/delta + angle_coeff 2*4 75.0 100.0 + +Description +""""""""""" + +The *cosine/delta* angle style uses the potential + +.. image:: Eqs/angle_cosine_delta.jpg + :align: center + +where theta0 is the equilibrium value of the angle, and K is a +prefactor. Note that the usual 1/2 factor is included in K. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy) +* theta0 (degrees) + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff `, :doc:`angle_style cosine/squared ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_cosine_periodic.txt b/doc/_sources/angle_cosine_periodic.txt new file mode 100644 index 0000000000..8faddb9117 --- /dev/null +++ b/doc/_sources/angle_cosine_periodic.txt @@ -0,0 +1,109 @@ +.. index:: angle_style cosine/periodic + +angle_style cosine/periodic command +=================================== + +angle_style cosine/periodic/omp command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + angle_style cosine/periodic + +Examples +"""""""" + +.. parsed-literal:: + + angle_style cosine/periodic + angle_coeff * 75.0 1 6 + +Description +""""""""""" + +The *cosine/periodic* angle style uses the following potential, which +is commonly used in the :ref:`DREIDING ` force +field, particularly for organometallic systems where *n* = 4 might be +used for an octahedral complex and *n* = 3 might be used for a +trigonal center: + +.. image:: Eqs/angle_cosine_periodic.jpg + :align: center + +where C, B and n are coefficients defined for each angle type. + +See :ref:`(Mayo) ` for a description of the DREIDING force field + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* C (energy) +* B = 1 or -1 +* n = 1, 2, 3, 4, 5 or 6 for periodicity + +Note that the prefactor C is specified and not the overall force +constant K = C / n^2. When B = 1, it leads to a minimum for the +linear geometry. When B = -1, it leads to a maximum for the linear +geometry. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +---------- + + +.. _Mayo: + + + +**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_cosine_shift.txt b/doc/_sources/angle_cosine_shift.txt new file mode 100644 index 0000000000..ee65f69eaf --- /dev/null +++ b/doc/_sources/angle_cosine_shift.txt @@ -0,0 +1,90 @@ +.. index:: angle_style cosine/shift + +angle_style cosine/shift command +================================ + +angle_style cosine/shift/omp command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style cosine/shift + +Examples +"""""""" + +.. parsed-literal:: + + angle_style cosine/shift + angle_coeff * 10.0 45.0 + +Description +""""""""""" + +The *cosine/shift* angle style uses the potential + +.. image:: Eqs/angle_cosine_shift.jpg + :align: center + +where theta0 is the equilibrium angle. The potential is bounded +between -Umin and zero. In the neighborhood of the minimum E=- Umin + +Umin/4(theta-theta0)^2 hence the spring constant is umin/2. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* umin (energy) +* theta (angle) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff `, +:doc:`angle_cosineshiftexp ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_cosine_shift_exp.txt b/doc/_sources/angle_cosine_shift_exp.txt new file mode 100644 index 0000000000..7d22bcc15d --- /dev/null +++ b/doc/_sources/angle_cosine_shift_exp.txt @@ -0,0 +1,103 @@ +.. index:: angle_style cosine/shift/exp + +angle_style cosine/shift/exp command +==================================== + +angle_style cosine/shift/exp/omp command +======================================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style cosine/shift/exp + +Examples +"""""""" + +.. parsed-literal:: + + angle_style cosine/shift/exp + angle_coeff * 10.0 45.0 2.0 + +Description +""""""""""" + +The *cosine/shift/exp* angle style uses the potential + +.. image:: Eqs/angle_cosine_shift_exp.jpg + :align: center + +where Umin, theta, and a are defined for each angle type. + +The potential is bounded between [-Umin:0] and the minimum is +located at the angle theta0. The a parameter can be both positive or +negative and is used to control the spring constant at the +equilibrium. + +The spring constant is given by k = A exp(A) Umin / [2 (Exp(a)-1)]. +For a > 3, k/Umin = a/2 to better than 5% relative error. For negative +values of the a parameter, the spring constant is essentially zero, +and anharmonic terms takes over. The potential is furthermore well +behaved in the limit a -> 0, where it has been implemented to linear +order in a for a < 0.001. In this limit the potential reduces to the +cosineshifted potential. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* umin (energy) +* theta (angle) +* A (real number) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff `, +:doc:`angle_cosineshift `, +:doc:`dihedral_cosineshift ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_cosine_squared.txt b/doc/_sources/angle_cosine_squared.txt new file mode 100644 index 0000000000..55f6926552 --- /dev/null +++ b/doc/_sources/angle_cosine_squared.txt @@ -0,0 +1,90 @@ +.. index:: angle_style cosine/squared + +angle_style cosine/squared command +================================== + +angle_style cosine/squared/omp command +====================================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style cosine/squared + +Examples +"""""""" + +.. parsed-literal:: + + angle_style cosine/squared + angle_coeff 2*4 75.0 100.0 + +Description +""""""""""" + +The *cosine/squared* angle style uses the potential + +.. image:: Eqs/angle_cosine_squared.jpg + :align: center + +where theta0 is the equilibrium value of the angle, and K is a +prefactor. Note that the usual 1/2 factor is included in K. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy) +* theta0 (degrees) + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_dipole.txt b/doc/_sources/angle_dipole.txt new file mode 100644 index 0000000000..bf01e7926f --- /dev/null +++ b/doc/_sources/angle_dipole.txt @@ -0,0 +1,152 @@ +.. index:: angle_style dipole + +angle_style dipole command +========================== + +angle_style dipole/omp command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style dipole + +Examples +"""""""" + +.. parsed-literal:: + + angle_style dipole + angle_coeff 6 2.1 180.0 + +Description +""""""""""" + +The *dipole* angle style is used to control the orientation of a dipolar +atom within a molecule :ref:`(Orsi) `. Specifically, the *dipole* angle +style restrains the orientation of a point dipole mu_j (embedded in atom +'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i' +is another atom of the same molecule (typically, 'i' and 'j' are also +covalently bonded). + +It is convenient to define an angle gamma between the 'free' vector mu_j +and the reference (bond) vector r_ij: + +.. image:: Eqs/angle_dipole_gamma.jpg + :align: center + +The *dipole* angle style uses the potential: + +.. image:: Eqs/angle_dipole_potential.jpg + :align: center + +where K is a rigidity constant and gamma0 is an equilibrium (reference) +angle. + +The torque on the dipole can be obtained by differentiating the +potential using the 'chain rule' as in appendix C.3 of +:ref:`(Allen) `: + +.. image:: Eqs/angle_dipole_torque.jpg + :align: center + +Example: if gamma0 is set to 0 degrees, the torque generated by +the potential will tend to align the dipole along the reference +direction defined by the (bond) vector r_ij (in other words, mu_j is +restrained to point towards atom 'i'). + +The dipolar torque T_j must be counterbalanced in order to conserve +the local angular momentum. This is achieved via an additional force +couple generating a torque equivalent to the opposite of T_j: + +.. image:: Eqs/angle_dipole_couple.jpg + :align: center + +where F_i and F_j are applied on atoms i and j, respectively. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy) +* gamma0 (degrees) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS <2_3>` +section for more info on packages. + +.. note:: + + In the "Angles" section of the data file, the atom ID 'j' + corresponding to the dipole to restrain must come before the atom ID + of the reference atom 'i'. A third atom ID 'k' must also be provided, + although 'k' is just a 'dummy' atom which can be any atom; it may be + useful to choose a convention (e.g., 'k'='i') and adhere to it. For + example, if ID=1 for the dipolar atom to restrain, and ID=2 for the + reference atom, the corresponding line in the "Angles" section of the + data file would read: X X 1 2 2 + +The "newton" command for intramolecular interactions must be "on" +(which is the default). + +This angle style should not be used with SHAKE. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff `, :doc:`angle_hybrid ` + +**Default:** none + + +---------- + + +.. _Orsi: + + + +**(Orsi)** Orsi & Essex, The ELBA force field for coarse-grain modeling of +lipid membranes, PloS ONE 6(12): e28637, 2011. + +.. _Allen: + + + +**(Allen)** Allen & Tildesley, Computer Simulation of Liquids, +Clarendon Press, Oxford, 1987. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_fourier.txt b/doc/_sources/angle_fourier.txt new file mode 100644 index 0000000000..fefde623df --- /dev/null +++ b/doc/_sources/angle_fourier.txt @@ -0,0 +1,85 @@ +.. index:: angle_style fourier + +angle_style fourier command +=========================== + +angle_style fourier/omp command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style fourier + +Examples +"""""""" + +angle_style fourier +angle_coeff 75.0 1.0 1.0 1.0 + +Description +""""""""""" + +The *fourier* angle style uses the potential + +.. image:: Eqs/angle_fourier.jpg + :align: center + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy) +* C0 (real) +* C1 (real) +* C2 (real) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER_MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_fourier_simple.txt b/doc/_sources/angle_fourier_simple.txt new file mode 100644 index 0000000000..476214f23f --- /dev/null +++ b/doc/_sources/angle_fourier_simple.txt @@ -0,0 +1,84 @@ +.. index:: angle_style fourier/simple + +angle_style fourier/simple command +================================== + +angle_style fourier/simple/omp command +====================================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style fourier/simple + +Examples +"""""""" + +angle_style fourier/simple +angle_coeff 100.0 -1.0 1.0 + +Description +""""""""""" + +The *fourier/simple* angle style uses the potential + +.. image:: Eqs/angle_fourier_simple.jpg + :align: center + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy) +* c (real) +* n (real) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER_MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_harmonic.txt b/doc/_sources/angle_harmonic.txt new file mode 100644 index 0000000000..025b37fed7 --- /dev/null +++ b/doc/_sources/angle_harmonic.txt @@ -0,0 +1,93 @@ +.. index:: angle_style harmonic + +angle_style harmonic command +============================ + +angle_style harmonic/kk command +=============================== + +angle_style harmonic/omp command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + angle_style harmonic + +Examples +"""""""" + +.. parsed-literal:: + + angle_style harmonic + angle_coeff 1 300.0 107.0 + +Description +""""""""""" + +The *harmonic* angle style uses the potential + +.. image:: Eqs/angle_harmonic.jpg + :align: center + +where theta0 is the equilibrium value of the angle, and K is a +prefactor. Note that the usual 1/2 factor is included in K. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy/radian^2) +* theta0 (degrees) + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + none + +This angle style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_hybrid.txt b/doc/_sources/angle_hybrid.txt new file mode 100644 index 0000000000..bedaa512e7 --- /dev/null +++ b/doc/_sources/angle_hybrid.txt @@ -0,0 +1,109 @@ +.. index:: angle_style hybrid + +angle_style hybrid command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style hybrid style1 style2 ... + +* style1,style2 = list of one or more angle styles + +Examples +"""""""" + +.. parsed-literal:: + + angle_style hybrid harmonic cosine + angle_coeff 1 harmonic 80.0 30.0 + angle_coeff 2* cosine 50.0 + +Description +""""""""""" + +The *hybrid* style enables the use of multiple angle styles in one +simulation. An angle style is assigned to each angle type. For +example, angles in a polymer flow (of angle type 1) could be computed +with a *harmonic* potential and angles in the wall boundary (of angle +type 2) could be computed with a *cosine* potential. The assignment +of angle type to style is made via the :doc:`angle_coeff ` +command or in the data file. + +In the angle_coeff commands, the name of an angle style must be added +after the angle type, with the remaining coefficients being those +appropriate to that style. In the example above, the 2 angle_coeff +commands set angles of angle type 1 to be computed with a *harmonic* +potential with coefficients 80.0, 30.0 for K, theta0. All other angle +types (2-N) are computed with a *cosine* potential with coefficient +50.0 for K. + +If angle coefficients are specified in the data file read via the +:doc:`read_data ` command, then the same rule applies. +E.g. "harmonic" or "cosine", must be added after the angle type, for each +line in the "Angle Coeffs" section, e.g. + +.. parsed-literal:: + + Angle Coeffs + +.. parsed-literal:: + + 1 harmonic 80.0 30.0 + 2 cosine 50.0 + ... + +If *class2* is one of the angle hybrid styles, the same rule holds for +specifying additional BondBond (and BondAngle) coefficients either via +the input script or in the data file. I.e. *class2* must be added to +each line after the angle type. For lines in the BondBond (or +BondAngle) section of the data file for angle types that are not +*class2*, you must use an angle style of *skip* as a placeholder, e.g. + +.. parsed-literal:: + + BondBond Coeffs + +.. parsed-literal:: + + 1 skip + 2 class2 3.6512 1.0119 1.0119 + ... + +Note that it is not necessary to use the angle style *skip* in the +input script, since BondBond (or BondAngle) coefficients need not be +specified at all for angle types that are not *class2*. + +An angle style of *none* with no additional coefficients can be used +in place of an angle style, either in a input script angle_coeff +command or in the data file, if you desire to turn off interactions +for specific angle types. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Unlike other angle styles, the hybrid angle style does not store angle +coefficient info for individual sub-styles in a :doc:`binary restart files `. Thus when retarting a simulation from a restart +file, you need to re-specify angle_coeff commands. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_none.txt b/doc/_sources/angle_none.txt new file mode 100644 index 0000000000..cf723a71e9 --- /dev/null +++ b/doc/_sources/angle_none.txt @@ -0,0 +1,38 @@ +.. index:: angle_style none + +angle_style none command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style none + +Examples +"""""""" + +.. parsed-literal:: + + angle_style none + +Description +""""""""""" + +Using an angle style of none means angle forces are not computed, even +if triplets of angle atoms were listed in the data file read by the +:doc:`read_data ` command. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_quartic.txt b/doc/_sources/angle_quartic.txt new file mode 100644 index 0000000000..67ccdfc164 --- /dev/null +++ b/doc/_sources/angle_quartic.txt @@ -0,0 +1,93 @@ +.. index:: angle_style quartic + +angle_style quartic command +=========================== + +angle_style quartic/omp command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style quartic + +Examples +"""""""" + +.. parsed-literal:: + + angle_style quartic + angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 + +Description +""""""""""" + +The *quartic* angle style uses the potential + +.. image:: Eqs/angle_quartic.jpg + :align: center + +where theta0 is the equilibrium value of the angle, and K is a +prefactor. Note that the usual 1/2 factor is included in K. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* theta0 (degrees) +* K2 (energy/radian^2) +* K3 (energy/radian^3) +* K4 (energy/radian^4) + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER_MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_sdk.txt b/doc/_sources/angle_sdk.txt new file mode 100644 index 0000000000..bec3958638 --- /dev/null +++ b/doc/_sources/angle_sdk.txt @@ -0,0 +1,70 @@ +.. index:: angle_style sdk + +angle_style sdk command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + angle_style sdk + +.. parsed-literal:: + + angle_style sdk/omp + +Examples +"""""""" + +.. parsed-literal:: + + angle_style sdk + angle_coeff 1 300.0 107.0 + +Description +""""""""""" + +The *sdk* angle style is a combination of the harmonic angle potential, + +.. image:: Eqs/angle_harmonic.jpg + :align: center + +where theta0 is the equilibrium value of the angle and K a prefactor, +with the *repulsive* part of the non-bonded *lj/sdk* pair style +between the atoms 1 and 3. This angle potential is intended for +coarse grained MD simulations with the CMM parametrization using the +:doc:`pair_style lj/sdk `. Relative to the pair_style +*lj/sdk*, however, the energy is shifted by *epsilon*, to avoid sudden +jumps. Note that the usual 1/2 factor is included in K. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above: + +* K (energy/radian^2) +* theta0 (degrees) + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. +The also required *lj/sdk* parameters will be extracted automatically +from the pair_style. + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER-CG-CMM package. See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff `, :doc:`angle_style harmonic `, :doc:`pair_style lj/sdk `, +:doc:`pair_style lj/sdk/coul/long ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_style.txt b/doc/_sources/angle_style.txt new file mode 100644 index 0000000000..c053eb399c --- /dev/null +++ b/doc/_sources/angle_style.txt @@ -0,0 +1,112 @@ +.. index:: angle_style + +angle_style command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + angle_style style + +* style = *none* or *hybrid* or *charmm* or *class2* or *cosine* or *cosine/squared* or *harmonic* + +Examples +"""""""" + +.. parsed-literal:: + + angle_style harmonic + angle_style charmm + angle_style hybrid harmonic cosine + +Description +""""""""""" + +Set the formula(s) LAMMPS uses to compute angle interactions between +triplets of atoms, which remain in force for the duration of the +simulation. The list of angle triplets is read in by a +:doc:`read_data ` or :doc:`read_restart ` command +from a data or restart file. + +Hybrid models where angles are computed using different angle +potentials can be setup using the *hybrid* angle style. + +The coefficients associated with a angle style can be specified in a +data or restart file or via the :doc:`angle_coeff ` command. + +All angle potentials store their coefficient data in binary restart +files which means angle_style and :doc:`angle_coeff ` +commands do not need to be re-specified in an input script that +restarts a simulation. See the :doc:`read_restart ` +command for details on how to do this. The one exception is that +angle_style *hybrid* only stores the list of sub-styles in the restart +file; angle coefficients need to be re-specified. + +.. note:: + + When both an angle and pair style is defined, the + :doc:`special_bonds ` command often needs to be used to + turn off (or weight) the pairwise interaction that would otherwise + exist between 3 bonded atoms. + +In the formulas listed for each angle style, *theta* is the angle +between the 3 atoms in the angle. + + +---------- + + +Here is an alphabetic list of angle styles defined in LAMMPS. Click on +the style to display the formula it computes and coefficients +specified by the associated :doc:`angle_coeff ` command. + +Note that there are also additional angle styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the angle section of :ref:`this page `. + +* :doc:`angle_style none ` - turn off angle interactions +* :doc:`angle_style hybrid ` - define multiple styles of angle interactions + +* :doc:`angle_style charmm ` - CHARMM angle +* :doc:`angle_style class2 ` - COMPASS (class 2) angle +* :doc:`angle_style cosine ` - cosine angle potential +* :doc:`angle_style cosine/delta ` - difference of cosines angle potential +* :doc:`angle_style cosine/periodic ` - DREIDING angle +* :doc:`angle_style cosine/squared ` - cosine squared angle potential +* :doc:`angle_style harmonic ` - harmonic angle +* :doc:`angle_style table ` - tabulated by angle + + +---------- + + +Restrictions +"""""""""""" + + +Angle styles can only be set for atom_styles that allow angles to be +defined. + +Most angle styles are part of the MOLECULE package. They are only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info on packages. +The doc pages for individual bond potentials tell if it is part of a +package. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +Default +""""""" + +.. parsed-literal:: + + angle_style none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/angle_table.txt b/doc/_sources/angle_table.txt new file mode 100644 index 0000000000..5c958b79cc --- /dev/null +++ b/doc/_sources/angle_table.txt @@ -0,0 +1,175 @@ +.. index:: angle_style table + +angle_style table command +========================= + +angle_style table/omp command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + angle_style table style N + +* style = *linear* or *spline* = method of interpolation +* N = use N values in table + +Examples +"""""""" + +.. parsed-literal:: + + angle_style table linear 1000 + angle_coeff 3 file.table ENTRY1 + +Description +""""""""""" + +Style *table* creates interpolation tables of length *N* from angle +potential and derivative values listed in a file(s) as a function of +angle The files are read by the :doc:`angle_coeff ` +command. + +The interpolation tables are created by fitting cubic splines to the +file values and interpolating energy and derivative values at each of +*N* angles. During a simulation, these tables are used to interpolate +energy and force values on individual atoms as needed. The +interpolation is done in one of 2 styles: *linear* or *spline*. + +For the *linear* style, the angle is used to find 2 surrounding table +values from which an energy or its derivative is computed by linear +interpolation. + +For the *spline* style, a cubic spline coefficients are computed and +stored at each of the *N* values in the table. The angle is used to +find the appropriate set of coefficients which are used to evaluate a +cubic polynomial which computes the energy or derivative. + +The following coefficients must be defined for each angle type via the +:doc:`angle_coeff ` command as in the example above. + +* filename +* keyword + +The filename specifies a file containing tabulated energy and +derivative values. The keyword specifies a section of the file. The +format of this file is described below. + + +---------- + + +The format of a tabulated file is as follows (without the +parenthesized comments): + +.. parsed-literal:: + + # Angle potential for harmonic (one or more comment or blank lines) + +.. parsed-literal:: + + HAM (keyword is the first text on line) + N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters) + (blank line) + N 181 FP 0 0 (N, FP parameters) + 1 0.0 200.5 2.5 (index, angle, energy, derivative) + 2 1.0 198.0 2.5 + ... + 181 180.0 0.0 0.0 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the +:doc:`angle_coeff ` command. The next line lists (in any +order) one or more parameters for the table. Each parameter is a +keyword followed by one or more numeric values. + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the *N* +specified in the :doc:`angle_style table ` command. Let +Ntable = *N* in the angle_style command, and Nfile = "N" in the +tabulated file. What LAMMPS does is a preliminary interpolation by +creating splines using the Nfile tabulated values as nodal points. It +uses these to interpolate as needed to generate energy and derivative +values at Ntable different points. The resulting tables of length +Ntable are then used as described above, when computing energy and +force for individual angles and their atoms. This means that if you +want the interpolation tables of length Ntable to match exactly what +is in the tabulated file (with effectively no preliminary +interpolation), you should set Ntable = Nfile. + +The "FP" parameter is optional. If used, it is followed by two values +fplo and fphi, which are the 2nd derivatives at the innermost and +outermost angle settings. These values are needed by the spline +construction routines. If not specified by the "FP" parameter, they +are estimated (less accurately) by the first two and last two +derivative values in the table. + +The "EQ" parameter is also optional. If used, it is followed by a the +equilibrium angle value, which is used, for example, by the :doc:`fix shake ` command. If not used, the equilibrium angle is +set to 180.0. + +Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +the angle value (in degrees), the 3rd value is the energy (in energy +units), and the 4th is -dE/d(theta) (also in energy units). The 3rd +term is the energy of the 3-atom configuration for the specified +angle. The last term is the derivative of the energy with respect to +the angle (in degrees, not radians). Thus the units of the last term +are still energy, not force. The angle values must increase from one +line to the next. The angle values must also begin with 0.0 and end +with 180.0, i.e. span the full range of possible angles. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`angle_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/atom_modify.txt b/doc/_sources/atom_modify.txt new file mode 100644 index 0000000000..63c7e6c441 --- /dev/null +++ b/doc/_sources/atom_modify.txt @@ -0,0 +1,186 @@ +.. index:: atom_modify + +atom_modify command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + atom_modify keyword values ... + +* one or more keyword/value pairs may be appended +* keyword = *id* or *map* or *first* or *sort* +.. parsed-literal:: + + *id* value = *yes* or *no* + *map* value = *array* or *hash* + *first* value = group-ID = group whose atoms will appear first in internal atom lists + *sort* values = Nfreq binsize + Nfreq = sort atoms spatially every this many time steps + binsize = bin size for spatial sorting (distance units) + + + +Examples +"""""""" + +.. parsed-literal:: + + atom_modify map hash + atom_modify map array sort 10000 2.0 + atom_modify first colloid + +Description +""""""""""" + +Modify certain attributes of atoms defined and stored within LAMMPS, +in addition to what is specified by the :doc:`atom_style ` +command. The *id* and *map* keywords must be specified before a +simulation box is defined; other keywords can be specified any time. + +The *id* keyword determines whether non-zero atom IDs can be assigned +to each atom. If the value is *yes*, which is the default, IDs are +assigned, whether you use the :doc:`create atoms ` or +:doc:`read_data ` or :doc:`read_restart ` +commands to initialize atoms. If the value is *no* the IDs for all +atoms are assumed to be 0. + +If atom IDs are used, they must all be positive integers. They should +also be unique, though LAMMPS does not check for this. Typically they +should also be consecutively numbered (from 1 to Natoms), though this +is not required. Molecular :doc:`atom styles ` are those +that store bond topology information (styles bond, angle, molecular, +full). These styles require atom IDs since the IDs are used to encode +the topology. Some other LAMMPS commands also require the use of atom +IDs. E.g. some many-body pair styles use them to avoid double +computation of the I-J interaction between two atoms. + +The only reason not to use atom IDs is if you are running an atomic +simulation so large that IDs cannot be uniquely assigned. For a +default LAMMPS build this limit is 2^31 or about 2 billion atoms. +However, even in this case, you can use 64-bit atom IDs, allowing 2^63 +or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG +switch. This is described in :ref:`Section 2.2 ` +of the manual. If atom IDs are not used, they must be specified as 0 +for all atoms, e.g. in a data or restart file. + +The *map* keyword determines how atom ID lookup is done for molecular +atom styles. Lookups are performed by bond (angle, etc) routines in +LAMMPS to find the local atom index associated with a global atom ID. + +When the *array* value is used, each processor stores a lookup table +of length N, where N is the largest atom ID in the system. This is a +fast, simple method for many simulations, but requires too much memory +for large simulations. The *hash* value uses a hash table to perform +the lookups. This can be slightly slower than the *array* method, but +its memory cost is proportional to the number of atoms owned by a +processor, i.e. N/P when N is the total number of atoms in the system +and P is the number of processors. + +When this setting is not specified in your input script, LAMMPS +creates a map, if one is needed, as an array or hash. See the +discussion of default values below for how LAMMPS chooses which kind +of map to build. Note that atomic systems do not normally need to +create a map. However, even in this case some LAMMPS commands will +create a map to find atoms (and then destroy it), or require a +permanent map. An example of the former is the :doc:`velocity loop all ` command, which uses a map when looping over all +atoms and insuring the same velocity values are assigned to an atom +ID, no matter which processor owns it. + +The *first* keyword allows a :doc:`group ` to be specified whose +atoms will be maintained as the first atoms in each processor's list +of owned atoms. This in only useful when the specified group is a +small fraction of all the atoms, and there are other operations LAMMPS +is performing that will be sped-up significantly by being able to loop +over the smaller set of atoms. Otherwise the reordering required by +this option will be a net slow-down. The :doc:`neigh_modify include ` and :doc:`comm_modify group ` +commands are two examples of commands that require this setting to +work efficiently. Several :doc:`fixes `, most notably time +integration fixes like :doc:`fix nve `, also take advantage of +this setting if the group they operate on is the group specified by +this command. Note that specifying "all" as the group-ID effectively +turns off the *first* option. + +It is OK to use the *first* keyword with a group that has not yet been +defined, e.g. to use the atom_modify first command at the beginning of +your input script. LAMMPS does not use the group until a simullation +is run. + +The *sort* keyword turns on a spatial sorting or reordering of atoms +within each processor's sub-domain every *Nfreq* timesteps. If +*Nfreq* is set to 0, then sorting is turned off. Sorting can improve +cache performance and thus speed-up a LAMMPS simulation, as discussed +in a paper by :ref:`(Meloni) `. Its efficacy depends on the problem +size (atoms/processor), how quickly the system becomes disordered, and +various other factors. As a general rule, sorting is typically more +effective at speeding up simulations of liquids as opposed to solids. +In tests we have done, the speed-up can range from zero to 3-4x. + +Reordering is peformed every *Nfreq* timesteps during a dynamics run +or iterations during a minimization. More precisely, reordering +occurs at the first reneighboring that occurs after the target +timestep. The reordering is performed locally by each processor, +using bins of the specified *binsize*. If *binsize* is set to 0.0, +then a binsize equal to half the :doc:`neighbor ` cutoff +distance (force cutoff plus skin distance) is used, which is a +reasonable value. After the atoms have been binned, they are +reordered so that atoms in the same bin are adjacent to each other in +the processor's 1d list of atoms. + +The goal of this procedure is for atoms to put atoms close to each +other in the processor's one-dimensional list of atoms that are also +near to each other spatially. This can improve cache performance when +pairwise intereractions and neighbor lists are computed. Note that if +bins are too small, there will be few atoms/bin. Likewise if bins are +too large, there will be many atoms/bin. In both cases, the goal of +cache locality will be undermined. + +.. note:: + + Running a simulation with sorting on versus off should not + change the simulation results in a statistical sense. However, a + different ordering will induce round-off differences, which will lead + to diverging trajectories over time when comparing two simluations. + Various commands, particularly those which use random numbers + (e.g. :doc:`velocity create `, and :doc:`fix langevin `), may generate (statistically identical) + results which depend on the order in which atoms are processed. The + order of atoms in a :doc:`dump ` file will also typically change + if sorting is enabled. + +Restrictions +"""""""""""" + + +The *first* and *sort* options cannot be used together. Since sorting +is on by default, it will be turned off if the *first* keyword is +used with a group-ID that is not "all". + +**Related commands:** none + +Default +""""""" + +By default, *id* is yes. By default, atomic systems (no bond topology +info) do not use a map. For molecular systems (with bond topology +info), a map is used. The default map style is array if no atom ID is +larger than 1 million, otherwise the default is hash. By default, a +"first" group is not defined. By default, sorting is enabled with a +frequency of 1000 and a binsize of 0.0, which means the neighbor +cutoff will be used to set the bin size. + + +---------- + + +.. _Meloni: + + + +**(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/atom_style.txt b/doc/_sources/atom_style.txt new file mode 100644 index 0000000000..b875001298 --- /dev/null +++ b/doc/_sources/atom_style.txt @@ -0,0 +1,336 @@ +.. index:: atom_style + +atom_style command +================== + +Syntax +"""""" + +.. parsed-literal:: + + atom_style style args + +* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *tri* or *template* or *hybrid* +.. parsed-literal:: + + args = none for any style except the following + *body* args = bstyle bstyle-args + bstyle = style of body particles + bstyle-args = additional arguments specific to the bstyle + see the :doc:`body ` doc page for details + *template* args = template-ID + template-ID = ID of molecule template specified in a separate :doc:`molecule ` command + *hybrid* args = list of one or more sub-styles, each with their args + +* accelerated styles (with same args) = *angle/cuda* or *angle/kk* or *atomic/cuda* or *atomic/kk* or *bond/kk* or *charge/cuda* or *charge/kk* or *full/cuda* or *full/kk* or *molecular/kk* + + +Examples +"""""""" + +.. parsed-literal:: + + atom_style atomic + atom_style bond + atom_style full + atom_style full/cuda + atom_style body nparticle 2 10 + atom_style hybrid charge bond + atom_style hybrid charge body nparticle 2 5 + atom_style template myMols + +Description +""""""""""" + +Define what style of atoms to use in a simulation. This determines +what attributes are associated with the atoms. This command must be +used before a simulation is setup via a :doc:`read_data `, +:doc:`read_restart `, or :doc:`create_box ` +command. + +.. note:: + + Many of the atom styles discussed here are only enabled if + LAMMPS was built with a specific package, as listed below in the + Restrictions section. + +Once a style is assigned, it cannot be changed, so use a style general +enough to encompass all attributes. E.g. with style *bond*, angular +terms cannot be used or added later to the model. It is OK to use a +style more general than needed, though it may be slightly inefficient. + +The choice of style affects what quantities are stored by each atom, +what quantities are communicated between processors to enable forces +to be computed, and what quantities are listed in the data file read +by the :doc:`read_data ` command. + +These are the additional attributes of each style and the typical +kinds of physical systems they are used to model. All styles store +coordinates, velocities, atom IDs and types. See the +:doc:`read_data `, :doc:`create_atoms `, and +:doc:`set ` commands for info on how to set these various +quantities. + ++--------------+-----------------------------------------------------+--------------------------------------+ +| *angle* | bonds and angles | bead-spring polymers with stiffness | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *atomic* | only the default values | coarse-grain liquids, solids, metals | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *bond* | bonds | bead-spring polymers | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *charge* | charge | atomic system with charges | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *dipole* | charge and dipole moment | system with dipolar particles | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *dpd* | internal temperature and internal energies | DPD particles | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *electron* | charge and spin and eradius | electronic force field | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *full* | molecular + charge | bio-molecules | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *line* | end points, angular velocity | rigid bodies | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *meso* | rho, e, cv | SPH particles | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *peri* | mass, volume | mesocopic Peridynamic models | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *sphere* | diameter, mass, angular velocity | granular models | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *template* | template index, template atom | small molecules with fixed topology | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *tri* | corner points, angular momentum | rigid bodies | ++--------------+-----------------------------------------------------+--------------------------------------+ +| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD | ++--------------+-----------------------------------------------------+--------------------------------------+ + +.. note:: + + It is possible to add some attributes, such as a molecule ID, to + atom styles that do not have them via the :doc:`fix property/atom ` command. This command also + allows new custom attributes consisting of extra integer or + floating-point values to be added to atoms. See the :doc:`fix property/atom ` doc page for examples of cases + where this is useful and details on how to initialize, access, and + output the custom values. + +All of the above styles define point particles, except the *sphere*, +*ellipsoid*, *electron*, *peri*, *wavepacket*, *line*, *tri*, and +*body* styles, which define finite-size particles. See :ref:`Section_howto 14 ` for an overview of using finite-size +particle models with LAMMPS. + +All of the point-particle styles assign mass to particles on a +per-type basis, using the :doc:`mass ` command, The finite-size +particle styles assign mass to individual particles on a per-particle +basis. + +For the *sphere* style, the particles are spheres and each stores a +per-particle diameter and mass. If the diameter > 0.0, the particle +is a finite-size sphere. If the diameter = 0.0, it is a point +particle. + +For the *ellipsoid* style, the particles are ellipsoids and each +stores a flag which indicates whether it is a finite-size ellipsoid or +a point particle. If it is an ellipsoid, it also stores a shape +vector with the 3 diamters of the ellipsoid and a quaternion 4-vector +with its orientation. + +For the *dipole* style, a point dipole is defined for each point +particle. Note that if you wish the particles to be finite-size +spheres as in a Stockmayer potential for a dipolar fluid, so that the +particles can rotate due to dipole-dipole interactions, then you need +to use atom_style hybrid sphere dipole, which will assign both a +diameter and dipole moment to each particle. + +For the *electron* style, the particles representing electrons are 3d +Gaussians with a specified position and bandwidth or uncertainty in +position, which is represented by the eradius = electron size. + +For the *peri* style, the particles are spherical and each stores a +per-particle mass and volume. + +The *dpd* style is for dissipative particle dynamics (DPD) particles +which store the particle internal temperature (dpdTheta), internal +conductive energy (uCond) and internal mechanical energy (uMech). + +The *meso* style is for smoothed particle hydrodynamics (SPH) +particles which store a density (rho), energy (e), and heat capacity +(cv). + +The *smd* style is for a general formulation of Smooth Particle +Hydrodynamics. Both fluids and solids can be modeled. Particles +store the mass and volume of an integration point, a kernel diameter +used for calculating the field variables (e.g. stress and deformation) +and a contact radius for calculating repulsive forces which prevent +individual physical bodies from penetretating each other. + +The *wavepacket* style is similar to *electron*, but the electrons may +consist of several Gaussian wave packets, summed up with coefficients +cs= (cs_re,cs_im). Each of the wave packets is treated as a separate +particle in LAMMPS, wave packets belonging to the same electron must +have identical *etag* values. + +For the *line* style, the particles are idealized line segments and +each stores a per-particle mass and length and orientation (i.e. the +end points of the line segment). + +For the *tri* style, the particles are planar triangles and each +stores a per-particle mass and size and orientation (i.e. the corner +points of the triangle). + +The *template* style allows molecular topolgy (bonds,angles,etc) to be +defined via a molecule template using the `molecule `_ +command. The template stores one or more molecules with a single copy +of the topology info (bonds,angles,etc) of each. Individual atoms +only store a template index and template atom to identify which +molecule and which atom-within-the-molecule they represent. Using the +*template* style instead of the *bond*, *angle*, *molecular* styles +can save memory for systems comprised of a large number of small +molecules, all of a single type (or small number of types). See the +paper by Grime and Voth, in :ref:`(Grime) `, for examples of how this +can be advantageous for large-scale coarse-grained systems. + +.. note:: + + When using the *template* style with a :doc:`molecule template ` that contains multiple molecules, you should + insure the atom types, bond types, angle_types, etc in all the + molecules are consistent. E.g. if one molecule represents H2O and + another CO2, then you probably do not want each molecule file to + define 2 atom types and a single bond type, because they will conflict + with each other when a mixture system of H2O and CO2 molecules is + defined, e.g. by the :doc:`read_data ` command. Rather the + H2O molecule should define atom types 1 and 2, and bond type 1. And + the CO2 molecule should define atom types 3 and 4 (or atom types 3 and + 2 if a single oxygen type is desired), and bond type 2. + +For the *body* style, the particles are arbitrary bodies with internal +attributes defined by the "style" of the bodies, which is specified by +the *bstyle* argument. Body particles can represent complex entities, +such as surface meshes of discrete points, collections of +sub-particles, deformable objects, etc. + +The :doc:`body ` doc page descibes the body styles LAMMPS +currently supports, and provides more details as to the kind of body +particles they represent. For all styles, each body particle stores +moments of inertia and a quaternion 4-vector, so that its orientation +and position can be time integrated due to forces and torques. + +Note that there may be additional arguments required along with the +*bstyle* specification, in the atom_style body command. These +arguments are described in the :doc:`body ` doc page. + + +---------- + + +Typically, simulations require only a single (non-hybrid) atom style. +If some atoms in the simulation do not have all the properties defined +by a particular style, use the simplest style that defines all the +needed properties by any atom. For example, if some atoms in a +simulation are charged, but others are not, use the *charge* style. +If some atoms have bonds, but others do not, use the *bond* style. + +The only scenario where the *hybrid* style is needed is if there is no +single style which defines all needed properties of all atoms. For +example, as mentioned above, if you want dipolar particles which will +rotate due to torque, you need to use "atom_style hybrid sphere +dipole". When a hybrid style is used, atoms store and communicate the +union of all quantities implied by the individual styles. + +When using the *hybrid* style, you cannot combine the *template* style +with another molecular style that stores bond,angle,etc info on a +per-atom basis. + +LAMMPS can be extended with new atom styles as well as new body +styles; see :doc:`this section `. + + +---------- + + +Styles with a *cuda* or *kk* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +Note that other acceleration packages in LAMMPS, specifically the GPU, +USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom +styles. + +The accelerated styles are part of the USER-CUDA and KOKKOS packages +respectively. They are only enabled if LAMMPS was built with those +packages. See the :ref:`Making LAMMPS ` section +for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restrictions +"""""""""""" + + +This command cannot be used after the simulation box is defined by a +:doc:`read_data ` or :doc:`create_box ` command. + +Many of the styles listed above are only enabled if LAMMPS was built +with a specific package, as listed below. See the :ref:`Making LAMMPS ` section for more info. + +The *angle*, *bond*, *full*, *molecular*, and *template* styles are +part of the MOLECULE package. + +The *line* and *tri* styles are part of the ASPHERE pacakge. + +The *body* style is part of the BODY package. + +The *dipole* style is part of the DIPOLE package. + +The *peri* style is part of the PERI package for Peridynamics. + +The *electron* style is part of the USER-EFF package for :doc:`electronic force fields `. + +The *dpd* style is part of the USER-DPD package for dissipative +particle dynamics (DPD). + +The *meso* style is part of the USER-SPH package for smoothed particle +hydrodyanmics (SPH). See `this PDF guide `_ to using SPH in LAMMPS. + +The *wavepacket* style is part of the USER-AWPMD package for the +:doc:`antisymmetrized wave packet MD method `. + +Related commands +"""""""""""""""" + +:doc:`read_data `, :doc:`pair_style ` + +Default +""""""" + +atom_style atomic + + +---------- + + +.. _Grime: + + + +**(Grime)** Grime and Voth, to appear in J Chem Theory & Computation +(2014). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/balance.txt b/doc/_sources/balance.txt new file mode 100644 index 0000000000..41e9fbc64a --- /dev/null +++ b/doc/_sources/balance.txt @@ -0,0 +1,386 @@ +.. index:: balance + +balance command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + balance thresh style args ... keyword value ... + +* thresh = imbalance threshhold that must be exceeded to perform a re-balance +* one style/arg pair can be used (or multiple for *x*,*y*,*z*) +* style = *x* or *y* or *z* or *shift* or *rcb* +.. parsed-literal:: + + *x* args = *uniform* or Px-1 numbers between 0 and 1 + *uniform* = evenly spaced cuts between processors in x dimension + numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension + *x* can be specified together with *y* or *z* + *y* args = *uniform* or Py-1 numbers between 0 and 1 + *uniform* = evenly spaced cuts between processors in y dimension + numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension + *y* can be specified together with *x* or *z* + *z* args = *uniform* or Pz-1 numbers between 0 and 1 + *uniform* = evenly spaced cuts between processors in z dimension + numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension + *z* can be specified together with *x* or *y* + *shift* args = dimstr Niter stopthresh + dimstr = sequence of letters containing "x" or "y" or "z", each not more than once + Niter = # of times to iterate within each dimension of dimstr sequence + stopthresh = stop balancing when this imbalance threshhold is reached + *rcb* args = none + +* zero or more keyword/value pairs may be appended +* keyword = *out* +.. parsed-literal:: + + *out* value = filename + filename = write each processor's sub-domain to a file + + + +Examples +"""""""" + +.. parsed-literal:: + + balance 0.9 x uniform y 0.4 0.5 0.6 + balance 1.2 shift xz 5 1.1 + balance 1.0 shift xz 5 1.1 + balance 1.1 rcb + balance 1.0 shift x 20 1.0 out tmp.balance + +Description +""""""""""" + +This command adjusts the size and shape of processor sub-domains +within the simulation box, to attempt to balance the number of +particles and thus the computational cost (load) evenly across +processors. The load balancing is "static" in the sense that this +command performs the balancing once, before or between simulations. +The processor sub-domains will then remain static during the +subsequent run. To perform "dynamic" balancing, see the :doc:`fix balance ` command, which can adjust processor +sub-domain sizes and shapes on-the-fly during a :doc:`run `. + +Load-balancing is typically only useful if the particles in the +simulation box have a spatially-varying density distribution. E.g. a +model of a vapor/liquid interface, or a solid with an irregular-shaped +geometry containing void regions. In this case, the LAMMPS default of +dividing the simulation box volume into a regular-spaced grid of 3d +bricks, with one equal-volume sub-domain per procesor, may assign very +different numbers of particles per processor. This can lead to poor +performance when the simulation is run in parallel. + +Note that the :doc:`processors ` command allows some control +over how the box volume is split across processors. Specifically, for +a Px by Py by Pz grid of processors, it allows choice of Px, Py, and +Pz, subject to the constraint that Px * Py * Pz = P, the total number +of processors. This is sufficient to achieve good load-balance for +some problems on some processor counts. However, all the processor +sub-domains will still have the same shape and same volume. + +The requested load-balancing operation is only performed if the +current "imbalance factor" in particles owned by each processor +exceeds the specified *thresh* parameter. The imbalance factor is +defined as the maximum number of particles owned by any processor, +divided by the average number of particles per processor. Thus an +imbalance factor of 1.0 is perfect balance. + +As an example, for 10000 particles running on 10 processors, if the +most heavily loaded processor has 1200 particles, then the factor is +1.2, meaning there is a 20% imbalance. Note that a re-balance can be +forced even if the current balance is perfect (1.0) be specifying a +*thresh* < 1.0. + +.. note:: + + Balancing is performed even if the imbalance factor does not + exceed the *thresh* parameter if a "grid" style is specified when the + current partitioning is "tiled". The meaning of "grid" vs "tiled" is + explained below. This is to allow forcing of the partitioning to + "grid" so that the :doc:`comm_style brick ` command can then + be used to replace a current :doc:`comm_style tiled ` + setting. + +When the balance command completes, it prints statistics about the +result, including the change in the imbalance factor and the change in +the maximum number of particles on any processor. For "grid" methods +(defined below) that create a logical 3d grid of processors, the +positions of all cutting planes in each of the 3 dimensions (as +fractions of the box length) are also printed. + +.. note:: + + This command attempts to minimize the imbalance factor, as + defined above. But depending on the method a perfect balance (1.0) + may not be achieved. For example, "grid" methods (defined below) that + create a logical 3d grid cannot achieve perfect balance for many + irregular distributions of particles. Likewise, if a portion of the + system is a perfect lattice, e.g. the intiial system is generated by + the :doc:`create_atoms ` command, then "grid" methods may + be unable to achieve exact balance. This is because entire lattice + planes will be owned or not owned by a single processor. + +.. note:: + + The imbalance factor is also an estimate of the maximum speed-up + you can hope to achieve by running a perfectly balanced simulation + versus an imbalanced one. In the example above, the 10000 particle + simulation could run up to 20% faster if it were perfectly balanced, + versus when imbalanced. However, computational cost is not strictly + proportional to particle count, and changing the relative size and + shape of processor sub-domains may lead to additional computational + and communication overheads, e.g. in the PPPM solver used via the + :doc:`kspace_style ` command. Thus you should benchmark + the run times of a simulation before and after balancing. + + +---------- + + +The method used to perform a load balance is specified by one of the +listed styles (or more in the case of *x*,*y*,*z*), which are +described in detail below. There are 2 kinds of styles. + +The *x*, *y*, *z*, and *shift* styles are "grid" methods which produce +a logical 3d grid of processors. They operate by changing the cutting +planes (or lines) between processors in 3d (or 2d), to adjust the +volume (area in 2d) assigned to each processor, as in the following 2d +diagram where processor sub-domains are shown and atoms are colored by +the processor that owns them. The leftmost diagram is the default +partitioning of the simulation box across processors (one sub-box for +each of 16 processors); the middle diagram is after a "grid" method +has been applied. + +.. thumbnail:: JPG/balance_uniform.jpg + :align: center +.. thumbnail:: JPG/balance_nonuniform.jpg + :align: center +.. thumbnail:: JPG/balance_rcb.jpg + :align: center +The *rcb* style is a "tiling" method which does not produce a logical +3d grid of processors. Rather it tiles the simulation domain with +rectangular sub-boxes of varying size and shape in an irregular +fashion so as to have equal numbers of particles in each sub-box, as +in the rightmost diagram above. + +The "grid" methods can be used with either of the +:doc:`comm_style ` command options, *brick* or *tiled*. The +"tiling" methods can only be used with :doc:`comm_style tiled `. Note that it can be useful to use a "grid" +method with :doc:`comm_style tiled ` to return the domain +partitioning to a logical 3d grid of processors so that "comm_style +brick" can afterwords be specified for subsequent :doc:`run ` +commands. + +When a "grid" method is specified, the current domain partitioning can +be either a logical 3d grid or a tiled partitioning. In the former +case, the current logical 3d grid is used as a starting point and +changes are made to improve the imbalance factor. In the latter case, +the tiled partitioning is discarded and a logical 3d grid is created +with uniform spacing in all dimensions. This becomes the starting +point for the balancing operation. + +When a "tiling" method is specified, the current domain partitioning +("grid" or "tiled") is ignored, and a new partitioning is computed +from scratch. + + +---------- + + +The *x*, *y*, and *z* styles invoke a "grid" method for balancing, as +described above. Note that any or all of these 3 styles can be +specified together, one after the other, but they cannot be used with +any other style. This style adjusts the position of cutting planes +between processor sub-domains in specific dimensions. Only the +specified dimensions are altered. + +The *uniform* argument spaces the planes evenly, as in the left +diagrams above. The *numeric* argument requires listing Ps-1 numbers +that specify the position of the cutting planes. This requires +knowing Ps = Px or Py or Pz = the number of processors assigned by +LAMMPS to the relevant dimension. This assignment is made (and the +Px, Py, Pz values printed out) when the simulation box is created by +the "create_box" or "read_data" or "read_restart" command and is +influenced by the settings of the :doc:`processors ` +command. + +Each of the numeric values must be between 0 and 1, and they must be +listed in ascending order. They represent the fractional position of +the cutting place. The left (or lower) edge of the box is 0.0, and +the right (or upper) edge is 1.0. Neither of these values is +specified. Only the interior Ps-1 positions are specified. Thus is +there are 2 procesors in the x dimension, you specify a single value +such as 0.75, which would make the left processor's sub-domain 3x +larger than the right processor's sub-domain. + + +---------- + + +The *shift* style invokes a "grid" method for balancing, as +described above. It changes the positions of cutting planes between +processors in an iterative fashion, seeking to reduce the imbalance +factor, similar to how the :doc:`fix balance shift ` +command operates. + +The *dimstr* argument is a string of characters, each of which must be +an "x" or "y" or "z". Eacn character can appear zero or one time, +since there is no advantage to balancing on a dimension more than +once. You should normally only list dimensions where you expect there +to be a density variation in the particles. + +Balancing proceeds by adjusting the cutting planes in each of the +dimensions listed in *dimstr*, one dimension at a time. For a single +dimension, the balancing operation (described below) is iterated on up +to *Niter* times. After each dimension finishes, the imbalance factor +is re-computed, and the balancing operation halts if the *stopthresh* +criterion is met. + +A rebalance operation in a single dimension is performed using a +recursive multisectioning algorithm, where the position of each +cutting plane (line in 2d) in the dimension is adjusted independently. +This is similar to a recursive bisectioning for a single value, except +that the bounds used for each bisectioning take advantage of +information from neighboring cuts if possible. At each iteration, the +count of particles on either side of each plane is tallied. If the +counts do not match the target value for the plane, the position of +the cut is adjusted to be halfway between a low and high bound. The +low and high bounds are adjusted on each iteration, using new count +information, so that they become closer together over time. Thus as +the recustion progresses, the count of particles on either side of the +plane gets closer to the target value. + +Once the rebalancing is complete and final processor sub-domains +assigned, particles are migrated to their new owning processor, and +the balance procedure ends. + +.. note:: + + At each rebalance operation, the bisectioning for each cutting + plane (line in 2d) typcially starts with low and high bounds separated + by the extent of a processor's sub-domain in one dimension. The size + of this bracketing region shrinks by 1/2 every iteration. Thus if + *Niter* is specified as 10, the cutting plane will typically be + positioned to 1 part in 1000 accuracy (relative to the perfect target + position). For *Niter* = 20, it will be accurate to 1 part in a + million. Thus there is no need ot set *Niter* to a large value. + LAMMPS will check if the threshold accuracy is reached (in a + dimension) is less iterations than *Niter* and exit early. However, + *Niter* should also not be set too small, since it will take roughly + the same number of iterations to converge even if the cutting plane is + initially close to the target value. + + +---------- + + +The *rcb* style invokes a "tiled" method for balancing, as described +above. It performs a recursive coordinate bisectioning (RCB) of the +simulation domain. The basic idea is as follows. + +The simulation domain is cut into 2 boxes by an axis-aligned cut in +the longest dimension, leaving one new box on either side of the cut. +All the processors are also partitioned into 2 groups, half assigned +to the box on the lower side of the cut, and half to the box on the +upper side. (If the processor count is odd, one side gets an extra +processor.) The cut is positioned so that the number of atoms in the +lower box is exactly the number that the processors assigned to that +box should own for load balance to be perfect. This also makes load +balance for the upper box perfect. The positioning is done +iteratively, by a bisectioning method. Note that counting atoms on +either side of the cut requires communication between all processors +at each iteration. + +That is the procedure for the first cut. Subsequent cuts are made +recursively, in exactly the same manner. The subset of processors +assigned to each box make a new cut in the longest dimension of that +box, splitting the box, the subset of processsors, and the atoms in +the box in two. The recursion continues until every processor is +assigned a sub-box of the entire simulation domain, and owns the atoms +in that sub-box. + + +---------- + + +The *out* keyword writes a text file to the specified *filename* with +the results of the balancing operation. The file contains the bounds +of the sub-domain for each processor after the balancing operation +completes. The format of the file is compatible with the +`Pizza.py `_ *mdump* tool which has support for manipulating and +visualizing mesh files. An example is shown here for a balancing by 4 +processors for a 2d problem: + +.. parsed-literal:: + + ITEM: TIMESTEP + 0 + ITEM: NUMBER OF NODES + 16 + ITEM: BOX BOUNDS + 0 10 + 0 10 + 0 10 + ITEM: NODES + 1 1 0 0 0 + 2 1 5 0 0 + 3 1 5 5 0 + 4 1 0 5 0 + 5 1 5 0 0 + 6 1 10 0 0 + 7 1 10 5 0 + 8 1 5 5 0 + 9 1 0 5 0 + 10 1 5 5 0 + 11 1 5 10 0 + 12 1 10 5 0 + 13 1 5 5 0 + 14 1 10 5 0 + 15 1 10 10 0 + 16 1 5 10 0 + ITEM: TIMESTEP + 0 + ITEM: NUMBER OF SQUARES + 4 + ITEM: SQUARES + 1 1 1 2 3 4 + 2 1 5 6 7 8 + 3 1 9 10 11 12 + 4 1 13 14 15 16 + +The coordinates of all the vertices are listed in the NODES section, 5 +per processor. Note that the 4 sub-domains share vertices, so there +will be duplicate nodes in the list. + +The "SQUARES" section lists the node IDs of the 4 vertices in a +rectangle for each processor (1 to 4). + +For a 3d problem, the syntax is similar with 8 vertices listed for +each processor, instead of 4, and "SQUARES" replaced by "CUBES". + + +---------- + + +Restrictions +"""""""""""" + + +For 2d simulations, the *z* style cannot be used. Nor can a "z" +appear in *dimstr* for the *shift* style. + +Related commands +"""""""""""""""" + +:doc:`processors `, :doc:`fix balance ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/body.txt b/doc/_sources/body.txt new file mode 100644 index 0000000000..7f1ad12d4e --- /dev/null +++ b/doc/_sources/body.txt @@ -0,0 +1,301 @@ +Body particles +============== + +**Overview:** + +This doc page is not about a LAMMPS input script command, but about +body particles, which are generalized finite-size particles. +Individual body particles can represent complex entities, such as +surface meshes of discrete points, collections of sub-particles, +deformable objects, etc. Note that other kinds of finite-size +spherical and aspherical particles are also supported by LAMMPS, such +as spheres, ellipsoids, line segments, and triangles, but they are +simpler entities that body particles. See :ref:`Section_howto 14 ` for a general overview of all these +particle types. + +Body particles are used via the :doc:`atom_style body ` +command. It takes a body style as an argument. The current body +styles supported by LAMMPS are as follows. The name in the first +column is used as the *bstyle* argument for the :doc:`atom_style body ` command. + ++-------------------+-----------------------------------+ +| *nparticle* | rigid body with N sub-particles | ++-------------------+-----------------------------------+ +| *rounded/polygon* | 2d convex polygon with N vertices | ++-------------------+-----------------------------------+ + +The body style determines what attributes are stored for each body and +thus how they can be used to compute pairwise body/body or +bond/non-body (point particle) interactions. More details of each +style are described below. + +.. note:: + + The rounded/polygon style listed in the table above and + described below has not yet been relesed in LAMMPS. It will be soon. + +We hope to add more styles in the future. See :ref:`Section_modify 12 ` for details on how to add a new body +style to the code. + + +---------- + + +**When to use body particles:** + +You should not use body particles to model a rigid body made of +simpler particles (e.g. point, sphere, ellipsoid, line segment, +triangular particles), if the interaction between pairs of rigid +bodies is just the summation of pairwise interactions between the +simpler particles. LAMMPS already supports this kind of model via the +:doc:`fix rigid ` command. Any of the numerous pair styles +that compute interactions between simpler particles can be used. The +:doc:`fix rigid ` command time integrates the motion of the +rigid bodies. All of the standard LAMMPS commands for thermostatting, +adding constraints, performing output, etc will operate as expected on +the simple particles. + +By contrast, when body particles are used, LAMMPS treats an entire +body as a single particle for purposes of computing pairwise +interactions, building neighbor lists, migrating particles between +processors, outputting particles to a dump file, etc. This means that +interactions between pairs of bodies or between a body and non-body +(point) particle need to be encoded in an appropriate pair style. If +such a pair style were to mimic the :doc:`fix rigid ` model, +it would need to loop over the entire collection of interactions +between pairs of simple particles within the two bodies, each time a +single body/body interaction was computed. + +Thus it only makes sense to use body particles and develop such a pair +style, when particle/particle interactions are more complex than what +the :doc:`fix rigid ` command can already calculate. For +example, if particles have one or more of the following attributes: + +* represented by a surface mesh +* represented by a collection of geometric entities (e.g. planes + spheres) +* deformable +* internal stress that induces fragmentation + +then the interaction between pairs of particles is likely to be more +complex than the summation of simple sub-particle interactions. An +example is contact or frictional forces between particles with planar +sufaces that inter-penetrate. + +These are additional LAMMPS commands that can be used with body +particles of different styles + ++------------------------------------------------+-----------------------------------------------------+ +| :doc:`fix nve/body ` | integrate motion of a body particle in NVE ensemble | ++------------------------------------------------+-----------------------------------------------------+ +| :doc:`fix nvt/body ` | ditto for NVT ensemble | ++------------------------------------------------+-----------------------------------------------------+ +| :doc:`fix npt/body ` | ditto for NPT ensemble | ++------------------------------------------------+-----------------------------------------------------+ +| :doc:`fix nph/body ` | ditto for NPH ensemble | ++------------------------------------------------+-----------------------------------------------------+ +| :doc:`compute body/local ` | store sub-particle attributes of a body particle | ++------------------------------------------------+-----------------------------------------------------+ +| :doc:`compute temp/body ` | compute temperature of body particles | ++------------------------------------------------+-----------------------------------------------------+ +| :doc:`dump local ` | output sub-particle attributes of a body particle | ++------------------------------------------------+-----------------------------------------------------+ +| :doc:`dump image ` | output body particle attributes as an image | ++------------------------------------------------+-----------------------------------------------------+ + +The pair styles defined for use with specific body styles are listed +in the sections below. + + +---------- + + +**Specifics of body style nparticle:** + +The *nparticle* body style represents body particles as a rigid body +with a variable number N of sub-particles. It is provided as a +vanillia, prototypical example of a body particle, although as +mentioned above, the :doc:`fix rigid ` command already +duplicates its functionality. + +The atom_style body command for this body style takes two additional +arguments: + +.. parsed-literal:: + + atom_style body nparticle Nmin Nmax + Nmin = minimum # of sub-particles in any body in the system + Nmax = maximum # of sub-particles in any body in the system + +The Nmin and Nmax arguments are used to bound the size of data +structures used internally by each particle. + +When the :doc:`read_data ` command reads a data file for this +body style, the following information must be provided for each entry +in the *Bodies* section of the data file: + +.. parsed-literal:: + + atom-ID 1 M + N + ixx iyy izz ixy ixz iyz + x1 y1 z1 + ... + xN yN zN + +N is the number of sub-particles in the body particle. M = 6 + 3*N. +The integer line has a single value N. The floating point line(s) +list 6 moments of inertia followed by the coordinates of the N +sub-particles (x1 to zN) as 3N values. These values can be listed on +as many lines as you wish; see the :doc:`read_data ` command +for more details. + +The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the +values consistent with the current orientation of the rigid body +around its center of mass. The values are with respect to the +simulation box XYZ axes, not with respect to the prinicpal axes of the +rigid body itself. LAMMPS performs the latter calculation internally. +The coordinates of each sub-particle are specified as its x,y,z +displacement from the center-of-mass of the body particle. The +center-of-mass position of the particle is specified by the x,y,z +values in the *Atoms* section of the data file, as is the total mass +of the body particle. + +The :doc:`pair_style body ` command can be used with this +body style to compute body/body and body/non-body interactions. + +For output purposes via the :doc:`compute body/local ` and :doc:`dump local ` +commands, this body style produces one datum for each of the N +sub-particles in a body particle. The datum has 3 values: + +.. parsed-literal:: + + 1 = x position of sub-particle + 2 = y position of sub-particle + 3 = z position of sub-particle + +These values are the current position of the sub-particle within the +simulation domain, not a displacement from the center-of-mass (COM) of +the body particle itself. These values are calculated using the +current COM and orientation of the body particle. + +For images created by the :doc:`dump image ` command, if the +*body* keyword is set, then each body particle is drawn as a +collection of spheres, one for each sub-particle. The size of each +sphere is determined by the *bflag1* parameter for the *body* keyword. +The *bflag2* argument is ignored. + + +---------- + + +**Specifics of body style rounded/polygon:** + +The *rounded/polygon* body style represents body particles as a convex +polygon with a variable number N > 2 of vertices, which can only be +used for 2d models. One example use of this body style is for 2d +discrete element models, as described in :ref:`Fraige `. Similar to +body style *nparticle*, the atom_style body command for this body +style takes two additional arguments: + +.. parsed-literal:: + + atom_style body rounded/polygon Nmin Nmax + Nmin = minimum # of vertices in any body in the system + Nmax = maximum # of vertices in any body in the system + +The Nmin and Nmax arguments are used to bound the size of data +structures used internally by each particle. + +When the :doc:`read_data ` command reads a data file for this +body style, the following information must be provided for each entry +in the *Bodies* section of the data file: + +.. parsed-literal:: + + atom-ID 1 M + N + ixx iyy izz ixy ixz iyz + x1 y1 z1 + ... + xN yN zN + i j j k k ... + radius + +N is the number of vertices in the body particle. M = 6 + 3*N + 2*N + +1. The integer line has a single value N. The floating point line(s) +list 6 moments of inertia followed by the coordinates of the N +vertices (x1 to zN) as 3N values, followed by 2N vertex indices +corresponding to the end points of the N edges, followed by a single +radius value = the smallest circle encompassing the polygon. That +last value is used to facilitate the body/body contact detection. +These floating-point values can be listed on as many lines as you +wish; see the :doc:`read_data ` command for more details. + +The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the +values consistent with the current orientation of the rigid body +around its center of mass. The values are with respect to the +simulation box XYZ axes, not with respect to the prinicpal axes of the +rigid body itself. LAMMPS performs the latter calculation internally. +The coordinates of each vertex are specified as its x,y,z displacement +from the center-of-mass of the body particle. The center-of-mass +position of the particle is specified by the x,y,z values in the +*Atoms* section of the data file. + +For example, the following information would specify a square +particles whose edge length is sqrt(2): + +.. parsed-literal:: + + 3 1 27 + 4 + 1 1 4 0 0 0 + -0.7071 -0.7071 0 + -0.7071 0.7071 0 + 0.7071 0.7071 0 + 0.7071 -0.7071 0 + 0 1 1 2 2 3 3 0 + 1.0 + +The :doc:`pair_style body/rounded/polygon ` command +can be used with this body style to compute body/body interactions. + +For output purposes via the :doc:`compute body/local ` and :doc:`dump local ` +commands, this body style produces one datum for each of the N +sub-particles in a body particle. The datum has 3 values: + +.. parsed-literal:: + + 1 = x position of vertex + 2 = y position of vertex + 3 = z position of vertex + +These values are the current position of the vertex within the +simulation domain, not a displacement from the center-of-mass (COM) of +the body particle itself. These values are calculated using the +current COM and orientation of the body particle. + +For images created by the :doc:`dump image ` command, if the +*body* keyword is set, then each body particle is drawn as a convex +polygon consisting of N line segments. Note that the line segments +are drawn between the N vertices, which does not correspond exactly to +the physical extent of the body (because the `pair_style rounded/polygon `_ defines finite-size +spheres at those point and the line segments between the spheres are +tangent to the spheres). The drawn diameter of each line segment is +determined by the *bflag1* parameter for the *body* keyword. The +*bflag2* argument is ignored. + + +---------- + + +.. _Fraige: + + + +**(Fraige)** F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, +Particuology, 6, 455 (2008). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_class2.txt b/doc/_sources/bond_class2.txt new file mode 100644 index 0000000000..95b0169866 --- /dev/null +++ b/doc/_sources/bond_class2.txt @@ -0,0 +1,101 @@ +.. index:: bond_style class2 + +bond_style class2 command +========================= + +bond_style class2/omp command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + bond_style class2 + +Examples +"""""""" + +.. parsed-literal:: + + bond_style class2 + bond_coeff 1 1.0 100.0 80.0 80.0 + +Description +""""""""""" + +The *class2* bond style uses the potential + +.. image:: Eqs/bond_class2.jpg + :align: center + +where r0 is the equilibrium bond distance. + +See :ref:`(Sun) ` for a description of the COMPASS class2 force field. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* R0 (distance) +* K2 (energy/distance^2) +* K3 (energy/distance^3) +* K4 (energy/distance^4) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the CLASS2 +package. See the :ref:`Making LAMMPS ` section +for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +---------- + + +.. _Sun: + + + +**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_coeff.txt b/doc/_sources/bond_coeff.txt new file mode 100644 index 0000000000..a57efc4e3f --- /dev/null +++ b/doc/_sources/bond_coeff.txt @@ -0,0 +1,112 @@ +.. index:: bond_coeff + +bond_coeff command +================== + +Syntax +"""""" + +.. parsed-literal:: + + bond_coeff N args + +* N = bond type (see asterisk form below) +* args = coefficients for one or more bond types + +Examples +"""""""" + +.. parsed-literal:: + + bond_coeff 5 80.0 1.2 + bond_coeff * 30.0 1.5 1.0 1.0 + bond_coeff 1*4 30.0 1.5 1.0 1.0 + bond_coeff 1 harmonic 200.0 1.0 + +Description +""""""""""" + +Specify the bond force field coefficients for one or more bond types. +The number and meaning of the coefficients depends on the bond style. +Bond coefficients can also be set in the data file read by the +:doc:`read_data ` command or in a restart file. + +N can be specified in one of two ways. An explicit numeric value can +be used, as in the 1st example above. Or a wild-card asterisk can be +used to set the coefficients for multiple bond types. This takes the +form "*" or "*n" or "n*" or "m*n". If N = the number of bond types, +then an asterisk with no numeric values means all types from 1 to N. A +leading asterisk means all types from 1 to n (inclusive). A trailing +asterisk means all types from n to N (inclusive). A middle asterisk +means all types from m to n (inclusive). + +Note that using a bond_coeff command can override a previous setting +for the same bond type. For example, these commands set the coeffs +for all bond types, then overwrite the coeffs for just bond type 2: + +.. parsed-literal:: + + bond_coeff * 100.0 1.2 + bond_coeff 2 200.0 1.2 + +A line in a data file that specifies bond coefficients uses the exact +same format as the arguments of the bond_coeff command in an input +script, except that wild-card asterisks should not be used since +coefficients for all N types must be listed in the file. For example, +under the "Bond Coeffs" section of a data file, the line that +corresponds to the 1st example above would be listed as + +.. parsed-literal:: + + 5 80.0 1.2 + + +---------- + + +Here is an alphabetic list of bond styles defined in LAMMPS. Click on +the style to display the formula it computes and coefficients +specified by the associated :doc:`bond_coeff ` command. + +Note that here are also additional bond styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the bond section of :ref:`this page `. + +* :doc:`bond_style none ` - turn off bonded interactions +* :doc:`bond_style hybrid ` - define multiple styles of bond interactions + +* :doc:`bond_style class2 ` - COMPASS (class 2) bond +* :doc:`bond_style fene ` - FENE (finite-extensible non-linear elastic) bond +* :doc:`bond_style fene/expand ` - FENE bonds with variable size particles +* :doc:`bond_style harmonic ` - harmonic bond +* :doc:`bond_style morse ` - Morse bond +* :doc:`bond_style nonlinear ` - nonlinear bond +* :doc:`bond_style quartic ` - breakable quartic bond +* :doc:`bond_style table ` - tabulated by bond length + + +---------- + + +Restrictions +"""""""""""" + + +This command must come after the simulation box is defined by a +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. + +A bond style must be defined before any bond coefficients are set, +either in the input script or in a data file. + +Related commands +"""""""""""""""" + +:doc:`bond_style ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_fene.txt b/doc/_sources/bond_fene.txt new file mode 100644 index 0000000000..6218a34e58 --- /dev/null +++ b/doc/_sources/bond_fene.txt @@ -0,0 +1,109 @@ +.. index:: bond_style fene + +bond_style fene command +======================= + +bond_style fene/kk command +========================== + +bond_style fene/omp command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + bond_style fene + +Examples +"""""""" + +.. parsed-literal:: + + bond_style fene + bond_coeff 1 30.0 1.5 1.0 1.0 + +Description +""""""""""" + +The *fene* bond style uses the potential + +.. image:: Eqs/bond_fene.jpg + :align: center + +to define a finite extensible nonlinear elastic (FENE) potential +:ref:`(Kremer) `, used for bead-spring polymer models. The first +term is attractive, the 2nd Lennard-Jones term is repulsive. The +first term extends to R0, the maximum extent of the bond. The 2nd +term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy/distance^2) +* R0 (distance) +* epsilon (energy) +* sigma (distance) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +You typically should specify `special_bonds fene `_ +or :doc:`special_bonds lj/coul 0 1 1 ` to use this bond +style. LAMMPS will issue a warning it that's not the case. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +---------- + + +.. _Kremer: + + + +**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_fene_expand.txt b/doc/_sources/bond_fene_expand.txt new file mode 100644 index 0000000000..20bb1472ee --- /dev/null +++ b/doc/_sources/bond_fene_expand.txt @@ -0,0 +1,111 @@ +.. index:: bond_style fene/expand + +bond_style fene/expand command +============================== + +bond_style fene/expand/omp command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + bond_style fene/expand + +Examples +"""""""" + +.. parsed-literal:: + + bond_style fene/expand + bond_coeff 1 30.0 1.5 1.0 1.0 0.5 + +Description +""""""""""" + +The *fene/expand* bond style uses the potential + +.. image:: Eqs/bond_fene_expand.jpg + :align: center + +to define a finite extensible nonlinear elastic (FENE) potential +:ref:`(Kremer) `, used for bead-spring polymer models. The first +term is attractive, the 2nd Lennard-Jones term is repulsive. + +The *fene/expand* bond style is similar to *fene* except that an extra +shift factor of delta (positive or negative) is added to *r* to +effectively change the bead size of the bonded atoms. The first term +now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma ++ delta. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy/distance^2) +* R0 (distance) +* epsilon (energy) +* sigma (distance) +* delta (distance) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +You typically should specify `special_bonds fene `_ +or :doc:`special_bonds lj/coul 0 1 1 ` to use this bond +style. LAMMPS will issue a warning it that's not the case. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +---------- + + +.. _Kremer: + + + +**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_harmonic.txt b/doc/_sources/bond_harmonic.txt new file mode 100644 index 0000000000..842cd9f6c1 --- /dev/null +++ b/doc/_sources/bond_harmonic.txt @@ -0,0 +1,93 @@ +.. index:: bond_style harmonic + +bond_style harmonic command +=========================== + +bond_style harmonic/intel command +================================= + +bond_style harmonic/kk command +============================== + +bond_style harmonic/omp command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + bond_style harmonic + +Examples +"""""""" + +.. parsed-literal:: + + bond_style harmonic + bond_coeff 5 80.0 1.2 + +Description +""""""""""" + +The *harmonic* bond style uses the potential + +.. image:: Eqs/bond_harmonic.jpg + :align: center + +where r0 is the equilibrium bond distance. Note that the usual 1/2 +factor is included in K. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy/distance^2) +* r0 (distance) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_harmonic_shift.txt b/doc/_sources/bond_harmonic_shift.txt new file mode 100644 index 0000000000..b62b14dfc1 --- /dev/null +++ b/doc/_sources/bond_harmonic_shift.txt @@ -0,0 +1,94 @@ +.. index:: bond_style harmonic/shift + +bond_style harmonic/shift command +================================= + +bond_style harmonic/shift/omp command +===================================== + +Syntax +"""""" + +.. parsed-literal:: + + bond_style harmonic/shift + +Examples +"""""""" + +.. parsed-literal:: + + bond_style harmonic/shift + bond_coeff 5 10.0 0.5 1.0 + +Description +""""""""""" + +The *harmonic/shift* bond style is a shifted harmonic bond that uses +the potential + +.. image:: Eqs/bond_harmonic_shift.jpg + :align: center + +where r0 is the equilibrium bond distance, and rc the critical distance. +The potential is -Umin at r0 and zero at rc. The spring constant is +k = Umin / [ 2 (r0-rc)^2]. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* Umin (energy) + +* r0 (distance) + +* rc (distance) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds `, +:doc:`bond_harmonic ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_harmonic_shift_cut.txt b/doc/_sources/bond_harmonic_shift_cut.txt new file mode 100644 index 0000000000..6f04183a21 --- /dev/null +++ b/doc/_sources/bond_harmonic_shift_cut.txt @@ -0,0 +1,93 @@ +.. index:: bond_style harmonic/shift/cut + +bond_style harmonic/shift/cut command +===================================== + +bond_style harmonic/shift/cut/omp command +========================================= + +Syntax +"""""" + +.. parsed-literal:: + + bond_style harmonic/shift/cut + +Examples +"""""""" + +.. parsed-literal:: + + bond_style harmonic/shift/cut + bond_coeff 5 10.0 0.5 1.0 + +Description +""""""""""" + +The *harmonic/shift/cut* bond style is a shifted harmonic bond that +uses the potential + +.. image:: Eqs/bond_harmonic_shift_cut.jpg + :align: center + +where r0 is the equilibrium bond distance, and rc the critical distance. +The bond potential is zero for distances r > rc. The potential is -Umin +at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)^2]. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* Umin (energy) +* r0 (distance) +* rc (distance) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds `, +:doc:`bond_harmonic `, +:doc:`bond_harmonicshift ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_hybrid.txt b/doc/_sources/bond_hybrid.txt new file mode 100644 index 0000000000..a07e051db6 --- /dev/null +++ b/doc/_sources/bond_hybrid.txt @@ -0,0 +1,88 @@ +.. index:: bond_style hybrid + +bond_style hybrid command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + bond_style hybrid style1 style2 ... + +* style1,style2 = list of one or more bond styles + +Examples +"""""""" + +.. parsed-literal:: + + bond_style hybrid harmonic fene + bond_coeff 1 harmonic 80.0 1.2 + bond_coeff 2* fene 30.0 1.5 1.0 1.0 + +Description +""""""""""" + +The *hybrid* style enables the use of multiple bond styles in one +simulation. A bond style is assigned to each bond type. For example, +bonds in a polymer flow (of bond type 1) could be computed with a +*fene* potential and bonds in the wall boundary (of bond type 2) could +be computed with a *harmonic* potential. The assignment of bond type +to style is made via the :doc:`bond_coeff ` command or in +the data file. + +In the bond_coeff commands, the name of a bond style must be added +after the bond type, with the remaining coefficients being those +appropriate to that style. In the example above, the 2 bond_coeff +commands set bonds of bond type 1 to be computed with a *harmonic* +potential with coefficients 80.0, 1.2 for K, r0. All other bond types +(2-N) are computed with a *fene* potential with coefficients 30.0, +1.5, 1.0, 1.0 for K, R0, epsilon, sigma. + +If bond coefficients are specified in the data file read via the +:doc:`read_data ` command, then the same rule applies. +E.g. "harmonic" or "fene" must be added after the bond type, for each +line in the "Bond Coeffs" section, e.g. + +.. parsed-literal:: + + Bond Coeffs + +.. parsed-literal:: + + 1 harmonic 80.0 1.2 + 2 fene 30.0 1.5 1.0 1.0 + ... + +A bond style of *none* with no additional coefficients can be used in +place of a bond style, either in a input script bond_coeff command or +in the data file, if you desire to turn off interactions for specific +bond types. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Unlike other bond styles, the hybrid bond style does not store bond +coefficient info for individual sub-styles in a :doc:`binary restart files `. Thus when retarting a simulation from a restart +file, you need to re-specify bond_coeff commands. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_morse.txt b/doc/_sources/bond_morse.txt new file mode 100644 index 0000000000..d31766a9d8 --- /dev/null +++ b/doc/_sources/bond_morse.txt @@ -0,0 +1,88 @@ +.. index:: bond_style morse + +bond_style morse command +======================== + +bond_style morse/omp command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + bond_style morse + +Examples +"""""""" + +.. parsed-literal:: + + bond_style morse + bond_coeff 5 1.0 2.0 1.2 + +Description +""""""""""" + +The *morse* bond style uses the potential + +.. image:: Eqs/bond_morse.jpg + :align: center + +where r0 is the equilibrium bond distance, alpha is a stiffness +parameter, and D determines the depth of the potential well. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* D (energy) +* alpha (inverse distance) +* r0 (distance) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_none.txt b/doc/_sources/bond_none.txt new file mode 100644 index 0000000000..7dc635a852 --- /dev/null +++ b/doc/_sources/bond_none.txt @@ -0,0 +1,38 @@ +.. index:: bond_style none + +bond_style none command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + bond_style none + +Examples +"""""""" + +.. parsed-literal:: + + bond_style none + +Description +""""""""""" + +Using a bond style of none means bond forces are not computed, even if +pairs of bonded atoms were listed in the data file read by the +:doc:`read_data ` command. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_nonlinear.txt b/doc/_sources/bond_nonlinear.txt new file mode 100644 index 0000000000..1db2d83ca2 --- /dev/null +++ b/doc/_sources/bond_nonlinear.txt @@ -0,0 +1,98 @@ +.. index:: bond_style nonlinear + +bond_style nonlinear command +============================ + +bond_style nonlinear/omp command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + bond_style nonlinear + +Examples +"""""""" + +.. parsed-literal:: + + bond_style nonlinear + bond_coeff 2 100.0 1.1 1.4 + +Description +""""""""""" + +The *nonlinear* bond style uses the potential + +.. image:: Eqs/bond_nonlinear.jpg + :align: center + +to define an anharmonic spring :ref:`(Rector) ` of equilibrium +length r0 and maximum extension lamda. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* epsilon (energy) +* r0 (distance) +* lamda (distance) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +---------- + + +.. _Rector: + + + +**(Rector)** Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_quartic.txt b/doc/_sources/bond_quartic.txt new file mode 100644 index 0000000000..9cfe81f22d --- /dev/null +++ b/doc/_sources/bond_quartic.txt @@ -0,0 +1,128 @@ +.. index:: bond_style quartic + +bond_style quartic command +========================== + +bond_style quartic/omp command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + bond_style quartic + +Examples +"""""""" + +.. parsed-literal:: + + bond_style quartic + bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 + +Description +""""""""""" + +The *quartic* bond style uses the potential + +.. image:: Eqs/bond_quartic.jpg + :align: center + +to define a bond that can be broken as the simulation proceeds (e.g. +due to a polymer being stretched). The sigma and epsilon used in the +LJ portion of the formula are both set equal to 1.0 by LAMMPS. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy/distance^4) +* B1 (distance) +* B2 (distance) +* Rc (distance) +* U0 (energy) + +This potential was constructed to mimic the FENE bond potential for +coarse-grained polymer chains. When monomers with sigma = epsilon = +1.0 are used, the following choice of parameters gives a quartic +potential that looks nearly like the FENE potential: K = 1200, B1 = +-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters +can be specified using the :doc:`bond_coeff ` command, but +you will need to choose them carefully so they form a suitable bond +potential. + +Rc is the cutoff length at which the bond potential goes smoothly to a +local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks" +the bond, which means two things. First, the bond potential is turned +off by setting its type to 0, and is no longer computed. Second, a +pairwise interaction between the two atoms is turned on, since they +are no longer bonded. + +LAMMPS does the second task via a computational sleight-of-hand. It +subtracts the pairwise interaction as part of the bond computation. +When the bond breaks, the subtraction stops. For this to work, the +pairwise interaction must always be computed by the +:doc:`pair_style ` command, whether the bond is broken or +not. This means that :doc:`special_bonds ` must be set +to 1,1,1, as indicated as a restriction below. + +Note that when bonds are dumped to a file via the :doc:`dump local ` command, bonds with type 0 are not included. The +:doc:`delete_bonds ` command can also be used to query the +status of broken bonds or permanently delete them, e.g.: + +.. parsed-literal:: + + delete_bonds all stats + delete_bonds all bond 0 remove + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +The *quartic* style requires that :doc:`special_bonds ` +parameters be set to 1,1,1. Three- and four-body interactions (angle, +dihedral, etc) cannot be used with *quartic* bonds. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_style.txt b/doc/_sources/bond_style.txt new file mode 100644 index 0000000000..eba8caf6e6 --- /dev/null +++ b/doc/_sources/bond_style.txt @@ -0,0 +1,121 @@ +.. index:: bond_style + +bond_style command +================== + +Syntax +"""""" + +.. parsed-literal:: + + bond_style style args + +* style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or *harmonic* or *morse* or *nonlinear* or *quartic* + +.. parsed-literal:: + + args = none for any style except *hybrid* + *hybrid* args = list of one or more styles + +Examples +"""""""" + +.. parsed-literal:: + + bond_style harmonic + bond_style fene + bond_style hybrid harmonic fene + +Description +""""""""""" + +Set the formula(s) LAMMPS uses to compute bond interactions between +pairs of atoms. In LAMMPS, a bond differs from a pairwise +interaction, which are set via the :doc:`pair_style ` +command. Bonds are defined between specified pairs of atoms and +remain in force for the duration of the simulation (unless the bond +breaks which is possible in some bond potentials). The list of bonded +atoms is read in by a :doc:`read_data ` or +:doc:`read_restart ` command from a data or restart file. +By contrast, pair potentials are typically defined between all pairs +of atoms within a cutoff distance and the set of active interactions +changes over time. + +Hybrid models where bonds are computed using different bond potentials +can be setup using the *hybrid* bond style. + +The coefficients associated with a bond style can be specified in a +data or restart file or via the :doc:`bond_coeff ` command. + +All bond potentials store their coefficient data in binary restart +files which means bond_style and :doc:`bond_coeff ` commands +do not need to be re-specified in an input script that restarts a +simulation. See the :doc:`read_restart ` command for +details on how to do this. The one exception is that bond_style +*hybrid* only stores the list of sub-styles in the restart file; bond +coefficients need to be re-specified. + +.. note:: + + When both a bond and pair style is defined, the + :doc:`special_bonds ` command often needs to be used to + turn off (or weight) the pairwise interaction that would otherwise + exist between 2 bonded atoms. + +In the formulas listed for each bond style, *r* is the distance +between the 2 atoms in the bond. + + +---------- + + +Here is an alphabetic list of bond styles defined in LAMMPS. Click on +the style to display the formula it computes and coefficients +specified by the associated :doc:`bond_coeff ` command. + +Note that there are also additional bond styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the bond section of :ref:`this page `. + +* :doc:`bond_style none ` - turn off bonded interactions +* :doc:`bond_style hybrid ` - define multiple styles of bond interactions + +* :doc:`bond_style class2 ` - COMPASS (class 2) bond +* :doc:`bond_style fene ` - FENE (finite-extensible non-linear elastic) bond +* :doc:`bond_style fene/expand ` - FENE bonds with variable size particles +* :doc:`bond_style harmonic ` - harmonic bond +* :doc:`bond_style morse ` - Morse bond +* :doc:`bond_style nonlinear ` - nonlinear bond +* :doc:`bond_style quartic ` - breakable quartic bond +* :doc:`bond_style table ` - tabulated by bond length + + +---------- + + +Restrictions +"""""""""""" + + +Bond styles can only be set for atom styles that allow bonds to be +defined. + +Most bond styles are part of the MOLECULE package. They are only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info on packages. +The doc pages for individual bond potentials tell if it is part of a +package. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +Default +""""""" + +bond_style none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/bond_table.txt b/doc/_sources/bond_table.txt new file mode 100644 index 0000000000..11aebc8b72 --- /dev/null +++ b/doc/_sources/bond_table.txt @@ -0,0 +1,172 @@ +.. index:: bond_style table + +bond_style table command +======================== + +bond_style table/omp command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + bond_style table style N + +* style = *linear* or *spline* = method of interpolation +* N = use N values in table + +Examples +"""""""" + +.. parsed-literal:: + + bond_style table linear 1000 + bond_coeff 1 file.table ENTRY1 + +Description +""""""""""" + +Style *table* creates interpolation tables of length *N* from bond +potential and force values listed in a file(s) as a function of bond +length. The files are read by the :doc:`bond_coeff ` +command. + +The interpolation tables are created by fitting cubic splines to the +file values and interpolating energy and force values at each of *N* +distances. During a simulation, these tables are used to interpolate +energy and force values as needed. The interpolation is done in one +of 2 styles: *linear* or *spline*. + +For the *linear* style, the bond length is used to find 2 surrounding +table values from which an energy or force is computed by linear +interpolation. + +For the *spline* style, a cubic spline coefficients are computed and +stored at each of the *N* values in the table. The bond length is +used to find the appropriate set of coefficients which are used to +evaluate a cubic polynomial which computes the energy or force. + +The following coefficients must be defined for each bond type via the +:doc:`bond_coeff ` command as in the example above. + +* filename +* keyword + +The filename specifies a file containing tabulated energy and force +values. The keyword specifies a section of the file. The format of +this file is described below. + + +---------- + + +The format of a tabulated file is as follows (without the +parenthesized comments): + +.. parsed-literal:: + + # Bond potential for harmonic (one or more comment or blank lines) + +.. parsed-literal:: + + HAM (keyword is the first text on line) + N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters) + (blank line) + 1 0.00 338.0000 1352.0000 (index, bond-length, energy, force) + 2 0.01 324.6152 1324.9600 + ... + 101 1.00 338.0000 -1352.0000 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the +:doc:`bond_coeff ` command. The next line lists (in any +order) one or more parameters for the table. Each parameter is a +keyword followed by one or more numeric values. + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the *N* +specified in the :doc:`bond_style table ` command. Let +Ntable = *N* in the bond_style command, and Nfile = "N" in the +tabulated file. What LAMMPS does is a preliminary interpolation by +creating splines using the Nfile tabulated values as nodal points. It +uses these to interpolate as needed to generate energy and force +values at Ntable different points. The resulting tables of length +Ntable are then used as described above, when computing energy and +force for individual bond lengths. This means that if you want the +interpolation tables of length Ntable to match exactly what is in the +tabulated file (with effectively no preliminary interpolation), you +should set Ntable = Nfile. + +The "FP" parameter is optional. If used, it is followed by two values +fplo and fphi, which are the derivatives of the force at the innermost +and outermost bond lengths. These values are needed by the spline +construction routines. If not specified by the "FP" parameter, they +are estimated (less accurately) by the first two and last two force +values in the table. + +The "EQ" parameter is also optional. If used, it is followed by a the +equilibrium bond length, which is used, for example, by the :doc:`fix shake ` command. If not used, the equilibrium bond +length is set to 0.0. + +Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +the bond length r (in distance units), the 3rd value is the energy (in +energy units), and the 4th is the force (in force units). The bond +lengths must range from a LO value to a HI value, and increase from +one line to the next. If the actual bond length is ever smaller than +the LO value or larger than the HI value, then the bond energy and +force is evaluated as if the bond were the LO or HI length. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This bond style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`bond_coeff `, :doc:`delete_bonds ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/boundary.txt b/doc/_sources/boundary.txt new file mode 100644 index 0000000000..99f5ff6f0b --- /dev/null +++ b/doc/_sources/boundary.txt @@ -0,0 +1,114 @@ +.. index:: boundary + +boundary command +================ + +Syntax +"""""" + +.. parsed-literal:: + + boundary x y z + +* x,y,z = *p* or *s* or *f* or *m*, one or two letters +.. parsed-literal:: + + *p* is periodic + *f* is non-periodic and fixed + *s* is non-periodic and shrink-wrapped + *m* is non-periodic and shrink-wrapped with a minimum value + + + +Examples +"""""""" + +.. parsed-literal:: + + boundary p p f + boundary p fs p + boundary s f fm + +Description +""""""""""" + +Set the style of boundaries for the global simulation box in each +dimension. A single letter assigns the same style to both the lower +and upper face of the box. Two letters assigns the first style to the +lower face and the second style to the upper face. The initial size +of the simulation box is set by the :doc:`read_data `, +:doc:`read_restart `, or :doc:`create_box ` +commands. + +The style *p* means the box is periodic, so that particles interact +across the boundary, and they can exit one end of the box and re-enter +the other end. A periodic dimension can change in size due to +constant pressure boundary conditions or box deformation (see the :doc:`fix npt ` and :doc:`fix deform ` commands). The *p* +style must be applied to both faces of a dimension. + +The styles *f*, *s*, and *m* mean the box is non-periodic, so that +particles do not interact across the boundary and do not move from one +side of the box to the other. + +For style *f*, the position of the face is fixed. If an atom moves +outside the face it will be deleted on the next timestep that +reneighboring occurs. This will typically generate an error unless +you have set the :doc:`thermo_modify lost ` option to +allow for lost atoms. + +For style *s*, the position of the face is set so as to encompass the +atoms in that dimension (shrink-wrapping), no matter how far they +move. + +For style *m*, shrink-wrapping occurs, but is bounded by the value +specified in the data or restart file or set by the +:doc:`create_box ` command. For example, if the upper z +face has a value of 50.0 in the data file, the face will always be +positioned at 50.0 or above, even if the maximum z-extent of all the +atoms becomes less than 50.0. This can be useful if you start a +simulation with an empty box or if you wish to leave room on one side +of the box, e.g. for atoms to evaporate from a surface. + +For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension +of a tilt factor (e.g. y for xy) is periodic, then the periodicity is +enforced with the tilt factor offset. If the 1st dimension is +shrink-wrapped, then the shrink wrapping is applied to the tilted box +face, to encompass the atoms. E.g. for a positive xy tilt, the xlo +and xhi faces of the box are planes tilting in the +y direction as y +increases. These tilted planes are shrink-wrapped around the atoms to +determine the x extent of the box. + +See :ref:`Section_howto 12 ` of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used +triclinic representations. + +Restrictions +"""""""""""" + + +This command cannot be used after the simulation box is defined by a +:doc:`read_data ` or :doc:`create_box ` command or +:doc:`read_restart ` command. See the +:doc:`change_box ` command for how to change the simulation +box boundaries after it has been defined. + +For 2d simulations, the z dimension must be periodic. + +Related commands +"""""""""""""""" + +See the :doc:`thermo_modify ` command for a discussion +of lost atoms. + +Default +""""""" + +.. parsed-literal:: + + boundary p p p + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/box.txt b/doc/_sources/box.txt new file mode 100644 index 0000000000..e77f24c1ad --- /dev/null +++ b/doc/_sources/box.txt @@ -0,0 +1,73 @@ +.. index:: box + +box command +=========== + +Syntax +"""""" + +.. parsed-literal:: + + box keyword value ... + +* one or more keyword/value pairs may be appended +* keyword = *tilt* +.. parsed-literal:: + + *tilt* value = *small* or *large* + + + +Examples +"""""""" + +.. parsed-literal:: + + box tilt large + box tilt small + +Description +""""""""""" + +Set attributes of the simulation box. + +For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword +allows simulation domains to be created with arbitrary tilt factors, +e.g. via the :doc:`create_box ` or +:doc:`read_data ` commands. Tilt factors determine how +skewed the triclinic box is; see :ref:`this section ` of the manual for a discussion of +triclinic boxes in LAMMPS. + +LAMMPS normally requires that no tilt factor can skew the box more +than half the distance of the parallel box length, which is the 1st +dimension in the tilt factor (x for xz). If *tilt* is set to +*small*, which is the default, then an error will be +generated if a box is created which exceeds this limit. If *tilt* +is set to *large*, then no limit is enforced. You can create +a box with any tilt factors you wish. + +Note that if a simulation box has a large tilt factor, LAMMPS will run +less efficiently, due to the large volume of communication needed to +acquire ghost atoms around a processor's irregular-shaped sub-domain. +For extreme values of tilt, LAMMPS may also lose atoms and generate an +error. + +Restrictions +"""""""""""" + + +This command cannot be used after the simulation box is defined by a +:doc:`read_data ` or :doc:`create_box ` command or +:doc:`read_restart ` command. + +**Related commands:** none + +Default +""""""" + +The default value is tilt = small. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/change_box.txt b/doc/_sources/change_box.txt new file mode 100644 index 0000000000..56f220f209 --- /dev/null +++ b/doc/_sources/change_box.txt @@ -0,0 +1,381 @@ +.. index:: change_box + +change_box command +================== + +Syntax +"""""" + +.. parsed-literal:: + + change_box group-ID parameter args ... keyword args ... + +* group-ID = ID of group of atoms to (optionally) displace +* one or more parameter/arg pairs may be appended +.. parsed-literal:: + + parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *boundary* or *ortho* or *triclinic* or *set* or *remap* + *x*, *y*, *z* args = style value(s) + style = *final* or *delta* or *scale* or *volume* + *final* values = lo hi + lo hi = box boundaries after displacement (distance units) + *delta* values = dlo dhi + dlo dhi = change in box boundaries after displacement (distance units) + *scale* values = factor + factor = multiplicative factor for change in box length after displacement + *volume* value = none = adjust this dim to preserve volume of system + *xy*, *xz*, *yz* args = style value + style = *final* or *delta* + *final* value = tilt + tilt = tilt factor after displacement (distance units) + *delta* value = dtilt + dtilt = change in tilt factor after displacement (distance units) + *boundary* args = x y z + x,y,z = *p* or *s* or *f* or *m*, one or two letters + *p* is periodic + *f* is non-periodic and fixed + *s* is non-periodic and shrink-wrapped + *m* is non-periodic and shrink-wrapped with a minimum value + *ortho* args = none = change box to orthogonal + *triclinic* args = none = change box to triclinic + *set* args = none = store state of current box + *remap* args = none = remap atom coords from last saved state to current box + +* zero or more keyword/value pairs may be appended +* keyword = *units* +.. parsed-literal:: + + *units* value = *lattice* or *box* + lattice = distances are defined in lattice units + box = distances are defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box + change_box all x scale 1.1 y volume z volume remap + +Description +""""""""""" + +Change the volume and/or shape and/or boundary conditions for the +simulation box. Orthogonal simulation boxes have 3 adjustable size +parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have +6 adjustable size/shape parameters (x,y,z,xy,xz,yz). Any or all of +them can be adjusted independently by this command. Thus it can be +used to expand or contract a box, or to apply a shear strain to a +non-orthogonal box. It can also be used to change the boundary +conditions for the simulation box, similar to the +:doc:`boundary ` command. + +The size and shape of the initial simulation box are specified by the +:doc:`create_box ` or :doc:`read_data ` or +:doc:`read_restart ` command used to setup the simulation. +The size and shape may be altered by subsequent runs, e.g. by use of +the :doc:`fix npt ` or :doc:`fix deform ` commands. +The :doc:`create_box `, :doc:`read data `, and +:doc:`read_restart ` commands also determine whether the +simulation box is orthogonal or triclinic and their doc pages explain +the meaning of the xy,xz,yz tilt factors. + +See :ref:`Section_howto 12 ` of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used +triclinic representations. + +The keywords used in this command are applied sequentially to the +simulation box and the atoms in it, in the order specified. + +Before the sequence of keywords are invoked, the current box +size/shape is stored, in case a *remap* keyword is used to map the +atom coordinates from a previously stored box size/shape to the +current one. + +After all the keywords have been processed, any shrink-wrap boundary +conditions are invoked (see the :doc:`boundary ` command) +which may change simulation box boundaries, and atoms are migrated to +new owning processors. + +.. note:: + + This means that you cannot use the change_box command to enlarge + a shrink-wrapped box, e.g. to make room to insert more atoms via the + :doc:`create_atoms ` command, because the simulation box + will be re-shrink-wrapped before the change_box command completes. + Instead you could do something like this, assuming the simulation box + is non-periodic and atoms extend from 0 to 20 in all dimensions: + +.. parsed-literal:: + + change_box all x final -10 20 + create_atoms 1 single -5 5 5 # this will fail to insert an atom + +.. parsed-literal:: + + change_box all x final -10 20 boundary f s s + create_atoms 1 single -5 5 5 + change_box boundary s s s # this will work + +.. note:: + + Unlike the earlier "displace_box" version of this command, atom + remapping is NOT performed by default. This command allows remapping + to be done in a more general way, exactly when you specify it (zero or + more times) in the sequence of transformations. Thus if you do not + use the *remap* keyword, atom coordinates will not be changed even if + the box size/shape changes. If a uniformly strained state is desired, + the *remap* keyword should be specified. + +.. note:: + + It is possible to lose atoms with this command. E.g. by + changing the box without remapping the atoms, and having atoms end up + outside of non-periodic boundaries. It is also possible to alter + bonds between atoms straddling a boundary in bad ways. E.g. by + converting a boundary from periodic to non-periodic. It is also + possible when remapping atoms to put them (nearly) on top of each + other. E.g. by converting a boundary from non-periodic to periodic. + All of these will typically lead to bad dynamics and/or generate error + messages. + +.. note:: + + The simulation box size/shape can be changed by arbitrarily + large amounts by this command. This is not a problem, except that the + mapping of processors to the simulation box is not changed from its + initial 3d configuration; see the :doc:`processors ` + command. Thus, if the box size/shape changes dramatically, the + mapping of processors to the simulation box may not end up as optimal + as the initial mapping attempted to be. + +.. note:: + + Because the keywords used in this command are applied one at a + time to the simulation box and the atoms in it, care must be taken + with triclinic cells to avoid exceeding the limits on skew after each + transformation in the sequence. If skew is exceeded before the final + transformation this can be avoided by changing the order of the + sequence, or breaking the transformation into two or more smaller + transformations. For more information on the allowed limits for box + skew see the discussion on triclinic boxes on :ref:`this page `. + + +---------- + + +For the *x*, *y*, and *z* parameters, this is the meaning of their +styles and values. + +For style *final*, the final lo and hi box boundaries of a dimension +are specified. The values can be in lattice or box distance units. +See the discussion of the units keyword below. + +For style *delta*, plus or minus changes in the lo/hi box boundaries +of a dimension are specified. The values can be in lattice or box +distance units. See the discussion of the units keyword below. + +For style *scale*, a multiplicative factor to apply to the box length +of a dimension is specified. For example, if the initial box length +is 10, and the factor is 1.1, then the final box length will be 11. A +factor less than 1.0 means compression. + +The *volume* style changes the specified dimension in such a way that +the overall box volume remains constant with respect to the operation +performed by the preceding keyword. The *volume* style can only be +used following a keyword that changed the volume, which is any of the +*x*, *y*, *z* keywords. If the preceding keyword "key" had a *volume* +style, then both it and the current keyword apply to the keyword +preceding "key". I.e. this sequence of keywords is allowed: + +.. parsed-literal:: + + change_box all x scale 1.1 y volume z volume + +The *volume* style changes the associated dimension so that the +overall box volume is unchanged relative to its value before the +preceding keyword was invoked. + +If the following command is used, then the z box length will shrink by +the same 1.1 factor the x box length was increased by: + +.. parsed-literal:: + + change_box all x scale 1.1 z volume + +If the following command is used, then the y,z box lengths will each +shrink by sqrt(1.1) to keep the volume constant. In this case, the +y,z box lengths shrink so as to keep their relative aspect ratio +constant: + +.. parsed-literal:: + + change_box all"x scale 1.1 y volume z volume + +If the following command is used, then the final box will be a factor +of 10% larger in x and y, and a factor of 21% smaller in z, so as to +keep the volume constant: + +.. parsed-literal:: + + change_box all x scale 1.1 z volume y scale 1.1 z volume + +.. note:: + + For solids or liquids, when one dimension of the box is + expanded, it may be physically undesirable to hold the other 2 box + lengths constant since that implies a density change. For solids, + adjusting the other dimensions via the *volume* style may make + physical sense (just as for a liquid), but may not be correct for + materials and potentials whose Poisson ratio is not 0.5. + +For the *scale* and *volume* styles, the box length is expanded or +compressed around its mid point. + + +---------- + + +For the *xy*, *xz*, and *yz* parameters, this is the meaning of their +styles and values. Note that changing the tilt factors of a triclinic +box does not change its volume. + +For style *final*, the final tilt factor is specified. The value +can be in lattice or box distance units. See the discussion of the +units keyword below. + +For style *delta*, a plus or minus change in the tilt factor is +specified. The value can be in lattice or box distance units. See +the discussion of the units keyword below. + +All of these styles change the xy, xz, yz tilt factors. In LAMMPS, +tilt factors (xy,xz,yz) for triclinic boxes are required to be no more +than half the distance of the parallel box length. For example, if +xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt +factor must be between -5 and 5. Similarly, both xz and yz must be +between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a +limitation, since if the maximum tilt factor is 5 (as in this +example), then configurations with tilt = ..., -15, -5, 5, 15, 25, +... are all equivalent. Any tilt factor specified by this command +must be within these limits. + + +---------- + + +The *boundary* keyword takes arguments that have exactly the same +meaning as they do for the :doc:`boundary ` command. In each +dimension, a single letter assigns the same style to both the lower +and upper face of the box. Two letters assigns the first style to the +lower face and the second style to the upper face. + +The style *p* means the box is periodic; the other styles mean +non-periodic. For style *f*, the position of the face is fixed. For +style *s*, the position of the face is set so as to encompass the +atoms in that dimension (shrink-wrapping), no matter how far they +move. For style *m*, shrink-wrapping occurs, but is bounded by the +current box edge in that dimension, so that the box will become no +smaller. See the :doc:`boundary ` command for more +explanation of these style options. + +Note that the "boundary" command itself can only be used before the +simulation box is defined via a :doc:`read_data ` or +:doc:`create_box ` or :doc:`read_restart ` +command. This command allows the boundary conditions to be changed +later in your input script. Also note that the +:doc:`read_restart ` will change boundary conditions to +match what is stored in the restart file. So if you wish to change +them, you should use the change_box command after the read_restart +command. + + +---------- + + +The *ortho* and *triclinic* keywords convert the simulation box to be +orthogonal or triclinic (non-orthongonal). See :ref:`this section ` for a discussion of how non-orthongal +boxes are represented in LAMMPS. + +The simulation box is defined as either orthogonal or triclinic when +it is created via the :doc:`create_box `, +:doc:`read_data `, or :doc:`read_restart ` +commands. + +These keywords allow you to toggle the existing simulation box from +orthogonal to triclinic and vice versa. For example, an initial +equilibration simulation can be run in an orthogonal box, the box can +be toggled to triclinic, and then a :ref:`non-equilibrium MD (NEMD) simulation ` can be run with deformation +via the :doc:`fix deform ` command. + +If the simulation box is currently triclinic and has non-zero tilt in +xy, yz, or xz, then it cannot be converted to an orthogonal box. + + +---------- + + +The *set* keyword saves the current box size/shape. This can be +useful if you wish to use the *remap* keyword more than once or if you +wish it to be applied to an intermediate box size/shape in a sequence +of keyword operations. Note that the box size/shape is saved before +any of the keywords are processed, i.e. the box size/shape at the time +the create_box command is encountered in the input script. + +The *remap* keyword remaps atom coordinates from the last saved box +size/shape to the current box state. For example, if you stretch the +box in the x dimension or tilt it in the xy plane via the *x* and *xy* +keywords, then the *remap* commmand will dilate or tilt the atoms to +conform to the new box size/shape, as if the atoms moved with the box +as it deformed. + +Note that this operation is performed without regard to periodic +boundaries. Also, any shrink-wrapping of non-periodic boundaries (see +the :doc:`boundary ` command) occurs after all keywords, +including this one, have been processed. + +Only atoms in the specified group are remapped. + + +---------- + + +The *units* keyword determines the meaning of the distance units used +to define various arguments. A *box* value selects standard distance +units as defined by the :doc:`units ` command, e.g. Angstroms for +units = real or metal. A *lattice* value means the distance units are +in lattice spacings. The :doc:`lattice ` command must have +been previously used to define the lattice spacing. + + +---------- + + +Restrictions +"""""""""""" + + +If you use the *ortho* or *triclinic* keywords, then at the point in +the input script when this command is issued, no :doc:`dumps ` can +be active, nor can a :doc:`fix ave/spatial ` or :doc:`fix deform ` be active. This is because these commands +test whether the simulation box is orthogonal when they are first +issued. Note that these commands can be used in your script before a +change_box command is issued, so long as an :doc:`undump ` or +:doc:`unfix ` command is also used to turn them off. + +Related commands +"""""""""""""""" + +:doc:`fix deform `, :doc:`boundary ` + +Default +""""""" + +The option default is units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/clear.txt b/doc/_sources/clear.txt new file mode 100644 index 0000000000..f145148cb9 --- /dev/null +++ b/doc/_sources/clear.txt @@ -0,0 +1,47 @@ +.. index:: clear + +clear command +============= + +Syntax +"""""" + +.. parsed-literal:: + + clear + +Examples +"""""""" + +.. parsed-literal:: + + (commands for 1st simulation) + clear + (commands for 2nd simulation) + +Description +""""""""""" + +This command deletes all atoms, restores all settings to their default +values, and frees all memory allocated by LAMMPS. Once a clear +command has been executed, it is almost as if LAMMPS were starting +over, with only the exceptions noted below. This command enables +multiple jobs to be run sequentially from one input script. + +These settings are not affected by a clear command: the working +directory (:doc:`shell ` command), log file status +(:doc:`log ` command), echo status (:doc:`echo ` command), and +input script variables (:doc:`variable ` command). + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/comm_modify.txt b/doc/_sources/comm_modify.txt new file mode 100644 index 0000000000..79a3f5be40 --- /dev/null +++ b/doc/_sources/comm_modify.txt @@ -0,0 +1,177 @@ +.. index:: comm_modify + +comm_modify command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + comm_modify keyword value ... + +* zero or more keyword/value pairs may be appended +* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel* +.. parsed-literal:: + + *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances + *cutoff* value = Rcut (distance units) = communicate atoms from this far away + *cutoff/multi* type value + type = atom type or type range (supports asterisk notation) + value = Rcut (distance units) = communicate atoms for selected types from this far away + *group* value = group-ID = only communicate atoms in the group + *vel* value = *yes* or *no* = do or do not communicate velocity info with ghost atoms + + + +Examples +"""""""" + +.. parsed-literal:: + + comm_modify mode multi + comm_modify mode multi group solvent + comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 + comm_modify vel yes + comm_modify mode single cutoff 5.0 vel yes + comm_modify cutoff/multi * 0.0 + +Description +""""""""""" + +This command sets parameters that affect the inter-processor +communication of atom information that occurs each timestep as +coordinates and other properties are exchanged between neighboring +processors and stored as properties of ghost atoms. + +.. note:: + + These options apply to the currently defined comm style. When + you specify a :doc:`comm_style ` command, all communication + settings are restored to their default values, including those + previously reset by a comm_modify command. Thus if your input script + specifies a comm_style command, you should use the comm_modify command + after it. + +The *mode* keyword determines whether a single or multiple cutoff +distances are used to determine which atoms to communicate. + +The default mode is *single* which means each processor acquires +information for ghost atoms that are within a single distance from its +sub-domain. The distance is by default the maximum of the neighbor +cutoff across all atom type pairs. + +For many systems this is an efficient algorithm, but for systems with +widely varying cutoffs for different type pairs, the *multi* mode can +be faster. In this case, each atom type is assigned its own distance +cutoff for communication purposes, and fewer atoms will be +communicated. See the :doc:`neighbor multi ` command for a +neighbor list construction option that may also be beneficial for +simulations of this kind. + +The *cutoff* keyword allows you to extend the ghost cutoff distance +for communication mode *single*, which is the distance from the borders +of a processor's sub-domain at which ghost atoms are acquired from other +processors. By default the ghost cutoff = neighbor cutoff = pairwise +force cutoff + neighbor skin. See the :doc:`neighbor ` command +for more information about the skin distance. If the specified Rcut is +greater than the neighbor cutoff, then extra ghost atoms will be acquired. +If the provided cutoff is smaller, the provided value will be ignored +and the ghost cutoff is set to the neighbor cutoff. Specifying a +cutoff value of 0.0 will reset any previous value to the default. + +The *cutoff/multi* option is equivalent to *cutoff*, but applies to +communication mode *multi* instead. Since in this case the communication +cutoffs are determined per atom type, a type specifier is needed and +cutoff for one or multiple types can be extended. Also ranges of types +using the usual asterisk notation can be given. + +These are simulation scenarios in which it may be useful or even +necessary to set a ghost cutoff > neighbor cutoff: + +* a single polymer chain with bond interactions, but no pairwise interactions +* bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff +* ghost atoms beyond the pairwise cutoff are needed for some computation + +In the first scenario, a pairwise potential is not defined. Thus the +pairwise neighbor cutoff will be 0.0. But ghost atoms are still +needed for computing bond, angle, etc interactions between atoms on +different processors, or when the interaction straddles a periodic +boundary. + +The appropriate ghost cutoff depends on the :doc:`newton bond ` +setting. For newton bond *off*, the distance needs to be the furthest +distance between any two atoms in the bond, angle, etc. E.g. the +distance between 1-4 atoms in a dihedral. For newton bond *on*, the +distance between the central atom in the bond, angle, etc and any +other atom is sufficient. E.g. the distance between 2-4 atoms in a +dihedral. + +In the second scenario, a pairwise potential is defined, but its +neighbor cutoff is not sufficiently long enough to enable bond, angle, +etc terms to be computed. As in the previous scenario, an appropriate +ghost cutoff should be set. + +In the last scenario, a :doc:`fix ` or :doc:`compute ` or +:doc:`pairwise potential ` needs to calculate with ghost +atoms beyond the normal pairwise cutoff for some computation it +performs (e.g. locate neighbors of ghost atoms in a multibody pair +potential). Setting the ghost cutoff appropriately can insure it will +find the needed atoms. + +.. note:: + + In these scenarios, if you do not set the ghost cutoff long + enough, and if there is only one processor in a periodic dimension + (e.g. you are running in serial), then LAMMPS may "find" the atom it + is looking for (e.g. the partner atom in a bond), that is on the far + side of the simulation box, across a periodic boundary. This will + typically lead to bad dynamics (i.e. the bond length is now the + simulation box length). To detect if this is happening, see the + :doc:`neigh_modify cluster ` command. + +The *group* keyword will limit communication to atoms in the specified +group. This can be useful for models where no ghost atoms are needed +for some kinds of particles. All atoms (not just those in the +specified group) will still migrate to new processors as they move. +The group specified with this option must also be specified via the +:doc:`atom_modify first ` command. + +The *vel* keyword enables velocity information to be communicated with +ghost particles. Depending on the :doc:`atom_style `, +velocity info includes the translational velocity, angular velocity, +and angular momentum of a particle. If the *vel* option is set to +*yes*, then ghost atoms store these quantities; if *no* then they do +not. The *yes* setting is needed by some pair styles which require +the velocity state of both the I and J particles to compute a pairwise +I,J interaction. + +Note that if the :doc:`fix deform ` command is being used +with its "remap v" option enabled, then the velocities for ghost atoms +(in the fix deform group) mirrored across a periodic boundary will +also include components due to any velocity shift that occurs across +that boundary (e.g. due to dilation or shear). + +Restrictions +"""""""""""" + + +Communication mode *multi* is currently only available for +:doc:`comm_style ` *brick*. + +Related commands +"""""""""""""""" + +:doc:`comm_style `, :doc:`neighbor ` + +Default +""""""" + +The option defauls are mode = single, group = all, cutoff = 0.0, vel = +no. The cutoff default of 0.0 means that ghost cutoff = neighbor +cutoff = pairwise force cutoff + neighbor skin. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/comm_style.txt b/doc/_sources/comm_style.txt new file mode 100644 index 0000000000..bdfca78d09 --- /dev/null +++ b/doc/_sources/comm_style.txt @@ -0,0 +1,73 @@ +.. index:: comm_style + +comm_style command +================== + +Syntax +"""""" + +.. parsed-literal:: + + comm_style style + +* style = *brick* or *tiled* + +Examples +"""""""" + +.. parsed-literal:: + + comm_style brick + comm_style tiled + +Description +""""""""""" + +This command sets the style of inter-processor communication of atom +information that occurs each timestep as coordinates and other +properties are exchanged between neighboring processors and stored as +properties of ghost atoms. + +For the default *brick* style, the domain decomposition used by LAMMPS +to partition the simulation box must be a regular 3d grid of bricks, +one per processor. Each processor communicates with its 6 Cartesian +neighbors in the grid to acquire information for nearby atoms. + +For the *tiled* style, a more general domain decomposition can be +used, as triggered by the :doc:`balance ` or :doc:`fix balance ` commands. The simulation box can be +partitioned into non-overlapping rectangular-shaped "tiles" or varying +sizes and shapes. Again there is one tile per processor. To acquire +information for nearby atoms, communication must now be done with a +more complex pattern of neighboring processors. + +Note that this command does not actually define a partitoining of the +simulation box (a domain decomposition), rather it determines what +kinds of decompositions are allowed and the pattern of communication +used to enable the decomposition. A decomposition is created when the +simulation box is first created, via the :doc:`create_box ` +or :doc:`read_data ` or :doc:`read_restart ` +commands. For both the *brick* and *tiled* styles, the initial +decomposition will be the same, as described by +:doc:`create_box ` and :doc:`processors ` +commands. The decomposition can be changed via the +:doc:`balance ` or :doc:`fix_balance ` commands. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`comm_modify `, :doc:`processors `, +:doc:`balance `, :doc:`fix balance ` + +Default +""""""" + +The default style is brick. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute.txt b/doc/_sources/compute.txt new file mode 100644 index 0000000000..3587cf199b --- /dev/null +++ b/doc/_sources/compute.txt @@ -0,0 +1,270 @@ +.. index:: compute + +compute command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID style args + +* ID = user-assigned name for the computation +* group-ID = ID of the group of atoms to perform the computation on +* style = one of a list of possible style names (see below) +* args = arguments used by a particular style + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all temp + compute newtemp flow temp/partial 1 1 0 + compute 3 all ke/atom + +Description +""""""""""" + +Define a computation that will be performed on a group of atoms. +Quantities calculated by a compute are instantaneous values, meaning +they are calculated from information about atoms on the current +timestep or iteration, though a compute may internally store some +information about a previous state of the system. Defining a compute +does not perform a computation. Instead computes are invoked by other +LAMMPS commands as needed, e.g. to calculate a temperature needed for +a thermostat fix or to generate thermodynamic or dump file output. +See this :ref:`howto section ` for a summary of +various LAMMPS output options, many of which involve computes. + +The ID of a compute can only contain alphanumeric characters and +underscores. + + +---------- + + +Computes calculate one of three styles of quantities: global, +per-atom, or local. A global quantity is one or more system-wide +values, e.g. the temperature of the system. A per-atom quantity is +one or more values per atom, e.g. the kinetic energy of each atom. +Per-atom values are set to 0.0 for atoms not in the specified compute +group. Local quantities are calculated by each processor based on the +atoms it owns, but there may be zero or more per atom, e.g. a list of +bond distances. Computes that produce per-atom quantities have the +word "atom" in their style, e.g. *ke/atom*. Computes that produce +local quantities have the word "local" in their style, +e.g. *bond/local*. Styles with neither "atom" or "local" in their +style produce global quantities. + +Note that a single compute produces either global or per-atom or local +quantities, but never more than one of these (with only a few +exceptions, as documented by individual compute commands). + +Global, per-atom, and local quantities each come in three kinds: a +single scalar value, a vector of values, or a 2d array of values. The +doc page for each compute describes the style and kind of values it +produces, e.g. a per-atom vector. Some computes produce more than one +kind of a single style, e.g. a global scalar and a global vector. + +When a compute quantity is accessed, as in many of the output commands +discussed below, it can be referenced via the following bracket +notation, where ID is the ID of the compute: + ++------------+--------------------------------------------+ +| c_ID | entire scalar, vector, or array | ++------------+--------------------------------------------+ +| c_ID[I] | one element of vector, one column of array | ++------------+--------------------------------------------+ +| c_ID[I][J] | one element of array | ++------------+--------------------------------------------+ + +In other words, using one bracket reduces the dimension of the +quantity once (vector -> scalar, array -> vector). Using two brackets +reduces the dimension twice (array -> scalar). Thus a command that +uses scalar compute values as input can also process elements of a +vector or array. + +Note that commands and :doc:`variables ` which use compute +quantities typically do not allow for all kinds, e.g. a command may +require a vector of values, not a scalar. This means there is no +ambiguity about referring to a compute quantity as c_ID even if it +produces, for example, both a scalar and vector. The doc pages for +various commands explain the details. + + +---------- + + +In LAMMPS, the values generated by a compute can be used in several +ways: + +* The results of computes that calculate a global temperature or + pressure can be used by fixes that do thermostatting or barostatting + or when atom velocities are created. +* Global values can be output via the :doc:`thermo_style custom ` or :doc:`fix ave/time ` command. + Or the values can be referenced in a :doc:`variable equal ` or + :doc:`variable atom ` command. +* Per-atom values can be output via the :doc:`dump custom ` command + or the :doc:`fix ave/spatial ` command. Or they can be + time-averaged via the :doc:`fix ave/atom ` command or + reduced by the :doc:`compute reduce ` command. Or the + per-atom values can be referenced in an :doc:`atom-style variable `. +* Local values can be reduced by the :doc:`compute reduce ` command, or histogrammed by the :doc:`fix ave/histo ` command, or output by the :doc:`dump local ` command. +The results of computes that calculate global quantities can be either +"intensive" or "extensive" values. Intensive means the value is +independent of the number of atoms in the simulation, +e.g. temperature. Extensive means the value scales with the number of +atoms in the simulation, e.g. total rotational kinetic energy. +:doc:`Thermodynamic output ` will normalize extensive +values by the number of atoms in the system, depending on the +"thermo_modify norm" setting. It will not normalize intensive values. +If a compute value is accessed in another way, e.g. by a +:doc:`variable `, you may want to know whether it is an +intensive or extensive value. See the doc page for individual +computes for further info. + + +---------- + + +LAMMPS creates its own computes internally for thermodynamic output. +Three computes are always created, named "thermo_temp", +"thermo_press", and "thermo_pe", as if these commands had been invoked +in the input script: + +.. parsed-literal:: + + compute thermo_temp all temp + compute thermo_press all pressure thermo_temp + compute thermo_pe all pe + +Additional computes for other quantities are created if the thermo +style requires it. See the documentation for the +:doc:`thermo_style ` command. + +Fixes that calculate temperature or pressure, i.e. for thermostatting +or barostatting, may also create computes. These are discussed in the +documentation for specific :doc:`fix ` commands. + +In all these cases, the default computes LAMMPS creates can be +replaced by computes defined by the user in the input script, as +described by the :doc:`thermo_modify ` and :doc:`fix modify ` commands. + +Properties of either a default or user-defined compute can be modified +via the :doc:`compute_modify ` command. + +Computes can be deleted with the :doc:`uncompute ` command. + +Code for new computes can be added to LAMMPS (see :doc:`this section ` of the manual) and the results of their +calculations accessed in the various ways described above. + + +---------- + + +Each compute style has its own doc page which describes its arguments +and what it does. Here is an alphabetic list of compute styles +available in LAMMPS. They are also given in more compact form in the +Compute section of :ref:`this page `. + +There are also additional compute styles (not listed here) submitted +by users which are included in the LAMMPS distribution. The list of +these with links to the individual styles are given in the compute +section of :ref:`this page `. + +* :doc:`angle/local ` - theta and energy of each angle +* :doc:`angmom/chunk ` - angular momentum for each chunk +* :doc:`body/local ` - attributes of body sub-particles +* :doc:`bond/local ` - distance and energy of each bond +* :doc:`centro/atom ` - centro-symmetry parameter for each atom +* :doc:`chunk/atom ` - assign chunk IDs to each atom +* :doc:`cluster/atom ` - cluster ID for each atom +* :doc:`cna/atom ` - common neighbor analysis (CNA) for each atom +* :doc:`com ` - center-of-mass of group of atoms +* :doc:`com/chunk ` - center-of-mass for each chunk +* :doc:`contact/atom ` - contact count for each spherical particle +* :doc:`coord/atom ` - coordination number for each atom +* :doc:`damage/atom ` - Peridynamic damage for each atom +* :doc:`dihedral/local ` - angle of each dihedral +* :doc:`dilatation/atom ` - Peridynamic dilatation for each atom +* :doc:`displace/atom ` - displacement of each atom +* :doc:`erotate/asphere ` - rotational energy of aspherical particles +* :doc:`erotate/rigid ` - rotational energy of rigid bodies +* :doc:`erotate/sphere ` - rotational energy of spherical particles +* :doc:`erotate/sphere/atom ` - rotational energy for each spherical particle +* :doc:`event/displace ` - detect event on atom displacement +* :doc:`group/group ` - energy/force between two groups of atoms +* :doc:`gyration ` - radius of gyration of group of atoms +* :doc:`gyration/chunk ` - radius of gyration for each chunk +* :doc:`heat/flux ` - heat flux through a group of atoms +* :doc:`hexorder/atom ` - bond orientational order parameter q6 +* :doc:`improper/local ` - angle of each improper +* :doc:`inertia/chunk ` - inertia tensor for each chunk +* :doc:`ke ` - translational kinetic energy +* :doc:`ke/atom ` - kinetic energy for each atom +* :doc:`ke/rigid ` - translational kinetic energy of rigid bodies +* :doc:`msd ` - mean-squared displacement of group of atoms +* :doc:`msd/chunk ` - mean-squared displacement for each chunk +* :doc:`msd/nongauss ` - MSD and non-Gaussian parameter of group of atoms +* :doc:`omega/chunk ` - angular velocity for each chunk +* :doc:`orientorder/atom ` - Steinhardt bond orientational order parameters Ql +* :doc:`pair ` - values computed by a pair style +* :doc:`pair/local ` - distance/energy/force of each pairwise interaction +* :doc:`pe ` - potential energy +* :doc:`pe/atom ` - potential energy for each atom +* :doc:`plasticity/atom ` - Peridynamic plasticity for each atom +* :doc:`pressure ` - total pressure and pressure tensor +* :doc:`property/atom ` - convert atom attributes to per-atom vectors/arrays +* :doc:`property/local ` - convert local attributes to localvectors/arrays +* :doc:`property/chunk ` - extract various per-chunk attributes +* :doc:`rdf ` - radial distribution function g(r) histogram of group of atoms +* :doc:`reduce ` - combine per-atom quantities into a single global value +* :doc:`reduce/region ` - same as compute reduce, within a region +* :doc:`slice ` - extract values from global vector or array +* :doc:`sna/atom ` - calculate bispectrum coefficients for each atom +* :doc:`snad/atom ` - derivative of bispectrum coefficients for each atom +* :doc:`snav/atom ` - virial contribution from bispectrum coefficients for each atom +* :doc:`stress/atom ` - stress tensor for each atom +* :doc:`temp ` - temperature of group of atoms +* :doc:`temp/asphere ` - temperature of aspherical particles +* :doc:`temp/chunk ` - temperature of each chunk +* :doc:`temp/com ` - temperature after subtracting center-of-mass velocity +* :doc:`temp/deform ` - temperature excluding box deformation velocity +* :doc:`temp/partial ` - temperature excluding one or more dimensions of velocity +* :doc:`temp/profile ` - temperature excluding a binned velocity profile +* :doc:`temp/ramp ` - temperature excluding ramped velocity component +* :doc:`temp/region ` - temperature of a region of atoms +* :doc:`temp/sphere ` - temperature of spherical particles +* :doc:`ti ` - thermodyanmic integration free energy values +* :doc:`torque/chunk ` - torque applied on each chunk +* :doc:`vacf ` - velocity-autocorrelation function of group of atoms +* :doc:`vcm/chunk ` - velocity of center-of-mass for each chunk +* :doc:`voronoi/atom ` - Voronoi volume and neighbors for each atom + +There are also additional compute styles submitted by users which are +included in the LAMMPS distribution. The list of these with links to +the individual styles are given in the compute section of :ref:`this page `. + +There are also additional accelerated compute styles included in the +LAMMPS distribution for faster performance on CPUs and GPUs. The list +of these with links to the individual styles are given in the pair +section of :ref:`this page `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`uncompute `, :doc:`compute_modify `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, +:doc:`fix ave/time `, :doc:`fix ave/histo ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_ackland_atom.txt b/doc/_sources/compute_ackland_atom.txt new file mode 100644 index 0000000000..b17519a738 --- /dev/null +++ b/doc/_sources/compute_ackland_atom.txt @@ -0,0 +1,87 @@ +.. index:: compute ackland/atom + +compute ackland/atom command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID ackland/atom + +* ID, group-ID are documented in :doc:`compute ` command +* ackland/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all ackland/atom + +Description +""""""""""" + +Defines a computation that calculates the local lattice structure +according to the formulation given in :ref:`(Ackland) `. + +In contrast to the :doc:`centro-symmetry parameter ` this method is stable against +temperature boost, because it is based not on the distance between +particles but the angles. Therefore statistical fluctuations are +averaged out a little more. A comparison with the Common Neighbor +Analysis metric is made in the paper. + +The result is a number which is mapped to the following different +lattice structures: + +* 0 = UNKNOWN +* 1 = BCC +* 2 = FCC +* 3 = HCP +* 4 = ICO + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each of +which computes this quantity.- + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +Restrictions +"""""""""""" + + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The per-atom vector values will be unitless since they are the +integers defined above. + +Related commands +"""""""""""""""" + +:doc:`compute centro/atom ` + +**Default:** none + + +---------- + + +.. _Ackland: + + + +**(Ackland)** Ackland, Jones, Phys Rev B, 73, 054104 (2006). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_angle_local.txt b/doc/_sources/compute_angle_local.txt new file mode 100644 index 0000000000..f0656219e8 --- /dev/null +++ b/doc/_sources/compute_angle_local.txt @@ -0,0 +1,86 @@ +.. index:: compute angle/local + +compute angle/local command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID angle/local input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* angle/local = style name of this compute command +* one or more keywords may be appended +* keyword = *theta* or *eng* +.. parsed-literal:: + + *theta* = tabulate angles + *eng* = tabulate angle energies + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all angle/local theta + compute 1 all angle/local eng theta + +Description +""""""""""" + +Define a computation that calculates properties of individual angle +interactions. The number of datums generated, aggregated across all +processors, equals the number of angles in the system, modified by the +group parameter as explained below. + +The local data stored by this command is generated by looping over all +the atoms owned on a processor and their angles. An angle will only +be included if all 3 atoms in the angle are in the specified compute +group. Any angles that have been broken (see the +:doc:`angle_style ` command) by setting their angle type to +0 are not included. Angles that have been turned off (see the :doc:`fix shake ` or :doc:`delete_bonds ` commands) by +setting their angle type negative are written into the file, but their +energy will be 0.0. + +Note that as atoms migrate from processor to processor, there will be +no consistent ordering of the entries within the local vector or array +from one timestep to the next. The only consistency that is +guaranteed is that the ordering on a particular timestep will be the +same for local vectors or arrays generated by other compute commands. +For example, angle output from the :doc:`compute property/local ` command can be combined +with data from this command and output by the :doc:`dump local ` +command in a consistent way. + +**Output info:** + +This compute calculates a local vector or local array depending on the +number of keywords. The length of the vector or number of rows in the +array is the number of angles. If a single keyword is specified, a +local vector is produced. If two or more keywords are specified, a +local array is produced where the number of columns = the number of +keywords. The vector or array can be accessed by any command that +uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The output for *theta* will be in degrees. The output for *eng* will +be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump local `, :doc:`compute property/local ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_angmom_chunk.txt b/doc/_sources/compute_angmom_chunk.txt new file mode 100644 index 0000000000..68894d1850 --- /dev/null +++ b/doc/_sources/compute_angmom_chunk.txt @@ -0,0 +1,97 @@ +.. index:: compute angmom/chunk + +compute angmom/chunk command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID angmom/chunk chunkID + +* ID, group-ID are documented in :doc:`compute ` command +* angmom/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 fluid angmom/chunk molchunk + +Description +""""""""""" + +Define a computation that calculates the angular momemtum of multiple +chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the 3 components of the angular momentum +vector for each chunk, due to the velocity/momentum of the individual +atoms in the chunk around the center-of-mass of the chunk. The +calculation includes all effects due to atoms passing thru periodic +boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The :doc:`compute chunk/atom ` command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +.. note:: + + The coordinates of an atom contribute to the chunk's angular + momentum in "unwrapped" form, by using the image flags associated with + each atom. See the :doc:`dump custom ` command for a discussion + of "unwrapped" coordinates. See the Atoms section of the + :doc:`read_data ` command for a discussion of image flags and + how they are set for each atom. You can reset the image flags + (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + +The simplest way to output the results of the compute angmom/chunk +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all angmom/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +**Output info:** + +This compute calculates a global array where the number of rows = the +number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = +3 for the 3 xyz components of the angular momentum for each chunk. +These values can be accessed by any command that uses global array +values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The array values are "intensive". The array values will be in +mass-velocity-distance :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`variable angmom() function ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_basal_atom.txt b/doc/_sources/compute_basal_atom.txt new file mode 100644 index 0000000000..046fc8236f --- /dev/null +++ b/doc/_sources/compute_basal_atom.txt @@ -0,0 +1,88 @@ +.. index:: compute basal/atom + +compute basal/atom command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID basal/atom + +* ID, group-ID are documented in :doc:`compute ` command +* basal/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all basal/atom + +Description +""""""""""" + +Defines a computation that calculates the hexagonal close-packed "c" +lattice vector for each atom in the group. It does this by +calculating the normal unit vector to the basal plane for each atom. +The results enable efficient identification and characterization of +twins and grains in hexagonal close-packed structures. + +The output of the compute is thus the 3 components of a unit vector +associdate with each atom. The components are set to 0.0 for +atoms not in the group. + +Details of the calculation are given in :ref:`(Barrett) `. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each of +which computes this quantity. + +An example input script that uses this compute is provided +in examples/USER/misc/basal. + +**Output info:** + +This compute calculates a per-atom array with 3 columns, which can be +accessed by indices 1-3 by any command that uses per-atom values from +a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The per-atom vector values are unitless since the 3 columns represent +components of a unit vector. + +Restrictions +"""""""""""" + + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The output of this compute will be meaningless unless the atoms are on +(or near) hcp lattice sites, since the calculation assumes a +well-defined basal plane. + +Related commands +"""""""""""""""" + +:doc:`compute centro/atom `, :doc:`compute ackland/atom ` + +**Default:** none + + +---------- + + +.. _Barrett: + + + +**(Barrett)** Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_body_local.txt b/doc/_sources/compute_body_local.txt new file mode 100644 index 0000000000..3f642a4cdb --- /dev/null +++ b/doc/_sources/compute_body_local.txt @@ -0,0 +1,106 @@ +.. index:: compute body/local + +compute body/local command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID body/local input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* body/local = style name of this compute command +* one or more keywords may be appended +* keyword = *id* or *type* or *integer* +.. parsed-literal:: + + *id* = atom ID of the body particle + *type* = atom type of the body particle + *integer* = 1,2,3,etc = index of fields defined by body style + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all body/local type 1 2 3 + compute 1 all body/local 3 6 + +Description +""""""""""" + +Define a computation that calculates properties of individual body +sub-particles. The number of datums generated, aggregated across all +processors, equals the number of body sub-particles plus the number of +non-body particles in the system, modified by the group parameter as +explained below. See :ref:`Section_howto 14 ` +of the manual and the :doc:`body ` doc page for more details on +using body particles. + +The local data stored by this command is generated by looping over all +the atoms. An atom will only be included if it is in the group. If +the atom is a body particle, then its N sub-particles will be looped +over, and it will contribute N datums to the count of datums. If it +is not a body particle, it will contribute 1 datum. + +For both body particles and non-body particles, the *id* keyword +will store the ID of the particle. + +For both body particles and non-body particles, the *type* keyword +will store the type of the particle. + +The *integer* keywords mean different things for body and non-body +particles. If the atom is not a body particle, only its *x*, *y*, *z* +coordinates can be referenced, using the *integer* keywords 1,2,3. +Note that this means that if you want to access more fields than this +for body particles, then you cannot include non-body particles in the +group. + +For a body particle, the *integer* keywords refer to fields calculated +by the body style for each sub-particle. The body style, as specified +by the :doc:`atom_style body `, determines how many fields +exist and what they are. See the :doc:`body ` doc page for +details of the different styles. + +Here is an example of how to output body information using the :doc:`dump local ` command with this compute. If fields 1,2,3 for the +body sub-particles are x,y,z coordinates, then the dump file will be +formatted similar to the output of a :doc:`dump atom or custom ` +command. + +.. parsed-literal:: + + compute 1 all body/local type 1 2 3 + dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] + +**Output info:** + +This compute calculates a local vector or local array depending on the +number of keywords. The length of the vector or number of rows in the +array is the number of datums as described above. If a single keyword +is specified, a local vector is produced. If two or more keywords are +specified, a local array is produced where the number of columns = the +number of keywords. The vector or array can be accessed by any +command that uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The :doc:`units ` for output values depend on the body style. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump local ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_bond_local.txt b/doc/_sources/compute_bond_local.txt new file mode 100644 index 0000000000..cfad7a48dc --- /dev/null +++ b/doc/_sources/compute_bond_local.txt @@ -0,0 +1,96 @@ +.. index:: compute bond/local + +compute bond/local command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID bond/local input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* bond/local = style name of this compute command +* one or more keywords may be appended +* keyword = *dist* or *eng* +.. parsed-literal:: + + *dist* = bond distance + *eng* = bond energy + *force* = bond force + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all bond/local eng + compute 1 all bond/local dist eng force + +Description +""""""""""" + +Define a computation that calculates properties of individual bond +interactions. The number of datums generated, aggregated across all +processors, equals the number of bonds in the system, modified +by the group parameter as explained below. + +The local data stored by this command is generated by looping over all +the atoms owned on a processor and their bonds. A bond will only be +included if both atoms in the bond are in the specified compute group. +Any bonds that have been broken (see the :doc:`bond_style ` +command) by setting their bond type to 0 are not included. Bonds that +have been turned off (see the :doc:`fix shake ` or +:doc:`delete_bonds ` commands) by setting their bond type +negative are written into the file, but their energy will be 0.0. + +Note that as atoms migrate from processor to processor, there will be +no consistent ordering of the entries within the local vector or array +from one timestep to the next. The only consistency that is +guaranteed is that the ordering on a particular timestep will be the +same for local vectors or arrays generated by other compute commands. +For example, bond output from the :doc:`compute property/local ` command can be combined +with data from this command and output by the :doc:`dump local ` +command in a consistent way. + +Here is an example of how to do this: + +.. parsed-literal:: + + compute 1 all property/local batom1 batom2 btype + compute 2 all bond/local dist eng + dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] + +**Output info:** + +This compute calculates a local vector or local array depending on the +number of keywords. The length of the vector or number of rows in the +array is the number of bonds. If a single keyword is specified, a +local vector is produced. If two or more keywords are specified, a +local array is produced where the number of columns = the number of +keywords. The vector or array can be accessed by any command that +uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The output for *dist* will be in distance :doc:`units `. The +output for *eng* will be in energy :doc:`units `. The output for +*force* will be in force :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump local `, :doc:`compute property/local ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_centro_atom.txt b/doc/_sources/compute_centro_atom.txt new file mode 100644 index 0000000000..176644ee7f --- /dev/null +++ b/doc/_sources/compute_centro_atom.txt @@ -0,0 +1,142 @@ +.. index:: compute centro/atom + +compute centro/atom command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID centro/atom lattice + +* ID, group-ID are documented in :doc:`compute ` command +* centro/atom = style name of this compute command +* lattice = *fcc* or *bcc* or N = # of neighbors per atom to include + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all centro/atom fcc + +.. parsed-literal:: + + compute 1 all centro/atom 8 + +Description +""""""""""" + +Define a computation that calculates the centro-symmetry parameter for +each atom in the group. In solid-state systems the centro-symmetry +parameter is a useful measure of the local lattice disorder around an +atom and can be used to characterize whether the atom is part of a +perfect lattice, a local defect (e.g. a dislocation or stacking +fault), or at a surface. + +The value of the centro-symmetry parameter will be 0.0 for atoms not +in the specified compute group. + +This parameter is computed using the following formula from +:ref:`(Kelchner) ` + +.. image:: Eqs/centro_symmetry.jpg + :align: center + +where the *N* nearest neighbors or each atom are identified and Ri and +Ri+N/2 are vectors from the central atom to a particular pair of +nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that +can contribute to this formula. The quantity in the sum is computed +for each, and the N/2 smallest are used. This will typically be for +pairs of atoms in symmetrically opposite positions with respect to the +central atom; hence the i+N/2 notation. + +*N* is an input parameter, which should be set to correspond to the +number of nearest neighbors in the underlying lattice of atoms. If +the keyword *fcc* or *bcc* is used, *N* is set to 12 and 8 +respectively. More generally, *N* can be set to a positive, even +integer. + +For an atom on a lattice site, surrounded by atoms on a perfect +lattice, the centro-symmetry parameter will be 0. It will be near 0 +for small thermal perturbations of a perfect lattice. If a point +defect exists, the symmetry is broken, and the parameter will be a +larger positive value. An atom at a surface will have a large +positive parameter. If the atom does not have *N* neighbors (within +the potential cutoff), then its centro-symmetry parameter is set to +0.0. + +Only atoms within the cutoff of the pairwise neighbor list are +considered as possible neighbors. Atoms not in the compute group are +included in the *N* neighbors used in this calculation. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (e.g. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each with a +*centro/atom* style. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values are unitless values >= 0.0. Their +magnitude depends on the lattice style due to the number of +contibuting neighbor pairs in the summation in the formula above. And +it depends on the local defects surrounding the central atom, as +described above. + +Here are typical centro-symmetry values, from a a nanoindentation +simulation into gold (FCC). These were provided by Jon Zimmerman +(Sandia): + +.. parsed-literal:: + + Bulk lattice = 0 + Dislocation core ~ 1.0 (0.5 to 1.25) + Stacking faults ~ 5.0 (4.0 to 6.0) + Free surface ~ 23.0 + +These values are *not* normalized by the square of the lattice +parameter. If they were, normalized values would be: + +.. parsed-literal:: + + Bulk lattice = 0 + Dislocation core ~ 0.06 (0.03 to 0.075) + Stacking faults ~ 0.3 (0.24 to 0.36) + Free surface ~ 1.38 + +For BCC materials, the values for dislocation cores and free surfaces +would be somewhat different, due to their being only 8 neighbors instead +of 12. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute cna/atom ` + +**Default:** none + + +---------- + + +.. _Kelchner: + + + +**(Kelchner)** Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_chunk_atom.txt b/doc/_sources/compute_chunk_atom.txt new file mode 100644 index 0000000000..71e80679df --- /dev/null +++ b/doc/_sources/compute_chunk_atom.txt @@ -0,0 +1,699 @@ +.. index:: compute chunk/atom + +compute chunk/atom command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID chunk/atom style args keyword values ... + +* ID, group-ID are documented in :doc:`compute ` command +* chunk/atom = style name of this compute command +.. parsed-literal:: + + style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *type* or *molecule* or *compute/fix/variable* + *bin/1d* args = dim origin delta + dim = *x* or *y* or *z* + origin = *lower* or *center* or *upper* or coordinate value (distance units) + delta = thickness of spatial bins in dim (distance units) + *bin/2d* args = dim origin delta dim origin delta + dim = *x* or *y* or *z* + origin = *lower* or *center* or *upper* or coordinate value (distance units) + delta = thickness of spatial bins in dim (distance units) + *bin/3d* args = dim origin delta dim origin delta dim origin delta + dim = *x* or *y* or *z* + origin = *lower* or *center* or *upper* or coordinate value (distance units) + delta = thickness of spatial bins in dim (distance units) + *bin/sphere* args = xorig yorig zorig rmin rmax nsbin + xorig,yorig,zorig = center point of sphere + srmin,srmax = bin from sphere radius rmin to rmax + nsbin = # of spherical shell bins between rmin and rmax + *bin/cylinder* args = dim origin delta c1 c2 rmin rmax ncbin + dim = *x* or *y* or *z* = axis of cylinder axis + origin = *lower* or *center* or *upper* or coordinate value (distance units) + delta = thickness of spatial bins in dim (distance units) + c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) + crmin,crmax = bin from cylinder radius rmin to rmax (distance units) + ncbin = # of concentric circle bins between rmin and rmax + *type* args = none + *molecule* args = none + *compute/fix/variable* = c_ID, c_ID[I], f_ID, f_ID[I], v_name with no args + c_ID = per-atom vector calculated by a compute with ID + c_ID[I] = Ith column of per-atom array calculated by a compute with ID + f_ID = per-atom vector calculated by a fix with ID + f_ID[I] = Ith column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name + +* zero or more keyword/values pairs may be appended +* keyword = *region* or *nchunk* or *static* or *compress* or *bound* or *discard* or *pbc* or *units* +.. parsed-literal:: + + *region* value = region-ID + region-ID = ID of region atoms must be in to be part of a chunk + *nchunk* value = *once* or *every* + once = only compute the number of chunks once + every = re-compute the number of chunks whenever invoked + *limit* values = 0 or Nc max or Nc exact + 0 = no limit on the number of chunks + Nc max = limit number of chunks to be <= Nc + Nc exact = set number of chunks to exactly Nc + *ids* value = *once* or *nfreq* or *every* + once = assign chunk IDs to atoms only once, they persist thereafter + nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by :doc:`fix ave/chunk ` which sets Nfreq) + every = assign chunk IDs to atoms whenever invoked + *compress* value = *yes* or *no* + yes = compress chunk IDs to eliminate IDs with no atoms + no = do not compress chunk IDs even if some IDs have no atoms + *discard* value = *yes* or *no* or *mixed* + yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0 + no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID + mixed = keep or discard such atoms according to spatial binning rule + *bound* values = x/y/z lo hi + x/y/z = *x* or *y* or *z* to bound sptial bins in this dimension + lo = *lower* or coordinate value (distance units) + hi = *upper* or coordinate value (distance units) + *pbc* value = *no* or *yes* + yes = use periodic distance for bin/sphere and bin/cylinder styles + *units* value = *box* or *lattice* or *reduced* + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all chunk/atom type + compute 1 all chunk/atom bin/1d z lower 0.02 units reduced + compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5 + compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes + compute 1 all chunk/atom bin/sphere 5 5 5 2.0 5.0 5 discard yes + compute 1 all chunk/atom bin/cylinder z lower 2 10 10 2.0 5.0 3 discard yes + +Description +""""""""""" + +Define a computation that calculates an integer chunk ID from 1 to +Nchunk for each atom in the group. Values of chunk IDs are determined +by the *style* of chunk, which can be based on atom type or molecule +ID or spatial binning or a per-atom property or value calculated by +another :doc:`compute `, :doc:`fix `, or :doc:`atom-style variable `. Per-atom chunk IDs can be used by other +computes with "chunk" in their style name, such as :doc:`compute com/chunk ` or :doc:`compute msd/chunk `. Or they can be used by the :doc:`fix ave/chunk ` command to sum and time average a +variety of per-atom properties over the atoms in each chunk. Or they +can simply be accessed by any command that uses per-atom values from a +compute as input, as discussed in :ref:`Section_howto 15 `. + +See :ref:`Section_howto 23 ` for an overview of +how this compute can be used with a variety of other commands to +tabulate properties of a simulation. The howto section gives several +examples of input script commands that can be used to calculate +interesting properties. + +Conceptually it is important to realize that this compute does two +simple things. First, it sets the value of *Nchunk* = the number of +chunks, which can be a constant value or change over time. Second, it +assigns each atom to a chunk via a chunk ID. Chunk IDs range from 1 +to *Nchunk* inclusive; some chunks may have no atoms assigned to them. +Atoms that do not belong to any chunk are assigned a value of 0. Note +that the two operations are not always performed together. For +example, spatial bins can be setup once (which sets *Nchunk*), and +atoms assigned to those bins many times thereafter (setting their +chunk IDs). + +All other commands in LAMMPS that use chunk IDs assume there are +*Nchunk* number of chunks, and that every atom is assigned to one of +those chunks, or not assigned to any chunk. + +There are many options for specifying for how and when *Nchunk* is +calculated, and how and when chunk IDs are assigned to atoms. The +details depend on the chunk *style* and its *args*, as well as +optional keyword settings. They can also depend on whether a :doc:`fix ave/chunk ` command is using this compute, since +that command requires *Nchunk* to remain static across windows of +timesteps it specifies, while it accumulates per-chunk averages. + +The details are described below. + + + + + +The different chunk styles operate as follows. For each style, how it +calculates *Nchunk* and assigns chunk IDs to atoms is explained. Note +that using the optional keywords can change both of those actions, as +described further below where the keywords are discussed. + + +---------- + + +The *binning* styles perform a spatial binning of atoms, and assign an +atom the chunk ID corresponding to the bin number it is in. *Nchunk* +is set to the number of bins, which can change if the simulation box +size changes. + +The *bin/1d*, *bin/2d*, and *bin/3d* styles define bins as 1d layers +(slabs), 2d pencils, or 3d boxes. The *dim*, *origin*, and *delta* +settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is +no restriction on specifying dim = x before dim = y or z, or dim = y +before dim = z. Bins in a particular *dim* have a bin size in that +dimension given by *delta*. In each dimension, bins are defined +relative to a specified *origin*, which may be the lower/upper edge of +the simulation box (in that dimension), or its center point, or a +specified coordinate value. Starting at the origin, sufficient bins +are created in both directions to completely span the simulation box +or the bounds specified by the optional *bounds* keyword. + +For orthogonal simulation boxes, the bins are layers, pencils, or +boxes aligned with the xyz coordinate axes. For triclinic +(non-orthogonal) simulation boxes, the bin faces are parallel to the +tilted faces of the simulation box. See :ref:`this section ` of the manual for a discussion of +the geometry of triclinic boxes in LAMMPS. As described there, a +tilted simulation box has edge vectors a,b,c. In that nomenclature, +bins in the x dimension have faces with normals in the "b" cross "c" +direction. Bins in y have faces normal to the "a" cross "c" +direction. And bins in z have faces normal to the "a" cross "b" +direction. Note that in order to define the size and position of +these bins in an unambiguous fashion, the *units* option must be set +to *reduced* when using a triclinic simulation box, as noted below. + +The meaning of *origin* and *delta* for triclinic boxes is as follows. +Consider a triclinic box with bins that are 1d layers or slabs in the +x dimension. No matter how the box is tilted, an *origin* of 0.0 +means start layers at the lower "b" cross "c" plane of the simulation +box and an *origin* of 1.0 means to start layers at the upper "b" +cross "c" face of the box. A *delta* value of 0.1 in *reduced* units +means there will be 10 layers from 0.0 to 1.0, regardless of the +current size or shape of the simulation box. + +The *bin/sphere* style defines a set of spherical shell bins around +the origin (*xorig*,*yorig*,*zorig*), using *nsbin* bins with radii +equally spaced between *srmin* and *srmax*. This is effectively a 1d +vector of bins. For example, if *srmin* = 1.0 and *srmax* = 10.0 and +*nsbin* = 9, then the first bin spans 1.0 < r < 2.0, and the last bin +spans 9.0 < r 10.0. The geometry of the bins is the same whether the +simulation box is orthogonal or triclinic; i.e. the spherical shells +are not tilted or scaled differently in different dimensions to +transform them into ellipsoidal shells. + +The *bin/cylinder* style defines bins for a cylinder oriented along +the axis *dim* with the axis coordinates in the other two radial +dimensions at (*c1*,*c2*). For dim = x, c1/c2 = y/z; for dim = y, +c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array +of bins. The first dimension is along the cylinder axis, the second +dimension is radially outward from the cylinder axis. The bin size +and positions along the cylinder axis are specified by the *origin* +and *delta* values, the same as for the *bin/1d*, *bin/2d*, and +*bin/3d* styles. There are *ncbin* concentric circle bins in the +radial direction from the cylinder axis with radii equally spaced +between *crmin* and *crmax*. For example, if *crmin* = 1.0 and +*crmax* = 10.0 and *ncbin* = 9, then the first bin spans 1.0 < r < +2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in +the radial dimensions is the same whether the simulation box is +orthogonal or triclinic; i.e. the concetric circles are not tilted or +scaled differently in the two different dimensions to transform them +into ellipses. + +The created bins (and hence the chunk IDs) are numbered consecutively +from 1 to the number of bins = *Nchunk*. For *bin2d* and *bin3d*, the +numbering varies most rapidly in the first dimension (which could be +x, y, or z), next rapidly in the 2nd dimension, and most slowly in the +3rd dimension. For *bin/sphere*, the bin with smallest radii is chunk +1 and the bni with largest radii is chunk Nchunk = *ncbin*. For +*bin/cylinder*, the numbering varies most rapidly in the dimension +along the cylinder axis and most slowly in the radial direction. + +Each time this compute is invoked, each atom is mapped to a bin based +on its current position. Note that between reneighboring timesteps, +atoms can move outside the current simulation box. If the box is +periodic (in that dimension) the atom is remapping into the periodic +box for purposes of binning. If the box in not periodic, the atom may +have moved outside the bounds of all bins. If an atom is not inside +any bin, the *discard* keyword is used to determine how a chunk ID is +assigned to the atom. + + +---------- + + +The *type* style uses the atom type as the chunk ID. *Nchunk* is set +to the number of atom types defined for the simulation, e.g. via the +:doc:`create_box ` or :doc:`read_data ` commands. + + +---------- + + +The *molecule* style uses the molecule ID of each atom as its chunk +ID. *Nchunk* is set to the largest chunk ID. Note that this excludes +molecule IDs for atoms which are not in the specified group or +optional region. + +There is no requirement that all atoms in a particular molecule are +assigned the same chunk ID (zero or non-zero), though you probably +want that to be the case, if you wish to compute a per-molecule +property. LAMMPS will issue a warning if that is not the case, but +only the first time that *Nchunk* is calculated. + +Note that atoms with a molecule ID = 0, which may be non-molecular +solvent atoms, have an out-of-range chunk ID. These atoms are +discarded (not assigned to any chunk) or assigned to *Nchunk*, +depending on the value of the *discard* keyword. + + +---------- + + +The *compute/fix/variable* styles set the chunk ID of each atom based +on a quantity calculated and stored by a compute, fix, or variable. +In each case, it must be a per-atom quantity. In each case the +referenced floating point values are converted to an integer chunk ID +as follows. The floating point value is truncated (rounded down) to +an integer value. If the integer value is <= 0, then a chunk ID of 0 +is assigned to the atom. If the integer value is > 0, it becomes the +chunk ID to the atom. *Nchunk* is set to the largest chunk ID. Note +that this excludes atoms which are not in the specified group or +optional region. + +If the style begins with "c_", a compute ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the compute is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and :doc:`add them to LAMMPS `. + +If the style begins with "f_", a fix ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the fix is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with the +timestep on which this compute accesses the fix, else an error +results. Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name for an *atom* or +*atomfile* style :doc:`variable ` must follow which has been +previously defined in the input script. Variables of style *atom* can +reference thermodynamic keywords and various per-atom attributes, or +invoke other computes, fixes, or variables when they are evaluated, so +this is a very general means of generating per-atom quantities to +treat as a chunk ID. + + + + + +Normally, *Nchunk* = the number of chunks, is re-calculated every time +this fix is invoked, though the value may or may not change. As +explained below, the *nchunk* keyword can be set to *once* which means +*Nchunk* will never change. + +If a :doc:`fix ave/chunk ` command uses this compute, it +can also turn off the re-calculation of *Nchunk* for one or more +windows of timesteps. The extent of the windows, during which Nchunk +is held constant, are determined by the *Nevery*, *Nrepeat*, *Nfreq* +values and the *ave* keyword setting that are used by the :doc:`fix ave/chunk ` command. + +Specifically, if *ave* = *one*, then for each span of *Nfreq* +timesteps, *Nchunk* is held constant between the first timestep when +averaging is done (within the Nfreq-length window), and the last +timestep when averaging is done (multiple of Nfreq). If *ave* = +*running* or *window*, then *Nchunk* is held constant forever, +starting on the first timestep when the :doc:`fix ave/chunk ` command invokes this compute. + +Note that multiple :doc:`fix ave/chunk ` commands can use +the same compute chunk/atom compute. However, the time windows they +induce for holding *Nchunk* constant must be identical, else an error +will be generated. + + + + + +The various optional keywords operate as follows. Note that some of +them function differently or are ignored by different chunk styles. +Some of them also have different default values, depending on +the chunk style, as listed below. + +The *region* keyword applies to all chunk styles. If used, an atom +must be in both the specified group and the specified geometric +:doc:`region ` to be assigned to a chunk. + + +---------- + + +The *nchunk* keyword applies to all chunk styles. It specifies how +often *Nchunk* is recalculated, which in turn can affect the chunk IDs +assigned to individual atoms. + +If *nchunk* is set to *once*, then *Nchunk* is only calculated once, +the first time this compute is invoked. If *nchunk* is set to +*every*, then *Nchunk* is re-calculated every time the compute is +invoked. Note that, as described above, the use of this compute +by the :doc:`fix ave/chunk ` command can override +the *every* setting. + +The default values for *nchunk* are listed below and depend on the +chunk style and other system and keyword settings. They attempt to +represent typical use cases for the various chunk styles. The +*nchunk* value can always be set explicitly if desired. + + +---------- + + +The *limit* keyword can be used to limit the calculated value of +*Nchunk* = the number of chunks. The limit is applied each time +*Nchunk* is calculated, which also limits the chunk IDs assigned to +any atom. The *limit* keyword is used by all chunk styles except the +*binning* styles, which ignore it. This is because the number of bins +can be tailored using the *bound* keyword (described below) which +effectively limits the size of *Nchunk*. + +If *limit* is set to *Nc* = 0, then no limit is imposed on *Nchunk*, +though the *compress* keyword can still be used to reduce *Nchunk*, as +described below. + +If *Nc* > 0, then the effect of the *limit* keyword depends on whether +the *compress* keyword is also used with a setting of *yes*, and +whether the *compress* keyword is specified before the *limit* keyword +or after. + +In all cases, *Nchunk* is first calculated in the usual way for each +chunk style, as described above. + +First, here is what occurs if *compress yes* is not set. If *limit* +is set to *Nc max*, then *Nchunk* is reset to the smaller of *Nchunk* +and *Nc*. If *limit* is set to *Nc exact*, then *Nchunk* is reset to +*Nc*, whether the original *Nchunk* was larger or smaller than *Nc*. +If *Nchunk* shrank due to the *limit* setting, then atom chunk IDs > +*Nchunk* will be reset to 0 or *Nchunk*, depending on the setting of +the *discard* keyword. If *Nchunk* grew, there will simply be some +chunks with no atoms assigned to them. + +If *compress yes* is set, and the *compress* keyword comes before the +*limit* keyword, the compression operation is performed first, as +described below, which resets *Nchunk*. The *limit* keyword is then +applied to the new *Nchunk* value, exactly as described in the +preceeding paragraph. Note that in this case, all atoms will end up +with chunk IDs <= *Nc*, but their original values (e.g. molecule ID or +compute/fix/variable value) may have been > *Nc*, because of the +compression operation. + +If *compress yes* is set, and the *compress* keyword comes after the +*limit* keyword, then the *limit* value of *Nc* is applied first to +the uncompressed value of *Nchunk*, but only if *Nc* < *Nchunk* +(whether *Nc max* or *Nc exact* is used). This effectively means all +atoms with chunk IDs > *Nc* have their chunk IDs reset to 0 or *Nc*, +depending on the setting of the *discard* keyword. The compression +operation is then performed, which may shrink *Nchunk* further. If +the new *Nchunk* < *Nc* and *limit* = *Nc exact* is specified, then +*Nchunk* is reset to *Nc*, which results in extra chunks with no atoms +assigned to them. Note that in this case, all atoms will end up with +chunk IDs <= *Nc*, and their original values (e.g. molecule ID or +compute/fix/variable value) will also have been <= *Nc*. + + +---------- + + +The *ids* keyword applies to all chunk styles. If the setting is +*once* then the chunk IDs assigned to atoms the first time this +compute is invoked will be permanent, and never be re-computed. + +If the setting is *nfreq* and if a :doc:`fix ave/chunk ` +command is using this compute, then in each of the *Nchunk* = constant +time windows (discussed above), the chunk ID's assigned to atoms on +the first step of the time window will persist until the end of the +time window. + +If the setting is *every*, which is the default, then chunk IDs are +re-calculated on any timestep this compute is invoked. + +.. note:: + + If you want the persistent chunk-IDs calculated by this compute + to be continuous when running from a :doc:`restart file `, + then you should use the same ID for this compute, as in the original + run. This is so that the fix this compute creates to store per-atom + quantities will also have the same ID, and thus be initialized + correctly with chunk IDs from the restart file. + + +---------- + + +The *compress* keyword applies to all chunk styles and affects how +*Nchunk* is calculated, which in turn affects the chunk IDs assigned +to each atom. It is useful for converting a "sparse" set of chunk IDs +(with many IDs that have no atoms assigned to them), into a "dense" +set of IDs, where every chunk has one or more atoms assigned to it. + +Two possible use cases are as follows. If a large simulation box is +mostly empty space, then the *binning* style may produce many bins +with no atoms. If *compress* is set to *yes*, only bins with atoms +will be contribute to *Nchunk*. Likewise, the *molecule* or +*compute/fix/variable* styles may produce large *Nchunk* values. For +example, the :doc:`compute cluster/atom ` command +assigns every atom an atom ID for one of the atoms it is clustered +with. For a million-atom system with 5 clusters, there would only be +5 unique chunk IDs, but the largest chunk ID might be 1 million, +resulting in *Nchunk* = 1 million. If *compress* is set to *yes*, +*Nchunk* will be reset to 5. + +If *compress* is set to *no*, which is the default, no compression is +done. If it is set to *yes*, all chunk IDs with no atoms are removed +from the list of chunk IDs, and the list is sorted. The remaining +chunk IDs are renumbered from 1 to *Nchunk* where *Nchunk* is the new +length of the list. The chunk IDs assigned to each atom reflect +the new renumbering from 1 to *Nchunk*. + +The original chunk IDs (before renumbering) can be accessed by the +:doc:`compute property/chunk ` command and its +*id* keyword, or by the :doc:`fix ave/chunk ` command +which outputs the original IDs as one of the columns in its global +output array. For example, using the "compute cluster/atom" command +discussed above, the original 5 unique chunk IDs might be atom IDs +(27,4982,58374,857838,1000000). After compresion, these will be +renumbered to (1,2,3,4,5). The original values (27,...,1000000) can +be output to a file by the :doc:`fix ave/chunk ` command, +or by using the :doc:`fix ave/time ` command in +conjunction with the :doc:`compute property/chunk ` command. + +.. note:: + + The compression operation requires global communication across + all processors to share their chunk ID values. It can require large + memory on every processor to store them, even after they are + compressed, if there are are a large number of unique chunk IDs with + atoms assigned to them. It uses a STL map to find unique chunk IDs + and store them in sorted order. Each time an atom is assigned a + compressed chunk ID, it must access the STL map. All of this means + that compression can be expensive, both in memory and CPU time. The + use of the *limit* keyword in conjunction with the *compress* keyword + can affect these costs, depending on which keyword is used first. So + use this option with care. + + +---------- + + +The *discard* keyword applies to all chunk styles. It affects what +chunk IDs are assigned to atoms that do not match one of the valid +chunk IDs from 1 to *Nchunk*. Note that it does not apply to atoms +that are not in the specified group or optionally specified region. +Those atoms are always assigned a chunk ID = 0. + +If the calculated chunk ID for an atom is not within the range 1 to +*Nchunk* then it is a "discard" atom. Note that *Nchunk* may have +been shrunk by the *limit* keyword. Or the *compress* keyword may +have eliminated chunk IDs that were valid before the compression took +place, and are now not in the compressed list. Also note that for the +*molecule* chunk style, if new molecules are added to the system, +their chunk IDs may exceed a previously calculated *Nchunk*. +Likewise, evaluation of a compute/fix/variable on a later timestep may +return chunk IDs that are invalid for the previously calculated +*Nchunk*. + +All the chunk styles except the *binning* styles, must use *discard* +set to either *yes* or *no*. If *discard* is set to *yes*, which is +the default, then every "discard" atom has its chunk ID set to 0. If +*discard* is set to *no*, every "discard" atom has its chunk ID set to +*Nchunk*. I.e. it becomes part of the last chunk. + +The *binning* styles use the *discard* keyword to decide whether to +discard atoms outside the spatial domain covered by bins, or to assign +them to the bin they are nearest to. + +For the *bin/1d*, *bin/2d*, *bin/3d* styles the details are as +follows. If *discard* is set to *yes*, an out-of-domain atom will +have its chunk ID set to 0. If *discard* is set to *no*, the atom +will have its chunk ID set to the first or last bin in that dimension. +If *discard* is set to *mixed*, which is the default, it will only +have its chunk ID set to the first or last bin if bins extend to the +simulation box boundary in that dimension. This is the case if the +*bound* keyword settings are *lower* and *upper*, which is the +default. If the *bound* keyword settings are numeric values, then the +atom will have its chunk ID set to 0 if it is outside the bounds of +any bin. Note that in this case, it is possible that the first or +last bin extends beyond the numeric *bounds* settings, depending on +the specified *origin*. If this is the case, the chunk ID of the atom +is only set to 0 if it is outside the first or last bin, not if it is +simply outside the numeric *bounds* setting. + +For the *bin/sphere* style the details are as follows. If *discard* +is set to *yes*, an out-of-domain atom will have its chunk ID set to +0. If *discard* is set to *no* or *mixed*, the atom will have its +chunk ID set to the first or last bin, i.e. the innermost or outermost +spherical shell. If the distance of the atom from the origin is less +than *rmin*, it will be assigned to the first bin. If the distance of +the atom from the origin is greater than *rmax*, it will be assigned +to the last bin. + +For the *bin/cylinder* style the details are as follows. If *discard* +is set to *yes*, an out-of-domain atom will have its chunk ID set to +0. If *discard* is set to *no*, the atom will have its chunk ID set +to the first or last bin in both the radial and axis dimensions. If +*discard* is set to *mixed*, which is the default, the the radial +dimension is treated the same as for *discard* = no. But for the axis +dimensinon, it will only have its chunk ID set to the first or last +bin if bins extend to the simulation box boundary in the axis +dimension. This is the case if the *bound* keyword settings are +*lower* and *upper*, which is the default. If the *bound* keyword +settings are numeric values, then the atom will have its chunk ID set +to 0 if it is outside the bounds of any bin. Note that in this case, +it is possible that the first or last bin extends beyond the numeric +*bounds* settings, depending on the specified *origin*. If this is +the case, the chunk ID of the atom is only set to 0 if it is outside +the first or last bin, not if it is simply outside the numeric +*bounds* setting. + +If *discard* is set to *no* or *mixed*, the atom will have its +chunk ID set to the first or last bin, i.e. the innermost or outermost +spherical shell. If the distance of the atom from the origin is less +than *rmin*, it will be assigned to the first bin. If the distance of +the atom from the origin is greater than *rmax*, it will be assigned +to the last bin. + + +---------- + + +The *bound* keyword only applies to the *bin/1d*, *bin/2d*, *bin/3d* +styles and to the axis dimension of the *bin/cylinder* style; +otherwise it is ignored. It can be used one or more times to limit +the extent of bin coverage in a specified dimension, i.e. to only bin +a portion of the box. If the *lo* setting is *lower* or the *hi* +setting is *upper*, the bin extent in that direction extends to the +box boundary. If a numeric value is used for *lo* and/or *hi*, then +the bin extent in the *lo* or *hi* direction extends only to that +value, which is assumed to be inside (or at least near) the simulation +box boundaries, though LAMMPS does not check for this. Note that +using the *bound* keyword typically reduces the total number of bins +and thus the number of chunks *Nchunk*. + +The *pbc* keyword only applies to the *bin/sphere* and *bin/cylinder* +styles. If set to *yes*, the distance an atom is from the sphere +origin or cylinder axis is calculated in a minimum image sense with +respect to periodic dimensions, when determining which bin the atom is +in. I.e. if x is a periodic dimension and the distance between the +atom and the sphere center in the x dimension is greater than 0.5 * +simulation box length in x, then a box length is subtracted to give a +distance < 0.5 * simulation box length. This allosws the sphere or +cylinder center to be near a box edge, and atoms on the other side of +the periodic box will still be close to the center point/axis. Note +that with a setting of *yes*, the outer sphere or cylinder radius must +also be <= 0.5 * simulation box length in any periodic dimension +except for the cylinder axis dimension, or an error is generated. + +The *units* keyword only applies to the *binning* styles; otherwise it +is ignored. For the *bin/1d*, *bin/2d*, *bin/3d* styles, it +determines the meaning of the distance units used for the bin sizes +*delta* and for *origin* and *bounds* values if they are coordinate +values. For the *bin/sphere* style it determines the meaning of the +distance units used for *xorig*,*yorig*,*zorig* and the radii *srmin* +and *srmax*. For the *bin/cylinder* style it determines the meaning +of the distance units used for *delta*,*c1*,*c2* and the radii *crmin* +and *crmax*. + +For orthogonal simulation boxes, any of the 3 options may +be used. For non-orthogonal (triclinic) simulation boxes, only the +*reduced* option may be used. + +A *box* value selects standard distance units as defined by the +:doc:`units ` command, e.g. Angstroms for units = real or metal. +A *lattice* value means the distance units are in lattice spacings. +The :doc:`lattice ` command must have been previously used to +define the lattice spacing. A *reduced* value means normalized +unitless values between 0 and 1, which represent the lower and upper +faces of the simulation box respectively. Thus an *origin* value of +0.5 means the center of the box in any dimension. A *delta* value of +0.1 means 10 bins span the box in that dimension. + +Note that for the *bin/sphere* style, the radii *srmin* and *srmax* are +scaled by the lattice spacing or reduced value of the *x* dimension. + +Note that for the *bin/cylinder* style, the radii *crmin* and *crmax* +are scaled by the lattice spacing or reduced value of the 1st +dimension perpendicular to the cylinder axis. E.g. y for an x-axis +cylinder, x for a y-axis cylinder, and x for a z-axis cylinder. + + +---------- + + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values are unitless chunk IDs, ranging from 1 to +*Nchunk* (inclusive) for atoms assigned to chunks, and 0 for atoms not +belonging to a chunk. + +Restrictions +"""""""""""" + + +Even if the *nchunk* keyword is set to *once*, the chunk IDs assigned +to each atom are not stored in a restart files. This means you cannot +expect those assignments to persist in a restarted simulation. +Instead you must re-specify this command and assign atoms to chunks when +the restarted simulation begins. + +Related commands +"""""""""""""""" + +:doc:`fix ave/chunk ` + +Default +""""""" + +The option defaults are as follows: + +* region = none +* nchunk = every, if compress is yes, overriding other defaults listed here +* nchunk = once, for type style +* nchunk = once, for mol style if region is none +* nchunk = every, for mol style if region is set +* nchunk = once, for binning style if the simulation box size is static or units = reduced +* nchunk = every, for binning style if the simulation box size is dynamic and units is lattice or box +* nchunk = every, for compute/fix/variable style +* limit = 0 +* ids = every +* compress = no +* discard = yes, for all styles except binning +* discard = mixed, for binning styles +* bound = lower and upper in all dimensions +* pbc = no +* units = lattice + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_cluster_atom.txt b/doc/_sources/compute_cluster_atom.txt new file mode 100644 index 0000000000..a402ee3d25 --- /dev/null +++ b/doc/_sources/compute_cluster_atom.txt @@ -0,0 +1,85 @@ +.. index:: compute cluster/atom + +compute cluster/atom command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID cluster/atom cutoff + +* ID, group-ID are documented in :doc:`compute ` command +* cluster/atom = style name of this compute command +* cutoff = distance within which to label atoms as part of same cluster (distance units) + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all cluster/atom 1.0 + +Description +""""""""""" + +Define a computation that assigns each atom a cluster ID. + +A cluster is defined as a set of atoms, each of which is within the +cutoff distance from one or more other atoms in the cluster. If an +atom has no neighbors within the cutoff distance, then it is a 1-atom +cluster. The ID of every atom in the cluster will be the smallest +atom ID of any atom in the cluster. + +Only atoms in the compute group are clustered and assigned cluster +IDs. Atoms not in the compute group are assigned a cluster ID = 0. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each of a +*clsuter/atom* style. + +.. note:: + + If you have a bonded system, then the settings of + :doc:`special_bonds ` command can remove pairwise + interactions between atoms in the same bond, angle, or dihedral. This + is the default setting for the :doc:`special_bonds ` + command, and means those pairwise interactions do not appear in the + neighbor list. Because this fix uses the neighbor list, it also means + those pairs will not be included when computing the clusters. This + does not apply when using long-range coulomb (*coul/long*, *coul/msm*, + *coul/wolf* or similar. One way to get around this would be to set + special_bond scaling factors to very tiny numbers that are not exactly + zero (e.g. 1.0e-50). Another workaround is to write a dump file, and + use the :doc:`rerun ` command to compute the clusters for + snapshots in the dump file. The rerun script can use a + :doc:`special_bonds ` command that includes all pairs in + the neighbor list. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be an ID > 0, as explained above. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute coord/atom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_cna_atom.txt b/doc/_sources/compute_cna_atom.txt new file mode 100644 index 0000000000..336ce82632 --- /dev/null +++ b/doc/_sources/compute_cna_atom.txt @@ -0,0 +1,117 @@ +.. index:: compute cna/atom + +compute cna/atom command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID cna/atom cutoff + +* ID, group-ID are documented in :doc:`compute ` command +* cna/atom = style name of this compute command +* cutoff = cutoff distance for nearest neighbors (distance units) + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all cna/atom 3.08 + +Description +""""""""""" + +Define a computation that calculates the CNA (Common Neighbor +Analysis) pattern for each atom in the group. In solid-state systems +the CNA pattern is a useful measure of the local crystal structure +around an atom. The CNA methodology is described in :ref:`(Faken) ` +and :ref:`(Tsuzuki) `. + +Currently, there are five kinds of CNA patterns LAMMPS recognizes: + +* fcc = 1 +* hcp = 2 +* bcc = 3 +* icosohedral = 4 +* unknown = 5 + +The value of the CNA pattern will be 0 for atoms not in the specified +compute group. Note that normally a CNA calculation should only be +performed on mono-component systems. + +The CNA calculation can be sensitive to the specified cutoff value. +You should insure the appropriate nearest neighbors of an atom are +found within the cutoff distance for the presumed crystal strucure. +E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest +neighbors for perfect BCC crystals. These formulas can be used to +obtain a good cutoff distance: + +.. image:: Eqs/cna_cutoff1.jpg + :align: center + +where a is the lattice constant for the crystal structure concerned +and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a +for HCP crystals. + +Also note that since the CNA calculation in LAMMPS uses the neighbors +of an owned atom to find the nearest neighbors of a ghost atom, the +following relation should also be satisfied: + +.. image:: Eqs/cna_cutoff2.jpg + :align: center + +where Rc is the cutoff distance of the potential, Rs is the skin +distance as specified by the :doc:`neighbor ` command, and +cutoff is the argument used with the compute cna/atom command. LAMMPS +will issue a warning if this is not the case. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (e.g. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each with a +*cna/atom* style. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be a number from 0 to 5, as explained +above. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute centro/atom ` + +**Default:** none + + +---------- + + +.. _Faken: + + + +**(Faken)** Faken, Jonsson, Comput Mater Sci, 2, 279 (1994). + +.. _Tsuzuki: + + + +**(Tsuzuki)** Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_com.txt b/doc/_sources/compute_com.txt new file mode 100644 index 0000000000..0a34de74dc --- /dev/null +++ b/doc/_sources/compute_com.txt @@ -0,0 +1,67 @@ +.. index:: compute com + +compute com command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID com + +* ID, group-ID are documented in :doc:`compute ` command +* com = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all com + +Description +""""""""""" + +Define a computation that calculates the center-of-mass of the group +of atoms, including all effects due to atoms passing thru periodic +boundaries. + +A vector of three quantites is calculated by this compute, which +are the x,y,z coordinates of the center of mass. + +.. note:: + + The coordinates of an atom contribute to the center-of-mass in + "unwrapped" form, by using the image flags associated with each atom. + See the :doc:`dump custom ` command for a discussion of + "unwrapped" coordinates. See the Atoms section of the + :doc:`read_data ` command for a discussion of image flags and + how they are set for each atom. You can reset the image flags + (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + +**Output info:** + +This compute calculates a global vector of length 3, which can be +accessed by indices 1-3 by any command that uses global vector values +from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The vector values are "intensive". The vector values will be in +distance :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute com/chunk ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_com_chunk.txt b/doc/_sources/compute_com_chunk.txt new file mode 100644 index 0000000000..5a70472115 --- /dev/null +++ b/doc/_sources/compute_com_chunk.txt @@ -0,0 +1,95 @@ +.. index:: compute com/chunk + +compute com/chunk command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID com/chunk chunkID + +* ID, group-ID are documented in :doc:`compute ` command +* com/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 fluid com/chunk molchunk + +Description +""""""""""" + +Define a computation that calculates the center-of-mass for multiple +chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the x,y,z coordinates of the center-of-mass +for each chunk, which includes all effects due to atoms passing thru +periodic boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The :doc:`compute chunk/atom ` command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +.. note:: + + The coordinates of an atom contribute to the chunk's + center-of-mass in "unwrapped" form, by using the image flags + associated with each atom. See the :doc:`dump custom ` command + for a discussion of "unwrapped" coordinates. See the Atoms section of + the :doc:`read_data ` command for a discussion of image flags + and how they are set for each atom. You can reset the image flags + (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + +The simplest way to output the results of the compute com/chunk +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all com/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +**Output info:** + +This compute calculates a global array where the number of rows = the +number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = +3 for the x,y,z center-of-mass coordinates of each chunk. These +values can be accessed by any command that uses global array values +from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The array values are "intensive". The array values will be in +distance :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute com ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_contact_atom.txt b/doc/_sources/compute_contact_atom.txt new file mode 100644 index 0000000000..ea633116ab --- /dev/null +++ b/doc/_sources/compute_contact_atom.txt @@ -0,0 +1,64 @@ +.. index:: compute contact/atom + +compute contact/atom command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID contact/atom + +* ID, group-ID are documented in :doc:`compute ` command +* contact/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all contact/atom + +Description +""""""""""" + +Define a computation that calculates the number of contacts +for each atom in a group. + +The contact number is defined for finite-size spherical particles as +the number of neighbor atoms which overlap the central particle, +meaning that their distance of separation is less than or equal to the +sum of the radii of the two particles. + +The value of the contact number will be 0.0 for atoms not in the +specified compute group. + +**Output info:** + +This compute calculates a per-atom vector, whose values can be +accessed by any command that uses per-atom values from a compute as +input. See :ref:`Section_howto 15 ` for an +overview of LAMMPS output options. + +The per-atom vector values will be a number >= 0.0, as explained +above. + +Restrictions +"""""""""""" + + +This compute requires that atoms store a radius as defined by the +:doc:`atom_style sphere ` command. + +Related commands +"""""""""""""""" + +:doc:`compute coord/atom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_coord_atom.txt b/doc/_sources/compute_coord_atom.txt new file mode 100644 index 0000000000..4a12143af2 --- /dev/null +++ b/doc/_sources/compute_coord_atom.txt @@ -0,0 +1,103 @@ +.. index:: compute coord/atom + +compute coord/atom command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID coord/atom cutoff type1 type2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* coord/atom = style name of this compute command +* cutoff = distance within which to count coordination neighbors (distance units) +* typeN = atom type for Nth coordination count (see asterisk form below) + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all coord/atom 2.0 + compute 1 all coord/atom 6.0 1 2 + compute 1 all coord/atom 6.0 2*4 5*8 * + +Description +""""""""""" + +Define a computation that calculates one or more coordination numbers +for each atom in a group. + +A coordination number is defined as the number of neighbor atoms with +specified atom type(s) that are within the specified cutoff distance +from the central atom. Atoms not in the group are included in a +coordination number of atoms in the group. + +The *typeN* keywords allow you to specify which atom types contribute +to each coordination number. One coordination number is computed for +each of the *typeN* keywords listed. If no *typeN* keywords are +listed, a single coordination number is calculated, which includes +atoms of all types (same as the "*" format, see below). + +The *typeN* keywords can be specified in one of two ways. An explicit +numeric value can be used, as in the 2nd example above. Or a +wild-card asterisk can be used to specify a range of atom types. This +takes the form "*" or "*n" or "n*" or "m*n". If N = the number of +atom types, then an asterisk with no numeric values means all types +from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). + +The value of all coordination numbers will be 0.0 for atoms not in the +specified compute group. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently. + +.. note:: + + If you have a bonded system, then the settings of + :doc:`special_bonds ` command can remove pairwise + interactions between atoms in the same bond, angle, or dihedral. This + is the default setting for the :doc:`special_bonds ` + command, and means those pairwise interactions do not appear in the + neighbor list. Because this fix uses the neighbor list, it also means + those pairs will not be included in the coordination count. One way + to get around this, is to write a dump file, and use the + :doc:`rerun ` command to compute the coordination for snapshots + in the dump file. The rerun script can use a + :doc:`special_bonds ` command that includes all pairs in + the neighbor list. + +**Output info:** + +If single *type1* keyword is specified (or if none are specified), +this compute calculates a per-atom vector. If multiple *typeN* +keywords are specified, this compute calculates a per-atom array, with +N columns. These values can be accessed by any command that uses +per-atom values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The per-atom vector or array values will be a number >= 0.0, as +explained above. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute cluster/atom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_damage_atom.txt b/doc/_sources/compute_damage_atom.txt new file mode 100644 index 0000000000..114f070202 --- /dev/null +++ b/doc/_sources/compute_damage_atom.txt @@ -0,0 +1,69 @@ +.. index:: compute damage/atom + +compute damage/atom command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID damage/atom + +* ID, group-ID are documented in :doc:`compute ` command +* damage/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all damage/atom + +Description +""""""""""" + +Define a computation that calculates the per-atom damage for each atom +in a group. This is a quantity relevant for :doc:`Peridynamics models `. See `this document `_ +for an overview of LAMMPS commands for Peridynamics modeling. + +The "damage" of a Peridymaics particles is based on the bond breakage +between the particle and its neighbors. If all the bonds are broken +the particle is considered to be fully damaged. + +See the `PDLAMMPS user guide `_ for a formal +definition of "damage" and more details about Peridynamics as it is +implemented in LAMMPS. + +This command can be used with all the Peridynamic pair styles. + +The damage value will be 0.0 for atoms not in the specified compute +group. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values are unitlesss numbers (damage) >= 0.0. + +Restrictions +"""""""""""" + + +This compute is part of the PERI package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute dilatation `, :doc:`compute plasticity ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_dihedral_local.txt b/doc/_sources/compute_dihedral_local.txt new file mode 100644 index 0000000000..ee95d0c3a8 --- /dev/null +++ b/doc/_sources/compute_dihedral_local.txt @@ -0,0 +1,79 @@ +.. index:: compute dihedral/local + +compute dihedral/local command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID dihedral/local input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* dihedral/local = style name of this compute command +* one or more keywords may be appended +* keyword = *phi* +.. parsed-literal:: + + *phi* = tabulate dihedral angles + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all dihedral/local phi + +Description +""""""""""" + +Define a computation that calculates properties of individual dihedral +interactions. The number of datums generated, aggregated across all +processors, equals the number of angles in the system, modified by the +group parameter as explained below. + +The local data stored by this command is generated by looping over all +the atoms owned on a processor and their dihedrals. A dihedral will +only be included if all 4 atoms in the dihedral are in the specified +compute group. + +Note that as atoms migrate from processor to processor, there will be +no consistent ordering of the entries within the local vector or array +from one timestep to the next. The only consistency that is +guaranteed is that the ordering on a particular timestep will be the +same for local vectors or arrays generated by other compute commands. +For example, dihedral output from the :doc:`compute property/local ` command can be combined +with data from this command and output by the :doc:`dump local ` +command in a consistent way. + +**Output info:** + +This compute calculates a local vector or local array depending on the +number of keywords. The length of the vector or number of rows in the +array is the number of dihedrals. If a single keyword is specified, a +local vector is produced. If two or more keywords are specified, a +local array is produced where the number of columns = the number of +keywords. The vector or array can be accessed by any command that +uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The output for *phi* will be in degrees. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump local `, :doc:`compute property/local ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_dilatation_atom.txt b/doc/_sources/compute_dilatation_atom.txt new file mode 100644 index 0000000000..54fe89e9ce --- /dev/null +++ b/doc/_sources/compute_dilatation_atom.txt @@ -0,0 +1,71 @@ +.. index:: compute dilatation/atom + +compute dilatation/atom command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID dilatation/atom + +* ID, group-ID are documented in compute command +* dilation/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all dilatation/atom + +Description +""""""""""" + +Define a computation that calculates the per-atom dilatation for each +atom in a group. This is a quantity relevant for :doc:`Peridynamics models `. See `this document `_ +for an overview of LAMMPS commands for Peridynamics modeling. + +For small deformation, dilatation of is the measure of the volumetric +strain. + +The dilatation "theta" for each peridynamic particle I is calculated +as a sum over its neighbors with unbroken bonds, where the +contribution of the IJ pair is a function of the change in bond length +(versus the initial length in the reference state), the volume +fraction of the particles and an influence function. See the +`PDLAMMPS user guide `_ for a formal +definition of dilatation. + +This command can only be used with a subset of the Peridynamic :doc:`pair styles `: peri/lps, peri/ves and peri/eps. + +The dilatation value will be 0.0 for atoms not in the specified +compute group. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +Section_howto 15 for an overview of LAMMPS output options. + +The per-atom vector values are unitlesss numbers (theta) >= 0.0. + +Restrictions +"""""""""""" + + +This compute is part of the PERI package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute damage `, :doc:`compute plasticity ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_displace_atom.txt b/doc/_sources/compute_displace_atom.txt new file mode 100644 index 0000000000..8c0e84bc54 --- /dev/null +++ b/doc/_sources/compute_displace_atom.txt @@ -0,0 +1,80 @@ +.. index:: compute displace/atom + +compute displace/atom command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID displace/atom + +* ID, group-ID are documented in :doc:`compute ` command +* displace/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all displace/atom + +Description +""""""""""" + +Define a computation that calculates the current displacement of each +atom in the group from its original coordinates, including all effects +due to atoms passing thru periodic boundaries. + +A vector of four quantites per atom is calculated by this compute. +The first 3 elements of the vector are the dx,dy,dz displacements. +The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy + +dz*dz). + +The displacement of an atom is from its original position at the time +the compute command was issued. The value of the displacement will be +0.0 for atoms not in the specified compute group. + +.. note:: + + Initial coordinates are stored in "unwrapped" form, by using the + image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. + See the Atoms section of the :doc:`read_data ` command for a + discussion of image flags and how they are set for each atom. You can + reset the image flags (e.g. to 0) before invoking this compute by + using the :doc:`set image ` command. + +.. note:: + + If you want the quantities calculated by this compute to be + continuous when running from a :doc:`restart file `, then + you should use the same ID for this compute, as in the original run. + This is so that the fix this compute creates to store per-atom + quantities will also have the same ID, and thus be initialized + correctly with time=0 atom coordinates from the restart file. + +**Output info:** + +This compute calculates a per-atom array with 4 columns, which can be +accessed by indices 1-4 by any command that uses per-atom values from +a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The per-atom array values will be in distance :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute msd `, :doc:`dump custom `, :doc:`fix store/state ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_dpd.txt b/doc/_sources/compute_dpd.txt new file mode 100644 index 0000000000..5028ed787c --- /dev/null +++ b/doc/_sources/compute_dpd.txt @@ -0,0 +1,85 @@ +.. index:: compute dpd + +compute dpd command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID dpd + +* ID, group-ID are documented in :doc:`compute ` command +* dpd = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all dpd + +Description +""""""""""" + +Define a computation that accumulates the total internal conductive +energy (U_cond), the total internal mechanical energy (U_mech), the +total internal energy (U) and the *harmonic* average of the internal +temperature (dpdTheta) for the entire system of particles. See the +:doc:`compute dpd/atom ` command if you want +per-particle internal energies and internal temperatures. + +The system internal properties are computed according to the following +relations: + +.. image:: Eqs/compute_dpd.jpg + :align: center + +where N is the number of particles in the system + + +---------- + + +**Output info:** + +This compute calculates a global vector of length 5 (U_cond, U_mech, +U, dpdTheta, N_particles), which can be accessed by indices 1-5. See +:ref:`this section ` for an overview of LAMMPS +output options. + +The vector values will be in energy and temperature :doc:`units `. + +Restrictions +"""""""""""" + + +The compute *dpd* is only available if LAMMPS is built with the +USER-DPD package and requires the :doc:`atom_style dpd `. + +Related commands +"""""""""""""""" + +:doc:`compute dpd/atom `, +:doc:`thermo_style ` + +**Default:** none + + +---------- + + +.. _Larentzos: + + + +**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and +W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative +Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research +Laboratory, Aberdeen Proving Ground, MD (2014). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_dpd_atom.txt b/doc/_sources/compute_dpd_atom.txt new file mode 100644 index 0000000000..1cdf02264e --- /dev/null +++ b/doc/_sources/compute_dpd_atom.txt @@ -0,0 +1,73 @@ +.. index:: compute dpd/atom + +compute dpd/atom command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID dpd/atom + +* ID, group-ID are documented in :doc:`compute ` command +* dpd/atom = style name of this compute command + +Examples +"""""""" + +compute 1 all dpd/atom + +Description +""""""""""" + +Define a computation that accesses the per-particle internal +conductive energy (u_cond), internal mechanical energy (u_mech) and +internal temperatures (dpdTheta) for each particle in a group. See +the :doc:`compute dpd ` command if you want the total +internal conductive energy, the total internal mechanical energy, and +average internal temperature of the entire system or group of dpd +particles. + +**Output info:** + +This compute calculates a per-particle array with 3 columns (u_cond, +u_mech, dpdTheta), which can be accessed by indices 1-3 by any command +that uses per-particle values from a compute as input. See +:ref:`Section_howto15 ` for an overview of +LAMMPS output options. + +The per-particle array values will be in energy (u_cond, u_mech) and +temperature (dpdTheta) :doc:`units `. + +Restrictions +"""""""""""" + + +The compute *dpd/atom* is only available if LAMMPS is built with the +USER-DPD package. + +Related commands +"""""""""""""""" + +:doc:`dump custom `, :doc:`compute dpd ` + +**Default:** none + + +---------- + + +.. _Larentzos: + + + +**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and +W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative +Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research +Laboratory, Aberdeen Proving Ground, MD (2014). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_erotate_asphere.txt b/doc/_sources/compute_erotate_asphere.txt new file mode 100644 index 0000000000..f75175b3f0 --- /dev/null +++ b/doc/_sources/compute_erotate_asphere.txt @@ -0,0 +1,80 @@ +.. index:: compute erotate/asphere + +compute erotate/asphere command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID erotate/asphere + +* ID, group-ID are documented in :doc:`compute ` command +* erotate/asphere = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all erotate/asphere + +Description +""""""""""" + +Define a computation that calculates the rotational kinetic energy of +a group of aspherical particles. The aspherical particles can be +ellipsoids, or line segments, or triangles. See the +:doc:`atom_style ` and :doc:`read_data ` commands +for descriptions of these options. + +For all 3 types of particles, the rotational kinetic energy is +computed as 1/2 I w^2, where I is the inertia tensor for the +aspherical particle and w is its angular velocity, which is computed +from its angular momentum if needed. + +.. note:: + + For :doc:`2d models `, ellipsoidal particles are + treated as ellipsoids, not ellipses, meaning their moments of inertia + will be the same as in 3d. + +**Output info:** + +This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See :ref:`Section_howto 15 ` for an +overview of LAMMPS output options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute requires that ellipsoidal particles atoms store a shape +and quaternion orientation and angular momentum as defined by the +:doc:`atom_style ellipsoid ` command. + +This compute requires that line segment particles atoms store a length +and orientation and angular velocity as defined by the :doc:`atom_style line ` command. + +This compute requires that triangular particles atoms store a size and +shape and quaternion orientation and angular momentum as defined by +the :doc:`atom_style tri ` command. + +All particles in the group must be finite-size. They cannot be point +particles. + +**Related commands:** none + +:doc:`compute erotate/sphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_erotate_rigid.txt b/doc/_sources/compute_erotate_rigid.txt new file mode 100644 index 0000000000..093860fef0 --- /dev/null +++ b/doc/_sources/compute_erotate_rigid.txt @@ -0,0 +1,69 @@ +.. index:: compute erotate/rigid + +compute erotate/rigid command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID erotate/rigid fix-ID + +* ID, group-ID are documented in :doc:`compute ` command +* erotate/rigid = style name of this compute command +* fix-ID = ID of rigid body fix + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all erotate/rigid myRigid + +Description +""""""""""" + +Define a computation that calculates the rotational kinetic energy of +a collection of rigid bodies, as defined by one of the :doc:`fix rigid ` command variants. + +The rotational energy of each rigid body is computed as 1/2 I Wbody^2, +where I is the inertia tensor for the rigid body, and Wbody is its +angular velocity vector. Both I and Wbody are in the frame of +reference of the rigid body, i.e. I is diagonalized. + +The *fix-ID* should be the ID of one of the :doc:`fix rigid ` +commands which defines the rigid bodies. The group specified in the +compute command is ignored. The rotational energy of all the rigid +bodies defined by the fix rigid command in included in the +calculation. + +**Output info:** + +This compute calculates a global scalar (the summed rotational energy +of all the rigid bodies). This value can be used by any command that +uses a global scalar value from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the RIGID package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute ke/rigid ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_erotate_sphere.txt b/doc/_sources/compute_erotate_sphere.txt new file mode 100644 index 0000000000..5ed6d6a10e --- /dev/null +++ b/doc/_sources/compute_erotate_sphere.txt @@ -0,0 +1,69 @@ +.. index:: compute erotate/sphere + +compute erotate/sphere command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID erotate/sphere + +* ID, group-ID are documented in :doc:`compute ` command +* erotate/sphere = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all erotate/sphere + +Description +""""""""""" + +Define a computation that calculates the rotational kinetic energy of +a group of spherical particles. + +The rotational energy is computed as 1/2 I w^2, where I is the moment +of inertia for a sphere and w is the particle's angular velocity. + +.. note:: + + For :doc:`2d models `, particles are treated as + spheres, not disks, meaning their moment of inertia will be the same + as in 3d. + +**Output info:** + +This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See :ref:`Section_howto 15 ` for an +overview of LAMMPS output options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute requires that atoms store a radius and angular velocity +(omega) as defined by the :doc:`atom_style sphere ` command. + +All particles in the group must be finite-size spheres or point +particles. They cannot be aspherical. Point particles will not +contribute to the rotational energy. + +Related commands +"""""""""""""""" + +:doc:`compute erotate/asphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_erotate_sphere_atom.txt b/doc/_sources/compute_erotate_sphere_atom.txt new file mode 100644 index 0000000000..ba529198cb --- /dev/null +++ b/doc/_sources/compute_erotate_sphere_atom.txt @@ -0,0 +1,65 @@ +.. index:: compute erotate/sphere/atom + +compute erotate/sphere/atom command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID erotate/sphere/atom + +* ID, group-ID are documented in :doc:`compute ` command +* erotate/sphere/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all erotate/sphere/atom + +Description +""""""""""" + +Define a computation that calculates the rotational kinetic energy for +each particle in a group. + +The rotational energy is computed as 1/2 I w^2, where I is the moment +of inertia for a sphere and w is the particle's angular velocity. + +.. note:: + + For :doc:`2d models `, particles are treated as + spheres, not disks, meaning their moment of inertia will be the same + as in 3d. + +The value of the rotational kinetic energy will be 0.0 for atoms not +in the specified compute group or for point particles with a radius = +0.0. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump custom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_event_displace.txt b/doc/_sources/compute_event_displace.txt new file mode 100644 index 0000000000..ac54510eda --- /dev/null +++ b/doc/_sources/compute_event_displace.txt @@ -0,0 +1,74 @@ +.. index:: compute event/displace + +compute event/displace command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID event/displace threshold + +* ID, group-ID are documented in :doc:`compute ` command +* event/displace = style name of this compute command +* threshold = minimum distance anyparticle must move to trigger an event (distance units) + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all event/displace 0.5 + +Description +""""""""""" + +Define a computation that flags an "event" if any particle in the +group has moved a distance greater than the specified threshold +distance when compared to a previously stored reference state +(i.e. the previous event). This compute is typically used in +conjunction with the :doc:`prd ` and :doc:`tad ` commands, +to detect if a transition +to a new minimum energy basin has occurred. + +This value calculated by the compute is equal to 0 if no particle has +moved far enough, and equal to 1 if one or more particles have moved +further than the threshold distance. + +.. note:: + + If the system is undergoing significant center-of-mass motion, + due to thermal motion, an external force, or an initial net momentum, + then this compute will not be able to distinguish that motion from + local atom displacements and may generate "false postives." + +**Output info:** + +This compute calculates a global scalar (the flag). This value can be +used by any command that uses a global scalar value from a compute as +input. See :ref:`Section_howto 15 ` for an +overview of LAMMPS output options. + +The scalar value calculated by this compute is "intensive". The +scalar value will be a 0 or 1 as explained above. + +Restrictions +"""""""""""" + + +This command can only be used if LAMMPS was built with the REPLICA +package. See the :ref:`Making LAMMPS ` section +for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`prd `, :doc:`tad ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_fep.txt b/doc/_sources/compute_fep.txt new file mode 100644 index 0000000000..f145f8d7c6 --- /dev/null +++ b/doc/_sources/compute_fep.txt @@ -0,0 +1,315 @@ +.. index:: compute fep + +compute fep command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID fep temp attribute args ... keyword value ... + +* ID, group-ID are documented in the :doc:`compute ` command +* fep = name of this compute command +* temp = external temperature (as specified for constant-temperature run) +* one or more attributes with args may be appended +* attribute = *pair* or *atom* +.. parsed-literal:: + + *pair* args = pstyle pparam I J v_delta + pstyle = pair style name, e.g. lj/cut + pparam = parameter to perturb + I,J = type pair(s) to set parameter for + v_delta = variable with perturbation to apply (in the units of the parameter) + *atom* args = aparam I v_delta + aparam = parameter to perturb + I = type to set parameter for + v_delta = variable with perturbation to apply (in the units of the parameter) + +* zero or more keyword/value pairs may be appended +* keyword = *tail* or *volume* +.. parsed-literal:: + + *tail* value = *no* or *yes* + *no* = ignore tail correction to pair energies (usually small in fep) + *yes* = include tail correction to pair energies + *volume* value = *no* or *yes* + *no* = ignore volume changes (e.g. in *NVE* or *NVT* trajectories) + *yes* = include volume changes (e.g. in *NpT* trajectories) + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes + compute 1 all fep 300 atom charge 2 v_delta + +Description +""""""""""" + +Apply a perturbation to parameters of the interaction potential and +recalculate the pair potential energy without changing the atomic +coordinates from those of the reference, unperturbed system. This +compute can be used to calculate free energy differences using several +methods, such as free-energy perturbation (FEP), finite-difference +thermodynamic integration (FDTI) or Bennet's acceptance ratio method +(BAR). + +The potential energy of the system is decomposed in three terms: a +background term corresponding to interaction sites whose parameters +remain constant, a reference term *U*0 corresponding to the +initial interactions of the atoms that will undergo perturbation, and +a term *U*1 corresponding to the final interactions of +these atoms: + +.. image:: Eqs/compute_fep_u.jpg + :align: center + +A coupling parameter λ varying from 0 to 1 connects the +reference and perturbed systems: + +.. image:: Eqs/compute_fep_lambda.jpg + :align: center + +It is possible but not necessary that the coupling parameter (or a +function thereof) appears as a multiplication factor of the potential +energy. Therefore, this compute can apply perturbations to interaction +parameters that are not directly proportional to the potential energy +(e.g. σ in Lennard-Jones potentials). + +This command can be combined with :doc:`fix adapt ` to +perform multistage free-energy perturbation calculations along +stepwise alchemical transformations during a simulation run: + +.. image:: Eqs/compute_fep_fep.jpg + :align: center + +This compute is suitable for the finite-difference thermodynamic +integration (FDTI) method :ref:`(Mezei) `, which is based on an +evaluation of the numerical derivative of the free energy by a +perturbation method using a very small δ: + +.. image:: Eqs/compute_fep_fdti.jpg + :align: center + +where *w*i are weights of a numerical quadrature. The :doc:`fix adapt ` command can be used to define the stages of +λ at which the derivative is calculated and averaged. + +The compute fep calculates the exponential Boltzmann term and also the +potential energy difference *U*1-*U*0. By +choosing a very small perturbation δ the thermodynamic +integration method can be implemented using a numerical evaluation of +the derivative of the potential energy with respect to λ: + +.. image:: Eqs/compute_fep_ti.jpg + :align: center + +Another technique to calculate free energy differences is the +acceptance ratio method :ref:`(Bennet) `, which can be implemented +by calculating the potential energy differences with δ = 1.0 on +both the forward and reverse routes: + +.. image:: Eqs/compute_fep_bar.jpg + :align: center + +The value of the free energy difference is determined by numerical +root finding to establish the equality. + +Concerning the choice of how the atomic parameters are perturbed in +order to setup an alchemical transformation route, several strategies +are available, such as single-topology or double-topology strategies +:ref:`(Pearlman) `. The latter does not require modification of +bond lengths, angles or other internal coordinates. + +NOTES: This compute command does not take kinetic energy into account, +therefore the masses of the particles should not be modified between +the reference and perturbed states, or along the alchemical +transformation route. This compute command does not change bond +lengths or other internal coordinates :ref:`(Boresch, Karplus) `. + + +---------- + + +The *pair* attribute enables various parameters of potentials defined +by the :doc:`pair_style ` and :doc:`pair_coeff ` +commands to be changed, if the pair style supports it. + +The *pstyle* argument is the name of the pair style. For example, +*pstyle* could be specified as "lj/cut". The *pparam* argument is the +name of the parameter to change. This is a (non-exclusive) list of +pair styles and parameters that can be used with this compute. See +the doc pages for individual pair styles and their energy formulas for +the meaning of these parameters: + ++------------------------------------------------+----------------------+------------+ +| :doc:`lj/cut ` | epsilon,sigma | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`lj/cut/coul/cut ` | epsilon,sigma | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`lj/cut/coul/long ` | epsilon,sigma | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`lj/cut/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`coul/cut/soft ` | lambda | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`coul/long/soft ` | lambda | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`lj/cut/coul/cut/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`lj/cut/coul/long/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`lj/cut/tip4p/long/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`tip4p/long/soft ` | lambda | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`lj/charmm/coul/long/soft ` | epsilon,sigma,lambda | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`born ` | a,b,c | type pairs | ++------------------------------------------------+----------------------+------------+ +| :doc:`buck ` | a,c | type pairs | ++------------------------------------------------+----------------------+------------+ + +Note that it is easy to add new potentials and their parameters to +this list. All it typically takes is adding an extract() method to +the pair_*.cpp file associated with the potential. + +Similar to the :doc:`pair_coeff ` command, I and J can be +specified in one of two ways. Explicit numeric values can be used for +each, as in the 1st example above. I <= J is required. LAMMPS sets +the coefficients for the symmetric J,I interaction to the same +values. A wild-card asterisk can be used in place of or in conjunction +with the I,J arguments to set the coefficients for multiple pairs of +atom types. This takes the form "*" or "*n" or "n*" or "m*n". If N = +the number of atom types, then an asterisk with no numeric values +means all types from 1 to N. A leading asterisk means all types from +1 to n (inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). Note that only type pairs with I <= J are considered; if +asterisks imply type pairs where J < I, they are ignored. + +If :doc:`pair_style hybrid or hybrid/overlay ` is being +used, then the *pstyle* will be a sub-style name. You must specify +I,J arguments that correspond to type pair values defined (via the +:doc:`pair_coeff ` command) for that sub-style. + +The *v_name* argument for keyword *pair* is the name of an +:doc:`equal-style variable ` which will be evaluated each time +this compute is invoked. It should be specified as v_name, where name +is the variable name. + + +---------- + + +The *atom* attribute enables atom properties to be changed. The +*aparam* argument is the name of the parameter to change. This is the +current list of atom parameters that can be used with this compute: + +* charge = charge on particle + +The *v_name* argument for keyword *pair* is the name of an +:doc:`equal-style variable ` which will be evaluated each time +this compute is invoked. It should be specified as v_name, where name +is the variable name. + + +---------- + + +The *tail* keyword controls the calculation of the tail correction to +"van der Waals" pair energies beyond the cutoff, if this has been +activated via the :doc:`pair_modify ` command. If the +perturbation is small, the tail contribution to the energy difference +between the reference and perturbed systems should be negligible. + +If the keyword *volume* = *yes*, then the Boltzmann term is multiplied +by the volume so that correct ensemble averaging can be performed over +trajectories during which the volume fluctuates or changes :ref:`(Allen and Tildesley) `: + +.. image:: Eqs/compute_fep_vol.jpg + :align: center + + +---------- + + +**Output info:** + +This compute calculates a global vector of length 3 which contains the +energy difference (*U*1-*U*0) as c_ID[1], the +Boltzmann factor exp(-(*U*1-*U*0)/*kT*), or +*V*exp(-(*U*1-*U*0)/*kT*), as c_ID[2] and the +volume of the simulation box *V* as c_ID[3]. *U*1 is the +pair potential energy obtained with the perturbed parameters and +*U*0 is the pair potential energy obtained with the +unperturbed parameters. The energies include kspace terms if these +are used in the simulation. + +These output results can be used by any command that uses a global +scalar or vector from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. For example, the computed values can be averaged using :doc:`fix ave/time `. + +The values calculated by this compute are "extensive". + +Restrictions +"""""""""""" + + +This compute is distributed as the USER-FEP package. It is only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix adapt/fep `, :doc:`fix ave/time `, +`pair_lj_soft_coul_soft `_ + +Default +""""""" + +The option defaults are *tail* = *no*, *volume* = *no*. + + +---------- + + +.. _Pearlman: + + + +**(Pearlman)** Pearlman, J Chem Phys, 98, 1487 (1994) + +.. _Mezei: + + + +**(Mezei)** Mezei, J Chem Phys, 86, 7084 (1987) + +.. _Bennet: + + + +**(Bennet)** Bennet, J Comput Phys, 22, 245 (1976) + +.. _BoreschKarplus: + + + +**(BoreschKarplus)** Boresch and Karplus, J Phys Chem A, 103, 103 (1999) + +.. _AllenTildesley: + + + +**(AllenTildesley)** Allen and Tildesley, Computer Simulation of +Liquids, Oxford University Press (1987) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_group_group.txt b/doc/_sources/compute_group_group.txt new file mode 100644 index 0000000000..03bebbbeca --- /dev/null +++ b/doc/_sources/compute_group_group.txt @@ -0,0 +1,144 @@ +.. index:: compute group/group + +compute group/group command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID group/group group2-ID keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* group/group = style name of this compute command +* group2-ID = group ID of second (or same) group +* zero or more keyword/value pairs may be appended +* keyword = *pair* or *kspace* or *boundary* +.. parsed-literal:: + + *pair* value = *yes* or *no* + *kspace* value = *yes* or *no* + *boundary* value = *yes* or *no* + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 lower group/group upper + compute 1 lower group/group upper kspace yes + compute mine fluid group/group wall + +Description +""""""""""" + +Define a computation that calculates the total energy and force +interaction between two groups of atoms: the compute group and the +specified group2. The two groups can be the same. + +If the *pair* keyword is set to *yes*, which is the default, then the +the interaction energy will include a pair component which is defined +as the pairwise energy between all pairs of atoms where one atom in +the pair is in the first group and the other is in the second group. +Likewise, the interaction force calculated by this compute will +include the force on the compute group atoms due to pairwise +interactions with atoms in the specified group2. + +If the *kspace* keyword is set to *yes*, which is not the default, and +if a :doc:`kspace_style ` is defined, then the interaction +energy will include a Kspace component which is the long-range +Coulombic energy between all the atoms in the first group and all the +atoms in the 2nd group. Likewise, the interaction force calculated by +this compute will include the force on the compute group atoms due to +long-range Coulombic interactions with atoms in the specified group2. + +Normally the long-range Coulombic energy converges only when the net +charge of the unit cell is zero. However, one can assume the net +charge of the system is neutralized by a uniform background plasma, +and a correction to the system energy can be applied to reduce +artifacts. For more information see :ref:`(Bogusz) `. If the +*boundary* keyword is set to *yes*, which is the default, and *kspace* +contributions are included, then this energy correction term will be +added to the total group-group energy. This correction term does not +affect the force calculation and will be zero if one or both of the +groups are charge neutral. This energy correction term is the same as +that included in the regular Ewald and PPPM routines. + +This compute does not calculate any bond or angle or dihedral or +improper interactions between atoms in the two groups. + + +---------- + + +The pairwise contributions to the group-group interactions are +calculated by looping over a neighbor list. The Kspace contribution +to the group-group interactions require essentially the same amount of +work (FFTs, Ewald summation) as computing long-range forces for the +entire system. Thus it can be costly to invoke this compute too +frequently. + +If you desire a breakdown of the interactions into a pairwise and +Kspace component, simply invoke the compute twice with the appropriate +yes/no settings for the *pair* and *kspace* keywords. This is no more +costly than using a single compute with both keywords set to *yes*. +The individual contributions can be summed in a +:doc:`variable ` if desired. + +This `document `_ describes how the long-range +group-group calculations are performed. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the energy) and a global +vector of length 3 (force), which can be accessed by indices 1-3. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +Both the scalar and vector values calculated by this compute are +"extensive". The scalar value will be in energy :doc:`units `. +The vector values will be in force :doc:`units `. + +Restrictions +"""""""""""" + + +Not all pair styles can be evaluated in a pairwise mode as required by +this compute. For example, 3-body and other many-body potentials, +such as :doc:`Tersoff ` and +:doc:`Stillinger-Weber ` cannot be used. :doc:`EAM ` +potentials only include the pair potential portion of the EAM +interaction when used by this compute, not the embedding term. + +Not all Kspace styles support calculation of group/group interactions. +The *ewald* and *pppm* styles do. + +**Related commands:** none + +Default +""""""" + +The option defaults are pair = yes, kspace = no, and boundary = yes. + + +---------- + + +.. _Bogusz: + + + +Bogusz et al, J Chem Phys, 108, 7070 (1998) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_gyration.txt b/doc/_sources/compute_gyration.txt new file mode 100644 index 0000000000..d28bef60cc --- /dev/null +++ b/doc/_sources/compute_gyration.txt @@ -0,0 +1,83 @@ +.. index:: compute gyration + +compute gyration command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID gyration + +* ID, group-ID are documented in :doc:`compute ` command +* gyration = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 molecule gyration + +Description +""""""""""" + +Define a computation that calculates the radius of gyration Rg of the +group of atoms, including all effects due to atoms passing thru +periodic boundaries. + +Rg is a measure of the size of the group of atoms, and is computed as +the square root of the Rg^2 value in this formula + +.. image:: Eqs/compute_gyration.jpg + :align: center + +where M is the total mass of the group, Rcm is the center-of-mass +position of the group, and the sum is over all atoms in the group. + +A Rg^2 tensor, stored as a 6-element vector, is also calculated by +this compute. The formula for the components of the tensor is the +same as the above formula, except that (Ri - Rcm)^2 is replaced by +(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6 +components of the vector are ordered xx, yy, zz, xy, xz, yz. Note +that unlike the scalar Rg, each of the 6 values of the tensor is +effectively a "squared" value, since the cross-terms may be negative +and taking a sqrt() would be invalid. + +.. note:: + + The coordinates of an atom contribute to Rg in "unwrapped" form, + by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. + See the Atoms section of the :doc:`read_data ` command for a + discussion of image flags and how they are set for each atom. You can + reset the image flags (e.g. to 0) before invoking this compute by + using the :doc:`set image ` command. + +**Output info:** + +This compute calculates a global scalar (Rg) and a global vector of +length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These +values can be used by any command that uses a global scalar value or +vector values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The scalar and vector values calculated by this compute are +"intensive". The scalar and vector values will be in distance and +distance^2 :doc:`units ` respectively. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute gyration/chunk ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_gyration_chunk.txt b/doc/_sources/compute_gyration_chunk.txt new file mode 100644 index 0000000000..cbd683db3f --- /dev/null +++ b/doc/_sources/compute_gyration_chunk.txt @@ -0,0 +1,122 @@ +.. index:: compute gyration/chunk + +compute gyration/chunk command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID gyration/chunk chunkID keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* gyration/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command +* zero or more keyword/value pairs may be appended +* keyword = *tensor* +.. parsed-literal:: + + *tensor* value = none + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 molecule gyration/chunk molchunk + compute 2 molecule gyration/chunk molchunk tensor + +Description +""""""""""" + +Define a computation that calculates the radius of gyration Rg for +multiple chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the radius of gyration Rg for each chunk, +which includes all effects due to atoms passing thru periodic +boundaries. + +Rg is a measure of the size of a chunk, and is computed by this +formula + +.. image:: Eqs/compute_gyration.jpg + :align: center + +where M is the total mass of the chunk, Rcm is the center-of-mass +position of the chunk, and the sum is over all atoms in the +chunk. + +Note that only atoms in the specified group contribute to the +calculation. The :doc:`compute chunk/atom ` command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +If the *tensor* keyword is specified, then the scalar Rg value is not +calculated, but an Rg tensor is instead calculated for each chunk. +The formula for the components of the tensor is the same as the above +formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy - +Rcmy) for the xy component, etc. The 6 components of the tensor are +ordered xx, yy, zz, xy, xz, yz. + +.. note:: + + The coordinates of an atom contribute to Rg in "unwrapped" form, + by using the image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. + See the Atoms section of the :doc:`read_data ` command for a + discussion of image flags and how they are set for each atom. You can + reset the image flags (e.g. to 0) before invoking this compute by + using the :doc:`set image ` command. + +The simplest way to output the results of the compute gyration/chunk +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all gyration/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +**Output info:** + +This compute calculates a global vector if the *tensor* keyword is not +specified and a global array if it is. The length of the vector or +number of rows in the array = the number of chunks *Nchunk* as +calculated by the specified :doc:`compute chunk/atom ` command. If the *tensor* keyword +is specified, the global array has 6 columns. The vector or array can +be accessed by any command that uses global values from a compute as +input. See :ref:`this section ` for an overview +of LAMMPS output options. + +All the vector or array values calculated by this compute are +"intensive". The vector or array values will be in distance +:doc:`units `, since they are the square root of values +represented by the formula above. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +:doc:`compute gyration ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_heat_flux.txt b/doc/_sources/compute_heat_flux.txt new file mode 100644 index 0000000000..00a1f01137 --- /dev/null +++ b/doc/_sources/compute_heat_flux.txt @@ -0,0 +1,225 @@ +.. index:: compute heat/flux + +compute heat/flux command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID heat/flux ke-ID pe-ID stress-ID + +* ID, group-ID are documented in :doc:`compute ` command +* heat/flux = style name of this compute command +* ke-ID = ID of a compute that calculates per-atom kinetic energy +* pe-ID = ID of a compute that calculates per-atom potential energy +* stress-ID = ID of a compute that calculates per-atom stress + +Examples +"""""""" + +.. parsed-literal:: + + compute myFlux all heat/flux myKE myPE myStress + +Description +""""""""""" + +Define a computation that calculates the heat flux vector based on +contributions from atoms in the specified group. This can be used by +itself to measure the heat flux into or out of a reservoir of atoms, +or to calculate a thermal conductivity using the Green-Kubo formalism. + +See the :doc:`fix thermal/conductivity ` +command for details on how to compute thermal conductivity in an +alternate way, via the Muller-Plathe method. See the :doc:`fix heat ` command for a way to control the heat added or +subtracted to a group of atoms. + +The compute takes three arguments which are IDs of other +:doc:`computes `. One calculates per-atom kinetic energy +(*ke-ID*), one calculates per-atom potential energy (*pe-ID)*, and the +third calcualtes per-atom stress (*stress-ID*). These should be +defined for the same group used by compute heat/flux, though LAMMPS +does not check for this. + +The Green-Kubo formulas relate the ensemble average of the +auto-correlation of the heat flux J to the thermal conductivity kappa: + +.. image:: Eqs/heat_flux_J.jpg + :align: center + +.. image:: Eqs/heat_flux_k.jpg + :align: center + +Ei in the first term of the equation for J is the per-atom energy +(potential and kinetic). This is calculated by the computes *ke-ID* +and *pe-ID*. Si in the second term of the equation for J is the +per-atom stress tensor calculated by the compute *stress-ID*. The +tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a +vector. Note that as discussed below, the 1/V scaling factor in the +equation for J is NOT included in the calculation performed by this +compute; you need to add it for a volume appropriate to the atoms +included in the calculation. + +.. note:: + + The :doc:`compute pe/atom ` and :doc:`compute stress/atom ` commands have options for which + terms to include in their calculation (pair, bond, etc). The heat + flux calculation will thus include exactly the same terms. Normally + you should use :doc:`compute stress/atom virial ` + so as not to include a kinetic energy term in the heat flux. + +This compute calculates 6 quantities and stores them in a 6-component +vector. The first 3 components are the x, y, z components of the full +heat flux vector, i.e. (Jx, Jy, Jz). The next 3 components are the x, +y, z components of just the convective portion of the flux, i.e. the +first term in the equation for J above. + + +---------- + + +The heat flux can be output every so many timesteps (e.g. via the +:doc:`thermo_style custom ` command). Then as a +post-processing operation, an autocorrelation can be performed, its +integral estimated, and the Green-Kubo formula above evaluated. + +The :doc:`fix ave/correlate ` command can calclate +the autocorrelation. The trap() function in the +:doc:`variable ` command can calculate the integral. + +An example LAMMPS input script for solid Ar is appended below. The +result should be: average conductivity ~0.29 in W/mK. + + +---------- + + +**Output info:** + +This compute calculates a global vector of length 6 (total heat flux +vector, followed by convective heat flux vector), which can be +accessed by indices 1-6. These values can be used by any command that +uses global vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The vector values calculated by this compute are "extensive", meaning +they scale with the number of atoms in the simulation. They can be +divided by the appropriate volume to get a flux, which would then be +an "intensive" value, meaning independent of the number of atoms in +the simulation. Note that if the compute is "all", then the +appropriate volume to divide by is the simulation box volume. +However, if a sub-group is used, it should be the volume containing +those atoms. + +The vector values will be in energy*velocity :doc:`units `. Once +divided by a volume the units will be that of flux, namely +energy/area/time :doc:`units ` + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix thermal/conductivity `, +:doc:`fix ave/correlate `, +:doc:`variable ` + +**Default:** none + + +---------- + + +.. parsed-literal:: + + # Sample LAMMPS input script for thermal conductivity of solid Ar + +.. parsed-literal:: + + units real + variable T equal 70 + variable V equal vol + variable dt equal 4.0 + variable p equal 200 # correlation length + variable s equal 10 # sample interval + variable d equal $p*$s # dump interval + +.. parsed-literal:: + + # convert from LAMMPS real units to SI + +.. parsed-literal:: + + variable kB equal 1.3806504e-23 # [J/K] Boltzmann + variable kCal2J equal 4186.0/6.02214e23 + variable A2m equal 1.0e-10 + variable fs2s equal 1.0e-15 + variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m} + +.. parsed-literal:: + + # setup problem + +.. parsed-literal:: + + dimension 3 + boundary p p p + lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 + region box block 0 4 0 4 0 4 + create_box 1 box + create_atoms 1 box + mass 1 39.948 + pair_style lj/cut 13.0 + pair_coeff * * 0.2381 3.405 + timestep ${dt} + thermo $d + +.. parsed-literal:: + + # equilibration and thermalization + +.. parsed-literal:: + + velocity all create $T 102486 mom yes rot yes dist gaussian + fix NVT all nvt temp $T $T 10 drag 0.2 + run 8000 + +.. parsed-literal:: + + # thermal conductivity calculation, switch to NVE if desired + +.. parsed-literal:: + + #unfix NVT + #fix NVE all nve + +.. parsed-literal:: + + reset_timestep 0 + compute myKE all ke/atom + compute myPE all pe/atom + compute myStress all stress/atom NULL virial + compute flux all heat/flux myKE myPE myStress + variable Jx equal c_flux[1]/vol + variable Jy equal c_flux[2]/vol + variable Jz equal c_flux[3]/vol + fix JJ all ave/correlate $s $p $d & + c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running + variable scale equal ${convert}/${kB}/$T/$T/$V*$s*${dt} + variable k11 equal trap(f_JJ[3])*${scale} + variable k22 equal trap(f_JJ[4])*${scale} + variable k33 equal trap(f_JJ[5])*${scale} + thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 + run 100000 + variable k equal (v_k11+v_k22+v_k33)/3.0 + variable ndens equal count(all)/vol + print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3" + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_hexorder_atom.txt b/doc/_sources/compute_hexorder_atom.txt new file mode 100644 index 0000000000..dd5555ce0e --- /dev/null +++ b/doc/_sources/compute_hexorder_atom.txt @@ -0,0 +1,136 @@ +.. index:: compute hexorder/atom + +compute hexorder/atom command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID hexorder/atom keyword values ... + +* ID, group-ID are documented in :doc:`compute ` command +* hexorder/atom = style name of this compute command +* one or more keyword/value pairs may be appended +.. parsed-literal:: + + keyword = *degree* or *nnn* or *cutoff* + *cutoff* value = distance cutoff + *nnn* value = number of nearest neighbors + *degree* value = degree *n* of order parameter + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all hexorder/atom + compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 + +Description +""""""""""" + +Define a computation that calculates *qn* the bond-orientational +order parameter for each atom in a group. The hexatic (*n* = 6) order +parameter was introduced by :ref:`Nelson and Halperin ` as a way to detect +hexagonal symmetry in two-dimensional systems. For each atom, *qn* +is a complex number (stored as two real numbers) defined as follows: + +.. image:: Eqs/hexorder.jpg + :align: center + +where the sum is over the *nnn* nearest neighbors +of the central atom. The angle theta +is formed by the bond vector rij and the *x* axis. theta is calculated +only using the *x* and *y* components, whereas the distance from the +central atom is calculated using all three +*x*, *y*, and *z* components of the bond vector. +Neighbor atoms not in the group +are included in the order parameter of atoms in the group. + +The optional keyword *cutoff* defines the distance cutoff +used when searching for neighbors. The default value, also +the maximum allowable value, is the cutoff specified +by the pair style. + +The optional keyword *nnn* defines the number of nearest +neighbors used to calculate *qn*. The default value is 6. +If the value is NULL, then all neighbors up to the +distance cutoff are used. + +The optional keyword *degree* sets the degree *n* of the order parameter. +The default value is 6. For a perfect hexagonal lattice with +*nnn* = 6, +*q*6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 +depends only on the orientation of the lattice relative to the *x* axis. +In an isotropic liquid, local neighborhoods may still exhibit +weak hexagonal symmetry, but because the orientational correlation +decays quickly with distance, the value of phi will be different for +different atoms, and so when *q*6 is averaged over all the atoms +in the system, |<*q*6>| << 1. + +The value of *qn* is set to zero for atoms not in the +specified compute group, as well as for atoms that have less than +*nnn* neighbors within the distance cutoff. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently. + +.. note:: + + If you have a bonded system, then the settings of + :doc:`special_bonds ` command can remove pairwise + interactions between atoms in the same bond, angle, or dihedral. This + is the default setting for the :doc:`special_bonds ` + command, and means those pairwise interactions do not appear in the + neighbor list. Because this fix uses the neighbor list, it also means + those pairs will not be included in the order parameter. This + difficulty can be circumvented by writing a dump file, and using the + :doc:`rerun ` command to compute the order parameter for + snapshots in the dump file. The rerun script can use a + :doc:`special_bonds ` command that includes all pairs in + the neighbor list. + +**Output info:** + +This compute calculates a per-atom array with 2 columns, giving the +real and imaginary parts *qn*, a complex number restricted to the +unit disk of the complex plane i.e. Re(*qn*)^2 + Im(*qn*)^2 <= 1 . + +These values can be accessed by any command that uses +per-atom values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute orientorder/atom `, :doc:`compute coord/atom `, :doc:`compute centro/atom ` + +Default +""""""" + +The option defaults are *cutoff* = pair style cutoff, *nnn* = 6, *degree* = 6 + + +---------- + + +.. _Nelson: + + + +**(Nelson)** Nelson, Halperin, Phys Rev B, 19, 2457 (1979). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_improper_local.txt b/doc/_sources/compute_improper_local.txt new file mode 100644 index 0000000000..d2128538c0 --- /dev/null +++ b/doc/_sources/compute_improper_local.txt @@ -0,0 +1,79 @@ +.. index:: compute improper/local + +compute improper/local command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID improper/local input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* improper/local = style name of this compute command +* one or more keywords may be appended +* keyword = *chi* +.. parsed-literal:: + + *chi* = tabulate improper angles + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all improper/local chi + +Description +""""""""""" + +Define a computation that calculates properties of individual improper +interactions. The number of datums generated, aggregated across all +processors, equals the number of impropers in the system, modified by +the group parameter as explained below. + +The local data stored by this command is generated by looping over all +the atoms owned on a processor and their impropers. An improper will +only be included if all 4 atoms in the improper are in the specified +compute group. + +Note that as atoms migrate from processor to processor, there will be +no consistent ordering of the entries within the local vector or array +from one timestep to the next. The only consistency that is +guaranteed is that the ordering on a particular timestep will be the +same for local vectors or arrays generated by other compute commands. +For example, improper output from the :doc:`compute property/local ` command can be combined +with data from this command and output by the :doc:`dump local ` +command in a consistent way. + +**Output info:** + +This compute calculates a local vector or local array depending on the +number of keywords. The length of the vector or number of rows in the +array is the number of impropers. If a single keyword is specified, a +local vector is produced. If two or more keywords are specified, a +local array is produced where the number of columns = the number of +keywords. The vector or array can be accessed by any command that +uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The output for *chi* will be in degrees. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump local `, :doc:`compute property/local ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_inertia_chunk.txt b/doc/_sources/compute_inertia_chunk.txt new file mode 100644 index 0000000000..e55f6f413b --- /dev/null +++ b/doc/_sources/compute_inertia_chunk.txt @@ -0,0 +1,96 @@ +.. index:: compute inertia/chunk + +compute inertia/chunk command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID inertia/chunk chunkID + +* ID, group-ID are documented in :doc:`compute ` command +* inertia/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 fluid inertia/chunk molchunk + +Description +""""""""""" + +Define a computation that calculates the inertia tensor for multiple +chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the 6 components of the symmetric intertia +tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The +calculation includes all effects due to atoms passing thru periodic +boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The :doc:`compute chunk/atom ` command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +.. note:: + + The coordinates of an atom contribute to the chunk's inertia + tensor in "unwrapped" form, by using the image flags associated with + each atom. See the :doc:`dump custom ` command for a discussion + of "unwrapped" coordinates. See the Atoms section of the + :doc:`read_data ` command for a discussion of image flags and + how they are set for each atom. You can reset the image flags + (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + +The simplest way to output the results of the compute inertia/chunk +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all inertia/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +**Output info:** + +This compute calculates a global array where the number of rows = the +number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = +6 for the 6 components of the inertia tensor for each chunk, ordered +as listed above. These values can be accessed by any command that +uses global array values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The array values are "intensive". The array values will be in +mass*distance^2 :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`variable inertia() function ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_ke.txt b/doc/_sources/compute_ke.txt new file mode 100644 index 0000000000..9283108be8 --- /dev/null +++ b/doc/_sources/compute_ke.txt @@ -0,0 +1,69 @@ +.. index:: compute ke + +compute ke command +================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID ke + +* ID, group-ID are documented in :doc:`compute ` command +* ke = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all ke + +Description +""""""""""" + +Define a computation that calculates the translational kinetic energy +of a group of particles. + +The kinetic energy of each particle is computed as 1/2 m v^2, where m +and v are the mass and velocity of the particle. + +There is a subtle difference between the quantity calculated by this +compute and the kinetic energy calculated by the *ke* or *etotal* +keyword used in thermodynamic output, as specified by the +:doc:`thermo_style ` command. For this compute, kinetic +energy is "translational" kinetic energy, calculated by the simple +formula above. For thermodynamic output, the *ke* keyword infers +kinetic energy from the temperature of the system with 1/2 Kb T of +energy for each degree of freedom. For the default temperature +computation via the :doc:`compute temp ` command, these +are the same. But different computes that calculate temperature can +subtract out different non-thermal components of velocity and/or +include different degrees of freedom (translational, rotational, etc). + +**Output info:** + +This compute calculates a global scalar (the summed KE). This value +can be used by any command that uses a global scalar value from a +compute as input. See :ref:`Section_howto 15 ` +for an overview of LAMMPS output options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute erotate/sphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_ke_atom.txt b/doc/_sources/compute_ke_atom.txt new file mode 100644 index 0000000000..ddee572c60 --- /dev/null +++ b/doc/_sources/compute_ke_atom.txt @@ -0,0 +1,58 @@ +.. index:: compute ke/atom + +compute ke/atom command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID ke/atom + +* ID, group-ID are documented in :doc:`compute ` command +* ke/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all ke/atom + +Description +""""""""""" + +Define a computation that calculates the per-atom translational +kinetic energy for each atom in a group. + +The kinetic energy is simply 1/2 m v^2, where m is the mass and v is +the velocity of each atom. + +The value of the kinetic energy will be 0.0 for atoms not in the +specified compute group. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump custom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_ke_atom_eff.txt b/doc/_sources/compute_ke_atom_eff.txt new file mode 100644 index 0000000000..b776b17128 --- /dev/null +++ b/doc/_sources/compute_ke_atom_eff.txt @@ -0,0 +1,88 @@ +.. index:: compute ke/atom/eff + +compute ke/atom/eff command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID ke/atom/eff + +* ID, group-ID are documented in :doc:`compute ` command +* ke/atom/eff = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all ke/atom/eff + +Description +""""""""""" + +Define a computation that calculates the per-atom translational +(nuclei and electrons) and radial kinetic energy (electron only) in a +group. The particles are assumed to be nuclei and electrons modeled +with the :doc:`electronic force field `. + +The kinetic energy for each nucleus is computed as 1/2 m v^2, where m +corresponds to the corresponding nuclear mass, and the kinetic energy +for each electron is computed as 1/2 (me v^2 + 3/4 me s^2), where me +and v correspond to the mass and translational velocity of each +electron, and s to its radial velocity, respectively. + +There is a subtle difference between the quantity calculated by this +compute and the kinetic energy calculated by the *ke* or *etotal* +keyword used in thermodynamic output, as specified by the +:doc:`thermo_style ` command. For this compute, kinetic +energy is "translational" plus electronic "radial" kinetic energy, +calculated by the simple formula above. For thermodynamic output, the +*ke* keyword infers kinetic energy from the temperature of the system +with 1/2 Kb T of energy for each (nuclear-only) degree of freedom in +eFF. + +.. note:: + + The temperature in eFF should be monitored via the :doc:`compute temp/eff ` command, which can be printed with + thermodynamic output by using the :doc:`thermo_modify ` + command, as shown in the following example: + +.. parsed-literal:: + + compute effTemp all temp/eff + thermo_style custom step etotal pe ke temp press + thermo_modify temp effTemp + +The value of the kinetic energy will be 0.0 for atoms (nuclei or +electrons) not in the specified compute group. + +**Output info:** + +This compute calculates a scalar quantity for each atom, which can be +accessed by any command that uses per-atom computes as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`dump custom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_ke_eff.txt b/doc/_sources/compute_ke_eff.txt new file mode 100644 index 0000000000..4497ecf5bd --- /dev/null +++ b/doc/_sources/compute_ke_eff.txt @@ -0,0 +1,87 @@ +.. index:: compute ke/eff + +compute ke/eff command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID ke/eff + +* ID, group-ID are documented in :doc:`compute ` command +* ke/eff = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all ke/eff + +Description +""""""""""" + +Define a computation that calculates the kinetic energy of motion of a +group of eFF particles (nuclei and electrons), as modeled with the +:doc:`electronic force field `. + +The kinetic energy for each nucleus is computed as 1/2 m v^2 and the +kinetic energy for each electron is computed as 1/2(me v^2 + 3/4 me +s^2), where m corresponds to the nuclear mass, me to the electron +mass, v to the translational velocity of each particle, and s to the +radial velocity of the electron, respectively. + +There is a subtle difference between the quantity calculated by this +compute and the kinetic energy calculated by the *ke* or *etotal* +keyword used in thermodynamic output, as specified by the +:doc:`thermo_style ` command. For this compute, kinetic +energy is "translational" and "radial" (only for electrons) kinetic +energy, calculated by the simple formula above. For thermodynamic +output, the *ke* keyword infers kinetic energy from the temperature of +the system with 1/2 Kb T of energy for each degree of freedom. For +the eFF temperature computation via the :doc:`compute temp_eff ` command, these are the same. But +different computes that calculate temperature can subtract out +different non-thermal components of velocity and/or include other +degrees of freedom. + +IMPRORTANT NOTE: The temperature in eFF models should be monitored via +the :doc:`compute temp/eff ` command, which can be +printed with thermodynamic output by using the +:doc:`thermo_modify ` command, as shown in the following +example: + +.. parsed-literal:: + + compute effTemp all temp/eff + thermo_style custom step etotal pe ke temp press + thermo_modify temp effTemp + +See :doc:`compute temp/eff `. + +**Output info:** + +This compute calculates a global scalar (the KE). This value can be +used by any command that uses a global scalar value from a compute as +input. See :ref:`Section_howto 15 ` for an +overview of LAMMPS output options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_ke_rigid.txt b/doc/_sources/compute_ke_rigid.txt new file mode 100644 index 0000000000..d40e1768c6 --- /dev/null +++ b/doc/_sources/compute_ke_rigid.txt @@ -0,0 +1,67 @@ +.. index:: compute ke/rigid + +compute ke/rigid command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID ke/rigid fix-ID + +* ID, group-ID are documented in :doc:`compute ` command +* ke = style name of this compute command +* fix-ID = ID of rigid body fix + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all ke/rigid myRigid + +Description +""""""""""" + +Define a computation that calculates the translational kinetic energy +of a collection of rigid bodies, as defined by one of the :doc:`fix rigid ` command variants. + +The kinetic energy of each rigid body is computed as 1/2 M Vcm^2, +where M is the total mass of the rigid body, and Vcm is its +center-of-mass velocity. + +The *fix-ID* should be the ID of one of the :doc:`fix rigid ` +commands which defines the rigid bodies. The group specified in the +compute command is ignored. The kinetic energy of all the rigid +bodies defined by the fix rigid command in included in the +calculation. + +**Output info:** + +This compute calculates a global scalar (the summed KE of all the +rigid bodies). This value can be used by any command that uses a +global scalar value from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the RIGID package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute erotate/rigid ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_meso_e_atom.txt b/doc/_sources/compute_meso_e_atom.txt new file mode 100644 index 0000000000..833e0d363b --- /dev/null +++ b/doc/_sources/compute_meso_e_atom.txt @@ -0,0 +1,65 @@ +.. index:: compute meso/e/atom + +compute meso/e/atom command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID meso/e/atom + +* ID, group-ID are documented in :doc:`compute ` command +* meso/e/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all meso/e/atom + +Description +""""""""""" + +Define a computation that calculates the per-atom internal energy +for each atom in a group. + +The internal energy is the energy associated with the internal degrees +of freedom of a mesoscopic particles, e.g. a Smooth-Particle +Hydrodynamics particle. + +See `this PDF guide `_ to using SPH in +LAMMPS. + +The value of the internal energy will be 0.0 for atoms not in the +specified compute group. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SPH package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`dump custom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_meso_rho_atom.txt b/doc/_sources/compute_meso_rho_atom.txt new file mode 100644 index 0000000000..cbfa469267 --- /dev/null +++ b/doc/_sources/compute_meso_rho_atom.txt @@ -0,0 +1,65 @@ +.. index:: compute meso/rho/atom + +compute meso/rho/atom command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID meso/rho/atom + +* ID, group-ID are documented in :doc:`compute ` command +* meso/rho/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all meso/rho/atom + +Description +""""""""""" + +Define a computation that calculates the per-atom mesoscopic density +for each atom in a group. + +The mesoscopic density is the mass density of a mesoscopic particle, +calculated by kernel function interpolation using "pair style +sph/rhosum". + +See `this PDF guide `_ to using SPH in +LAMMPS. + +The value of the mesoscopic density will be 0.0 for atoms not in the +specified compute group. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be in mass/volume :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SPH package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`dump custom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_meso_t_atom.txt b/doc/_sources/compute_meso_t_atom.txt new file mode 100644 index 0000000000..817d6f2567 --- /dev/null +++ b/doc/_sources/compute_meso_t_atom.txt @@ -0,0 +1,67 @@ +.. index:: compute meso/t/atom + +compute meso/t/atom command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID meso/t/atom + +* ID, group-ID are documented in :doc:`compute ` command +* meso/t/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all meso/t/atom + +Description +""""""""""" + +Define a computation that calculates the per-atom internal temperature +for each atom in a group. + +The internal temperature is the ratio of internal energy over the heat +capacity associated with the internal degrees of freedom of a mesoscopic +particles, e.g. a Smooth-Particle Hydrodynamics particle. + +T_*int* = E_*int* / C_*V, int* + +See `this PDF guide `_ to using SPH in +LAMMPS. + +The value of the internal energy will be 0.0 for atoms not in the +specified compute group. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be in temperature :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SPH package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`dump custom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_modify.txt b/doc/_sources/compute_modify.txt new file mode 100644 index 0000000000..a95364c843 --- /dev/null +++ b/doc/_sources/compute_modify.txt @@ -0,0 +1,82 @@ +.. index:: compute_modify + +compute_modify command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + compute_modify compute-ID keyword value ... + +* compute-ID = ID of the compute to modify +* one or more keyword/value pairs may be listed +* keyword = *extra* or *dynamic* +.. parsed-literal:: + + *extra* value = N + N = # of extra degrees of freedom to subtract + *dynamic* value = *yes* or *no* + yes/no = do or do not recompute the number of atoms contributing to the temperature + *thermo* value = *yes* or *no* + yes/no = do or do not add contributions from fixes to the potential energy + + + +Examples +"""""""" + +.. parsed-literal:: + + compute_modify myTemp extra 0 + compute_modify newtemp dynamic yes extra 600 + +Description +""""""""""" + +Modify one or more parameters of a previously defined compute. Not +all compute styles support all parameters. + +The *extra* keyword refers to how many degrees-of-freedom are +subtracted (typically from 3N) as a normalizing factor in a +temperature computation. Only computes that compute a temperature use +this option. The default is 2 or 3 for :doc:`2d or 3d systems ` which is a correction factor for an ensemble +of velocities with zero total linear momentum. You can use a negative +number for the *extra* parameter if you need to add +degrees-of-freedom. See the :doc:`compute temp/asphere ` command for an example. + +The *dynamic* keyword determines whether the number of atoms N in the +compute group is re-computed each time a temperature is computed. +Only compute styles that compute a temperature use this option. By +default, N is assumed to be constant. If you are adding atoms to the +system (see the :doc:`fix pour ` or :doc:`fix deposit ` commands) or expect atoms to be lost +(e.g. due to evaporation), then this option should be used to insure +the temperature is correctly normalized. + +The *thermo* keyword determines whether the potential energy +contribution calculated by some :doc:`fixes ` is added to the +potential energy calculated by the compute. Currently, only the +compute of style *pe* uses this option. See the doc pages for +:doc:`individual fixes ` for details. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute ` + +Default +""""""" + +The option defaults are extra = 2 or 3 for 2d or 3d systems and +dynamic = no. Thermo is *yes* if the compute of style *pe* was +defined with no extra keywords; otherwise it is *no*. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_msd.txt b/doc/_sources/compute_msd.txt new file mode 100644 index 0000000000..1e3e718373 --- /dev/null +++ b/doc/_sources/compute_msd.txt @@ -0,0 +1,126 @@ +.. index:: compute msd + +compute msd command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID msd keyword values ... + +* ID, group-ID are documented in :doc:`compute ` command +* msd = style name of this compute command +* zero or more keyword/value pairs may be appended +* keyword = *com* or *average* +.. parsed-literal:: + + *com* value = *yes* or *no* + *average* value = *yes* or *no* + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all msd + compute 1 upper msd com yes average yes + +Description +""""""""""" + +Define a computation that calculates the mean-squared displacement +(MSD) of the group of atoms, including all effects due to atoms +passing thru periodic boundaries. For computation of the non-Gaussian +parameter of mean-squared displacement, see the :doc:`compute msd/nongauss ` command. + +A vector of four quantites is calculated by this compute. The first 3 +elements of the vector are the squared dx,dy,dz displacements, summed +and averaged over atoms in the group. The 4th element is the total +squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and +averaged over atoms in the group. + +The slope of the mean-squared displacement (MSD) versus time is +proportional to the diffusion coefficient of the diffusing atoms. + +The displacement of an atom is from its reference position. This is +normally the original position at the time +the compute command was issued, unless the *average* keyword is set to *yes*. +The value of the displacement will be +0.0 for atoms not in the specified compute group. + +If the *com* option is set to *yes* then the effect of any drift in +the center-of-mass of the group of atoms is subtracted out before the +displacment of each atom is calculated. + +If the *average* option is set to *yes* then the reference position of +an atom is based on the average position of that atom, corrected for +center-of-mass motion if requested. The average position is a running +average over all previous calls to the compute, including the current +call. So on the first call it is current position, on the second call +it is the arithmetic average of the current position and the position +on the first call, and so on. Note that when using this option, the +precise value of the mean square displacement will depend on the +number of times the compute is called. So, for example, changing the +frequency of thermo output may change the computed displacement. Also, +the precise values will be changed if a single simulation is broken up +into two parts, using either multiple run commands or a restart +file. It only makes sense to use this option if the atoms are not +diffusing, so that their average positions relative to the center of +mass of the system are stationary. The most common case is crystalline +solids undergoing thermal motion. + +.. note:: + + Initial coordinates are stored in "unwrapped" form, by using the + image flags associated with each atom. See the :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. + See the Atoms section of the :doc:`read_data ` command for a + discussion of image flags and how they are set for each atom. You can + reset the image flags (e.g. to 0) before invoking this compute by + using the :doc:`set image ` command. + +.. note:: + + If you want the quantities calculated by this compute to be + continuous when running from a :doc:`restart file `, then + you should use the same ID for this compute, as in the original run. + This is so that the fix this compute creates to store per-atom + quantities will also have the same ID, and thus be initialized + correctly with atom reference positions from the restart file. When + *average* is set to yes, then the atom reference positions are + restored correctly, but not the number of samples used obtain them. As + a result, the reference positions from the restart file are combined + with subsequent positions as if they were from a single sample, + instead of many, which will change the values of msd somewhat. + +**Output info:** + +This compute calculates a global vector of length 4, which can be +accessed by indices 1-4 by any command that uses global vector values +from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The vector values are "intensive". The vector values will be in +distance^2 :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute msd/nongauss `, :doc:`compute displace_atom `, :doc:`fix store/state `, :doc:`compute msd/chunk ` + +Default +""""""" + +The option default are com = no, average = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_msd_chunk.txt b/doc/_sources/compute_msd_chunk.txt new file mode 100644 index 0000000000..4c491d0a4a --- /dev/null +++ b/doc/_sources/compute_msd_chunk.txt @@ -0,0 +1,134 @@ +.. index:: compute msd/chunk + +compute msd/chunk command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID msd/chunk chunkID + +* ID, group-ID are documented in :doc:`compute ` command +* msd/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all msd/chunk molchunk + +Description +""""""""""" + +Define a computation that calculates the mean-squared displacement +(MSD) for multiple chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +Four quantites are calculated by this compute for each chunk. The +first 3 quantities are the squared dx,dy,dz displacements of the +center-of-mass. The 4th component is the total squared displacement, +i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These +calculations include all effects due to atoms passing thru periodic +boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The :doc:`compute chunk/atom ` command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +The slope of the mean-squared displacement (MSD) versus time is +proportional to the diffusion coefficient of the diffusing chunks. + +The displacement of the center-of-mass of the chunk is from its +original center-of-mass position, calculated on the timestep this +compute command was first invoked. + +.. note:: + + The number of chunks *Nchunk* calculated by the :doc:`compute chunk/atom ` command must remain constant each + time this compute is invoked, so that the displacement for each chunk + from its original position can be computed consistently. If *Nchunk* + does not remain constant, an error will be generated. If needed, you + can enforce a constant *Nchunk* by using the *nchunk once* or *ids + once* options when specifying the :doc:`compute chunk/atom ` command. + +.. note:: + + This compute stores the original position (of the + center-of-mass) of each chunk. When a displacement is calculated on a + later timestep, it is assumed that the same atoms are assigned to the + same chunk ID. However LAMMPS has no simple way to insure this is the + case, though you can use the *ids once* option when specifying the + :doc:`compute chunk/atom ` command. Note that if + this is not the case, the MSD calculation does not have a sensible + meaning. + +.. note:: + + The initial coordinates of the atoms in each chunk are stored in + "unwrapped" form, by using the image flags associated with each atom. + See the :doc:`dump custom ` command for a discussion of + "unwrapped" coordinates. See the Atoms section of the + :doc:`read_data ` command for a discussion of image flags and + how they are set for each atom. You can reset the image flags + (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + +.. note:: + + If you want the quantities calculated by this compute to be + continuous when running from a :doc:`restart file `, then + you should use the same ID for this compute, as in the original run. + This is so that the fix this compute creates to store per-chunk + quantities will also have the same ID, and thus be initialized + correctly with chunk reference positions from the restart file. + +The simplest way to output the results of the compute com/msd +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all com/msd cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +**Output info:** + +This compute calculates a global array where the number of rows = the +number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = +4 for dx,dy,dz and the total displacement. These values can be +accessed by any command that uses global array values from a compute +as input. See :ref:`this section ` for an +overview of LAMMPS output options. + +The array values are "intensive". The array values will be in +distance^2 :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute msd ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_msd_nongauss.txt b/doc/_sources/compute_msd_nongauss.txt new file mode 100644 index 0000000000..a330cb2a95 --- /dev/null +++ b/doc/_sources/compute_msd_nongauss.txt @@ -0,0 +1,93 @@ +.. index:: compute msd/nongauss + +compute msd/nongauss command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID msd/nongauss keyword values ... + +* ID, group-ID are documented in :doc:`compute ` command +* msd/nongauss = style name of this compute command +* zero or more keyword/value pairs may be appended +* keyword = *com* +.. parsed-literal:: + + *com* value = *yes* or *no* + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all msd/nongauss + compute 1 upper msd/nongauss com yes + +Description +""""""""""" + +Define a computation that calculates the mean-squared displacement +(MSD) and non-Gaussian parameter (NGP) of the group of atoms, +including all effects due to atoms passing thru periodic boundaries. + +A vector of three quantites is calculated by this compute. The first +element of the vector is the total squared dx,dy,dz displacements +drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the +fourth power of these displacements drfourth = (dx*dx + dy*dy + +dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the +group. The 3rd component is the nonGaussian diffusion paramter NGP = +3*drfourth/(5*drsquared*drsquared), i.e. + +.. image:: Eqs/compute_msd_nongauss.jpg + :align: center + +The NGP is a commonly used quantity in studies of dynamical +heterogeneity. Its minimum theoretical value (-0.4) occurs when all +atoms have the same displacement magnitude. NGP=0 for Brownian +diffusion, while NGP > 0 when some mobile atoms move faster than +others. + +If the *com* option is set to *yes* then the effect of any drift in +the center-of-mass of the group of atoms is subtracted out before the +displacment of each atom is calcluated. + +See the :doc:`compute msd ` doc page for further important +NOTEs, which also apply to this compute. + +**Output info:** + +This compute calculates a global vector of length 3, which can be +accessed by indices 1-3 by any command that uses global vector values +from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The vector values are "intensive". The first vector value will be in +distance^2 :doc:`units `, the second is in distance^4 units, and +the 3rd is dimensionless. + +Restrictions +"""""""""""" + + +This compute is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute msd ` + +Default +""""""" + +The option default is com = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_omega_chunk.txt b/doc/_sources/compute_omega_chunk.txt new file mode 100644 index 0000000000..ea3cc572a3 --- /dev/null +++ b/doc/_sources/compute_omega_chunk.txt @@ -0,0 +1,97 @@ +.. index:: compute omega/chunk + +compute omega/chunk command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID omega/chunk chunkID + +* ID, group-ID are documented in :doc:`compute ` command +* omega/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 fluid omega/chunk molchunk + +Description +""""""""""" + +Define a computation that calculates the angular velocity (omega) of +multiple chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the 3 components of the angular velocity +vector for each chunk, via the formula L = Iw where L is the angular +momentum vector of the chunk, I is its moment of inertia tensor, and w +is omega = angular velocity of the chunk. The calculation includes +all effects due to atoms passing thru periodic boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The :doc:`compute chunk/atom ` command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +.. note:: + + The coordinates of an atom contribute to the chunk's angular + velocity in "unwrapped" form, by using the image flags associated with + each atom. See the :doc:`dump custom ` command for a discussion + of "unwrapped" coordinates. See the Atoms section of the + :doc:`read_data ` command for a discussion of image flags and + how they are set for each atom. You can reset the image flags + (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + +The simplest way to output the results of the compute omega/chunk +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all omega/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +**Output info:** + +This compute calculates a global array where the number of rows = the +number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = +3 for the 3 xyz components of the angular velocity for each chunk. +These values can be accessed by any command that uses global array +values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The array values are "intensive". The array values will be in +velocity/distance :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`variable omega() function ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_orientorder_atom.txt b/doc/_sources/compute_orientorder_atom.txt new file mode 100644 index 0000000000..ddc76d6570 --- /dev/null +++ b/doc/_sources/compute_orientorder_atom.txt @@ -0,0 +1,144 @@ +.. index:: compute orientorder/atom + +compute orientorder/atom command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID orientorder/atom keyword values ... + +* ID, group-ID are documented in :doc:`compute ` command +* orientorder/atom = style name of this compute command +* one or more keyword/value pairs may be appended +.. parsed-literal:: + + keyword = *cutoff* or *nnn* or *ql* + *cutoff* value = distance cutoff + *nnn* value = number of nearest neighbors + *degrees* values = nlvalues, l1, l2,... + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all orientorder/atom + compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 + +Description +""""""""""" + +Define a computation that calculates a set of bond-orientational +order parameters *Ql* for each atom in a group. These order parameters +were introduced by :ref:`Steinhardt et al. ` as a way to +characterize the local orientational order in atomic structures. +For each atom, *Ql* is a real number defined as follows: + +.. image:: Eqs/orientorder.jpg + :align: center + +The first equation defines the spherical harmonic order parameters. +These are complex number components of the 3D analog of the 2D order +parameter *qn*, which is implemented as LAMMPS compute +:doc:`hexorder/atom `. +The summation is over the *nnn* nearest +neighbors of the central atom. +The angles theta and phi are the standard spherical polar angles +defining the direction of the bond vector *rij*. +The second equation defines *Ql*, which is a +rotationally invariant scalar quantity obtained by summing +over all the components of degree *l*. + +The optional keyword *cutoff* defines the distance cutoff +used when searching for neighbors. The default value, also +the maximum allowable value, is the cutoff specified +by the pair style. + +The optional keyword *nnn* defines the number of nearest +neighbors used to calculate *Ql*. The default value is 12. +If the value is NULL, then all neighbors up to the +specified distance cutoff are used. + +The optional keyword *degrees* defines the list of order parameters to +be computed. The first argument *nlvalues* is the number of order +parameters. This is followed by that number of integers giving the +degree of each order parameter. Because *Q*2 and all odd-degree +order parameters are zero for atoms in cubic crystals +(see :ref:`Steinhardt `), the default order parameters +are *Q*4, *Q*6, *Q*8, *Q*10, and *Q*12. For the +FCC crystal with *nnn*=12, *Q*4 = sqrt(7/3)/8 = 0.19094.... +The numerical values of all order parameters up to *Q*12 +for a range of commonly encountered high-symmetry structures are given +in Table I of :ref:`Mickel et al. `. + +The value of *Ql* is set to zero for atoms not in the +specified compute group, as well as for atoms that have less than +*nnn* neighbors within the distance cutoff. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently. + +.. note:: + + If you have a bonded system, then the settings of + :doc:`special_bonds ` command can remove pairwise + interactions between atoms in the same bond, angle, or dihedral. This + is the default setting for the :doc:`special_bonds ` + command, and means those pairwise interactions do not appear in the + neighbor list. Because this fix uses the neighbor list, it also means + those pairs will not be included in the order parameter. This + difficulty can be circumvented by writing a dump file, and using the + :doc:`rerun ` command to compute the order parameter for + snapshots in the dump file. The rerun script can use a + :doc:`special_bonds ` command that includes all pairs in + the neighbor list. + +**Output info:** + +This compute calculates a per-atom array with *nlvalues* columns, giving the +*Ql* values for each atom, which are real numbers on the range 0 <= *Ql* <= 1. + +These values can be accessed by any command that uses +per-atom values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute coord/atom `, :doc:`compute centro/atom `, :doc:`compute hexorder/atom ` + +Default +""""""" + +The option defaults are *cutoff* = pair style cutoff, *nnn* = 12, *degrees* = 5 4 6 8 9 10 12 i.e. *Q*4, *Q*6, *Q*8, *Q*10, and *Q*12. + + +---------- + + +.. _Steinhardt: + + + +.. _Mickel: + +**(Steinhardt)** P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983). + + +**(Mickel)** W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_pair.txt b/doc/_sources/compute_pair.txt new file mode 100644 index 0000000000..5262e0c035 --- /dev/null +++ b/doc/_sources/compute_pair.txt @@ -0,0 +1,90 @@ +.. index:: compute pair + +compute pair command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID pair pstyle evalue + +* ID, group-ID are documented in :doc:`compute ` command +* pair = style name of this compute command +* pstyle = style name of a pair style that calculates additional values +* evalue = *epair* or *evdwl* or *ecoul* or blank (optional setting) + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all pair gauss + compute 1 all pair lj/cut/coul/cut ecoul + compute 1 all pair reax + +Description +""""""""""" + +Define a computation that extracts additional values calculated by a +pair style, sums them across processors, and makes them accessible for +output or further processing by other commands. The group specified +for this command is ignored. + +The specified *pstyle* must be a pair style used in your simulation +either by itself or as a sub-style in a :doc:`pair_style hybrid or hybrid/overlay ` command. + +The *evalue* setting is optional; it may be left off the command. All +pair styles tally a potential energy *epair* which may be broken into +two parts: *evdwl* and *ecoul* such that *epair* = *evdwl* + *ecoul*. +If the pair style calculates Coulombic interactions, their energy will +be tallied in *ecoul*. Everything else (whether it is a Lennard-Jones +style van der Waals interaction or not) is tallied in *evdwl*. If +*evalue* is specified as *epair* or left out, then *epair* is stored +as a global scalar by this compute. This is useful when using +:doc:`pair_style hybrid ` if you want to know the portion +of the total energy contributed by one sub-style. If *evalue* is +specfied as *evdwl* or *ecoul*, then just that portion of the energy +is stored as a global scalar. + +Some pair styles tally additional quantities, e.g. a breakdown of +potential energy into a dozen or so components is tallied by the +:doc:`pair_style reax ` commmand. These values (1 or more) +are stored as a global vector by this compute. See the doc page for +:doc:`individual pair styles ` for info on these values. + +**Output info:** + +This compute calculates a global scalar which is *epair* or *evdwl* or +*ecoul*. If the pair style supports it, it also calculates a global +vector of length >= 1, as determined by the pair style. These values +can be used by any command that uses global scalar or vector values +from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar and vector values calculated by this compute are +"extensive". + +The scalar value will be in energy :doc:`units `. The vector +values will typically also be in energy :doc:`units `, but +see the doc page for the pair style for details. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute pe ` + +Default +""""""" + +The default for *evalue* is *epair*. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_pair_local.txt b/doc/_sources/compute_pair_local.txt new file mode 100644 index 0000000000..99a3d2af70 --- /dev/null +++ b/doc/_sources/compute_pair_local.txt @@ -0,0 +1,129 @@ +.. index:: compute pair/local + +compute pair/local command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID pair/local input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* pair/local = style name of this compute command +* zero or more keywords may be appended +* keyword = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN* +.. parsed-literal:: + + *dist* = pairwise distance + *eng* = pairwise energy + *force* = pairwise force + *fx*,*fy*,*fz* = components of pairwise force + *pN* = pair style specific quantities for allowed N values + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all pair/local eng + compute 1 all pair/local dist eng force + compute 1 all pair/local dist eng fx fy fz + compute 1 all pair/local dist fx fy fz p1 p2 p3 + +Description +""""""""""" + +Define a computation that calculates properties of individual pairwise +interactions. The number of datums generated, aggregated across all +processors, equals the number of pairwise interactions in the system. + +The local data stored by this command is generated by looping over the +pairwise neighbor list. Info about an individual pairwise interaction +will only be included if both atoms in the pair are in the specified +compute group, and if the current pairwise distance is less than the +force cutoff distance for that interaction, as defined by the +:doc:`pair_style ` and :doc:`pair_coeff ` +commands. + +The output *dist* is the distance bewteen the pair of atoms. + +The output *eng* is the interaction energy for the pair of atoms. + +The output *force* is the force acting between the pair of atoms, +which is positive for a repulsive force and negative for an attractive +force. The outputs *fx*, *fy*, and *fz* are the xyz components of +*force* on atom I. + +A pair style may define additional pairwise quantities which can be +accessed as *p1* to *pN*, where N is defined by the pair style. Most +pair styles do not define any additional quantities, so N = 0. An +example of ones that do are the :doc:`granular pair styles ` +which calculate the tangential force between two particles and return +its components and magnitude acting on atom I for N = 1,2,3,4. See +individual pair styles for detils. + +The output *dist* will be in distance :doc:`units `. The output +*eng* will be in energy :doc:`units `. The outputs *force*, +*fx*, *fy*, and *fz* will be in force :doc:`units `. The output +*pN* will be in whatever units the pair style defines. + +Note that as atoms migrate from processor to processor, there will be +no consistent ordering of the entries within the local vector or array +from one timestep to the next. The only consistency that is +guaranteed is that the ordering on a particular timestep will be the +same for local vectors or arrays generated by other compute commands. +For example, pair output from the :doc:`compute property/local ` command can be combined +with data from this command and output by the :doc:`dump local ` +command in a consistent way. + +.. note:: + + For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4 + interactions within the molecular topology, their pairwise interaction + may be turned off, and thus they may not appear in the neighbor list, + and will not be part of the local data created by this command. More + specifically, this will be true of I,J pairs with a weighting factor + of 0.0; pairs with a non-zero weighting factor are included. The + weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set + by the :doc:`special_bonds ` command. An exception is if + long-range Coulombics are being computed via the + :doc:`kspace_style ` command, then atom pairs with + weighting factors of zero are still included in the neighbor list, so + that a portion of the long-range interaction contribution can be + computed in the pair style. Hence in that case, those atom pairs will + be part of the local data created by this command. + +**Output info:** + +This compute calculates a local vector or local array depending on the +number of keywords. The length of the vector or number of rows in the +array is the number of pairs. If a single keyword is specified, a +local vector is produced. If two or more keywords are specified, a +local array is produced where the number of columns = the number of +keywords. The vector or array can be accessed by any command that +uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The output for *dist* will be in distance :doc:`units `. The +output for *eng* will be in energy :doc:`units `. The output for +*force* will be in force :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump local `, :doc:`compute property/local ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_pe.txt b/doc/_sources/compute_pe.txt new file mode 100644 index 0000000000..440c6b86b7 --- /dev/null +++ b/doc/_sources/compute_pe.txt @@ -0,0 +1,117 @@ +.. index:: compute pe + +compute pe command +================== + +compute pe/cuda command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID pe keyword ... + +* ID, group-ID are documented in :doc:`compute ` command +* pe = style name of this compute command +* zero or more keywords may be appended +* keyword = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all pe + compute molPE all pe bond angle dihedral improper + +Description +""""""""""" + +Define a computation that calculates the potential energy of the +entire system of atoms. The specified group must be "all". See the +:doc:`compute pe/atom ` command if you want per-atom +energies. These per-atom values could be summed for a group of atoms +via the :doc:`compute reduce ` command. + +The energy is calculated by the various pair, bond, etc potentials +defined for the simulation. If no extra keywords are listed, then the +potential energy is the sum of pair, bond, angle, dihedral, improper, +and kspace (long-range) energy. If any extra keywords are listed, +then only those components are summed to compute the potential energy. + +The Kspace contribution requires 1 extra FFT each timestep the energy +is calculated, if using the PPPM solver via the :doc:`kspace_style pppm ` command. Thus it can increase the cost of the +PPPM calculation if it is needed on a large fraction of the simulation +timesteps. + +Various fixes can contribute to the total potential energy of the +system. See the doc pages for :doc:`individual fixes ` for +details. The *thermo* option of the +:doc:`compute_modify ` command determines whether these +contributions are added into the computed potential energy. If no +keywords are specified the default is *yes*. If any keywords are +specified, the default is *no*. + +A compute of this style with the ID of "thermo_pe" is created when +LAMMPS starts up, as if this command were in the input script: + +.. parsed-literal:: + + compute thermo_pe all pe + +See the "thermo_style" command for more details. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the potential energy). This +value can be used by any command that uses a global scalar value from +a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "extensive". The +scalar value will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute pe/atom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_pe_atom.txt b/doc/_sources/compute_pe_atom.txt new file mode 100644 index 0000000000..aefbc60f8d --- /dev/null +++ b/doc/_sources/compute_pe_atom.txt @@ -0,0 +1,109 @@ +.. index:: compute pe/atom + +compute pe/atom command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID pe/atom keyword ... + +* ID, group-ID are documented in :doc:`compute ` command +* pe/atom = style name of this compute command +* zero or more keywords may be appended +* keyword = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all pe/atom + compute 1 all pe/atom pair + compute 1 all pe/atom pair bond + +Description +""""""""""" + +Define a computation that computes the per-atom potential energy for +each atom in a group. See the :doc:`compute pe ` command if +you want the potential energy of the entire system. + +The per-atom energy is calculated by the various pair, bond, etc +potentials defined for the simulation. If no extra keywords are +listed, then the potential energy is the sum of pair, bond, angle, +dihedral,improper, and kspace energy. If any extra keywords are +listed, then only those components are summed to compute the potential +energy. + +Note that the energy of each atom is due to its interaction with all +other atoms in the simulation, not just with other atoms in the group. + +For an energy contribution produced by a small set of atoms (e.g. 4 +atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that +energy is assigned in equal portions to each atom in the set. +E.g. 1/4 of the dihedral energy to each of the 4 atoms. + +The :doc:`dihedral_style charmm ` style calculates +pairwise interactions between 1-4 atoms. The energy contribution of +these terms is included in the pair energy, not the dihedral energy. + +The KSpace contribution is calculated using the method in +:ref:`(Heyes) ` for the Ewald method and a related method for PPPM, +as specified by the :doc:`kspace_style pppm ` command. +For PPPM, the calcluation requires 1 extra FFT each timestep that +per-atom energy is calculated. Thie `document `_ +describes how the long-range per-atom energy calculation is performed. + +As an example of per-atom potential energy compared to total potential +energy, these lines in an input script should yield the same result +in the last 2 columns of thermo output: + +.. parsed-literal:: + + compute peratom all pe/atom + compute pe all reduce sum c_peratom + thermo_style custom step temp etotal press pe c_pe + +.. note:: + + The per-atom energy does not any Lennard-Jones tail corrections + invoked by the :doc:`pair_modify tail yes ` command, since + those are global contributions to the system energy. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-atom vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +Related commands +"""""""""""""""" + +:doc:`compute pe `, :doc:`compute stress/atom ` + +**Default:** none + + +---------- + + +.. _Heyes: + + + +**(Heyes)** Heyes, Phys Rev B 49, 755 (1994), + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_plasticity_atom.txt b/doc/_sources/compute_plasticity_atom.txt new file mode 100644 index 0000000000..843c7d868d --- /dev/null +++ b/doc/_sources/compute_plasticity_atom.txt @@ -0,0 +1,78 @@ +.. index:: compute plasticity/atom + +compute plasticity/atom command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID plasticity/atom + +* ID, group-ID are documented in compute command +* plasticity/atom = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all plasticity/atom + +Description +""""""""""" + +Define a computation that calculates the per-atom plasticity for each +atom in a group. This is a quantity relevant for :doc:`Peridynamics models `. See `this document `_ +for an overview of LAMMPS commands for Peridynamics modeling. + +The plasticity for a Peridynamic particle is the so-called consistency +parameter (lambda). For elastic deformation lambda = 0, otherwise +lambda > 0 for plastic deformation. For details, see +:ref:`(Mitchell) ` and the PDF doc included in the LAMMPS +distro in `doc/PDF/PDLammps_EPS.pdf `_. + +This command can be invoked for one of the Peridynamic :doc:`pair styles `: peri/eps. + +The plasticity value will be 0.0 for atoms not in the specified +compute group. + +**Output info:** + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +Section_howto 15 for an overview of LAMMPS output options. + +The per-atom vector values are unitlesss numbers (lambda) >= 0.0. + +Restrictions +"""""""""""" + + +This compute is part of the PERI package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute damage `, :doc:`compute dilatation ` + +**Default:** none + + +---------- + + +.. _Mitchell: + + + +**(Mitchell)** Mitchell, "A non-local, ordinary-state-based +viscoelasticity model for peridynamics", Sandia National Lab Report, +8064:1-28 (2011). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_pressure.txt b/doc/_sources/compute_pressure.txt new file mode 100644 index 0000000000..fd366853ca --- /dev/null +++ b/doc/_sources/compute_pressure.txt @@ -0,0 +1,166 @@ +.. index:: compute pressure + +compute pressure command +======================== + +compute pressure/cuda command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID pressure temp-ID keyword ... + +* ID, group-ID are documented in :doc:`compute ` command +* pressure = style name of this compute command +* temp-ID = ID of compute that calculates temperature, can be NULL if not needed +* zero or more keywords may be appended +* keyword = *ke* or *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *fix* or *virial* + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all pressure thermo_temp + compute 1 all pressure NULL pair bond + +Description +""""""""""" + +Define a computation that calculates the pressure of the entire system +of atoms. The specified group must be "all". See the :doc:`compute stress/atom ` command if you want per-atom +pressure (stress). These per-atom values could be summed for a group +of atoms via the :doc:`compute reduce ` command. + +The pressure is computed by the formula + +.. image:: Eqs/pressure.jpg + :align: center + +where N is the number of atoms in the system (see discussion of DOF +below), Kb is the Boltzmann constant, T is the temperature, d is the +dimensionality of the system (2 or 3 for 2d/3d), V is the system +volume (or area in 2d), and the second term is the virial, computed +within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body, +and long-range interactions. :doc:`Fixes ` that impose constraints +(e.g. the :doc:`fix shake ` command) also contribute to the +virial term. + +A symmetric pressure tensor, stored as a 6-element vector, is also +calculated by this compute. The 6 components of the vector are +ordered xx, yy, zz, xy, xz, yz. The equation for the I,J components +(where I and J = x,y,z) is similar to the above formula, except that +the first term uses components of the kinetic energy tensor and the +second term uses components of the virial tensor: + +.. image:: Eqs/pressure_tensor.jpg + :align: center + +If no extra keywords are listed, the entire equations above are +calculated. This includes a kinetic energy (temperature) term and the +virial as the sum of pair, bond, angle, dihedral, improper, kspace +(long-range), and fix contributions to the force on each atom. If any +extra keywords are listed, then only those components are summed to +compute temperature or ke and/or the virial. The *virial* keyword +means include all terms except the kinetic energy *ke*. + +Details of how LAMMPS computes the virial efficiently for the entire +system, including the effects of periodic boundary conditions is +discussed in :ref:`(Thompson) `. + +The temperature and kinetic energy tensor is not calculated by this +compute, but rather by the temperature compute specified with the +command. If the kinetic energy is not included in the pressure, than +the temperature compute is not used and can be specified as NULL. +Normally the temperature compute used by compute pressure should +calculate the temperature of all atoms for consistency with the virial +term, but any compute style that calculates temperature can be used, +e.g. one that excludes frozen atoms or other degrees of freedom. + +Note that if desired the specified temperature compute can be one that +subtracts off a bias to calculate a temperature using only the thermal +velocity of the atoms, e.g. by subtracting a background streaming +velocity. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. + +Also note that the N in the first formula above is really +degrees-of-freedom divided by d = dimensionality, where the DOF value +is calcluated by the temperature compute. See the various :doc:`compute temperature ` styles for details. + +A compute of this style with the ID of "thermo_press" is created when +LAMMPS starts up, as if this command were in the input script: + +.. parsed-literal:: + + compute thermo_press all pressure thermo_temp + +where "thermo_temp" is the ID of a similarly defined compute of style +"temp". See the "thermo_style" command for more details. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the pressure) and a global +vector of length 6 (pressure tensor), which can be accessed by indices +1-6. These values can be used by any command that uses global scalar +or vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar and vector values calculated by this compute are +"intensive". The scalar and vector values will be in pressure +:doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`compute stress/atom `, +:doc:`thermo_style `, + +**Default:** none + + +---------- + + +.. _Thompson: + + + +**(Thompson)** Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_property_atom.txt b/doc/_sources/compute_property_atom.txt new file mode 100644 index 0000000000..546faaa32b --- /dev/null +++ b/doc/_sources/compute_property_atom.txt @@ -0,0 +1,182 @@ +.. index:: compute property/atom + +compute property/atom command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID property/atom input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* property/atom = style name of this compute command +* input = one or more atom attributes +.. parsed-literal:: + + possible attributes = id, mol, proc, type, mass, + x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, + vx, vy, vz, fx, fy, fz, + q, mux, muy, muz, mu, + radius, diameter, omegax, omegay, omegaz, + angmomx, angmomy, angmomz, + shapex,shapey, shapez, + quatw, quati, quatj, quatk, tqx, tqy, tqz, + end1x, end1y, end1z, end2x, end2y, end2z, + corner1x, corner1y, corner1z, + corner2x, corner2y, corner2z, + corner3x, corner3y, corner3z, + nbonds, + vfrac, s0, + spin, eradius, ervel, erforce, + rho, drho, e, de, cv, + i_name, d_name + +.. parsed-literal:: + + id = atom ID + mol = molecule ID + proc = ID of processor that owns atom + type = atom type + mass = atom mass + x,y,z = unscaled atom coordinates + xs,ys,zs = scaled atom coordinates + xu,yu,zu = unwrapped atom coordinates + ix,iy,iz = box image that the atom is in + vx,vy,vz = atom velocities + fx,fy,fz = forces on atoms + q = atom charge + mux,muy,muz = orientation of dipole moment of atom + mu = magnitude of dipole moment of atom + radius,diameter = radius,diameter of spherical particle + omegax,omegay,omegaz = angular velocity of spherical particle + angmomx,angmomy,angmomz = angular momentum of aspherical particle + shapex,shapey,shapez = 3 diameters of aspherical particle + quatw,quati,quatj,quatk = quaternion components for aspherical or body particles + tqx,tqy,tqz = torque on finite-size particles + end12x, end12y, end12z = end points of line segment + corner123x, corner123y, corner123z = corner points of triangle + nbonds = number of bonds assigned to an atom + +.. parsed-literal:: + + PERI package per-atom properties: + vfrac = ??? + s0 = ??? + +.. parsed-literal:: + + USER-EFF and USER-AWPMD package per-atom properties: + spin = electron spin + eradius = electron radius + ervel = electron radial velocity + erforce = electron radial force + +.. parsed-literal:: + + USER-SPH package per-atom properties: + rho = ??? + drho = ??? + e = ??? + de = ??? + cv = ??? + +.. parsed-literal:: + + :doc:`fix property/atom ` per-atom properties: + i_name = custom integer vector with name + d_name = custom integer vector with name + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all property/atom xs vx fx mux + compute 2 all property/atom type + compute 1 all property/atom ix iy iz + +Description +""""""""""" + +Define a computation that simply stores atom attributes for each atom +in the group. This is useful so that the values can be used by other +:ref:`output commands ` that take computes as +inputs. See for example, the :doc:`compute reduce `, +:doc:`fix ave/atom `, :doc:`fix ave/histo `, +:doc:`fix ave/spatial `, and :doc:`atom-style variable ` commands. + +The list of possible attributes is the same as that used by the :doc:`dump custom ` command, which describes their meaning, with some +additional quantities that are only defined for certain :doc:`atom styles `. Basically, this augmented list gives an +input script access to any per-atom quantity stored by LAMMPS. + +The values are stored in a per-atom vector or array as discussed +below. Zeroes are stored for atoms not in the specified group or for +quantities that are not defined for a particular particle in the group +(e.g. *shapex* if the particle is not an ellipsoid). + +The additional quantities only accessible via this command, and not +directly via the :doc:`dump custom ` command, are as follows. + +*Shapex*, *shapey*, and *shapez* are defined for ellipsoidal particles +and define the 3d shape of each particle. + +*Quatw*, *quati*, *quatj*, and *quatk* are defined for ellipsoidal +particles and body particles and store the 4-vector quaternion +representing the orientation of each particle. See the :doc:`set ` +command for an explanation of the quaternion vector. + +*End1x*, *end1y*, *end1z*, *end2x*, *end2y*, *end2z*, are defined for +line segment particles and define the end points of each line segment. + +*Corner1x*, *corner1y*, *corner1z*, *corner2x*, *corner2y*, +*corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for +triangular particles and define the corner points of each triangle. + +*Nbonds* is available for all molecular atom styles and refers to the +number of explicit bonds assigned to an atom. Note that if the +:doc:`newton bond ` command is set to *on*, which is the +default, then every bond in the system is assigned to only one of the +two atoms in the bond. Thus a bond between atoms I,J may be tallied +for either atom I or atom J. If :doc:`newton bond off ` is set, +it will be tallied with both atom I and atom J. + +The *i_name* and *d_name* attributes refer to custom integer and +floating-point properties that have been added to each atom via the +:doc:`fix property/atom ` command. When that command +is used specific names are given to each attribute which are what is +specified as the "name" portion of *i_name* or *d_name*. + +**Output info:** + +This compute calculates a per-atom vector or per-atom array depending +on the number of input values. If a single input is specified, a +per-atom vector is produced. If two or more inputs are specified, a +per-atom array is produced where the number of columns = the number of +inputs. The vector or array can be accessed by any command that uses +per-atom values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The vector or array values will be in whatever :doc:`units ` the +corresponding attribute is in, e.g. velocity units for vx, charge +units for q, etc. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump custom `, :doc:`compute reduce `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, +:doc:`fix property/atom ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_property_chunk.txt b/doc/_sources/compute_property_chunk.txt new file mode 100644 index 0000000000..7bb22eeaab --- /dev/null +++ b/doc/_sources/compute_property_chunk.txt @@ -0,0 +1,125 @@ +.. index:: compute property/chunk + +compute property/chunk command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID property/chunk chunkID input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* property/chunk = style name of this compute command +* input = one or more attributes +.. parsed-literal:: + + attributes = count, id, coord1, coord2, coord3 + count = # of atoms in chunk + id = original chunk IDs before compression by :doc:`compute chunk/atom ` + coord123 = coordinates for spatial bins calculated by :doc:`compute chunk/atom ` + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all property/chunk count + compute 1 all property/chunk ID coord1 + +Description +""""""""""" + +Define a computation that stores the specified attributes of chunks of +atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates and stores the specified attributes of chunks +as global data so they can be accessed by other :ref:`output commands ` and used in conjunction with +other commands that generate per-chunk data, such as :doc:`compute com/chunk ` or :doc:`compute msd/chunk `. + +Note that only atoms in the specified group contribute to the +calculation of the *count* attribute. The :doc:`compute chunk/atom ` command defines its own group; +atoms will have a chunk ID = 0 if they are not in that group, +signifying they are not assigned to a chunk, and will thus also not +contribute to this calculation. You can specify the "all" group for +this command if you simply want to include atoms with non-zero chunk +IDs. + +The *count* attribute is the number of atoms in the chunk. + +The *id* attribute stores the original chunk ID for each chunk. It +can only be used if the *compress* keyword was set to *yes* for the +:doc:`compute chunk/atom ` command referenced by +chunkID. This means that the original chunk IDs (e.g. molecule IDs) +will have been compressed to remove chunk IDs with no atoms assigned +to them. Thus a compresed chunk ID of 3 may correspond to an original +chunk ID (molecule ID in this case) of 415. The *id* attribute will +then be 415 for the 3rd chunk. + +The *coordN* attributes can only be used if a *binning* style was used +in the :doc:`compute chunk/atom ` command referenced +by chunkID. For *bin/1d*, *bin/2d*, and *bin/3d* styles the attribute +is the center point of the bin in the corresponding dimension. Style +*bin/1d* only defines a *coord1* attribute. Style *bin/2d* adds a +*coord2* attribute. Style *bin/3d* adds a *coord3* attribute. + +Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*, the +*coordN* attributes will be in distance :doc:`units `. If the +value of the *units* keyword is *reduced*, the *coordN* attributes +will be in unitless reduced units (0-1). + +The simplest way to output the results of the compute property/chunk +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk1 all property/chunk cc1 + compute myChunk2 all com/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2 file tmp.out mode vector + +**Output info:** + +This compute calculates a global vector or global array depending on +the number of input values. The length of the vector or number of +rows in the array is the number of chunks. + +This compute calculates a global vector or global array where the +number of rows = the number of chunks *Nchunk* as calculated by the +specified :doc:`compute chunk/atom ` command. If a +single input is specified, a global vector is produced. If two or +more inputs are specified, a global array is produced where the number +of columns = the number of inputs. The vector or array can be +accessed by any command that uses global values from a compute as +input. See :ref:`this section ` for an overview +of LAMMPS output options. + +The vector or array values are "intensive". The values will be +unitless or in the units discussed above. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix ave/chunk ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_property_local.txt b/doc/_sources/compute_property_local.txt new file mode 100644 index 0000000000..3463764279 --- /dev/null +++ b/doc/_sources/compute_property_local.txt @@ -0,0 +1,153 @@ +.. index:: compute property/local + +compute property/local command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID property/local input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* property/local = style name of this compute command +* input = one or more attributes +.. parsed-literal:: + + possible attributes = natom1 natom2 ntype1 ntype2 + patom1 patom2 ptype1 ptype2 + batom1 batom2 btype + aatom1 aatom2 aatom3 atype + datom1 datom2 datom3 dtype + iatom1 iatom2 iatom3 itype + +.. parsed-literal:: + + natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff) + ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff) + patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff) + ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff) + batom1, batom2 = IDs of 2 atoms in each bond + btype = bond type of each bond + aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle + atype = angle type of each angle + datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral + dtype = dihedral type of each dihedral + iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper + itype = improper type of each improper + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all property/local btype batom1 batom2 + compute 1 all property/local atype aatom2 + +Description +""""""""""" + +Define a computation that stores the specified attributes as local +data so it can be accessed by other :ref:`output commands `. If the input attributes refer +to bond information, then the number of datums generated, aggregated +across all processors, equals the number of bonds in the system. +Ditto for pairs, angles, etc. + +If multiple input attributes are specified then they must all generate +the same amount of information, so that the resulting local array has +the same number of rows for each column. This means that only bond +attributes can be specified together, or angle attributes, etc. Bond +and angle attributes can not be mixed in the same compute +property/local command. + +If the inputs are pair attributes, the local data is generated by +looping over the pairwise neighbor list. Info about an individual +pairwise interaction will only be included if both atoms in the pair +are in the specified compute group. For *natom1* and *natom2*, all +atom pairs in the neighbor list are considered (out to the neighbor +cutoff = force cutoff + :doc:`neighbor skin `). For *patom1* +and *patom2*, the distance between the atoms must be less than the +force cutoff distance for that pair to be included, as defined by the +:doc:`pair_style ` and :doc:`pair_coeff ` +commands. + +If the inputs are bond, angle, etc attributes, the local data is +generated by looping over all the atoms owned on a processor and +extracting bond, angle, etc info. For bonds, info about an individual +bond will only be included if both atoms in the bond are in the +specified compute group. Likewise for angles, dihedrals, etc. + +For bonds and angles, a bonds/angles that have been broken by setting +their bond/angle type to 0 will not be included. Bonds/angles that +have been turned off (see the :doc:`fix shake ` or +:doc:`delete_bonds ` commands) by setting their bond/angle +type negative are written into the file. This is consistent with the +:doc:`compute bond/local ` and :doc:`compute angle/local ` commands + +Note that as atoms migrate from processor to processor, there will be +no consistent ordering of the entries within the local vector or array +from one timestep to the next. The only consistency that is +guaranteed is that the ordering on a particular timestep will be the +same for local vectors or arrays generated by other compute commands. +For example, output from the :doc:`compute bond/local ` command can be combined with bond +atom indices from this command and output by the :doc:`dump local ` command in a consistent way. + +The *natom1* and *natom2*, or *patom1* and *patom2* attributes refer +to the atom IDs of the 2 atoms in each pairwise interaction computed +by the :doc:`pair_style ` command. The *ntype1* and +*ntype2*, or *ptype1* and *ptype2* attributes refer to the atom types +of the 2 atoms in each pairwise interaction. + +.. note:: + + For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4 + interactions within the molecular topology, their pairwise interaction + may be turned off, and thus they may not appear in the neighbor list, + and will not be part of the local data created by this command. More + specifically, this may be true of I,J pairs with a weighting factor of + 0.0; pairs with a non-zero weighting factor are included. The + weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set + by the :doc:`special_bonds ` command. + +The *batom1* and *batom2* attributes refer to the atom IDs of the 2 +atoms in each :doc:`bond `. The *btype* attribute refers to +the type of the bond, from 1 to Nbtypes = # of bond types. The number +of bond types is defined in the data file read by the +:doc:`read_data ` command. + +The attributes that start with "a", "d", "i", refer to similar values +for :doc:`angles `, :doc:`dihedrals `, and +:doc:`impropers `. + +**Output info:** + +This compute calculates a local vector or local array depending on the +number of input values. The length of the vector or number of rows in +the array is the number of bonds, angles, etc. If a single input is +specified, a local vector is produced. If two or more inputs are +specified, a local array is produced where the number of columns = the +number of inputs. The vector or array can be accessed by any command +that uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The vector or array values will be integers that correspond to the +specified attribute. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump local `, :doc:`compute reduce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_rdf.txt b/doc/_sources/compute_rdf.txt new file mode 100644 index 0000000000..861e7c7f59 --- /dev/null +++ b/doc/_sources/compute_rdf.txt @@ -0,0 +1,170 @@ +.. index:: compute rdf + +compute rdf command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* rdf = style name of this compute command +* Nbin = number of RDF bins +* itypeN = central atom type for Nth RDF histogram (see asterisk form below) +* jtypeN = distribution atom type for Nth RDF histogram (see asterisk form below) + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all rdf 100 + compute 1 all rdf 100 1 1 + compute 1 all rdf 100 * 3 + compute 1 fluid rdf 500 1 1 1 2 2 1 2 2 + compute 1 fluid rdf 500 1*3 2 5 *10 + +Description +""""""""""" + +Define a computation that calculates the radial distribution function +(RDF), also called g(r), and the coordination number for a group of +particles. Both are calculated in histogram form by binning pairwise +distances into *Nbin* bins from 0.0 to the maximum force cutoff +defined by the :doc:`pair_style ` command. The bins are of +uniform size in radial distance. Thus a single bin encompasses a thin +shell of distances in 3d and a thin ring of distances in 2d. + +.. note:: + + If you have a bonded system, then the settings of + :doc:`special_bonds ` command can remove pairwise + interactions between atoms in the same bond, angle, or dihedral. This + is the default setting for the :doc:`special_bonds ` + command, and means those pairwise interactions do not appear in the + neighbor list. Because this fix uses the neighbor list, it also means + those pairs will not be included in the RDF. This does not apply when + using long-range coulomb (*coul/long*, *coul/msm*, *coul/wolf* or + similar. One way to get around this would be to set special_bond + scaling factors to very tiny numbers that are not exactly zero + (e.g. 1.0e-50). Another workaround is to write a dump file, and use + the :doc:`rerun ` command to compute the RDF for snapshots in the + dump file. The rerun script can use a + :doc:`special_bonds ` command that includes all pairs in + the neighbor list. + +The *itypeN* and *jtypeN* arguments are optional. These arguments +must come in pairs. If no pairs are listed, then a single histogram +is computed for g(r) between all atom types. If one or more pairs are +listed, then a separate histogram is generated for each +*itype*,*jtype* pair. + +The *itypeN* and *jtypeN* settings can be specified in one of two +ways. An explicit numeric value can be used, as in the 4th example +above. Or a wild-card asterisk can be used to specify a range of atom +types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the +number of atom types, then an asterisk with no numeric values means +all types from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). + +If both *itypeN* and *jtypeN* are single values, as in the 4th example +above, this means that a g(r) is computed where atoms of type *itypeN* +are the central atom, and atoms of type *jtypeN* are the distribution +atom. If either *itypeN* and *jtypeN* represent a range of values via +the wild-card asterisk, as in the 5th example above, this means that a +g(r) is computed where atoms of any of the range of types represented +by *itypeN* are the central atom, and atoms of any of the range of +types represented by *jtypeN* are the distribution atom. + +Pairwise distances are generated by looping over a pairwise neighbor +list, just as they would be in a :doc:`pair_style ` +computation. The distance between two atoms I and J is included in a +specific histogram if the following criteria are met: + +* atoms I,J are both in the specified compute group +* the distance between atoms I,J is less than the maximum force cutoff +* the type of the I atom matches itypeN (one or a range of types) +* the type of the J atom matches jtypeN (one or a range of types) + +It is OK if a particular pairwise distance is included in more than +one individual histogram, due to the way the *itypeN* and *jtypeN* +arguments are specified. + +The g(r) value for a bin is calculated from the histogram count by +scaling it by the idealized number of how many counts there would be +if atoms of type *jtypeN* were uniformly distributed. Thus it +involves the count of *itypeN* atoms, the count of *jtypeN* atoms, the +volume of the entire simulation box, and the volume of the bin's thin +shell in 3d (or the area of the bin's thin ring in 2d). + +A coordination number coord(r) is also calculated, which is the number +of atoms of type *jtypeN* within the current bin or closer, averaged +over atoms of type *itypeN*. This is calculated as the area- or +volume-weighted sum of g(r) values over all bins up to and including +the current bin, multiplied by the global average volume density of +atoms of type jtypeN. + +The simplest way to output the results of the compute rdf calculation +to a file is to use the :doc:`fix ave/time ` command, for +example: + +.. parsed-literal:: + + compute myRDF all rdf 50 + fix 1 all ave/time 100 1 100 c_myRDF file tmp.rdf mode vector + +**Output info:** + +This compute calculates a global array with the number of rows = +*Nbins*, and the number of columns = 1 + 2*Npairs, where Npairs is the +number of I,J pairings specified. The first column has the bin +coordinate (center of the bin), Each successive set of 2 columns has +the g(r) and coord(r) values for a specific set of *itypeN* versus +*jtypeN* interactions, as described above. These values can be used +by any command that uses a global values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The array values calculated by this compute are all "intensive". + +The first column of array values will be in distance +:doc:`units `. The g(r) columns of array values are normalized +numbers >= 0.0. The coordination number columns of array values are +also numbers >= 0.0. + +Restrictions +"""""""""""" + + +The RDF is not computed for distances longer than the force cutoff, +since processors (in parallel) don't know about atom coordinates for +atoms further away than that distance. If you want an RDF for larger +distances, you can use the :doc:`rerun ` command to post-process +a dump file and set the cutoff for the potential to be longer in the +rerun script. Note that in the rerun context, the force cutoff is +arbitrary, since you aren't running dynamics and thus are not changing +your model. The definition of g(r) used by LAMMPS is only appropriate +for characterizing atoms that are uniformly distributed throughout the +simulation cell. In such cases, the coordination number is still +correct and meaningful. As an example, if a large simulation cell +contains only one atom of type *itypeN* and one of *jtypeN*, then g(r) +will register an arbitrarily large spike at whatever distance they +happen to be at, and zero everywhere else. Coord(r) will show a step +change from zero to one at the location of the spike in g(r). + +Related commands +"""""""""""""""" + +:doc:`fix ave/time ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_reduce.txt b/doc/_sources/compute_reduce.txt new file mode 100644 index 0000000000..79eaec6f56 --- /dev/null +++ b/doc/_sources/compute_reduce.txt @@ -0,0 +1,206 @@ +.. index:: compute reduce + +compute reduce command +====================== + +compute reduce/region command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID style arg mode input1 input2 ... keyword args ... + +* ID, group-ID are documented in :doc:`compute ` command +* style = *reduce* or *reduce/region* +.. parsed-literal:: + + *reduce* arg = none + *reduce/region* arg = region-ID + region-ID = ID of region to use for choosing atoms + +* mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq* +* one or more inputs can be listed +* input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name +.. parsed-literal:: + + x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) + c_ID = per-atom or local vector calculated by a compute with ID + c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID + f_ID = per-atom or local vector calculated by a fix with ID + f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name + +* zero or more keyword/args pairs may be appended +* keyword = *replace* +.. parsed-literal:: + + *replace* args = vec1 vec2 + vec1 = reduced value from this input vector will be replaced + vec2 = replace it with vec1[N] where N is index of max/min value from vec2 + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all reduce sum c_force + compute 1 all reduce/region subbox sum c_force + compute 2 all reduce min c_press[2] f_ave v_myKE + compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3 + +Description +""""""""""" + +Define a calculation that "reduces" one or more vector inputs into +scalar values, one per listed input. The inputs can be per-atom or +local quantities; they cannot be global quantities. Atom attributes +are per-atom quantities, :doc:`computes ` and :doc:`fixes ` +may generate any of the three kinds of quantities, and :doc:`atom-style variables ` generate per-atom quantities. See the +`variable `_ command and its special functions which can +perform the same operations as the compute reduce command on global +vectors. + +The reduction operation is specified by the *mode* setting. The *sum* +option adds the values in the vector into a global total. The *min* +or *max* options find the minimum or maximum value across all vector +values. The *ave* setting adds the vector values into a global total, +then divides by the number of values in the vector. The *sumsq* +option sums the square of the values in the vector into a global +total. The *avesq* setting does the same as *sumsq*, then divdes the +sum of squares by the number of values. The last two options can be +useful for calculating the variance of some quantity, e.g. variance = +sumsq - ave^2. + +Each listed input is operated on independently. For per-atom inputs, +the group specified with this command means only atoms within the +group contribute to the result. For per-atom inputs, if the compute +reduce/region command is used, the atoms must also currently be within +the region. Note that an input that produces per-atom quantities may +define its own group which affects the quantities it returns. For +example, if a compute is used as an input which generates a per-atom +vector, it will generate values of 0.0 for atoms that are not in the +group specified for that compute. + +Each listed input can be an atom attribute (position, velocity, force +component) or can be the result of a :doc:`compute ` or +:doc:`fix ` or the evaluation of an atom-style +:doc:`variable `. + +The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are +self-explanatory. Note that other atom attributes can be used as +inputs to this fix by using the :doc:`compute property/atom ` command and then specifying +an input value from that compute. + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. Computes can generate +per-atom or local quantities. See the individual +:doc:`compute ` doc page for details. If no bracketed integer +is appended, the vector calculated by the compute is used. If a +bracketed integer is appended, the Ith column of the array calculated +by the compute is used. Users can also write code for their own +compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. Fixes can generate per-atom +or local quantities. See the individual :doc:`fix ` doc page for +details. Note that some fixes only produce their values on certain +timesteps, which must be compatible with when compute reduce +references the values, else an error results. If no bracketed integer +is appended, the vector calculated by the fix is used. If a bracketed +integer is appended, the Ith column of the array calculated by the fix +is used. Users can also write code for their own fix style and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script. It must be an +:doc:`atom-style variable `. Atom-style variables can +reference thermodynamic keywords and various per-atom attributes, or +invoke other computes, fixes, or variables when they are evaluated, so +this is a very general means of generating per-atom quantities to +reduce. + + +---------- + + +If the *replace* keyword is used, two indices *vec1* and *vec2* are +specified, where each index ranges from 1 to the # of input values. +The replace keyword can only be used if the *mode* is *min* or *max*. +It works as follows. A min/max is computed as usual on the *vec2* +input vector. The index N of that value within *vec2* is also stored. +Then, instead of performing a min/max on the *vec1* input vector, the +stored index is used to select the Nth element of the *vec1* vector. + +Thus, for example, if you wish to use this compute to find the bond +with maximum stretch, you can do it as follows: + +.. parsed-literal:: + + compute 1 all property/local batom1 batom2 + compute 2 all bond/local dist + compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3 + thermo_style custom step temp c_3[1] c_3[2] c_3[3] + +The first two input values in the compute reduce command are vectors +with the IDs of the 2 atoms in each bond, using the :doc:`compute property/local ` command. The last input +value is bond distance, using the :doc:`compute bond/local ` command. Instead of taking the +max of the two atom ID vectors, which does not yield useful +information in this context, the *replace* keywords will extract the +atom IDs for the two atoms in the bond of maximum stretch. These atom +IDs and the bond stretch will be printed with thermodynamic output. + + +---------- + + +If a single input is specified this compute produces a global scalar +value. If multiple inputs are specified, this compute produces a +global vector of values, the length of which is equal to the number of +inputs specified. + +As discussed below, for the *sum* and *sumsq* modes, the value(s) +produced by this compute are all "extensive", meaning their value +scales linearly with the number of atoms involved. If normalized +values are desired, this compute can be accessed by the :doc:`thermo_style custom ` command with :doc:`thermo_modify norm yes ` set as an option. Or it can be accessed by a +:doc:`variable ` that divides by the appropriate atom count. + + +---------- + + +**Output info:** + +This compute calculates a global scalar if a single input value is +specified or a global vector of length N where N is the number of +inputs, and which can be accessed by indices 1 to N. These values can +be used by any command that uses global scalar or vector values from a +compute as input. See :ref:`Section_howto 15 ` +for an overview of LAMMPS output options. + +All the scalar or vector values calculated by this compute are +"intensive", except when the *sum* or *sumsq* modes are used on +per-atom or local vectors, in which case the calculated values are +"extensive". + +The scalar or vector values will be in whatever :doc:`units ` the +quantities being reduced are in. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`fix `, :doc:`variable ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_saed.txt b/doc/_sources/compute_saed.txt new file mode 100644 index 0000000000..d8ed8b0abc --- /dev/null +++ b/doc/_sources/compute_saed.txt @@ -0,0 +1,211 @@ +.. index:: compute saed + +compute saed command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID saed lambda type1 type2 ... typeN keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* saed = style name of this compute command +* lambda = wavelength of incident radiation (length units) +* type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) +* zero or more keyword/value pairs may be appended +* keyword = *Kmax* or *Zone* or *dR_Ewald* or *c* or *manual* or *echo* +.. parsed-literal:: + + *Kmax* value = Maximum distance explored from reciprocal space origin + (inverse length units) + *Zone* values = z1 z2 z3 + z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all + reciprocal space will be meshed up to *Kmax* + *dR_Ewald* value = Thickness of Ewald sphere slice intercepting + reciprocal space (inverse length units) + *c* values = c1 c2 c3 + c1,c2,c3 = parameters to adjust the spacing of the reciprocal + lattice nodes in the h, k, and l directions respectively + *manual* = flag to use manual spacing of reciprocal lattice points + based on the values of the *c* parameters + *echo* = flag to provide extra output for debugging purposes + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 + compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo + +.. parsed-literal:: + + fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed + fix saed/vtk 1 1 1 c_2 file Ni_000.saed + +Description +""""""""""" + +Define a computation that calculates electron diffraction intensity as +described in :ref:`(Coleman) ` on a mesh of reciprocal lattice nodes +defined by the entire simulation domain (or manually) using simulated +radiation of wavelength lambda. + +The electron diffraction intensity I at each reciprocal lattice point +is computed from the structure factor F using the equations: + +.. image:: Eqs/compute_saed1.jpg + :align: center + +.. image:: Eqs/compute_saed2.jpg + :align: center + +Here, K is the location of the reciprocal lattice node, rj is the +position of each atom, fj are atomic scattering factors. + +Diffraction intensities are calculated on a three-dimensional mesh of +reciprocal lattice nodes. The mesh spacing is defined either (a) by +the entire simulation domain or (b) manually using selected values as +shown in the 2D diagram below. + +.. thumbnail:: JPG/saed_mesh.jpg + :align: center + +For a mesh defined by the simulation domain, a rectilinear grid is +constructed with spacing *c**inv(A) along each reciprocal lattice +axis. Where A are the vectors corresponding to the edges of the +simulation cell. If one or two directions has non-periodic boundary +conditions, then the spacing in these directions is defined from the +average of the (inversed) box lengths with periodic boundary conditions. +Meshes defined by the simulation domain must contain at least one periodic +boundary. + +If the *manual* flag is included, the mesh of reciprocal lattice nodes +will defined using the *c* values for the spacing along each reciprocal +lattice axis. Note that manual mapping of the reciprocal space mesh is +good for comparing diffraction results from multiple simulations; however +it can reduce the likelihood that Bragg reflections will be satisfied +unless small spacing parameters <0.05 Angstrom^(-1) are implemented. +Meshes with manual spacing do not require a periodic boundary. + +The limits of the reciprocal lattice mesh are determined by the use of +the *Kmax*, *Zone*, and *dR_Ewald* parameters. The rectilinear mesh +created about the origin of reciprocal space is terminated at the +boundary of a sphere of radius *Kmax* centered at the origin. If +*Zone* parameters z1=z2=z3=0 are used, diffraction intensities are +computed throughout the entire spherical volume - note this can +greatly increase the cost of computation. Otherwise, *Zone* +parameters will denote the z1=h, z2=k, and z3=l (in a global since) +zone axis of an intersecting Ewald sphere. Diffraction intensities +will only be computed at the intersection of the reciprocal lattice +mesh and a *dR_Ewald* thick surface of the Ewald sphere. See the +example 3D intestiety data and the intersection of a [010] zone axis +in the below image. + +.. thumbnail:: JPG/saed_ewald_intersect.jpg + :align: center + +The atomic scattering factors, fj, accounts for the reduction in +diffraction intensity due to Compton scattering. Compute saed uses +analytical approximations of the atomic scattering factors that vary +for each atom type (type1 type2 ... typeN) and angle of diffraction. +The analytic approximation is computed using the formula +:ref:`(Brown) `: + +.. image:: Eqs/compute_saed3.jpg + :align: center + +Coefficients parameterized by :ref:`(Fox) ` are assigned for each +atom type designating the chemical symbol and charge of each atom +type. Valid chemical symbols for compute saed are: + +H: He: Li: Be: B: + C: N: O: F: Ne: + Na: Mg: Al: Si: P: + S: Cl: Ar: K: Ca: + Sc: Ti: V: Cr: Mn: + Fe: Co: Ni: Cu: Zn: + Ga: Ge: As: Se: Br: + Kr: Rb: Sr: Y: Zr: + Nb: Mo: Tc: Ru: Rh: + Pd: Ag: Cd: In: Sn: + Sb: Te: I: Xe: Cs: + Ba: La: Ce: Pr: Nd: + Pm: Sm: Eu: Gd: Tb: + Dy: Ho: Er: Tm: Yb: + Lu: Hf: Ta: W: Re: + Os: Ir: Pt: Au: Hg: + Tl: Pb: Bi: Po: At: + Rn: Fr: Ra: Ac: Th: + Pa: U: Np: Pu: Am: + Cm: Bk: Cf:tb(c=5,s=:) + +If the *echo* keyword is specified, compute saed will provide extra +reporting information to the screen. + +**Output info:** + +This compute calculates a global vector. The length of the vector is +the number of reciprocal lattice nodes that are explored by the mesh. +The entries of the global vector are the computed diffraction +intensities as described above. + +The vector can be accessed by any command that uses global values +from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +All array values calculated by this compute are "intensive". + +Restrictions +"""""""""""" + + +This compute is part of the USER-DIFFRACTION package. It is only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The compute_saed command does not work for triclinic cells. + +Related commands +"""""""""""""""" + +:doc:`fix saed_vtk `, :doc:`compute xrd ` + +Default +""""""" + +The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald = +0.01. + + +---------- + + +.. _Coleman: + + + +**(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020 +(2013). + +.. _Brown: + + + +**(Brown)** Brown et al. International Tables for Crystallography +Volume C: Mathematical and Chemical Tables, 554-95 (2004). + +.. _Fox: + + + +**(Fox)** Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93 +(1989). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_slice.txt b/doc/_sources/compute_slice.txt new file mode 100644 index 0000000000..c4fe7b4708 --- /dev/null +++ b/doc/_sources/compute_slice.txt @@ -0,0 +1,123 @@ +.. index:: compute slice + +compute slice command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID slice Nstart Nstop Nskip input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* slice = style name of this compute command +* Nstart = starting index within input vector(s) +* Nstop = stopping index within input vector(s) +* Nskip = extract every Nskip elements from input vector(s) +* input = c_ID, c_ID[N], f_ID, f_ID[N] +.. parsed-literal:: + + c_ID = global vector calculated by a compute with ID + c_ID[I] = Ith column of global array calculated by a compute with ID + f_ID = global vector calculated by a fix with ID + f_ID[I] = Ith column of global array calculated by a fix with ID + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all slice 1 100 10 c_msdmol[4] + compute 1 all slice 301 400 1 c_msdmol[4] + +Description +""""""""""" + +Define a calculation that "slices" one or more vector inputs into +smaller vectors, one per listed input. The inputs can be global +quantities; they cannot be per-atom or local quantities. +:doc:`Computes ` and :doc:`fixes ` may generate any of the +three kinds of quantities. :doc:`Variables ` do not generate +global vectors. The group specified with this command is ignored. + +The values extracted from the input vector(s) are determined by the +*Nstart*, *Nstop*, and *Nskip* parameters. The elements of an input +vector of length N are indexed from 1 to N. Starting at element +*Nstart*, every Mth element is extracted, where M = *Nskip*, until +element *Nstop* is reached. The extracted quantities are stored as a +vector, which is typically shorter than the input vector. + +Each listed input is operated on independently to produce one output +vector. Each listed input must be a global vector or column of a +global array calculated by another :doc:`compute ` or +:doc:`fix `. + +If an input value begins with "c_", a compute ID must follow which has +been previously defined in the input script and which generates a +global vector or array. See the individual :doc:`compute ` doc +page for details. If no bracketed integer is appended, the vector +calculated by the compute is used. If a bracketed integer is +appended, the Ith column of the array calculated by the compute is +used. Users can also write code for their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script and which generates a global +vector or array. See the individual :doc:`fix ` doc page for +details. Note that some fixes only produce their values on certain +timesteps, which must be compatible with when compute slice references +the values, else an error results. If no bracketed integer is +appended, the vector calculated by the fix is used. If a bracketed +integer is appended, the Ith column of the array calculated by the fix +is used. Users can also write code for their own fix style and :doc:`add them to LAMMPS `. + +If a single input is specified this compute produces a global vector, +even if the length of the vector is 1. If multiple inputs are +specified, then a global array of values is produced, with the number +of columns equal to the number of inputs specified. + + +---------- + + +**Output info:** + +This compute calculates a global vector if a single input value is +specified or a global array with N columns where N is the number of +inputs. The length of the vector or the number of rows in the array +is equal to the number of values extracted from each input vector. +These values can be used by any command that uses global vector or +array values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The vector or array values calculated by this compute are simply +copies of values generated by computes or fixes that are input vectors +to this compute. If there is a single input vector of intensive +and/or extensive values, then each value in the vector of values +calculated by this compute will be "intensive" or "extensive", +depending on the corresponding input value. If there are multiple +input vectors, and all the values in them are intensive, then the +array values calculated by this compute are "intensive". If there are +multiple input vectors, and any value in them is extensive, then the +array values calculated by this compute are "extensive". + +The vector or array values will be in whatever :doc:`units ` the +input quantities are in. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`fix `, :doc:`compute reduce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_contact_radius.txt b/doc/_sources/compute_smd_contact_radius.txt new file mode 100644 index 0000000000..ff888621ea --- /dev/null +++ b/doc/_sources/compute_smd_contact_radius.txt @@ -0,0 +1,64 @@ +.. index:: compute smd/contact/radius + +compute smd/contact/radius command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/contact/radius + +* ID, group-ID are documented in :doc:`compute ` command +* smd/contact/radius = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/contact/radius + +Description +""""""""""" + +Define a computation which outputs the contact radius, i.e., the +radius used to prevent particles from penetrating each other. The +contact radius is used only to prevent particles belonging to +different physical bodies from penetrating each other. It is used by +the contact pair styles, e.g., smd/hertz and smd/tri_surface. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +The value of the contact radius will be 0.0 for particles not in the +specified compute group. + +**Output info:** + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +:ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-particle vector values will be in distance :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`dump custom ` smd/hertz smd/tri_surface + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_damage.txt b/doc/_sources/compute_smd_damage.txt new file mode 100644 index 0000000000..0744858101 --- /dev/null +++ b/doc/_sources/compute_smd_damage.txt @@ -0,0 +1,58 @@ +.. index:: compute smd/damage + +compute smd/damage command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/damage + +* ID, group-ID are documented in :doc:`compute ` command +* smd/damage = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/damage + +Description +""""""""""" + +Define a computation that calculates the damage status of SPH particles +according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion. + +See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. + +**Output Info:** + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +:ref:`How-to discussions, section 6.15 ` +for an overview of LAMMPS output options. + +The per-particle values are dimensionless an in the range of zero to one. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` +section for more info. + +Related commands +"""""""""""""""" + +:doc:`smd/plastic_strain `, :doc:`smd/tlsph_stress ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_hourglass_error.txt b/doc/_sources/compute_smd_hourglass_error.txt new file mode 100644 index 0000000000..34cd46606c --- /dev/null +++ b/doc/_sources/compute_smd_hourglass_error.txt @@ -0,0 +1,70 @@ +.. index:: compute smd/hourglass/error + +compute smd/hourglass/error command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/hourglass/error + +* ID, group-ID are documented in :doc:`compute ` command +* smd/hourglass/error = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/hourglass/error + +Description +""""""""""" + +Define a computation which outputs the error of the approximated +relative separation with respect to the actual relative separation of +the particles i and j. Ideally, if the deformation gradient is exact, +and there exists a unique mapping between all particles' positions +within the neighborhood of the central node and the deformation +gradient, the approximated relative separation will coincide with the +actual relative separation of the particles i and j in the deformed +configuration. This compute is only really useful for debugging the +hourglass control mechanim which is part of the Total-Lagrangian SPH +pair style. + +See `this PDF guide `_ to use Smooth +Mach Dynamics in LAMMPS. + +**Output Info:** + +This compute calculates a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. See +:ref:`How-to discussions, section 6.15 ` +for an overview of LAMMPS output options. + +The per-particle vector values will are dimensionless. See +:doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This quantity will be computed only for particles which interact with +tlsph pair style. + +**Related Commands:** + +:doc:`smd/tlsph_defgrad ` + +Default +""""""" + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_internal_energy.txt b/doc/_sources/compute_smd_internal_energy.txt new file mode 100644 index 0000000000..075adc72b4 --- /dev/null +++ b/doc/_sources/compute_smd_internal_energy.txt @@ -0,0 +1,58 @@ +.. index:: compute smd/internal/energy + +compute smd/internal/energy command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/internal/energy + +* ID, group-ID are documented in :doc:`compute ` command +* smd/smd/internal/energy = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/internal/energy + +Description +""""""""""" + +Define a computation which outputs the per-particle enthalpy, i.e., +the sum of potential energy and heat. + +See `this PDF guide `_ to use Smooth +Mach Dynamics in LAMMPS. + +**Output Info:** + +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See :ref:`How-to discussions, section 6.15 ` for +an overview of LAMMPS output options. + +The per-particle vector values will be given in :doc:`units ` of energy. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles. + +**Related Commands:** + +Default +""""""" + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_plastic_strain.txt b/doc/_sources/compute_smd_plastic_strain.txt new file mode 100644 index 0000000000..f666f62ae1 --- /dev/null +++ b/doc/_sources/compute_smd_plastic_strain.txt @@ -0,0 +1,63 @@ +.. index:: compute smd/plastic/strain + +compute smd/plastic/strain command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/plastic/strain + +* ID, group-ID are documented in :doc:`compute ` command +* smd/plastic/strain = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/plastic/strain + +Description +""""""""""" + +Define a computation that outputs the equivalent plastic strain per +particle. This command is only meaningful if a material model with +plasticity is defined. + +See `this PDF guide `_ to use Smooth +Mach Dynamics in LAMMPS. + +**Output Info:** + +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See :ref:`How-to discussions, section 6.15 ` for +an overview of LAMMPS output options. + +The per-particle values will be given dimensionless. See :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles. + +Related commands +"""""""""""""""" + +:doc:`smd/plastic/strain/rate `, +:doc:`smd/tlsph/strain/rate `, +:doc:`smd/tlsph/strain ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_plastic_strain_rate.txt b/doc/_sources/compute_smd_plastic_strain_rate.txt new file mode 100644 index 0000000000..71b708b193 --- /dev/null +++ b/doc/_sources/compute_smd_plastic_strain_rate.txt @@ -0,0 +1,63 @@ +.. index:: compute smd/plastic/strain/rate + +compute smd/plastic/strain/rate command +======================================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/plastic/strain/rate + +* ID, group-ID are documented in :doc:`compute ` command +* smd/plastic/strain/rate = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/plastic/strain/rate + +Description +""""""""""" + +Define a computation that outputs the time rate of the equivalent +plastic strain. This command is only meaningful if a material model +with plasticity is defined. + +See `this PDF guide `_ to use Smooth +Mach Dynamics in LAMMPS. + +**Output Info:** + +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See :ref:`How-to discussions, section 6.15 ` for +an overview of LAMMPS output options. + +The per-particle values will be given in :doc:`units ` of one over time. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles. + +Related commands +"""""""""""""""" + +:doc:`smd/plastic/strain `, +:doc:`smd/tlsph/strain/rate `, +:doc:`smd/tlsph/strain ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_rho.txt b/doc/_sources/compute_smd_rho.txt new file mode 100644 index 0000000000..f253983764 --- /dev/null +++ b/doc/_sources/compute_smd_rho.txt @@ -0,0 +1,60 @@ +.. index:: compute smd/rho + +compute smd/rho command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/rho + +* ID, group-ID are documented in :doc:`compute ` command +* smd/rho = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/rho + +Description +""""""""""" + +Define a computation that calculates the per-particle mass density. +The mass density is the mass of a particle which is constant during +the course of a simulation, divided by its volume, which can change +due to mechanical deformation. + +See `this PDF guide `_ to use Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See :ref:`How-to discussions, section 6.15 ` for +an overview of LAMMPS output options. + +The per-particle values will be in :doc:`units ` of mass over volume. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute smd/vol ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_tlsph_defgrad.txt b/doc/_sources/compute_smd_tlsph_defgrad.txt new file mode 100644 index 0000000000..33501df12a --- /dev/null +++ b/doc/_sources/compute_smd_tlsph_defgrad.txt @@ -0,0 +1,65 @@ +.. index:: compute smd/tlsph/defgrad + +compute smd/tlsph/defgrad command +================================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/tlsph/defgrad + +* ID, group-ID are documented in :doc:`compute ` command +* smd/tlsph/defgrad = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/tlsph/defgrad + +Description +""""""""""" + +Define a computation that calculates the deformation gradient. It is +only meaningful for particles which interact according to the +Total-Lagrangian SPH pair style. + +See `this PDF guide `_ to use Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute outputss a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See :ref:`How-to discussions, section 6.15 ` for an overview of LAMMPS output +options. + +The per-particle vector values will be given dimensionless. See +:doc:`units `. The per-particle vector has 10 entries. The first +nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz +components of the asymmetric deformation gradient tensor. The tenth +entry is the determinant of the deformation gradient. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. TThis +compute can only be used for particles which interact via the total +Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`smd/hourglass/error ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_tlsph_dt.txt b/doc/_sources/compute_smd_tlsph_dt.txt new file mode 100644 index 0000000000..e8e4069818 --- /dev/null +++ b/doc/_sources/compute_smd_tlsph_dt.txt @@ -0,0 +1,67 @@ +.. index:: compute smd/tlsph/dt + +compute smd/tlsph/dt command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/tlsph/dt + +* ID, group-ID are documented in :doc:`compute ` command +* smd/tlsph/dt = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/tlsph/dt + +Description +""""""""""" + +Define a computation that outputs the CFL-stable time increment per +particle. This time increment is essentially given by the speed of +sound, divided by the SPH smoothing length. Because both the speed of +sound and the smoothing length typically change during the course of a +simulation, the stable time increment needs to be recomputed every +time step. This calculation is performed automatically in the +relevant SPH pair styles and this compute only serves to make the +stable time increment accessible for output purposes. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See :ref:`How-to discussions, section 6.15 ` for +an overview of LAMMPS output options. + +The per-particle values will be given in :doc:`units ` of time. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This compute can only be used for particles interacting with the +Total-Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`smd/adjust/dt ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_tlsph_num_neighs.txt b/doc/_sources/compute_smd_tlsph_num_neighs.txt new file mode 100644 index 0000000000..78fb764750 --- /dev/null +++ b/doc/_sources/compute_smd_tlsph_num_neighs.txt @@ -0,0 +1,62 @@ +.. index:: compute smd/tlsph/num/neighs + +compute smd/tlsph/num/neighs command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/tlsph/num/neighs + +* ID, group-ID are documented in :doc:`compute ` command +* smd/tlsph/num/neighs = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/tlsph/num/neighs + +Description +""""""""""" + +Define a computation that calculates the number of particles inside of +the smoothing kernel radius for particles interacting via the +Total-Lagrangian SPH pair style. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See :ref:`How-to discussions, section 6.15 ` for +an overview of LAMMPS output options. + +The per-particle values are dimensionless. See :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This quantity will be computed only for particles which interact with +the Total-Lagrangian pair style. + +Related commands +"""""""""""""""" + +:doc:`smd/ulsph/num/neighs ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_tlsph_shape.txt b/doc/_sources/compute_smd_tlsph_shape.txt new file mode 100644 index 0000000000..7067b524c2 --- /dev/null +++ b/doc/_sources/compute_smd_tlsph_shape.txt @@ -0,0 +1,69 @@ +.. index:: compute smd/tlsph/shape + +compute smd/tlsph/shape command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/tlsph/shape + +* ID, group-ID are documented in :doc:`compute ` command +* smd/tlsph/shape = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/tlsph/shape + +Description +""""""""""" + +Define a computation that outputs the current shape of the volume +associated with a particle as a rotated ellipsoid. It is only +meaningful for particles which interact according to the +Total-Lagrangian SPH pair style. + +See `this PDF guide `_ to use Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector of vectors, which can be +accessed by any command that uses per-particle values from a compute +as input. See :ref:`How-to discussions, section 6.15 ` for an overview of LAMMPS output +options. + +The per-particle vector has 7 entries. The first three entries +correspond to the lengths of the ellipsoid's axes and have units of +length. These axis valus are computed as the contact radius times the +xx, yy, or zz components of the Green-Lagrange strain tensor +associated with the particle. The next 4 values are quaternions +(order: q, x, y, z) which describe the spatial rotation of the +particle relative to its initial state. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`smd/contact/radius ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_tlsph_strain.txt b/doc/_sources/compute_smd_tlsph_strain.txt new file mode 100644 index 0000000000..7e92bae14f --- /dev/null +++ b/doc/_sources/compute_smd_tlsph_strain.txt @@ -0,0 +1,66 @@ +.. index:: compute smd/tlsph/strain + +compute smd/tlsph/strain command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/tlsph/strain + +* ID, group-ID are documented in :doc:`compute ` command +* smd/tlsph/strain = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/tlsph/strain + +Description +""""""""""" + +Define a computation that calculates the Green-Lagrange strain tensor +for particles interacting via the Total-Lagrangian SPH pair style. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See :ref:`How-to discussions, section 6.15 ` for an overview of LAMMPS output +options. + +The per-particle tensor values will be given dimensionless. See +:doc:`units `. + +The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain tensor. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`smd/tlsph/strain/rate `, +:doc:`smd/tlsph/stress ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_tlsph_strain_rate.txt b/doc/_sources/compute_smd_tlsph_strain_rate.txt new file mode 100644 index 0000000000..fc2731c838 --- /dev/null +++ b/doc/_sources/compute_smd_tlsph_strain_rate.txt @@ -0,0 +1,64 @@ +.. index:: compute smd/tlsph/strain/rate + +compute smd/tlsph/strain/rate command +===================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/tlsph/strain/rate + +* ID, group-ID are documented in :doc:`compute ` command +* smd/tlsph/strain/rate = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/tlsph/strain/rate + +Description +""""""""""" + +Define a computation that calculates the rate of the strain tensor for +particles interacting via the Total-Lagrangian SPH pair style. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See :ref:`How-to discussions, section 6.15 ` for an overview of LAMMPS output +options. + +The values will be given in :doc:`units ` of one over time. + +The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This quantity will be computed only for particles which interact with +Total-Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`compute smd/tlsph/strain `, :doc:`compute smd/tlsph/stress ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_tlsph_stress.txt b/doc/_sources/compute_smd_tlsph_stress.txt new file mode 100644 index 0000000000..a155b3a64d --- /dev/null +++ b/doc/_sources/compute_smd_tlsph_stress.txt @@ -0,0 +1,67 @@ +.. index:: compute smd/tlsph/stress + +compute smd/tlsph/stress command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/tlsph/stress + +* ID, group-ID are documented in :doc:`compute ` command +* smd/tlsph/stress = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/tlsph/stress + +Description +""""""""""" + +Define a computation that outputs the Cauchy stress tensor for +particles interacting via the Total-Lagrangian SPH pair style. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector of vectors (tensors), which can be +accessed by any command that uses per-particle values from a compute +as input. See +:ref:`How-to discussions, section 6.15 ` +for an overview of LAMMPS output options. + +The values will be given in :doc:`units ` of pressure. + +The per-particle vector has 7 entries. The first six entries +correspond to the xx, yy, zz, xy, xz and yz components of the +symmetric Cauchy stress tensor. The seventh entry is the second +invariant of the stress tensor, i.e., the von Mises equivalent stress. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`compute smd/tlsph/strain `, :doc:`cmopute smd/tlsph/strain/rate ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_triangle_mesh_vertices.txt b/doc/_sources/compute_smd_triangle_mesh_vertices.txt new file mode 100644 index 0000000000..5c02009857 --- /dev/null +++ b/doc/_sources/compute_smd_triangle_mesh_vertices.txt @@ -0,0 +1,68 @@ +compute smd/triangle/mesh/vertices +================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/triangle/mesh/vertices + +* ID, group-ID are documented in :doc:`compute ` command +* smd/triangle/mesh/vertices = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/triangle/mesh/vertices + +Description +""""""""""" + +Define a computation that returns the coordinates of the vertices +corresponding to the triangle-elements of a mesh created by the `fix smd/wall_surface `_. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute returns a per-particle vector of vectors, which can be +accessed by any command that uses per-particle values from a compute as +input. See :ref:`How-to discussions, section 6.15 ` +for an overview of LAMMPS output options. + +The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and +(x3/y3/z3) corresponding to the first, second, and third vertex of +each triangle. + +It is only meaningful to use this compute for a group of particles +which is created via the `fix smd/wall_surface `_ command. + +The output of this compute can be used with the dump2vtk_tris tool to +generate a VTK representation of the smd/wall_surace mesh for +visualization purposes. + +The values will be given in :doc:`units ` of distance. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute smd/move/tri/surf `, +`compute smd/wall/surface `_ + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_ulsph_num_neighs.txt b/doc/_sources/compute_smd_ulsph_num_neighs.txt new file mode 100644 index 0000000000..90c7a202d4 --- /dev/null +++ b/doc/_sources/compute_smd_ulsph_num_neighs.txt @@ -0,0 +1,61 @@ +.. index:: compute smd/ulsph/num/neighs + +compute smd/ulsph/num/neighs command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/ulsph/num/neighs + +* ID, group-ID are documented in :doc:`compute ` command +* smd/ulsph/num/neighs = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/ulsph/num/neighs + +Description +""""""""""" + +Define a computation that returns the number of neighbor particles +inside of the smoothing kernel radius for particles interacting via +the updated Lagrangian SPH pair style. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute returns a per-particle vector, which can be accessed by +any command that uses per-particle values from a compute as input. +See :ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-particle values will be given dimentionless, see :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`compute smd/tlsph/num/neighs ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_ulsph_strain.txt b/doc/_sources/compute_smd_ulsph_strain.txt new file mode 100644 index 0000000000..1c8ec914ec --- /dev/null +++ b/doc/_sources/compute_smd_ulsph_strain.txt @@ -0,0 +1,64 @@ +.. index:: compute smd/ulsph/strain + +compute smd/ulsph/strain command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/ulsph/strain + +* ID, group-ID are documented in :doc:`compute ` command +* smd/ulsph/strain = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/ulsph/strain + +Description +""""""""""" + +Define a computation that outputs the logarithmic strain tensor. for +particles interacting via the updated Lagrangian SPH pair style. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle tensor, which can be accessed +by any command that uses per-particle values from a compute as input. +See :ref:`Section_howto 15 ` for an overview of +LAMMPS output options. + +The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor. + +The per-particle tensor values will be given dimensionless, see +:doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`compute smd/tlsph/strain ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_ulsph_strain_rate.txt b/doc/_sources/compute_smd_ulsph_strain_rate.txt new file mode 100644 index 0000000000..7308385bcb --- /dev/null +++ b/doc/_sources/compute_smd_ulsph_strain_rate.txt @@ -0,0 +1,64 @@ +.. index:: compute smd/ulsph/strain/rate + +compute smd/ulsph/strain/rate command +===================================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/ulsph/strain/rate + +* ID, group-ID are documented in :doc:`compute ` command +* smd/ulsph/strain/rate = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/ulsph/strain/rate + +Description +""""""""""" + +Define a computation that outputs the rate of the logarithmic strain +tensor for particles interacting via the updated Lagrangian SPH pair +style. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The values will be given in :doc:`units ` of one over time. + +The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`compute smd/tlsph/strain/rate ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_ulsph_stress.txt b/doc/_sources/compute_smd_ulsph_stress.txt new file mode 100644 index 0000000000..a3385985fc --- /dev/null +++ b/doc/_sources/compute_smd_ulsph_stress.txt @@ -0,0 +1,64 @@ +.. index:: compute smd/ulsph/stress + +compute smd/ulsph/stress command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/ulsph/stress + +* ID, group-ID are documented in :doc:`compute ` command +* smd/ulsph/stress = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/ulsph/stress + +Description +""""""""""" + +Define a computation that outputs the Cauchy stress tensor. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The values will be given in :doc:`units ` of pressure. + +The per-particle vector has 7 entries. The first six entries +correspond to the xx, yy, zz, xy, xz, yz components of the symmetric +Cauchy stress tensor. The seventh entry is the second invariant of the +stress tensor, i.e., the von Mises equivalent stress. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style. + +Related commands +"""""""""""""""" + +:doc:`compute smd/ulsph/strain `, :doc:`compute smd/ulsph/strain/rate ` :doc:`compute smd/tlsph/stress ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_smd_vol.txt b/doc/_sources/compute_smd_vol.txt new file mode 100644 index 0000000000..ec2be61e15 --- /dev/null +++ b/doc/_sources/compute_smd_vol.txt @@ -0,0 +1,62 @@ +.. index:: compute smd/vol + +compute smd/vol command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID smd/vol + +* ID, group-ID are documented in :doc:`compute ` command +* smd/vol = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all smd/vol + +Description +""""""""""" + +Define a computation that provides the per-particle volume and the sum +of the per-particle volumes of the group for which the fix is defined. + +See `this PDF guide `_ to using Smooth +Mach Dynamics in LAMMPS. + +**Output info:** + +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See :ref:`How-to discussions, section 6.15 ` for +an overview of LAMMPS output options. + +The per-particle vector values will be given in :doc:`units ` of +volume. + +Additionally, the compute returns a scalar, which is the sum of the +per-particle volumes of the group for which the fix is defined. + +Restrictions +"""""""""""" + + +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute smd/rho ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_sna_atom.txt b/doc/_sources/compute_sna_atom.txt new file mode 100644 index 0000000000..fedd758542 --- /dev/null +++ b/doc/_sources/compute_sna_atom.txt @@ -0,0 +1,281 @@ +.. index:: compute sna/atom + +compute sna/atom command +======================== + +compute snad/atom command +========================= + +compute snav/atom command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID sna/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... + compute ID group-ID snad/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... + compute ID group-ID snav/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... + +* ID, group-ID are documented in :doc:`compute ` command +* sna/atom = style name of this compute command +* rcutfac = scale factor applied to all cutoff radii (positive real) +* rfac0 = parameter in distance to angle conversion (0 < rcutfac < 1) +* twojmax = band limit for bispectrum components (non-negative integer) +* R_1, R_2,... = list of cutoff radii, one for each type (distance units) +* w_1, w_2,... = list of neighbor weights, one for each type +* zero or more keyword/value pairs may be appended +* keyword = *diagonal* or *rmin0* or *switchflag* +.. parsed-literal:: + + *diagonal* value = *0* or *1* or *2* or *3* + *0* = all j1, j2, j <= twojmax, j2 <= j1 + *1* = subset satisfying j1 == j2 + *2* = subset satisfying j1 == j2 == j3 + *3* = subset satisfying j2 <= j1 <= j + *rmin0* value = parameter in distance to angle conversion (distance units) + *switchflag* value = *0* or *1* + *0* = do not use switching function + *1* = use switching function + + + +Examples +"""""""" + +.. parsed-literal:: + + compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 diagonal 3 rmin0 0.0 + compute db all sna/atom 1.4 0.95 6 2.0 1.0 + compute vb all sna/atom 1.4 0.95 6 2.0 1.0 + +Description +""""""""""" + +Define a computation that calculates a set of bispectrum components +for each atom in a group. + +Bispectrum components of an atom are order parameters characterizing +the radial and angular distribution of neighbor atoms. The detailed +mathematical definition is given in the paper by Thompson et +al. :ref:`(Thompson) ` + +The position of a neighbor atom *i'* relative to a central atom *i* is +a point within the 3D ball of radius *R_ii' = rcutfac*(R_i + R_i')* + +Bartok et al. :ref:`(Bartok) `, proposed mapping this 3D ball +onto the 3-sphere, the surface of the unit ball in a four-dimensional +space. The radial distance *r* within *R_ii'* is mapped on to a third +polar angle *theta0* defined by, + +.. image:: Eqs/compute_sna_atom1.jpg + :align: center + +In this way, all possible neighbor positions are mapped on to a subset +of the 3-sphere. Points south of the latitude *theta0max=rfac0*Pi* +are excluded. + +The natural basis for functions on the 3-sphere is formed by the 4D +hyperspherical harmonics *U^j_m,m'(theta, phi, theta0).* These +functions are better known as *D^j_m,m',* the elements of the Wigner +*D*-matrices :ref:`(Meremianin `, +:ref:`Varshalovich) `. + +The density of neighbors on the 3-sphere can be written as a sum of +Dirac-delta functions, one for each neighbor, weighted by species and +radial distance. Expanding this density function as a generalized +Fourier series in the basis functions, we can write each Fourier +coefficient as + +.. image:: Eqs/compute_sna_atom2.jpg + :align: center + +The *w_i'* neighbor weights are dimensionless numbers that are chosen +to distinguish atoms of different types, while the central atom is +arbitrarily assigned a unit weight. The function *fc(r)* ensures that +the contribution of each neighbor atom goes smoothly to zero at +*R_ii'*: + +.. image:: Eqs/compute_sna_atom4.jpg + :align: center + +The expansion coefficients *u^j_m,m'* are complex-valued and they are +not directly useful as descriptors, because they are not invariant +under rotation of the polar coordinate frame. However, the following +scalar triple products of expansion coefficients can be shown to be +real-valued and invariant under rotation :ref:`(Bartok) `. + +.. image:: Eqs/compute_sna_atom3.jpg + :align: center + +The constants *H^jmm'_j1m1m1'_j2m2m2'* are coupling coefficients, +analogous to Clebsch-Gordan coefficients for rotations on the +2-sphere. These invariants are the components of the bispectrum and +these are the quantities calculated by the compute *sna/atom*. They +characterize the strength of density correlations at three points on +the 3-sphere. The j2=0 subset form the power spectrum, which +characterizes the correlations of two points. The lowest-order +components describe the coarsest features of the density function, +while higher-order components reflect finer detail. Note that the +central atom is included in the expansion, so three point-correlations +can be either due to three neighbors, or two neighbors and the central +atom. + +Compute *snad/atom* calculates the derivative of the bispectrum components +summed separately for each atom type: + +.. image:: Eqs/compute_sna_atom5.jpg + :align: center + +The sum is over all atoms *i'* of atom type *I*. For each atom *i*, +this compute evaluates the above expression for each direction, each +atom type, and each bispectrum component. See section below on output +for a detailed explanation. + +Compute *snav/atom* calculates the virial contribution due to the +derivatives: + +.. image:: Eqs/compute_sna_atom6.jpg + :align: center + +Again, the sum is over all atoms *i'* of atom type *I*. For each atom +*i*, this compute evaluates the above expression for each of the six +virial components, each atom type, and each bispectrum component. See +section below on output for a detailed explanation. + +The value of all bispectrum components will be zero for atoms not in +the group. Neighbor atoms not in the group do not contribute to the +bispectrum of atoms in the group. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (i.e. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently. + +The argument *rcutfac* is a scale factor that controls the ratio of +atomic radius to radial cutoff distance. + +The argument *rfac0* and the optional keyword *rmin0* define the +linear mapping from radial distance to polar angle *theta0* on the +3-sphere. + +The argument *twojmax* and the keyword *diagonal* define which +bispectrum components are generated. See section below on output for a +detailed explanation of the number of bispectrum components and the +ordered in which they are listed + +The keyword *switchflag* can be used to turn off the switching +function. + +.. note:: + + If you have a bonded system, then the settings of + :doc:`special_bonds ` command can remove pairwise + interactions between atoms in the same bond, angle, or dihedral. This + is the default setting for the :doc:`special_bonds ` + command, and means those pairwise interactions do not appear in the + neighbor list. Because this fix uses the neighbor list, it also means + those pairs will not be included in the calculation. One way to get + around this, is to write a dump file, and use the :doc:`rerun ` + command to compute the bispectrum components for snapshots in the dump + file. The rerun script can use a :doc:`special_bonds ` + command that includes all pairs in the neighbor list. + +;line + +**Output info:** + +Compute *sna/atom* calculates a per-atom array, each column +corresponding to a particular bispectrum component. The total number +of columns and the identities of the bispectrum component contained in +each column depend on the values of *twojmax* and *diagonal*, as +described by the following piece of python code: + +.. parsed-literal:: + + for j1 in range(0,twojmax+1): + if(diagonal==2): + print j1/2,j1/2,j1/2 + elif(diagonal==1): + for j in range(0,min(twojmax,2*j1)+1,2): + print j1/2,j1/2,j/2 + elif(diagonal==0): + for j2 in range(0,j1+1): + for j in range(j1-j2,min(twojmax,j1+j2)+1,2): + print j1/2,j2/2,j/2 + elif(diagonal==3): + for j2 in range(0,j1+1): + for j in range(j1-j2,min(twojmax,j1+j2)+1,2): + if (j>=j1): print j1/2,j2/2,j/2 + +Compute *snad/atom* evaluates a per-atom array. The columns are +arranged into *ntypes* blocks, listed in order of atom type *I*. Each +block contains three sub-blocks corresponding to the *x*, *y*, and *z* +components of the atom position. Each of these sub-blocks contains +one column for each bispectrum component, the same as for compute +*sna/atom* + +Compute *snav/atom* evaluates a per-atom array. The columns are +arranged into *ntypes* blocks, listed in order of atom type *I*. Each +block contains six sub-blocks corresponding to the *xx*, *yy*, *zz*, +*yz*, *xz*, and *xy* components of the virial tensor in Voigt +notation. Each of these sub-blocks contains one column for each +bispectrum component, the same as for compute *sna/atom* + +These values can be accessed by any command that uses per-atom values +from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +Restrictions +"""""""""""" + + +These computes are part of the SNAP package. They are only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`pair_style snap ` + +Default +""""""" + +The optional keyword defaults are *diagonal* = 0, *rmin0* = 0, +*switchflag* = 1. + + +---------- + + +.. _Thompson2014: + + + +**(Thompson)** Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint +available at `arXiv:1409.3880 `_ + +.. _Bartok2010: + + + +**(Bartok)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010). + +.. _Meremianin2006: + + + +**(Meremianin)** Meremianin, J. Phys. A, 39, 3099 (2006). + +.. _Varshalovich1987: + + + +**(Varshalovich)** Varshalovich, Moskalev, Khersonskii, Quantum Theory +of Angular Momentum, World Scientific, Singapore (1987). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_stress_atom.txt b/doc/_sources/compute_stress_atom.txt new file mode 100644 index 0000000000..602d79f9bc --- /dev/null +++ b/doc/_sources/compute_stress_atom.txt @@ -0,0 +1,187 @@ +.. index:: compute stress/atom + +compute stress/atom command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID stress/atom temp-ID keyword ... + +* ID, group-ID are documented in :doc:`compute ` command +* stress/atom = style name of this compute command +* temp-ID = ID of compute that calculates temperature, can be NULL if not needed +* zero or more keywords may be appended +* keyword = *ke* or *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *fix* or *virial* + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 mobile stress/atom NULL + compute 1 mobile stress/atom myRamp + compute 1 all stress/atom NULL pair bond + +Description +""""""""""" + +Define a computation that computes the symmetric per-atom stress +tensor for each atom in a group. The tensor for each atom has 6 +components and is stored as a 6-element vector in the following order: +xx, yy, zz, xy, xz, yz. See the :doc:`compute pressure ` command if you want the stress tensor +(pressure) of the entire system. + +The stress tensor for atom *I* is given by the following formula, +where *a* and *b* take on values x,y,z to generate the 6 components of +the symmetric tensor: + +.. image:: Eqs/stress_tensor.jpg + :align: center + +The first term is a kinetic energy contribution for atom *I*. See +details below on how the specified *temp-ID* can affect the velocities +used in this calculation. The second term is a pairwise energy +contribution where *n* loops over the *Np* neighbors of atom *I*, *r1* +and *r2* are the positions of the 2 atoms in the pairwise interaction, +and *F1* and *F2* are the forces on the 2 atoms resulting from the +pairwise interaction. The third term is a bond contribution of +similar form for the *Nb* bonds which atom *I* is part of. There are +similar terms for the *Na* angle, *Nd* dihedral, and *Ni* improper +interactions atom *I* is part of. There is also a term for the KSpace +contribution from long-range Coulombic interactions, if defined. +Finally, there is a term for the *Nf* :doc:`fixes ` that apply +internal constraint forces to atom *I*. Currently, only the :doc:`fix shake ` and :doc:`fix rigid ` commands +contribute to this term. + +As the coefficients in the formula imply, a virial contribution +produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3 +atoms in a Tersoff 3-body interaction) is assigned in equal portions +to each atom in the set. E.g. 1/4 of the dihedral virial to each of +the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied +to atoms in a a water molecule via the :doc:`fix shake ` +command. + +If no extra keywords are listed, all of the terms in this formula are +included in the per-atom stress tensor. If any extra keywords are +listed, only those terms are summed to compute the tensor. The +*virial* keyword means include all terms except the kinetic energy +*ke*. + +Note that the stress for each atom is due to its interaction with all +other atoms in the simulation, not just with other atoms in the group. + +Details of how LAMMPS computes the virial for individual atoms for +either pairwise or manybody potentials, and including the effects of +periodic boundary conditions is discussed in :ref:`(Thompson) `. +The basic idea for manybody potentials is to treat each component of +the force computation between a small cluster of atoms in the same +manner as in the formula above for bond, angle, dihedral, etc +interactions. Namely the quantity R dot F is summed over the atoms in +the interaction, with the R vectors unwrapped by periodic boundaries +so that the cluster of atoms is close together. The total +contribution for the cluster interaction is divided evenly among those +atoms. + +The :doc:`dihedral_style charmm ` style calculates +pairwise interactions between 1-4 atoms. The virial contribution of +these terms is included in the pair virial, not the dihedral virial. + +The KSpace contribution is calculated using the method in +:ref:`(Heyes) ` for the Ewald method and by the methodology described +in :ref:`(Sirk) ` for PPPM. The choice of KSpace solver is specified +by the :doc:`kspace_style pppm ` command. Note that for +PPPM, the calcluation requires 6 extra FFTs each timestep that +per-atom stress is calculated. Thus it can significantly increase the +cost of the PPPM calculation if it is needed on a large fraction of +the simulation timesteps. + +The *temp-ID* argument can be used to affect the per-atom velocities +used in the kinetic energy contribution to the total stress. If the +kinetic energy is not included in the stress, than the temperature +compute is not used and can be specified as NULL. If the kinetic +energy is included and you wish to use atom velocities as-is, then +*temp-ID* can also be specified as NULL. If desired, the specified +temperature compute can be one that subtracts off a bias to leave each +atom with only a thermal velocity to use in the formula above, e.g. by +subtracting a background streaming velocity. See the doc pages for +individual :doc:`compute commands ` to determine which ones +include a bias. + + +---------- + + +Note that as defined in the formula, per-atom stress is the negative +of the per-atom pressure tensor. It is also really a stress*volume +formulation, meaning the computed quantity is in units of +pressure*volume. It would need to be divided by a per-atom volume to +have units of stress (pressure), but an individual atom's volume is +not well defined or easy to compute in a deformed solid or a liquid. +See the :doc:`compute voronoi/atom ` command for +one possible way to estimate a per-atom volume. + +Thus, if the diagonal components of the per-atom stress tensor are +summed for all atoms in the system and the sum is divided by dV, where +d = dimension and V is the volume of the system, the result should be +-P, where P is the total pressure of the system. + +These lines in an input script for a 3d system should yield that +result. I.e. the last 2 columns of thermo output will be the same: + +.. parsed-literal:: + + compute peratom all stress/atom NULL + compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] + variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) + thermo_style custom step temp etotal press v_press + +**Output info:** + +This compute calculates a per-atom array with 6 columns, which can be +accessed by indices 1-6 by any command that uses per-atom values from +a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The per-atom array values will be in pressure*volume +:doc:`units ` as discussed above. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute pe `, :doc:`compute pressure ` + +**Default:** none + + +---------- + + +.. _Heyes: + + + +**(Heyes)** Heyes, Phys Rev B 49, 755 (1994), + +.. _Sirk: + + + +**(Sirk)** Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013). + +.. _Thompson: + + + +**(Thompson)** Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_tally.txt b/doc/_sources/compute_tally.txt new file mode 100644 index 0000000000..677c2e6182 --- /dev/null +++ b/doc/_sources/compute_tally.txt @@ -0,0 +1,102 @@ +.. index:: compute force/tally + +compute force/tally command +=========================== + +compute heat/flux/tally command +=============================== + +compute pe/tally command +======================== + +compute stress/tally command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID style group2-ID + +* ID, group-ID are documented in :doc:`compute ` command +* style = *force/tally* or *pe/tally* or *stress/tally* +* group2-ID = group ID of second (or same) group + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 lower force/tally upper + compute 1 left pe/tally right + compute 1 lower stress/tally lower + +Description +""""""""""" + +Define a computation that calculates properties between two groups of +atoms by accumulating them from pairwise non-bonded computations. The +two groups can be the same. This is similar to :doc:`compute group/group ` only that the data is +accumulated directly during the non-bonded force computation. The +computes *force/tally*, *pe/tally*, *stress/tally*, and +*heat/flux/tally* are primarily provided as example how to program +additional, more sophisticated computes using the tally mechanism. + + +---------- + + +The pairwise contributions are computing via a callback that the +compute registers with the non-bonded pairwise force computation. +This limits the use to systems that have no bonds, no Kspace, and no +manybody interactions. On the other hand, the computation does not +have to compute forces or energies a second time and thus can be much +more efficient. The callback mechanism allows to write more complex +pairwise property computations. + + +---------- + + +**Output info:** + +Compute *pe/tally* calculates a global scalar (the energy) and a per +atom scalar (the contributions of the single atom to the global +scalar). Compute *force/tally* calculates a global scalar (the force +magnitude) and a per atom 3-element vector (force contribution from +each atom). Compute *stress/tally* calculates a global scalar +(average of the diagonal elements of the stress tensor) and a per atom +vector (the 6 elements of stress tensor contributions from the +individual atom). + +Both the scalar and vector values calculated by this compute are +"extensive". + +Restrictions +"""""""""""" + + +This compute is part of the USER-TALLY package. It is only enabled +if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Not all pair styles can be evaluated in a pairwise mode as required by +this compute. For example, 3-body and other many-body potentials, +such as :doc:`Tersoff ` and +:doc:`Stillinger-Weber ` cannot be used. :doc:`EAM ` +potentials only include the pair potential portion of the EAM +interaction when used by this compute, not the embedding term. Also +bonded or Kspace interactions do not contribute to this compute. + +Related commands +"""""""""""""""" + +*compute group/group*_compute_group_group.html, *compute +heat/flux*_compute_heat_flux.html + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp.txt b/doc/_sources/compute_temp.txt new file mode 100644 index 0000000000..e5cb44a723 --- /dev/null +++ b/doc/_sources/compute_temp.txt @@ -0,0 +1,128 @@ +.. index:: compute temp + +compute temp command +==================== + +compute temp/cuda command +========================= + +compute temp/kk command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp + +* ID, group-ID are documented in :doc:`compute ` command +* temp = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all temp + compute myTemp mobile temp + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms. A compute of this style can be used by any command that +computes a temperature, e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. + +The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = 2 or 3 = dimensionality of the simulation, N = number of atoms +in the group, k = Boltzmann constant, and T = temperature. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as :doc:`fix shake ` and +:doc:`fix rigid `. This means the temperature of groups of +atoms that include these constraints will be computed correctly. If +needed, the subtracted degrees-of-freedom can be altered using the +*extra* option of the :doc:`compute_modify ` command. + +A compute of this style with the ID of "thermo_temp" is created when +LAMMPS starts up, as if this command were in the input script: + +.. parsed-literal:: + + compute thermo_temp all temp + +See the "thermo_style" command for more details. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute temp/partial `, :doc:`compute temp/region `, :doc:`compute pressure ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_asphere.txt b/doc/_sources/compute_temp_asphere.txt new file mode 100644 index 0000000000..d9954deef7 --- /dev/null +++ b/doc/_sources/compute_temp_asphere.txt @@ -0,0 +1,170 @@ +.. index:: compute temp/asphere + +compute temp/asphere command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/asphere keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* temp/asphere = style name of this compute command +* zero or more keyword/value pairs may be appended +* keyword = *bias* or *dof* +.. parsed-literal:: + + *bias* value = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias + *dof* value = *all* or *rotate* + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all temp/asphere + compute myTemp mobile temp/asphere bias tempCOM + compute myTemp mobile temp/asphere dof rotate + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +aspherical particles, including a contribution from both their +translational and rotational kinetic energy. This differs from the +usual :doc:`compute temp ` command, which assumes point +particles with only translational kinetic energy. + +Only finite-size particles (aspherical or spherical) can be included +in the group. For 3d finite-size particles, each has 6 degrees of +freedom (3 translational, 3 rotational). For 2d finite-size +particles, each has 3 degrees of freedom (2 translational, 1 +rotational). + +.. note:: + + This choice for degrees of freedom (dof) assumes that all + finite-size aspherical or spherical particles in your model will + freely rotate, sampling all their rotational dof. It is possible to + use a combination of interaction potentials and fixes that induce no + torque or otherwise constrain some of all of your particles so that + this is not the case. Then there are less dof and you should use the + :doc:`compute_modify extra ` command to adjust the dof + accordingly. + +For example, an aspherical particle with all three of its shape +parameters the same is a sphere. If it does not rotate, then it +should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A +uniaxial aspherical particle has two of its three shape parameters the +same. If it does not rotate around the axis perpendicular to its +circular cross section, then it should have 5 dof instead of 6 in 3d. +The latter is the case for uniaxial ellipsoids in a :doc:`GayBerne model ` since there is no induced torque around the +optical axis. It will also be the case for biaxial ellipsoids when +exactly two of the semiaxes have the same length and the corresponding +relative well depths are equal. + +The translational kinetic energy is computed the same as is described +by the :doc:`compute temp ` command. The rotational +kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor +for the aspherical particle and w is its angular velocity, which is +computed from its angular momentum. + +.. note:: + + For :doc:`2d models `, particles are treated as + ellipsoids, not ellipses, meaning their moments of inertia will be the + same as in 3d. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute. The formula for the components of the +tensor is the same as the above formula, except that v^2 and w^2 are +replaced by vx*vy and wx*wy for the xy component, and the appropriate +elements of the inertia tensor are used. The 6 components of the +vector are ordered xx, yy, zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +This compute subtracts out translational degrees-of-freedom due to +fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the +temperature of groups of atoms that include these constraints will be +computed correctly. If needed, the subtracted degrees-of-freedom can +be altered using the *extra* option of the +:doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + + +---------- + + +The keyword/value option pairs are used in the following ways. + +For the *bias* keyword, *bias-ID* refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This allows +compute temp/sphere to compute its thermal temperature after the +translational kinetic energy components have been altered in a +prescribed way, e.g. to remove a flow velocity profile. Thermostats +that use this compute will work with this bias term. See the doc +pages for individual computes that calculate a temperature and the doc +pages for fixes that perform thermostatting for more details. + +For the *dof* keyword, a setting of *all* calculates a temperature +that includes both translational and rotational degrees of freedom. A +setting of *rotate* calculates a temperature that includes only +rotational degrees of freedom. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the ASPHERE package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This compute requires that atoms store angular momementum and a +quaternion as defined by the :doc:`atom_style ellipsoid ` +command. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical as defined by their +shape attribute. + +Related commands +"""""""""""""""" + +:doc:`compute temp ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_body.txt b/doc/_sources/compute_temp_body.txt new file mode 100644 index 0000000000..89d49d8092 --- /dev/null +++ b/doc/_sources/compute_temp_body.txt @@ -0,0 +1,146 @@ +.. index:: compute temp/body + +compute temp/body command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/body keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* temp/body = style name of this compute command +* zero or more keyword/value pairs may be appended +* keyword = *bias* or *dof* +.. parsed-literal:: + + *bias* value = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias + *dof* value = *all* or *rotate* + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all temp/body + compute myTemp mobile temp/body bias tempCOM + compute myTemp mobile temp/body dof rotate + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +body particles, including a contribution from both their +translational and rotational kinetic energy. This differs from the +usual :doc:`compute temp ` command, which assumes point +particles with only translational kinetic energy. + +Only body particles can be included in the group. For 3d particles, +each has 6 degrees of freedom (3 translational, 3 rotational). For 2d +body particles, each has 3 degrees of freedom (2 translational, 1 +rotational). + +.. note:: + + This choice for degrees of freedom (dof) assumes that all body + particles in your model will freely rotate, sampling all their + rotational dof. It is possible to use a combination of interaction + potentials and fixes that induce no torque or otherwise constrain some + of all of your particles so that this is not the case. Then there are + less dof and you should use the :doc:`compute_modify extra ` command to adjust the dof accordingly. + +The translational kinetic energy is computed the same as is described +by the :doc:`compute temp ` command. The rotational +kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor +for the aspherical particle and w is its angular velocity, which is +computed from its angular momentum. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute. The formula for the components of the +tensor is the same as the above formula, except that v^2 and w^2 are +replaced by vx*vy and wx*wy for the xy component, and the appropriate +elements of the inertia tensor are used. The 6 components of the +vector are ordered xx, yy, zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +This compute subtracts out translational degrees-of-freedom due to +fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the +temperature of groups of atoms that include these constraints will be +computed correctly. If needed, the subtracted degrees-of-freedom can +be altered using the *extra* option of the +:doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + + +---------- + + +The keyword/value option pairs are used in the following ways. + +For the *bias* keyword, *bias-ID* refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This allows +compute temp/sphere to compute its thermal temperature after the +translational kinetic energy components have been altered in a +prescribed way, e.g. to remove a flow velocity profile. Thermostats +that use this compute will work with this bias term. See the doc +pages for individual computes that calculate a temperature and the doc +pages for fixes that perform thermostatting for more details. + +For the *dof* keyword, a setting of *all* calculates a temperature +that includes both translational and rotational degrees of freedom. A +setting of *rotate* calculates a temperature that includes only +rotational degrees of freedom. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the BODY package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This compute requires that atoms store angular momementum and a +quaternion as defined by the :doc:`atom_style body ` +command. + +Related commands +"""""""""""""""" + +:doc:`compute temp ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_chunk.txt b/doc/_sources/compute_temp_chunk.txt new file mode 100644 index 0000000000..c779a82703 --- /dev/null +++ b/doc/_sources/compute_temp_chunk.txt @@ -0,0 +1,255 @@ +.. index:: compute temp/chunk + +compute temp/chunk command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/chunk chunkID value1 value2 ... keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* temp/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command +* zero or more values can be listed as value1,value2,etc +* value = *temp* or *kecom* or *internal* +.. parsed-literal:: + + temp = temperature of each chunk + kecom = kinetic energy of each chunk based on velocity of center of mass + internal = internal kinetic energy of each chunk + +* zero or more keyword/value pairs may be appended +* keyword = *com* or *bias* or *adof* or *cdof* +.. parsed-literal:: + + *com* value = *yes* or *no* + yes = subtract center-of-mass velocity from each chunk before calculating temperature + no = do not subtract center-of-mass velocity + *bias* value = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias + *adof* value = dof_per_atom + dof_per_atom = define this many degrees-of-freedom per atom + *cdof* value = dof_per_chunk + dof_per_chunk = define this many degrees-of-freedom per chunk + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 fluid temp/chunk molchunk + compute 1 fluid temp/chunk molchunk temp internal + compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms that are also in chunks, after optionally subtracting out the +center-of-mass velocity of each chunk. By specifying optional values, +it can also calulate the per-chunk temperature or energies of the +multiple chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +The temperature is calculated by the formula KE = DOF/2 k T, where KE = +total kinetic energy of all atoms assigned to chunks (sum of 1/2 m +v^2), DOF = the total number of degrees of freedom for those atoms, k += Boltzmann constant, and T = temperature. + +The DOF is calculated as N*adof + Nchunk*cdof, where N = number of +atoms contributing to the KE, adof = degrees of freedom per atom, and +cdof = degrees of freedom per chunk. By default adof = 2 or 3 = +dimensionality of system, as set via the :doc:`dimension ` +command, and cdof = 0.0. This gives the usual formula for +temperature. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. + +Note that the number of atoms contributing to the temperature is +calculated each time the temperature is evaluated since it is assumed +the atoms may be dynamically assigned to chunks. Thus there is no +need to use the *dynamic* option of the +:doc:`compute_modify ` command for this compute style. + +If any optional values are specified, then per-chunk quantities are +also calculated and stored in a global array, as described below. + +The *temp* value calculates the temperature for each chunk by the +formula KE = DOF/2 k T, where KE = total kinetic energy of the chunk +of atoms (sum of 1/2 m v^2), DOF = the total number of degrees of +freedom for all atoms in the chunk, k = Boltzmann constant, and T = +temperature. + +The DOF in this case is calculated as N*adof + cdof, where N = number +of atoms in the chunk, adof = degrees of freedom per atom, and cdof = +degrees of freedom per chunk. By default adof = 2 or 3 = +dimensionality of system, as set via the :doc:`dimension ` +command, and cdof = 0.0. This gives the usual formula for +temperature. + +The *kecom* value calculates the kinetic energy of each chunk as if +all its atoms were moving with the velocity of the center-of-mass of +the chunk. + +The *internal* value calculates the internal kinetic energy of each +chunk. The interal KE is summed over the atoms in the chunk using an +internal "thermal" velocity for each atom, which is its velocity minus +the center-of-mass velocity of the chunk. + + +---------- + + +Note that currently the global and per-chunk temperatures calculated +by this compute only include translational degrees of freedom for each +atom. No rotational degrees of freedom are included for finite-size +particles. Also no degrees of freedom are subtracted for any velocity +bias or constraints that are applied, such as :doc:`compute temp/partial `, or :doc:`fix shake ` +or :doc:`fix rigid `. This is because those degrees of +freedom (e.g. a constrained bond) could apply to sets of atoms that +are both included and excluded from a specific chunk, and hence the +concept is somewhat ill-defined. In some cases, you can use the +*adof* and *cdof* keywords to adjust the calculated degress of freedom +appropriately, as explained below. + +Note that the per-chunk temperature calulated by this compute and the +:doc:`fix ave/chunk temp ` command can be different. +This compute calculates the temperature for each chunk for a single +snapshot. Fix ave/chunk can do that but can also time average those +values over many snapshots, or it can compute a temperature as if the +atoms in the chunk on different timesteps were collected together as +one set of atoms to calculate their temperature. This compute allows +the center-of-mass velocity of each chunk to be subtracted before +calculating the temperature; fix ave/chunk does not. + +.. note:: + + Only atoms in the specified group contribute to the calculations + performed by this compute. The :doc:`compute chunk/atom ` command defines its own group; + atoms will have a chunk ID = 0 if they are not in that group, + signifying they are not assigned to a chunk, and will thus also not + contribute to this calculation. You can specify the "all" group for + this command if you simply want to include atoms with non-zero chunk + IDs. + +The simplest way to output the per-chunk results of the compute +temp/chunk calculation to a file is to use the :doc:`fix ave/time ` command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all temp/chunk cc1 temp + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + + +---------- + + +The keyword/value option pairs are used in the following ways. + +The *com* keyword can be used with a value of *yes* to subtract the +velocity of the center-of-mass for each chunk from the velocity of the +atoms in that chunk, before calculating either the global or per-chunk +temperature. This can be useful if the atoms are streaming or +otherwise moving collectively, and you wish to calculate only the +thermal temperature. + +For the *bias* keyword, *bias-ID* refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This also +allows calculation of the global or per-chunk temperature using only +the thermal temperature of atoms in each chunk after the translational +kinetic energy components have been altered in a prescribed way, +e.g. to remove a velocity profile. It also applies to the calculation +of the other per-chunk values, such as *kecom* or *internal*, which +involve the center-of-mass velocity of each chunk, which is calculated +after the velocity bias is removed from each atom. Note that the +temperature compute will apply its bias globally to the entire system, +not on a per-chunk basis. + +The *adof* and *cdof* keywords define the values used in the degree of +freedom (DOF) formulas used for the global or per-chunk temperature, +as described above. They can be used to calculate a more appropriate +temperature for some kinds of chunks. Here are 3 examples: + +If spatially binned chunks contain some number of water molecules and +:doc:`fix shake ` is used to make each molecule rigid, then +you could calculate a temperature with 6 degrees of freedom (DOF) (3 +translational, 3 rotational) per molecule by setting *adof* to 2.0. + +If :doc:`compute temp/partial ` is used with the +*bias* keyword to only allow the x component of velocity to contribute +to the temperature, then *adof* = 1.0 would be appropriate. + +If each chunk consists of a large molecule, with some number of its +bonds constrained by :doc:`fix shake ` or the entire molecule +by :doc:`fix rigid/small `, *adof* = 0.0 and *cdof* could be +set to the remaining degrees of freedom for the entire molecule +(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid +molecule. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +This compute also optionally calculates a global array, if one or more +of the optional values are specified. The number of rows in the array += the number of chunks *Nchunk* as calculated by the specified +:doc:`compute chunk/atom ` command. The number of +columns is the number of specifed values (1 or more). These values +can be accessed by any command that uses global array values from a +compute as input. Again, see :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The array values are "intensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. The array values +will be in temperature :doc:`units ` for the *temp* value, and in +energy :doc:`units ` for the *kecom* and *internal* values. + +Restrictions +"""""""""""" + + +The *com* and *bias* keywords cannot be used together. + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`fix ave/chunk temp ` + +Default +""""""" + +The option defaults are com no, no bias, adof = dimensionality of the +system (2 or 3), and cdof = 0.0. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_com.txt b/doc/_sources/compute_temp_com.txt new file mode 100644 index 0000000000..63fef44bcd --- /dev/null +++ b/doc/_sources/compute_temp_com.txt @@ -0,0 +1,98 @@ +.. index:: compute temp/com + +compute temp/com command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/com + +* ID, group-ID are documented in :doc:`compute ` command +* temp/com = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all temp/com + compute myTemp mobile temp/com + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms, after subtracting out the center-of-mass velocity of the group. +This is useful if the group is expected to have a non-zero net +velocity for some reason. A compute of this style can be used by any +command that computes a temperature, +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. + +After the center-of-mass velocity has been subtracted from each atom, +the temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = 2 or 3 = dimensionality of the simulation, N = number of atoms +in the group, k = Boltzmann constant, and T = temperature. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +The removal of the center-of-mass velocity by this fix is essentially +computing the temperature after a "bias" has been removed from the +velocity of the atoms. If this compute is used with a fix command +that performs thermostatting then this bias will be subtracted from +each atom, thermostatting of the remaining thermal velocity will be +performed, and the bias will be added back in. Thermostatting fixes +that work in this way include :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix temp/berendsen `, and :doc:`fix langevin `. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as :doc:`fix shake ` and +:doc:`fix rigid `. This means the temperature of groups of +atoms that include these constraints will be computed correctly. If +needed, the subtracted degrees-of-freedom can be altered using the +*extra* option of the :doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute temp ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_cs.txt b/doc/_sources/compute_temp_cs.txt new file mode 100644 index 0000000000..c9eeedf0d4 --- /dev/null +++ b/doc/_sources/compute_temp_cs.txt @@ -0,0 +1,128 @@ +.. index:: compute temp/cs + +compute temp/cs command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/cs group1 group2 + +* ID, group-ID are documented in :doc:`compute ` command +* temp/cs = style name of this compute command +* group1 = group-ID of either cores or shells +* group2 = group-ID of either shells or cores + +Examples +"""""""" + +.. parsed-literal:: + + compute oxygen_c-s all temp/cs O_core O_shell + compute core_shells all temp/cs cores shells + +Description +""""""""""" + +Define a computation that calculates the temperature of a system based +on the center-of-mass velocity of atom pairs that are bonded to each +other. This compute is designed to be used with the adiabatic +core/shell model of :ref:`(Mitchell and Finchham) `. See +:ref:`Section_howto 25 ` of the manual for an +overview of the model as implemented in LAMMPS. Specifically, this +compute enables correct temperature calculation and thermostatting of +core/shell pairs where it is desirable for the internal degrees of +freedom of the core/shell pairs to not be influenced by a thermostat. +A compute of this style can be used by any command that computes a +temperature via :doc:`fix_modify ` e.g. :doc:`fix temp/rescale `, :doc:`fix npt `, etc. + +Note that this compute does not require all ions to be polarized, +hence defined as core/shell pairs. One can mix core/shell pairs and +ions without a satellite particle if desired. The compute will +consider the non-polarized ions according to the physical system. + +For this compute, core and shell particles are specified by two +respective group IDs, which can be defined using the +:doc:`group ` command. The number of atoms in the two groups +must be the same and there should be one bond defined between a pair +of atoms in the two groups. Non-polarized ions which might also be +included in the treated system should not be included into either of +these groups, they are taken into account by the *group-ID* (2nd +argument) of the compute. + +The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = 2 or 3 = dimensionality of the simulation, N = number of atoms +in the group, k = Boltzmann constant, and T = temperature. Note that +the velocity of each core or shell atom used in the KE calculation is +the velocity of the center-of-mass (COM) of the core/shell pair the +atom is part of. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. In contrast to the temperature, the velocity of +each core or shell atom is taken individually. + +The change this fix makes to core/shell atom velocities is essentially +computing the temperature after a "bias" has been removed from the +velocity of the atoms. This "bias" is the velocity of the atom +relative to the COM velocity of the core/shell pair. If this compute +is used with a fix command that performs thermostatting then this bias +will be subtracted from each atom, thermostatting of the remaining COM +velocity will be performed, and the bias will be added back in. This +means the thermostating will effectively be performed on the +core/shell pairs, instead of on the individual core and shell atoms. +Thermostatting fixes that work in this way include :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix temp/berendsen `, and :doc:`fix langevin `. + +The internal energy of core/shell pairs can be calculated by the +:doc:`compute temp/chunk ` command, if chunks are +defined as core/shell pairs. See :ref:`Section_howto 25 ` for more discussion on how to do this. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +The number of core/shell pairs contributing to the temperature is +assumed to be constant for the duration of the run. No fixes should +be used which generate new molecules or atoms during a simulation. + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`compute temp/chunk ` + +**Default:** none + + +---------- + + +.. _MitchellFinchham: + + + +**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter, +5, 1031-1038 (1993). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_deform.txt b/doc/_sources/compute_temp_deform.txt new file mode 100644 index 0000000000..54eb1dba76 --- /dev/null +++ b/doc/_sources/compute_temp_deform.txt @@ -0,0 +1,140 @@ +.. index:: compute temp/deform + +compute temp/deform command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/deform + +* ID, group-ID are documented in :doc:`compute ` command +* temp/deform = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute myTemp all temp/deform + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms, after subtracting out a streaming velocity induced by the +simulation box changing size and/or shape, for example in a +non-equilibrium MD (NEMD) simulation. The size/shape change is +induced by use of the :doc:`fix deform ` command. A compute +of this style is created by the :doc:`fix nvt/sllod ` +command to compute the thermal temperature of atoms for thermostatting +purposes. A compute of this style can also be used by any command +that computes a temperature, e.g. :doc:`thermo_modify `, +:doc:`fix temp/rescale `, :doc:`fix npt `, etc. + +The deformation fix changes the box size and/or shape over time, so +each atom in the simulation box can be thought of as having a +"streaming" velocity. For example, if the box is being sheared in x, +relative to y, then atoms at the bottom of the box (low y) have a +small x velocity, while atoms at the top of the box (hi y) have a +large x velocity. This position-dependent streaming velocity is +subtracted from each atom's actual velocity to yield a thermal +velocity which is used to compute the temperature. + +.. note:: + + :doc:`Fix deform ` has an option for remapping either + atom coordinates or velocities to the changing simulation box. When + using this compute in conjunction with a deforming box, fix deform + should NOT remap atom positions, but rather should let atoms respond + to the changing box by adjusting their own velocities (or let :doc:`fix deform ` remap the atom velocities, see it's remap + option). If fix deform does remap atom positions, then they appear to + move with the box but their velocity is not changed, and thus they do + NOT have the streaming velocity assumed by this compute. LAMMPS will + warn you if fix deform is defined and its remap setting is not + consistent with this compute. + +After the streaming velocity has been subtracted from each atom, the +temperature is calculated by the formula KE = dim/2 N k T, where KE = +total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 +or 3 = dimensionality of the simulation, N = number of atoms in the +group, k = Boltzmann constant, and T = temperature. Note that v in +the kinetic energy formula is the atom's thermal velocity. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +The removal of the box deformation velocity component by this fix is +essentially computing the temperature after a "bias" has been removed +from the velocity of the atoms. If this compute is used with a fix +command that performs thermostatting then this bias will be subtracted +from each atom, thermostatting of the remaining thermal velocity will +be performed, and the bias will be added back in. Thermostatting +fixes that work in this way include :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix temp/berendsen `, and :doc:`fix langevin `. + +.. note:: + + The temperature calculated by this compute is only accurate if + the atoms are indeed moving with a stream velocity profile that + matches the box deformation. If not, then the compute will subtract + off an incorrect stream velocity, yielding a bogus thermal + temperature. You should NOT assume that your atoms are streaming at + the same rate the box is deforming. Rather, you should monitor their + velocity profile, e.g. via the :doc:`fix ave/spatial ` + command. And you can compare the results of this compute to :doc:`compute temp/profile `, which actually calculates the + stream profile before subtracting it. If the two computes do not give + roughly the same temperature, then your atoms are not streaming + consistent with the box deformation. See the :doc:`fix deform ` command for more details on ways to get atoms + to stream consistently with the box deformation. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as :doc:`fix shake ` and +:doc:`fix rigid `. This means the temperature of groups of +atoms that include these constraints will be computed correctly. If +needed, the subtracted degrees-of-freedom can be altered using the +*extra* option of the :doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute temp/ramp `, :doc:`compute temp/profile `, :doc:`fix deform `, +:doc:`fix nvt/sllod ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_deform_eff.txt b/doc/_sources/compute_temp_deform_eff.txt new file mode 100644 index 0000000000..5eaa0c4c07 --- /dev/null +++ b/doc/_sources/compute_temp_deform_eff.txt @@ -0,0 +1,77 @@ +.. index:: compute temp/deform/eff + +compute temp/deform/eff command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/deform/eff + +* ID, group-ID are documented in :doc:`compute ` command +* temp/deform/eff = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute myTemp all temp/deform/eff + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +nuclei and electrons in the :doc:`electron force field ` +model, after subtracting out a streaming velocity induced by the +simulation box changing size and/or shape, for example in a +non-equilibrium MD (NEMD) simulation. The size/shape change is +induced by use of the :doc:`fix deform/eff ` command. A +compute of this style is created by the :doc:`fix nvt/sllod/eff ` command to compute the thermal +temperature of atoms for thermostatting purposes. A compute of this +style can also be used by any command that computes a temperature, +e.g. :doc:`thermo_modify `, :doc:`fix npt/eff `, +etc. + +The calculation performed by this compute is exactly like that +described by the :doc:`compute temp/deform ` +command, except that the formula for the temperature includes the +radial electron velocity contributions, as discussed by the :doc:`compute temp/eff ` command. Note that only the +translational degrees of freedom for each nuclei or electron are +affected by the streaming velocity adjustment. The radial velocity +component of the electrons is not affected. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute temp/ramp `, :doc:`fix deform/eff `, :doc:`fix nvt/sllod/eff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_drude.txt b/doc/_sources/compute_temp_drude.txt new file mode 100644 index 0000000000..24a911d32e --- /dev/null +++ b/doc/_sources/compute_temp_drude.txt @@ -0,0 +1,85 @@ +.. index:: compute temp/drude + +compute temp/drude command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/drude + +* ID, group-ID are documented in :doc:`compute ` command +* temp/drude = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute TDRUDE all temp/drude + +Description +""""""""""" + +Define a computation that calculates the temperatures of core-Drude +pairs. This compute is designed to be used with the +:doc:`thermalized Drude oscillator model `. Polarizable +models in LAMMPS are described in :ref:`this Section `. + +Drude oscillators consist of a core particle and a Drude particle +connected by a harmonic bond, and the relative motion of these Drude +oscillators is usually maintained cold by a specific thermostat that +acts on the relative motion of the core-Drude particle +pairs. Therefore, because LAMMPS considers Drude particles as normal +atoms in its default temperature compute (:doc:`compute temp ` command), the reduced temperature of the +core-Drude particle pairs is not calculated correctly. + +By contrast, this compute calculates the temperature of the cores +using center-of-mass velocities of the core-Drude pairs, and the +reduced temperature of the Drude particles using the relative +velocities of the Drude particles with respect to their cores. +Non-polarizable atoms are considered as cores. Their velocities +contribute to the temperature of the cores. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6, which can be accessed by indices 1-6, whose components +are + +1. temperature of the centers of mass (temperature units) +2. temperature of the dipoles (temperature units) +3. number of degrees of freedom of the centers of mass +4. number of degrees of freedom of the dipoles +5. kinetic energy of the centers of mass (energy units) +6. kinetic energy of the dipoles (energy units) + +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +Both the scalar value and the first two values of the vector +calculated by this compute are "intensive". The other 4 vector values +are "extensive". + +Restrictions +"""""""""""" + + +The number of degrees of freedom contributing to the temperature is +assumed to be constant for the duration of the run unless the +*fix_modify* command sets the option *dynamic yes*. + +Related commands +"""""""""""""""" + +:doc:`fix drude `, :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`pair_style thole `, :doc:`compute temp ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_eff.txt b/doc/_sources/compute_temp_eff.txt new file mode 100644 index 0000000000..81ba026c13 --- /dev/null +++ b/doc/_sources/compute_temp_eff.txt @@ -0,0 +1,105 @@ +.. index:: compute temp/eff + +compute temp/eff command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/eff + +* ID, group-ID are documented in :doc:`compute ` command +* temp/eff = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all temp/eff + compute myTemp mobile temp/eff + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +nuclei and electrons in the :doc:`electron force field ` +model. A compute of this style can be used by commands that compute a +temperature, e.g. :doc:`thermo_modify `, :doc:`fix npt/eff `, etc. + +The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for +nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s +includes the radial electron velocity contributions), dim = 2 or 3 = +dimensionality of the simulation, N = number of atoms (only total +number of nuclei in the eFF (see the :doc:`pair_eff ` +command) in the group, k = Boltzmann constant, and T = temperature. +This expression is summed over all nuclear and electronic degrees of +freedom, essentially by setting the kinetic contribution to the heat +capacity to 3/2k (where only nuclei contribute). This subtlety is +valid for temperatures well below the Fermi temperature, which for +densities two to five times the density of liquid H2 ranges from +86,000 to 170,000 K. + +.. note:: + + For eFF models, in order to override the default temperature + reported by LAMMPS in the thermodynamic quantities reported via the + :doc:`thermo ` command, the user should apply a + :doc:`thermo_modify ` command, as shown in the following + example: + +.. parsed-literal:: + + compute effTemp all temp/eff + thermo_style custom step etotal pe ke temp press + thermo_modify temp effTemp + +A 6-component kinetic energy tensor is also calculated by this compute +for use in the computation of a pressure tensor. The formula for the +components of the tensor is the same as the above formula, except that +v^2 is replaced by vx * vy for the xy component, etc. For the eFF, +again, the radial electronic velocities are also considered. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as :doc:`fix shake ` and +:doc:`fix rigid `. This means the temperature of groups of +atoms that include these constraints will be computed correctly. If +needed, the subtracted degrees-of-freedom can be altered using the +*extra* option of the :doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +**Output info:** + +The scalar value calculated by this compute is "intensive", meaning it +is independent of the number of atoms in the simulation. The vector +values are "extensive", meaning they scale with the number of atoms in +the simulation. + +Restrictions +"""""""""""" + + +This compute is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute temp/partial `, :doc:`compute temp/region `, :doc:`compute pressure ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_partial.txt b/doc/_sources/compute_temp_partial.txt new file mode 100644 index 0000000000..269ddcc80b --- /dev/null +++ b/doc/_sources/compute_temp_partial.txt @@ -0,0 +1,128 @@ +.. index:: compute temp/partial + +compute temp/partial command +============================ + +compute temp/partial/cuda command +================================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/partial xflag yflag zflag + +* ID, group-ID are documented in :doc:`compute ` command +* temp/partial = style name of this compute command +* xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension + +Examples +"""""""" + +.. parsed-literal:: + + compute newT flow temp/partial 1 1 0 + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms, after excluding one or more velocity components. A compute of +this style can be used by any command that computes a temperature, +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. + +The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = dimensionality of the simulation, N = number of atoms in the +group, k = Boltzmann constant, and T = temperature. The calculation +of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag = +0. The dim parameter is adjusted to give the correct number of +degrees of freedom. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the calculation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +The removal of velocity components by this fix is essentially +computing the temperature after a "bias" has been removed from the +velocity of the atoms. If this compute is used with a fix command +that performs thermostatting then this bias will be subtracted from +each atom, thermostatting of the remaining thermal velocity will be +performed, and the bias will be added back in. Thermostatting fixes +that work in this way include :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix temp/berendsen `, and :doc:`fix langevin `. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as :doc:`fix shake ` and +:doc:`fix rigid `. This means the temperature of groups of +atoms that include these constraints will be computed correctly. If +needed, the subtracted degrees-of-freedom can be altered using the +*extra* option of the :doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`compute temp/region `, :doc:`compute pressure ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_profile.txt b/doc/_sources/compute_temp_profile.txt new file mode 100644 index 0000000000..7887745921 --- /dev/null +++ b/doc/_sources/compute_temp_profile.txt @@ -0,0 +1,198 @@ +.. index:: compute temp/profile + +compute temp/profile command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/profile xflag yflag zflag binstyle args + +* ID, group-ID are documented in :doc:`compute ` command +* temp/profile = style name of this compute command +* xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension +* binstyle = *x* or *y* or *z* or *xy* or *yz* or *xz* or *xyz* +.. parsed-literal:: + + *x* arg = Nx + *y* arg = Ny + *z* arg = Nz + *xy* args = Nx Ny + *yz* args = Ny Nz + *xz* args = Nx Nz + *xyz* args = Nx Ny Nz + Nx,Ny,Nz = number of velocity bins in x,y,z dimensions + +* zero or more keyword/value pairs may be appended +* keyword = *out* +.. parsed-literal:: + + *out* value = *tensor* or *bin* + + + +Examples +"""""""" + +.. parsed-literal:: + + compute myTemp flow temp/profile 1 1 1 x 10 + compute myTemp flow temp/profile 1 1 1 x 10 out bin + compute myTemp flow temp/profile 0 1 1 xyz 20 20 20 + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms, after subtracting out a spatially-averaged center-of-mass +velocity field, before computing the kinetic energy. This can be +useful for thermostatting a collection of atoms undergoing a complex +flow, e.g. via a profile-unbiased thermostat (PUT) as described in +:ref:`(Evans) `. A compute of this style can be used by any command +that computes a temperature, e.g. :doc:`thermo_modify `, +:doc:`fix temp/rescale `, :doc:`fix npt `, etc. + +The *xflag*, *yflag*, *zflag* settings determine which components of +average velocity are subtracted out. + +The *binstyle* setting and its *Nx*, *Ny*, *Nz* arguments determine +how bins are setup to perform spatial averaging. "Bins" can be 1d +slabs, 2d pencils, or 3d bricks depending on which *binstyle* is used. +The simulation box is partitioned conceptually into *Nx* by *Ny* by +*Nz* bins. Depending on the *binstyle*, you may only specify one or +two of these values; the others are effectively set to 1 (no binning +in that dimension). For non-orthogonal (triclinic) simulation boxes, +the bins are "tilted" slabs or pencils or bricks that are parallel to +the tilted faces of the box. See the :doc:`region prism ` +command for a discussion of the geometry of tilted boxes in LAMMPS. + +When a temperature is computed, the center-of-mass velocity for the +set of atoms that are both in the compute group and in the same +spatial bin is calculated. This bias velocity is then subtracted from +the velocities of individual atoms in the bin to yield a thermal +velocity for each atom. Note that if there is only one atom in the +bin, its thermal velocity will thus be 0.0. + +After the spatially-averaged velocity field has been subtracted from +each atom, the temperature is calculated by the formula KE = (dim/2 N +- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of +atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the +simulation, N = number of atoms in the group, k = Boltzmann constant, +and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom +subtracted to adjust for the removal of the center-of-mass velocity in +each of Nx*Ny*Nz bins, as discussed in the :ref:`(Evans) ` paper. + +If the *out* keyword is used with a *tensor* value, which is the +default, a kinetic energy tensor, stored as a 6-element vector, is +also calculated by this compute for use in the computation of a +pressure tensor. The formula for the components of the tensor is the +same as the above formula, except that v^2 is replaced by vx*vy for +the xy component, etc. The 6 components of the vector are ordered xx, +yy, zz, xy, xz, yz. + +If the *out* keyword is used with a *bin* value, the count of atoms +and computed temperature for each bin are stored for output, as an +array of values, as described below. The temperature of each bin is +calculated as described above, where the bias velocity is subtracted +and only the remaining thermal velocity of atoms in the bin +contributes to the temperature. See the note below for how the +temperature is normalized by the degrees-of-freedom of atoms in the +bin. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +The removal of the spatially-averaged velocity field by this fix is +essentially computing the temperature after a "bias" has been removed +from the velocity of the atoms. If this compute is used with a fix +command that performs thermostatting then this bias will be subtracted +from each atom, thermostatting of the remaining thermal velocity will +be performed, and the bias will be added back in. Thermostatting +fixes that work in this way include :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix temp/berendsen `, and :doc:`fix langevin `. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as :doc:`fix shake ` and +:doc:`fix rigid `. This means the temperature of groups of +atoms that include these constraints will be computed correctly. If +needed, the subtracted degrees-of-freedom can be altered using the +*extra* option of the :doc:`compute_modify ` command. + +.. note:: + + When using the *out* keyword with a value of *bin*, the + calculated temperature for each bin does not include the + degrees-of-freedom adjustment described in the preceeding paragraph, + for fixes that constrain molecular motion. It does include the + adjustment due to the *extra* option, which is applied to each bin. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. Using this compute in conjunction with a +thermostatting fix, as explained there, will effectively implement a +profile-unbiased thermostat (PUT), as described in :ref:`(Evans) `. + +**Output info:** + +This compute calculates a global scalar (the temperature). Depending +on the setting of the *out* keyword, it also calculates a global +vector or array. For *out* = *tensor*, it calculates a vector of +length 6 (KE tensor), which can be accessed by indices 1-6. For *out* += *bin* it calculates a global array which has 2 columns and N rows, +where N is the number of bins. The first column contains the number +of atoms in that bin. The second contains the temperature of that +bin, calculated as described above. The ordering of rows in the array +is as follows. Bins in x vary fastest, then y, then z. Thus for a +10x10x10 3d array of bins, there will be 1000 rows. The bin with +indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10 ++ ix = 322, where the rows are numbered from 1 to 1000 and the bin +indices are numbered from 1 to 10 in each dimension. + +These values can be used by any command that uses global scalar or +vector or array values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". The array values are "intensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. The first column +of array values are counts; the values in the second column will be in +temperature :doc:`units `. + +Restrictions +"""""""""""" + + +You should not use too large a velocity-binning grid, especially in +3d. In the current implementation, the binned velocity averages are +summed across all processors, so this will be inefficient if the grid +is too large, and the operation is performed every timestep, as it +will be for most thermostats. + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`compute temp/ramp `, :doc:`compute temp/deform `, :doc:`compute pressure ` + +Default +""""""" + +The option default is out = tensor. + + +---------- + + +.. _Evans: + + + +**(Evans)** Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_ramp.txt b/doc/_sources/compute_temp_ramp.txt new file mode 100644 index 0000000000..1f0a09cbdd --- /dev/null +++ b/doc/_sources/compute_temp_ramp.txt @@ -0,0 +1,122 @@ +.. index:: compute temp/ramp + +compute temp/ramp command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/ramp vdim vlo vhi dim clo chi keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* temp/ramp = style name of this compute command +* vdim = *vx* or *vy* or *vz* +* vlo,vhi = subtract velocities between vlo and vhi (velocity units) +* dim = *x* or *y* or *z* +* clo,chi = lower and upper bound of domain to subtract from (distance units) +* zero or more keyword/value pairs may be appended +* keyword = *units* + +.. parsed-literal:: + + *units* value = *lattice* or *box* + +Examples +"""""""" + +.. parsed-literal:: + + compute 2nd middle temp/ramp vx 0 8 y 2 12 units lattice + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms, after subtracting out an ramped velocity profile before +computing the kinetic energy. A compute of this style can be used by +any command that computes a temperature, +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. + +The meaning of the arguments for this command which define the +velocity ramp are the same as for the :doc:`velocity ramp ` +command which was presumably used to impose the velocity. + +After the ramp velocity has been subtracted from the specified +dimension for each atom, the temperature is calculated by the formula +KE = dim/2 N k T, where KE = total kinetic energy of the group of +atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the +simulation, N = number of atoms in the group, k = Boltzmann constant, +and T = temperature. + +The *units* keyword determines the meaning of the distance units used +for coordinates (c1,c2) and velocities (vlo,vhi). A *box* value +selects standard distance units as defined by the :doc:`units ` +command, e.g. Angstroms for units = real or metal. A *lattice* value +means the distance units are in lattice spacings; e.g. velocity = +lattice spacings / tau. The :doc:`lattice ` command must have +been previously used to define the lattice spacing. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +The removal of the ramped velocity component by this fix is +essentially computing the temperature after a "bias" has been removed +from the velocity of the atoms. If this compute is used with a fix +command that performs thermostatting then this bias will be subtracted +from each atom, thermostatting of the remaining thermal velocity will +be performed, and the bias will be added back in. Thermostatting +fixes that work in this way include :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix temp/berendsen `, and :doc:`fix langevin `. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as :doc:`fix shake ` and +:doc:`fix rigid `. This means the temperature of groups of +atoms that include these constraints will be computed correctly. If +needed, the subtracted degrees-of-freedom can be altered using the +*extra* option of the :doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`compute temp/profie `, :doc:`compute temp/deform `, :doc:`compute pressure ` + +Default +""""""" + +The option default is units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_region.txt b/doc/_sources/compute_temp_region.txt new file mode 100644 index 0000000000..6a09213634 --- /dev/null +++ b/doc/_sources/compute_temp_region.txt @@ -0,0 +1,112 @@ +.. index:: compute temp/region + +compute temp/region command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/region region-ID + +* ID, group-ID are documented in :doc:`compute ` command +* temp/region = style name of this compute command +* region-ID = ID of region to use for choosing atoms + +Examples +"""""""" + +.. parsed-literal:: + + compute mine flow temp/region boundary + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms in a geometric region. This can be useful for thermostatting +one portion of the simulation box. E.g. a McDLT simulation where one +side is cooled, and the other side is heated. A compute of this style +can be used by any command that computes a temperature, +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, etc. + +Note that a *region*-style temperature can be used to thermostat with +:doc:`fix temp/rescale ` or :doc:`fix langevin `, but should probably not be used with +Nose/Hoover style fixes (:doc:`fix nvt `, :doc:`fix npt `, or :doc:`fix nph `), if the +degrees-of-freedom included in the computed T varies with time. + +The temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = 2 or 3 = dimensionality of the simulation, N = number of atoms +in both the group and region, k = Boltzmann constant, and T = +temperature. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. + +The number of atoms contributing to the temperature is calculated each +time the temperature is evaluated since it is assumed atoms can +enter/leave the region. Thus there is no need to use the *dynamic* +option of the :doc:`compute_modify ` command for this +compute style. + +The removal of atoms outside the region by this fix is essentially +computing the temperature after a "bias" has been removed, which in +this case is the velocity of any atoms outside the region. If this +compute is used with a fix command that performs thermostatting then +this bias will be subtracted from each atom, thermostatting of the +remaining thermal velocity will be performed, and the bias will be +added back in. Thermostatting fixes that work in this way include +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix temp/berendsen `, and :doc:`fix langevin `. This means that when this compute +is used to calculate the temperature for any of the thermostatting +fixes via the :doc:`fix modify temp ` command, the thermostat +will operate only on atoms that are currently in the geometric +region. + +Unlike other compute styles that calculate temperature, this compute +does not subtract out degrees-of-freedom due to fixes that constrain +motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This is because those degrees of freedom +(e.g. a constrained bond) could apply to sets of atoms that straddle +the region boundary, and hence the concept is somewhat ill-defined. +If needed the number of subtracted degrees-of-freedom can be set +explicitly using the *extra* option of the +:doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`compute pressure ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_region_eff.txt b/doc/_sources/compute_temp_region_eff.txt new file mode 100644 index 0000000000..d0a0bac432 --- /dev/null +++ b/doc/_sources/compute_temp_region_eff.txt @@ -0,0 +1,69 @@ +.. index:: compute temp/region/eff + +compute temp/region/eff command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/region/eff region-ID + +* ID, group-ID are documented in :doc:`compute ` command +* temp/region/eff = style name of this compute command +* region-ID = ID of region to use for choosing atoms + +Examples +"""""""" + +.. parsed-literal:: + + compute mine flow temp/region/eff boundary + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +nuclei and electrons in the :doc:`electron force field ` +model, within a geometric region using the electron force field. A +compute of this style can be used by commands that compute a +temperature, e.g. :doc:`thermo_modify `. + +The operation of this compute is exactly like that described by the +:doc:`compute temp/region ` command, except that +the formula for the temperature itself includes the radial electron +velocity contributions, as discussed by the :doc:`compute temp/eff ` command. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute temp/region `, :doc:`compute temp/eff `, :doc:`compute pressure ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_rotate.txt b/doc/_sources/compute_temp_rotate.txt new file mode 100644 index 0000000000..65803d96dd --- /dev/null +++ b/doc/_sources/compute_temp_rotate.txt @@ -0,0 +1,100 @@ +.. index:: compute temp/rotate + +compute temp/rotate command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/rotate + +* ID, group-ID are documented in :doc:`compute ` command +* temp/rotate = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute Tbead bead temp/rotate + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +atoms, after subtracting out the center-of-mass velocity and angular velocity of the group. +This is useful if the group is expected to have a non-zero net +velocity and/or global rotation motion for some reason. A compute of this style can be used by any +command that computes a temperature, +e.g. :doc:`thermo_modify `, :doc:`fix temp/rescale `, :doc:`fix npt `, etc. + +After the center-of-mass velocity and angular velocity has been subtracted from each atom, +the temperature is calculated by the formula KE = dim/2 N k T, where +KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), +dim = 2 or 3 = dimensionality of the simulation, N = number of atoms +in the group, k = Boltzmann constant, and T = temperature. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute for use in the computation of a pressure +tensor. The formula for the components of the tensor is the same as +the above formula, except that v^2 is replaced by vx*vy for the xy +component, etc. The 6 components of the vector are ordered xx, yy, +zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +The removal of the center-of-mass velocity and angular velocity by this fix is essentially +computing the temperature after a "bias" has been removed from the +velocity of the atoms. If this compute is used with a fix command +that performs thermostatting then this bias will be subtracted from +each atom, thermostatting of the remaining thermal velocity will be +performed, and the bias will be added back in. Thermostatting fixes +that work in this way include :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix temp/berendsen `, and :doc:`fix langevin `. + +This compute subtracts out degrees-of-freedom due to fixes that +constrain molecular motion, such as :doc:`fix shake ` and +:doc:`fix rigid `. This means the temperature of groups of +atoms that include these constraints will be computed correctly. If +needed, the subtracted degrees-of-freedom can be altered using the +*extra* option of the :doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute temp ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_temp_sphere.txt b/doc/_sources/compute_temp_sphere.txt new file mode 100644 index 0000000000..d95d17b889 --- /dev/null +++ b/doc/_sources/compute_temp_sphere.txt @@ -0,0 +1,156 @@ +.. index:: compute temp/sphere + +compute temp/sphere command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID temp/sphere keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* temp/sphere = style name of this compute command +* zero or more keyword/value pairs may be appended +* keyword = *bias* or *dof* +.. parsed-literal:: + + *bias* value = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias + *dof* value = *all* or *rotate* + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all temp/sphere + compute myTemp mobile temp/sphere bias tempCOM + compute myTemp mobile temp/sphere dof rotate + +Description +""""""""""" + +Define a computation that calculates the temperature of a group of +spherical particles, including a contribution from both their +translational and rotational kinetic energy. This differs from the +usual :doc:`compute temp ` command, which assumes point +particles with only translational kinetic energy. + +Both point and finite-size particles can be included in the group. +Point particles do not rotate, so they have only 3 translational +degrees of freedom. For 3d spherical particles, each has 6 degrees of +freedom (3 translational, 3 rotational). For 2d spherical particles, +each has 3 degrees of freedom (2 translational, 1 rotational). + +.. note:: + + This choice for degrees of freedom (dof) assumes that all + finite-size spherical particles in your model will freely rotate, + sampling all their rotational dof. It is possible to use a + combination of interaction potentials and fixes that induce no torque + or otherwise constrain some of all of your particles so that this is + not the case. Then there are less dof and you should use the + :doc:`compute_modify extra ` command to adjust the dof + accordingly. + +The translational kinetic energy is computed the same as is described +by the :doc:`compute temp ` command. The rotational +kinetic energy is computed as 1/2 I w^2, where I is the moment of +inertia for a sphere and w is the particle's angular velocity. + +.. note:: + + For :doc:`2d models `, particles are treated as + spheres, not disks, meaning their moment of inertia will be the same + as in 3d. + +A kinetic energy tensor, stored as a 6-element vector, is also +calculated by this compute. The formula for the components of the +tensor is the same as the above formulas, except that v^2 and w^2 are +replaced by vx*vy and wx*wy for the xy component. The 6 components of +the vector are ordered xx, yy, zz, xy, xz, yz. + +The number of atoms contributing to the temperature is assumed to be +constant for the duration of the run; use the *dynamic* option of the +:doc:`compute_modify ` command if this is not the case. + +This compute subtracts out translational degrees-of-freedom due to +fixes that constrain molecular motion, such as :doc:`fix shake ` and :doc:`fix rigid `. This means the +temperature of groups of atoms that include these constraints will be +computed correctly. If needed, the subtracted degrees-of-freedom can +be altered using the *extra* option of the +:doc:`compute_modify ` command. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + + +---------- + + +The keyword/value option pairs are used in the following ways. + +For the *bias* keyword, *bias-ID* refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This allows +compute temp/sphere to compute its thermal temperature after the +translational kinetic energy components have been altered in a +prescribed way, e.g. to remove a flow velocity profile. Thermostats +that use this compute will work with this bias term. See the doc +pages for individual computes that calculate a temperature and the doc +pages for fixes that perform thermostatting for more details. + +For the *dof* keyword, a setting of *all* calculates a temperature +that includes both translational and rotational degrees of freedom. A +setting of *rotate* calculates a temperature that includes only +rotational degrees of freedom. + + +---------- + + +**Output info:** + +This compute calculates a global scalar (the temperature) and a global +vector of length 6 (KE tensor), which can be accessed by indices 1-6. +These values can be used by any command that uses global scalar or +vector values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "intensive". The +vector values are "extensive". + +The scalar value will be in temperature :doc:`units `. The +vector values will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This fix requires that atoms store torque and angular velocity (omega) +and a radius as defined by the :doc:`atom_style sphere ` +command. + +All particles in the group must be finite-size spheres, or point +particles with radius = 0.0. + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`compute temp/asphere ` + +Default +""""""" + +The option defaults are no bias and dof = all. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_ti.txt b/doc/_sources/compute_ti.txt new file mode 100644 index 0000000000..4da45a5e6a --- /dev/null +++ b/doc/_sources/compute_ti.txt @@ -0,0 +1,157 @@ +.. index:: compute ti + +compute ti command +================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group ti keyword args ... + +* ID, group-ID are documented in :doc:`compute ` command +* ti = style name of this compute command +* one or more attribute/arg pairs may be appended +* keyword = pair style (lj/cut, gauss, born, etc) or *tail* or *kspace* +.. parsed-literal:: + + pair style args = atype v_name1 v_name2 + atype = atom type (see asterisk form below) + v_name1 = variable with name1 that is energy scale factor and function of lambda + v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda + *tail* args = atype v_name1 v_name2 + atype = atom type (see asterisk form below) + v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda + v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda + *kspace* args = atype v_name1 v_name2 + atype = atom type (see asterisk form below) + v_name1 = variable with name1 that is K-Space scale factor and function of lambda + v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks + compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks + +Description +""""""""""" + +Define a computation that calculates the derivative of the interaction +potential with respect to *lambda*, the coupling parameter used in a +thermodynamic integration. This derivative can be used to infer a +free energy difference resulting from an alchemical simulation, as +described in :ref:`Eike `. + +Typically this compute will be used in conjunction with the :doc:`fix adapt ` command which can perform alchemical +transformations by adusting the strength of an interaction potential +as a simulation runs, as defined by one or more +:doc:`pair_style ` or :doc:`kspace_style ` +commands. This scaling is done via a prefactor on the energy, forces, +virial calculated by the pair or K-Space style. The prefactor is +often a function of a *lambda* parameter which may be adjusted from 0 +to 1 (or vice versa) over the course of a :doc:`run `. The +time-dependent adjustment is what the :doc:`fix adapt ` +command does. + +Assume that the unscaled energy of a pair_style or kspace_style is +given by U. Then the scaled energy is + +.. parsed-literal:: + + Us = f(lambda) U + +where f() is some function of lambda. What this compute calculates is + +.. parsed-literal:: + + dUs / d(lambda) = U df(lambda)/dlambda = Us / f(lambda) df(lambda)/dlambda + +which is the derivative of the system's scaled potential energy Us +with respect to *lambda*. + +To perform this calculation, you provide one or more atom types as +*atype*. *Atype* can be specified in one of two ways. An explicit +numeric values can be used, as in the 1st example above. Or a +wildcard asterisk can be used in place of or in conjunction with the +*atype* argument to select multiple atom types. This takes the form +"*" or "*n" or "n*" or "m*n". If N = the number of atom types, then +an asterisk with no numeric values means all types from 1 to N. A +leading asterisk means all types from 1 to n (inclusive). A trailing +asterisk means all types from n to N (inclusive). A middle asterisk +means all types from m to n (inclusive). + +You also specify two functions, as :doc:`equal-style variables `. The first is specified as *v_name1*, where +*name1* is the name of the variable, and is f(lambda) in the notation +above. The second is specified as *v_name2*, where *name2* is the +name of the variable, and is df(lambda) / dlambda in the notation +above. I.e. it is the analytic derivative of f() with respect to +lambda. Note that the *name1* variable is also typically given as an +argument to the :doc:`fix adapt ` command. + +An alchemical simulation may use several pair potentials together, +invoked via the :doc:`pair_style hybrid or hybrid/overlay ` +command. The total dUs/dlambda for the overall system is calculated +as the sum of each contributing term as listed by the keywords in the +compute ti command. Individual pair potentials can be listed, which +will be sub-styles in the hybrid case. You can also include a K-space +term via the *kspace* keyword. You can also include a pairwise +long-range tail correction to the energy via the *tail* keyword. + +For each term you can specify a different (or the same) scale factor +by the two variables that you list. Again, these will typically +correspond toe the scale factors applied to these various potentials +and the K-Space contribution via the :doc:`fix_adapt ` +command. + +More details about the exact functional forms for the computation of +du/dl can be found in the paper by :ref:`Eike `. + + +---------- + + +**Output info:** + +This compute calculates a global scalar, namely dUs/dlambda. This +value can be used by any command that uses a global scalar value from +a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The scalar value calculated by this compute is "extensive". + +The scalar value will be in energy :doc:`units `. + +Restrictions +"""""""""""" + + +This compute is part of the MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix adapt ` + +**Default:** none + + +---------- + + +.. _Eike: + + + +**(Eike)** Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_torque_chunk.txt b/doc/_sources/compute_torque_chunk.txt new file mode 100644 index 0000000000..13a1106bae --- /dev/null +++ b/doc/_sources/compute_torque_chunk.txt @@ -0,0 +1,96 @@ +.. index:: compute torque/chunk + +compute torque/chunk command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID torque/chunk chunkID + +* ID, group-ID are documented in :doc:`compute ` command +* torque/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 fluid torque/chunk molchunk + +Description +""""""""""" + +Define a computation that calculates the torque on multiple chunks of +atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the 3 components of the torque vector for eqch +chunk, due to the forces on the individual atoms in the chunk around +the center-of-mass of the chunk. The calculation includes all effects +due to atoms passing thru periodic boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The :doc:`compute chunk/atom ` command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +.. note:: + + The coordinates of an atom contribute to the chunk's torque in + "unwrapped" form, by using the image flags associated with each atom. + See the :doc:`dump custom ` command for a discussion of + "unwrapped" coordinates. See the Atoms section of the + :doc:`read_data ` command for a discussion of image flags and + how they are set for each atom. You can reset the image flags + (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + +The simplest way to output the results of the compute torque/chunk +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all torque/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +**Output info:** + +This compute calculates a global array where the number of rows = the +number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = +3 for the 3 xyz components of the torque for each chunk. These values +can be accessed by any command that uses global array values from a +compute as input. See :ref:`Section_howto 15 ` +for an overview of LAMMPS output options. + +The array values are "intensive". The array values will be in +force-distance :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`variable torque() function ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_vacf.txt b/doc/_sources/compute_vacf.txt new file mode 100644 index 0000000000..2065562b4a --- /dev/null +++ b/doc/_sources/compute_vacf.txt @@ -0,0 +1,84 @@ +.. index:: compute vacf + +compute vacf command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID vacf + +* ID, group-ID are documented in :doc:`compute ` command +* vacf = style name of this compute command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all vacf + compute 1 upper vacf + +Description +""""""""""" + +Define a computation that calculates the velocity auto-correlation +function (VACF), averaged over a group of atoms. Each atom's +contribution to the VACF is its current velocity vector dotted into +its initial velocity vector at the time the compute was specified. + +A vector of four quantites is calculated by this compute. The first 3 +elements of the vector are vx * vx0 (and similarly for the y and z +components), summed and averaged over atoms in the group. Vx is the +current x-component of velocity for the atom, vx0 is the initial +x-component of velocity for the atom. The 4th element of the vector +is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and +averaged over atoms in the group. + +The integral of the VACF versus time is proportional to the diffusion +coefficient of the diffusing atoms. This can be computed in the +following manner, using the :doc:`variable trap() ` function: + +.. parsed-literal:: + + compute 2 all vacf + fix 5 all vector 1 c_2[4] + variable diff equal dt*trap(f_5) + thermo_style custom step v_diff + +.. note:: + + If you want the quantities calculated by this compute to be + continuous when running from a :doc:`restart file `, then + you should use the same ID for this compute, as in the original run. + This is so that the fix this compute creates to store per-atom + quantities will also have the same ID, and thus be initialized + correctly with time=0 atom velocities from the restart file. + +**Output info:** + +This compute calculates a global vector of length 4, which can be +accessed by indices 1-4 by any command that uses global vector values +from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. + +The vector values are "intensive". The vector values will be in +velocity^2 :doc:`units `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute msd ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_vcm_chunk.txt b/doc/_sources/compute_vcm_chunk.txt new file mode 100644 index 0000000000..5eb1749ac5 --- /dev/null +++ b/doc/_sources/compute_vcm_chunk.txt @@ -0,0 +1,83 @@ +.. index:: compute vcm/chunk + +compute vcm/chunk command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID vcm/chunk chunkID + +* ID, group-ID are documented in :doc:`compute ` command +* vcm/chunk = style name of this compute command +* chunkID = ID of :doc:`compute chunk/atom ` command + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 fluid vcm/chunk molchunk + +Description +""""""""""" + +Define a computation that calculates the center-of-mass velocity for +multiple chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the x,y,z components of the center-of-mass +velocity for each chunk. This is done by summing mass*velocity for +each atom in the chunk and dividing the sum by the total mass of the +chunk. + +Note that only atoms in the specified group contribute to the +calculation. The :doc:`compute chunk/atom ` command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +The simplest way to output the results of the compute vcm/chunk +calculation to a file is to use the :doc:`fix ave/time ` +command, for example: + +.. parsed-literal:: + + compute cc1 all chunk/atom molecule + compute myChunk all vcm/chunk cc1 + fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector + +**Output info:** + +This compute calculates a global array where the number of rows = the +number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = +3 for the x,y,z center-of-mass velocity coordinates of each chunk. +These values can be accessed by any command that uses global array +values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. + +The array values are "intensive". The array values will be in +velocity :doc:`units `. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_voronoi_atom.txt b/doc/_sources/compute_voronoi_atom.txt new file mode 100644 index 0000000000..16f1ecc9a0 --- /dev/null +++ b/doc/_sources/compute_voronoi_atom.txt @@ -0,0 +1,252 @@ +.. index:: compute voronoi/atom + +compute voronoi/atom command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID voronoi/atom keyword arg ... + +* ID, group-ID are documented in :doc:`compute ` command +* voronoi/atom = style name of this compute command +* zero or more keyword/value pairs may be appended +* keyword = *only_group* or *surface* or *radius* or *edge_histo* or *edge_threshold* + or *face_threshold* or *neighbors* or *peratom* +.. parsed-literal:: + + *only_group* = no arg + *occupation* = no arg + *surface* arg = sgroup-ID + sgroup-ID = compute the dividing surface between group-ID and sgroup-ID + this keyword adds a third column to the compute output + *radius* arg = v_r + v_r = radius atom style variable for a poly-disperse Voronoi tessellation + *edge_histo* arg = maxedge + maxedge = maximum number of Voronoi cell edges to be accounted in the histogram + *edge_threshold* arg = minlength + minlength = minimum length for an edge to be counted + *face_threshold* arg = minarea + minarea = minimum area for a face to be counted + *neighbors* value = *yes* or *no* = store list of all neighbors or no + *peratom* value = *yes* or *no* = per-atom quantities accessible or no + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all voronoi/atom + compute 2 precipitate voronoi/atom surface matrix + compute 3b precipitate voronoi/atom radius v_r + compute 4 solute voronoi/atom only_group + +.. parsed-literal:: + + compute 5 defects voronoi/atom occupation + +compute 6 all voronoi/atom neighbors yes + +Description +""""""""""" + +Define a computation that calculates the Voronoi tessellation of the +atoms in the simulation box. The tessellation is calculated using all +atoms in the simulation, but non-zero values are only stored for atoms +in the group. + +By default two per-atom quantities are calculated by this compute. +The first is the volume of the Voronoi cell around each atom. Any +point in an atom's Voronoi cell is closer to that atom than any other. +The second is the number of faces of the Voronoi cell. This is +equal to the number of nearest neighbors of the central atom, +plus any exterior faces (see note below). If the *peratom* keyword +is set to "no", the per-atom quantities are still calculated, +but they are not accessible. + + +---------- + + +If the *only_group* keyword is specified the tessellation is performed +only with respect to the atoms contained in the compute group. This is +equivalent to deleting all atoms not contained in the group prior to +evaluating the tessellation. + +If the *surface* keyword is specified a third quantity per atom is +computed: the Voronoi cell surface of the given atom. *surface* takes +a group ID as an argument. If a group other than *all* is specified, +only the Voronoi cell facets facing a neighbor atom from the specified +group are counted towards the surface area. + +In the example above, a precipitate embedded in a matrix, only atoms +at the surface of the precipitate will have non-zero surface area, and +only the outward facing facets of the Voronoi cells are counted (the +hull of the precipitate). The total surface area of the precipitate +can be obtained by running a "reduce sum" compute on c_2[3] + +If the *radius* keyword is specified with an atom style variable as +the argument, a poly-disperse Voronoi tessellation is +performed. Examples for radius variables are + +.. parsed-literal:: + + variable r1 atom (type==1)*0.1+(type==2)*0.4 + compute radius all property/atom radius + variable r2 atom c_radius + +Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms +and 0.4 units for type 2 atoms, and v_r2 accesses the radius property +present in atom_style sphere for granular models. + +The *edge_histo* keyword activates the compilation of a histogram of +number of edges on the faces of the Voronoi cells in the compute +group. The argument *maxedge* of the this keyword is the largest number +of edges on a single Voronoi cell face expected to occur in the +sample. This keyword adds the generation of a global vector with +*maxedge*+1 entries. The last entry in the vector contains the number of +faces with with more than *maxedge* edges. Since the polygon with the +smallest amount of edges is a triangle, entries 1 and 2 of the vector +will always be zero. + +The *edge_threshold* and *face_threshold* keywords allow the +suppression of edges below a given minimum length and faces below a +given minimum area. Ultra short edges and ultra small faces can occur +as artifacts of the Voronoi tessellation. These keywords will affect +the neighbor count and edge histogram outputs. + +If the *occupation* keyword is specified the tessellation is only +performed for the first invocation of the compute and then stored. +For all following invocations of the compute the number of atoms in +each Voronoi cell in the stored tessellation is counted. In this mode +the compute returns a per-atom array with 2 columns. The first column +is the number of atoms currently in the Voronoi volume defined by this +atom at the time of the first invocation of the compute (note that the +atom may have moved significantly). The second column contains the +total number of atoms sharing the Voronoi cell of the stored +tessellation at the location of the current atom. Numbers in column +one can be any positive integer including zero, while column two +values will always be greater than zero. Column one data can be used +to locate vacancies (the coordinates are given by the atom coordinates +at the time step when the compute was first invoked), while column two +data can be used to identify interstitial atoms. + +If the *neighbors* value is set to yes, then +this compute creates a local array with 3 columns. There +is one row for each face of each Voronoi cell. The +3 columns are the atom ID of the atom that owns the cell, +the atom ID of the atom in the neighboring cell +(or zero if the face is external), and the area of the face. +The array can be accessed by any command that +uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output +options. More specifically, the array can be accessed by a +:doc:`dump local ` command to write a file containing +all the Voronoi neighbors in a system: + +.. parsed-literal:: + + compute 6 all voronoi/atom neighbors yes + dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3] + +If the *face_threshold* keyword is used, then only faces +with areas greater than the threshold are stored. + + +---------- + + +The Voronoi calculation is performed by the freely available `Voro++ package `_, written by Chris Rycroft at UC Berkeley and LBL, +which must be installed on your system when building LAMMPS for use +with this compute. See instructions on obtaining and installing the +Voro++ software in the src/VORONOI/README file. + +.. _voronoi: http://math.lbl.gov/voro++ + + + +.. note:: + + The calculation of Voronoi volumes is performed by each + processor for the atoms it owns, and includes the effect of ghost + atoms stored by the processor. This assumes that the Voronoi cells of + owned atoms are not affected by atoms beyond the ghost atom cut-off + distance. This is usually a good assumption for liquid and solid + systems, but may lead to underestimation of Voronoi volumes in low + density systems. By default, the set of ghost atoms stored by each + processor is determined by the cutoff used for + :doc:`pair_style ` interactions. The cutoff can be set + explicitly via the :doc:`comm_modify cutoff ` command. The + Voronoi cells for atoms adjacent to empty regions will extend into + those regions up to the communication cutoff in x, y, or z. In that + situation, an exterior face is created at the cutoff distance normal + to the x, y, or z direction. For triclinic systems, the exterior face + is parallel to the corresponding reciprocal lattice vector. + +.. note:: + + The Voro++ package performs its calculation in 3d. This will + still work for a 2d LAMMPS simulation, provided all the atoms have the + same z coordinate. The Voronoi cell of each atom will be a columnar + polyhedron with constant cross-sectional area along the z direction + and two exterior faces at the top and bottom of the simulation box. If + the atoms do not all have the same z coordinate, then the columnar + cells will be accordingly distorted. The cross-sectional area of each + Voronoi cell can be obtained by dividing its volume by the z extent of + the simulation box. Note that you define the z extent of the + simulation box for 2d simulations when using the + :doc:`create_box ` or :doc:`read_data ` commands. + +**Output info:** + +By default, this compute calculates a per-atom array with 2 +columns. In regular dynamic tessellation mode the first column is the +Voronoi volume, the second is the neighbor count, as described above +(read above for the output data in case the *occupation* keyword is +specified). These values can be accessed by any command that uses +per-atom values from a compute as input. See :ref:`Section_howto 15 ` for an overview of LAMMPS output +options. If the *peratom* keyword is set to "no", the per-atom array +is still created, but it is not accessible. + +If the *edge_histo* keyword is used, then this compute generates a +global vector of length *maxedge*+1, containing a histogram of the +number of edges per face. + +If the *neighbors* value is set to yes, then this compute calculates a +local array with 3 columns. There is one row for each face of each +Voronoi cell. + +.. note:: + + Some LAMMPS commands such as the :doc:`compute reduce ` command can accept either a per-atom or + local quantity. If this compute produces both quantities, the command + may access the per-atom quantity, even if you want to access the local + quantity. This effect can be eliminated by using the *peratom* + keyword to turn off the production of the per-atom quantities. For + the default value *yes* both quantities are produced. For the value + *no*, only the local array is produced. + +The Voronoi cell volume will be in distance :doc:`units ` cubed. +The Voronoi face area will be in distance :doc:`units ` squared. + +Restrictions +"""""""""""" + + +This compute is part of the VORONOI package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`dump custom `, :doc:`dump local ` + +**Default:** *neighbors* no, *peratom* yes + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/compute_xrd.txt b/doc/_sources/compute_xrd.txt new file mode 100644 index 0000000000..3c8759c0ce --- /dev/null +++ b/doc/_sources/compute_xrd.txt @@ -0,0 +1,236 @@ +.. index:: compute xrd + +compute xrd command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID xrd lambda type1 type2 ... typeN keyword value ... + +* ID, group-ID are documented in :doc:`compute ` command +* xrd = style name of this compute command +* lambda = wavelength of incident radiation (length units) +* type1 type2 ... typeN = chemical symbol of each atom type (see valid options below) +* zero or more keyword/value pairs may be appended +* keyword = *2Theta* or *c* or *LP* or *manual* or *echo* +.. parsed-literal:: + + *2Theta* values = Min2Theta Max2Theta + Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore + (radians or degrees) + *c* values = c1 c2 c3 + c1,c2,c3 = parameters to adjust the spacing of the reciprocal + lattice nodes in the h, k, and l directions respectively + *LP* value = switch to apply Lorentz-polarization factor + 0/1 = off/on + *manual* = flag to use manual spacing of reciprocal lattice points + based on the values of the *c* parameters + *echo* = flag to provide extra output for debugging purposes + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo + compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual + +.. parsed-literal:: + + fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd + fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd + +.. parsed-literal:: + + +Description +""""""""""" + +Define a computation that calculates x-ray diffraction intensity as described +in :ref:`(Coleman) ` on a mesh of reciprocal lattice nodes defined +by the entire simulation domain (or manually) using a simulated radiation +of wavelength lambda. + +The x-ray diffraction intensity, I, at each reciprocal lattice point, k, +is computed from the structure factor, F, using the equations: + +.. image:: Eqs/compute_xrd1.jpg + :align: center + +.. image:: Eqs/compute_xrd2.jpg + :align: center + +.. image:: Eqs/compute_xrd3.jpg + :align: center + +.. image:: Eqs/compute_xrd4.jpg + :align: center + +Here, K is the location of the reciprocal lattice node, rj is the +position of each atom, fj are atomic scattering factors, LP is the +Lorentz-polarization factor, and theta is the scattering angle of +diffraction. The Lorentz-polarization factor can be turned off using +the optional *LP* keyword. + +Diffraction intensities are calculated on a three-dimensional mesh of +reciprocal lattice nodes. The mesh spacing is defined either (a) +by the entire simulation domain or (b) manually using selected values as +shown in the 2D diagram below. + +.. thumbnail:: JPG/xrd_mesh.jpg + :align: center + +For a mesh defined by the simulation domain, a rectilinear grid is +constructed with spacing *c**inv(A) along each reciprocal lattice +axis. Where A are the vectors corresponding to the edges of the +simulation cell. If one or two directions has non-periodic boundary +conditions, then the spacing in these directions is defined from the +average of the (inversed) box lengths with periodic boundary conditions. +Meshes defined by the simulation domain must contain at least one periodic +boundary. + +If the *manual* flag is included, the mesh of reciprocal lattice nodes +will defined using the *c* values for the spacing along each +reciprocal lattice axis. Note that manual mapping of the reciprocal +space mesh is good for comparing diffraction results from multiple +simulations; however it can reduce the likelihood that Bragg +reflections will be satisfied unless small spacing parameters (< 0.05 +Angstrom^(-1)) are implemented. Meshes with manual spacing do not +require a periodic boundary. + +The limits of the reciprocal lattice mesh are determined by range of +scattering angles explored. The *2Theta* parameters allows the user +to reduce the scattering angle range to only the region of interest +which reduces the cost of the computation. + +The atomic scattering factors, fj, accounts for the reduction in +diffraction intensity due to Compton scattering. Compute xrd uses +analytical approximations of the atomic scattering factors that vary +for each atom type (type1 type2 ... typeN) and angle of diffraction. +The analytic approximation is computed using the formula +:ref:`(Colliex) `: + +.. image:: Eqs/compute_xrd5.jpg + :align: center + +Coefficients parameterized by :ref:`(Peng) ` are assigned for each +atom type designating the chemical symbol and charge of each atom +type. Valid chemical symbols for compute xrd are: + +H: He1-: He: Li: Li1+: + Be: Be2+: B: C: Cval: + N: O: O1-: F: F1-: + Ne: Na: Na1+: Mg: Mg2+: + Al: Al3+: Si: Sival: Si4+: + P: S: Cl: Cl1-: Ar: + K: Ca: Ca2+: Sc: Sc3+: + Ti: Ti2+: Ti3+: Ti4+: V: + V2+: V3+: V5+: Cr: Cr2+: + Cr3+: Mn: Mn2+: Mn3+: Mn4+: + Fe: Fe2+: Fe3+: Co: Co2+: + Co: Ni: Ni2+: Ni3+: Cu: + Cu1+: Cu2+: Zn: Zn2+: Ga: + Ga3+: Ge: Ge4+: As: Se: + Br: Br1-: Kr: Rb: Rb1+: + Sr: Sr2+: Y: Y3+: Zr: + Zr4+: Nb: Nb3+: Nb5+: Mo: + Mo3+: Mo5+: Mo6+: Tc: Ru: + Ru3+: Ru4+: Rh: Rh3+: Rh4+: + Pd: Pd2+: Pd4+: Ag: Ag1+: + Ag2+: Cd: Cd2+: In: In3+: + Sn: Sn2+: Sn4+: Sb: Sb3+: + Sb5+: Te: I: I1-: Xe: + Cs: Cs1+: Ba: Ba2+: La: + La3+: Ce: Ce3+: Ce4+: Pr: + Pr3+: Pr4+: Nd: Nd3+: Pm: + Pm3+: Sm: Sm3+: Eu: Eu2+: + Eu3+: Gd: Gd3+: Tb: Tb3+: + Dy: Dy3+: Ho: Ho3+: Er: + Er3+: Tm: Tm3+: Yb: Yb2+: + Yb3+: Lu: Lu3+: Hf: Hf4+: + Ta: Ta5+: W: W6+: Re: + Os: Os4+: Ir: Ir3+: Ir4+: + Pt: Pt2+: Pt4+: Au: Au1+: + Au3+: Hg: Hg1+: Hg2+: Tl: + Tl1+: Tl3+: Pb: Pb2+: Pb4+: + Bi: Bi3+: Bi5+: Po: At: + Rn: Fr: Ra: Ra2+: Ac: + Ac3+: Th: Th4+: Pa: U: + U3+: U4+: U6+: Np: Np3+: + Np4+: Np6+: Pu: Pu3+: Pu4+: + Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:) + +If the *echo* keyword is specified, compute xrd will provide extra +reporting information to the screen. + +**Output info:** + +This compute calculates a global array. The number of rows in the +array is the number of reciprocal lattice nodes that are explored +which by the mesh. The global array has 2 columns. + +The first column contains the diffraction angle in the units (radians +or degrees) provided with the *2Theta* values. The second column contains +the computed diffraction intensities as described above. + +The array can be accessed by any command that uses global values from +a compute as input. See :ref:`this section ` +for an overview of LAMMPS output options. + +All array values calculated by this compute are "intensive". + +Restrictions +"""""""""""" + + +This compute is part of the USER-DIFFRACTION package. It is only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The compute_xrd command does not work for triclinic cells. + +Related commands +"""""""""""""""" + +:doc:`fix ave/histo `, +:doc:`compute saed ` + +Default +""""""" + +The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1, +no manual flag, no echo flag. + + +---------- + + +.. _Coleman: + + + +**(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020 +(2013). + +.. _Colliex: + + + +**(Colliex)** Colliex et al. International Tables for Crystallography +Volume C: Mathematical and Chemical Tables, 249-429 (2004). + +.. _Peng: + + + +**(Peng)** Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 +(1996). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/create_atoms.txt b/doc/_sources/create_atoms.txt new file mode 100644 index 0000000000..eac291ee71 --- /dev/null +++ b/doc/_sources/create_atoms.txt @@ -0,0 +1,349 @@ +.. index:: create_atoms + +create_atoms command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + create_atoms type style args keyword values ... + +* type = atom type (1-Ntypes) of atoms to create (offset for molecule creation) +* style = *box* or *region* or *single* or *random* +.. parsed-literal:: + + *box* args = none + *region* args = region-ID + region-ID = particles will only be created if contained in the region + *single* args = x y z + x,y,z = coordinates of a single particle (distance units) + *random* args = N seed region-ID + N = number of particles to create + seed = random # seed (positive integer) + region-ID = create atoms within this region, use NULL for entire simulation box + +* zero or more keyword/value pairs may be appended +* keyword = *mol* or *basis* or *remap* or *var* or *set* or *units* +.. parsed-literal:: + + *mol* value = template-ID seed + template-ID = ID of molecule template specified in a separate :doc:`molecule ` command + seed = random # seed (positive integer) + *basis* values = M itype + M = which basis atom + itype = atom type (1-N) to assign to this basis atom + *remap* value = *yes* or *no* + *var* value = name = variable name to evaluate for test of atom creation + *set* values = dim vname + dim = *x* or *y* or *z* + name = name of variable to set with x,y,z atom position + *rotate* values = Rx Ry Rz theta + Rx,Ry,Rz = rotation vector for single molecule + theta = rotation angle for single molecule (degrees) + *units* value = *lattice* or *box* + *lattice* = the geometry is defined in lattice units + *box* = the geometry is defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + create_atoms 1 box + create_atoms 3 region regsphere basis 2 3 + create_atoms 3 single 0 0 5 + create_atoms 1 box var v set x xpos set y ypos + +Description +""""""""""" + +This command creates atoms (or molecules) on a lattice, or a single +atom (or molecule), or a random collection of atoms (or molecules), as +an alternative to reading in their coordinates explicitly via a +:doc:`read_data ` or :doc:`read_restart ` +command. A simulation box must already exist, which is typically +created via the :doc:`create_box ` command. Before using +this command, a lattice must also be defined using the +:doc:`lattice ` command, unless you specify the *single* style +with units = box or the *random* style. For the remainder of this doc +page, a created atom or molecule is referred to as a "particle". + +If created particles are individual atoms, they are assigned the +specified atom *type*, though this can be altered via the *basis* +keyword as discussed below. If molecules are being created, the type +of each atom in the created molecule is specified in the file read by +the :doc:`molecule ` command, and those values are added to +the specified atom *type*. E.g. if *type* = 2, and the file specifies +atom types 1,2,3, then each created molecule will have atom types +3,4,5. + +For the *box* style, the create_atoms command fills the entire +simulation box with particles on the lattice. If your simulation box +is periodic, you should insure its size is a multiple of the lattice +spacings, to avoid unwanted atom overlaps at the box boundaries. If +your box is periodic and a multiple of the lattice spacing in a +particular dimension, LAMMPS is careful to put exactly one particle at +the boundary (on either side of the box), not zero or two. + +For the *region* style, a geometric volume is filled with particles on +the lattice. This volume what is inside the simulation box and is +also consistent with the region volume. See the :doc:`region ` +command for details. Note that a region can be specified so that its +"volume" is either inside or outside a geometric boundary. Also note +that if your region is the same size as a periodic simulation box (in +some dimension), LAMMPS does not implement the same logic described +above as for the *box* style, to insure exactly one particle at +periodic boundaries. if this is what you desire, you should either +use the *box* style, or tweak the region size to get precisely the +particles you want. + +For the *single* style, a single particle is added to the system at +the specified coordinates. This can be useful for debugging purposes +or to create a tiny system with a handful of particles at specified +positions. + +For the *random* style, N particles are added to the system at +randomly generated coordinates, which can be useful for generating an +amorphous system. The particles are created one by one using the +speficied random number *seed*, resulting in the same set of particles +coordinates, independent of how many processors are being used in the +simulation. If the *region-ID* argument is specified as NULL, then +the created particles will be anywhere in the simulation box. If a +*region-ID* is specified, a geometric volume is filled which is both +inside the simulation box and is also consistent with the region +volume. See the :doc:`region ` command for details. Note that +a region can be specified so that its "volume" is either inside or +outside a geometric boundary. + +.. note:: + + Particles generated by the *random* style will typically be + highly overlapped which will cause many interatomic potentials to + compute large energies and forces. Thus you should either perform an + :doc:`energy minimization ` or run dynamics with :doc:`fix nve/limit ` to equilibrate such a system, before + running normal dynamics. + +Note that this command adds particles to those that already exist. +This means it can be used to add particles to a system previously read +in from a data or restart file. Or the create_atoms command can be +used multiple times, to add multiple sets of particles to the +simulation. For example, grain boundaries can be created, by +interleaving create_atoms with :doc:`lattice ` commands +specifying different orientations. By using the create_atoms command +in conjunction with the :doc:`delete_atoms ` command, +reasonably complex geometries can be created, or a protein can be +solvated with a surrounding box of water molecules. + +In all these cases, care should be taken to insure that new atoms do +not overlap existing atoms inappropriately, especially if molecules +are being added. The :doc:`delete_atoms ` command can be +used to remove overlapping atoms or molecules. + + +---------- + + +Individual atoms are inserted by this command, unless the *mol* +keyword is used. It specifies a *template-ID* previously defined +using the :doc:`molecule ` command, which reads a file that +defines the molecule. The coordinates, atom types, charges, etc, as +well as any bond/angle/etc and special neighbor information for the +molecule can be specified in the molecule file. See the +:doc:`molecule ` command for details. The only settings +required to be in this file are the coordinates and types of atoms in +the molecule. + +Using a lattice to add molecules, e.g. via the *box* or *region* or +*single* styles, is exactly the same as adding atoms on lattice +points, except that entire molecules are added at each point, i.e. on +the point defined by each basis atom in the unit cell as it tiles the +simulation box or region. This is done by placing the geometric +center of the molecule at the lattice point, and giving the molecule a +random orientation about the point. The random *seed* specified with +the *mol* keyword is used for this operation, and the random numbers +generated by each processor are different. This means the coordinates +of individual atoms (in the molecules) will be different when running +on different numbers of processors, unlike when atoms are being +created in parallel. + +Also note that because of the random rotations, it may be important to +use a lattice with a large enough spacing that adjacent molecules will +not overlap, regardless of their relative orientations. + +.. note:: + + If the :doc:`create_box ` command is used to create + the simulation box, followed by the create_atoms command with its + *mol* option for adding molecules, then you typically need to use the + optional keywords allowed by the :doc:`create_box ` command + for extra bonds (angles,etc) or extra special neighbors. This is + because by default, the :doc:`create_box ` command sets up a + non-molecular system which doesn't allow molecules to be added. + + +---------- + + +This is the meaning of the other allowed keywords. + +The *basis* keyword is only used when atoms (not molecules) are being +created. It specifies an atom type that will be assigned to specific +basis atoms as they are created. See the :doc:`lattice ` +command for specifics on how basis atoms are defined for the unit cell +of the lattice. By default, all created atoms are assigned the +argument *type* as their atom type. + +The *remap* keyword only applies to the *single* style. If it is set +to *yes*, then if the specified position is outside the simulation +box, it will mapped back into the box, assuming the relevant +dimensions are periodic. If it is set to *no*, no remapping is done +and no particle is created if its position is outside the box. + +The *var* and *set* keywords can be used to provide a criterion for +accepting or rejecting the addition of an individual atom, based on +its coordinates. The *vname* specified for the *var* keyword is the +name of an :doc:`equal-style variable ` which should evaluate +to a zero or non-zero value based on one or two or three variables +which will store the x, y, or z coordinates of an atom (one variable +per coordinate). These other variables must be :doc:`equal-style variables ` defined in the input script, but their +formula can by anything. The *set* keyword is used to identify the +names of these other variables, one variable for the x-coordinate of a +created atom, one for y, and one for z. + +When an atom is created, its x, y, or z coordinates override the +formula for any *set* variable that is defined. The *var* variable is +then evaluated. If the returned value is 0.0, the atom is not +created. If it is non-zero, the atom is created. After all atoms are +created, the formulas defined for all of the *set* variables are +restored to their original strings. + +As an example, these commands can be used in a 2d simulation, to +create a sinusoidal surface. Note that the surface is "rough" due to +individual lattice points being "above" or "below" the mathematical +expression for the sinusoidal curve. If a finer lattice were used, +the sinusoid would appear to be "smoother". Also note the use of the +"xlat" and "ylat" :doc:`thermo_style ` keywords which +converts lattice spacings to distance. Click on the image for a +larger version. + +.. parsed-literal:: + + variable x equal 100 + variable y equal 25 + lattice hex 0.8442 + region box block 0 $x 0 $y -0.5 0.5 + create_box 1 box + +.. parsed-literal:: + + variable xx equal 0.0 + variable yy equal 0.0 + variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0" + create_atoms 1 box var v set x xx set y yy + +.. thumbnail:: JPG/sinusoid.jpg + :align: center + +The *rotate* keyword can be used with the *single* style, when adding +a single molecule to specify the orientation at which the molecule is +inserted. The axis of rotation is determined by the rotation vector +(Rx,Ry,Rz) that goes through the insertion point. The specified +*theta* determines the angle of rotation around that axis. Note that +the direction of rotation for the atoms around the rotation axis is +consistent with the right-hand rule: if your right-hand's thumb points +along *R*, then your fingers wrap around the axis in the direction of +rotation. + +The *units* keyword determines the meaning of the distance units used +to specify the coordinates of the one particle created by the *single* +style. A *box* value selects standard distance units as defined by +the :doc:`units ` command, e.g. Angstroms for units = real or +metal. A *lattice* value means the distance units are in lattice +spacings. + + +---------- + + +Atom IDs are assigned to created atoms in the following way. The +collection of created atoms are assigned consecutive IDs that start +immediately following the largest atom ID existing before the +create_atoms command was invoked. When a simulation is performed on +different numbers of processors, there is no guarantee a particular +created atom will be assigned the same ID. If molecules are being +created, molecule IDs are assigned to created molecules in a similar +fashion. + +Aside from their ID, atom type, and xyz position, other properties of +created atoms are set to default values, depending on which quantities +are defined by the chosen :doc:`atom style `. See the :doc:`atom style ` command for more details. See the +:doc:`set ` and :doc:`velocity ` commands for info on how +to change these values. + +* charge = 0.0 +* dipole moment magnitude = 0.0 +* diameter = 1.0 +* shape = 0.0 0.0 0.0 +* density = 1.0 +* volume = 1.0 +* velocity = 0.0 0.0 0.0 +* angular velocity = 0.0 0.0 0.0 +* angular momentum = 0.0 0.0 0.0 +* quaternion = (1,0,0,0) +* bonds, angles, dihedrals, impropers = none + +If molecules are being created, these defaults can be overridden by +values specified in the file read by the :doc:`molecule ` +command. E.g. the file typically defines bonds (angles,etc) between +atoms in the molecule, and can optionally define charges on each atom. + +Note that the *sphere* atom style sets the default particle diameter +to 1.0 as well as the density. This means the mass for the particle +is not 1.0, but is PI/6 * diameter^3 = 0.5236. + +Note that the *ellipsoid* atom style sets the default particle shape +to (0.0 0.0 0.0) and the density to 1.0 which means it is a point +particle, not an ellipsoid, and has a mass of 1.0. + +Note that the *peri* style sets the default volume and density to 1.0 +and thus also set the mass for the particle to 1.0. + +The :doc:`set ` command can be used to override many of these +default settings. + + +---------- + + +Restrictions +"""""""""""" + + +An :doc:`atom_style ` must be previously defined to use this +command. + +A rotation vector specified for a single molecule must be in +the z-direction for a 2d model. + +Related commands +"""""""""""""""" + +:doc:`lattice `, :doc:`region `, :doc:`create_box `, +:doc:`read_data `, :doc:`read_restart ` + +Default +""""""" + +The default for the *basis* keyword is that all created atoms are +assigned the argument *type* as their atom type (when single atoms are +being created). The other defaults are *remap* = no, *rotate* = +random, and *units* = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/create_bonds.txt b/doc/_sources/create_bonds.txt new file mode 100644 index 0000000000..378873d243 --- /dev/null +++ b/doc/_sources/create_bonds.txt @@ -0,0 +1,120 @@ +.. index:: create_bonds + +create_bonds command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + create_bonds group-ID group2-ID btype rmin rmax + +* group-ID = ID of first group +* group2-ID = ID of second group, bonds will be between atoms in the 2 groups +* btype = bond type of created bonds +* rmin = minimum distance between pair of atoms to bond together +* rmax = minimum distance between pair of atoms to bond together + +Examples +"""""""" + +.. parsed-literal:: + + create_bonds all all 1 1.0 1.2 + create_bonds surf solvent 3 2.0 2.4 + +Description +""""""""""" + +Create bonds between pairs of atoms that meet specified distance +criteria. The bond interactions can then be computed during a +simulation by the bond potential defined by the +:doc:`bond_style ` and :doc:`bond_coeff ` +commands. This command is useful for adding bonds to a system, +e.g. between nearest neighbors in a lattice of atoms, without having +to enumerate all the bonds in the data file read by the +:doc:`read_data ` command. + +Note that the flexibility of this command is limited. It can be used +several times to create different types of bond at different +distances. But it cannot typically create all the bonds that would +normally be defined in a complex system of molecules. Also note that +this command does not add any 3-body or 4-body interactions which, +depending on your model, may be induced by added bonds, +e.g. :doc:`angle `, :doc:`dihedral `, or +:doc:`improper ` interactions. + +All created bonds will be between pairs of atoms I,J where I is in one +of the two specified groups, and J is in the other. The two groups +can be the same, e.g. group "all". The created bonds will be of bond +type *btype*, where *btype* must be a value between 1 and the number +of bond types defined. This maximum value is set by the "bond types" +field in the header of the data file read by the +:doc:`read_data ` command, or via the optional "bond/types" +argument of the :doc:`create_box ` command. + +For a bond to be created, an I,J pair of atoms must be a distance D +apart such that *rmin* <= D <= *rmax*. + +The following settings must have been made in an input +script before this command is used: + +* special_bonds weight for 1-2 interactions must be 0.0 +* a :doc:`pair_style ` must be defined +* no :doc:`kspace_style ` defined +* minimum :doc:`pair_style ` cutoff + :doc:`neighbor ` skin >= *rmax* + +These settings are required so that a neighbor list can be created to +search for nearby atoms. Pairs of atoms that are already bonded +cannot appear in the neighbor list, to avoid creation of duplicate +bonds. The neighbor list for all atom type pairs must also extend to +a distance that encompasses the *rmax* for new bonds to create. + +An additional requirement is that your system must be ready to perform +a simulation. This means, for example, that all +:doc:`pair_style ` coefficients be set via the +:doc:`pair_coeff ` command. A :doc:`bond_style ` +command and all bond coefficients must also be set, even if no bonds +exist before this command is invoked. This is because the building of +neighbor list requires initialization and setup of a simulation, +similar to what a :doc:`run ` command would require. + +Note that you can change any of these settings after this command +executes, e.g. if you wish to use long-range Coulombic interactions +via the :doc:`kspace_style ` command for your subsequent +simulation. + +.. note:: + + If the system has no bonds to begin with, or if more bonds per + atom are being added than currently exist, then you must insure that + the number of bond types and the maximum number of bonds per atom are + set to large enough values. Otherwise an error may occur when too + many bonds are added to an atom. If the :doc:`read_data ` + command is used to define the system, these 2 parameters can be set + via the "bond types" and "extra bond per atom" fields in the header + section of the data file. If the :doc:`create_box ` command + is used to define the system, these 2 parameters can be set via its + optional "bond/types" and "extra/bond/per/atom" arguments. See the + doc pages for the 2 commands for details. + +Restrictions +"""""""""""" + + +This command cannot be used with molecular systems defined using +molecule template files via the :doc:`molecule ` and +:doc:`atom_style template ` commands. + +Related commands +"""""""""""""""" + +:doc:`create_atoms `, :doc:`delete_bonds ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/create_box.txt b/doc/_sources/create_box.txt new file mode 100644 index 0000000000..8cda653ca8 --- /dev/null +++ b/doc/_sources/create_box.txt @@ -0,0 +1,167 @@ +.. index:: create_box + +create_box command +================== + +Syntax +"""""" + +.. parsed-literal:: + + create_box N region-ID keyword value ... + +* N = # of atom types to use in this simulation +* region-ID = ID of region to use as simulation domain +* zero or more keyword/value pairs may be appended +* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* +.. parsed-literal:: + + *bond/types* value = # of bond types + *angle/types* value = # of angle types + *dihedral/types* value = # of dihedral types + *improper/types* value = # of improper types + *extra/bond/per/atom* value = # of bonds per atom + *extra/angle/per/atom* value = # of angles per atom + *extra/dihedral/per/atom* value = # of dihedrals per atom + *extra/improper/per/atom* value = # of impropers per atom + *extra/special/per/atom* value = # of special neighbors per atom + + + +Examples +"""""""" + +.. parsed-literal:: + + create_box 2 mybox + create_box 2 mybox bond/types 2 extra/bond/per/atom 1 + +Description +""""""""""" + +This command creates a simulation box based on the specified region. +Thus a :doc:`region ` command must first be used to define a +geometric domain. It also partitions the simulation box into a +regular 3d grid of rectangular bricks, one per processor, based on the +number of processors being used and the settings of the +:doc:`processors ` command. The partitioning can later be +changed by the :doc:`balance ` or :doc:`fix balance ` commands. + +The argument N is the number of atom types that will be used in the +simulation. + +If the region is not of style *prism*, then LAMMPS encloses the region +(block, sphere, etc) with an axis-aligned orthogonal bounding box +which becomes the simulation domain. + +If the region is of style *prism*, LAMMPS creates a non-orthogonal +simulation domain shaped as a parallelepiped with triclinic symmetry. +As defined by the :doc:`region prism ` command, the +parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3 +edge vectors starting from the origin given by A = (xhi-xlo,0,0); B = +(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). *Xy,xz,yz* can be 0.0 or +positive or negative values and are called "tilt factors" because they +are the amount of displacement applied to faces of an originally +orthogonal box to transform it into the parallelipiped. + +By default, a *prism* region used with the create_box command must +have tilt factors (xy,xz,yz) that do not skew the box more than half +the distance of the parallel box length. For example, if xlo = 2 and +xhi = 12, then the x box length is 10 and the xy tilt factor must be +between -5 and 5. Similarly, both xz and yz must be between +-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, +since if the maximum tilt factor is 5 (as in this example), then +configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all +geometrically equivalent. If you wish to define a box with tilt +factors that exceed these limits, you can use the :doc:`box tilt ` +command, with a setting of *large*; a setting of *small* is the +default. + +See :ref:`Section_howto 12 ` of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used +triclinic representations. + +When a prism region is used, the simulation domain should normally be +periodic in the dimension that the tilt is applied to, which is given +by the second dimension of the tilt factor (e.g. y for xy tilt). This +is so that pairs of atoms interacting across that boundary will have +one of them shifted by the tilt factor. Periodicity is set by the +:doc:`boundary ` command. For example, if the xy tilt factor +is non-zero, then the y dimension should be periodic. Similarly, the +z dimension should be periodic if xz or yz is non-zero. LAMMPS does +not require this periodicity, but you may lose atoms if this is not +the case. + +Also note that if your simulation will tilt the box, e.g. via the :doc:`fix deform ` command, the simulation box must be setup to +be triclinic, even if the tilt factors are initially 0.0. You can +also change an orthogonal box to a triclinic box or vice versa by +using the :doc:`change box ` command with its *ortho* and +*triclinic* options. + +.. note:: + + If the system is non-periodic (in a dimension), then you should + not make the lo/hi box dimensions (as defined in your + :doc:`region ` command) radically smaller/larger than the extent + of the atoms you eventually plan to create, e.g. via the + :doc:`create_atoms ` command. For example, if your atoms + extend from 0 to 50, you should not specify the box bounds as -10000 + and 10000. This is because as described above, LAMMPS uses the + specified box size to layout the 3d grid of processors. A huge + (mostly empty) box will be sub-optimal for performance when using + "fixed" boundary conditions (see the :doc:`boundary ` + command). When using "shrink-wrap" boundary conditions (see the + :doc:`boundary ` command), a huge (mostly empty) box may cause + a parallel simulation to lose atoms the first time that LAMMPS + shrink-wraps the box around the atoms. + + +---------- + + +The optional keywords can be used to create a system that allows for +bond (angle, dihedral, improper) interactions, or for molecules with +special 1-2,1-3,1-4 neighbors to be added later. These optional +keywords serve the same purpose as the analogous keywords that can be +used in a data file which are recognized by the +:doc:`read_data ` command when it sets up a system. + +Note that if these keywords are not used, then the create_box command +creates an atomic (non-molecular) simulation that does not allow bonds +between pairs of atoms to be defined, or a :doc:`bond potential ` to be specified, or for molecules with +special neighbors to be added to the system by commands such as +:doc:`create_atoms mol `, :doc:`fix deposit ` +or :doc:`fix pour `. + +As an example, see the examples/deposit/in.deposit.molecule script, +which deposits molecules onto a substrate. Initially there are no +molecules in the system, but they are added later by the :doc:`fix deposit ` command. The create_box command in the +script uses the bond/types and extra/bond/per/atom keywords to allow +this. If the added molecule contained more than 1 special bond +(allowed by default), an extra/special/per/atom keyword would also +need to be specified. + + +---------- + + +Restrictions +"""""""""""" + + +An :doc:`atom_style ` and :doc:`region ` must have +been previously defined to use this command. + +Related commands +"""""""""""""""" + +:doc:`read_data `, :doc:`create_atoms `, +:doc:`region ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/delete_atoms.txt b/doc/_sources/delete_atoms.txt new file mode 100644 index 0000000000..14d88f9331 --- /dev/null +++ b/doc/_sources/delete_atoms.txt @@ -0,0 +1,163 @@ +.. index:: delete_atoms + +delete_atoms command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + delete_atoms style args keyword value ... + +* style = *group* or *region* or *overlap* or *porosity* +.. parsed-literal:: + + *group* args = group-ID + *region* args = region-ID + *overlap* args = cutoff group1-ID group2-ID + cutoff = delete one atom from pairs of atoms within the cutoff (distance units) + group1-ID = one atom in pair must be in this group + group2-ID = other atom in pair must be in this group + *porosity* args = region-ID fraction seed + region-ID = region within which to perform deletions + fraction = delete this fraction of atoms + seed = random number seed (positive integer) + +* zero or more keyword/value pairs may be appended +* keyword = *compress* or *bond* or *mol* +.. parsed-literal:: + + *compress* value = *no* or *yes* + *bond* value = *no* or *yes* + *mol* value = *no* or *yes* + + + +Examples +"""""""" + +.. parsed-literal:: + + delete_atoms group edge + delete_atoms region sphere compress no + delete_atoms overlap 0.3 all all + delete_atoms overlap 0.5 solvent colloid + delete_atoms porosity cube 0.1 482793 bond yes + +Description +""""""""""" + +Delete the specified atoms. This command can be used to carve out +voids from a block of material or to delete created atoms that are too +close to each other (e.g. at a grain boundary). + +For style *group*, all atoms belonging to the group are deleted. + +For style *region*, all atoms in the region volume are deleted. +Additional atoms can be deleted if they are in a molecule for which +one or more atoms were deleted within the region; see the *mol* +keyword discussion below. + +For style *overlap* pairs of atoms whose distance of separation is +within the specified cutoff distance are searched for, and one of the +2 atoms is deleted. Only pairs where one of the two atoms is in the +first group specified and the other atom is in the second group are +considered. The atom that is in the first group is the one that is +deleted. + +Note that it is OK for the two group IDs to be the same (e.g. group +*all*), or for some atoms to be members of both groups. In these +cases, either atom in the pair may be deleted. Also note that if +there are atoms which are members of both groups, the only guarantee +is that at the end of the deletion operation, enough deletions will +have occurred that no atom pairs within the cutoff will remain +(subject to the group restriction). There is no guarantee that the +minimum number of atoms will be deleted, or that the same atoms will +be deleted when running on different numbers of processors. + +For style *porosity* a specified *fraction* of atoms are deleted +within the specified region. For example, if fraction is 0.1, then +10% of the atoms will be deleted. The atoms to delete are chosen +randomly. There is no guarantee that the exact fraction of atoms will +be deleted, or that the same atoms will be deleted when running on +different numbers of processors. + +If the *compress* keyword is set to *yes*, then after atoms are +deleted, then atom IDs are re-assigned so that they run from 1 to the +number of atoms in the system. Note that this is not done for +molecular systems (see the :doc:`atom_style ` command), +regardless of the *compress* setting, since it would foul up the bond +connectivity that has already been assigned. + +A molecular system with fixed bonds, angles, dihedrals, or improper +interactions, is one where the topology of the interactions is +typically defined in the data file read by the +:doc:`read_data ` command, and where the interactions +themselves are defined with the :doc:`bond_style `, +:doc:`angle_style `, etc commands. If you delete atoms +from such a system, you must be careful not to end up with bonded +interactions that are stored by remaining atoms but which include +deleted atoms. This will cause LAMMPS to generate a "missing atoms" +error when the bonded interaction is computed. The *bond* and *mol* +keywords offer two ways to do that. + +It the *bond* keyword is set to *yes* then any bond or angle or +dihedral or improper interaction that includes a deleted atom is also +removed from the lists of such interactions stored by non-deleted +atoms. Note that simply deleting interactions due to dangling bonds +(e.g. at a surface) may result in a inaccurate or invalid model for +the remaining atoms. + +It the *mol* keyword is set to *yes*, then for every atom that is +deleted, all other atoms in the same molecule (with the same molecule +ID) will also be deleted. This is not done for atoms with molecule ID += 0, since such an ID is assumed to flag isolated atoms that are not +part of molecules. + +.. note:: + + The molecule deletion operation in invoked after all individual + atoms have been deleted using the rules described above for each + style. This means additional atoms may be deleted that are not in the + group or region, that are not required by the overlap cutoff + criterion, or that will create a higher fraction of porosity than was + requested. + +Restrictions +"""""""""""" + + +The *overlap* styles requires inter-processor communication to acquire +ghost atoms and build a neighbor list. This means that your system +must be ready to perform a simulation before using this command (force +fields setup, atom masses set, etc). Since a neighbor list is used to +find overlapping atom pairs, it also means that you must define a +:doc:`pair style ` with the minimum force cutoff distance +between any pair of atoms types (plus the :doc:`neighbor ` +skin) >= the specified overlap cutoff. + +If the :doc:`special_bonds ` command is used with a +setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not +appear in the neighbor list, and thus will not be considered for +deletion by the *overlap* styles. You probably don't want to be +deleting one atom in a bonded pair anyway. + +The *bond yes* option cannot be used with molecular systems defined +using molecule template files via the :doc:`molecule ` and +:doc:`atom_style template ` commands. + +Related commands +"""""""""""""""" + +:doc:`create_atoms ` + +Default +""""""" + +The option defaults are compress = yes, bond = no, mol = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/delete_bonds.txt b/doc/_sources/delete_bonds.txt new file mode 100644 index 0000000000..cecdddc060 --- /dev/null +++ b/doc/_sources/delete_bonds.txt @@ -0,0 +1,165 @@ +.. index:: delete_bonds + +delete_bonds command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + delete_bonds group-ID style arg keyword ... + +* group-ID = group ID +* style = *multi* or *atom* or *bond* or *angle* or *dihedral* or + *improper* or *stats* +.. parsed-literal:: + + *multi* arg = none + *atom* arg = an atom type or range of types (see below) + *bond* arg = a bond type or range of types (see below) + *angle* arg = an angle type or range of types (see below) + *dihedral* arg = a dihedral type or range of types (see below) + *improper* arg = an improper type or range of types (see below) + *stats* arg = none + +* zero or more keywords may be appended +* keyword = *any* or *undo* or *remove* or *special* + + +Examples +"""""""" + +.. parsed-literal:: + + delete_bonds frozen multi remove + delete_bonds all atom 4 special + delete_bonds all bond 0*3 special + delete_bonds all stats + +Description +""""""""""" + +Turn off (or on) molecular topology interactions, i.e. bonds, angles, +dihedrals, impropers. This command is useful for deleting +interactions that have been previously turned off by bond-breaking +potentials. It is also useful for turning off topology interactions +between frozen or rigid atoms. Pairwise interactions can be turned +off via the :doc:`neigh_modify exclude ` command. The +:doc:`fix shake ` command also effectively turns off certain +bond and angle interactions. + +For all styles, by default, an interaction is only turned off (or on) +if all the atoms involved are in the specified group. See the *any* +keyword to change the behavior. + +Several of the styles (*atom*, *bond*, *angle*, *dihedral*, +*improper*) take a *type* as an argument. The specified *type* should +be an integer from 0 to N, where N is the number of relevant types +(atom types, bond types, etc). A value of 0 is only relevant for +style *bond*; see details below. In all cases, a wildcard asterisk +can be used in place of or in conjunction with the *type* argument to +specify a range of types. This takes the form "*" or "*n" or "n*" or +"m*n". If N = the number of types, then an asterisk with no numeric +values means all types from 0 to N. A leading asterisk means all +types from 0 to n (inclusive). A trailing asterisk means all types +from n to N (inclusive). A middle asterisk means all types from m to +n (inclusive). Note that it is fine to include a type of 0 for +non-bond styles; it will simply be ignored. + +For style *multi* all bond, angle, dihedral, and improper interactions +of any type, involving atoms in the group, are turned off. + +Style *atom* is the same as style *multi* except that in addition, one +or more of the atoms involved in the bond, angle, dihedral, or +improper interaction must also be of the specified atom type. + +For style *bond*, only bonds are candidates for turn-off, and the bond +must also be of the specified type. Styles *angle*, *dihedral*, and +*improper* are treated similarly. + +For style *bond*, you can set the type to 0 to delete bonds that have +been previously broken by a bond-breaking potential (which sets the +bond type to 0 when a bond is broken); e.g. see the :doc:`bond_style quartic ` command. + +For style *stats* no interactions are turned off (or on); the status +of all interactions in the specified group is simply reported. This +is useful for diagnostic purposes if bonds have been turned off by a +bond-breaking potential during a previous run. + +The default behavior of the delete_bonds command is to turn off +interactions by toggling their type to a negative value, but not to +permanently remove the interaction. E.g. a bond_type of 2 is set to +-2. The neighbor list creation routines will not include such an +interaction in their interaction lists. The default is also to not +alter the list of 1-2, 1-3, 1-4 neighbors computed by the +:doc:`special_bonds ` command and used to weight pairwise +force and energy calculations. This means that pairwise computations +will proceed as if the bond (or angle, etc) were still turned on. + +Several keywords can be appended to the argument list to alter the +default behaviors. + +The *any* keyword changes the requirement that all atoms in the bond +(angle, etc) must be in the specified group in order to turn-off the +interaction. Instead, if any of the atoms in the interaction are in +the specified group, it will be turned off (or on if the *undo* +keyword is used). + +The *undo* keyword inverts the delete_bonds command so that the +specified bonds, angles, etc are turned on if they are currently +turned off. This means a negative value is toggled to positive. For +example, for style *angle*, if *type* is specified as 2, then all +angles with current type = -2, are reset to type = 2. Note that the +:doc:`fix shake ` command also sets bond and angle types +negative, so this option should not be used on those interactions. + +The *remove* keyword is invoked at the end of the delete_bonds +operation. It causes turned-off bonds (angles, etc) to be removed +from each atom's data structure and then adjusts the global bond +(angle, etc) counts accordingly. Removal is a permanent change; +removed bonds cannot be turned back on via the *undo* keyword. +Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list. + +The *special* keyword is invoked at the end of the delete_bonds +operation, after (optional) removal. It re-computes the pairwise 1-2, +1-3, 1-4 weighting list. The weighting list computation treats +turned-off bonds the same as turned-on. Thus, turned-off bonds must +be removed if you wish to change the weighting list. + +Note that the choice of *remove* and *special* options affects how +1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that +have been modified by the delete_bonds command. + +Restrictions +"""""""""""" + + +This command requires inter-processor communication to acquire ghost +atoms, to coordinate the deleting of bonds, angles, etc between atoms +shared by multiple processors. This means that your system must be +ready to perform a simulation before using this command (force fields +setup, atom masses set, etc). Just as would be needed to run +dynamics, the force field you define should define a cutoff +(e.g. through a :doc:`pair_style ` command) which is long +enough for a processor to acquire the ghost atoms its needs to compute +bond, angle, etc interactions. + +If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4 +weighting list is not recomputed, this can cause a later :doc:`fix shake ` command to fail due to an atom's bonds being +inconsistent with the weighting list. This should only happen if the +group used in the fix command includes both atoms in the bond, in +which case you probably should be recomputing the weighting list. + +Related commands +"""""""""""""""" + +:doc:`neigh_modify ` exclude, +:doc:`special_bonds `, :doc:`fix shake ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dielectric.txt b/doc/_sources/dielectric.txt new file mode 100644 index 0000000000..c9b09437e5 --- /dev/null +++ b/doc/_sources/dielectric.txt @@ -0,0 +1,52 @@ +.. index:: dielectric + +dielectric command +================== + +Syntax +"""""" + +.. parsed-literal:: + + dielectric value + +* value = dielectric constant + +Examples +"""""""" + +.. parsed-literal:: + + dielectric 2.0 + +Description +""""""""""" + +Set the dielectric constant for Coulombic interactions (pairwise and +long-range) to this value. The constant is unitless, since it is used +to reduce the strength of the interactions. The value is used in the +denominator of the formulas for Coulombic interactions - e.g. a value +of 4.0 reduces the Coulombic interactions to 25% of their default +strength. See the :doc:`pair_style ` command for more +details. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`pair_style ` + +Default +""""""" + +.. parsed-literal:: + + dielectric 1.0 + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_charmm.txt b/doc/_sources/dihedral_charmm.txt new file mode 100644 index 0000000000..4e26eac780 --- /dev/null +++ b/doc/_sources/dihedral_charmm.txt @@ -0,0 +1,141 @@ +.. index:: dihedral_style charmm + +dihedral_style charmm command +============================= + +dihedral_style charmm/intel command +=================================== + +dihedral_style charmm/kk command +================================ + +dihedral_style charmm/omp command +================================= + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style charmm + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style charmm + dihedral_coeff 1 120.0 1 60 0.5 + +Description +""""""""""" + +The *charmm* dihedral style uses the potential + +.. image:: Eqs/dihedral_charmm.jpg + :align: center + +See :ref:`(MacKerell) ` for a description of the CHARMM force +field. This dihedral style can also be used for the AMBER force field +(see comment on weighting factors below). See :ref:`(Cornell) ` +for a description of the AMBER force field. + +The following coefficients must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy) +* n (integer >= 0) +* d (integer value of degrees) +* weighting factor (0.0 to 1.0) + +The weighting factor is applied to pairwise interaction between the +1st and 4th atoms in the dihedral, which are computed by a CHARMM +:doc:`pair_style ` with epsilon and sigma values specified +with a :doc:`pair_coeff ` command. Note that this +weighting factor is unrelated to the weighting factor specified by the +:doc:`special bonds ` command which applies to all 1-4 +interactions in the system. + +For CHARMM force fields, the special_bonds 1-4 weighting factor should +be set to 0.0. This is because the pair styles that contain "charmm" +(e.g. :doc:`pair_style lj/charmm/coul/long `) define extra +1-4 interaction coefficients that are used by this dihedral style to +compute those interactions explicitly. This means that if any of the +weighting factors defined as dihedral coefficients (4th coeff above) +are non-zero, then you must use a charmm pair style. Note that if you +do not set the special_bonds 1-4 weighting factor to 0.0 (which is the +default) then 1-4 interactions in dihedrals will be computed twice, +once by the pair routine and once by the dihedral routine, which is +probably not what you want. + +For AMBER force fields, the special_bonds 1-4 weighting factor should +be set to the AMBER defaults (1/2 and 5/6) and all the dihedral +weighting factors (4th coeff above) should be set to 0.0. In this +case, you can use any pair style you wish, since the dihedral does not +need any 1-4 information. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +---------- + + +.. _Cornell: + + + +**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, +Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). + +.. _MacKerell: + + + +**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, +Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_class2.txt b/doc/_sources/dihedral_class2.txt new file mode 100644 index 0000000000..4e0ae04ae2 --- /dev/null +++ b/doc/_sources/dihedral_class2.txt @@ -0,0 +1,198 @@ +.. index:: dihedral_style class2 + +dihedral_style class2 command +============================= + +dihedral_style class2/omp command +================================= + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style class2 + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style class2 + dihedral_coeff 1 100 75 100 70 80 60 + dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 + dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 + dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 + dihedral_coeff * aat -13.5271 110.2453 105.1270 + dihedral_coeff * bb13 0.0 1.0119 1.1010 + +Description +""""""""""" + +The *class2* dihedral style uses the potential + +.. image:: Eqs/dihedral_class2.jpg + :align: center + +where Ed is the dihedral term, Embt is a middle-bond-torsion term, +Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat +is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term. + +Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium +bond lengths. + +See :ref:`(Sun) ` for a description of the COMPASS class2 force field. + +Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas +must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, +or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands. + +These are the 6 coefficients for the Ed formula: + +* K1 (energy) +* phi1 (degrees) +* K2 (energy) +* phi2 (degrees) +* K3 (energy) +* phi3 (degrees) + +For the Embt formula, each line in a +:doc:`dihedral_coeff ` command in the input script lists +5 coefficients, the first of which is "mbt" to indicate they are +MiddleBondTorsion coefficients. In a data file, these coefficients +should be listed under a "MiddleBondTorsion Coeffs" heading and you +must leave out the "mbt", i.e. only list 4 coefficients after the +dihedral type. + +* mbt +* A1 (energy/distance) +* A2 (energy/distance) +* A3 (energy/distance) +* r2 (distance) + +For the Eebt formula, each line in a +:doc:`dihedral_coeff ` command in the input script lists +9 coefficients, the first of which is "ebt" to indicate they are +EndBondTorsion coefficients. In a data file, these coefficients +should be listed under a "EndBondTorsion Coeffs" heading and you must +leave out the "ebt", i.e. only list 8 coefficients after the dihedral +type. + +* ebt +* B1 (energy/distance) +* B2 (energy/distance) +* B3 (energy/distance) +* C1 (energy/distance) +* C2 (energy/distance) +* C3 (energy/distance) +* r1 (distance) +* r3 (distance) + +For the Eat formula, each line in a +:doc:`dihedral_coeff ` command in the input script lists +9 coefficients, the first of which is "at" to indicate they are +AngleTorsion coefficients. In a data file, these coefficients should +be listed under a "AngleTorsion Coeffs" heading and you must leave out +the "at", i.e. only list 8 coefficients after the dihedral type. + +* at +* D1 (energy/radian) +* D2 (energy/radian) +* D3 (energy/radian) +* E1 (energy/radian) +* E2 (energy/radian) +* E3 (energy/radian) +* theta1 (degrees) +* theta2 (degrees) + +Theta1 and theta2 are specified in degrees, but LAMMPS converts them +to radians internally; hence the units of D and E are in +energy/radian. + +For the Eaat formula, each line in a +:doc:`dihedral_coeff ` command in the input script lists +4 coefficients, the first of which is "aat" to indicate they are +AngleAngleTorsion coefficients. In a data file, these coefficients +should be listed under a "AngleAngleTorsion Coeffs" heading and you +must leave out the "aat", i.e. only list 3 coefficients after the +dihedral type. + +* aat +* M (energy/radian^2) +* theta1 (degrees) +* theta2 (degrees) + +Theta1 and theta2 are specified in degrees, but LAMMPS converts them +to radians internally; hence the units of M are in energy/radian^2. + +For the Ebb13 formula, each line in a +:doc:`dihedral_coeff ` command in the input script lists +4 coefficients, the first of which is "bb13" to indicate they are +BondBond13 coefficients. In a data file, these coefficients should be +listed under a "BondBond13 Coeffs" heading and you must leave out the +"bb13", i.e. only list 3 coefficients after the dihedral type. + +* bb13 +* N (energy/distance^2) +* r1 (distance) +* r3 (distance) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +CLASS2 package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +---------- + + +.. _Sun: + + + +**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_coeff.txt b/doc/_sources/dihedral_coeff.txt new file mode 100644 index 0000000000..20aa5911c4 --- /dev/null +++ b/doc/_sources/dihedral_coeff.txt @@ -0,0 +1,130 @@ +.. index:: dihedral_coeff + +dihedral_coeff command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_coeff N args + +* N = dihedral type (see asterisk form below) +* args = coefficients for one or more dihedral types + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_coeff 1 80.0 1 3 + dihedral_coeff * 80.0 1 3 0.5 + dihedral_coeff 2* 80.0 1 3 0.5 + +Description +""""""""""" + + +---------- + + +Specify the dihedral force field coefficients for one or more dihedral types. +The number and meaning of the coefficients depends on the dihedral style. +Dihedral coefficients can also be set in the data file read by the +:doc:`read_data ` command or in a restart file. + +N can be specified in one of two ways. An explicit numeric value can +be used, as in the 1st example above. Or a wild-card asterisk can be +used to set the coefficients for multiple dihedral types. This takes the +form "*" or "*n" or "n*" or "m*n". If N = the number of dihedral types, +then an asterisk with no numeric values means all types from 1 to N. A +leading asterisk means all types from 1 to n (inclusive). A trailing +asterisk means all types from n to N (inclusive). A middle asterisk +means all types from m to n (inclusive). + +Note that using a dihedral_coeff command can override a previous setting +for the same dihedral type. For example, these commands set the coeffs +for all dihedral types, then overwrite the coeffs for just dihedral type 2: + +.. parsed-literal:: + + dihedral_coeff * 80.0 1 3 + dihedral_coeff 2 200.0 1 3 + +A line in a data file that specifies dihedral coefficients uses the exact +same format as the arguments of the dihedral_coeff command in an input +script, except that wild-card asterisks should not be used since +coefficients for all N types must be listed in the file. For example, +under the "Dihedral Coeffs" section of a data file, the line that +corresponds to the 1st example above would be listed as + +.. parsed-literal:: + + 1 80.0 1 3 + +The :doc:`dihedral_style class2 ` is an exception to +this rule, in that an additional argument is used in the input script +to allow specification of the cross-term coefficients. See its doc +page for details. + +.. note:: + + When comparing the formulas and coefficients for various LAMMPS + dihedral styles with dihedral equations defined by other force fields, + note that some force field implementations divide/multiply the energy + prefactor *K* by the multiple number of torsions that contain the J-K + bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed + dihedral equation applies to each individual dihedral. Thus you need + to define *K* appropriately to account for this difference if + necessary. + + +---------- + + +Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on +the style to display the formula it computes and coefficients +specified by the associated :doc:`dihedral_coeff ` command. + +Note that there are also additional dihedral styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the dihedral section of +:ref:`this page `. + +* :doc:`dihedral_style none ` - turn off dihedral interactions +* :doc:`dihedral_style hybrid ` - define multiple styles of dihedral interactions + +* :doc:`dihedral_style charmm ` - CHARMM dihedral +* :doc:`dihedral_style class2 ` - COMPASS (class 2) dihedral +* :doc:`dihedral_style harmonic ` - harmonic dihedral +* :doc:`dihedral_style helix ` - helix dihedral +* :doc:`dihedral_style multi/harmonic ` - multi-harmonic dihedral +* :doc:`dihedral_style opls ` - OPLS dihedral + + +---------- + + +Restrictions +"""""""""""" + + +This command must come after the simulation box is defined by a +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. + +A dihedral style must be defined before any dihedral coefficients are +set, either in the input script or in a data file. + +Related commands +"""""""""""""""" + +:doc:`dihedral_style ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_cosine_shift_exp.txt b/doc/_sources/dihedral_cosine_shift_exp.txt new file mode 100644 index 0000000000..613cf25a5b --- /dev/null +++ b/doc/_sources/dihedral_cosine_shift_exp.txt @@ -0,0 +1,101 @@ +.. index:: dihedral_style cosine/shift/exp + +dihedral_style cosine/shift/exp command +======================================= + +dihedral_style cosine/shift/exp/omp command +=========================================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style cosine/shift/exp + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style cosine/shift/exp + dihedral_coeff 1 10.0 45.0 2.0 + +Description +""""""""""" + +The *cosine/shift/exp* dihedral style uses the potential + +.. image:: Eqs/dihedral_cosine_shift_exp.jpg + :align: center + +where Umin, theta, and a are defined for each dihedral type. + +The potential is bounded between [-Umin:0] and the minimum is located +at the angle theta0. The a parameter can be both positive or negative +and is used to control the spring constant at the equilibrium. + +The spring constant is given by k=a exp(a) Umin/ [2 (Exp(a)-1)]. +For a>3 k/Umin = a/2 to better than 5% relative error. For negative +values of the a parameter, the spring constant is essentially zero, +and anharmonic terms takes over. The potential is furthermore well +behaved in the limit a->0, where it has been implemented to linear +order in a for a < 0.001. + +The following coefficients must be defined for each dihedral type via +the :doc:`dihedral_coeff ` command as in the example +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* umin (energy) +* theta (angle) +* A (real number) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff `, +:doc:`angle_cosineshiftexp ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_fourier.txt b/doc/_sources/dihedral_fourier.txt new file mode 100644 index 0000000000..f71f318794 --- /dev/null +++ b/doc/_sources/dihedral_fourier.txt @@ -0,0 +1,91 @@ +.. index:: dihedral_style fourier + +dihedral_style fourier command +============================== + +dihedral_style fourier/omp command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style fourier + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style fourier + dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 + +Description +""""""""""" + +The *fourier* dihedral style uses the potential: + +.. image:: Eqs/dihedral_fourier.jpg + :align: center + +The following coefficients must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* m (integer >=1) +* K1 (energy) +* n1 (integer >= 0) +* d1 (degrees) +* .... +* Km (energy) +* nm (integer >= 0) +* dm (degrees) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER_MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_harmonic.txt b/doc/_sources/dihedral_harmonic.txt new file mode 100644 index 0000000000..fbfdeb943e --- /dev/null +++ b/doc/_sources/dihedral_harmonic.txt @@ -0,0 +1,97 @@ +.. index:: dihedral_style harmonic + +dihedral_style harmonic command +=============================== + +dihedral_style harmonic/omp command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style harmonic + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style harmonic + dihedral_coeff 1 80.0 1 2 + +Description +""""""""""" + +The *harmonic* dihedral style uses the potential + +.. image:: Eqs/dihedral_harmonic.jpg + :align: center + +The following coefficients must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K (energy) +* d (+1 or -1) +* n (integer >= 0) + +.. note:: + + Here are important points to take note of when defining LAMMPS + dihedral coefficients for the harmonic style, so that they are + compatible with how harmonic dihedrals are defined by other force + fields: + +* The LAMMPS convention is that the trans position = 180 degrees, while + in some force fields trans = 0 degrees. +* Some force fields reverse the sign convention on *d*. +* Some force fields let *n* be positive or negative which corresponds to + *d* = 1 or -1 for the harmonic style. + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_helix.txt b/doc/_sources/dihedral_helix.txt new file mode 100644 index 0000000000..a034610a11 --- /dev/null +++ b/doc/_sources/dihedral_helix.txt @@ -0,0 +1,103 @@ +.. index:: dihedral_style helix + +dihedral_style helix command +============================ + +dihedral_style helix/omp command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style helix + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style helix + dihedral_coeff 1 80.0 100.0 40.0 + +Description +""""""""""" + +The *helix* dihedral style uses the potential + +.. image:: Eqs/dihedral_helix.jpg + :align: center + +This coarse-grain dihedral potential is described in :ref:`(Guo) `. +For dihedral angles in the helical region, the energy function is +represented by a standard potential consisting of three minima, one +corresponding to the trans (t) state and the other to gauche states +(g+ and g-). The paper describes how the A,B,C parameters are chosen +so as to balance secondary (largely driven by local interactions) and +tertiary structure (driven by long-range interactions). + +The following coefficients must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* A (energy) +* B (energy) +* C (energy) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +---------- + + +.. _Guo: + + + +**(Guo)** Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_hybrid.txt b/doc/_sources/dihedral_hybrid.txt new file mode 100644 index 0000000000..a654aedaa5 --- /dev/null +++ b/doc/_sources/dihedral_hybrid.txt @@ -0,0 +1,110 @@ +.. index:: dihedral_style hybrid + +dihedral_style hybrid command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style hybrid style1 style2 ... + +* style1,style2 = list of one or more dihedral styles + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style hybrid harmonic helix + dihedral_coeff 1 harmonic 6.0 1 3 + dihedral_coeff 2* helix 10 10 10 + +Description +""""""""""" + +The *hybrid* style enables the use of multiple dihedral styles in one +simulation. An dihedral style is assigned to each dihedral type. For +example, dihedrals in a polymer flow (of dihedral type 1) could be +computed with a *harmonic* potential and dihedrals in the wall +boundary (of dihedral type 2) could be computed with a *helix* +potential. The assignment of dihedral type to style is made via the +:doc:`dihedral_coeff ` command or in the data file. + +In the dihedral_coeff commands, the name of a dihedral style must be +added after the dihedral type, with the remaining coefficients being +those appropriate to that style. In the example above, the 2 +dihedral_coeff commands set dihedrals of dihedral type 1 to be +computed with a *harmonic* potential with coefficients 6.0, 1, 3 for +K, d, n. All other dihedral types (2-N) are computed with a *helix* +potential with coefficients 10, 10, 10 for A, B, C. + +If dihedral coefficients are specified in the data file read via the +:doc:`read_data ` command, then the same rule applies. +E.g. "harmonic" or "helix", must be added after the dihedral type, for +each line in the "Dihedral Coeffs" section, e.g. + +.. parsed-literal:: + + Dihedral Coeffs + +.. parsed-literal:: + + 1 harmonic 6.0 1 3 + 2 helix 10 10 10 + ... + +If *class2* is one of the dihedral hybrid styles, the same rule holds +for specifying additional AngleTorsion (and EndBondTorsion, etc) +coefficients either via the input script or in the data file. +I.e. *class2* must be added to each line after the dihedral type. For +lines in the AngleTorsion (or EndBondTorsion, etc) section of the data +file for dihedral types that are not *class2*, you must use an +dihedral style of *skip* as a placeholder, e.g. + +.. parsed-literal:: + + AngleTorsion Coeffs + +.. parsed-literal:: + + 1 skip + 2 class2 1.0 1.0 1.0 3.0 3.0 3.0 30.0 50.0 + ... + +Note that it is not necessary to use the dihedral style *skip* in the +input script, since AngleTorsion (or EndBondTorsion, etc) coefficients +need not be specified at all for dihedral types that are not *class2*. + +A dihedral style of *none* with no additional coefficients can be used +in place of a dihedral style, either in a input script dihedral_coeff +command or in the data file, if you desire to turn off interactions +for specific dihedral types. + + +---------- + + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Unlike other dihedral styles, the hybrid dihedral style does not store +dihedral coefficient info for individual sub-styles in a :doc:`binary restart files `. Thus when retarting a simulation from a +restart file, you need to re-specify dihedral_coeff commands. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_multi_harmonic.txt b/doc/_sources/dihedral_multi_harmonic.txt new file mode 100644 index 0000000000..2fa1a27e9b --- /dev/null +++ b/doc/_sources/dihedral_multi_harmonic.txt @@ -0,0 +1,87 @@ +.. index:: dihedral_style multi/harmonic + +dihedral_style multi/harmonic command +===================================== + +dihedral_style multi/harmonic/omp command +========================================= + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style multi/harmonic + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style multi/harmonic + dihedral_coeff 1 20 20 20 20 20 + +Description +""""""""""" + +The *multi/harmonic* dihedral style uses the potential + +.. image:: Eqs/dihedral_multi_harmonic.jpg + :align: center + +The following coefficients must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* A1 (energy) +* A2 (energy) +* A3 (energy) +* A4 (energy) +* A5 (energy) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_nharmonic.txt b/doc/_sources/dihedral_nharmonic.txt new file mode 100644 index 0000000000..8724f70fd7 --- /dev/null +++ b/doc/_sources/dihedral_nharmonic.txt @@ -0,0 +1,88 @@ +.. index:: dihedral_style nharmonic + +dihedral_style nharmonic command +================================ + +dihedral_style nharmonic/omp command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style nharmonic + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style nharmonic + dihedral_coeff 3 10.0 20.0 30.0 + +Description +""""""""""" + +The *nharmonic* dihedral style uses the potential: + +.. image:: Eqs/dihedral_nharmonic.jpg + :align: center + +The following coefficients must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* n (integer >=1) +* A1 (energy) +* A2 (energy) +* ... +* An (energy) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER_MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_none.txt b/doc/_sources/dihedral_none.txt new file mode 100644 index 0000000000..cbc7c0facb --- /dev/null +++ b/doc/_sources/dihedral_none.txt @@ -0,0 +1,38 @@ +.. index:: dihedral_style none + +dihedral_style none command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style none + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style none + +Description +""""""""""" + +Using an dihedral style of none means dihedral forces are not +computed, even if quadruplets of dihedral atoms were listed in the +data file read by the :doc:`read_data ` command. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_opls.txt b/doc/_sources/dihedral_opls.txt new file mode 100644 index 0000000000..8ef51b504c --- /dev/null +++ b/doc/_sources/dihedral_opls.txt @@ -0,0 +1,106 @@ +.. index:: dihedral_style opls + +dihedral_style opls command +=========================== + +dihedral_style opls/kk command +============================== + +dihedral_style opls/omp command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style opls + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style opls + dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT + dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC + dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC + +Description +""""""""""" + +The *opls* dihedral style uses the potential + +.. image:: Eqs/dihedral_opls.jpg + :align: center + +Note that the usual 1/2 factor is not included in the K values. + +This dihedral potential is used in the OPLS force field and is +described in :ref:`(Watkins) `. + +The following coefficients must be defined for each dihedral type via the +:doc:`dihedral_coeff ` command as in the example above, or in +the data file or restart files read by the :doc:`read_data ` +or :doc:`read_restart ` commands: + +* K1 (energy) +* K2 (energy) +* K3 (energy) +* K4 (energy) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +---------- + + +.. _Watkins: + + + +**(Watkins)** Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_quadratic.txt b/doc/_sources/dihedral_quadratic.txt new file mode 100644 index 0000000000..5f680e43c1 --- /dev/null +++ b/doc/_sources/dihedral_quadratic.txt @@ -0,0 +1,89 @@ +.. index:: dihedral_style quadratic + +dihedral_style quadratic command +================================ + +dihedral_style quadratic/omp command +==================================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style quadratic + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style quadratic + dihedral_coeff 100.0 80.0 + +Description +""""""""""" + +The *quadratic* dihedral style uses the potential: + +.. image:: Eqs/dihedral_quadratic.jpg + :align: center + +This dihedral potential can be used to keep a dihedral in a predefined +value (cis=zero, right-hand convention is used). + +The following coefficients must be defined for each dihedral type via +the :doc:`dihedral_coeff ` command as in the example +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* K (energy/radian^2) +* phi0 (degrees) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER_MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_style.txt b/doc/_sources/dihedral_style.txt new file mode 100644 index 0000000000..2d525c1854 --- /dev/null +++ b/doc/_sources/dihedral_style.txt @@ -0,0 +1,135 @@ +.. index:: dihedral_style + +dihedral_style command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style style + +* style = *none* or *hybrid* or *charmm* or *class2* or *harmonic* or *helix* or *multi/harmonic* or *opls* + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style harmonic + dihedral_style multi/harmonic + dihedral_style hybrid harmonic charmm + +Description +""""""""""" + +Set the formula(s) LAMMPS uses to compute dihedral interactions +between quadruplets of atoms, which remain in force for the duration +of the simulation. The list of dihedral quadruplets is read in by a +:doc:`read_data ` or :doc:`read_restart ` command +from a data or restart file. + +Hybrid models where dihedrals are computed using different dihedral +potentials can be setup using the *hybrid* dihedral style. + +The coefficients associated with a dihedral style can be specified in +a data or restart file or via the :doc:`dihedral_coeff ` +command. + +All dihedral potentials store their coefficient data in binary restart +files which means dihedral_style and +:doc:`dihedral_coeff ` commands do not need to be +re-specified in an input script that restarts a simulation. See the +:doc:`read_restart ` command for details on how to do +this. The one exception is that dihedral_style *hybrid* only stores +the list of sub-styles in the restart file; dihedral coefficients need +to be re-specified. + +.. note:: + + When both a dihedral and pair style is defined, the + :doc:`special_bonds ` command often needs to be used to + turn off (or weight) the pairwise interaction that would otherwise + exist between 4 bonded atoms. + +In the formulas listed for each dihedral style, *phi* is the torsional +angle defined by the quadruplet of atoms. This angle has a sign +convention as shown in this diagram: + +.. image:: Eqs/dihedral_sign.jpg + :align: center + +where the I,J,K,L ordering of the 4 atoms that define the dihedral +is from left to right. + +This sign convention effects several of the dihedral styles listed +below (e.g. charmm, helix) in the sense that the energy formula +depends on the sign of phi, which may be reflected in the value of the +coefficients you specify. + +.. note:: + + When comparing the formulas and coefficients for various LAMMPS + dihedral styles with dihedral equations defined by other force fields, + note that some force field implementations divide/multiply the energy + prefactor *K* by the multiple number of torsions that contain the J-K + bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed + dihedral equation applies to each individual dihedral. Thus you need + to define *K* appropriately via the + :doc:`dihedral_coeff ` command to account for this + difference if necessary. + + +---------- + + +Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on +the style to display the formula it computes and coefficients +specified by the associated :doc:`dihedral_coeff ` command. + +Note that there are also additional dihedral styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the dihedral section of +:ref:`this page `. + +* :doc:`dihedral_style none ` - turn off dihedral interactions +* :doc:`dihedral_style hybrid ` - define multiple styles of dihedral interactions + +* :doc:`dihedral_style charmm ` - CHARMM dihedral +* :doc:`dihedral_style class2 ` - COMPASS (class 2) dihedral +* :doc:`dihedral_style harmonic ` - harmonic dihedral +* :doc:`dihedral_style helix ` - helix dihedral +* :doc:`dihedral_style multi/harmonic ` - multi-harmonic dihedral +* :doc:`dihedral_style opls ` - OPLS dihedral + + +---------- + + +Restrictions +"""""""""""" + + +Dihedral styles can only be set for atom styles that allow dihedrals +to be defined. + +Most dihedral styles are part of the MOLECULE package. They are only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info on packages. +The doc pages for individual dihedral potentials tell if it is part of +a package. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +Default +""""""" + +dihedral_style none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dihedral_table.txt b/doc/_sources/dihedral_table.txt new file mode 100644 index 0000000000..0e3c537b24 --- /dev/null +++ b/doc/_sources/dihedral_table.txt @@ -0,0 +1,229 @@ +.. index:: dihedral_style table + +dihedral_style table command +============================ + +dihedral_style table/omp command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + dihedral_style table style Ntable + +* style = *linear* or *spline* = method of interpolation +* Ntable = size of the internal lookup table + +Examples +"""""""" + +.. parsed-literal:: + + dihedral_style table spline 400 + dihedral_style table linear 1000 + dihedral_coeff 1 file.table DIH_TABLE1 + dihedral_coeff 2 file.table DIH_TABLE2 + +Description +""""""""""" + +The *table* dihedral style creates interpolation tables of length +*Ntable* from dihedral potential and derivative values listed in a +file(s) as a function of the dihedral angle "phi". The files are read +by the :doc:`dihedral_coeff ` command. + +The interpolation tables are created by fitting cubic splines to the +file values and interpolating energy and derivative values at each of +*Ntable* dihedral angles. During a simulation, these tables are used +to interpolate energy and force values on individual atoms as +needed. The interpolation is done in one of 2 styles: *linear* or +*spline*. + +For the *linear* style, the dihedral angle (phi) is used to find 2 +surrounding table values from which an energy or its derivative is +computed by linear interpolation. + +For the *spline* style, cubic spline coefficients are computed and +stored at each of the *Ntable* evenly-spaced values in the +interpolated table. For a given dihedral angle (phi), the appropriate +coefficients are chosen from this list, and a cubic polynomial is used +to compute the energy and the derivative at this angle. + +The following coefficients must be defined for each dihedral type via +the :doc:`dihedral_coeff ` command as in the example +above. + +* filename +* keyword + +The filename specifies a file containing tabulated energy and +derivative values. The keyword specifies a section of the file. The +format of this file is described below. + + +---------- + + +The format of a tabulated file is as follows (without the +parenthesized comments). It can begin with one or more comment +or blank lines. + +.. parsed-literal:: + + # Table of the potential and its negative derivative + +.. parsed-literal:: + + DIH_TABLE1 (keyword is the first text on line) + N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F) + (blank line) + 1 -168.0 -1.40351172223 -0.0423346818422 + 2 -156.0 -1.70447981034 -0.00811786522531 + 3 -144.0 -1.62956100432 0.0184129719987 + ... + 30 180.0 -0.707106781187 -0.0719306095245 + +.. parsed-literal:: + + # Example 2: table of the potential. Forces omitted + +.. parsed-literal:: + + DIH_TABLE2 + N 30 NOF CHECKU testU.dat CHECKF testF.dat + +.. parsed-literal:: + + 1 -168.0 -1.40351172223 + 2 -156.0 -1.70447981034 + 3 -144.0 -1.62956100432 + ... + 30 180.0 -0.707106781187 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the +:doc:`dihedral_coeff ` command. The next line lists (in +any order) one or more parameters for the table. Each parameter is a +keyword followed by one or more numeric values. + +Following a blank line, the next N lines list the tabulated values. On +each line, the 1st value is the index from 1 to N, the 2nd value is +the angle value, the 3rd value is the energy (in energy units), and +the 4th is -dE/d(phi) also in energy units). The 3rd term is the +energy of the 4-atom configuration for the specified angle. The 4th +term (when present) is the negative derivative of the energy with +respect to the angle (in degrees, or radians depending on whether the +user selected DEGREES or RADIANS). Thus the units of the last term +are still energy, not force. The dihedral angle values must increase +from one line to the next. + +Dihedral table splines are cyclic. There is no discontinuity at 180 +degrees (or at any other angle). Although in the examples above, the +angles range from -180 to 180 degrees, in general, the first angle in +the list can have any value (positive, zero, or negative). However +the *range* of angles represented in the table must be *strictly* less +than 360 degrees (2pi radians) to avoid angle overlap. (You may not +supply entries in the table for both 180 and -180, for example.) If +the user's table covers only a narrow range of dihedral angles, +strange numerical behavior can occur in the large remaining gap. + +**Parameters:** + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the N +specified in the :doc:`dihedral_style table ` command. +Let *Ntable* is the number of table entries requested dihedral_style +command, and let *Nfile* be the parameter following "N" in the +tabulated file ("30" in the sparse example above). What LAMMPS does +is a preliminary interpolation by creating splines using the *Nfile* +tabulated values as nodal points. It uses these to interpolate as +needed to generate energy and derivative values at *Ntable* different +points (which are evenly spaced over a 360 degree range, even if the +angles in the file are not). The resulting tables of length *Ntable* +are then used as described above, when computing energy and force for +individual dihedral angles and their atoms. This means that if you +want the interpolation tables of length *Ntable* to match exactly what +is in the tabulated file (with effectively nopreliminary +interpolation), you should set *Ntable* = *Nfile*. To insure the +nodal points in the user's file are aligned with the interpolated +table entries, the angles in the table should be integer multiples of +360/*Ntable* degrees, or 2*PI/*Ntable* radians (depending on your +choice of angle units). + +The optional "NOF" keyword allows the user to omit the forces +(negative energy derivatives) from the table file (normally located in +the 4th column). In their place, forces will be calculated +automatically by differentiating the potential energy function +indicated by the 3rd column of the table (using either linear or +spline interpolation). + +The optional "DEGREES" keyword allows the user to specify angles in +degrees instead of radians (default). + +The optional "RADIANS" keyword allows the user to specify angles in +radians instead of degrees. (Note: This changes the way the forces +are scaled in the 4th column of the data file.) + +The optional "CHECKU" keyword is followed by a filename. This allows +the user to save all of the the *Ntable* different entries in the +interpolated energy table to a file to make sure that the interpolated +function agrees with the user's expectations. (Note: You can +temporarily increase the *Ntable* parameter to a high value for this +purpose. "*Ntable*" is explained above.) + +The optional "CHECKF" keyword is analogous to the "CHECKU" keyword. +It is followed by a filename, and it allows the user to check the +interpolated force table. This option is available even if the user +selected the "NOF" option. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds one +that matches the specified keyword. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restrictions +"""""""""""" + + +This dihedral style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS <2_3>` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`dihedral_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dimension.txt b/doc/_sources/dimension.txt new file mode 100644 index 0000000000..2a421360ba --- /dev/null +++ b/doc/_sources/dimension.txt @@ -0,0 +1,63 @@ +.. index:: dimension + +dimension command +================= + +Syntax +"""""" + +.. parsed-literal:: + + dimension N + +* N = 2 or 3 + +Examples +"""""""" + +.. parsed-literal:: + + dimension 2 + +Description +""""""""""" + +Set the dimensionality of the simulation. By default LAMMPS runs 3d +simulations. To run a 2d simulation, this command should be used +prior to setting up a simulation box via the +:doc:`create_box ` or :doc:`read_data ` commands. +Restart files also store this setting. + +See the discussion in :doc:`Section_howto ` for +additional instructions on how to run 2d simulations. + +.. note:: + + Some models in LAMMPS treat particles as finite-size spheres or + ellipsoids, as opposed to point particles. In 2d, the particles will + still be spheres or ellipsoids, not circular disks or ellipses, + meaning their moment of inertia will be the same as in 3d. + +Restrictions +"""""""""""" + + +This command must be used before the simulation box is defined by a +:doc:`read_data ` or :doc:`create_box ` command. + +Related commands +"""""""""""""""" + +:doc:`fix enforce2d ` + +Default +""""""" + +.. parsed-literal:: + + dimension 3 + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/displace_atoms.txt b/doc/_sources/displace_atoms.txt new file mode 100644 index 0000000000..acb703e732 --- /dev/null +++ b/doc/_sources/displace_atoms.txt @@ -0,0 +1,163 @@ +.. index:: displace_atoms + +displace_atoms command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + displace_atoms group-ID style args keyword value ... + +* group-ID = ID of group of atoms to displace +* style = *move* or *ramp* or *random* or *rotate* +.. parsed-literal:: + + *move* args = delx dely delz + delx,dely,delz = distance to displace in each dimension (distance units) + any of delx,dely,delz can be a variable (see below) + *ramp* args = ddim dlo dhi dim clo chi + ddim = *x* or *y* or *z* + dlo,dhi = displacement distance between dlo and dhi (distance units) + dim = *x* or *y* or *z* + clo,chi = lower and upper bound of domain to displace (distance units) + *random* args = dx dy dz seed + dx,dy,dz = random displacement magnitude in each dimension (distance units) + seed = random # seed (positive integer) + *rotate* args = Px Py Pz Rx Ry Rz theta + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + theta = angle of rotation (degrees) + +* zero or more keyword/value pairs may be appended +.. parsed-literal:: + + keyword = *units* + value = *box* or *lattice* + + + +Examples +"""""""" + +.. parsed-literal:: + + displace_atoms top move 0 -5 0 units box + displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 + +Description +""""""""""" + +Displace a group of atoms. This can be used to move atoms a large +distance before beginning a simulation or to randomize atoms initially +on a lattice. For example, in a shear simulation, an initial strain +can be imposed on the system. Or two groups of atoms can be brought +into closer proximity. + +The *move* style displaces the group of atoms by the specified 3d +displacement vector. Any of the 3 quantities defining the vector +components can be specified as an equal-style or atom-style +:doc:`variable `. If the value is a variable, it should be +specified as v_name, where name is the variable name. In this case, +the variable will be evaluated, and its value(s) used for the +displacement(s). The scale factor implied by the *units* keyword will +also be applied to the variable result. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Atom-style variables can specify the same formulas as +equal-style variables but can also include per-atom values, such as +atom coordinates or per-atom values read from a file. Note that if +the variable references other :doc:`compute ` or :doc:`fix ` +commands, those values must be up-to-date for the current timestep. +See the "Variable Accuracy" section of the :doc:`variable ` +doc page for more details. + +The *ramp* style displaces atoms a variable amount in one dimension +depending on the atom's coordinate in a (possibly) different +dimension. For example, the second example command displaces atoms in +the x-direction an amount between 0.0 and 5.0 distance units. Each +atom's displacement depends on the fractional distance its y +coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside +those bounds will be moved the minimum (0.0) or maximum (5.0) amount. + +The *random* style independently moves each atom in the group by a +random displacement, uniformly sampled from a value between -dx and ++dx in the x dimension, and similarly for y and z. Random numbers are +used in such a way that the displacement of a particular atom is the +same, regardless of how many processors are being used. + +The *rotate* style rotates each atom in the group by the angle *theta* +around a rotation axis *R* = (Rx,Ry,Rz) that goes thru a point *P* = +(Px,Py,Pz). The direction of rotation for the atoms around the +rotation axis is consistent with the right-hand rule: if your +right-hand thumb points along *R*, then your fingers wrap around the +axis in the direction of positive theta. + +If the defined :doc:`atom_style ` assigns an orientation to +each atom (:doc:`atom styles ` ellipsoid, line, tri, body), +then that property is also updated appropriately to correspond to the +atom's rotation. + +Distance units for displacements and the origin point of the *rotate* +style are determined by the setting of *box* or *lattice* for the +*units* keyword. *Box* means distance units as defined by the +:doc:`units ` command - e.g. Angstroms for *real* units. +*Lattice* means distance units are in lattice spacings. The +:doc:`lattice ` command must have been previously used to +define the lattice spacing. + + +---------- + + +.. note:: + + Care should be taken not to move atoms on top of other atoms. + After the move, atoms are remapped into the periodic simulation box if + needed, and any shrink-wrap boundary conditions (see the + :doc:`boundary ` command) are enforced which may change the + box size. Other than this effect, this command does not change the + size or shape of the simulation box. See the + :doc:`change_box ` command if that effect is desired. + +.. note:: + + Atoms can be moved arbitrarily long distances by this command. + If the simulation box is non-periodic and shrink-wrapped (see the + :doc:`boundary ` command), this can change its size or shape. + This is not a problem, except that the mapping of processors to the + simulation box is not changed by this command from its initial 3d + configuration; see the :doc:`processors ` command. Thus, if + the box size/shape changes dramatically, the mapping of processors to + the simulation box may not end up as optimal as the initial mapping + attempted to be. + + +---------- + + +Restrictions +"""""""""""" + + +You cannot rotate around any rotation vector except the z-axis for a +2d simulation. + +Related commands +"""""""""""""""" + +:doc:`lattice `, :doc:`change_box `, +:doc:`fix_move ` + +Default +""""""" + +The option defaults are units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dump.txt b/doc/_sources/dump.txt new file mode 100644 index 0000000000..2c05cd317c --- /dev/null +++ b/doc/_sources/dump.txt @@ -0,0 +1,684 @@ +.. index:: dump + +dump command +============ + +:doc:`dump h5md ` command +==================================== + +:doc:`dump image ` command +====================================== + +:doc:`dump movie ` command +====================================== + +:doc:`dump molfile ` command +========================================== + +Syntax +"""""" + +.. parsed-literal:: + + dump ID group-ID style N file args + +* ID = user-assigned name for the dump +* group-ID = ID of the group of atoms to be dumped +* style = *atom* or *atom/gz* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/mpiio* or *dcd* or *xtc* or *xyz* or *xyz/gz* or *xyz/mpiio* or *h5md* or *image* or *movie* or *molfile* or *local* or *custom* or *custom/gz* or *custom/mpiio* +* N = dump every this many timesteps +* file = name of file to write dump info to +* args = list of arguments for a particular style +.. parsed-literal:: + + *atom* args = none + *atom/gz* args = none + *atom/mpiio* args = none + *cfg* args = same as *custom* args, see below + *cfg/gz* args = same as *custom* args, see below + *cfg/mpiio* args = same as *custom* args, see below + *dcd* args = none + *xtc* args = none + *xyz* args = none + +.. parsed-literal:: + + *xyz/gz* args = none + +.. parsed-literal:: + + *xyz/mpiio* args = none + +.. parsed-literal:: + + *h5md* args = discussed on :doc:`dump h5md ` doc page + +.. parsed-literal:: + + *image* args = discussed on :doc:`dump image ` doc page + +.. parsed-literal:: + + *movie* args = discussed on :doc:`dump image ` doc page + +.. parsed-literal:: + + *molfile* args = discussed on :doc:`dump molfile ` doc page + +.. parsed-literal:: + + *local* args = list of local attributes + possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N] + index = enumeration of local values + c_ID = local vector calculated by a compute with ID + c_ID[N] = Nth column of local array calculated by a compute with ID + f_ID = local vector calculated by a fix with ID + f_ID[N] = Nth column of local array calculated by a fix with ID + +.. parsed-literal:: + + *custom* or *custom/gz* or *custom/mpiio* args = list of atom attributes + possible attributes = id, mol, proc, procp1, type, element, mass, + x, y, z, xs, ys, zs, xu, yu, zu, + xsu, ysu, zsu, ix, iy, iz, + vx, vy, vz, fx, fy, fz, + q, mux, muy, muz, mu, + radius, diameter, omegax, omegay, omegaz, + angmomx, angmomy, angmomz, tqx, tqy, tqz, + c_ID, c_ID[N], f_ID, f_ID[N], v_name + +.. parsed-literal:: + + id = atom ID + mol = molecule ID + proc = ID of processor that owns atom + procp1 = ID+1 of processor that owns atom + type = atom type + element = name of atom element, as defined by :doc:`dump_modify ` command + mass = atom mass + x,y,z = unscaled atom coordinates + xs,ys,zs = scaled atom coordinates + xu,yu,zu = unwrapped atom coordinates + xsu,ysu,zsu = scaled unwrapped atom coordinates + ix,iy,iz = box image that the atom is in + vx,vy,vz = atom velocities + fx,fy,fz = forces on atoms + q = atom charge + mux,muy,muz = orientation of dipole moment of atom + mu = magnitude of dipole moment of atom + radius,diameter = radius,diameter of spherical particle + omegax,omegay,omegaz = angular velocity of spherical particle + angmomx,angmomy,angmomz = angular momentum of aspherical particle + tqx,tqy,tqz = torque on finite-size particles + c_ID = per-atom vector calculated by a compute with ID + c_ID[N] = Nth column of per-atom array calculated by a compute with ID + f_ID = per-atom vector calculated by a fix with ID + f_ID[N] = Nth column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name + d_name = per-atom floating point vector with name, managed by fix property/atom + i_name = per-atom integer vector with name, managed by fix property/atom + + + +Examples +"""""""" + +.. parsed-literal:: + + dump myDump all atom 100 dump.atom + dump myDump all atom/mpiio 100 dump.atom.mpiio + dump myDump all atom/gz 100 dump.atom.gz + dump 2 subgroup atom 50 dump.run.bin + dump 2 subgroup atom 50 dump.run.mpiio.bin + dump 4a all custom 100 dump.myforce.* id type x y vx fx + dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke + dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz + dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2] + dump 1 all xtc 1000 file.xtc + +Description +""""""""""" + +Dump a snapshot of atom quantities to one or more files every N +timesteps in one of several styles. The *image* and *movie* styles are +the exception: the *image* style renders a JPG, PNG, or PPM image file +of the atom configuration every N timesteps while the *movie* style +combines and compresses them into a movie file; both are discussed in +detail on the :doc:`dump image ` doc page. The timesteps on +which dump output is written can also be controlled by a variable. +See the :doc:`dump_modify every ` command. + +Only information for atoms in the specified group is dumped. The +:doc:`dump_modify thresh and region ` commands can also +alter what atoms are included. Not all styles support all these +options; see details below. + +As described below, the filename determines the kind of output (text +or binary or gzipped, one big file or one per timestep, one big file +or multiple smaller files). + +.. note:: + + Because periodic boundary conditions are enforced only on + timesteps when neighbor lists are rebuilt, the coordinates of an atom + written to a dump file may be slightly outside the simulation box. + +.. note:: + + Unless the :doc:`dump_modify sort ` option is + invoked, the lines of atom information written to dump files + (typically one line per atom) will be in an indeterminate order for + each snapshot. This is even true when running on a single processor, + if the :doc:`atom_modify sort ` option is on, which it is + by default. In this case atoms are re-ordered periodically during a + simulation, due to spatial sorting. It is also true when running in + parallel, because data for a single snapshot is collected from + multiple processors, each of which owns a subset of the atoms. + +For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by +default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting by +atom ID is on by default. See the :doc:`dump_modify ` doc +page for details. + +The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are identical +in command syntax to the corresponding styles without "gz", however, +they generate compressed files using the zlib library. Thus the filename +suffix ".gz" is mandatory. This is an alternative approach to writing +compressed files via a pipe, as done by the regular dump styles, which +may be required on clusters where the interface to the high-speed network +disallows using the fork() library call (which is needed for a pipe). +For the remainder of this doc page, you should thus consider the *atom* +and *atom/gz* styles (etc) to be inter-changeable, with the exception +of the required filename suffix. + +As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and +*xyz/mpiio* styles are identical in command syntax and in the format +of the dump files they create, to the corresponding styles without +"mpiio", except the single dump file they produce is written in +parallel via the MPI-IO library. For the remainder of this doc page, +you should thus consider the *atom* and *atom/mpiio* styles (etc) to +be inter-changeable. The one exception is how the filename is +specified for the MPI-IO styles, as explained below. + + +---------- + + +The *style* keyword determines what atom quantities are written to the +file and in what format. Settings made via the +:doc:`dump_modify ` command can also alter the format of +individual values and the file itself. + +The *atom*, *local*, and *custom* styles create files in a simple text +format that is self-explanatory when viewing a dump file. Many of the +LAMMPS :doc:`post-processing tools `, including +`Pizza.py `_, work with this +format, as does the :doc:`rerun ` command. + +For post-processing purposes the *atom*, *local*, and *custom* text +files are self-describing in the following sense. + +The dimensions of the simulation box are included in each snapshot. +For an orthogonal simulation box this information is is formatted as: + +.. parsed-literal:: + + ITEM: BOX BOUNDS xx yy zz + xlo xhi + ylo yhi + zlo zhi + +where xlo,xhi are the maximum extents of the simulation box in the +x-dimension, and similarly for y and z. The "xx yy zz" represent 6 +characters that encode the style of boundary for each of the 6 +simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of +the 6 characters is either p = periodic, f = fixed, s = shrink wrap, +or m = shrink wrapped with a minimum value. See the +:doc:`boundary ` command for details. + +For triclinic simulation boxes (non-orthogonal), an orthogonal +bounding box which encloses the triclinic simulation box is output, +along with the 3 tilt factors (xy, xz, yz) of the triclinic box, +formatted as follows: + +.. parsed-literal:: + + ITEM: BOX BOUNDS xy xz yz xx yy zz + xlo_bound xhi_bound xy + ylo_bound yhi_bound xz + zlo_bound zhi_bound yz + +The presence of the text "xy xz yz" in the ITEM line indicates that +the 3 tilt factors will be included on each of the 3 following lines. +This bounding box is convenient for many visualization programs. The +meaning of the 6 character flags for "xx yy zz" is the same as above. + +Note that the first two numbers on each line are now xlo_bound instead +of xlo, etc, since they repesent a bounding box. See :ref:`this section ` of the doc pages for a geometric +description of triclinic boxes, as defined by LAMMPS, simple formulas +for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are +calculated from the triclinic parameters, and how to transform those +parameters to and from other commonly used triclinic representations. + +The "ITEM: ATOMS" line in each snapshot lists column descriptors for +the per-atom lines that follow. For example, the descriptors would be +"id type xs ys zs" for the default *atom* style, and would be the atom +attributes you specify in the dump command for the *custom* style. + +For style *atom*, atom coordinates are written to the file, along with +the atom ID and atom type. By default, atom coords are written in a +scaled format (from 0 to 1). I.e. an x value of 0.25 means the atom +is at a location 1/4 of the distance from xlo to xhi of the box +boundaries. The format can be changed to unscaled coords via the +:doc:`dump_modify ` settings. Image flags can also be +added for each atom via dump_modify. + +Style *custom* allows you to specify a list of atom attributes to be +written to the dump file for each atom. Possible attributes are +listed above and will appear in the order specified. You cannot +specify a quantity that is not defined for a particular simulation - +such as *q* for atom style *bond*, since that atom style doesn't +assign charges. Dumps occur at the very end of a timestep, so atom +attributes will include effects due to fixes that are applied during +the timestep. An explanation of the possible dump custom attributes +is given below. + +For style *local*, local output generated by :doc:`computes ` +and :doc:`fixes ` is used to generate lines of output that is +written to the dump file. This local data is typically calculated by +each processor based on the atoms it owns, but there may be zero or +more entities per atom, e.g. a list of bond distances. An explanation +of the possible dump local attributes is given below. Note that by +using input from the :doc:`compute property/local ` command with dump local, +it is possible to generate information on bonds, angles, etc that can +be cut and pasted directly into a data file read by the +:doc:`read_data ` command. + +Style *cfg* has the same command syntax as style *custom* and writes +extended CFG format files, as used by the +`AtomEye `_ visualization +package. Since the extended CFG format uses a single snapshot of the +system per file, a wildcard "*" must be included in the filename, as +discussed below. The list of atom attributes for style *cfg* must +begin with either "mass type xs ys zs" or "mass type xsu ysu zsu" +since these quantities are needed to write the CFG files in the +appropriate format (though the "mass" and "type" fields do not appear +explicitly in the file). Any remaining attributes will be stored as +"auxiliary properties" in the CFG files. Note that you will typically +want to use the :doc:`dump_modify element ` command with +CFG-formatted files, to associate element names with atom types, so +that AtomEye can render atoms appropriately. When unwrapped +coordinates *xsu*, *ysu*, and *zsu* are requested, the nominal AtomEye +periodic cell dimensions are expanded by a large factor UNWRAPEXPAND = +10.0, which ensures atoms that are displayed correctly for up to +UNWRAPEXPAND/2 periodic boundary crossings in any direction. Beyond +this, AtomEye will rewrap the unwrapped coordinates. The expansion +causes the atoms to be drawn farther away from the viewer, but it is +easy to zoom the atoms closer, and the interatomic distances are +unaffected. + +The *dcd* style writes DCD files, a standard atomic trajectory format +used by the CHARMM, NAMD, and XPlor molecular dynamics packages. DCD +files are binary and thus may not be portable to different machines. +The number of atoms per snapshot cannot change with the *dcd* style. +The *unwrap* option of the :doc:`dump_modify ` command +allows DCD coordinates to be written "unwrapped" by the image flags +for each atom. Unwrapped means that if the atom has passed through +a periodic boundary one or more times, the value is printed for what +the coordinate would be if it had not been wrapped back into the +periodic box. Note that these coordinates may thus be far outside +the box size stored with the snapshot. + +The *xtc* style writes XTC files, a compressed trajectory format used +by the GROMACS molecular dynamics package, and described +`here `_. +The precision used in XTC files can be adjusted via the +:doc:`dump_modify ` command. The default value of 1000 +means that coordinates are stored to 1/1000 nanometer accuracy. XTC +files are portable binary files written in the NFS XDR data format, +so that any machine which supports XDR should be able to read them. +The number of atoms per snapshot cannot change with the *xtc* style. +The *unwrap* option of the :doc:`dump_modify ` command allows +XTC coordinates to be written "unwrapped" by the image flags for each +atom. Unwrapped means that if the atom has passed thru a periodic +boundary one or more times, the value is printed for what the +coordinate would be if it had not been wrapped back into the periodic +box. Note that these coordinates may thus be far outside the box size +stored with the snapshot. + +The *xyz* style writes XYZ files, which is a simple text-based +coordinate format that many codes can read. Specifically it has +a line with the number of atoms, then a comment line that is +usually ignored followed by one line per atom with the atom type +and the x-, y-, and z-coordinate of that atom. You can use the +:doc:`dump_modify element ` option to change the output +from using the (numerical) atom type to an element name (or some +other label). This will help many visualization programs to guess +bonds and colors. + +Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files +can be read directly by `VMD `_, a +popular molecular viewing program. See :ref:`Section tools ` of the manual and the +tools/lmp2vmd/README.txt file for more information about support in +VMD for reading and visualizing LAMMPS dump files. + + +---------- + + +Dumps are performed on timesteps that are a multiple of N (including +timestep 0) and on the last timestep of a minimization if the +minimization converges. Note that this means a dump will not be +performed on the initial timestep after the dump command is invoked, +if the current timestep is not a multiple of N. This behavior can be +changed via the :doc:`dump_modify first ` command, which +can also be useful if the dump command is invoked after a minimization +ended on an arbitrary timestep. N can be changed between runs by +using the :doc:`dump_modify every ` command (not allowed +for *dcd* style). The :doc:`dump_modify every ` command +also allows a variable to be used to determine the sequence of +timesteps on which dump files are written. In this mode a dump on the +first timestep of a run will also not be written unless the +:doc:`dump_modify first ` command is used. + +The specified filename determines how the dump file(s) is written. +The default is to write one large text file, which is opened when the +dump command is invoked and closed when an :doc:`undump ` +command is used or when LAMMPS exits. For the *dcd* and *xtc* styles, +this is a single large binary file. + +Dump filenames can contain two wildcard characters. If a "*" +character appears in the filename, then one file per snapshot is +written and the "*" character is replaced with the timestep value. +For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000, +tmp.dump.20000, etc. This option is not available for the *dcd* and +*xtc* styles. Note that the :doc:`dump_modify pad ` +command can be used to insure all timestep numbers are the same length +(e.g. 00010), which can make it easier to read a series of dump files +in order with some post-processing tools. + +If a "%" character appears in the filename, then each of P processors +writes a portion of the dump file, and the "%" character is replaced +with the processor ID from 0 to P-1. For example, tmp.dump.% becomes +tmp.dump.0, tmp.dump.1, ... tmp.dump.P-1, etc. This creates smaller +files and can be a fast mode of output on parallel machines that +support parallel I/O for output. This option is not available for the +*dcd*, *xtc*, and *xyz* styles. + +By default, P = the number of processors meaning one file per +processor, but P can be set to a smaller value via the *nfile* or +*fileper* keywords of the :doc:`dump_modify ` command. +These options can be the most efficient way of writing out dump files +when running on large numbers of processors. + +Note that using the "*" and "%" characters together can produce a +large number of small dump files! + +For the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* +styles, a single dump file is written in parallel via the MPI-IO +library, which is part of the MPI standard for versions 2.0 and above. +Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO +package installed, e.g. + +.. parsed-literal:: + + make yes-mpiio # installs the MPIIO package + make g++ # build LAMMPS for your platform + +Second, use a dump filename which contains ".mpiio". Note that it +does not have to end in ".mpiio", just contain those characters. +Unlike MPI-IO restart files, which must be both written and read using +MPI-IO, the dump files produced by these MPI-IO styles are identical +in format to the files produced by their non-MPI-IO style +counterparts. This means you can write a dump file using MPI-IO and +use the :doc:`read_dump ` command or perform other +post-processing, just as if the dump file was not written using +MPI-IO. + +Note that MPI-IO dump files are one large file which all processors +write to. You thus cannot use the "%" wildcard character described +above in the filename since that specifies generation of multiple +files. You can use the ".bin" suffix described below in an MPI-IO +dump file; again this file will be written in parallel and have the +same binary format as if it were written without MPI-IO. + +If the filename ends with ".bin", the dump file (or files, if "*" or +"%" is also used) is written in binary format. A binary dump file +will be about the same size as a text version, but will typically +write out much faster. Of course, when post-processing, you will need +to convert it back to text format (see the :ref:`binary2txt tool `) or write your own code to read the +binary file. The format of the binary file can be understood by +looking at the tools/binary2txt.cpp file. This option is only +available for the *atom* and *custom* styles. + +If the filename ends with ".gz", the dump file (or files, if "*" or "%" +is also used) is written in gzipped format. A gzipped dump file will +be about 3x smaller than the text version, but will also take longer +to write. This option is not available for the *dcd* and *xtc* +styles. + + +---------- + + +This section explains the local attributes that can be specified as +part of the *local* style. + +The *index* attribute can be used to generate an index number from 1 +to N for each line written into the dump file, where N is the total +number of local datums from all processors, or lines of output that +will appear in the snapshot. Note that because data from different +processors depend on what atoms they currently own, and atoms migrate +between processor, there is no guarantee that the same index will be +used for the same info (e.g. a particular bond) in successive +snapshots. + +The *c_ID* and *c_ID[N]* attributes allow local vectors or arrays +calculated by a :doc:`compute ` to be output. The ID in the +attribute should be replaced by the actual ID of the compute that has +been defined previously in the input script. See the +:doc:`compute ` command for details. There are computes for +calculating local information such as indices, types, and energies for +bonds and angles. + +Note that computes which calculate global or per-atom quantities, as +opposed to local quantities, cannot be output in a dump local command. +Instead, global quantities can be output by the :doc:`thermo_style custom ` command, and per-atom quantities can be +output by the dump custom command. + +If *c_ID* is used as a attribute, then the local vector calculated by +the compute is printed. If *c_ID[N]* is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length local +array calculated by the compute. + +The *f_ID* and *f_ID[N]* attributes allow local vectors or arrays +calculated by a :doc:`fix ` to be output. The ID in the attribute +should be replaced by the actual ID of the fix that has been defined +previously in the input script. + +If *f_ID* is used as a attribute, then the local vector calculated by +the fix is printed. If *f_ID[N]* is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length local +array calculated by the fix. + +Here is an example of how to dump bond info for a system, +including the distance and energy of each bond: + +.. parsed-literal:: + + compute 1 all property/local batom1 batom2 btype + compute 2 all bond/local dist eng + dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] + + +---------- + + +This section explains the atom attributes that can be specified as +part of the *custom* and *cfg* styles. + +The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*, +*vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory. + +*Id* is the atom ID. *Mol* is the molecule ID, included in the data +file for molecular systems. *Proc* is the ID of the processor (0 to +Nprocs-1) that currently owns the atom. *Procp1* is the proc ID+1, +which can be convenient in place of a *type* attribute (1 to Ntypes) +for coloring atoms in a visualization program. *Type* is the atom +type (1 to Ntypes). *Element* is typically the chemical name of an +element, which you must assign to each type via the :doc:`dump_modify element ` command. More generally, it can be any +string you wish to associated with an atom type. *Mass* is the atom +mass. *Vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components of +atom velocity and force and atomic charge. + +There are several options for outputting atom coordinates. The *x*, +*y*, *z* attributes write atom coordinates "unscaled", in the +appropriate distance :doc:`units ` (Angstroms, sigma, etc). Use +*xs*, *ys*, *zs* if you want the coordinates "scaled" to the box size, +so that each value is 0.0 to 1.0. If the simulation box is triclinic +(tilted), then all atom coords will still be between 0.0 and 1.0. Use +*xu*, *yu*, *zu* if you want the coordinates "unwrapped" by the image +flags for each atom. Unwrapped means that if the atom has passed thru +a periodic boundary one or more times, the value is printed for what +the coordinate would be if it had not been wrapped back into the +periodic box. Note that using *xu*, *yu*, *zu* means that the +coordinate values may be far outside the box bounds printed with the +snapshot. Using *xsu*, *ysu*, *zsu* is similar to using *xu*, *yu*, *zu*, +except that the unwrapped coordinates are scaled by the box size. Atoms +that have passed through a periodic boundary will have the corresponding +cooordinate increased or decreased by 1.0. + +The image flags can be printed directly using the *ix*, *iy*, *iz* +attributes. For periodic dimensions, they specify which image of the +simulation box the atom is considered to be in. An image of 0 means +it is inside the box as defined. A value of 2 means add 2 box lengths +to get the true value. A value of -1 means subtract 1 box length to +get the true value. LAMMPS updates these flags as atoms cross +periodic boundaries during the simulation. + +The *mux*, *muy*, *muz* attributes are specific to dipolar systems +defined with an atom style of *dipole*. They give the orientation of +the atom's point dipole moment. The *mu* attribute gives the +magnitude of the atom's dipole moment. + +The *radius* and *diameter* attributes are specific to spherical +particles that have a finite size, such as those defined with an atom +style of *sphere*. + +The *omegax*, *omegay*, and *omegaz* attributes are specific to +finite-size spherical particles that have an angular velocity. Only +certain atom styles, such as *sphere* define this quantity. + +The *angmomx*, *angmomy*, and *angmomz* attributes are specific to +finite-size aspherical particles that have an angular momentum. Only +the *ellipsoid* atom style defines this quantity. + +The *tqx*, *tqy*, *tqz* attributes are for finite-size particles that +can sustain a rotational torque due to interactions with other +particles. + +The *c_ID* and *c_ID[N]* attributes allow per-atom vectors or arrays +calculated by a :doc:`compute ` to be output. The ID in the +attribute should be replaced by the actual ID of the compute that has +been defined previously in the input script. See the +:doc:`compute ` command for details. There are computes for +calculating the per-atom energy, stress, centro-symmetry parameter, +and coordination number of individual atoms. + +Note that computes which calculate global or local quantities, as +opposed to per-atom quantities, cannot be output in a dump custom +command. Instead, global quantities can be output by the +:doc:`thermo_style custom ` command, and local quantities +can be output by the dump local command. + +If *c_ID* is used as a attribute, then the per-atom vector calculated +by the compute is printed. If *c_ID[N]* is used, then N must be in +the range from 1-M, which will print the Nth column of the M-length +per-atom array calculated by the compute. + +The *f_ID* and *f_ID[N]* attributes allow vector or array per-atom +quantities calculated by a :doc:`fix ` to be output. The ID in the +attribute should be replaced by the actual ID of the fix that has been +defined previously in the input script. The :doc:`fix ave/atom ` command is one that calculates per-atom +quantities. Since it can time-average per-atom quantities produced by +any :doc:`compute `, :doc:`fix `, or atom-style +:doc:`variable `, this allows those time-averaged results to +be written to a dump file. + +If *f_ID* is used as a attribute, then the per-atom vector calculated +by the fix is printed. If *f_ID[N]* is used, then N must be in the +range from 1-M, which will print the Nth column of the M-length +per-atom array calculated by the fix. + +The *v_name* attribute allows per-atom vectors calculated by a +:doc:`variable ` to be output. The name in the attribute +should be replaced by the actual name of the variable that has been +defined previously in the input script. Only an atom-style variable +can be referenced, since it is the only style that generates per-atom +values. Variables of style *atom* can reference individual atom +attributes, per-atom atom attributes, thermodynamic keywords, or +invoke other computes, fixes, or variables when they are evaluated, so +this is a very general means of creating quantities to output to a +dump file. + +The *d_name* and *i_name* attributes allow to output custom per atom +floating point or integer properties that are managed by +:doc:`fix property/atom `. + +See :doc:`Section_modify ` of the manual for information +on how to add new compute and fix styles to LAMMPS to calculate +per-atom quantities which could then be output into dump files. + + +---------- + + +Restrictions +"""""""""""" + + +To write gzipped dump files, you must either compile LAMMPS with the +-DLAMMPS_GZIP option or use the styles from the COMPRESS package +- see the :ref:`Making LAMMPS ` section of +the documentation. + +The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are part +of the COMPRESS package. They are only enabled if LAMMPS was built +with that package. See the :ref:`Making LAMMPS ` section for more info. + +The *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and *xyz/mpiio* styles +are part of the MPIIO package. They are only enabled if LAMMPS was +built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The *xtc* style is part of the XTC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. This is +because some machines may not support the low-level XDR data format +that XTC files are written with, which will result in a compile-time +error when a low-level include file is not found. Putting this style +in a package makes it easy to exclude from a LAMMPS build for those +machines. However, the XTC package also includes two compatibility +header files and associated functions, which should be a suitable +substitute on machines that do not have the appropriate native header +files. This option can be invoked at build time by adding +-DLAMMPS_XDR to the CCFLAGS variable in the appropriate low-level +Makefile, e.g. src/MAKE/Makefile.foo. This compatibility mode has +been tested successfully on Cray XT3/XT4/XT5 and IBM BlueGene/L +machines and should also work on IBM BG/P, and Windows XP/Vista/7 +machines. + +Related commands +"""""""""""""""" + +:doc:`dump h5md `, :doc:`dump image `, +:doc:`dump molfile `, :doc:`dump_modify `, +:doc:`undump ` + +Default +""""""" + +The defaults for the *image* and *movie* styles are listed on the +:doc:`dump image ` doc page. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dump_h5md.txt b/doc/_sources/dump_h5md.txt new file mode 100644 index 0000000000..78085bf130 --- /dev/null +++ b/doc/_sources/dump_h5md.txt @@ -0,0 +1,153 @@ +.. index:: dump h5md + +dump h5md command +================= + +Syntax +"""""" + +.. parsed-literal:: + + dump ID group-ID h5md N file.h5 args + +* ID = user-assigned name for the dump +* group-ID = ID of the group of atoms to be imaged +* h5md = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) +* N = dump every this many timesteps +* file.h5 = name of file to write to +* args = list of data elements to dump, with their dump "subintervals". + At least one element must be given and image may only be present if + position is specified first. +.. parsed-literal:: + + position options + image + velocity options + force options + species options + file_from ID: do not open a new file, re-use the already opened file from dump ID + box value = *yes* or *no* + create_group value = *yes* or *no* + author value = quoted string + +For the elements *position*, *velocity*, *force* and *species*, one +may specify a sub-interval to write the data only every N_element +iterations of the dump (i.e. every N*N_element time steps). This is +specified by the option + +.. parsed-literal:: + + every N_element + +that follows directly the element declaration. + + + +Examples +"""""""" + +.. parsed-literal:: + + dump h5md1 all h5md 100 dump_h5md.h5 position image + dump h5md1 all h5md 100 dump_h5md.h5 position velocity every 10 + dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" + +Description +""""""""""" + +Dump a snapshot of atom coordinates every N timesteps in the +`HDF5 `_ based `H5MD `_ file format :ref:`(de Buyl) `. +HDF5 files are binary, portable and self-describing. This dump style +will write only one file, on the root node. + +Several dumps may write to the same file, by using file_from and +referring to a previously defined dump. Several groups may also be +stored within the same file by defining several dumps. A dump that +refers (via *file_from*) to an already open dump ID and that concerns +another particle group must specify *create_group yes*. + +.. _h5md: http://nongnu.org/h5md/ + + + +Each data element is written every N*N_element steps. For *image*, no +subinterval is needed as it must be present at the same interval as +*position*. *image* must be given after *position* in any case. The +box information (edges in each dimension) is stored at the same +interval than the *position* element, if present. Else it is stored +every N steps. + +.. note:: + + Because periodic boundary conditions are enforced only on + timesteps when neighbor lists are rebuilt, the coordinates of an atom + written to a dump file may be slightly outside the simulation box. + +**Use from write_dump:** + +It is possible to use this dump style with the +:doc:`write_dump ` command. In this case, the subintervals +must not be set at all. The write_dump command can be used either to +create a new file or to add current data to an existing dump file by +using the *file_from* keyword. + +Typically, the *species* data is fixed. The following two commands +store the position data every 100 timesteps, with the image data, and +store once the species data in the same file. + +.. parsed-literal:: + + dump h5md1 all h5md 100 dump.h5 position image + write_dump all h5md dump.h5 file_from h5md1 species + + +---------- + + +Restrictions +"""""""""""" + + +The number of atoms per snapshot cannot change with the h5md style. +The position data is stored wrapped (box boundaries not enforced, see +note above). Only orthogonal domains are currently supported. This is +a limitation of the present dump h5md command and not of H5MD itself. + +The *h5md* dump style is part of the USER-H5MD package. It is only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. It also +requires (i) building the ch5md library provided with LAMMPS (See the +:ref:`Making LAMMPS ` section for more info.) and +(ii) having the `HDF5 `_ library installed (C bindings are +sufficient) on your system. The library ch5md is compiled with the +h5cc wrapper provided by the HDF5 library. + +.. _HDF5_ws: http://www.hdfgroup.org/HDF5/ + + + + +---------- + + +Related commands +"""""""""""""""" + +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` + + +---------- + + +.. _h5md_cpc: + + + +**(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured, +efficient, and portable file format for molecular data, +Comp. Phys. Comm. 185(6), 1546-1553 (2014) - +`[arXiv:1308.6382] `_. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dump_image.txt b/doc/_sources/dump_image.txt new file mode 100644 index 0000000000..90f7b78e35 --- /dev/null +++ b/doc/_sources/dump_image.txt @@ -0,0 +1,674 @@ +.. index:: dump image + +dump image command +================== + +dump movie command +================== + +Syntax +"""""" + +.. parsed-literal:: + + dump ID group-ID style N file color diameter keyword value ... + +* ID = user-assigned name for the dump +* group-ID = ID of the group of atoms to be imaged +* style = *image* or *movie* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) +* N = dump every this many timesteps +* file = name of file to write image to +* color = atom attribute that determines color of each atom +* diameter = atom attribute that determines size of each atom +* zero or more keyword/value pairs may be appended +* keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *size* or *view* or *center* or *up* or *zoom* or *persp* or *box* or *axes* or *subbox* or *shiny* or *ssao* +.. parsed-literal:: + + *atom* = yes/no = do or do not draw atoms + *adiam* size = numeric value for atom diameter (distance units) + *bond* values = color width = color and width of bonds + color = *atom* or *type* or *none* + width = number or *atom* or *type* or *none* + number = numeric value for bond width (distance units) + *line* = color width + color = *type* + width = numeric value for line width (distance units) + *tri* = color tflag width + color = *type* + tflag = 1 for just triangle, 2 for just tri edges, 3 for both + width = numeric value for tringle edge width (distance units) + *body* = color bflag1 bflag2 + color = *type* + bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn + *size* values = width height = size of images + width = width of image in # of pixels + height = height of image in # of pixels + *view* values = theta phi = view of simulation box + theta = view angle from +z axis (degrees) + phi = azimuthal view angle (degrees) + theta or phi can be a variable (see below) + *center* values = flag Cx Cy Cz = center point of image + flag = "s" for static, "d" for dynamic + Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box) + Cx,Cy,Cz can be variables (see below) + *up* values = Ux Uy Uz = direction that is "up" in image + Ux,Uy,Uz = components of up vector + Ux,Uy,Uz can be variables (see below) + *zoom* value = zfactor = size that simulation box appears in image + zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink + zfactor can be a variable (see below) + *persp* value = pfactor = amount of "perspective" in image + pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed) + pfactor can be a variable (see below) + *box* values = yes/no diam = draw outline of simulation box + yes/no = do or do not draw simulation box lines + diam = diameter of box lines as fraction of shortest box length + *axes* values = yes/no length diam = draw xyz axes + yes/no = do or do not draw xyz axes lines next to simulation box + length = length of axes lines as fraction of respective box lengths + diam = diameter of axes lines as fraction of shortest box length + *subbox* values = yes/no diam = draw outline of processor sub-domains + yes/no = do or do not draw sub-domain lines + diam = diameter of sub-domain lines as fraction of shortest box length + *shiny* value = sfactor = shinyness of spheres and cylinders + sfactor = shinyness of spheres and cylinders from 0.0 to 1.0 + *ssao* value = yes/no seed dfactor = SSAO depth shading + yes/no = turn depth shading on/off + seed = random # seed (positive integer) + dfactor = strength of shading from 0.0 to 1.0 + + + +Examples +"""""""" + +.. parsed-literal:: + + dump d0 all image 100 dump.*.jpg type type + dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6 + dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720 + dump m0 all movie 1000 movie.mpg type type size 640 480 + dump m1 all movie 1000 movie.avi type type size 640 480 + dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720 + +Description +""""""""""" + +Dump a high-quality rendered image of the atom configuration every N +timesteps and save the images either as a sequence of JPEG or PNG or +PPM files, or as a single movie file. The options for this command as +well as the :doc:`dump_modify ` command control what is +included in the image or movie and how it appears. A series of such +images can easily be manually converted into an animated movie of your +simulation or the process can be automated without writing the +intermediate files using the dump movie style; see further details +below. Other dump styles store snapshots of numerical data asociated +with atoms in various formats, as discussed on the :doc:`dump ` +doc page. + +Note that a set of images or a movie can be made after a simulation +has been run, using the :doc:`rerun ` command to read snapshots +from an existing dump file, and using these dump commands in the rerun +script to generate the images/movie. + +Here are two sample images, rendered as 1024x1024 JPEG files. Click +to see the full-size images: + +.. raw:: html + +
      + +.. thumbnail:: JPG/dump1.jpg + +.. thumbnail:: JPG/dump2.jpg + +.. raw:: html + +
      + +Only atoms in the specified group are rendered in the image. The +:doc:`dump_modify region and thresh ` commands can also +alter what atoms are included in the image. +The filename suffix determines whether a JPEG, PNG, or PPM file is +created with the *image* dump style. If the suffix is ".jpg" or +".jpeg", then a JPEG format file is created, if the suffix is ".png", +then a PNG format is created, else a PPM (aka NETPBM) format file is +created. The JPEG and PNG files are binary; PPM has a text mode +header followed by binary data. JPEG images have lossy compression; +PNG has lossless compression; and PPM files are uncompressed but can +be compressed with gzip, if LAMMPS has been compiled with +-DLAMMPS_GZIP and a ".gz" suffix is used. + +Similarly, the format of the resulting movie is chosen with the +*movie* dump style. This is handled by the underlying FFmpeg converter +and thus details have to be looked up in the FFmpeg documentation. +Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif +Additional settings of the movie compression like bitrate and +framerate can be set using the :doc:`dump_modify ` command. + +To write out JPEG and PNG format files, you must build LAMMPS with +support for the corresponding JPEG or PNG library. To convert images +into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG +flag. See :ref:`this section ` of the manual +for instructions on how to do this. + +.. note:: + + Because periodic boundary conditions are enforced only on + timesteps when neighbor lists are rebuilt, the coordinates of an atom + in the image may be slightly outside the simulation box. + + +---------- + + +Dumps are performed on timesteps that are a multiple of N (including +timestep 0) and on the last timestep of a minimization if the +minimization converges. Note that this means a dump will not be +performed on the initial timestep after the dump command is invoked, +if the current timestep is not a multiple of N. This behavior can be +changed via the :doc:`dump_modify first ` command, which +can be useful if the dump command is invoked after a minimization +ended on an arbitrary timestep. N can be changed between runs by +using the :doc:`dump_modify every ` command. + +Dump *image* filenames must contain a wildcard character "*", so that +one image file per snapshot is written. The "*" character is replaced +with the timestep value. For example, tmp.dump.*.jpg becomes +tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note +that the :doc:`dump_modify pad ` command can be used to +insure all timestep numbers are the same length (e.g. 00010), which +can make it easier to convert a series of images into a movie in the +correct ordering. + +Dump *movie* filenames on the other hand, must not have any wildcard +character since only one file combining all images into a single +movie will be written by the movie encoder. + + +---------- + + +The *color* and *diameter* settings determine the color and size of +atoms rendered in the image. They can be any atom attribute defined +for the :doc:`dump custom ` command, including *type* and +*element*. This includes per-atom quantities calculated by a +:doc:`compute `, :doc:`fix `, or :doc:`variable `, +which are prefixed by "c_", "f_", or "v_" respectively. Note that the +*diameter* setting can be overridden with a numeric value applied to +all atoms by the optional *adiam* keyword. + +If *type* is specified for the *color* setting, then the color of each +atom is determined by its atom type. By default the mapping of types +to colors is as follows: + +* type 1 = red +* type 2 = green +* type 3 = blue +* type 4 = yellow +* type 5 = aqua +* type 6 = cyan + +and repeats itself for types > 6. This mapping can be changed by the +:doc:`dump_modify acolor ` command. + +If *type* is specified for the *diameter* setting then the diameter of +each atom is determined by its atom type. By default all types have +diameter 1.0. This mapping can be changed by the :doc:`dump_modify adiam ` command. + +If *element* is specified for the *color* and/or *diameter* setting, +then the color and/or diameter of each atom is determined by which +element it is, which in turn is specified by the element-to-type +mapping specified by the "dump_modify element" command. By default +every atom type is C (carbon). Every element has a color and diameter +associated with it, which is the same as the colors and sizes used by +the `AtomEye `_ visualization package. + +.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A + + + +If other atom attributes are used for the *color* or *diameter* +settings, they are interpreted in the following way. + +If "vx", for example, is used as the *color* setting, then the color +of the atom will depend on the x-component of its velocity. The +association of a per-atom value with a specific color is determined by +a "color map", which can be specified via the +:doc:`dump_modify ` command. The basic idea is that the +atom-attribute will be within a range of values, and every value +within the range is mapped to a specific color. Depending on how the +color map is defined, that mapping can take place via interpolation so +that a value of -3.2 is halfway between "red" and "blue", or +discretely so that the value of -3.2 is "orange". + +If "vx", for example, is used as the *diameter* setting, then the atom +will be rendered using the x-component of its velocity as the +diameter. If the per-atom value <= 0.0, them the atom will not be +drawn. Note that finite-size spherical particles, as defined by +:doc:`atom_style sphere ` define a per-particle radius or +diameter, which can be used as the *diameter* setting. + + +---------- + + +The various kewords listed above control how the image is rendered. +As listed below, all of the keywords have defaults, most of which you +will likely not need to change. The :doc:`dump modify ` +also has options specific to the dump image style, particularly for +assigning colors to atoms, bonds, and other image features. + + +---------- + + +The *atom* keyword allow you to turn off the drawing of all atoms, if +the specified value is *no*. Note that this will not turn off the +drawing of particles that are represented as lines, triangles, or +bodies, as discussed below. These particles can be drawn separately +if the *line*, *tri*, or *body* keywords are used. + +The *adiam* keyword allows you to override the *diameter* setting to +set a single numeric *size*. All atoms will be drawn with that +diameter, e.g. 1.5, which is in whatever distance :doc:`units ` +the input script defines, e.g. Angstroms. + +The *bond* keyword allows to you to alter how bonds are drawn. A bond +is only drawn if both atoms in the bond are being drawn due to being +in the specified group and due to other selection criteria +(e.g. region, threshhold settings of the +:doc:`dump_modify ` command). By default, bonds are drawn +if they are defined in the input data file as read by the +:doc:`read_data ` command. Using *none* for both the bond +*color* and *width* value will turn off the drawing of all bonds. + +If *atom* is specified for the bond *color* value, then each bond is +drawn in 2 halves, with the color of each half being the color of the +atom at that end of the bond. + +If *type* is specified for the *color* value, then the color of each +bond is determined by its bond type. By default the mapping of bond +types to colors is as follows: + +* type 1 = red +* type 2 = green +* type 3 = blue +* type 4 = yellow +* type 5 = aqua +* type 6 = cyan + +and repeats itself for bond types > 6. This mapping can be changed by +the :doc:`dump_modify bcolor ` command. + +The bond *width* value can be a numeric value or *atom* or *type* (or +*none* as indicated above). + +If a numeric value is specified, then all bonds will be drawn as +cylinders with that diameter, e.g. 1.0, which is in whatever distance +:doc:`units ` the input script defines, e.g. Angstroms. + +If *atom* is specified for the *width* value, then each bond +will be drawn with a width corresponding to the minimum diameter +of the 2 atoms in the bond. + +If *type* is specified for the *width* value then the diameter of each +bond is determined by its bond type. By default all types have +diameter 0.5. This mapping can be changed by the :doc:`dump_modify bdiam ` command. + +The *line* keyword can be used when :doc:`atom_style line ` +is used to define particles as line segments, and will draw them as +lines. If this keyword is not used, such particles will be drawn as +spheres, the same as if they were regular atoms. The only setting +currently allowed for the *color* value is *type*, which will color +the lines according to the atom type of the particle. By default the +mapping of types to colors is as follows: + +* type 1 = red +* type 2 = green +* type 3 = blue +* type 4 = yellow +* type 5 = aqua +* type 6 = cyan + +and repeats itself for types > 6. There is not yet an option to +change this via the :doc:`dump_modify ` command. + +The line *width* can only be a numeric value, which specifies that all +lines will be drawn as cylinders with that diameter, e.g. 1.0, which +is in whatever distance :doc:`units ` the input script defines, +e.g. Angstroms. + +The *tri* keyword can be used when :doc:`atom_style tri ` is +used to define particles as triangles, and will draw them as triangles +or edges (3 lines) or both, depending on the setting for *tflag*. If +edges are drawn, the *width* setting determines the diameters of the +line segments. If this keyword is not used, triangle particles will +be drawn as spheres, the same as if they were regular atoms. The only +setting currently allowed for the *color* value is *type*, which will +color the triangles according to the atom type of the particle. By +default the mapping of types to colors is as follows: + +* type 1 = red +* type 2 = green +* type 3 = blue +* type 4 = yellow +* type 5 = aqua +* type 6 = cyan + +and repeats itself for types > 6. There is not yet an option to +change this via the :doc:`dump_modify ` command. + +The *body* keyword can be used when :doc:`atom_style body ` +is used to define body particles with internal state +(e.g. sub-particles), and will drawn them in a manner specific to the +body style. If this keyword is not used, such particles will be drawn +as spheres, the same as if they were regular atoms. + +The :doc:`body ` doc page descibes the body styles LAMMPS +currently supports, and provides more details as to the kind of body +particles they represent and how they are drawn by this dump image +command. For all the body styles, individual atoms can be either a +body particle or a usual point (non-body) particle. Non-body +particles will be drawn the same way they would be as a regular atom. +The *bflag1* and *bflag2* settings are numerical values which are +passed to the body style to affect how the drawing of a body particle +is done. See the :doc:`body ` doc page for a description of what +these parameters mean for each body style. + + +---------- + + +The *size* keyword sets the width and height of the created images, +i.e. the number of pixels in each direction. + + +---------- + + +The *view*, *center*, *up*, *zoom*, and *persp* values determine how +3d simulation space is mapped to the 2d plane of the image. Basically +they control how the simulation box appears in the image. + +All of the *view*, *center*, *up*, *zoom*, and *persp* values can be +specified as numeric quantities, whose meaning is explained below. +Any of them can also be specified as an :doc:`equal-style variable `, by using v_name as the value, where "name" is +the variable name. In this case the variable will be evaluated on the +timestep each image is created to create a new value. If the +equal-style variable is time-dependent, this is a means of changing +the way the simulation box appears from image to image, effectively +doing a pan or fly-by view of your simulation. + +The *view* keyword determines the viewpoint from which the simulation +box is viewed, looking towards the *center* point. The *theta* value +is the vertical angle from the +z axis, and must be an angle from 0 to +180 degrees. The *phi* value is an azimuthal angle around the z axis +and can be positive or negative. A value of 0.0 is a view along the ++x axis, towards the *center* point. If *theta* or *phi* are +specified via variables, then the variable values should be in +degrees. + +The *center* keyword determines the point in simulation space that +will be at the center of the image. *Cx*, *Cy*, and *Cz* are +speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is +the center of the simulation box. These values do not have to be +between 0.0 and 1.0, if you want the simulation box to be offset from +the center of the image. Note, however, that if you choose strange +values for *Cx*, *Cy*, or *Cz* you may get a blank image. Internally, +*Cx*, *Cy*, and *Cz* are converted into a point in simulation space. +If *flag* is set to "s" for static, then this conversion is done once, +at the time the dump command is issued. If *flag* is set to "d" for +dynamic then the conversion is performed every time a new image is +created. If the box size or shape is changing, this will adjust the +center point in simulation space. + +The *up* keyword determines what direction in simulation space will be +"up" in the image. Internally it is stored as a vector that is in the +plane perpendicular to the view vector implied by the *theta* and +*pni* values, and which is also in the plane defined by the view +vector and user-specified up vector. Thus this internal vector is +computed from the user-specified *up* vector as + +.. parsed-literal:: + + up_internal = view cross (up cross view) + +This means the only restriction on the specified *up* vector is that +it cannot be parallel to the *view* vector, implied by the *theta* and +*phi* values. + +The *zoom* keyword scales the size of the simulation box as it appears +in the image. The default *zfactor* value of 1 should display an +image mostly filled by the atoms in the simulation box. A *zfactor* > +1 will make the simulation box larger; a *zfactor* < 1 will make it +smaller. *Zfactor* must be a value > 0.0. + +The *persp* keyword determines how much depth perspective is present +in the image. Depth perspective makes lines that are parallel in +simulation space appear non-parallel in the image. A *pfactor* value +of 0.0 means that parallel lines will meet at infininty (1.0/pfactor), +which is an orthographic rendering with no persepctive. A *pfactor* +value between 0.0 and 1.0 will introduce more perspective. A *pfactor* +value > 1 will create a highly skewed image with a large amount of +perspective. + +.. note:: + + The *persp* keyword is not yet supported as an option. + + +---------- + + +The *box* keyword determines if and how the simulation box boundaries +are rendered as thin cylinders in the image. If *no* is set, then the +box boundaries are not drawn and the *diam* setting is ignored. If +*yes* is set, the 12 edges of the box are drawn, with a diameter that +is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for +2d). The color of the box boundaries can be set with the :doc:`dump_modify boxcolor ` command. + +The *axes* keyword determines if and how the coordinate axes are +rendered as thin cylinders in the image. If *no* is set, then the +axes are not drawn and the *length* and *diam* settings are ignored. +If *yes* is set, 3 thin cylinders are drawn to represent the x,y,z +axes in colors red,green,blue. The origin of these cylinders will be +offset from the lower left corner of the box by 10%. The *length* +setting determines how long the cylinders will be as a fraction of the +respective box lengths. The *diam* setting determines their thickness +as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for +2d). + +The *subbox* keyword determines if and how processor sub-domain +boundaries are rendered as thin cylinders in the image. If *no* is +set (default), then the sub-domain boundaries are not drawn and the +*diam* setting is ignored. If *yes* is set, the 12 edges of each +processor sub-domain are drawn, with a diameter that is a fraction of +the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color +of the sub-domain boundaries can be set with the :doc:`dump_modify boxcolor ` command. + + +---------- + + +The *shiny* keyword determines how shiny the objects rendered in the +image will appear. The *sfactor* value must be a value 0.0 <= +*sfactor* <= 1.0, where *sfactor* = 1 is a highly reflective surface +and *sfactor* = 0 is a rough non-shiny surface. + +The *ssao* keyword turns on/off a screen space ambient occlusion +(SSAO) model for depth shading. If *yes* is set, then atoms further +away from the viewer are darkened via a randomized process, which is +perceived as depth. The calculation of this effect can increase the +cost of computing the image by roughly 2x. The strength of the effect +can be scaled by the *dfactor* parameter. If *no* is set, no depth +shading is performed. + + +---------- + + +A series of JPEG, PNG, or PPM images can be converted into a movie +file and then played as a movie using commonly available tools. Using +dump style *movie* automates this step and avoids the intermediate +step of writing (many) image snapshot file. But LAMMPS has to be +compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be +installed. + +To manually convert JPEG, PNG or PPM files into an animated GIF or +MPEG or other movie file you can use: + +* a) Use the ImageMagick convert program. +.. parsed-literal:: + + % convert *.jpg foo.gif + % convert -loop 1 *.ppm foo.mpg + +Animated GIF files from ImageMagick are unoptimized. You can use a +program like gifsicle to optimize and massively shrink them. +MPEG files created by ImageMagick are in MPEG-1 format with rather +inefficient compression and low quality. + +* b) Use QuickTime. +Select "Open Image Sequence" under the File menu Load the images into +QuickTime to animate them Select "Export" under the File menu Save the +movie as a QuickTime movie (*.mov) or in another format. QuickTime +can generate very high quality and efficiently compressed movie +files. Some of the supported formats require to buy a license and some +are not readable on all platforms until specific runtime libraries are +installed. + +* c) Use FFmpeg +FFmpeg is a command line tool that is available on many platforms and +allows extremely flexible encoding and decoding of movies. + +.. parsed-literal:: + + cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v + cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi + +Frontends for FFmpeg exist for multiple platforms. For more +information see the `FFmpeg homepage `_ + + + + +---------- + + +Play the movie: + +* a) Use your browser to view an animated GIF movie. +Select "Open File" under the File menu +Load the animated GIF file + +* b) Use the freely available mplayer or ffplay tool to view a + movie. Both are available for multiple OSes and support a large + variety of file formats and decoders. +.. parsed-literal:: + + % mplayer foo.mpg + % ffplay bar.avi + +* c) Use the `Pizza.py `_ + `animate tool `_, + which works directly on a series of image files. +.. parsed-literal:: + + a = animate("foo*.jpg") + +* d) QuickTime and other Windows- or MacOS-based media players can + obviously play movie files directly. Similarly for corresponding tools + bundled with Linux desktop environments. However, due to licensing + issues with some file formats, the formats may require installing + additional libraries, purchasing a license, or may not be + supported. + +---------- + + +See :doc:`Section_modify ` of the manual for information +on how to add new compute and fix styles to LAMMPS to calculate +per-atom quantities which could then be output into dump files. + + +---------- + + +Restrictions +"""""""""""" + + +To write JPEG images, you must use the -DLAMMPS_JPEG switch when +building LAMMPS and link with a JPEG library. To write PNG images, you +must use the -DLAMMPS_PNG switch when building LAMMPS and link with a +PNG library. + +To write *movie* dumps, you must use the -DLAMMPS_FFMPEG switch when +building LAMMPS and have the FFmpeg executable available on the +machine where LAMMPS is being run. Typically it's name is lowercase, +i.e. ffmpeg. + +See the :ref:`Making LAMMPS ` section of the +documentation for details on how to compile with optional switches. + +Note that since FFmpeg is run as an external program via a pipe, +LAMMPS has limited control over its execution and no knowledge about +errors and warnings printed by it. Those warnings and error messages +will be printed to the screen only. Due to the way image data is +communicated to FFmpeg, it will often print the message + +.. parsed-literal:: + + pipe:: Input/output error + +which can be safely ignored. Other warnings +and errors have to be addressed according to the FFmpeg documentation. +One known issue is that certain movie file formats (e.g. MPEG level 1 +and 2 format streams) have video bandwith limits that can be crossed +when rendering too large of image sizes. Typical warnings look like +this: + +.. parsed-literal:: + + [mpeg @ 0x98b5e0] packet too large, ignoring buffer limits to mux it + [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018 + [mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018 + +In this case it is recommended to either reduce the size of the image +or encode in a different format that is also supported by your copy of +FFmpeg, and which does not have this limitation (e.g. .avi, .mkv, +mp4). + +Related commands +"""""""""""""""" + +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` + +Default +""""""" + +The defaults for the keywords are as follows: + +* adiam = not specified (use diameter setting) +* atom = yes +* bond = none none (if no bonds in system) +* bond = atom 0.5 (if bonds in system) +* size = 512 512 +* view = 60 30 (for 3d) +* view = 0 0 (for 2d) +* center = s 0.5 0.5 0.5 +* up = 0 0 1 (for 3d) +* up = 0 1 0 (for 2d) +* zoom = 1.0 +* persp = 0.0 +* box = yes 0.02 +* axes = no 0.0 0.0 +* subbox no 0.0 +* shiny = 1.0 +* ssao = no + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dump_modify.txt b/doc/_sources/dump_modify.txt new file mode 100644 index 0000000000..2fec637576 --- /dev/null +++ b/doc/_sources/dump_modify.txt @@ -0,0 +1,924 @@ +.. index:: dump_modify + +dump_modify command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + dump_modify dump-ID keyword values ... + +* dump-ID = ID of dump to modify +* one or more keyword/value pairs may be appended +* these keywords apply to various dump styles +* keyword = *append* or *buffer* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *nfile* or *pad* or *precision* or *region* or *scale* or *sort* or *thresh* or *unwrap* +.. parsed-literal:: + + *append* arg = *yes* or *no* + *buffer* arg = *yes* or *no* + *element* args = E1 E2 ... EN, where N = # of atom types + E1,...,EN = element name, e.g. C or Fe or Ga + *every* arg = N + N = dump every this many timesteps + N can be a variable (see below) + *fileper* arg = Np + Np = write one file for every this many processors + *first* arg = *yes* or *no* + *format* arg = C-style format string for one line of output + *flush* arg = *yes* or *no* + *image* arg = *yes* or *no* + *label* arg = string + string = character string (e.g. BONDS) to use in header of dump local file + *nfile* arg = Nf + Nf = write this many files, one from each of Nf processors + *pad* arg = Nchar = # of characters to convert timestep to + *precision* arg = power-of-10 value from 10 to 1000000 + *region* arg = region-ID or "none" + *scale* arg = *yes* or *no* + *sfactor* arg = coordinate scaling factor (> 0.0) + *tfactor* arg = time scaling factor (> 0.0) + *sort* arg = *off* or *id* or N or -N + off = no sorting of per-atom lines within a snapshot + id = sort per-atom lines by atom ID + N = sort per-atom lines in ascending order by the Nth column + -N = sort per-atom lines in descending order by the Nth column + *thresh* args = attribute operation value + attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style + operation = "<" or "<=" or ">" or ">=" or "==" or "!=" + value = numeric value to compare to + these 3 args can be replaced by the word "none" to turn off thresholding + *unwrap* arg = *yes* or *no* + +* these keywords apply only to the *image* and *movie* :doc:`styles ` +* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* +.. parsed-literal:: + + *acolor* args = type color + type = atom type or range of types (see below) + color = name of color or color1/color2/... + *adiam* args = type diam + type = atom type or range of types (see below) + diam = diameter of atoms of that type (distance units) + *amap* args = lo hi style delta N entry1 entry2 ... entryN + lo = number or *min* = lower bound of range of color map + hi = number or *max* = upper bound of range of color map + style = 2 letters = "c" or "d" or "s" plus "a" or "f" + "c" for continuous + "d" for discrete + "s" for sequential + "a" for absolute + "f" for fractional + delta = binsize (only used for style "s", otherwise ignored) + binsize = range is divided into bins of this width + N = # of subsequent entries + entry = value color (for continuous style) + value = number or *min* or *max* = single value within range + color = name of color used for that value + entry = lo hi color (for discrete style) + lo/hi = number or *min* or *max* = lower/upper bound of subset of range + color = name of color used for that subset of values + entry = color (for sequential style) + color = name of color used for a bin of values + *backcolor* arg = color + color = name of color for background + *bcolor* args = type color + type = bond type or range of types (see below) + color = name of color or color1/color2/... + *bdiam* args = type diam + type = bond type or range of types (see below) + diam = diameter of bonds of that type (distance units) + *boxcolor* arg = color + color = name of color for simulation box lines and processor sub-domain lines + *color* args = name R G B + name = name of color + R,G,B = red/green/blue numeric values from 0.0 to 1.0 + *bitrate* arg = rate + rate = target bitrate for movie in kbps + *framerate* arg = fps + fps = frames per second for movie + + + +Examples +"""""""" + +.. parsed-literal:: + + dump_modify 1 format "%d %d %20.15g %g %g" scale yes + dump_modify myDump image yes scale no flush yes + dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2 + dump_modify xtcdump precision 10000 sfactor 0.1 + dump_modify 1 every 1000 nfile 20 + dump_modify 1 every v_myVar + dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red + +Description +""""""""""" + +Modify the parameters of a previously defined dump command. Not all +parameters are relevant to all dump styles. + +As explained on the :doc:`dump ` doc page, the *atom/mpiio*, +*custom/mpiio*, and *xyz/mpiio* dump styles are identical in command +syntax and in the format of the dump files they create, to the +corresponding styles without "mpiio", except the single dump file they +produce is written in parallel via the MPI-IO library. Thus if a +dump_modify option below is valid for the *atom* style, it is also +valid for the *atom/mpiio* style, and similarly for the other styles +which allow for use of MPI-IO. + + + + + +These keywords apply to various dump styles, including the :doc:`dump image ` and :doc:`dump movie ` styles. The +description gives details. + + +---------- + + +The *append* keyword applies to all dump styles except *cfg* and *xtc* +and *dcd*. It also applies only to text output files, not to binary +or gzipped or image/movie files. If specified as *yes*, then dump +snapshots are appended to the end of an existing dump file. If +specified as *no*, then a new dump file will be created which will +overwrite an existing file with the same name. This keyword can only +take effect if the dump_modify command is used after the +:doc:`dump ` command, but before the first command that causes +dump snapshots to be output, e.g. a :doc:`run ` or +:doc:`minimize ` command. Once the dump file has been opened, +this keyword has no further effect. + + +---------- + + +The *buffer* keyword applies only to dump styles *atom*, *cfg*, +*custom*, *local*, and *xyz*. It also applies only to text output +files, not to binary or gzipped files. If specified as *yes*, which +is the default, then each processor writes its output into an internal +text buffer, which is then sent to the processor(s) which perform file +writes, and written by those processors(s) as one large chunk of text. +If specified as *no*, each processor sends its per-atom data in binary +format to the processor(s) which perform file wirtes, and those +processor(s) format and write it line by line into the output file. + +The buffering mode is typically faster since each processor does the +relatively expensive task of formatting the output for its own atoms. +However it requires about twice the memory (per processor) for the +extra buffering. + + +---------- + + +The *element* keyword applies only to the the dump *cfg*, *xyz*, and +*image* styles. It associates element names (e.g. H, C, Fe) with +LAMMPS atom types. See the list of element names at the bottom of +this page. + +In the case of dump *cfg*, this allows the `AtomEye `_ +visualization package to read the dump file and render atoms with the +appropriate size and color. + +In the case of dump *image*, the output images will follow the same +`AtomEye `_ convention. An element name is specified for each +atom type (1 to Ntype) in the simulation. The same element name can +be given to multiple atom types. + +In the case of *xyz* format dumps, there are no restrictions to what +label can be used as an element name. Any whitespace separated text +will be accepted. + +.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A + + + + +---------- + + +The *every* keyword changes the dump frequency originally specified by +the :doc:`dump ` command to a new value. The every keyword can be +specified in one of two ways. It can be a numeric value in which case +it must be > 0. Or it can be an :doc:`equal-style variable `, +which should be specified as v_name, where name is the variable name. + +In this case, the variable is evaluated at the beginning of a run to +determine the next timestep at which a dump snapshot will be written +out. On that timestep the variable will be evaluated again to +determine the next timestep, etc. Thus the variable should return +timestep values. See the stagger() and logfreq() and stride() math +functions for :doc:`equal-style variables `, as examples of +useful functions to use in this context. Other similar math functions +could easily be added as options for :doc:`equal-style variables `. Also see the next() function, which allows +use of a file-style variable which reads successive values from a +file, each time the variable is evaluated. Used with the *every* +keyword, if the file contains a list of ascending timesteps, you can +output snapshots whenever you wish. + +Note that when using the variable option with the *every* keyword, you +need to use the *first* option if you want an initial snapshot written +to the dump file. The *every* keyword cannot be used with the dump +*dcd* style. + +For example, the following commands will +write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc: + +.. parsed-literal:: + + variable s equal logfreq(10,3,10) + dump 1 all atom 100 tmp.dump + dump_modify 1 every v_s first yes + +The following commands would write snapshots at the timesteps listed +in file tmp.times: + +.. parsed-literal:: + + variable f file tmp.times + variable s equal next(f) + dump 1 all atom 100 tmp.dump + dump_modify 1 every v_s + +.. note:: + + When using a file-style variable with the *every* keyword, the + file of timesteps must list a first timestep that is beyond the + current timestep (e.g. it cannot be 0). And it must list one or more + timesteps beyond the length of the run you perform. This is because + the dump command will generate an error if the next timestep it reads + from the file is not a value greater than the current timestep. Thus + if you wanted output on steps 0,15,100 of a 100-timestep run, the file + should contain the values 15,100,101 and you should also use the + dump_modify first command. Any final value > 100 could be used in + place of 101. + + +---------- + + +The *first* keyword determines whether a dump snapshot is written on +the very first timestep after the dump command is invoked. This will +always occur if the current timestep is a multiple of N, the frequency +specified in the :doc:`dump ` command, including timestep 0. But +if this is not the case, a dump snapshot will only be written if the +setting of this keyword is *yes*. If it is *no*, which is the +default, then it will not be written. + + +---------- + + +The *flush* keyword determines whether a flush operation is invoked +after a dump snapshot is written to the dump file. A flush insures +the output in that file is current (no buffering by the OS), even if +LAMMPS halts before the simulation completes. Flushes cannot be +performed with dump style *xtc*. + + +---------- + + +The text-based dump styles have a default C-style format string which +simply specifies %d for integers and %g for floating-point values. +The *format* keyword can be used to override the default with a new +C-style format string. Do not include a trailing "\\n" newline +character in the format string. This option has no effect on the +*dcd* and *xtc* dump styles since they write binary files. Note that +for the *cfg* style, the first two fields (atom id and type) are not +actually written into the CFG file, though you must include formats +for them in the format string. + +.. note:: + + Any value written to a text-based dump file that is a per-atom + quantity calculated by a :doc:`compute ` or :doc:`fix ` is + stored internally as a floating-point value. If the value is actually + an integer and you wish it to appear in the text dump file as a + (large) integer, then you need to use an appropriate format. For + example, these commands: + +.. parsed-literal:: + + compute 1 all property/local batom1 batom2 + dump 1 all local 100 tmp.bonds index c_1[1] c_1[2] + dump_modify 1 format "%d %0.0f %0.0f" + +will output the two atom IDs for atoms in each bond as integers. If +the dump_modify command were omitted, they would appear as +floating-point values, assuming they were large integers (more than 6 +digits). The "index" keyword should use the "%d" format since it is +not generated by a compute or fix, and is stored internally as an +integer. + + +---------- + + +The *fileper* keyword is documented below with the *nfile* keyword. + + +---------- + + +The *image* keyword applies only to the dump *atom* style. If the +image value is *yes*, 3 flags are appended to each atom's coords which +are the absolute box image of the atom in each dimension. For +example, an x image flag of -2 with a normalized coord of 0.5 means +the atom is in the center of the box, but has passed thru the box +boundary 2 times and is really 2 box lengths to the left of its +current coordinate. Note that for dump style *custom* these various +values can be printed in the dump file by using the appropriate atom +attributes in the dump command itself. + + +---------- + + +The *label* keyword applies only to the dump *local* style. When +it writes local information, such as bond or angle topology +to a dump file, it will use the specified *label* to format +the header. By default this includes 2 lines: + +.. parsed-literal:: + + ITEM: NUMBER OF ENTRIES + ITEM: ENTRIES ... + +The word "ENTRIES" will be replaced with the string specified, +e.g. BONDS or ANGLES. + + +---------- + + +The *nfile* or *fileper* keywords can be used in conjunction with the +"%" wildcard character in the specified dump file name, for all dump +styles except the *dcd*, *image*, *movie*, *xtc*, and *xyz* styles +(for which "%" is not allowed). As explained on the :doc:`dump ` +command doc page, the "%" character causes the dump file to be written +in pieces, one piece for each of P processors. By default P = the +number of processors the simulation is running on. The *nfile* or +*fileper* keyword can be used to set P to a smaller value, which can +be more efficient when running on a large number of processors. + +The *nfile* keyword sets P to the specified Nf value. For example, if +Nf = 4, and the simulation is running on 100 processors, 4 files will +be written, by processors 0,25,50,75. Each will collect information +from itself and the next 24 processors and write it to a dump file. + +For the *fileper* keyword, the specified value of Np means write one +file for every Np processors. For example, if Np = 4, every 4th +processor (0,4,8,12,etc) will collect information from itself and the +next 3 processors and write it to a dump file. + + +---------- + + +The *pad* keyword only applies when the dump filename is specified +with a wildcard "*" character which becomes the timestep. If *pad* is +0, which is the default, the timestep is converted into a string of +unpadded length, e.g. 100 or 12000 or 2000000. When *pad* is +specified with *Nchar* > 0, the string is padded with leading zeroes +so they are all the same length = *Nchar*. For example, pad 7 would +yield 0000100, 0012000, 2000000. This can be useful so that +post-processing programs can easily read the files in ascending +timestep order. + + +---------- + + +The *precision* keyword only applies to the dump *xtc* style. A +specified value of N means that coordinates are stored to 1/N +nanometer accuracy, e.g. for N = 1000, the coordinates are written to +1/1000 nanometer accuracy. + + +---------- + + +The *sfactor* and *tfactor* keywords only apply to the dump *xtc* +style. They allow customization of the unit conversion factors used +when writing to XTC files. By default they are initialized for +whatever :doc:`units ` style is being used, to write out +coordinates in nanometers and time in picoseconds. I.e. for *real* +units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the +Angstroms and fmsec used by *real* units are 0.1 nm and 0.001 psec +respectively. If you are using a units system with distance and time +units far from nm and psec, you may wish to write XTC files with +different units, since the compression algorithm used in XTC files is +most effective when the typical magnitude of position data is between +10.0 and 0.1. + + +---------- + + +The *region* keyword only applies to the dump *custom*, *cfg*, +*image*, and *movie* styles. If specified, only atoms in the region +will be written to the dump file or included in the image/movie. Only +one region can be applied as a filter (the last one specified). See +the :doc:`region ` command for more details. Note that a region +can be defined as the "inside" or "outside" of a geometric shape, and +it can be the "union" or "intersection" of a series of simpler +regions. + + +---------- + + +The *scale* keyword applies only to the dump *atom* style. A scale +value of *yes* means atom coords are written in normalized units from +0.0 to 1.0 in each box dimension. If the simluation box is triclinic +(tilted), then all atom coords will still be between 0.0 and 1.0. A +value of *no* means they are written in absolute distance units +(e.g. Angstroms or sigma). + + +---------- + + +The *sort* keyword determines whether lines of per-atom output in a +snapshot are sorted or not. A sort value of *off* means they will +typically be written in indeterminate order, either in serial or +parallel. This is the case even in serial if the :doc:`atom_modify sort ` option is turned on, which it is by default, to +improve performance. A sort value of *id* means sort the output by +atom ID. A sort value of N or -N means sort the output by the value +in the Nth column of per-atom info in either ascending or descending +order. + +The dump *local* style cannot be sorted by atom ID, since there are +typically multiple lines of output per atom. Some dump styles, such +as *dcd* and *xtc*, require sorting by atom ID to format the output +file correctly. If multiple processors are writing the dump file, via +the "%" wildcard in the dump filename, then sorting cannot be +performed. + +.. note:: + + Unless it is required by the dump style, sorting dump file + output requires extra overhead in terms of CPU and communication cost, + as well as memory, versus unsorted output. + + +---------- + + +The *thresh* keyword only applies to the dump *custom*, *cfg*, +*image*, and *movie* styles. Multiple thresholds can be specified. +Specifying "none" turns off all threshold criteria. If thresholds are +specified, only atoms whose attributes meet all the threshold criteria +are written to the dump file or included in the image. The possible +attributes that can be tested for are the same as those that can be +specified in the :doc:`dump custom ` command, with the exception +of the *element* attribute, since it is not a numeric value. Note +that different attributes can be output by the dump custom command +than are used as threshold criteria by the dump_modify command. +E.g. you can output the coordinates and stress of atoms whose energy +is above some threshold. + + +---------- + + +The *unwrap* keyword only applies to the dump *dcd* and *xtc* styles. +If set to *yes*, coordinates will be written "unwrapped" by the image +flags for each atom. Unwrapped means that if the atom has passed thru +a periodic boundary one or more times, the value is printed for what +the coordinate would be if it had not been wrapped back into the +periodic box. Note that these coordinates may thus be far outside the +box size stored with the snapshot. + + + + + +These keywords apply only to the :doc:`dump image ` and +:doc:`dump movie ` styles. Any keyword that affects an +image, also affects a movie, since the movie is simply a collection of +images. Some of the keywords only affect the :doc:`dump movie ` style. The descriptions give details. + + +---------- + + +The *acolor* keyword can be used with the :doc:`dump image ` +command, when its atom color setting is *type*, to set the color that +atoms of each type will be drawn in the image. + +The specified *type* should be an integer from 1 to Ntypes = the +number of atom types. A wildcard asterisk can be used in place of or +in conjunction with the *type* argument to specify a range of atom +types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the +number of atom types, then an asterisk with no numeric values means +all types from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). + +The specified *color* can be a single color which is any of the 140 +pre-defined colors (see below) or a color name defined by the +dump_modify color option. Or it can be two or more colors separated +by a "/" character, e.g. red/green/blue. In the former case, that +color is assigned to all the specified atom types. In the latter +case, the list of colors are assigned in a round-robin fashion to each +of the specified atom types. + + +---------- + + +The *adiam* keyword can be used with the :doc:`dump image ` +command, when its atom diameter setting is *type*, to set the size +that atoms of each type will be drawn in the image. The specified +*type* should be an integer from 1 to Ntypes. As with the *acolor* +keyword, a wildcard asterisk can be used as part of the *type* +argument to specify a range of atomt types. The specified *diam* is +the size in whatever distance :doc:`units ` the input script is +using, e.g. Angstroms. + + +---------- + + +The *amap* keyword can be used with the :doc:`dump image ` +command, with its *atom* keyword, when its atom setting is an +atom-attribute, to setup a color map. The color map is used to assign +a specific RGB (red/green/blue) color value to an individual atom when +it is drawn, based on the atom's attribute, which is a numeric value, +e.g. its x-component of velocity if the atom-attribute "vx" was +specified. + +The basic idea of a color map is that the atom-attribute will be +within a range of values, and that range is associated with a a series +of colors (e.g. red, blue, green). An atom's specific value (vx = +-3.2) can then mapped to the series of colors (e.g. halfway between +red and blue), and a specific color is determined via an interpolation +procedure. + +There are many possible options for the color map, enabled by the +*amap* keyword. Here are the details. + +The *lo* and *hi* settings determine the range of values allowed for +the atom attribute. If numeric values are used for *lo* and/or *hi*, +then values that are lower/higher than that value are set to the +value. I.e. the range is static. If *lo* is specified as *min* or +*hi* as *max* then the range is dynamic, and the lower and/or +upper bound will be calculated each time an image is drawn, based +on the set of atoms being visualized. + +The *style* setting is two letters, such as "ca". The first letter is +either "c" for continuous, "d" for discrete, or "s" for sequential. +The second letter is either "a" for absolute, or "f" for fractional. + +A continuous color map is one in which the color changes continuously +from value to value within the range. A discrete color map is one in +which discrete colors are assigned to sub-ranges of values within the +range. A sequential color map is one in which discrete colors are +assigned to a sequence of sub-ranges of values covering the entire +range. + +An absolute color map is one in which the values to which colors are +assigned are specified explicitly as values within the range. A +fractional color map is one in which the values to which colors are +assigned are specified as a fractional portion of the range. For +example if the range is from -10.0 to 10.0, and the color red is to be +assigned to atoms with a value of 5.0, then for an absolute color map +the number 5.0 would be used. But for a fractional map, the number +0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0. + +The *delta* setting must be specified for all styles, but is only used +for the sequential style; otherwise the value is ignored. It +specifies the bin size to use within the range for assigning +consecutive colors to. For example, if the range is from -10.0 to +10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to +the range. The first will be from -10.0 <= color1 < -9.0, then 2nd +from -9.0 <= color2 < -8.0, etc. + +The *N* setting is how many entries follow. The format of the entries +depends on whether the color map style is continuous, discrete or +sequential. In all cases the *color* setting can be any of the 140 +pre-defined colors (see below) or a color name defined by the +dump_modify color option. + +For continuous color maps, each entry has a *value* and a *color*. +The *value* is either a number within the range of values or *min* or +*max*. The *value* of the first entry must be *min* and the *value* +of the last entry must be *max*. Any entries in between must have +increasing values. Note that numeric values can be specified either +as absolute numbers or as fractions (0.0 to 1.0) of the range, +depending on the "a" or "f" in the style setting for the color map. + +Here is how the entries are used to determine the color of an +individual atom, given the value X of its atom attribute. X will fall +between 2 of the entry values. The color of the atom is linearly +interpolated (in each of the RGB values) between the 2 colors +associated with those entries. For example, if X = -5.0 and the 2 +surrounding entries are "red" at -10.0 and "blue" at 0.0, then the +atom's color will be halfway between "red" and "blue", which happens +to be "purple". + +For discrete color maps, each entry has a *lo* and *hi* value and a +*color*. The *lo* and *hi* settings are either numbers within the +range of values or *lo* can be *min* or *hi* can be *max*. The *lo* +and *hi* settings of the last entry must be *min* and *max*. Other +entries can have any *lo* and *hi* values and the sub-ranges of +different values can overlap. Note that numeric *lo* and *hi* values +can be specified either as absolute numbers or as fractions (0.0 to +1.0) of the range, depending on the "a" or "f" in the style setting +for the color map. + +Here is how the entries are used to determine the color of an +individual atom, given the value X of its atom attribute. The entries +are scanned from first to last. The first time that *lo* <= X <= +*hi*, X is assigned the color associated with that entry. You can +think of the last entry as assigning a default color (since it will +always be matched by X), and the earlier entries as colors that +override the default. Also note that no interpolation of a color RGB +is done. All atoms will be drawn with one of the colors in the list +of entries. + +For sequential color maps, each entry has only a *color*. Here is how +the entries are used to determine the color of an individual atom, +given the value X of its atom attribute. The range is partitioned +into N bins of width *binsize*. Thus X will fall in a specific bin +from 1 to N, say the Mth bin. If it falls on a boundary between 2 +bins, it is considered to be in the higher of the 2 bins. Each bin is +assigned a color from the E entries. If E < N, then the colors are +repeated. For example if 2 entries with colors red and green are +specified, then the odd numbered bins will be red and the even bins +green. The color of the atom is the color of its bin. Note that the +sequential color map is really a shorthand way of defining a discrete +color map without having to specify where all the bin boundaries are. + +Here is an example of using a sequential color map to color all the +atoms in individual molecules with a different color. See the +examples/pour/in.pour.2d.molecule input script for an example of how +this is used. + +.. parsed-literal:: + + variable colors string & + "red green blue yellow white & + purple pink orange lime gray" + variable mol atom mol%10 + dump 1 all image 250 image.*.jpg v_mol type & + zoom 1.6 adiam 1.5 + dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors} + +In this case, 10 colors are defined, and molecule IDs are +mapped to one of the colors, even if there are 1000s of molecules. + + +---------- + + +The *backcolor* sets the background color of the images. The color +name can be any of the 140 pre-defined colors (see below) or a color +name defined by the dump_modify color option. + + +---------- + + +The *bcolor* keyword can be used with the :doc:`dump image ` +command, with its *bond* keyword, when its color setting is *type*, to +set the color that bonds of each type will be drawn in the image. + +The specified *type* should be an integer from 1 to Nbondtypes = the +number of bond types. A wildcard asterisk can be used in place of or +in conjunction with the *type* argument to specify a range of bond +types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the +number of bond types, then an asterisk with no numeric values means +all types from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). + +The specified *color* can be a single color which is any of the 140 +pre-defined colors (see below) or a color name defined by the +dump_modify color option. Or it can be two or more colors separated +by a "/" character, e.g. red/green/blue. In the former case, that +color is assigned to all the specified bond types. In the latter +case, the list of colors are assigned in a round-robin fashion to each +of the specified bond types. + + +---------- + + +The *bdiam* keyword can be used with the :doc:`dump image ` +command, with its *bond* keyword, when its diam setting is *type*, to +set the diameter that bonds of each type will be drawn in the image. +The specified *type* should be an integer from 1 to Nbondtypes. As +with the *bcolor* keyword, a wildcard asterisk can be used as part of +the *type* argument to specify a range of bond types. The specified +*diam* is the size in whatever distance :doc:`units ` you are +using, e.g. Angstroms. + + +---------- + + +The *bitrate* keyword can be used with the :doc:`dump movie ` command to define the size of the resulting +movie file and its quality via setting how many kbits per second are +to be used for the movie file. Higher bitrates require less +compression and will result in higher quality movies. The quality is +also determined by the compression format and encoder. The default +setting is 2000 kbit/s, which will result in average quality with +older compression formats. + +.. note:: + + Not all movie file formats supported by dump movie allow the + bitrate to be set. If not, the setting is silently ignored. + + +---------- + + +The *boxcolor* keyword sets the color of the simulation box drawn +around the atoms in each image as well as the color of processor +sub-domain boundaries. See the "dump image box" command for how to +specify that a box be drawn via the *box* keyword, and the sub-domain +boundaries via the *subbox* keyword. The color name can be any of the +140 pre-defined colors (see below) or a color name defined by the +dump_modify color option. + + +---------- + + +The *color* keyword allows definition of a new color name, in addition +to the 140-predefined colors (see below), and associates 3 +red/green/blue RGB values with that color name. The color name can +then be used with any other dump_modify keyword that takes a color +name as a value. The RGB values should each be floating point values +between 0.0 and 1.0 inclusive. + +When a color name is converted to RGB values, the user-defined color +names are searched first, then the 140 pre-defined color names. This +means you can also use the *color* keyword to overwrite one of the +pre-defined color names with new RBG values. + + +---------- + + +The *framerate* keyword can be used with the :doc:`dump movie ` command to define the duration of the resulting +movie file. Movie files written by the dump *movie* command have a +default frame rate of 24 frames per second and the images generated +will be converted at that rate. Thus a sequence of 1000 dump images +will result in a movie of about 42 seconds. To make a movie run +longer you can either generate images more frequently or lower the +frame rate. To speed a movie up, you can do the inverse. Using a +frame rate higher than 24 is not recommended, as it will result in +simply dropping the rendered images. It is more efficient to dump +images less frequently. + + + + + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump `, :doc:`dump image `, :doc:`undump ` + +Default +""""""" + +The option defaults are + +* append = no +* buffer = yes for dump styles *atom*, *custom*, *loca*, and *xyz* +* element = "C" for every atom type +* every = whatever it was set to via the :doc:`dump ` command +* fileper = # of processors +* first = no +* flush = yes +* format = %d and %g for each integer or floating point value +* image = no +* label = ENTRIES +* nfile = 1 +* pad = 0 +* precision = 1000 +* region = none +* scale = yes +* sort = off for dump styles *atom*, *custom*, *cfg*, and *local* +* sort = id for dump styles *dcd*, *xtc*, and *xyz* +* thresh = none +* unwrap = no + +* acolor = * red/green/blue/yellow/aqua/cyan +* adiam = * 1.0 +* amap = min max cf 0.0 2 min blue max red +* backcolor = black +* bcolor = * red/green/blue/yellow/aqua/cyan +* bdiam = * 0.5 +* bitrate = 2000 +* boxcolor = yellow +* color = 140 color names are pre-defined as listed below +* framerate = 24 + + +---------- + + +These are the standard 109 element names that LAMMPS pre-defines for +use with the :doc:`dump image ` and dump_modify commands. + +* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne" +* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca" +* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn" +* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr" +* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn" +* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd" +* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb" +* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg" +* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th" +* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm" +* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt" + + +---------- + + +These are the 140 colors that LAMMPS pre-defines for use with the +:doc:`dump image ` and dump_modify commands. Additional +colors can be defined with the dump_modify color command. The 3 +numbers listed for each name are the RGB (red/green/blue) values. +Divide each value by 255 to get the equivalent 0.0 to 1.0 value. + ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| aliceblue = 240, 248, 255 | antiquewhite = 250, 235, 215 | aqua = 0, 255, 255 | aquamarine = 127, 255, 212 | azure = 240, 255, 255 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| beige = 245, 245, 220 | bisque = 255, 228, 196 | black = 0, 0, 0 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| blueviolet = 138, 43, 226 | brown = 165, 42, 42 | burlywood = 222, 184, 135 | cadetblue = 95, 158, 160 | chartreuse = 127, 255, 0 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| chocolate = 210, 105, 30 | coral = 255, 127, 80 | cornflowerblue = 100, 149, 237 | cornsilk = 255, 248, 220 | crimson = 220, 20, 60 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| cyan = 0, 255, 255 | darkblue = 0, 0, 139 | darkcyan = 0, 139, 139 | darkgoldenrod = 184, 134, 11 | darkgray = 169, 169, 169 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| darkgreen = 0, 100, 0 | darkkhaki = 189, 183, 107 | darkmagenta = 139, 0, 139 | darkolivegreen = 85, 107, 47 | darkorange = 255, 140, 0 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| darkorchid = 153, 50, 204 | darkred = 139, 0, 0 | darksalmon = 233, 150, 122 | darkseagreen = 143, 188, 143 | darkslateblue = 72, 61, 139 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| darkslategray = 47, 79, 79 | darkturquoise = 0, 206, 209 | darkviolet = 148, 0, 211 | deeppink = 255, 20, 147 | deepskyblue = 0, 191, 255 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| dimgray = 105, 105, 105 | dodgerblue = 30, 144, 255 | firebrick = 178, 34, 34 | floralwhite = 255, 250, 240 | forestgreen = 34, 139, 34 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| fuchsia = 255, 0, 255 | gainsboro = 220, 220, 220 | ghostwhite = 248, 248, 255 | gold = 255, 215, 0 | goldenrod = 218, 165, 32 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| gray = 128, 128, 128 | green = 0, 128, 0 | greenyellow = 173, 255, 47 | honeydew = 240, 255, 240 | hotpink = 255, 105, 180 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| indianred = 205, 92, 92 | indigo = 75, 0, 130 | ivory = 255, 240, 240 | khaki = 240, 230, 140 | lavender = 230, 230, 250 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0 | lemonchiffon = 255, 250, 205 | lightblue = 173, 216, 230 | lightcoral = 240, 128, 128 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| lightcyan = 224, 255, 255 | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144 | lightgrey = 211, 211, 211 | lightpink = 255, 182, 193 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| lightsalmon = 255, 160, 122 | lightseagreen = 32, 178, 170 | lightskyblue = 135, 206, 250 | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| lightyellow = 255, 255, 224 | lime = 0, 255, 0 | limegreen = 50, 205, 50 | linen = 250, 240, 230 | magenta = 255, 0, 255 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| maroon = 128, 0, 0 | mediumaquamarine = 102, 205, 170 | mediumblue = 0, 0, 205 | mediumorchid = 186, 85, 211 | mediumpurple = 147, 112, 219 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238 | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| midnightblue = 25, 25, 112 | mintcream = 245, 255, 250 | mistyrose = 255, 228, 225 | moccasin = 255, 228, 181 | navajowhite = 255, 222, 173 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| navy = 0, 0, 128 | oldlace = 253, 245, 230 | olive = 128, 128, 0 | olivedrab = 107, 142, 35 | orange = 255, 165, 0 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| orangered = 255, 69, 0 | orchid = 218, 112, 214 | palegoldenrod = 238, 232, 170 | palegreen = 152, 251, 152 | paleturquoise = 175, 238, 238 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213 | peachpuff = 255, 239, 213 | peru = 205, 133, 63 | pink = 255, 192, 203 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| plum = 221, 160, 221 | powderblue = 176, 224, 230 | purple = 128, 0, 128 | red = 255, 0, 0 | rosybrown = 188, 143, 143 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| royalblue = 65, 105, 225 | saddlebrown = 139, 69, 19 | salmon = 250, 128, 114 | sandybrown = 244, 164, 96 | seagreen = 46, 139, 87 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| seashell = 255, 245, 238 | sienna = 160, 82, 45 | silver = 192, 192, 192 | skyblue = 135, 206, 235 | slateblue = 106, 90, 205 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| slategray = 112, 128, 144 | snow = 255, 250, 250 | springgreen = 0, 255, 127 | steelblue = 70, 130, 180 | tan = 210, 180, 140 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| teal = 0, 128, 128 | thistle = 216, 191, 216 | tomato = 253, 99, 71 | turquoise = 64, 224, 208 | violet = 238, 130, 238 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/dump_molfile.txt b/doc/_sources/dump_molfile.txt new file mode 100644 index 0000000000..10be826c51 --- /dev/null +++ b/doc/_sources/dump_molfile.txt @@ -0,0 +1,146 @@ +.. index:: dump molfile + +dump molfile command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + dump ID group-ID molfile N file format path + +* ID = user-assigned name for the dump +* group-ID = ID of the group of atoms to be imaged +* molfile = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) +* N = dump every this many timesteps +* file = name of file to write to +* format = file format to be used +* path = file path with plugins (optional) + + +Examples +"""""""" + +.. parsed-literal:: + + dump mf1 all molfile 10 melt1.xml hoomd + dump mf2 all molfile 10 melt2-*.pdb pdb . + dump mf3 all molfile 50 melt3.xyz xyz .:/home/akohlmey/vmd/plugins/LINUX/molfile + +Description +""""""""""" + +Dump a snapshot of atom coordinates and selected additional quantities +to one or more files every N timesteps in one of several formats. +Only information for atoms in the specified group is dumped. This +specific dump style uses molfile plugins that are bundled with the +`VMD `_ molecular visualization and +analysis program. See :ref:`Section tools ` of the +manual and the tools/lmp2vmd/README.txt file for more information +about support in VMD for reading and visualizing native LAMMPS dump +files. + +Unless the filename contains a * character, the output will be written +to one single file with the specified format. Otherwise there will be +one file per snapshot and the * will be replaced by the time step number +when the snapshot is written. + +.. note:: + + Because periodic boundary conditions are enforced only on + timesteps when neighbor lists are rebuilt, the coordinates of an atom + written to a dump file may be slightly outside the simulation box. + +The molfile plugin API has a few restrictions that have to be honored +by this dump style: the number of atoms must not change, the atoms +must be sorted, outside of the coordinates no change in atom properties +(like type, mass, charge) will be recorded. + + +---------- + + +The *format* keyword determines what format is used to write out the +dump. For this to work, LAMMPS must be able to find and load a +compatible molfile plugin that supports this format. Settings made via +the :doc:`dump_modify ` command can alter per atom properties +like element names. + +The *path* keyword determines which in directories. This is a "path" +like other search paths, i.e. it can contain multiple directories +separated by a colon (or semi-colon on windows). This keyword is +optional and default to ".", the current directory. + +The *unwrap* option of the :doc:`dump_modify ` command allows +coordinates to be written "unwrapped" by the image flags for each atom. +Unwrapped means that if the atom has passed through a periodic boundary +one or more times, the value is printed for what the coordinate would be +if it had not been wrapped back into the periodic box. Note that these +coordinates may thus be far outside the box size stored with the +snapshot. + + +---------- + + +Dumps are performed on timesteps that are a multiple of N (including +timestep 0) and on the last timestep of a minimization if the +minimization converges. Note that this means a dump will not be +performed on the initial timestep after the dump command is invoked, +if the current timestep is not a multiple of N. This behavior can be +changed via the :doc:`dump_modify first ` command, which can +be useful if the dump command is invoked after a minimization ended on +an arbitrary timestep. N can be changed between runs by using the +:doc:`dump_modify every ` command. The :doc:`dump_modify every ` command also allows a variable to be used to +determine the sequence of timesteps on which dump files are written. + + +---------- + + +Restrictions +"""""""""""" + + +The *molfile* dump style is part of the USER-MOLFILE package. It is +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Molfile plugins provide a consistent programming interface to read and +write file formats commonly used in molecular simulations. The +USER-MOLFILE package only provides the interface code, not the plugins. +These can be obtained from a VMD installation which has to match the +platform that you are using to compile LAMMPS for. By adding plugins +to VMD, support for new file formats can be added to LAMMPS (or VMD +or other programs that use them) without having to recompile the +application itself. The plugins are installed in the directory: +/plugins//molfile + +.. note:: + + while the programming interface (API) to the plugins is backward + compatible, the binary interface (ABI) has been changing over time, so + it is necessary to compile this package with the plugin header files + from VMD that match the binary plugins. These header files in the + directory: /plugins/include For convenience, the package ships + with a set of header files that are compatible with VMD 1.9 and 1.9.1 + (June 2012) + + +---------- + + +Related commands +"""""""""""""""" + +:doc:`dump `, :doc:`dump_modify `, :doc:`undump ` + +Default +""""""" + +The default path is ".". All other properties have to be specified. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/echo.txt b/doc/_sources/echo.txt new file mode 100644 index 0000000000..a3bbead623 --- /dev/null +++ b/doc/_sources/echo.txt @@ -0,0 +1,50 @@ +.. index:: echo + +echo command +============ + +Syntax +"""""" + +.. parsed-literal:: + + echo style + +* style = *none* or *screen* or *log* or *both* + +Examples +"""""""" + +.. parsed-literal:: + + echo both + echo log + +Description +""""""""""" + +This command determines whether LAMMPS echoes each input script +command to the screen and/or log file as it is read and processed. If +an input script has errors, it can be useful to look at echoed output +to see the last command processed. + +The :ref:`command-line switch ` -echo can be used +in place of this command. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +Default +""""""" + +.. parsed-literal:: + + echo log + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix.txt b/doc/_sources/fix.txt new file mode 100644 index 0000000000..a96411f8c3 --- /dev/null +++ b/doc/_sources/fix.txt @@ -0,0 +1,285 @@ +.. index:: fix + +fix command +=========== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style args + +* ID = user-assigned name for the fix +* group-ID = ID of the group of atoms to apply the fix to +* style = one of a long list of possible style names (see below) +* args = arguments used by a particular style + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve + fix 3 all nvt temp 300.0 300.0 0.01 + fix mine top setforce 0.0 NULL 0.0 + +Description +""""""""""" + +Set a fix that will be applied to a group of atoms. In LAMMPS, a +"fix" is any operation that is applied to the system during +timestepping or minimization. Examples include updating of atom +positions and velocities due to time integration, controlling +temperature, applying constraint forces to atoms, enforcing boundary +conditions, computing diagnostics, etc. There are dozens of fixes +defined in LAMMPS and new ones can be added; see :doc:`this section ` for a discussion. + +Fixes perform their operations at different stages of the timestep. +If 2 or more fixes operate at the same stage of the timestep, they are +invoked in the order they were specified in the input script. + +The ID of a fix can only contain alphanumeric characters and +underscores. + +Fixes can be deleted with the :doc:`unfix ` command. + +.. note:: + + The :doc:`unfix ` command is the only way to turn off a + fix; simply specifying a new fix with a similar style will not turn + off the first one. This is especially important to realize for + integration fixes. For example, using a :doc:`fix nve ` + command for a second run after using a :doc:`fix nvt ` command + for the first run, will not cancel out the NVT time integration + invoked by the "fix nvt" command. Thus two time integrators would be + in place! + +If you specify a new fix with the same ID and style as an existing +fix, the old fix is deleted and the new one is created (presumably +with new settings). This is the same as if an "unfix" command were +first performed on the old fix, except that the new fix is kept in the +same order relative to the existing fixes as the old one originally +was. Note that this operation also wipes out any additional changes +made to the old fix via the :doc:`fix_modify ` command. + +The :doc:`fix modify ` command allows settings for some +fixes to be reset. See the doc page for individual fixes for details. + +Some fixes store an internal "state" which is written to binary +restart files via the :doc:`restart ` or +:doc:`write_restart ` commands. This allows the fix to +continue on with its calculations in a restarted simulation. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file. See the doc pages +for individual fixes for info on which ones can be restarted. + + +---------- + + +Some fixes calculate one of three styles of quantities: global, +per-atom, or local, which can be used by other commands or output as +described below. A global quantity is one or more system-wide values, +e.g. the energy of a wall interacting with particles. A per-atom +quantity is one or more values per atom, e.g. the displacement vector +for each atom since time 0. Per-atom values are set to 0.0 for atoms +not in the specified fix group. Local quantities are calculated by +each processor based on the atoms it owns, but there may be zero or +more per atoms. + +Note that a single fix may produces either global or per-atom or local +quantities (or none at all), but never more than one of these. + +Global, per-atom, and local quantities each come in three kinds: a +single scalar value, a vector of values, or a 2d array of values. The +doc page for each fix describes the style and kind of values it +produces, e.g. a per-atom vector. Some fixes produce more than one +kind of a single style, e.g. a global scalar and a global vector. + +When a fix quantity is accessed, as in many of the output commands +discussed below, it can be referenced via the following bracket +notation, where ID is the ID of the fix: + ++------------+--------------------------------------------+ +| f_ID | entire scalar, vector, or array | ++------------+--------------------------------------------+ +| f_ID[I] | one element of vector, one column of array | ++------------+--------------------------------------------+ +| f_ID[I][J] | one element of array | ++------------+--------------------------------------------+ + +In other words, using one bracket reduces the dimension of the +quantity once (vector -> scalar, array -> vector). Using two brackets +reduces the dimension twice (array -> scalar). Thus a command that +uses scalar fix values as input can also process elements of a vector +or array. + +Note that commands and :doc:`variables ` which use fix +quantities typically do not allow for all kinds, e.g. a command may +require a vector of values, not a scalar. This means there is no +ambiguity about referring to a fix quantity as f_ID even if it +produces, for example, both a scalar and vector. The doc pages for +various commands explain the details. + + +---------- + + +In LAMMPS, the values generated by a fix can be used in several ways: + +* Global values can be output via the :doc:`thermo_style custom ` or :doc:`fix ave/time ` command. + Or the values can be referenced in a :doc:`variable equal ` or + :doc:`variable atom ` command. +* Per-atom values can be output via the :doc:`dump custom ` command + or the :doc:`fix ave/spatial ` command. Or they can be + time-averaged via the :doc:`fix ave/atom ` command or + reduced by the :doc:`compute reduce ` command. Or the + per-atom values can be referenced in an :doc:`atom-style variable `. +* Local values can be reduced by the :doc:`compute reduce ` command, or histogrammed by the :doc:`fix ave/histo ` command. +See this :ref:`howto section ` for a summary of +various LAMMPS output options, many of which involve fixes. + +The results of fixes that calculate global quantities can be either +"intensive" or "extensive" values. Intensive means the value is +independent of the number of atoms in the simulation, +e.g. temperature. Extensive means the value scales with the number of +atoms in the simulation, e.g. total rotational kinetic energy. +:doc:`Thermodynamic output ` will normalize extensive +values by the number of atoms in the system, depending on the +"thermo_modify norm" setting. It will not normalize intensive values. +If a fix value is accessed in another way, e.g. by a +:doc:`variable `, you may want to know whether it is an +intensive or extensive value. See the doc page for individual fixes +for further info. + + +---------- + + +Each fix style has its own documentation page which describes its +arguments and what it does, as listed below. Here is an alphabetic +list of fix styles available in LAMMPS. They are also given in more +compact form in the Fix section of :ref:`this page `. + +There are also additional fix styles (not listed here) submitted by +users which are included in the LAMMPS distribution. The list of +these with links to the individual styles are given in the fix section +of :ref:`this page `. + +* :doc:`adapt ` - change a simulation parameter over time +* :doc:`addforce ` - add a force to each atom +* :doc:`append/atoms ` - append atoms to a running simulation +* :doc:`aveforce ` - add an averaged force to each atom +* :doc:`ave/atom ` - compute per-atom time-averaged quantities +* :doc:`ave/correlate ` - compute/output time correlations +* :doc:`ave/histo ` - compute/output time-averaged histograms +* :doc:`ave/spatial ` - compute/output time-averaged per-atom quantities by layer +* :doc:`ave/time ` - compute/output global time-averaged quantities +* :doc:`balance ` - perform dynamic load-balancing +* :doc:`bond/break ` - break bonds on the fly +* :doc:`bond/create ` - create bonds on the fly +* :doc:`bond/swap ` - Monte Carlo bond swapping +* :doc:`box/relax ` - relax box size during energy minimization +* :doc:`deform ` - change the simulation box size/shape +* :doc:`deposit ` - add new atoms above a surface +* :doc:`drag ` - drag atoms towards a defined coordinate +* :doc:`dt/reset ` - reset the timestep based on velocity, forces +* :doc:`efield ` - impose electric field on system +* :doc:`enforce2d ` - zero out z-dimension velocity and force +* :doc:`evaporate ` - remove atoms from simulation periodically +* :doc:`external ` - callback to an external driver program +* :doc:`freeze ` - freeze atoms in a granular simulation +* :doc:`gcmc ` - grand canonical insertions/deletions +* :doc:`gld ` - generalized Langevin dynamics integrator +* :doc:`gravity ` - add gravity to atoms in a granular simulation +* :doc:`heat ` - add/subtract momentum-conserving heat +* :doc:`indent ` - impose force due to an indenter +* :doc:`langevin ` - Langevin temperature control +* :doc:`lineforce ` - constrain atoms to move in a line +* :doc:`momentum ` - zero the linear and/or angular momentum of a group of atoms +* :doc:`move ` - move atoms in a prescribed fashion +* :doc:`msst ` - multi-scale shock technique (MSST) integration +* :doc:`neb ` - nudged elastic band (NEB) spring forces +* :doc:`nph ` - constant NPH time integration via Nose/Hoover +* :doc:`nphug ` - constant-stress Hugoniostat integration +* :doc:`nph/asphere ` - NPH for aspherical particles +* :doc:`nph/sphere ` - NPH for spherical particles +* :doc:`npt ` - constant NPT time integration via Nose/Hoover +* :doc:`npt/asphere ` - NPT for aspherical particles +* :doc:`npt/sphere ` - NPT for spherical particles +* :doc:`nve ` - constant NVE time integration +* :doc:`nve/asphere ` - NVE for aspherical particles +* :doc:`nve/asphere/noforce ` - NVE for aspherical particles without forces" +* :doc:`nve/body ` - NVE for body particles +* :doc:`nve/limit ` - NVE with limited step length +* :doc:`nve/line ` - NVE for line segments +* :doc:`nve/noforce ` - NVE without forces (v only) +* :doc:`nve/sphere ` - NVE for spherical particles +* :doc:`nve/tri ` - NVE for triangles +* :doc:`nvt ` - constant NVT time integration via Nose/Hoover +* :doc:`nvt/asphere ` - NVT for aspherical particles +* :doc:`nvt/sllod ` - NVT for NEMD with SLLOD equations +* :doc:`nvt/sphere ` - NVT for spherical particles +* :doc:`orient/fcc ` - add grain boundary migration force +* :doc:`planeforce ` - constrain atoms to move in a plane +* :doc:`poems ` - constrain clusters of atoms to move as coupled rigid bodies +* :doc:`pour ` - pour new atoms/molecules into a granular simulation domain +* :doc:`press/berendsen ` - pressure control by Berendsen barostat +* :doc:`print ` - print text and variables during a simulation +* :doc:`property/atom ` - add customized per-atom values +* :doc:`qeq/comb ` - charge equilibration for COMB potential :doc:`qeq/dynamic ` - charge equilibration via dynamic method :doc:`qeq/point ` - charge equilibration via point method :doc:`qeq/shielded ` - charge equilibration via shielded method :doc:`qeq/slater ` - charge equilibration via Slater method :doc:`reax/bonds ` - write out ReaxFF bond information :doc:`recenter ` - constrain the center-of-mass position of a group of atoms +* :doc:`restrain ` - constrain a bond, angle, dihedral +* :doc:`rigid ` - constrain one or more clusters of atoms to move as a rigid body with NVE integration +* :doc:`rigid/nph ` - constrain one or more clusters of atoms to move as a rigid body with NPH integration +* :doc:`rigid/npt ` - constrain one or more clusters of atoms to move as a rigid body with NPT integration +* :doc:`rigid/nve ` - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration +* :doc:`rigid/nvt ` - constrain one or more clusters of atoms to move as a rigid body with NVT integration +* :doc:`rigid/small ` - constrain many small clusters of atoms to move as a rigid body with NVE integration +* :doc:`setforce ` - set the force on each atom +* :doc:`shake ` - SHAKE constraints on bonds and/or angles +* :doc:`spring ` - apply harmonic spring force to group of atoms +* :doc:`spring/rg ` - spring on radius of gyration of group of atoms +* :doc:`spring/self ` - spring from each atom to its origin +* :doc:`srd ` - stochastic rotation dynamics (SRD) +* :doc:`store/force ` - store force on each atom +* :doc:`store/state ` - store attributes for each atom +* :doc:`temp/berendsen ` - temperature control by Berendsen thermostat +* :doc:`temp/rescale ` - temperature control by velocity rescaling +* :doc:`thermal/conductivity ` - Muller-Plathe kinetic energy exchange for thermal conductivity calculation +* :doc:`tmd ` - guide a group of atoms to a new configuration +* :doc:`ttm ` - two-temperature model for electronic/atomic coupling +* :doc:`tune/kspace ` - auto-tune KSpace parameters +* :doc:`vector ` - accumulate a global vector every N timesteps +* :doc:`viscosity ` - Muller-Plathe momentum exchange for viscosity calculation +* :doc:`viscous ` - viscous damping for granular simulations +* :doc:`wall/colloid ` - Lennard-Jones wall interacting with finite-size particles +* :doc:`wall/gran ` - frictional wall(s) for granular simulations +* :doc:`wall/harmonic ` - harmonic spring wall +* :doc:`wall/lj1043 ` - Lennard-Jones 10-4-3 wall +* :doc:`wall/lj126 ` - Lennard-Jones 12-6 wall +* :doc:`wall/lj93 ` - Lennard-Jones 9-3 wall +* :doc:`wall/piston ` - moving reflective piston wall +* :doc:`wall/reflect ` - reflecting wall(s) +* :doc:`wall/region ` - use region surface as wall +* :doc:`wall/srd ` - slip/no-slip wall for SRD particles + +Restrictions +"""""""""""" + + +Some fix styles are part of specific packages. They are only enabled +if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info on packages. +The doc pages for individual fixes tell if it is part of a package. + +Related commands +"""""""""""""""" + +:doc:`unfix `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_adapt.txt b/doc/_sources/fix_adapt.txt new file mode 100644 index 0000000000..d1e7734b6a --- /dev/null +++ b/doc/_sources/fix_adapt.txt @@ -0,0 +1,292 @@ +.. index:: fix adapt + +fix adapt command +================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID adapt N attribute args ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* adapt = style name of this fix command +* N = adapt simulation settings every this many timesteps +* one or more attribute/arg pairs may be appended +* attribute = *pair* or *kspace* or *atom* +.. parsed-literal:: + + *pair* args = pstyle pparam I J v_name + pstyle = pair style name, e.g. lj/cut + pparam = parameter to adapt over time + I,J = type pair(s) to set parameter for + v_name = variable with name that calculates value of pparam + *kspace* arg = v_name + v_name = variable with name that calculates scale factor on K-space terms + *atom* args = aparam v_name + aparam = parameter to adapt over time + v_name = variable with name that calculates value of aparam + +* zero or more keyword/value pairs may be appended +* keyword = *scale* or *reset* +.. parsed-literal:: + + *scale* value = *no* or *yes* + *no* = the variable value is the new setting + *yes* = the variable value multiplies the original setting + *reset* value = *no* or *yes* + *no* = values will remain altered at the end of a run + *yes* = reset altered values to their original values at the end of a run + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all adapt 1 pair soft a 1 1 v_prefactor + fix 1 all adapt 1 pair soft a 2* 3 v_prefactor + fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes + fix 1 all adapt 10 atom diameter v_size + +Description +""""""""""" + +Change or adapt one or more specific simulation attributes or settings +over time as a simulation runs. Pair potential and K-space and atom +attributes which can be varied by this fix are discussed below. Many +other fixes can also be used to time-vary simulation parameters, +e.g. the "fix deform" command will change the simulation box +size/shape and the "fix move" command will change atom positions and +velocities in a prescribed manner. Also note that many commands allow +variables as arguments for specific parameters, if described in that +manner on their doc pages. An equal-style variable can calculate a +time-dependent quantity, so this is another way to vary a simulation +parameter over time. + +If *N* is specified as 0, the specified attributes are only changed +once, before the simulation begins. This is all that is needed if the +associated variables are not time-dependent. If *N* > 0, then changes +are made every *N* steps during the simulation, presumably with a +variable that is time-dependent. + +Depending on the value of the *reset* keyword, attributes changed by +this fix will or will not be reset back to their original values at +the end of a simulation. Even if *reset* is specified as *yes*, a +restart file written during a simulation will contain the modified +settings. + +If the *scale* keyword is set to *no*, then the value the parameter is +set to will be whatever the variable generates. If the *scale* +keyword is set to *yes*, then the value of the altered parameter will +be the initial value of that parameter multiplied by whatever the +variable generates. I.e. the variable is now a "scale factor" applied +in (presumably) a time-varying fashion to the parameter. + +Note that whether scale is *no* or *yes*, internally, the parameters +themselves are actually altered by this fix. Make sure you use the +*reset yes* option if you want the parameters to be restored to their +initial values after the run. + + +---------- + + +The *pair* keyword enables various parameters of potentials defined by +the :doc:`pair_style ` command to be changed, if the pair +style supports it. Note that the :doc:`pair_style ` and +:doc:`pair_coeff ` commands must be used in the usual manner +to specify these parameters initially; the fix adapt command simply +overrides the parameters. + +The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay ` is used, *pstyle* should be +a sub-style name. If there are multiple sub-styles using the same +pair style, then *pstyle* should be specified as "style:N" where N is +which instance of the pair style you wish to adapt, e.g. the first, +second, etc. For example, *pstyle* could be specified as "soft" or +"lubricate" or "lj/cut:1" or "lj/cut:2". The *pparam* argument is the +name of the parameter to change. This is the current list of pair +styles and parameters that can be varied by this fix. See the doc +pages for individual pair styles and their energy formulas for the +meaning of these parameters: + ++-----------------------------------+---------------------+------------+ +| :doc:`born ` | a,b,c | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`buck ` | a,c | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`coul/cut ` | scale | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`coul/debye ` | scale | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`coul/long ` | scale | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`lj/cut ` | epsilon,sigma | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`lubricate ` | mu | global | ++-----------------------------------+---------------------+------------+ +| :doc:`gauss ` | a | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`morse ` | d0,r0,alpha | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`soft ` | a | type pairs | ++-----------------------------------+---------------------+------------+ + +.. note:: + + It is easy to add new potentials and their parameters to this + list. All it typically takes is adding an extract() method to the + pair_*.cpp file associated with the potential. + +Some parameters are global settings for the pair style, e.g. the +viscosity setting "mu" for :doc:`pair_style lubricate `. +Other parameters apply to atom type pairs within the pair style, +e.g. the prefactor "a" for :doc:`pair_style soft `. + +Note that for many of the potentials, the parameter that can be varied +is effectively a prefactor on the entire energy expression for the +potential, e.g. the lj/cut epsilon. The parameters listed as "scale" +are exactly that, since the energy expression for the +:doc:`coul/cut ` potential (for example) has no labeled +prefactor in its formula. To apply an effective prefactor to some +potentials, multiple parameters need to be altered. For example, the +:doc:`Buckingham potential ` needs both the A and C terms +altered together. To scale the Buckingham potential, you should thus +list the pair style twice, once for A and once for C. + +If a type pair parameter is specified, the *I* and *J* settings should +be specified to indicate which type pairs to apply it to. If a global +parameter is specified, the *I* and *J* settings still need to be +specified, but are ignored. + +Similar to the :doc:`pair_coeff command `, I and J can be +specified in one of two ways. Explicit numeric values can be used for +each, as in the 1st example above. I <= J is required. LAMMPS sets +the coefficients for the symmetric J,I interaction to the same values. + +A wild-card asterisk can be used in place of or in conjunction with +the I,J arguments to set the coefficients for multiple pairs of atom +types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the +number of atom types, then an asterisk with no numeric values means +all types from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). Note that only type pairs with I <= J are considered; if +asterisks imply type pairs where J < I, they are ignored. + +IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will +be a sub-style name. You must specify I,J arguments that correspond +to type pair values defined (via the :doc:`pair_coeff ` +command) for that sub-style. + +The *v_name* argument for keyword *pair* is the name of an +:doc:`equal-style variable ` which will be evaluated each time +this fix is invoked to set the parameter to a new value. It should be +specified as v_name, where name is the variable name. Equal-style +variables can specify formulas with various mathematical functions, +and include :doc:`thermo_style ` command keywords for the +simulation box parameters and timestep and elapsed time. Thus it is +easy to specify parameters that change as a function of time or span +consecutive runs in a continuous fashion. For the latter, see the +*start* and *stop* keywords of the :doc:`run ` command and the +*elaplong* keyword of :doc:`thermo_style custom ` for +details. + +For example, these commands would change the prefactor coefficient of +the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a +linear fashion over the course of a simulation: + +.. parsed-literal:: + + variable prefactor equal ramp(10,30) + fix 1 all adapt 1 pair soft a * * v_prefactor + + +---------- + + +The *kspace* keyword used the specified variable as a scale factor on +the energy, forces, virial calculated by whatever K-Space solver is +defined by the :doc:`kspace_style ` command. If the +variable has a value of 1.0, then the solver is unaltered. + +The *kspace* keyword works this way whether the *scale* keyword +is set to *no* or *yes*. + + +---------- + + +The *atom* keyword enables various atom properties to be changed. The +*aparam* argument is the name of the parameter to change. This is the +current list of atom parameters that can be varied by this fix: + +* charge = charge on particle +* diameter = diameter of particle + +The *v_name* argument of the *atom* keyword is the name of an +:doc:`equal-style variable ` which will be evaluated each time +this fix is invoked to set the parameter to a new value. It should be +specified as v_name, where name is the variable name. See the +discussion above describing the formulas associated with equal-style +variables. The new value is assigned to the corresponding attribute +for all atoms in the fix group. + +.. note:: + + The *atom* keyword works this way whether the *scale* keyword is + set to *no* or *yes*. I.e. the use of scale yes is not yet supported + by the *atom* keyword. + +If the atom parameter is *diameter* and per-atom density and per-atom +mass are defined for particles (e.g. :doc:`atom_style granular `), then the mass of each particle is also +changed when the diameter changes (density is assumed to stay +constant). + +For example, these commands would shrink the diameter of all granular +particles in the "center" group from 1.0 to 0.1 in a linear fashion +over the course of a 1000-step simulation: + +.. parsed-literal:: + + variable size equal ramp(1.0,0.1) + fix 1 center adapt 10 atom diameter v_size + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +For :doc:`rRESPA time integration `, this fix changes +parameters on the outermost rRESPA level. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute ti ` + +Default +""""""" + +The option defaults are scale = no, reset = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_adapt_fep.txt b/doc/_sources/fix_adapt_fep.txt new file mode 100644 index 0000000000..cf4e6d939f --- /dev/null +++ b/doc/_sources/fix_adapt_fep.txt @@ -0,0 +1,294 @@ +.. index:: fix adapt/fep + +fix adapt/fep command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID adapt/fep N attribute args ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* adapt/fep = style name of this fix command +* N = adapt simulation settings every this many timesteps +* one or more attribute/arg pairs may be appended +* attribute = *pair* or *kspace* or *atom* +.. parsed-literal:: + + *pair* args = pstyle pparam I J v_name + pstyle = pair style name, e.g. lj/cut + pparam = parameter to adapt over time + I,J = type pair(s) to set parameter for + v_name = variable with name that calculates value of pparam + *kspace* arg = v_name + v_name = variable with name that calculates scale factor on K-space terms + *atom* args = aparam v_name + aparam = parameter to adapt over time + I = type(s) to set parameter for + v_name = variable with name that calculates value of aparam + +* zero or more keyword/value pairs may be appended +* keyword = *scale* or *reset* or *after* +.. parsed-literal:: + + *scale* value = *no* or *yes* + *no* = the variable value is the new setting + *yes* = the variable value multiplies the original setting + *reset* value = *no* or *yes* + *no* = values will remain altered at the end of a run + *yes* = reset altered values to their original values at the end + of a run + *after* value = *no* or *yes* + *no* = parameters are adapted at timestep N + *yes* = parameters are adapted one timestep after N + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor + fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor + fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes + fix 1 all adapt/fep 10 atom diameter 1 v_size + +Description +""""""""""" + +Change or adapt one or more specific simulation attributes or settings +over time as a simulation runs. + +This is an enhanced version of the :doc:`fix_adapt ` command +with two differences, + +* It is possible to modify the charges of chosen atom types only, + instead of scaling all the charges in the system. +* There is a new option *after* for better compatibility with "fix + ave/time". +This version is suited for free energy calculations using +:doc:`compute_ti ` or :doc:`compute_fep `. + +If *N* is specified as 0, the specified attributes are only changed +once, before the simulation begins. This is all that is needed if the +associated variables are not time-dependent. If *N* > 0, then changes +are made every *N* steps during the simulation, presumably with a +variable that is time-dependent. + +Depending on the value of the *reset* keyword, attributes changed by +this fix will or will not be reset back to their original values at +the end of a simulation. Even if *reset* is specified as *yes*, a +restart file written during a simulation will contain the modified +settings. + +If the *scale* keyword is set to *no*, then the value the parameter is +set to will be whatever the variable generates. If the *scale* +keyword is set to *yes*, then the value of the altered parameter will +be the initial value of that parameter multiplied by whatever the +variable generates. I.e. the variable is now a "scale factor" applied +in (presumably) a time-varying fashion to the parameter. Internally, +the parameters themselves are actually altered; make sure you use the +*reset yes* option if you want the parameters to be restored to their +initial values after the run. + +If the *after* keyword is set to *yes*, then the parameters are +changed one timestep after the multiple of N. In this manner, if a fix +such as "fix ave/time" is used to calculate averages at every N +timesteps, all the contributions to the average will be obtained with +the same values of the parameters. + + +---------- + + +The *pair* keyword enables various parameters of potentials defined by +the :doc:`pair_style ` command to be changed, if the pair +style supports it. Note that the :doc:`pair_style ` and +:doc:`pair_coeff ` commands must be used in the usual manner +to specify these parameters initially; the fix adapt command simply +overrides the parameters. + +The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay ` is used, *pstyle* should be +a sub-style name. For example, *pstyle* could be specified as "soft" +or "lubricate". The *pparam* argument is the name of the parameter to +change. This is the current list of pair styles and parameters that +can be varied by this fix. See the doc pages for individual pair +styles and their energy formulas for the meaning of these parameters: + ++-----------------------------------+---------------------+------------+ +| :doc:`born ` | a,b,c | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`buck ` | a,c | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`coul/cut ` | scale | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`coul/debye ` | scale | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`coul/long ` | scale | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`lj/cut ` | epsilon,sigma | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`lj/expand ` | epsilon,sigma,delta | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`lubricate ` | mu | global | ++-----------------------------------+---------------------+------------+ +| :doc:`gauss ` | a | type pairs | ++-----------------------------------+---------------------+------------+ +| :doc:`soft ` | a | type pairs | ++-----------------------------------+---------------------+------------+ + +.. note:: + + It is easy to add new potentials and their parameters to this + list. All it typically takes is adding an extract() method to the + pair_*.cpp file associated with the potential. + +Some parameters are global settings for the pair style, e.g. the +viscosity setting "mu" for :doc:`pair_style lubricate `. +Other parameters apply to atom type pairs within the pair style, +e.g. the prefactor "a" for :doc:`pair_style soft `. + +Note that for many of the potentials, the parameter that can be varied +is effectively a prefactor on the entire energy expression for the +potential, e.g. the lj/cut epsilon. The parameters listed as "scale" +are exactly that, since the energy expression for the +:doc:`coul/cut ` potential (for example) has no labeled +prefactor in its formula. To apply an effective prefactor to some +potentials, multiple parameters need to be altered. For example, the +:doc:`Buckingham potential ` needs both the A and C terms +altered together. To scale the Buckingham potential, you should thus +list the pair style twice, once for A and once for C. + +If a type pair parameter is specified, the *I* and *J* settings should +be specified to indicate which type pairs to apply it to. If a global +parameter is specified, the *I* and *J* settings still need to be +specified, but are ignored. + +Similar to the :doc:`pair_coeff command `, I and J can be +specified in one of two ways. Explicit numeric values can be used for +each, as in the 1st example above. I <= J is required. LAMMPS sets +the coefficients for the symmetric J,I interaction to the same values. + +A wild-card asterisk can be used in place of or in conjunction with +the I,J arguments to set the coefficients for multiple pairs of atom +types. This takes the form "*" or "*n" or "n*" or "m*n". If N = the +number of atom types, then an asterisk with no numeric values means +all types from 1 to N. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). Note that only type pairs with I <= J are considered; if +asterisks imply type pairs where J < I, they are ignored. + +IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will +be a sub-style name. You must specify I,J arguments that correspond +to type pair values defined (via the :doc:`pair_coeff ` +command) for that sub-style. + +The *v_name* argument for keyword *pair* is the name of an +:doc:`equal-style variable ` which will be evaluated each time +this fix is invoked to set the parameter to a new value. It should be +specified as v_name, where name is the variable name. Equal-style +variables can specify formulas with various mathematical functions, +and include :doc:`thermo_style ` command keywords for the +simulation box parameters and timestep and elapsed time. Thus it is +easy to specify parameters that change as a function of time or span +consecutive runs in a continuous fashion. For the latter, see the +*start* and *stop* keywords of the :doc:`run ` command and the +*elaplong* keyword of :doc:`thermo_style custom ` for +details. + +For example, these commands would change the prefactor coefficient of +the :doc:`pair_style soft ` potential from 10.0 to 30.0 in a +linear fashion over the course of a simulation: + +.. parsed-literal:: + + variable prefactor equal ramp(10,30) + fix 1 all adapt 1 pair soft a * * v_prefactor + + +---------- + + +The *kspace* keyword used the specified variable as a scale factor on +the energy, forces, virial calculated by whatever K-Space solver is +defined by the :doc:`kspace_style ` command. If the +variable has a value of 1.0, then the solver is unaltered. + +The *kspace* keyword works this way whether the *scale* keyword +is set to *no* or *yes*. + + +---------- + + +The *atom* keyword enables various atom properties to be changed. The +*aparam* argument is the name of the parameter to change. This is the +current list of atom parameters that can be varied by this fix: + +* charge = charge on particle +* diameter = diameter of particle + +The *I* argument indicates which atom types are affected. A wild-card +asterisk can be used in place of or in conjunction with the I argument +to set the coefficients for multiple atom types. + +The *v_name* argument of the *atom* keyword is the name of an +:doc:`equal-style variable ` which will be evaluated each time +this fix is invoked to set the parameter to a new value. It should be +specified as v_name, where name is the variable name. See the +discussion above describing the formulas associated with equal-style +variables. The new value is assigned to the corresponding attribute +for all atoms in the fix group. + +If the atom parameter is *diameter* and per-atom density and per-atom +mass are defined for particles (e.g. :doc:`atom_style granular `), then the mass of each particle is also +changed when the diameter changes (density is assumed to stay +constant). + +For example, these commands would shrink the diameter of all granular +particles in the "center" group from 1.0 to 0.1 in a linear fashion +over the course of a 1000-step simulation: + +.. parsed-literal:: + + variable size equal ramp(1.0,0.1) + fix 1 center adapt 10 atom diameter * v_size + +For :doc:`rRESPA time integration `, this fix changes +parameters on the outermost rRESPA level. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute fep `, :doc:`fix_adapt `, :doc:`compute ti ` + +Default +""""""" + +The option defaults are scale = no, reset = no, after = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_addforce.txt b/doc/_sources/fix_addforce.txt new file mode 100644 index 0000000000..9e710492ae --- /dev/null +++ b/doc/_sources/fix_addforce.txt @@ -0,0 +1,194 @@ +.. index:: fix addforce + +fix addforce command +==================== + +fix addforce/cuda command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID addforce fx fy fz keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* addforce = style name of this fix command +* fx,fy,fz = force component values (force units) +.. parsed-literal:: + + any of fx,fy,fz can be a variable (see below) + +* zero or more keyword/value pairs may be appended to args +* keyword = *every* or *region* or *energy* +.. parsed-literal:: + + *every* value = Nevery + Nevery = add force every this many timesteps + *region* value = region-ID + region-ID = ID of region atoms must be in to have added force + *energy* value = v_name + v_name = variable with name that calculates the potential energy of each atom in the added force field + + + +Examples +"""""""" + +.. parsed-literal:: + + fix kick flow addforce 1.0 0.0 0.0 + fix kick flow addforce 1.0 0.0 v_oscillate + fix ff boundary addforce 0.0 0.0 v_push energy v_espace + +Description +""""""""""" + +Add fx,fy,fz to the corresponding component of force for each atom in +the group. This command can be used to give an additional push to +atoms in a simulation, such as for a simulation of Poiseuille flow in +a channel. + +Any of the 3 quantities defining the force components can be specified +as an equal-style or atom-style :doc:`variable `, namely *fx*, +*fy*, *fz*. If the value is a variable, it should be specified as +v_name, where name is the variable name. In this case, the variable +will be evaluated each timestep, and its value(s) used to determine +the force component. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent force field. + +Atom-style variables can specify the same formulas as equal-style +variables but can also include per-atom values, such as atom +coordinates. Thus it is easy to specify a spatially-dependent force +field with optional time-dependence as well. + +If the *every* keyword is used, the *Nevery* setting determines how +often the forces are applied. The default value is 1, for every +timestep. + +If the *region* keyword is used, the atom must also be in the +specified geometric :doc:`region ` in order to have force added +to it. + + +---------- + + +Adding a force to atoms implies a change in their potential energy as +they move due to the applied force field. For dynamics via the "run" +command, this energy can be optionally added to the system's potential +energy for thermodynamic output (see below). For energy minimization +via the "minimize" command, this energy must be added to the system's +potential energy to formulate a self-consistent minimization problem +(see below). + +The *energy* keyword is not allowed if the added force is a constant +vector F = (fx,fy,fz), with all components defined as numeric +constants and not as variables. This is because LAMMPS can compute +the energy for each atom directly as E = -x dot F = -(x*fx + y*fy + +z*fz), so that -Grad(E) = F. + +The *energy* keyword is optional if the added force is defined with +one or more variables, and if you are performing dynamics via the +:doc:`run ` command. If the keyword is not used, LAMMPS will set +the energy to 0.0, which is typically fine for dynamics. + +The *energy* keyword is required if the added force is defined with +one or more variables, and you are performing energy minimization via +the "minimize" command. The keyword specifies the name of an +atom-style :doc:`variable ` which is used to compute the +energy of each atom as function of its position. Like variables used +for *fx*, *fy*, *fz*, the energy variable is specified as v_name, +where name is the variable name. + +Note that when the *energy* keyword is used during an energy +minimization, you must insure that the formula defined for the +atom-style :doc:`variable ` is consistent with the force +variable formulas, i.e. that -Grad(E) = F. For example, if the force +were a spring-like F = kx, then the energy formula should be E = +-0.5kx^2. If you don't do this correctly, the minimization will not +converge properly. + + +---------- + + +Styles with a *cuda* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +These accelerated styles are part of the USER-CUDA package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the potential "energy" inferred by the added force to the +system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is +needed so that the :doc:`minimize ` command can include the +forces added by this fix in a consistent manner. I.e. there is a +decrease in potential energy when atoms move in the direction of the +added force. + +This fix computes a global scalar and a global 3-vector of forces, +which can be accessed by various :ref:`output commands `. The scalar is the potential +energy discussed above. The vector is the total force on the group of +atoms before the forces on individual atoms are changed by the fix. +The scalar and vector values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. You should not +specify force components with a variable that has time-dependence for +use with a minimizer, since the minimizer increments the timestep as +the iteration count during the minimization. + +.. note:: + + If you want the fictitious potential energy associated with the + added forces to be included in the total potential energy of the + system (the quantity being minimized), you MUST enable the + :doc:`fix_modify ` *energy* option for this fix. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix setforce `, :doc:`fix aveforce ` + +Default +""""""" + +The option default for the every keyword is every = 1. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_addtorque.txt b/doc/_sources/fix_addtorque.txt new file mode 100644 index 0000000000..58a50c01e5 --- /dev/null +++ b/doc/_sources/fix_addtorque.txt @@ -0,0 +1,101 @@ +.. index:: fix addtorque + +fix addtorque command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID addtorque Tx Ty Tz + +* ID, group-ID are documented in :doc:`fix ` command +* addtorque = style name of this fix command +* Tx,Ty,Tz = torque component values (torque units) +* any of Tx,Ty,Tz can be a variable (see below) + + +Examples +"""""""" + +.. parsed-literal:: + + fix kick bead addtorque 2.0 3.0 5.0 + fix kick bead addtorque 0.0 0.0 v_oscillate + +Description +""""""""""" + +Add a set of forces to each atom in +the group such that: + +* the components of the total torque applied on the group (around its + center of mass) are Tx,Ty,Tz +* the group would move as a rigid body in the absence of other + forces. +This command can be used to drive a group of atoms into rotation. + +Any of the 3 quantities defining the torque components can be specified +as an equal-style :doc:`variable `, namely *Tx*, +*Ty*, *Tz*. If the value is a variable, it should be specified as +v_name, where name is the variable name. In this case, the variable +will be evaluated each timestep, and its value used to determine the +torque component. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent torque. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the potential "energy" inferred by the added forces to the +system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is +needed so that the :doc:`minimize ` command can include the +forces added by this fix in a consistent manner. I.e. there is a +decrease in potential energy when atoms move in the direction of the +added forces. + +This fix computes a global scalar and a global 3-vector, which can be +accessed by various :ref:`output commands `. +The scalar is the potential energy discussed above. The vector is the +total torque on the group of atoms before the forces on individual +atoms are changed by the fix. The scalar and vector values calculated +by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. You should not +specify force components with a variable that has time-dependence for +use with a minimizer, since the minimizer increments the timestep as +the iteration count during the minimization. + +Restrictions +"""""""""""" + + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix addforce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_append_atoms.txt b/doc/_sources/fix_append_atoms.txt new file mode 100644 index 0000000000..907acca70c --- /dev/null +++ b/doc/_sources/fix_append_atoms.txt @@ -0,0 +1,126 @@ +.. index:: fix append/atoms + +fix append/atoms command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID append/atoms face ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* append/atoms = style name of this fix command +* face = *zhi* +* zero or more keyword/value pairs may be appended +* keyword = *basis* or *size* or *freq* or *temp* or *random* or *units* +.. parsed-literal:: + + *basis* values = M itype + M = which basis atom + itype = atom type (1-N) to assign to this basis atom + *size* args = Lz + Lz = z size of lattice region appended in a single event(distance units) + *freq* args = freq + freq = the number of timesteps between append events + *temp* args = target damp seed extent + target = target temperature for the region between zhi-extent and zhi (temperature units) + damp = damping parameter (time units) + seed = random number seed for langevin kicks + extent = extent of thermostated region (distance units) + *random* args = xmax ymax zmax seed + *xmax*, *ymax*, *zmax* = maximum displacement in particular direction (distance units) + *seed* = random number seed for random displacement + *units* value = *lattice* or *box* + *lattice* = the wall position is defined in lattice units + *box* = the wall position is defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all append/atoms zhi size 5.0 freq 295 units lattice + fix 4 all append/atoms zhi size 15.0 freq 5 units box + fix A all append/atoms zhi size 1.0 freq 1000 units lattice + +Description +""""""""""" + +This fix creates atoms on a lattice, appended on the zhi edge of the +system box. This can be useful when a shock or wave is propagating +from zlo. This allows the system to grow with time to accommodate an +expanding wave. A simulation box must already exist, which is +typically created via the :doc:`create_box ` command. +Before using this command, a lattice must also be defined using the +:doc:`lattice ` command. + +This fix will automatically freeze atoms on the zhi edge of the +system, so that overlaps are avoided when new atoms are appended. + +The *basis* keyword specifies an atom type that will be assigned to +specific basis atoms as they are created. See the +:doc:`lattice ` command for specifics on how basis atoms are +defined for the unit cell of the lattice. By default, all created +atoms are assigned type = 1 unless this keyword specifies differently. + +The *size* keyword defines the size in z of the chunk of material to +be added. + +The *random* keyword will give the atoms random displacements around +their lattice points to simulate some initial temperature. + +The *temp* keyword will cause a region to be thermostated with a +Langevin thermostat on the zhi boundary. The size of the region is +measured from zhi and is set with the *extent* argument. + +The *units* keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant is used. +A *box* value selects standard distance units as defined by the +:doc:`units ` command, e.g. Angstroms for units = real or metal. +A *lattice* value means the distance units are in lattice spacings. +The :doc:`lattice ` command must have been previously used to +define the lattice spacings. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix style is part of the SHOCK package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The boundary on which atoms are added with append/atoms must be +shrink/minimum. The opposite boundary may be any boundary type other +than periodic. + +Related commands +"""""""""""""""" + +:doc:`fix wall/piston ` command + +Default +""""""" + +The keyword defaults are size = 0.0, freq = 0, units = lattice. All +added atoms are of type 1 unless the basis keyword is used. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_atc.txt b/doc/_sources/fix_atc.txt new file mode 100644 index 0000000000..9450c38c65 --- /dev/null +++ b/doc/_sources/fix_atc.txt @@ -0,0 +1,312 @@ +.. index:: fix atc + +fix atc command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix atc + +* fixID = name of fix +* group = name of group fix is to be applied +* type = *thermal* or *two_temperature* or *hardy* or *field* +.. parsed-literal:: + + *thermal* = thermal coupling with fields: temperature + *two_temperature* = electron-phonon coupling with field: temperature and electron_temperature + *hardy* = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) + *field* = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) + +* parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file +Examples +"""""""" + +.. parsed-literal:: + + fix AtC internal atc thermal Ar_thermal.dat + fix AtC internal atc two_temperature Ar_ttm.mat + fix AtC internal atc hardy + fix AtC internal atc field + +Description +""""""""""" + +This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. + +.. image:: JPG/atc_nanotube.jpg + :align: center + +.. parsed-literal:: + + The following coupling example is typical, but non-exhaustive: + # ... commands to create and initialize the MD system + +.. parsed-literal:: + + # initial fix to designate coupling type and group to apply it to + # tag group physics material_file + fix AtC internal atc thermal Ar_thermal.mat + +.. parsed-literal:: + + # create a uniform 12 x 2 x 2 mesh that covers region contain the group + # nx ny nz region periodicity + fix_modify AtC mesh create 12 2 2 mdRegion f p p + +.. parsed-literal:: + + # specify the control method for the type of coupling + # physics control_type + fix_modify AtC thermal control flux + +.. parsed-literal:: + + # specify the initial values for the empirical field "temperature" + # field node_group value + fix_modify AtC initial temperature all 30 + +.. parsed-literal:: + + # create an output stream for nodal fields + # filename output_frequency + fix_modify AtC output atc_fe_output 100 + +.. parsed-literal:: + + run 1000 + +likewise for this post-processing example: + +.. parsed-literal:: + + # ... commands to create and initialize the MD system + +.. parsed-literal:: + + # initial fix to designate post-processing and the group to apply it to + # no material file is allowed nor required + fix AtC internal atc hardy + +.. parsed-literal:: + + # for hardy fix, specific kernel function (function type and range) to # be used as a localization function + fix AtC kernel quartic_sphere 10.0 + +.. parsed-literal:: + + # create a uniform 1 x 1 x 1 mesh that covers region contain the group + # with periodicity this effectively creats a system average + fix_modify AtC mesh create 1 1 1 box p p p + +.. parsed-literal:: + + # change from default lagrangian map to eulerian + # refreshed every 100 steps + fix_modify AtC atom_element_map eulerian 100 + +.. parsed-literal:: + + # start with no field defined + # add mass density, potential energy density, stress and temperature + fix_modify AtC fields add density energy stress temperature + +.. parsed-literal:: + + # create an output stream for nodal fields + # filename output_frequency + fix_modify AtC output nvtFE 100 text + +.. parsed-literal:: + + run 1000 + +the mesh's linear interpolation functions can be used as the localization function + by using the field option: + +fix AtC internal atc field + +fix_modify AtC mesh create 1 1 1 box p p p + +... + +Note coupling and post-processing can be combined in the same simulations using separate fixes. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. The :doc:`fix_modify ` options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various :ref:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. + +* Currently, +* - the coupling is restricted to thermal physics +* - the FE computations are done in serial on each processor. + +Related commands +"""""""""""""""" + +After specifying this fix in your input script, several other :doc:`fix_modify ` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions. + +fix_modify commands for setup: + +* :doc:`fix_modify AtC mesh create ` +* :doc:`fix_modify AtC mesh quadrature ` +* :doc:`fix_modify AtC mesh read ` +* :doc:`fix_modify AtC mesh write ` +* :doc:`fix_modify AtC mesh create_nodeset ` +* :doc:`fix_modify AtC mesh add_to_nodeset ` +* :doc:`fix_modify AtC mesh create_faceset box ` +* :doc:`fix_modify AtC mesh create_faceset plane ` +* :doc:`fix_modify AtC mesh create_elementset ` +* :doc:`fix_modify AtC mesh delete_elements ` +* :doc:`fix_modify AtC mesh nodeset_to_elementset ` +* :doc:`fix_modify AtC boundary ` +* :doc:`fix_modify AtC internal_quadrature ` +* :doc:`fix_modify AtC time_integration (thermal) ` +* :doc:`fix_modify AtC time_integration (momentum) ` +* :doc:`fix_modify AtC extrinsic electron_integration ` +* :doc:`fix_modify AtC internal_element_set ` +* :doc:`fix_modify AtC decomposition ` + +fix_modify commands for boundary and initial conditions: + +* :doc:`fix_modify AtC initial ` +* :doc:`fix_modify AtC fix ` +* :doc:`fix_modify AtC unfix ` +* :doc:`fix_modify AtC fix_flux ` +* :doc:`fix_modify AtC unfix_flux ` +* :doc:`fix_modify AtC source ` +* :doc:`fix_modify AtC remove_source ` + +fix_modify commands for control and filtering: + +* :doc:`fix_modify AtC control ` +* :doc:`fix_modify AtC control thermal ` +* :doc:`fix_modify AtC control thermal correction_max_iterations ` +* :doc:`fix_modify AtC control momentum ` +* :doc:`fix_modify AtC control localized_lambda ` +* :doc:`fix_modify AtC control lumped_lambda_solve ` +* :doc:`fix_modify AtC control mask_direction ` control +* :doc:`fix_modify AtC filter ` +* :doc:`fix_modify AtC filter scale ` +* :doc:`fix_modify AtC filter type ` +* :doc:`fix_modify AtC equilibrium_start ` +* :doc:`fix_modify AtC extrinsic exchange ` +* :doc:`fix_modify AtC poisson_solver ` + +fix_modify commands for output: + +* :doc:`fix_modify AtC output ` +* :doc:`fix_modify AtC output nodeset ` +* :doc:`fix_modify AtC output elementset ` +* :doc:`fix_modify AtC output boundary_integral ` +* :doc:`fix_modify AtC output contour_integral ` +* :doc:`fix_modify AtC mesh output ` +* :doc:`fix_modify AtC write_restart ` +* :doc:`fix_modify AtC read_restart ` + +fix_modify commands for post-processing: + +* :doc:`fix_modify AtC kernel ` +* :doc:`fix_modify AtC fields ` +* :doc:`fix_modify AtC grdients ` +* :doc:`fix_modify AtC rates ` +* :doc:`fix_modify AtC computes ` +* :doc:`fix_modify AtC on_the_fly ` +* :doc:`fix_modify AtC pair_interactions/bond_interactions ` +* :doc:`fix_modify AtC sample_frequency ` +* :doc:`fix_modify AtC set ` + +miscellaneous fix_modify commands: + +* :doc:`fix_modify AtC atom_element_map ` +* :doc:`fix_modify AtC atom_weight ` +* :doc:`fix_modify AtC write_atom_weights ` +* :doc:`fix_modify AtC reset_time ` +* :doc:`fix_modify AtC reset_atomic_reference_positions ` +* :doc:`fix_modify AtC fe_md_boundary ` +* :doc:`fix_modify AtC boundary_faceset ` +* :doc:`fix_modify AtC consistent_fe_initialization ` +* :doc:`fix_modify AtC mass_matrix ` +* :doc:`fix_modify AtC material ` +* :doc:`fix_modify AtC atomic_charge ` +* :doc:`fix_modify AtC source_integration ` +* :doc:`fix_modify AtC temperature_definition ` +* :doc:`fix_modify AtC track_displacement ` +* :doc:`fix_modify AtC boundary_dynamics ` +* :doc:`fix_modify AtC add_species ` +* :doc:`fix_modify AtC add_molecule ` +* :doc:`fix_modify AtC remove_species ` +* :doc:`fix_modify AtC remove_molecule ` + +Note: a set of example input files with the attendant material files are included with this package + +Default +""""""" +None + + +---------- + + +For detailed exposition of the theory and algorithms please see: + +.. _Wagner: + + + +**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. + +.. _Zimmeman2004: + + + +**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. + +.. _Zimmerman2010: + + + +**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364. + +.. _Templeton2010: + + + +**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. + +.. _Jones: + + + +**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940. + +.. _Templeton2011: + + + +**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736. + +.. _Mandadapu: + + + +**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. + +Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_atom_swap.txt b/doc/_sources/fix_atom_swap.txt new file mode 100644 index 0000000000..e5a3216210 --- /dev/null +++ b/doc/_sources/fix_atom_swap.txt @@ -0,0 +1,203 @@ +.. index:: fix atom/swap + +fix atom/swap command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID atom/swap N X seed T keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* atom/swap = style name of this fix command +* N = invoke this fix every N steps +* X = number of swaps to attempt every N steps +* seed = random # seed (positive integer) +* T = scaling temperature of the MC swaps (temperature units) +* one or more keyword/value pairs may be appended to args +* keyword = *types* or *mu* or *ke* or *semi-grand* or *region* +.. parsed-literal:: + + *types* values = two or more atom types + *mu* values = chemical potential of swap types (energy units) + *ke* value = *no* or *yes* + *no* = no conservation of kinetic energy after atom swaps + *yes* = kinetic energy is conserved after atom swaps + *semi-grand* value = *no* or *yes* + *no* = particle type counts and fractions conserved + *yes* = semi-grand canonical ensemble, particle fractions not conserved + *region* value = region-ID + region-ID = ID of region to use as an exchange/move volume + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2 + fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6 + fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0 + +Description +""""""""""" + +This fix performs Monte Carlo swaps of atoms of one given atom type +with atoms of the other given atom types. The specified T is used in +the Metropolis criterion dictating swap probabilities. + +Perform X swaps of atoms of one type with atoms of another type +according to a Monte Carlo probability. Swap candidates must be in the +fix group, must be in the region (if specified), and must be of one of +the listed types. Swaps are attempted between candidates that are +chosen randomly with equal probability among the candidate +atoms. Swaps are not attempted between atoms of the same type since +nothing would happen. + +All atoms in the simulation domain can be moved using regular time +integration displacements, e.g. via :doc:`fix_nvt `, resulting +in a hybrid MC+MD simulation. A smaller-than-usual timestep size may +be needed when running such a hybrid simulation, especially if the +swapped atoms are not well equilibrated. + +The *types* keyword is required. At least two atom types must be +specified. + +The *ke* keyword can be set to *no* to turn off kinetic energy +conservation for swaps. The default is *yes*, which means that swapped +atoms have their velocities scaled by the ratio of the masses of the +swapped atom types. This ensures that the kinetic energy of each atom +is the same after the swap as it was before the swap, even though the +atom masses have changed. + +The *semi-grand* keyword can be set to *yes* to switch to the +semi-grand canonical ensemble as discussed in :ref:`(Sadigh) `. This +means that the total number of each particle type does not need to be +conserved. The default is *no*, which means that the only kind of swap +allowed exchanges an atom of one type with an atom of a different +given type. In other words, the relative mole fractions of the swapped +atoms remains constant. Whereas in the semi-grand canonical ensemble, +the composition of the system can change. Note that when using +*semi-grand*, atoms in the fix group whose type is not listed +in the *types* keyword are ineligible for attempted +conversion. An attempt is made to switch +the selected atom (if eligible) to one of the other listed types +with equal probability. Acceptance of each attempt depends upon the Metropolis criterion. + +The *mu* keyword allows users to specify chemical +potentials. This is required and allowed only when using *semi-grand*. +All chemical potentials are absolute, so there is one for +each swap type listed following the *types* keyword. +In semi-grand canonical ensemble simulations the chemical composition +of the system is controlled by the difference in these values. So +shifting all values by a constant amount will have no effect +on the simulation. + +This command may optionally use the *region* keyword to define swap +volume. The specified region must have been previously defined with a +:doc:`region ` command. It must be defined with side = *in*. +Swap attempts occur only between atoms that are both within the +specified region. Swaps are not otherwise attempted. + +You should ensure you do not swap atoms belonging to a molecule, or +LAMMPS will soon generate an error when it tries to find those atoms. +LAMMPS will warn you if any of the atoms eligible for swapping have a +non-zero molecule ID, but does not check for this at the time of +swapping. + +If not using *semi-grand* this fix checks to ensure all atoms of the +given types have the same atomic charge. LAMMPS doesn't enforce this +in general, but it is needed for this fix to simplify the +swapping procedure. Successful swaps will swap the atom type and charge +of the swapped atoms. Conversely, when using *semi-grand*, it is assumed that all the atom +types involved in switches have the same charge. Otherwise, charge +would not be conserved. As a consequence, no checks on atomic charges are +performed, and successful switches update the atom type but not the +atom charge. While it is possible to use *semi-grand* with groups of +atoms that have different charges, these charges will not be changed when the +atom types change. + +Since this fix computes total potential energies before and after +proposed swaps, so even complicated potential energy calculations are +OK, including the following: + +* long-range electrostatics (kspace) +* many body pair styles +* hybrid pair styles +* eam pair styles +* triclinic systems +* need to include potential energy contributions from other fixes + +Some fixes have an associated potential energy. Examples of such fixes +include: :doc:`efield `, :doc:`gravity `, +:doc:`addforce `, :doc:`langevin `, +:doc:`restrain `, :doc:`temp/berendsen `, +:doc:`temp/rescale `, and :doc:`wall fixes `. +For that energy to be included in the total potential energy of the +system (the quantity used when performing GCMC moves), +you MUST enable the :doc:`fix_modify ` *energy* option for +that fix. The doc pages for individual :doc:`fix ` commands +specify if this should be done. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random +number generator seed, the next timestep for MC exchanges, etc. See +the :doc:`read_restart ` command for info on how to +re-specify a fix in an input script that reads a restart file, so that +the operation of the fix continues in an uninterrupted fashion. + +None of the :doc:`fix_modify ` options are relevant to this +fix. + +This fix computes a global vector of length 2, which can be accessed +by various :ref:`output commands `. The vector +values are the following global cumulative quantities: + +* 1 = swap attempts +* 2 = swap successes + +The vector values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix_nvt `, :doc:`neighbor `, +:doc:`fix_deposit `, :doc:`fix_evaporate `, +:doc:`delete_atoms `, :doc:`fix_gcmc ` + +Default +""""""" + +The option defaults are ke = yes, semi-grand = no, mu = 0.0 for +all atom types. + + +---------- + + +.. _Sadigh: + + + +**(Sadigh)** B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and +L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ave_atom.txt b/doc/_sources/fix_ave_atom.txt new file mode 100644 index 0000000000..ba4fbf8f17 --- /dev/null +++ b/doc/_sources/fix_ave_atom.txt @@ -0,0 +1,163 @@ +.. index:: fix ave/atom + +fix ave/atom command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ... + +* ID, group-ID are documented in :doc:`fix ` command +* ave/atom = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of times to use input values for calculating averages +* Nfreq = calculate averages every this many timesteps + one or more input values can be listed +* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name +.. parsed-literal:: + + x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) + c_ID = per-atom vector calculated by a compute with ID + c_ID[I] = Ith column of per-atom array calculated by a compute with ID + f_ID = per-atom vector calculated by a fix with ID + f_ID[I] = Ith column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all ave/atom 1 100 100 vx vy vz + fix 1 all ave/atom 10 20 1000 c_my_stress[1] + +Description +""""""""""" + +Use one or more per-atom vectors as inputs every few timesteps, and +average them atom by atom over longer timescales. The resulting +per-atom averages can be used by other :ref:`output commands ` such as the :doc:`fix ave/spatial ` or :doc:`dump custom ` commands. + +The group specified with the command means only atoms within the group +have their averages computed. Results are set to 0.0 for atoms not in +the group. + +Each input value can be an atom attribute (position, velocity, force +component) or can be the result of a :doc:`compute ` or +:doc:`fix ` or the evaluation of an atom-style +:doc:`variable `. In the latter cases, the compute, fix, or +variable must produce a per-atom vector, not a global quantity or +local quantity. If you wish to time-average global quantities from a +compute, fix, or variable, then see the :doc:`fix ave/time ` command. + +:doc:`Computes ` that produce per-atom vectors or arrays are +those which have the word *atom* in their style name. See the doc +pages for individual :doc:`fixes ` to determine which ones produce +per-atom vectors or arrays. :doc:`Variables ` of style *atom* +are the only ones that can be used with this fix since they produce +per-atom vectors. + +Each per-atom value of each input vector is averaged independently. + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be used in order to contribute to the +average. The final averaged quantities are generated on timesteps +that are a multiple of *Nfreq*. The average is over *Nrepeat* +quantities, computed in the preceding portion of the simulation every +*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and +*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps +contributing to the average value cannot overlap, +i.e. Nrepeat*Nevery can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on +timesteps 90,92,94,96,98,100 will be used to compute the final average +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on +timestep 200, etc. + + +---------- + + +The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are +self-explanatory. Note that other atom attributes can be used as +inputs to this fix by using the :doc:`compute property/atom ` command and then specifying +an input value from that compute. + +.. note:: + + The x,y,z attributes are values that are re-wrapped inside the + periodic box whenever an atom crosses a periodic boundary. Thus if + you time average an atom that spends half its time on either side of + the periodic box, you will get a value in the middle of the box. If + this is not what you want, consider averaging unwrapped coordinates, + which can be provided by the :doc:`compute property/atom ` command via its xu,yu,zu + attributes. + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. If no bracketed term is +appended, the per-atom vector calculated by the compute is used. If a +bracketed term containing an index I is appended, the Ith column of +the per-atom array calculated by the compute is used. Users can also +write code for their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. If no bracketed term is +appended, the per-atom vector calculated by the fix is used. If a +bracketed term containing an index I is appended, the Ith column of +the per-atom array calculated by the fix is used. Note that some +fixes only produce their values on certain timesteps, which must be +compatible with *Nevery*, else an error will result. Users can also +write code for their own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script as an :doc:`atom-style variable ` Variables of style *atom* can reference +thermodynamic keywords, or invoke other computes, fixes, or variables +when they are evaluated, so this is a very general means of generating +per-atom quantities to time average. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global scalar or vector quantities are +stored by this fix for access by various :ref:`output commands `. + +This fix produces a per-atom vector or array which can be accessed by +various :ref:`output commands `. A vector is +produced if only a single quantity is averaged by this fix. If two or +more quantities are averaged, then an array of values is produced. +The per-atom values can only be accessed on timesteps that are +multiples of *Nfreq* since that is when averaging is performed. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`fix ave/histo `, :doc:`fix ave/spatial `, :doc:`fix ave/time `, +:doc:`variable `, + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ave_chunk.txt b/doc/_sources/fix_ave_chunk.txt new file mode 100644 index 0000000000..ef9253c214 --- /dev/null +++ b/doc/_sources/fix_ave_chunk.txt @@ -0,0 +1,471 @@ +.. index:: fix ave/chunk + +fix ave/chunk command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* ave/chunk = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of times to use input values for calculating averages +* Nfreq = calculate averages every this many timesteps +* chunkID = ID of :doc:`compute chunk/atom ` command +* one or more input values can be listed +* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name +.. parsed-literal:: + + vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) + density/number, density/mass = number or mass density + temp = temperature + c_ID = per-atom vector calculated by a compute with ID + c_ID[I] = Ith column of per-atom array calculated by a compute with ID + f_ID = per-atom vector calculated by a fix with ID + f_ID[I] = Ith column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name + +* zero or more keyword/arg pairs may be appended +* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *title1* or *title2* or *title3* +.. parsed-literal:: + + *norm* arg = *all* or *sample* or *none* = how output on *Nfreq* steps is normalized + all = output is sum of atoms across all *Nrepeat* samples, divided by atom count + sample = output is sum of *Nrepeat* sample averages, divided by *Nrepeat* + none = output is sum of *Nrepeat* sample sums, divided by *Nrepeat* + *ave* args = *one* or *running* or *window M* + one = output new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps + *bias* arg = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation + *adof* value = dof_per_atom + dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation + *cdof* value = dof_per_chunk + dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation + *file* arg = filename + filename = file to write results to + *overwrite* arg = none = overwrite output file with only latest output + *format* arg = string + string = C-style format string + *title1* arg = string + string = text to print as 1st line of output file + *title2* arg = string + string = text to print as 2nd line of output file + *title3* arg = string + string = text to print as 3rd line of output file + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values" + fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile + fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running + fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running + +**NOTE:** + +If you are trying to replace an older fix ave/spatial command with the +newer, more flexible fix ave/chunk and :doc:`compute chunk/atom ` commands, you simply need to split +the fix ave/spatial arguments across the two new commands. For +example, this command: + +.. parsed-literal:: + + fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile + +could be replaced by: + +.. parsed-literal:: + + compute cc1 flow chunk/atom bin/1d y 0.0 1.0 + fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile + +Description +""""""""""" + +Use one or more per-atom vectors as inputs every few timesteps, sum +the values over the atoms in each chunk at each timestep, then average +the per-chunk values over longer timescales. The resulting chunk +averages can be used by other :ref:`output commands ` such as :doc:`thermo_style custom `, and can also be written to a file. + +In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom ` command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` doc page and ":ref:`Section_howto 23 ` for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +Note that only atoms in the specified group contribute to the summing +and averaging calculations. The :doc:`compute chunk/atom ` command defines its own group as +well as an optional region. Atoms will have a chunk ID = 0, meaning +they belong to no chunk, if they are not in that group or region. +Thus you can specify the "all" group for this command if you simply +want to use the chunk definitions provided by chunkID. + +Each specified per-atom value can be an atom attribute (position, +velocity, force component), a mass or number density, or the result of +a :doc:`compute ` or :doc:`fix ` or the evaluation of an +atom-style :doc:`variable `. In the latter cases, the +compute, fix, or variable must produce a per-atom quantity, not a +global quantity. Note that the :doc:`compute property/atom ` command provides access to +any attribute defined and stored by atoms. If you wish to +time-average global quantities from a compute, fix, or variable, then +see the :doc:`fix ave/time ` command. + +:doc:`Computes ` that produce per-atom quantities are those +which have the word *atom* in their style name. See the doc pages for +individual :doc:`fixes ` to determine which ones produce per-atom +quantities. :doc:`Variables ` of style *atom* are the only +ones that can be used with this fix since all other styles of variable +produce global quantities. + +The per-atom values of each input vector are summed and averaged +independently of the per-atom values in other input vectors. + +.. note:: + + This fix works by creating an array of size *Nchunk* by Nvalues + on each processor. *Nchunk* is the number of chunks which is defined + by the :doc:`compute chunk/atom ` command. + Nvalues is the number of input values specified. Each processor loops + over its atoms, tallying its values to the appropriate chunk. Then + the entire array is summed across all processors. This means that + using a large number of chunks will incur an overhead in memory and + computational cost (summing across processors), so be careful to + define a reasonable number of chunks. + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be accessed and contribute to the +average. The final averaged quantities are generated on timesteps +that are a multiples of *Nfreq*. The average is over *Nrepeat* +quantities, computed in the preceding portion of the simulation every +*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and +*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps +contributing to the average value cannot overlap, i.e. Nrepeat*Nevery +can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on +timesteps 90,92,94,96,98,100 will be used to compute the final average +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on +timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time +averaging is done; values are simply generated on timesteps +100,200,etc. + +Each input value can also be averaged over the atoms in each chunk. +The way the averaging is done across the *Nrepeat* timesteps to +produce output on the *Nfreq* timesteps, and across multiple *Nfreq* +outputs, is determined by the *norm* and *ave* keyword settings, as +discussed below. + +.. note:: + + To perform per-chunk averaging within a *Nfreq* time window, the + number of chunks *Nchunk* defined by the :doc:`compute chunk/atom ` command must remain constant. If + the *ave* keyword is set to *running* or *window* then *Nchunk* must + remain constant for the duration of the simulation. This fix forces + the chunk/atom compute specified by chunkID to hold *Nchunk* constant + for the appropriate time windows, by not allowing it to re-calcualte + *Nchunk*, which can also affect how it assigns chunk IDs to atoms. + More details are given on the :doc:`compute chunk/atom ` doc page. + + +---------- + + +The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. +As noted above, any other atom attributes can be used as input values +to this fix by using the :doc:`compute property/atom ` command and then specifying +an input value from that compute. + +The *density/number* value means the number density is computed for +each chunk, i.e. number/volume. The *density/mass* value means the +mass density is computed for each chunk, i.e. total-mass/volume. The +output values are in units of 1/volume or density (mass/volume). See +the :doc:`units ` command doc page for the definition of density +for each choice of units, e.g. gram/cm^3. If the chunks defined by +the :doc:`compute chunk/atom ` command are spatial +bins, the volume is the bin volume. Otherwise it is the volume of the +entire simulation box. + +The *temp* value means the temperature is computed for each chunk, by +the formula KE = DOF/2 k T, where KE = total kinetic energy of the +chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees +of freedom for all atoms in the chunk, k = Boltzmann constant, and T = +temperature. + +The DOF is calculated as N*adof + cdof, where N = number of atoms in +the chunk, adof = degrees of freedom per atom, and cdof = degrees of +freedom per chunk. By default adof = 2 or 3 = dimensionality of +system, as set via the :doc:`dimension ` command, and cdof = +0.0. This gives the usual formula for temperature. + +Note that currently this temperature only includes translational +degrees of freedom for each atom. No rotational degrees of freedom +are included for finite-size particles. Also no degrees of freedom +are subtracted for any velocity bias or constraints that are applied, +such as :doc:`compute temp/partial `, or :doc:`fix shake ` or :doc:`fix rigid `. This is because +those degrees of freedom (e.g. a constrained bond) could apply to sets +of atoms that are both included and excluded from a specific chunk, +and hence the concept is somewhat ill-defined. In some cases, you can +use the *adof* and *cdof* keywords to adjust the calculated degress of +freedom appropriately, as explained below. + +Also note that a bias can be subtracted from atom velocities before +they are used in the above formula for KE, by using the *bias* +keyword. This allows, for example, a thermal temperature to be +computed after removal of a flow velocity profile. + +Note that the per-chunk temperature calculated by this fix and the +:doc:`compute temp/chunk ` command can be different. +The compute calculates the temperature for each chunk for a single +snapshot. This fix can do that but can also time average those values +over many snapshots, or it can compute a temperature as if the atoms +in the chunk on different timesteps were collected together as one set +of atoms to calculate their temperature. The compute allows the +center-of-mass velocity of each chunk to be subtracted before +calculating the temperature; this fix does not. + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the compute is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the fix is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with +*Nevery*, else an error results. Users can also write code for their +own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script. Variables of style +*atom* can reference thermodynamic keywords and various per-atom +attributes, or invoke other computes, fixes, or variables when they +are evaluated, so this is a very general means of generating per-atom +quantities to average within chunks. + + +---------- + + +Additional optional keywords also affect the operation of this fix +and its outputs. + +The *norm* keyword affects how averaging is done for the per-chunk +values that are output every *Nfreq* timesteps. + +It the *norm* setting is *all*, which is the default, a chunk value is +summed over all atoms in all *Nrepeat* samples, as is the count of +atoms in the chunk. The averaged output value for the chunk on the +*Nfreq* timesteps is Total-sum / Total-count. In other words it is an +average over atoms across the entire *Nfreq* timescale. + +If the *norm* setting is *sample*, the chunk value is summed over atoms +for each sample, as is the count, and an "average sample value" is +computed for each sample, i.e. Sample-sum / Sample-count. The output +value for the chunk on the *Nfreq* timesteps is the average of the +*Nrepeat* "average sample values", i.e. the sum of *Nrepeat* "average +sample values" divided by *Nrepeat*. In other words it is an average +of an average. + +If the *norm* setting is *none*, a similar computation as for the +*sample* seting is done, except the individual "average sample values" +are "summed sample values". A summed sample value is simply the chunk +value summed over atoms in the sample, without dividing by the number +of atoms in the sample. The output value for the chunk on the +*Nfreq* timesteps is the average of the *Nrepeat* "summed sample +values", i.e. the sum of *Nrepeat* "summed sample values" divided by +*Nrepeat*. + +The *ave* keyword determines how the per-chunk values produced every +*Nfreq* steps are averaged with values produced on previous steps that +were multiples of *Nfreq*, before they are accessed by another output +command or written to a file. + +If the *ave* setting is *one*, which is the default, then the chunk +values produced on timesteps that are multiples of *Nfreq* are +independent of each other; they are output as-is without further +averaging. + +If the *ave* setting is *running*, then the chunk values produced on +timesteps that are multiples of *Nfreq* are summed and averaged in a +cumulative sense before being output. Each output chunk value is thus +the average of the chunk value produced on that timestep with all +preceding values for the same chunk. This running average begins when +the fix is defined; it can only be restarted by deleting the fix via +the :doc:`unfix ` command, or re-defining the fix by +re-specifying it. + +If the *ave* setting is *window*, then the chunk values produced on +timesteps that are multiples of *Nfreq* are summed and averaged within +a moving "window" of time, so that the last M values for the same +chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000, +then the output on step 10000 will be the average of the individual +chunk values on steps 8000,9000,10000. Outputs on early steps will +average over less than M values if they are not available. + +The *bias* keyword specifies the ID of a temperature compute that +removes a "bias" velocity from each atom, specified as *bias-ID*. It +is only used when the *temp* value is calculated, to compute the +thermal temperature of each chunk after the translational kinetic +energy components have been altered in a prescribed way, e.g. to +remove a flow velocity profile. See the doc pages for individual +computes that calculate a temperature to see which ones implement a +bias. + +The *adof* and *cdof* keywords define the values used in the degree of +freedom (DOF) formula described above for for temperature calculation +for each chunk. They are only used when the *temp* value is +calculated. They can be used to calculate a more appropriate +temperature for some kinds of chunks. Here are 3 examples: + +If spatially binned chunks contain some number of water molecules and +:doc:`fix shake ` is used to make each molecule rigid, then +you could calculate a temperature with 6 degrees of freedom (DOF) (3 +translational, 3 rotational) per molecule by setting *adof* to 2.0. + +If :doc:`compute temp/partial ` is used with the +*bias* keyword to only allow the x component of velocity to contribute +to the temperature, then *adof* = 1.0 would be appropriate. + +If each chunk consists of a large molecule, with some number of its +bonds constrained by :doc:`fix shake ` or the entire molecule +by :doc:`fix rigid/small `, *adof* = 0.0 and *cdof* could be +set to the remaining degrees of freedom for the entire molecule +(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid +molecule. + +The *file* keyword allows a filename to be specified. Every *Nfreq* +timesteps, a section of chunk info will be written to a text file in +the following format. A line with the timestep and number of chunks +is written. Then one line per chunk is written, containing the chunk +ID (1-Nchunk), an optional original ID value, optional coordinate +values for chunks that represent spatial bins, the number of atoms in +the chunk, and one or more calculated values. More explanation of the +optional values is given below. The number of values in each line +corresponds to the number of values specified in the fix ave/chunk +command. The number of atoms and the value(s) are summed or average +quantities, as explained above. + +The *overwrite* keyword will continuously overwrite the output file +with the latest output, so that it only contains one timestep worth of +output. This option can only be used with the *ave running* setting. + +The *format* keyword sets the numeric format of each value when it is +printed to a file via the *file* keyword. Note that all values are +floating point quantities. The default format is %g. You can specify +a higher precision if desired, e.g. %20.16g. + +The *title1* and *title2* and *title3* keywords allow specification of +the strings that will be printed as the first 3 lines of the output +file, assuming the *file* keyword was used. LAMMPS uses default +values for each of these, so they do not need to be specified. + +By default, these header lines are as follows: + +.. parsed-literal:: + + # Chunk-averaged data for fix ID and group name + # Timestep Number-of-chunks + # Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount value1 value2 ... + +In the first line, ID and name are replaced with the fix-ID and group +name. The second line describes the two values that are printed at +the first of each section of output. In the third line the values are +replaced with the appropriate value names, e.g. fx or c_myCompute**2**. + +The words in parenthesis only appear with corresponding columns if the +chunk style specified for the :doc:`compute chunk/atom ` command supports them. The OrigID +column is only used if the *compress* keyword was set to *yes* for the +:doc:`compute chunk/atom ` command. This means that +the original chunk IDs (e.g. molecule IDs) will have been compressed +to remove chunk IDs with no atoms assigned to them. Thus a compresed +chunk ID of 3 may correspond to an original chunk ID or molecule ID of +415. The OrigID column will list 415 for the 3rd chunk. + +The CoordN columns only appear if a *binning* style was used in the +:doc:`compute chunk/atom ` command. For *bin/1d*, +*bin/2d*, and *bin/3d* styles the column values are the center point +of the bin in the corresponding dimension. Just Coord1 is used for +*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*. +For *bin/sphere*, just Coord1 is used, and it is the radial +coordinate. For *bin/cylinder*, Coord1 and Coord2 are used. Coord1 +is the radial coordinate (away from the cylinder axis), and coord2 is +the coordinate along the cylinder axis. + +Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command ` is *box* or *lattice*, the +coordinate values will be in distance :doc:`units `. If the +value of the *units* keyword is *reduced*, the coordinate values will +be in unitless reduced units (0-1). This is not true for the Coord1 value +of style *bin/sphere* or *bin/cylinder* which both represent radial +dimensions. Those values are always in distance :doc:`units `. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global array of values which can be accessed by +various :ref:`output commands `. The values can +only be accessed on timesteps that are multiples of *Nfreq* since that +is when averaging is performed. The global array has # of rows = +the number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The # of columns = +M+1+Nvalues, where M = 1 to 4, depending on whether the optional +columns for OrigID and CoordN are used, as explained above. +Following the optional columns, the next column contains the count of +atoms in the chunk, and the remaining columns are the Nvalue +quantities. When the array is accessed with a row I that exceeds the +current number of chunks, than a 0.0 is returned by the fix instead of +an error, since the number of chunks can vary as a simulation runs +depending on how that value is computed by the compute chunk/atom +command. + +The array values calculated by this fix are treated as "intensive", +since they are typically already normalized by the count of atoms in +each chunk. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/histo `, :doc:`fix ave/time `, +:doc:`variable `, :doc:`fix ave/correlate ` + +Default +""""""" + +The option defaults are norm = all, ave = one, bias = none, no file output, and +title 1,2,3 = strings as described above. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ave_correlate.txt b/doc/_sources/fix_ave_correlate.txt new file mode 100644 index 0000000000..53e74246a7 --- /dev/null +++ b/doc/_sources/fix_ave_correlate.txt @@ -0,0 +1,350 @@ +.. index:: fix ave/correlate + +fix ave/correlate command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ave/correlate Nevery Nrepeat Nfreq value1 value2 ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* ave/correlate = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of correlation time windows to accumulate +* Nfreq = calculate time window averages every this many timesteps +* one or more input values can be listed +* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name +.. parsed-literal:: + + c_ID = global scalar calculated by a compute with ID + c_ID[I] = Ith component of global vector calculated by a compute with ID + f_ID = global scalar calculated by a fix with ID + f_ID[I] = Ith component of global vector calculated by a fix with ID + v_name = global value calculated by an equal-style variable with name + +* zero or more keyword/arg pairs may be appended +* keyword = *type* or *ave* or *start* or *prefactor* or *file* or *overwrite* or *title1* or *title2* or *title3* +.. parsed-literal:: + + *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* + auto = correlate each value with itself + upper = correlate each value with each succeeding value + lower = correlate each value with each preceding value + auto/upper = auto + upper + auto/lower = auto + lower + full = correlate each value with every other value, including itself = auto + upper + lower + *ave* args = *one* or *running* + one = zero the correlation accumulation every Nfreq steps + running = accumulate correlations continuously + *start* args = Nstart + Nstart = start accumulating correlations on this timestep + *prefactor* args = value + value = prefactor to scale all the correlation data by + *file* arg = filename + filename = name of file to output correlation data to + *overwrite* arg = none = overwrite output file with only latest output + *title1* arg = string + string = text to print as 1st line of output file + *title2* arg = string + string = text to print as 2nd line of output file + *title3* arg = string + string = text to print as 3rd line of output file + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate + fix 1 all ave/correlate 1 50 10000 & + c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] & + type upper ave running title1 "My correlation data" + +Description +""""""""""" + +Use one or more global scalar values as inputs every few timesteps, +calculate time correlations bewteen them at varying time intervals, +and average the correlation data over longer timescales. The +resulting correlation values can be time integrated by +:doc:`variables ` or used by other :ref:`output commands ` such as :doc:`thermo_style custom `, and can also be written to a file. See the +:doc:`fix ave/correlate/long ` command for an +alternate method for computing correlation functions efficiently over +very long time windows. + +The group specified with this command is ignored. However, note that +specified values may represent calculations performed by computes and +fixes which store their own "group" definitions. + +Each listed value can be the result of a :doc:`compute ` or +:doc:`fix ` or the evaluation of an equal-style +:doc:`variable `. In each case, the compute, fix, or variable +must produce a global quantity, not a per-atom or local quantity. If +you wish to spatial- or time-average or histogram per-atom quantities +from a compute, fix, or variable, then see the :doc:`fix ave/spatial `, :doc:`fix ave/atom `, +or :doc:`fix ave/histo ` commands. If you wish to sum a +per-atom quantity into a single global quantity, see the :doc:`compute reduce ` command. + +:doc:`Computes ` that produce global quantities are those which +do not have the word *atom* in their style name. Only a few +:doc:`fixes ` produce global quantities. See the doc pages for +individual fixes for info on which ones produce such values. +:doc:`Variables ` of style *equal* are the only ones that can +be used with this fix. Variables of style *atom* cannot be used, +since they produce per-atom values. + +The input values must either be all scalars. What kinds of +correlations between input values are calculated is determined by the +*type* keyword as discussed below. + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be used to calculate correlation data. +The input values are sampled every *Nevery* timesteps. The +correlation data for the preceding samples is computed on timesteps +that are a multiple of *Nfreq*. Consider a set of samples from some +initial time up to an output timestep. The initial time could be the +beginning of the simulation or the last output time; see the *ave* +keyword for options. For the set of samples, the correlation value +Cij is calculated as: + +.. parsed-literal:: + + Cij(delta) = ave(Vi(t)*Vj(t+delta)) + +which is the correlation value between input values Vi and Vj, +separated by time delta. Note that the second value Vj in the pair is +always the one sampled at the later time. The ave() represents an +average over every pair of samples in the set that are separated by +time delta. The maximum delta used is of size (*Nrepeat*-1)**Nevery*. +Thus the correlation between a pair of input values yields *Nrepeat* +correlation datums: + +.. parsed-literal:: + + Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery) + +For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on +timesteps 0,5,10,15,...,100 will be used to compute the final averages +on timestep 100. Six averages will be computed: Cij(0), Cij(5), +Cij(10), Cij(15), Cij(20), and Cij(25). Cij(10) on timestep 100 will +be the average of 19 samples, namely Vi(0)*Vj(10), Vi(5)*Vj(15), +Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100). + +*Nfreq* must be a multiple of *Nevery*; *Nevery* and *Nrepeat* must be +non-zero. Also, if the *ave* keyword is set to *one* which is the +default, then *Nfreq* >= (*Nrepeat*-1)**Nevery* is required. + + +---------- + + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. If no bracketed term is +appended, the global scalar calculated by the compute is used. If a +bracketed term is appended, the Ith element of the global vector +calculated by the compute is used. + +Note that there is a :doc:`compute reduce ` command +which can sum per-atom quantities into a global scalar or vector which +can thus be accessed by fix ave/correlate. Or it can be a compute +defined not in your input script, but by :doc:`thermodynamic output ` or other fixes such as :doc:`fix nvt ` +or :doc:`fix temp/rescale `. See the doc pages for +these commands which give the IDs of these computes. Users can also +write code for their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. If no bracketed term is +appended, the global scalar calculated by the fix is used. If a +bracketed term is appended, the Ith element of the global vector +calculated by the fix is used. + +Note that some fixes only produce their values on certain timesteps, +which must be compatible with *Nevery*, else an error will result. +Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script. Only equal-style +variables can be referenced. See the :doc:`variable ` command +for details. Note that variables of style *equal* define a formula +which can reference individual atom properties or thermodynamic +keywords, or they can invoke other computes, fixes, or variables when +they are evaluated, so this is a very general means of specifying +quantities to time correlate. + + +---------- + + +Additional optional keywords also affect the operation of this fix. + +The *type* keyword determines which pairs of input values are +correlated with each other. For N input values Vi, for i = 1 to N, +let the number of pairs = Npair. Note that the second value in the +pair Vi(t)*Vj(t+delta) is always the one sampled at the later time. + +* If *type* is set to *auto* then each input value is correlated with + itself. I.e. Cii = Vi*Vi, for i = 1 to N, so Npair = N. +* If *type* is set + to *upper* then each input value is correlated with every succeeding + value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. +* If *type* is set + to *lower* then each input value is correlated with every preceeding + value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. +* If *type* is set to *auto/upper* then each input value is correlated + with itself and every succeeding value. I.e. Cij = Vi*Vj, for i >= j, + so Npair = N*(N+1)/2. +* If *type* is set to *auto/lower* then each input value is correlated + with itself and every preceding value. I.e. Cij = Vi*Vj, for i <= j, + so Npair = N*(N+1)/2. +* If *type* is set to *full* then each input value is correlated with + itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so + Npair = N^2. +The *ave* keyword determines what happens to the accumulation of +correlation samples every *Nfreq* timesteps. If the *ave* setting is +*one*, then the accumulation is restarted or zeroed every *Nfreq* +timesteps. Thus the outputs on successive *Nfreq* timesteps are +essentially independent of each other. The exception is that the +Cij(0) = Vi(T)*Vj(T) value at a timestep T, where T is a multiple of +*Nfreq*, contributes to the correlation output both at time T and at +time T+Nfreq. + +If the *ave* setting is *running*, then the accumulation is never +zeroed. Thus the output of correlation data at any timestep is the +average over samples accumulated every *Nevery* steps since the fix +was defined. it can only be restarted by deleting the fix via the +:doc:`unfix ` command, or by re-defining the fix by re-specifying +it. + +The *start* keyword specifies what timestep the accumulation of +correlation samples will begin on. The default is step 0. Setting it +to a larger value can avoid adding non-equilibrated data to the +correlation averages. + +The *prefactor* keyword specifies a constant which will be used as a +multiplier on the correlation data after it is averaged. It is +effectively a scale factor on Vi*Vj, which can be used to account for +the size of the time window or other unit conversions. + +The *file* keyword allows a filename to be specified. Every *Nfreq* +steps, an array of correlation data is written to the file. The +number of rows is *Nrepeat*, as described above. The number of +columns is the Npair+2, also as described above. Thus the file ends +up to be a series of these array sections. + +The *overwrite* keyword will continuously overwrite the output file +with the latest output, so that it only contains one timestep worth of +output. This option can only be used with the *ave running* setting. + +The *title1* and *title2* and *title3* keywords allow specification of +the strings that will be printed as the first 3 lines of the output +file, assuming the *file* keyword was used. LAMMPS uses default +values for each of these, so they do not need to be specified. + +By default, these header lines are as follows: + +.. parsed-literal:: + + # Time-correlated data for fix ID + # TimeStep Number-of-time-windows + # Index TimeDelta Ncount valueI*valueJ valueI*valueJ ... + +In the first line, ID is replaced with the fix-ID. The second line +describes the two values that are printed at the first of each section +of output. In the third line the value pairs are replaced with the +appropriate fields from the fix ave/correlate command. + + +---------- + + +Let Sij = a set of time correlation data for input values I and J, +namely the *Nrepeat* values: + +.. parsed-literal:: + + Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery) + +As explained below, these datums are output as one column of a global +array, which is effectively the correlation matrix. + +The *trap* function defined for :doc:`equal-style variables ` +can be used to perform a time integration of this vector of datums, +using a trapezoidal rule. This is useful for calculating various +quantities which can be derived from time correlation data. If a +normalization factor is needed for the time integration, it can be +included in the variable formula or via the *prefactor* keyword. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global array of values which can be accessed by +various :ref:`output commands `. The values can +only be accessed on timesteps that are multiples of *Nfreq* since that +is when averaging is performed. The global array has # of rows = +*Nrepeat* and # of columns = Npair+2. The first column has the time +delta (in timesteps) between the pairs of input values used to +calculate the correlation, as described above. The 2nd column has the +number of samples contributing to the correlation average, as +described above. The remaining Npair columns are for I,J pairs of the +N input values, as determined by the *type* keyword, as described +above. + +* For *type* = *auto*, the Npair = N columns are ordered: C11, C22, ..., + CNN. +* For *type* = *upper*, the Npair = N*(N-1)/2 columns are ordered: C12, + C13, ..., C1N, C23, ..., C2N, C34, ..., CN-1N. +* For *type* = *lower*, the Npair = N*(N-1)/2 columns are ordered: C21, + C31, C32, C41, C42, C43, ..., CN1, CN2, ..., CNN-1. +* For *type* = *auto/upper*, the Npair = N*(N+1)/2 columns are ordered: + C11, C12, C13, ..., C1N, C22, C23, ..., C2N, C33, C34, ..., CN-1N, + CNN. +* For *type* = *auto/lower*, the Npair = N*(N+1)/2 columns are ordered: + C11, C21, C22, C31, C32, C33, C41, ..., C44, CN1, CN2, ..., CNN-1, + CNN. +* For *type* = *full*, the Npair = N^2 columns are ordered: C11, C12, + ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1, + CNN. +The array values calculated by this fix are treated as "intensive". +If you need to divide them by the number of atoms, you must do this in +a later processing step, e.g. when using them in a +:doc:`variable `. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix ave/correlate/long `, +:doc:`compute `, :doc:`fix ave/time `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, +:doc:`fix ave/histo `, :doc:`variable ` + +**Default:** none + +The option defaults are ave = one, type = auto, start = 0, no file +output, title 1,2,3 = strings as described above, and prefactor = 1.0. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ave_correlate_long.txt b/doc/_sources/fix_ave_correlate_long.txt new file mode 100644 index 0000000000..ae5eb2986f --- /dev/null +++ b/doc/_sources/fix_ave_correlate_long.txt @@ -0,0 +1,159 @@ +.. index:: fix ave/correlate/long + +fix ave/correlate/long command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ave/correlate/long Nevery Nfreq value1 value2 ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* ave/correlate/long = style name of this fix command +* Nevery = use input values every this many timesteps +* Nfreq = save state of the time correlation functions every this many timesteps +* one or more input values can be listed +* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name +.. parsed-literal:: + + c_ID = global scalar calculated by a compute with ID + c_ID[I] = Ith component of global vector calculated by a compute with ID + f_ID = global scalar calculated by a fix with ID + f_ID[I] = Ith component of global vector calculated by a fix with ID + v_name = global value calculated by an equal-style variable with name + +* zero or more keyword/arg pairs may be appended +* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *p* or *m* +.. parsed-literal:: + + *type* arg = *auto* or *upper* or *lower* or *auto/upper* or *auto/lower* or *full* + auto = correlate each value with itself + upper = correlate each value with each succeeding value + lower = correlate each value with each preceding value + auto/upper = auto + upper + auto/lower = auto + lower + full = correlate each value with every other value, including itself = auto + upper + lower + *start* args = Nstart + Nstart = start accumulating correlations on this timestep + *file* arg = filename + filename = name of file to output correlation data to + *overwrite* arg = none = overwrite output file with only latest output + *title1* arg = string + string = text to print as 1st line of output file + *title2* arg = string + string = text to print as 2nd line of output file + *ncorr* arg = Ncorrelators + Ncorrelators = number of correlators to store + *nlen* args = Nlen + Nlen = length of each correlator + *ncount* args = Ncount + Ncount = number of values over which succesive correlators are averaged + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate + fix 1 all ave/correlate/long 1 10000 & + c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] & + type upper title1 "My correlation data" nlen 15 ncount 3 + +Description +""""""""""" + +This fix is similar in spirit and syntax to the :doc:`fix ave/correlate `. However, this fix allows the +efficient calculation of time correlation functions on the fly over +extremely long time windows without too much CPU overhead, using a +multiple-tau method :ref:`(Ramirez) ` that decreases the resolution +of the stored correlation function with time. + +The group specified with this command is ignored. However, note that +specified values may represent calculations performed by computes and +fixes which store their own "group" definitions. + +Each listed value can be the result of a compute or fix or the +evaluation of an equal-style variable. See the :doc:`fix ave/correlate ` doc page for details. + +The *Nevery* and *Nfreq* arguments specify on what timesteps the input +values will be used to calculate correlation data, and the frequency +with which the time correlation functions will be output to a file. +Note that there is no *Nrepeat* argument, unlike the :doc:`fix ave/correlate ` command. + +The optional keywords *ncorr*, *nlen*, and *ncount* are unique to this +command and determine the number of correlation points calculated and +the memory and CPU overhead used by this calculation. *Nlen* and +*ncount* determine the amount of averaging done at longer correlation +times. The default values *nlen=16*, *ncount=2* ensure that the +systematic error of the multiple-tau correlator is always below the +level of the statistical error of a typical simulation (which depends +on the ensemble size and the simulation length). + +The maximum correlation time (in time steps) that can be reached is +given by the formula (nlen-1) * ncount^(ncorr-1). Longer correlation +times are discarded and not calculated. With the default values of +the parameters (ncorr=20, nlen=16 and ncount=2), this corresponds to +7864320 time steps. If longer correlation times are needed, the value +of ncorr should be increased. Using nlen=16 and ncount=2, with +ncorr=30, the maximum number of steps that can be correlated is +80530636808. If ncorr=40, correlation times in excess of 8e12 time +steps can be calculated. + +The total memory needed for each correlation pair is roughly +4*ncorr*nlen*8 bytes. With the default values of the parameters, this +corresponds to about 10 KB. + +For the meaning of the additional optional keywords, see the :doc:`fix ave/correlate ` doc page. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Since this fix in intended for the calculation of time correlation +functions over very long MD simulations, the information about this +fix is written automatically to binary restart files, so that the time +correlation calculation can continue in subsequent simulations. None +of the fix_modify options are relevant to this fix. + +No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy minimization. + +Restrictions +"""""""""""" + + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix ave/correlate ` + +**Default:** none + +The option defaults for keywords that are also keywords for the :doc:`fix ave/correlate ` command are as follows: type = +auto, start = 0, no file output, title 1,2 = strings as described on +the :doc:`fix ave/correlate ` doc page. + +The option defaults for keywords unique to this command are as +follows: ncorr=20, nlen=16, ncount=2. + + +---------- + + +.. _Ramirez: + + + +**(Ramirez)** J. Ramirez, S.K. Sukumaran, B. Vorselaars and +A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ave_histo.txt b/doc/_sources/fix_ave_histo.txt new file mode 100644 index 0000000000..9851fe22a2 --- /dev/null +++ b/doc/_sources/fix_ave_histo.txt @@ -0,0 +1,353 @@ +.. index:: fix ave/histo + +fix ave/histo command +===================== + +fix ave/histo/weight command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style Nevery Nrepeat Nfreq lo hi Nbin value1 value2 ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = *ave/histo* or *ave/histo/weight* = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of times to use input values for calculating histogram +* Nfreq = calculate histogram every this many timesteps +* lo,hi = lo/hi bounds within which to histogram +* Nbin = # of histogram bins +* one or more input values can be listed +* value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name +.. parsed-literal:: + + x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component) + c_ID = scalar or vector calculated by a compute with ID + c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID + f_ID = scalar or vector calculated by a fix with ID + f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID + v_name = value(s) calculated by an equal-style or atom-style variable with name + +* zero or more keyword/arg pairs may be appended +* keyword = *mode* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3* +.. parsed-literal:: + + *mode* arg = *scalar* or *vector* + scalar = all input values are scalars + vector = all input values are vectors + *file* arg = filename + filename = name of file to output histogram(s) to + *ave* args = *one* or *running* or *window* + one = output a new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps + *start* args = Nstart + Nstart = start averaging on this timestep + *beyond* arg = *ignore* or *end* or *extra* + ignore = ignore values outside histogram lo/hi bounds + end = count values outside histogram lo/hi bounds in end bins + extra = create 2 extra bins for value outside histogram lo/hi bounds + *overwrite* arg = none = overwrite output file with only latest output + *title1* arg = string + string = text to print as 1st line of output file + *title2* arg = string + string = text to print as 2nd line of output file + *title3* arg = string + string = text to print as 3rd line of output file, only for vector mode + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running + fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values" + fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra + fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2] + +Description +""""""""""" + +Use one or more values as inputs every few timesteps, histogram them, +and average the histogram over longer timescales. The resulting +histogram can be used by other :ref:`output commands `, and can also be written to a +file. The fix ave/histo/weight command has identical syntax to fix +ave/histo, except that exactly two values must be specified. See +details below. + +The group specified with this command is ignored for global and local +input values. For per-atom input values, only atoms in the group +contribute to the histogram. Note that regardless of the specified +group, specified values may represent calculations performed by +computes and fixes which store their own "group" definition. + +A histogram is simply a count of the number of values that fall within +a histogram bin. *Nbins* are defined, with even spacing between *lo* +and *hi*. Values that fall outside the lo/hi bounds can be treated in +different ways; see the discussion of the *beyond* keyword below. + +Each input value can be an atom attribute (position, velocity, force +component) or can be the result of a :doc:`compute ` or +:doc:`fix ` or the evaluation of an equal-style or atom-style +:doc:`variable `. The set of input values can be either all +global, all per-atom, or all local quantities. Inputs of different +kinds (e.g. global and per-atom) cannot be mixed. Atom attributes are +per-atom vector values. See the doc page for individual "compute" and +"fix" commands to see what kinds of quantities they generate. + +The input values must either be all scalars or all vectors (or +arrays), depending on the setting of the *mode* keyword. + +Note that the output of this command is a single histogram for all +input values combined together, not one histogram per input value. +See below for details on the format of the output of this fix. + +If *mode* = vector, then the input values may either be vectors or +arrays. If a global array is listed, then it is the same as if the +individual columns of the array had been listed one by one. +E.g. these 2 fix ave/histo commands are equivalent, since the :doc:`compute com/chunk ` command creates a global array +with 3 columns: + +.. parsed-literal:: + + compute myCOM all com/chunk + fix 1 all ave/histo 100 1 100 c_myCOM file tmp1.com mode vector + fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector + +If the fix ave/histo/weight command is used, exactly two values must +be specified. If the values are vectors, they must be the same +length. The first value (a scalar or vector) is what is histogrammed +into bins, in the same manner the fix ave/histo command operates. The +second value (a scalar or vector) is used as a "weight". This means +that instead of each value tallying a "1" to its bin, the +corresponding weight is tallied. E.g. the Nth entry in the first +vector tallies the Nth entry (weight) in the second vector. + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be used in order to contribute to the +histogram. The final histogram is generated on timesteps that are +multiple of *Nfreq*. It is averaged over *Nrepeat* histograms, +computed in the preceding portion of the simulation every *Nevery* +timesteps. *Nfreq* must be a multiple of *Nevery* and *Nevery* must +be non-zero even if *Nrepeat* is 1. Also, the timesteps +contributing to the histogram value cannot overlap, +i.e. Nrepeat*Nevery can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values +on timesteps 90,92,94,96,98,100 will be used to compute the final +histogram on timestep 100. Similarly for timesteps +190,192,194,196,198,200 on timestep 200, etc. If Nrepeat=1 and Nfreq += 100, then no time averaging of the histogram is done; a histogram is +simply generated on timesteps 100,200,etc. + + +---------- + + +The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are +self-explanatory. Note that other atom attributes can be used as +inputs to this fix by using the :doc:`compute property/atom ` command and then specifying +an input value from that compute. + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. If *mode* = scalar, then if +no bracketed term is appended, the global scalar calculated by the +compute is used. If a bracketed term is appended, the Ith element of +the global vector calculated by the compute is used. If *mode* = +vector, then if no bracketed term is appended, the global or per-atom +or local vector calculated by the compute is used. Or if the compute +calculates an array, all of the columns of the array are used as if +they had been specified as individual vectors (see description above). +If a bracketed term is appended, the Ith column of the global or +per-atom or local array calculated by the compute is used. + +Note that there is a :doc:`compute reduce ` command +which can sum per-atom quantities into a global scalar or vector which +can thus be accessed by fix ave/histo. Or it can be a compute defined +not in your input script, but by :doc:`thermodynamic output ` or other fixes such as :doc:`fix nvt ` or :doc:`fix temp/rescale `. See +the doc pages for these commands which give the IDs of these computes. +Users can also write code for their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. If *mode* = scalar, then if +no bracketed term is appended, the global scalar calculated by the fix +is used. If a bracketed term is appended, the Ith element of the +global vector calculated by the fix is used. If *mode* = vector, then +if no bracketed term is appended, the global or per-atom or local +vector calculated by the fix is used. Or if the fix calculates an +array, all of the columns of the array are used as if they had been +specified as individual vectors (see description above). If a +bracketed term is appended, the Ith column of the global or per-atom +or local array calculated by the fix is used. + +Note that some fixes only produce their values on certain timesteps, +which must be compatible with *Nevery*, else an error will result. +Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script. If *mode* = scalar, then +only equal-style variables can be used, which produce a global value. +If *mode* = vector, then only atom-style variables can be used, which +produce a per-atom vector. See the :doc:`variable ` command +for details. Note that variables of style *equal* and *atom* define a +formula which can reference individual atom properties or +thermodynamic keywords, or they can invoke other computes, fixes, or +variables when they are evaluated, so this is a very general means of +specifying quantities to histogram. + + +---------- + + +Additional optional keywords also affect the operation of this fix. + +If the *mode* keyword is set to *scalar*, then all input values must +be global scalars, or elements of global vectors. If the *mode* +keyword is set to *vector*, then all input values must be global or +per-atom or local vectors, or columns of global or per-atom or local +arrays. + +The *beyond* keyword determines how input values that fall outside the +*lo* to *hi* bounds are treated. Values such that *lo* <= value <= +*hi* are assigned to one bin. Values on a bin boundary are assigned +to the lower of the 2 bins. If *beyond* is set to *ignore* then +values < *lo* and values > *hi* are ignored, i.e. they are not binned. +If *beyond* is set to *end* then values < *lo* are counted in the +first bin and values > *hi* are counted in the last bin. If *beyond* +is set to *extend* then two extra bins are created, so that there are +Nbins+2 total bins. Values < *lo* are counted in the first bin and +values > *hi* are counted in the last bin (Nbins+1). Values between +*lo* and *hi* (inclusive) are counted in bins 2 thru Nbins+1. The +"coordinate" stored and printed for these two extra bins is *lo* and +*hi*. + +The *ave* keyword determines how the histogram produced every *Nfreq* +steps are averaged with histograms produced on previous steps that +were multiples of *Nfreq*, before they are accessed by another output +command or written to a file. + +If the *ave* setting is *one*, then the histograms produced on +timesteps that are multiples of *Nfreq* are independent of each other; +they are output as-is without further averaging. + +If the *ave* setting is *running*, then the histograms produced on +timesteps that are multiples of *Nfreq* are summed and averaged in a +cumulative sense before being output. Each bin value in the histogram +is thus the average of the bin value produced on that timestep with +all preceding values for the same bin. This running average begins +when the fix is defined; it can only be restarted by deleting the fix +via the :doc:`unfix ` command, or by re-defining the fix by +re-specifying it. + +If the *ave* setting is *window*, then the histograms produced on +timesteps that are multiples of *Nfreq* are summed within a moving +"window" of time, so that the last M histograms are used to produce +the output. E.g. if M = 3 and Nfreq = 1000, then the output on step +10000 will be the combined histogram of the individual histograms on +steps 8000,9000,10000. Outputs on early steps will be sums over less +than M histograms if they are not available. + +The *start* keyword specifies what timestep histogramming will begin +on. The default is step 0. Often input values can be 0.0 at time 0, +so setting *start* to a larger value can avoid including a 0.0 in +a running or windowed histogram. + +The *file* keyword allows a filename to be specified. Every *Nfreq* +steps, one histogram is written to the file. This includes a leading +line that contains the timestep, number of bins, the total count of +values contributing to the histogram, the count of values that were +not histogrammed (see the *beyond* keyword), the minimum value +encountered, and the maximum value encountered. The min/max values +include values that were not histogrammed. Following the leading +line, one line per bin is written into the file. Each line contains +the bin #, the coordinate for the center of the bin (between *lo* and +*hi*), the count of values in the bin, and the normalized count. The +normalized count is the bin count divided by the total count (not +including values not histogrammed), so that the normalized values sum +to 1.0 across all bins. + +The *overwrite* keyword will continuously overwrite the output file +with the latest output, so that it only contains one timestep worth of +output. This option can only be used with the *ave running* setting. + +The *title1* and *title2* and *title3* keywords allow specification of +the strings that will be printed as the first 3 lines of the output +file, assuming the *file* keyword was used. LAMMPS uses default +values for each of these, so they do not need to be specified. + +By default, these header lines are as follows: + +.. parsed-literal:: + + # Histogram for fix ID + # TimeStep Number-of-bins Total-counts Missing-counts Min-value Max-value + # Bin Coord Count Count/Total + +In the first line, ID is replaced with the fix-ID. The second line +describes the six values that are printed at the first of each section +of output. The third describes the 4 values printed for each bin in +the histogram. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix produces a global vector and global array which can be +accessed by various :ref:`output commands `. +The values can only be accessed on timesteps that are multiples of +*Nfreq* since that is when a histogram is generated. The global +vector has 4 values: + +* 1 = total counts in the histogram +* 2 = values that were not histogrammed (see *beyond* keyword) +* 3 = min value of all input values, including ones not histogrammed +* 4 = max value of all input values, including ones not histogrammed + +The global array has # of rows = Nbins and # of columns = 3. The +first column has the bin coordinate, the 2nd column has the count of +values in that histogram bin, and the 3rd column has the bin count +divided by the total count (not including missing counts), so that the +values in the 3rd column sum to 1.0. + +The vector and array values calculated by this fix are all treated as +"intensive". If this is not the case, e.g. due to histogramming +per-atom input values, then you will need to account for that when +interpreting the values produced by this fix. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, :doc:`fix ave/time `, +:doc:`variable `, :doc:`fix ave/correlate `, + +**Default:** none + +The option defaults are mode = scalar, ave = one, start = 0, no file +output, beyond = ignore, and title 1,2,3 = strings as described above. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ave_spatial.txt b/doc/_sources/fix_ave_spatial.txt new file mode 100644 index 0000000000..a88a61b4b1 --- /dev/null +++ b/doc/_sources/fix_ave_spatial.txt @@ -0,0 +1,447 @@ +.. index:: fix ave/spatial + +fix ave/spatial command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... value1 value2 ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* ave/spatial = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of times to use input values for calculating averages +* Nfreq = calculate averages every this many timesteps +* dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins +.. parsed-literal:: + + dim = *x* or *y* or *z* + origin = *lower* or *center* or *upper* or coordinate value (distance units) + delta = thickness of spatial bins in dim (distance units) + +* one or more input values can be listed +* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name +.. parsed-literal:: + + vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) + density/number, density/mass = number or mass density + c_ID = per-atom vector calculated by a compute with ID + c_ID[I] = Ith column of per-atom array calculated by a compute with ID + f_ID = per-atom vector calculated by a fix with ID + f_ID[I] = Ith column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name + +* zero or more keyword/arg pairs may be appended +* keyword = *region* or *bound* or *discard* or *norm* or *ave* or *units* or *file* or *overwrite* or *title1* or *title2* or *title3* +.. parsed-literal:: + + *region* arg = region-ID + *bound* args = x/y/z lo hi + x/y/z = *x* or *y* or *z* to bound bins in this dimension + lo = *lower* or coordinate value (distance units) + hi = *upper* or coordinate value (distance units) + *discard* arg = *mixed* or *no* or *yes* + mixed = discard atoms outside bins only if bin bounds are explicitly set + no = always keep out-of-bounds atoms + yes = always discard out-of-bounds atoms + *norm* arg = *all* or *sample* + region-ID = ID of region atoms must be in to contribute to spatial averaging + *ave* args = *one* or *running* or *window M* + one = output new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps + *units* arg = *box* or *lattice* or *reduced* + *file* arg = filename + filename = file to write results to + *overwrite* arg = none = overwrite output file with only latest output + *title1* arg = string + string = text to print as 1st line of output file + *title2* arg = string + string = text to print as 2nd line of output file + *title3* arg = string + string = text to print as 3rd line of output file + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced & + title1 "My output values" + fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile + fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running + fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running + +**NOTE:** + +The fix ave/spatial command has been replaced by the more flexible +:doc:`fix ave/chunk ` and :doc:`compute chunk/atom ` commands. The fix ave/spatial +command will be removed from LAMMPS sometime in the summer of 2015. + +Any fix ave/spatial command can be replaced by the two new commands. +You simply need to split the fix ave/spatial arguments across the two +new commands. For example, this command: + +.. parsed-literal:: + + fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile + +could be replaced by: + +.. parsed-literal:: + + compute cc1 flow chunk/atom bin/1d y 0.0 1.0 + fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile + +Description +""""""""""" + +Use one or more per-atom vectors as inputs every few timesteps, bin +their values spatially into 1d, 2d, or 3d bins based on current atom +coordinates, and average the bin values over longer timescales. The +resulting bin averages can be used by other :ref:`output commands ` such as :doc:`thermo_style custom `, and can also be written to a file. + +The group specified with the command means only atoms within the group +contribute to bin averages. If the *region* keyword is used, the atom +must be in both the specified group and the specified geometric +:doc:`region ` in order to contribute to bin averages. + +Each listed value can be an atom attribute (position, velocity, force +component), a mass or number density, or the result of a +:doc:`compute ` or :doc:`fix ` or the evaluation of an +atom-style :doc:`variable `. In the latter cases, the +compute, fix, or variable must produce a per-atom quantity, not a +global quantity. If you wish to time-average global quantities from a +compute, fix, or variable, then see the :doc:`fix ave/time ` command. + +:doc:`Computes ` that produce per-atom quantities are those +which have the word *atom* in their style name. See the doc pages for +individual :doc:`fixes ` to determine which ones produce per-atom +quantities. :doc:`Variables ` of style *atom* are the only +ones that can be used with this fix since all other styles of variable +produce global quantities. + +The per-atom values of each input vector are binned and averaged +independently of the per-atom values in other input vectors. + +The size and dimensionality of the bins (1d = layers or slabs, 2d = +pencils, 3d = boxes) are determined by the *dim*, *origin*, and +*delta* settings and how many times they are specified (1, 2, or 3). +See details below. + +.. note:: + + This fix works by creating an array of size Nbins by Nvalues on + each processor. Nbins is the total number of bins; Nvalues is the + number of input values specified. Each processor loops over its + atoms, tallying its values to the appropriate bin. Then the entire + array is summed across all processors. This means that using a large + number of bins (easy to do for 2d or 3d bins) will incur an overhead + in memory and computational cost (summing across processors), so be + careful to use reasonable numbers of bins. + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be used to bin them and contribute to +the average. The final averaged quantities are generated on timesteps +that are a multiples of *Nfreq*. The average is over *Nrepeat* +quantities, computed in the preceding portion of the simulation every +*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and +*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps +contributing to the average value cannot overlap, +i.e. Nrepeat*Nevery can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on +timesteps 90,92,94,96,98,100 will be used to compute the final average +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on +timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time +averaging is done; values are simply generated on timesteps +100,200,etc. + + +---------- + + +Each per-atom property is also averaged over atoms in each bin. The +way the averaging is one across the *Nrepeat* timesteps to produce +output on the *Nfreq* timesteps, and across multiple *Nfreq* outputs, +is determined by the *norm* and *av* keyword settings, as discussed +below. + +Bins can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends +on how many times (1, 2, or 3) the *dim*, *origin*, and *delta* +settings are specified in the fix ave/spatial command. For 2d or 3d +bins, there is no restriction on specifying dim = x before dim = y, or +dim = y before dim = z. Bins in a particular *dim* have a bin size in +that dimension given by *delta*. Every Nfreq steps, when averaging is +being performed and the per-atom property is calculated for the first +time, the number of bins and the bin sizes and boundaries are +computed. Thus if the simulation box changes size during a +simulation, the number of bins and their boundaries may also change. +In each dimension, bins are defined relative to a specified *origin*, +which may be the lower/upper edge of the simulation box in that +dimension, or its center point, or a specified coordinate value. +Starting at the origin, sufficient bins are created in both directions +to completely span the bin extent in that dimension. By default the +bin extent is the entire simulation box. + +The *bound* keyword can be used one or more times to limit the extent +of bin coverage in specified dimensions, i.e. to only bin a portion of +the box. If the *lo* setting is *lower* or the *hi* setting is +*upper*, the bin extent in that direction extends to the box boundary. +If a numeric value is used for *lo* and/or *hi*, then the bin extent +in the *lo* or *hi* direction extends only to that value, which is +assumed to be inside (or at least near) the simulation box boundaries, +though LAMMPS does not check for this. + +On each sampling timestep, each atom is mapped to the bin it currently +belongs to, based on its current position. Note that the group-ID and +region keyword can exclude specific atoms from this operation, as +discussed above. Note that between reneighboring timesteps, atoms can +move outside the current simulation box. If the box is periodic (in +that dimension) the atom is remapping into the periodic box for +purposes of binning. If the box in not periodic, the atom may have +moved outside the bounds of any bin. + +The *discard* keyword determines what is done with any atom which is +outside the bounds of any bin. If *discard* is set to *yes*, the atom +will be ignored and not contribute to any bin averages. If *discard* +is set to *no*, the atom will be counted as if it were in the first or +last bin in that dimension. If (discard* is set to *mixed*, which is +the default, it will only be counted in the first or last bin if bins +extend to the box boundary in that dimension. This is the case if the +*bound* keyword settings are *lower* and *upper*, which is the +default. If the *bound* keyword settings are numeric values, then the +atom will be ignored if it is outside the bounds of any bin. Note +that in this case, it is possible that the first or last bin extends +beyond the numeric *bounds* settings, depending on the specified +*origin*. If this is the case, the atom is only ignored if it is +outside the first or last bin, not if it is simply outside the numeric +*bounds* setting. + +For orthogonal simulation boxes, the bins are also layers, pencils, or +boxes aligned with the xyz coordinate axes. For triclinic +(non-orthogonal) simulation boxes, the bins are so that they are +parallel to the tilted faces of the simulation box. See :ref:`this section ` of the manual for a discussion of +the geometry of triclinic boxes in LAMMPS. As described there, a +tilted simulation box has edge vectors a,b,c. In that nomenclature, +bins in the x dimension have faces with normals in the "b" cross "c" +direction. Bins in y have faces normal to the "a" cross "c" +direction. And bins in z have faces normal to the "a" cross "b" +direction. Note that in order to define the size and position of +these bins in an unambiguous fashion, the *units* option must be set +to *reduced* when using a triclinic simulation box, as noted below. + + +---------- + + +The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. +Note that other atom attributes (including atom postitions x,y,z) can +be used as inputs to this fix by using the :doc:`compute property/atom ` command and then specifying +an input value from that compute. + +The *density/number* value means the number density is computed in +each bin, i.e. a weighting of 1 for each atom. The *density/mass* +value means the mass density is computed in each bind, i.e. each atom +is weighted by its mass. The resulting density is normalized by the +volume of the bin so that units of number/volume or density are +output. See the :doc:`units ` command doc page for the +definition of density for each choice of units, e.g. gram/cm^3. + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the compute is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the fix is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with +*Nevery*, else an error results. Users can also write code for their +own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script. Variables of style +*atom* can reference thermodynamic keywords and various per-atom +attributes, or invoke other computes, fixes, or variables when they +are evaluated, so this is a very general means of generating per-atom +quantities to spatially average. + + +---------- + + +Additional optional keywords also affect the operation of this fix. +The *region*, *bound*, and *discard* keywords were discussed above. + +The *norm* keyword affects how averaging is done for the output +produced every *Nfreq* timesteps. For an *all* setting, a bin +quantity is summed over all atoms in all *Nrepeat* samples, as is the +count of atoms in the bin. The printed value for the bin is +Total-quantity / Total-count. In other words it is an average over +the entire *Nfreq* timescale. + +For a *sample* setting, the bin quantity is summed over atoms for only +a single sample, as is the count, and a "average sample value" is +computed, i.e. Sample-quantity / Sample-count. The printed value for +the bin is the average of the *Nrepeat* "average sample values", In +other words it is an average of an average. + +The *ave* keyword determines how the bin values produced every *Nfreq* +steps are averaged with bin values produced on previous steps that +were multiples of *Nfreq*, before they are accessed by another output +command or written to a file. + +If the *ave* setting is *one*, then the bin values produced on +timesteps that are multiples of *Nfreq* are independent of each other; +they are output as-is without further averaging. + +If the *ave* setting is *running*, then the bin values produced on +timesteps that are multiples of *Nfreq* are summed and averaged in a +cumulative sense before being output. Each output bin value is thus +the average of the bin value produced on that timestep with all +preceding values for the same bin. This running average begins when +the fix is defined; it can only be restarted by deleting the fix via +the :doc:`unfix ` command, or re-defining the fix by +re-specifying it. + +If the *ave* setting is *window*, then the bin values produced on +timesteps that are multiples of *Nfreq* are summed and averaged within +a moving "window" of time, so that the last M values for the same bin +are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then +the output on step 10000 will be the average of the individual bin +values on steps 8000,9000,10000. Outputs on early steps will average +over less than M values if they are not available. + +The *units* keyword determines the meaning of the distance units used +for the bin size *delta* and for *origin* and *bounds* values if they +are coordinate value. For orthogonal simulation boxes, any of the 3 +options may be used. For non-orthogonal (triclinic) simulation boxes, +only the *reduced* option may be used. + +A *box* value selects standard distance units as defined by the +:doc:`units ` command, e.g. Angstroms for units = real or metal. +A *lattice* value means the distance units are in lattice spacings. +The :doc:`lattice ` command must have been previously used to +define the lattice spacing. A *reduced* value means normalized +unitless values between 0 and 1, which represent the lower and upper +faces of the simulation box respectively. Thus an *origin* value of +0.5 means the center of the box in any dimension. A *delta* value of +0.1 means 10 bins span the box in that dimension. + +Consider a non-orthogonal box, with bins that are 1d layers or slabs +in the x dimension. No matter how the box is tilted, an *origin* of +0.0 means start layers at the lower "b" cross "c" plane of the +simulation box and an *origin* of 1.0 means to start layers at the +upper "b" cross "c" face of the box. A *delta* value of 0.1 means +there will be 10 layers from 0.0 to 1.0, regardless of the current +size or shape of the simulation box. + +The *file* keyword allows a filename to be specified. Every *Nfreq* +timesteps, a section of bin info will be written to a text file in the +following format. A line with the timestep and number of bin is +written. Then one line per bin is written, containing the bin ID +(1-N), the coordinate of the center of the bin, the number of atoms +in the bin, and one or more calculated values. The number of values +in each line corresponds to the number of values specified in the fix +ave/spatial command. The number of atoms and the value(s) are average +quantities. If the value of the *units* keyword is *box* or +*lattice*, the "coord" is printed in box units. If the value of the +*units* keyword is *reduced*, the "coord" is printed in reduced units +(0-1). + +The *overwrite* keyword will continuously overwrite the output file +with the latest output, so that it only contains one timestep worth of +output. This option can only be used with the *ave running* setting. + +The *title1* and *title2* and *title3* keywords allow specification of +the strings that will be printed as the first 3 lines of the output +file, assuming the *file* keyword was used. LAMMPS uses default +values for each of these, so they do not need to be specified. + +By default, these header lines are as follows: + +.. parsed-literal:: + + # Spatial-averaged data for fix ID and group name + # Timestep Number-of-bins + # Bin Coord1 Coord2 Coord3 Count value1 value2 ... + +In the first line, ID and name are replaced with the fix-ID and group +name. The second line describes the two values that are printed at +the first of each section of output. In the third line the values are +replaced with the appropriate fields from the fix ave/spatial command. +The Coord2 and Coord3 entries in the third line only appear for 2d and +3d bins respectively. For 1d bins, the word Coord1 is replaced by +just Coord. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global array of values which can be accessed by +various :ref:`output commands `. The values can +only be accessed on timesteps that are multiples of *Nfreq* since that +is when averaging is performed. The global array has # of rows = +Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for +1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates +(center of the bin) in the appropriate dimensions, the next column has +the count of atoms in that bin, and the remaining columns are the +Nvalue quantities. When the array is accessed with an I that exceeds +the current number of bins, than a 0.0 is returned by the fix instead +of an error, since the number of bins can vary as a simulation runs, +depending on the simulation box size. 2d or 3d bins are ordered so +that the last dimension(s) vary fastest. The array values calculated +by this fix are "intensive", since they are already normalized by the +count of atoms in each bin. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +When the *ave* keyword is set to *running* or *window* then the number +of bins must remain the same during the simulation, so that the +appropriate averaging can be done. This will be the case if the +simulation box size doesn't change or if the *units* keyword is set to +*reduced*. + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/histo `, :doc:`fix ave/time `, +:doc:`variable `, :doc:`fix ave/correlate `, +:doc:`fix ave/spatial/sphere ` + +Default +""""""" + +The option defaults are bound = lower and upper in all dimensions, +discard = mixed, norm = all, ave = one, units = lattice, no file +output, and title 1,2,3 = strings as described above. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ave_spatial_sphere.txt b/doc/_sources/fix_ave_spatial_sphere.txt new file mode 100644 index 0000000000..ae930c7523 --- /dev/null +++ b/doc/_sources/fix_ave_spatial_sphere.txt @@ -0,0 +1,349 @@ +.. index:: fix ave/spatial/sphere + +fix ave/spatial/sphere command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ave/spatial/sphere Nevery Nrepeat Nfreq origin_x origin_y origin_z r_min r_max nbins value1 value2 ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* ave/spatial = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of times to use input values for calculating averages +* Nfreq = calculate averages every this many timesteps +* origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below) +* r_min = radial distance at which binning begins +* r_max = radial distance at which binning ends +* nbins = number of spherical shells to create between r_min and r_max +* one or more input values can be listed +* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name +.. parsed-literal:: + + vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) + density/number, density/mass = number or mass density + c_ID = per-atom vector calculated by a compute with ID + c_ID[I] = Ith column of per-atom array calculated by a compute with ID + f_ID = per-atom vector calculated by a fix with ID + f_ID[I] = Ith column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name + +* zero or more keyword/arg pairs may be appended +* keyword = *region* or *norm* or *units* or *ave* or *file* or *overwrite* or *title1* or *title2* or *title3* +.. parsed-literal:: + + *region* arg = region-ID + region-ID = ID of region atoms must be in to contribute to spatial averaging + *norm* arg = *all* or *sample* + *units* arg = *box* or *lattice* or *reduced* + *ave* args = *one* or *running* or *window M* + one = output new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps + *file* arg = filename + filename = file to write results to + *overwrite* arg = none = overwrite output file with only latest output + *title1* arg = string + string = text to print as 1st line of output file + *title2* arg = string + string = text to print as 2nd line of output file + *title3* arg = string + string = text to print as 3rd line of output file + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all ave/spatial/sphere 10000 1 10000 0.5 0.5 0.5 0.1 0.5 5 density/number vx vy vz units reduced title1 "My output values" + fix 1 flow ave/spatial/sphere 100 10 1000 20.0 20.0 20.0 0.0 20.0 20 vx vz norm sample file vel.profile + +Description +""""""""""" + +Use one or more per-atom vectors as inputs every few timesteps, bin +their values spatially into spherical shells based on current atom +coordinates, and average the bin values over longer timescales. The +resulting bin averages can be used by other :ref:`output commands ` such as :doc:`thermo_style custom `, and can also be written to a file. + +The group specified with the command means only atoms within the group +contribute to bin averages. If the *region* keyword is used, the atom +must be in both the group and the specified geometric +:doc:`region ` in order to contribute to bin averages. + +Each listed value can be an atom attribute (position, velocity, force +component), a mass or number density, or the result of a +:doc:`compute ` or :doc:`fix ` or the evaluation of an +atom-style :doc:`variable `. In the latter cases, the +compute, fix, or variable must produce a per-atom quantity, not a +global quantity. If you wish to time-average global quantities from a +compute, fix, or variable, then see the :doc:`fix ave/time ` command. + +:doc:`Computes ` that produce per-atom quantities are those +which have the word *atom* in their style name. See the doc pages for +individual :doc:`fixes ` to determine which ones produce per-atom +quantities. :doc:`Variables ` of style *atom* are the only +ones that can be used with this fix since all other styles of variable +produce global quantities. + +The per-atom values of each input vector are binned and averaged +independently of the per-atom values in other input vectors. + +*Nbins* specifies the number of spherical shells which will be created +between r_min and r_max centered at (origin_x, origin_y, origin_z). + +.. note:: + + This fix works by creating an array of size Nbins by Nvalues on + each processor. Nbins is the total number of bins; Nvalues is the + number of input values specified. Each processor loops over its + atoms, tallying its values to the appropriate bin. Then the entire + array is summed across all processors. This means that using a large + number of bins will incur an overhead in memory and computational cost + (summing across processors), so be careful to use reasonable numbers + of bins. + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be used to bin them and contribute to +the average. The final averaged quantities are generated on timesteps +that are a multiples of *Nfreq*. The average is over *Nrepeat* +quantities, computed in the preceding portion of the simulation every +*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and +*Nevery* must be non-zero even if *Nrepeat* is 1. +Also, the timesteps +contributing to the average value cannot overlap, +i.e. Nrepeat*Nevery can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on +timesteps 90,92,94,96,98,100 will be used to compute the final average +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on +timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time +averaging is done; values are simply generated on timesteps +100,200,etc. + + +---------- + + +The *origin_x*, *origin_y*, and *origin_z* parameters may be specified +by either a compute or a variable. This allows, for example, the +center of the spherical bins to be attached to the center of mass of a +group of atoms. If a variable origin is used and periodic boundary +conditions are in effect, then the origin will be wrapped across +periodic boundaries whenever it changes so that it is always inside +the simulation box. + + +---------- + + +The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. +Note that other atom attributes (including atom postitions x,y,z) can +be used as inputs to this fix by using the :doc:`compute property/atom ` command and then specifying +an input value from that compute. + +The *density/number* value means the number density is computed in +each bin, i.e. a weighting of 1 for each atom. The *density/mass* +value means the mass density is computed in each bin, i.e. each atom +is weighted by its mass. The resulting density is normalized by the +volume of the bin so that units of number/volume or density are +output. See the :doc:`units ` command doc page for the +definition of density for each choice of units, e.g. gram/cm^3. +The bin volume will always be calculated in box units, independent +of the use of the *units* keyword in this command. + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the compute is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the compute is used. Users can also write code for +their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. If no bracketed integer is +appended, the per-atom vector calculated by the fix is used. If a +bracketed integer is appended, the Ith column of the per-atom array +calculated by the fix is used. Note that some fixes only produce +their values on certain timesteps, which must be compatible with +*Nevery*, else an error results. Users can also write code for their +own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script. Variables of style +*atom* can reference thermodynamic keywords and various per-atom +attributes, or invoke other computes, fixes, or variables when they +are evaluated, so this is a very general means of generating per-atom +quantities to spatially average. + + +---------- + + +Additional optional keywords also affect the operation of this fix. +The *region* keyword was discussed above. + +The *norm* keyword affects how averaging is done for the output +produced every *Nfreq* timesteps. For an *all* setting, a bin +quantity is summed over all atoms in all *Nrepeat* samples, as is the +count of atoms in the bin. The printed value for the bin is +Total-quantity / Total-count. In other words it is an average over +the entire *Nfreq* timescale. + +For a *sample* setting, the bin quantity is summed over atoms for only +a single sample, as is the count, and a "average sample value" is +computed, i.e. Sample-quantity / Sample-count. The printed value for +the bin is the average of the *Nrepeat* "average sample values", In +other words it is an average of an average. + +The *ave* keyword determines how the bin values produced every *Nfreq* +steps are averaged with bin values produced on previous steps that +were multiples of *Nfreq*, before they are accessed by another output +command or written to a file. + +If the *ave* setting is *one*, then the bin values produced on +timesteps that are multiples of *Nfreq* are independent of each other; +they are output as-is without further averaging. + +If the *ave* setting is *running*, then the bin values produced on +timesteps that are multiples of *Nfreq* are summed and averaged in a +cumulative sense before being output. Each output bin value is thus +the average of the bin value produced on that timestep with all +preceding values for the same bin. This running average begins when +the fix is defined; it can only be restarted by deleting the fix via +the :doc:`unfix ` command, or re-defining the fix by +re-specifying it. + +If the *ave* setting is *window*, then the bin values produced on +timesteps that are multiples of *Nfreq* are summed and averaged within +a moving "window" of time, so that the last M values for the same bin +are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then +the output on step 10000 will be the average of the individual bin +values on steps 8000,9000,10000. Outputs on early steps will average +over less than M values if they are not available. + +The *units* keyword determines the meaning of the distance units used +for the sphere origin and the two radial lengths. For orthogonal +simulation boxes, any of the 3 options may be used. For +non-orthogonal (triclinic) simulation boxes, only the *reduced* option +may be used. + +A *box* value selects standard distance units as defined by the +:doc:`units ` command, e.g. Angstroms for units = real or metal. +A *lattice* value means the distance units are in lattice spacings. +The :doc:`lattice ` command must have been previously used to +define the lattice spacing. + +.. note:: + + The *lattice* style may only be used if the lattice spacing is + the same in each direction. + +A *reduced* value means normalized unitless values between 0 and 1, +which represent the lower and upper faces of the simulation box +respectively. Thus an *origin* value of 0.5 means the center of the +box in any dimension. + +The *file* keyword allows a filename to be specified. Every *Nfreq* +timesteps, a section of bin info will be written to a text file in the +following format. A line with the timestep and number of bin is +written. Then one line per bin is written, containing the bin ID +(1-N), the coordinate of the center of the bin, the number of atoms in +the bin, and one or more calculated values. The number of values in +each line corresponds to the number of values specified in the fix +ave/spatial command. The number of atoms and the value(s) are average +quantities. If the value of the *units* keyword is *box* or +*lattice*, the "coord" is printed in box units. If the value of the +*units* keyword is *reduced*, the "coord" is printed in reduced units +(0-1). + +The *overwrite* keyword will continuously overwrite the output file +with the latest output, so that it only contains one timestep worth of +output. This option can only be used with the *ave running* setting. + +The *title1* and *title2* and *title3* keywords allow specification of +the strings that will be printed as the first 3 lines of the output +file, assuming the *file* keyword was used. LAMMPS uses default +values for each of these, so they do not need to be specified. + +By default, these header lines are as follows: + +.. parsed-literal:: + + # Spatial-averaged data for fix ID and group name + # Timestep Number-of-bins + # Bin r Count value1 value2 ... + +In the first line, ID and name are replaced with the fix-ID and group +name. The second line describes the two values that are printed at +the first of each section of output. In the third line the values are +replaced with the appropriate fields from the fix ave/spatial command. +The Coord2 and Coord3 entries in the third line only appear for 2d and +3d bins respectively. For 1d bins, the word Coord1 is replaced by +just Coord. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global array of values which can be accessed by +various :ref:`output commands `. The values can +only be accessed on timesteps that are multiples of *Nfreq* since that +is when averaging is performed. The global array has # of rows = +Nbins and # of columns = 2+Nvalues. The first column contains the +radius at the center of the shell. For units *reduced*, this is in +reduced units, while for units *box* and *lattice* this is in box +units. The next column has the count of atoms in that bin, and the +remaining columns are the Nvalue quantities. When the array is +accessed with an I that exceeds the current number of bins, than a 0.0 +is returned by the fix instead of an error. The array values +calculated by this fix are "intensive", since they are already +normalized by the count of atoms in each bin. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +When the *ave* keyword is set to *running* or *window* then the number +of bins must remain the same during the simulation, so that the +appropriate averaging can be done. This will be the case if the +simulation box size doesn't change or if the *units* keyword is set to +*reduced*. + +This style is part of the USER-MISC package. It is only enabled if +LAMMPS is build with that package. See the :ref:`Making of LAMMPS <3>` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/histo `, :doc:`fix ave/time `, +:doc:`variable `, :doc:`fix ave/correlate `, +:doc:`fix ave/spatial `, + +Default +""""""" + +The option defaults are norm = all, ave = one, units = lattice, no +file output, and title 1,2,3 = strings as described above. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ave_time.txt b/doc/_sources/fix_ave_time.txt new file mode 100644 index 0000000000..db8e9074cb --- /dev/null +++ b/doc/_sources/fix_ave_time.txt @@ -0,0 +1,347 @@ +.. index:: fix ave/time + +fix ave/time command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* ave/time = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of times to use input values for calculating averages +* Nfreq = calculate averages every this many timesteps +* one or more input values can be listed +* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name +.. parsed-literal:: + + c_ID = global scalar, vector, or array calculated by a compute with ID + c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID + f_ID = global scalar, vector, or array calculated by a fix with ID + f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID + v_name = global value calculated by an equal-style variable with name + +* zero or more keyword/arg pairs may be appended +* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *title1* or *title2* or *title3* +.. parsed-literal:: + + *mode* arg = *scalar* or *vector* + scalar = all input values are global scalars + vector = all input values are global vectors or global arrays + *ave* args = *one* or *running* or *window M* + one = output a new average value every Nfreq steps + running = output cummulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps + *start* args = Nstart + Nstart = start averaging on this timestep + *off* arg = M = do not average this value + M = value # from 1 to Nvalues + *file* arg = filename + filename = name of file to output time averages to + *overwrite* arg = none = overwrite output file with only latest output + *format* arg = string + string = C-style format string + *title1* arg = string + string = text to print as 1st line of output file + *title2* arg = string + string = text to print as 2nd line of output file + *title3* arg = string + string = text to print as 3rd line of output file, only for vector mode + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile + fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 & + title1 "My output values" + fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1 + +Description +""""""""""" + +Use one or more global values as inputs every few timesteps, and +average them over longer timescales. The resulting averages can be +used by other :ref:`output commands ` such as +:doc:`thermo_style custom `, and can also be written to a +file. Note that if no time averaging is done, this command can be +used as a convenient way to simply output one or more global values to +a file. + +The group specified with this command is ignored. However, note that +specified values may represent calculations performed by computes and +fixes which store their own "group" definitions. + +Each listed value can be the result of a :doc:`compute ` or +:doc:`fix ` or the evaluation of an equal-style +:doc:`variable `. In each case, the compute, fix, or variable +must produce a global quantity, not a per-atom or local quantity. If +you wish to spatial- or time-average or histogram per-atom quantities +from a compute, fix, or variable, then see the :doc:`fix ave/spatial `, :doc:`fix ave/atom `, +or :doc:`fix ave/histo ` commands. If you wish to sum a +per-atom quantity into a single global quantity, see the :doc:`compute reduce ` command. + +:doc:`Computes ` that produce global quantities are those which +do not have the word *atom* in their style name. Only a few +:doc:`fixes ` produce global quantities. See the doc pages for +individual fixes for info on which ones produce such values. +:doc:`Variables ` of style *equal* are the only ones that can +be used with this fix. Variables of style *atom* cannot be used, +since they produce per-atom values. + +The input values must either be all scalars or all vectors (or +arrays), depending on the setting of the *mode* keyword. In both +cases, the averaging is performed independently on each input value. +I.e. each input scalar is averaged independently and each element of +each input vector (or array) is averaged independently. + +If *mode* = vector, then the input values may either be vectors or +arrays and all must be the same "length", which is the length of the +vector or number of rows in the array. If a global array is listed, +then it is the same as if the individual columns of the array had been +listed one by one. E.g. these 2 fix ave/time commands are equivalent, +since the :doc:`compute rdf ` command creates, in this +case, a global array with 3 columns, each of length 50: + +.. parsed-literal:: + + compute myRDF all rdf 50 1 2 + fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector + fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be used in order to contribute to the +average. The final averaged quantities are generated on timesteps +that are a mlutiple of *Nfreq*. The average is over *Nrepeat* +quantities, computed in the preceding portion of the simulation every +*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and +*Nevery* must be non-zero even if *Nrepeat* is 1. Also, the timesteps +contributing to the average value cannot overlap, +i.e. Nrepeat*Nevery can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on +timesteps 90,92,94,96,98,100 will be used to compute the final average +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on +timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time +averaging is done; values are simply generated on timesteps +100,200,etc. + + +---------- + + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. If *mode* = scalar, then if +no bracketed term is appended, the global scalar calculated by the +compute is used. If a bracketed term is appended, the Ith element of +the global vector calculated by the compute is used. If *mode* = +vector, then if no bracketed term is appended, the global vector +calculated by the compute is used. Or if the compute calculates an +array, all of the columns of the global array are used as if they had +been specified as individual vectors (see description above). If a +bracketed term is appended, the Ith column of the global array +calculated by the compute is used. + +Note that there is a :doc:`compute reduce ` command +which can sum per-atom quantities into a global scalar or vector which +can thus be accessed by fix ave/time. Or it can be a compute defined +not in your input script, but by :doc:`thermodynamic output ` or other fixes such as :doc:`fix nvt ` or :doc:`fix temp/rescale `. See +the doc pages for these commands which give the IDs of these computes. +Users can also write code for their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. If *mode* = scalar, then if +no bracketed term is appended, the global scalar calculated by the fix +is used. If a bracketed term is appended, the Ith element of the +global vector calculated by the fix is used. If *mode* = vector, then +if no bracketed term is appended, the global vector calculated by the +fix is used. Or if the fix calculates an array, all of the columns of +the global array are used as if they had been specified as individual +vectors (see description above). If a bracketed term is appended, the +Ith column of the global array calculated by the fix is used. + +Note that some fixes only produce their values on certain timesteps, +which must be compatible with *Nevery*, else an error will result. +Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script. Variables can only be +used as input for *mode* = scalar. Only equal-style variables can be +referenced. See the :doc:`variable ` command for details. +Note that variables of style *equal* define a formula which can +reference individual atom properties or thermodynamic keywords, or +they can invoke other computes, fixes, or variables when they are +evaluated, so this is a very general means of specifying quantities to +time average. + + +---------- + + +Additional optional keywords also affect the operation of this fix. + +If the *mode* keyword is set to *scalar*, then all input values must +be global scalars, or elements of global vectors. If the *mode* +keyword is set to *vector*, then all input values must be global +vectors, or columns of global arrays. They can also be global arrays, +which are converted into a series of global vectors (one per column), +as explained above. + +The *ave* keyword determines how the values produced every *Nfreq* +steps are averaged with values produced on previous steps that were +multiples of *Nfreq*, before they are accessed by another output +command or written to a file. + +If the *ave* setting is *one*, then the values produced on timesteps +that are multiples of *Nfreq* are independent of each other; they are +output as-is without further averaging. + +If the *ave* setting is *running*, then the values produced on +timesteps that are multiples of *Nfreq* are summed and averaged in a +cummulative sense before being output. Each output value is thus the +average of the value produced on that timestep with all preceding +values. This running average begins when the fix is defined; it can +only be restarted by deleting the fix via the :doc:`unfix ` +command, or by re-defining the fix by re-specifying it. + +If the *ave* setting is *window*, then the values produced on +timesteps that are multiples of *Nfreq* are summed and averaged within +a moving "window" of time, so that the last M values are used to +produce the output. E.g. if M = 3 and Nfreq = 1000, then the output +on step 10000 will be the average of the individual values on steps +8000,9000,10000. Outputs on early steps will average over less than M +values if they are not available. + +The *start* keyword specifies what timestep averaging will begin on. +The default is step 0. Often input values can be 0.0 at time 0, so +setting *start* to a larger value can avoid including a 0.0 in a +running or windowed average. + +The *off* keyword can be used to flag any of the input values. If a +value is flagged, it will not be time averaged. Instead the most +recent input value will always be stored and output. This is useful +if one of more of the inputs produced by a compute or fix or variable +are effectively constant or are simply current values. E.g. they are +being written to a file with other time-averaged values for purposes +of creating well-formatted output. + +The *file* keyword allows a filename to be specified. Every *Nfreq* +steps, one quantity or vector of quantities is written to the file for +each input value specified in the fix ave/time command. For *mode* = +scalar, this means a single line is written each time output is +performed. Thus the file ends up to be a series of lines, i.e. one +column of numbers for each input value. For *mode* = vector, an array +of numbers is written each time output is performed. The number of +rows is the length of the input vectors, and the number of columns is +the number of values. Thus the file ends up to be a series of these +array sections. + +The *overwrite* keyword will continuously overwrite the output file +with the latest output, so that it only contains one timestep worth of +output. This option can only be used with the *ave running* setting. + +The *format* keyword sets the numeric format of each value when it is +printed to a file via the *file* keyword. Note that all values are +floating point quantities. The default format is %g. You can specify +a higher precision if desired, e.g. %20.16g. + +The *title1* and *title2* and *title3* keywords allow specification of +the strings that will be printed as the first 2 or 3 lines of the +output file, assuming the *file* keyword was used. LAMMPS uses +default values for each of these, so they do not need to be specified. + +By default, these header lines are as follows for *mode* = scalar: + +.. parsed-literal:: + + # Time-averaged data for fix ID + # TimeStep value1 value2 ... + +In the first line, ID is replaced with the fix-ID. In the second line +the values are replaced with the appropriate fields from the fix +ave/time command. There is no third line in the header of the file, +so the *title3* setting is ignored when *mode* = scalar. + +By default, these header lines are as follows for *mode* = vector: + +.. parsed-literal:: + + # Time-averaged data for fix ID + # TimeStep Number-of-rows + # Row value1 value2 ... + +In the first line, ID is replaced with the fix-ID. The second line +describes the two values that are printed at the first of each section +of output. In the third line the values are replaced with the +appropriate fields from the fix ave/time command. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix produces a global scalar or global vector or global array +which can be accessed by various :ref:`output commands `. The values can only be +accessed on timesteps that are multiples of *Nfreq* since that is when +averaging is performed. + +A scalar is produced if only a single input value is averaged and +*mode* = scalar. A vector is produced if multiple input values are +averaged for *mode* = scalar, or a single input value for *mode* = +vector. In the first case, the length of the vector is the number of +inputs. In the second case, the length of the vector is the same as +the length of the input vector. An array is produced if multiple +input values are averaged and *mode* = vector. The global array has # +of rows = length of the input vectors and # of columns = number of +inputs. + +If the fix prouduces a scalar or vector, then the scalar and each +element of the vector can be either "intensive" or "extensive", +depending on whether the values contributing to the scalar or vector +element are "intensive" or "extensive". If the fix produces an array, +then all elements in the array must be the same, either "intensive" or +"extensive". If a compute or fix provides the value being time +averaged, then the compute or fix determines whether the value is +intensive or extensive; see the doc page for that compute or fix for +further info. Values produced by a variable are treated as intensive. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`fix ave/atom `, :doc:`fix ave/spatial `, :doc:`fix ave/histo `, +:doc:`variable `, :doc:`fix ave/correlate `, + +Default +""""""" + +The option defaults are mode = scalar, ave = one, start = 0, no file +output, format = %g, title 1,2,3 = strings as described above, and no +off settings for any input values. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_aveforce.txt b/doc/_sources/fix_aveforce.txt new file mode 100644 index 0000000000..03a7e9474c --- /dev/null +++ b/doc/_sources/fix_aveforce.txt @@ -0,0 +1,135 @@ +.. index:: fix aveforce + +fix aveforce command +==================== + +fix aveforce/cuda command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID aveforce fx fy fz keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* aveforce = style name of this fix command +* fx,fy,fz = force component values (force units) +.. parsed-literal:: + + any of fx,fy,fz can be a variable (see below) + +* zero or more keyword/value pairs may be appended to args +* keyword = *region* +.. parsed-literal:: + + *region* value = region-ID + region-ID = ID of region atoms must be in to have added force + + + +Examples +"""""""" + +.. parsed-literal:: + + fix pressdown topwall aveforce 0.0 -1.0 0.0 + fix 2 bottomwall aveforce NULL -1.0 0.0 region top + fix 2 bottomwall aveforce NULL -1.0 v_oscillate region top + +Description +""""""""""" + +Apply an additional external force to a group of atoms in such a way +that every atom experiences the same force. This is useful for +pushing on wall or boundary atoms so that the structure of the wall +does not change over time. + +The existing force is averaged for the group of atoms, component by +component. The actual force on each atom is then set to the average +value plus the component specified in this command. This means each +atom in the group receives the same force. + +Any of the fx,fy,fz values can be specified as NULL which means the +force in that dimension is not changed. Note that this is not the +same as specifying a 0.0 value, since that sets all forces to the same +average value without adding in any additional force. + +Any of the 3 quantities defining the force components can be specified +as an equal-style :doc:`variable `, namely *fx*, *fy*, *fz*. +If the value is a variable, it should be specified as v_name, where +name is the variable name. In this case, the variable will be +evaluated each timestep, and its value used to determine the average +force. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent average force. + +If the *region* keyword is used, the atom must also be in the +specified geometric :doc:`region ` in order to have force added +to it. + + +---------- + + +Styles with a *cuda* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +These accelerated styles are part of the USER-CUDA package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global 3-vector of forces, which can be accessed +by various :ref:`output commands `. This is the +total force on the group of atoms before the forces on individual +atoms are changed by the fix. The vector values calculated by this +fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. You should not +specify force components with a variable that has time-dependence for +use with a minimizer, since the minimizer increments the timestep as +the iteration count during the minimization. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix setforce `, :doc:`fix addforce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_balance.txt b/doc/_sources/fix_balance.txt new file mode 100644 index 0000000000..55deadd39c --- /dev/null +++ b/doc/_sources/fix_balance.txt @@ -0,0 +1,384 @@ +.. index:: fix balance + +fix balance command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID balance Nfreq thresh style args keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* balance = style name of this fix command +* Nfreq = perform dynamic load balancing every this many steps +* thresh = imbalance threshhold that must be exceeded to perform a re-balance +* style = *shift* or *rcb* +.. parsed-literal:: + + shift args = dimstr Niter stopthresh + dimstr = sequence of letters containing "x" or "y" or "z", each not more than once + Niter = # of times to iterate within each dimension of dimstr sequence + stopthresh = stop balancing when this imbalance threshhold is reached + rcb args = none + +* zero or more keyword/value pairs may be appended +* keyword = *out* +.. parsed-literal:: + + *out* value = filename + filename = write each processor's sub-domain to a file, at each re-balancing + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 2 all balance 1000 1.05 shift x 10 1.05 + fix 2 all balance 100 0.9 shift xy 20 1.1 out tmp.balance + fix 2 all balance 1000 1.1 rcb + +Description +""""""""""" + +This command adjusts the size and shape of processor sub-domains +within the simulation box, to attempt to balance the number of +particles and thus the computational cost (load) evenly across +processors. The load balancing is "dynamic" in the sense that +rebalancing is performed periodically during the simulation. To +perform "static" balancing, before or between runs, see the +:doc:`balance ` command. + +Load-balancing is typically only useful if the particles in the +simulation box have a spatially-varying density distribution. E.g. a +model of a vapor/liquid interface, or a solid with an irregular-shaped +geometry containing void regions. In this case, the LAMMPS default of +dividing the simulation box volume into a regular-spaced grid of 3d +bricks, with one equal-volume sub-domain per processor, may assign +very different numbers of particles per processor. This can lead to +poor performance when the simulation is run in parallel. + +Note that the :doc:`processors ` command allows some control +over how the box volume is split across processors. Specifically, for +a Px by Py by Pz grid of processors, it allows choice of Px, Py, and +Pz, subject to the constraint that Px * Py * Pz = P, the total number +of processors. This is sufficient to achieve good load-balance for +some problems on some processor counts. However, all the processor +sub-domains will still have the same shape and same volume. + +On a particular timestep, a load-balancing operation is only performed +if the current "imbalance factor" in particles owned by each processor +exceeds the specified *thresh* parameter. The imbalance factor is +defined as the maximum number of particles owned by any processor, +divided by the average number of particles per processor. Thus an +imbalance factor of 1.0 is perfect balance. + +As an example, for 10000 particles running on 10 processors, if the +most heavily loaded processor has 1200 particles, then the factor is +1.2, meaning there is a 20% imbalance. Note that re-balances can be +forced even if the current balance is perfect (1.0) be specifying a +*thresh* < 1.0. + +.. note:: + + This command attempts to minimize the imbalance factor, as + defined above. But depending on the method a perfect balance (1.0) + may not be achieved. For example, "grid" methods (defined below) that + create a logical 3d grid cannot achieve perfect balance for many + irregular distributions of particles. Likewise, if a portion of the + system is a perfect lattice, e.g. the initial system is generated by + the :doc:`create_atoms ` command, then "grid" methods may + be unable to achieve exact balance. This is because entire lattice + planes will be owned or not owned by a single processor. + +.. note:: + + The imbalance factor is also an estimate of the maximum speed-up + you can hope to achieve by running a perfectly balanced simulation + versus an imbalanced one. In the example above, the 10000 particle + simulation could run up to 20% faster if it were perfectly balanced, + versus when imbalanced. However, computational cost is not strictly + proportional to particle count, and changing the relative size and + shape of processor sub-domains may lead to additional computational + and communication overheads, e.g. in the PPPM solver used via the + :doc:`kspace_style ` command. Thus you should benchmark + the run times of a simulation before and after balancing. + + +---------- + + +The method used to perform a load balance is specified by one of the +listed styles, which are described in detail below. There are 2 kinds +of styles. + +The *shift* style is a "grid" method which produces a logical 3d grid +of processors. It operates by changing the cutting planes (or lines) +between processors in 3d (or 2d), to adjust the volume (area in 2d) +assigned to each processor, as in the following 2d diagram where +processor sub-domains are shown and atoms are colored by the processor +that owns them. The leftmost diagram is the default partitioning of +the simulation box across processors (one sub-box for each of 16 +processors); the middle diagram is after a "grid" method has been +applied. + +.. thumbnail:: JPG/balance_uniform.jpg + :align: center +.. thumbnail:: JPG/balance_nonuniform.jpg + :align: center +.. thumbnail:: JPG/balance_rcb.jpg + :align: center +The *rcb* style is a "tiling" method which does not produce a logical +3d grid of processors. Rather it tiles the simulation domain with +rectangular sub-boxes of varying size and shape in an irregular +fashion so as to have equal numbers of particles in each sub-box, as +in the rightmost diagram above. + +The "grid" methods can be used with either of the +:doc:`comm_style ` command options, *brick* or *tiled*. The +"tiling" methods can only be used with :doc:`comm_style tiled `. + +When a "grid" method is specified, the current domain partitioning can +be either a logical 3d grid or a tiled partitioning. In the former +case, the current logical 3d grid is used as a starting point and +changes are made to improve the imbalance factor. In the latter case, +the tiled partitioning is discarded and a logical 3d grid is created +with uniform spacing in all dimensions. This is the starting point +for the balancing operation. + +When a "tiling" method is specified, the current domain partitioning +("grid" or "tiled") is ignored, and a new partitioning is computed +from scratch. + + +---------- + + +The *group-ID* is currently ignored. In the future it may be used to +determine what particles are considered for balancing. Normally it +would only makes sense to use the *all* group. But in some cases it +may be useful to balance on a subset of the particles, e.g. when +modeling large nanoparticles in a background of small solvent +particles. + +The *Nfreq* setting determines how often a rebalance is performed. If +*Nfreq* > 0, then rebalancing will occur every *Nfreq* steps. Each +time a rebalance occurs, a reneighboring is triggered, so *Nfreq* +should not be too small. If *Nfreq* = 0, then rebalancing will be +done every time reneighboring normally occurs, as determined by the +the :doc:`neighbor ` and :doc:`neigh_modify ` +command settings. + +On rebalance steps, rebalancing will only be attempted if the current +imbalance factor, as defined above, exceeds the *thresh* setting. + + +---------- + + +The *shift* style invokes a "grid" method for balancing, as described +above. It changes the positions of cutting planes between processors +in an iterative fashion, seeking to reduce the imbalance factor. + +The *dimstr* argument is a string of characters, each of which must be +an "x" or "y" or "z". Eacn character can appear zero or one time, +since there is no advantage to balancing on a dimension more than +once. You should normally only list dimensions where you expect there +to be a density variation in the particles. + +Balancing proceeds by adjusting the cutting planes in each of the +dimensions listed in *dimstr*, one dimension at a time. For a single +dimension, the balancing operation (described below) is iterated on up +to *Niter* times. After each dimension finishes, the imbalance factor +is re-computed, and the balancing operation halts if the *stopthresh* +criterion is met. + +A rebalance operation in a single dimension is performed using a +density-dependent recursive multisectioning algorithm, where the +position of each cutting plane (line in 2d) in the dimension is +adjusted independently. This is similar to a recursive bisectioning +for a single value, except that the bounds used for each bisectioning +take advantage of information from neighboring cuts if possible, as +well as counts of particles at the bounds on either side of each cuts, +which themselves were cuts in previous iterations. The latter is used +to infer a density of pariticles near each of the current cuts. At +each iteration, the count of particles on either side of each plane is +tallied. If the counts do not match the target value for the plane, +the position of the cut is adjusted based on the local density. The +low and high bounds are adjusted on each iteration, using new count +information, so that they become closer together over time. Thus as +the recursion progresses, the count of particles on either side of the +plane gets closer to the target value. + +The density-dependent part of this algorithm is often an advantage +when you rebalance a system that is already nearly balanced. It +typically converges more quickly than the geometric bisectioning +algorithm used by the :doc:`balance ` command. However, if can +be a disadvantage if you attempt to rebalance a system that is far +from balanced, and converge more slowly. In this case you probably +want to use the :doc:`balance ` command before starting a run, +so that you begin the run with a balanced system. + +Once the rebalancing is complete and final processor sub-domains +assigned, particles migrate to their new owning processor as part of +the normal reneighboring procedure. + +.. note:: + + At each rebalance operation, the bisectioning for each cutting + plane (line in 2d) typcially starts with low and high bounds separated + by the extent of a processor's sub-domain in one dimension. The size + of this bracketing region shrinks based on the local density, as + described above, which should typically be 1/2 or more every + iteration. Thus if *Niter* is specified as 10, the cutting plane will + typically be positioned to better than 1 part in 1000 accuracy + (relative to the perfect target position). For *Niter* = 20, it will + be accurate to better than 1 part in a million. Thus there is no need + to set *Niter* to a large value. This is especially true if you are + rebalancing often enough that each time you expect only an incremental + adjustement in the cutting planes is necessary. LAMMPS will check if + the threshold accuracy is reached (in a dimension) is less iterations + than *Niter* and exit early. + + +---------- + + +The *rcb* style invokes a "tiled" method for balancing, as described +above. It performs a recursive coordinate bisectioning (RCB) of the +simulation domain. The basic idea is as follows. + +The simulation domain is cut into 2 boxes by an axis-aligned cut in +the longest dimension, leaving one new box on either side of the cut. +All the processors are also partitioned into 2 groups, half assigned +to the box on the lower side of the cut, and half to the box on the +upper side. (If the processor count is odd, one side gets an extra +processor.) The cut is positioned so that the number of atoms in the +lower box is exactly the number that the processors assigned to that +box should own for load balance to be perfect. This also makes load +balance for the upper box perfect. The positioning is done +iteratively, by a bisectioning method. Note that counting atoms on +either side of the cut requires communication between all processors +at each iteration. + +That is the procedure for the first cut. Subsequent cuts are made +recursively, in exactly the same manner. The subset of processors +assigned to each box make a new cut in the longest dimension of that +box, splitting the box, the subset of processsors, and the atoms in +the box in two. The recursion continues until every processor is +assigned a sub-box of the entire simulation domain, and owns the atoms +in that sub-box. + + +---------- + + +The *out* keyword writes a text file to the specified *filename* with +the results of each rebalancing operation. The file contains the +bounds of the sub-domain for each processor after the balancing +operation completes. The format of the file is compatible with the +`Pizza.py `_ *mdump* tool which has support for manipulating and +visualizing mesh files. An example is shown here for a balancing by 4 +processors for a 2d problem: + +.. parsed-literal:: + + ITEM: TIMESTEP + 0 + ITEM: NUMBER OF NODES + 16 + ITEM: BOX BOUNDS + 0 10 + 0 10 + 0 10 + ITEM: NODES + 1 1 0 0 0 + 2 1 5 0 0 + 3 1 5 5 0 + 4 1 0 5 0 + 5 1 5 0 0 + 6 1 10 0 0 + 7 1 10 5 0 + 8 1 5 5 0 + 9 1 0 5 0 + 10 1 5 5 0 + 11 1 5 10 0 + 12 1 10 5 0 + 13 1 5 5 0 + 14 1 10 5 0 + 15 1 10 10 0 + 16 1 5 10 0 + ITEM: TIMESTEP + 0 + ITEM: NUMBER OF SQUARES + 4 + ITEM: SQUARES + 1 1 1 2 3 4 + 2 1 5 6 7 8 + 3 1 9 10 11 12 + 4 1 13 14 15 16 + +The coordinates of all the vertices are listed in the NODES section, 5 +per processor. Note that the 4 sub-domains share vertices, so there +will be duplicate nodes in the list. + +The "SQUARES" section lists the node IDs of the 4 vertices in a +rectangle for each processor (1 to 4). + +For a 3d problem, the syntax is similar with 8 vertices listed for +each processor, instead of 4, and "SQUARES" replaced by "CUBES". + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global scalar which is the imbalance factor +after the most recent rebalance and a global vector of length 3 with +additional information about the most recent rebalancing. The 3 +values in the vector are as follows: + +* 1 = max # of particles per processor +* 2 = total # iterations performed in last rebalance +* 3 = imbalance factor right before the last rebalance was performed + +As explained above, the imbalance factor is the ratio of the maximum +number of particles on any processor to the average number of +particles per processor. + +These quantities can be accessed by various :ref:`output commands `. The scalar and vector values +calculated by this fix are "intensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + + +---------- + + +Restrictions +"""""""""""" + + +For 2d simulations, a "z" cannot appear in *dimstr* for the *shift* +style. + +Related commands +"""""""""""""""" + +:doc:`processors `, :doc:`balance ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_bond_break.txt b/doc/_sources/fix_bond_break.txt new file mode 100644 index 0000000000..4473d40546 --- /dev/null +++ b/doc/_sources/fix_bond_break.txt @@ -0,0 +1,160 @@ +.. index:: fix bond/break + +fix bond/break command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID bond/break Nevery bondtype Rmax keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* bond/break = style name of this fix command +* Nevery = attempt bond breaking every this many steps +* bondtype = type of bonds to break +* Rmax = bond longer than Rmax can break (distance units) +* zero or more keyword/value pairs may be appended to args +* keyword = *prob* +.. parsed-literal:: + + *prob* values = fraction seed + fraction = break a bond with this probability if otherwise eligible + seed = random number seed (positive integer) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 5 all bond/break 10 2 1.2 + fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829 + +Description +""""""""""" + +Break bonds between pairs of atoms as a simulation runs according to +specified criteria. This can be used to model the dissolution of a +polymer network due to stretching of the simulation box or other +deformations. In this context, a bond means an interaction between a +pair of atoms computed by the :doc:`bond_style ` command. +Once the bond is broken it will be permanently deleted, as will all +angle, dihedral, and improper interactions that bond is part of. + +This is different than a :doc:`pairwise ` bond-order +potential such as Tersoff or AIREBO which infers bonds and many-body +interactions based on the current geometry of a small cluster of atoms +and effectively creates and destroys bonds and higher-order many-body +interactions from timestep to timestep as atoms move. + +A check for possible bond breakage is performed every *Nevery* +timesteps. If two bonded atoms I,J are further than a distance *Rmax* +of each other, if the bond is of type *bondtype*, and if both I and J +are in the specified fix group, then I,J is labeled as a "possible" +bond to break. + +If several bonds involving an atom are stretched, it may have multiple +possible bonds to break. Every atom checks its list of possible bonds +to break and labels the longest such bond as its "sole" bond to break. +After this is done, if atom I is bonded to atom J in its sole bond, +and atom J is bonded to atom I in its sole bond, then the I,J bond is +"eligible" to be broken. + +Note that these rules mean an atom will only be part of at most one +broken bond on a given timestep. It also means that if atom I chooses +atom J as its sole partner, but atom J chooses atom K is its sole +partner (due to Rjk > Rij), then this means atom I will not be part of +a broken bond on this timestep, even if it has other possible bond +partners. + +The *prob* keyword can effect whether an eligible bond is actually +broken. The *fraction* setting must be a value between 0.0 and 1.0. +A uniform random number between 0.0 and 1.0 is generated and the +eligible bond is only broken if the random number < fraction. + +When a bond is broken, data structures within LAMMPS that store bond +topology are updated to reflect the breakage. Likewise, if the bond +is part of a 3-body (angle) or 4-body (dihedral, improper) +interaction, that interaction is removed as well. These changes +typically affect pairwise interactions between atoms that used to be +part of bonds, angles, etc. + +.. note:: + + One data structure that is not updated when a bond breaks are + the molecule IDs stored by each atom. Even though one molecule + becomes two moleclues due to the broken bond, all atoms in both new + moleclues retain their original molecule IDs. + +Computationally, each timestep this fix operates, it loops over all +the bonds in the system and computes distances between pairs of bonded +atoms. It also communicates between neighboring processors to +coordinate which bonds are broken. Moreover, if any bonds are broken, +neighbor lists must be immediately updated on the same timestep. This +is to insure that any pairwise interactions that should be turned "on" +due to a bond breaking, because they are no longer excluded by the +presence of the bond and the settings of the +:doc:`special_bonds ` command, will be immediately +recognized. All of these operations increase the cost of a timestep. +Thus you should be cautious about invoking this fix too frequently. + +You can dump out snapshots of the current bond topology via the :doc:`dump local ` command. + +.. note:: + + Breaking a bond typically alters the energy of a system. You + should be careful not to choose bond breaking criteria that induce a + dramatic change in energy. For example, if you define a very stiff + harmonic bond and break it when 2 atoms are separated by a distance + far from the equilibribum bond length, then the 2 atoms will be + dramatically released when the bond is broken. More generally, you + may need to thermostat your system to compensate for energy changes + resulting from broken bonds (and angles, dihedrals, impropers). + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes two statistics which it stores in a global vector of +length 2, which can be accessed by various :ref:`output commands `. The vector values calculated +by this fix are "intensive". + +These are the 2 quantities: + +* (1) # of bonds broken on the most recent breakage timestep +* (2) cummulative # of bonds broken + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix bond/create `, :doc:`fix bond/swap `, :doc:`dump local `, +:doc:`special_bonds ` + +Default +""""""" + +The option defaults are prob = 1.0. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_bond_create.txt b/doc/_sources/fix_bond_create.txt new file mode 100644 index 0000000000..77de5bfbdc --- /dev/null +++ b/doc/_sources/fix_bond_create.txt @@ -0,0 +1,263 @@ +.. index:: fix bond/create + +fix bond/create command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* bond/create = style name of this fix command +* Nevery = attempt bond creation every this many steps +* itype,jtype = atoms of itype can bond to atoms of jtype +* Rmin = 2 atoms separated by less than Rmin can bond (distance units) +* bondtype = type of created bonds +* zero or more keyword/value pairs may be appended to args +* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* +.. parsed-literal:: + + *iparam* values = maxbond, newtype + maxbond = max # of bonds of bondtype the itype atom can have + newtype = change the itype atom to this type when maxbonds exist + *jparam* values = maxbond, newtype + maxbond = max # of bonds of bondtype the jtype atom can have + newtype = change the jtype atom to this type when maxbonds exist + *prob* values = fraction seed + fraction = create a bond with this probability if otherwise eligible + seed = random number seed (positive integer) + *atype* value = angletype + angletype = type of created angles + *dtype* value = dihedraltype + dihedraltype = type of created dihedrals + *itype* value = impropertype + impropertype = type of created impropers + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 5 all bond/create 10 1 2 0.8 1 + fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 + fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2 + +Description +""""""""""" + +Create bonds between pairs of atoms as a simulation runs according to +specified criteria. This can be used to model cross-linking of +polymers, the formation of a percolation network, etc. In this +context, a bond means an interaction between a pair of atoms computed +by the :doc:`bond_style ` command. Once the bond is created +it will be permanently in place. Optionally, the creation of a bond +can also create angle, dihedral, and improper interactions that bond +is part of. See the discussion of the *atype*, *dtype*, and *itype* +keywords below. + +This is different than a :doc:`pairwise ` bond-order +potential such as Tersoff or AIREBO which infers bonds and many-body +interactions based on the current geometry of a small cluster of atoms +and effectively creates and destroys bonds and higher-order many-body +interactions from timestep to timestep as atoms move. + +A check for possible new bonds is performed every *Nevery* timesteps. +If two atoms I,J are within a distance *Rmin* of each other, if I is +of atom type *itype*, if J is of atom type *jtype*, if both I and J +are in the specified fix group, if a bond does not already exist +between I and J, and if both I and J meet their respective *maxbond* +requirement (explained below), then I,J is labeled as a "possible" +bond pair. + +If several atoms are close to an atom, it may have multiple possible +bond partners. Every atom checks its list of possible bond partners +and labels the closest such partner as its "sole" bond partner. After +this is done, if atom I has atom J as its sole partner, and atom J has +atom I as its sole partner, then the I,J bond is "eligible" to be +formed. + +Note that these rules mean an atom will only be part of at most one +created bond on a given timestep. It also means that if atom I +chooses atom J as its sole partner, but atom J chooses atom K is its +sole partner (due to Rjk < Rij), then this means atom I will not form +a bond on this timestep, even if it has other possible bond partners. + +It is permissible to have *itype* = *jtype*. *Rmin* must be <= the +pairwise cutoff distance between *itype* and *jtype* atoms, as defined +by the :doc:`pair_style ` command. + +The *iparam* and *jparam* keywords can be used to limit the bonding +functionality of the participating atoms. Each atom keeps track of +how many bonds of *bondtype* it already has. If atom I of +itype already has *maxbond* bonds (as set by the *iparam* +keyword), then it will not form any more. Likewise for atom J. If +*maxbond* is set to 0, then there is no limit on the number of bonds +that can be formed with that atom. + +The *newtype* value for *iparam* and *jparam* can be used to change +the atom type of atom I or J when it reaches *maxbond* number of bonds +of type *bondtype*. This means it can now interact in a pairwise +fashion with other atoms in a different way by specifying different +:doc:`pair_coeff ` coefficients. If you do not wish the +atom type to change, simply specify *newtype* as *itype* or *jtype*. + +The *prob* keyword can also effect whether an eligible bond is +actually created. The *fraction* setting must be a value between 0.0 +and 1.0. A uniform random number between 0.0 and 1.0 is generated and +the eligible bond is only created if the random number < fraction. + +Any bond that is created is assigned a bond type of *bondtype* + +When a bond is created, data structures within LAMMPS that store bond +topology are updated to reflect the creation. If the bond is part of +new 3-body (angle) or 4-body (dihedral, improper) interactions, you +can choose to create new angles, dihedrals, impropers as well, using +the *atype*, *dtype*, and *itype* keywords. All of these changes +typically affect pairwise interactions between atoms that are now part +of new bonds, angles, etc. + +.. note:: + + One data structure that is not updated when a bond breaks are + the molecule IDs stored by each atom. Even though two molecules + become one moleclue due to the created bond, all atoms in the new + moleclue retain their original molecule IDs. + +If the *atype* keyword is used and if an angle potential is defined +via the :doc:`angle_style ` command, then any new 3-body +interactions inferred by the creation of a bond will create new angles +of type *angletype*, with parameters assigned by the corresponding +:doc:`angle_coeff ` command. Likewise, the *dtype* and +*itype* keywords will create new dihedrals and impropers of type +*dihedraltype* and *impropertype*. + +.. note:: + + To create a new bond, the internal LAMMPS data structures that + store this information must have space for it. When LAMMPS is + initialized from a data file, the list of bonds is scanned and the + maximum number of bonds per atom is tallied. If some atom will + acquire more bonds than this limit as this fix operates, then the + "extra bond per atom" parameter must be set to allow for it. Ditto + for "extra angle per atom", "extra dihedral per atom", and "extra + improper per atom" if angles, dihedrals, or impropers are being added + when bonds are created. See the :doc:`read_data ` or + :doc:`create_box ` command for more details. Note that a + data file with no atoms can be used if you wish to add unbonded atoms + via the :doc:`create atoms ` command, e.g. for a + percolation simulation. + +.. note:: + + LAMMPS stores and maintains a data structure with a list of the + 1st, 2nd, and 3rd neighbors of each atom (within the bond topology of + the system) for use in weighting pairwise interactions for bonded + atoms. Note that adding a single bond always adds a new 1st neighbor + but may also induce *many* new 2nd and 3rd neighbors, depending on the + molecular topology of your system. The "extra special per atom" + parameter must typically be set to allow for the new maximum total + size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3 + ways to do this. See the :doc:`read_data ` or + :doc:`create_box ` or "special_bonds extra" commands for + details. + +.. note:: + + Even if you do not use the *atype*, *dtype*, or *itype* + keywords, the list of topological neighbors is updated for atoms + affected by the new bond. This in turn affects which neighbors are + considered for pairwise interactions, using the weighting rules set by + the :doc:`special_bonds ` command. Consider a new bond + created between atoms I,J. If J has a bonded neighbor K, then K + becomes a 2nd neighbor of I. Even if the *atype* keyword is not used + to create angle I-J-K, the pairwise interaction between I and K will + be potentially turned off or weighted by the 1-3 weighting specified + by the :doc:`special_bonds ` command. This is the case + even if the "angle yes" option was used with that command. The same + is true for 3rd neighbors (1-4 interactions), the *dtype* keyword, and + the "dihedral yes" option used with the + :doc:`special_bonds ` command. + +Note that even if your simulation starts with no bonds, you must +define a :doc:`bond_style ` and use the +:doc:`bond_coeff ` command to specify coefficients for the +*bondtype*. Similarly, if new atom types are specified by the +*iparam* or *jparam* keywords, they must be within the range of atom +types allowed by the simulation and pairwise coefficients must be +specified for the new types. + +Computationally, each timestep this fix operates, it loops over +neighbor lists and computes distances between pairs of atoms in the +list. It also communicates between neighboring processors to +coordinate which bonds are created. Moreover, if any bonds are +created, neighbor lists must be immediately updated on the same +timestep. This is to insure that any pairwise interactions that +should be turned "off" due to a bond creation, because they are now +excluded by the presence of the bond and the settings of the +:doc:`special_bonds ` command, will be immediately +recognized. All of these operations increase the cost of a timestep. +Thus you should be cautious about invoking this fix too frequently. + +You can dump out snapshots of the current bond topology via the :doc:`dump local ` command. + +.. note:: + + Creating a bond typically alters the energy of a system. You + should be careful not to choose bond creation criteria that induce a + dramatic change in energy. For example, if you define a very stiff + harmonic bond and create it when 2 atoms are separated by a distance + far from the equilibribum bond length, then the 2 atoms will oscillate + dramatically when the bond is formed. More generally, you may need to + thermostat your system to compensate for energy changes resulting from + created bonds (and angles, dihedrals, impropers). + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes two statistics which it stores in a global vector of +length 2, which can be accessed by various :ref:`output commands `. The vector values calculated +by this fix are "intensive". + +These are the 2 quantities: + +* (1) # of bonds created on the most recent creation timestep +* (2) cummulative # of bonds created + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix bond/break `, :doc:`fix bond/swap `, :doc:`dump local `, +:doc:`special_bonds ` + +Default +""""""" + +The option defaults are iparam = (0,itype), jparam = (0,jtype), and +prob = 1.0. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_bond_swap.txt b/doc/_sources/fix_bond_swap.txt new file mode 100644 index 0000000000..387c80af96 --- /dev/null +++ b/doc/_sources/fix_bond_swap.txt @@ -0,0 +1,212 @@ +.. index:: fix bond/swap + +fix bond/swap command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID bond/swap Nevery fraction cutoff seed + +* ID, group-ID are documented in :doc:`fix ` command +* bond/swap = style name of this fix command +* Nevery = attempt bond swapping every this many steps +* fraction = fraction of group atoms to consider for swapping +* cutoff = distance at which swapping will be considered (distance units) +* seed = random # seed (positive integer) + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all bond/swap 50 0.5 1.3 598934 + +Description +""""""""""" + +In a simulation of polymer chains, this command attempts to swap bonds +between two different chains, effectively grafting the end of one +chain onto another chain and vice versa. This is done via Monte Carlo +rules using the Boltzmann acceptance criterion. The purpose is to +equilibrate the polymer chain conformations more rapidly than dynamics +alone would do it, by enabling instantaneous large conformational +changes in a dense polymer melt. The polymer chains should thus more +rapidly converge to the proper end-to-end distances and radii of +gyration. It is designed for use with systems of +:doc:`FENE ` or :doc:`harmonic ` bead-spring +polymer chains where each polymer is a linear chain of monomers, but +LAMMPS does not enforce this requirement, i.e. any +:doc:`bond_style ` can be used. + +A schematic of the kinds of bond swaps that can occur is shown here: + +.. image:: JPG/bondswap.jpg + :align: center + +On the left, the red and blue chains have two monomers A1 and B1 close +to each other, which are currently bonded to monomers A2 and B2 +respectively within their own chains. The bond swap operation will +attempt to delete the A1-A2 and B1-B2 bonds and replace them with +A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the +two chains on the right are the result and each polymer chain has +undergone a dramatic conformational change. This reference, +:ref:`(Sides) ` provides more details on how the algorithm works and +its application: + +The bond swapping operation is invoked every *Nevery* timesteps. If +any bond is swapped, a re-build of the neighbor lists is triggered, +since a swap alters the list of which neighbors are considered for +pairwise interaction. At each invocation, each processor considers a +random specified *fraction* of its atoms as potential swapping +monomers for this timestep. Choosing a small *fraction* value can +reduce the likelihood of a reverse swap occurring soon after an +initial swap. + +For each monomer A1, its neighbors are examined to find a possible B1 +monomer. Both A1 and B1 must be in the fix group, their separation +must be less than the specified *cutoff*, and the molecule IDs of A1 +and B1 must be the same (see below). If a suitable partner is found, +the energy change due to swapping the 2 bonds is computed. This +includes changes in pairwise, bond, and angle energies due to the +altered connectivity of the 2 chains. Dihedral and improper +interactions are not allowed to be defined when this fix is used. + +If the energy decreases due to the swap operation, the bond swap is +accepted. If the energy increases it is accepted with probability +exp(-delta/kT) where delta is the increase in energy, k is the +Boltzmann constant, and T is the current temperature of the system. +Whether the swap is accepted or rejected, no other swaps are attempted +by this processor on this timestep. + +The criterion for matching molecule IDs is how bond swaps performed by +this fix conserve chain length. To use this features you must setup +the molecule IDs for your polymer chains in a certain way, typically +in the data file, read by the :doc:`read_data ` comand. +Consider a system of 6-mer chains. You have 2 choices. If the +molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then +swaps will conserve chain length. For a particular momoner there will +be only one other monomer on another chain which is a potential swap +partner. If the molecule IDs for monomers on each chain are set to +1,2,3,3,2,1 then swaps will conserve chain length but swaps will be +able to occur at either end of a chain. Thus for a particular monomer +there will be 2 possible swap partners on another chain. In this +scenario, swaps can also occur within a single chain, i.e. the two +ends of a chain swap with each other. + +.. note:: + + If your simulation uses molecule IDs in the usual way, where all + monomers on a single chain are assigned the same ID (different for + each chain), then swaps will only occur within the same chain. If you + assign the same molecule ID to all monomers in all chains then + inter-chain swaps will occur, but they will not conserve chain length. + Neither of these scenarios is probably what you want for this fix. + +.. note:: + + When a bond swap occurs the image flags of monomers in the new + polymer chains can become inconsistent. See the :doc:`dump ` + command for a discussion of image flags. This is not an issue for + running dynamics, but can affect calculation of some diagnostic + quantities or the printing of unwrapped coordinates to a dump file. + + +---------- + + +This fix computes a temperature each time it is invoked for use by the +Boltzmann criterion. To do this, the fix creates its own compute of +style *temp*, as if this command had been issued: + +.. parsed-literal:: + + compute fix-ID_temp all temp + +See the :doc:`compute temp ` command for details. Note +that the ID of the new compute is the fix-ID with underscore + "temp" +appended and the group for the new compute is "all", so that the +temperature of the entire system is used. + +Note that this is NOT the compute used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp*. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +:doc:`compute_modify ` command or print this temperature +during thermodyanmic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* will have no +effect on this fix. + + +---------- + + +**Restart, fix_modify, thermo output, run start/stop, minimize info:** + +No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. Also note that +each processor generates possible swaps independently of other +processors. Thus if you repeat the same simulation on a different number +of processors, the specific swaps performed will be different. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a :doc:`compute ` you have +defined to this fix which will be used to compute the temperature for +the Boltzmann criterion. + +This fix computes two statistical quantities as a global 2-vector of +output, which can be accessed by various :ref:`output commands `. The first component of the +vector is the cummulative number of swaps performed by all processors. +The second component of the vector is the cummulative number of swaps +attempted (whether accepted or rejected). Note that a swap "attempt" +only occurs when swap partners meeting the criteria described above +are found on a particular timestep. The vector values calculated by +this fix are "intensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The setings of the "special_bond" command must be 0,1,1 in order to +use this fix, which is typical of bead-spring chains with FENE or +harmonic bonds. This means that pairwise interactions between bonded +atoms are turned off, but are turned on between atoms two or three +hops away along the chain backbone. + +Currently, energy changes in dihedral and improper interactions due to +a bond swap are not considered. Thus a simulation that uses this fix +cannot use a dihedral or improper potential. + +Related commands +"""""""""""""""" + +:doc:`fix atom/swap ` + +**Default:** none + + +---------- + + +.. _Sides: + + + +**(Sides)** Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, +199-208 (2004). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_box_relax.txt b/doc/_sources/fix_box_relax.txt new file mode 100644 index 0000000000..ee273b500e --- /dev/null +++ b/doc/_sources/fix_box_relax.txt @@ -0,0 +1,406 @@ +.. index:: fix box/relax + +fix box/relax command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID box/relax keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* box/relax = style name of this fix command +.. parsed-literal:: + + one or more keyword value pairs may be appended + keyword = *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *nreset* or *vmax* or *dilate* or *scaleyz* or *scalexz* or *scalexy* or *fixedpoint* + *iso* or *aniso* or *tri* value = Ptarget = desired pressure (pressure units) + *x* or *y* or *z* or *xy* or *yz* or *xz* value = Ptarget = desired pressure (pressure units) + *couple* = *none* or *xyz* or *xy* or *yz* or *xz* + *nreset* value = reset reference cell every this many minimizer iterations + *vmax* value = fraction = max allowed volume change in one iteration + *dilate* value = *all* or *partial* + *scaleyz* value = *yes* or *no* = scale yz with lz + *scalexz* value = *yes* or *no* = scale xz with lz + *scalexy* value = *yes* or *no* = scale xy with ly + *fixedpoint* values = x y z + x,y,z = perform relaxation dilation/contraction around this point (distance units) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all box/relax iso 0.0 vmax 0.001 + fix 2 water box/relax aniso 0.0 dilate partial + fix 2 ice box/relax tri 0.0 couple xy nreset 100 + +Description +""""""""""" + +Apply an external pressure or stress tensor to the simulation box +during an :doc:`energy minimization `. This allows the box +size and shape to vary during the iterations of the minimizer so that +the final configuration will be both an energy minimum for the +potential energy of the atoms, and the system pressure tensor will be +close to the specified external tensor. Conceptually, specifying a +positive pressure is like squeezing on the simulation box; a negative +pressure typically allows the box to expand. + + +---------- + + +The external pressure tensor is specified using one or more of the +*iso*, *aniso*, *tri*, *x*, *y*, *z*, *xy*, *xz*, *yz*, and *couple* +keywords. These keywords give you the ability to specify all 6 +components of an external stress tensor, and to couple various of +these components together so that the dimensions they represent are +varied together during the mimimization. + +Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). +Triclinic (non-orthogonal) simulation boxes have 6 adjustable +dimensions (x,y,z,xy,xz,yz). The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands +specify whether the simulation box is orthogonal or non-orthogonal +(triclinic) and explain the meaning of the xy,xz,yz tilt factors. + +The target pressures *Ptarget* for each of the 6 components of the +stress tensor can be specified independently via the *x*, *y*, *z*, +*xy*, *xz*, *yz* keywords, which correspond to the 6 simulation box +dimensions. For example, if the *y* keyword is used, the y-box length +will change during the minimization. If the *xy* keyword is used, the +xy tilt factor will change. A box dimension will not change if that +component is not specified. + +Note that in order to use the *xy*, *xz*, or *yz* keywords, the +simulation box must be triclinic, even if its initial tilt factors are +0.0. + +When the size of the simulation box changes, all atoms are re-scaled +to new positions, unless the keyword *dilate* is specified with a +value of *partial*, in which case only the atoms in the fix group are +re-scaled. This can be useful for leaving the coordinates of atoms in +a solid substrate unchanged and controlling the pressure of a +surrounding fluid. + +The *scaleyz*, *scalexz*, and *scalexy* keywords control whether or +not the corresponding tilt factors are scaled with the associated box +dimensions when relaxing triclinic periodic cells. The default +values *yes* will turn on scaling, which corresponds to adjusting the +linear dimensions of the cell while preserving its shape. Choosing +*no* ensures that the tilt factors are not scaled with the box +dimensions. See below for restrictions and default values in different +situations. In older versions of LAMMPS, scaling of tilt factors was +not performed. The old behavior can be recovered by setting all three +scale keywords to *no*. + +The *fixedpoint* keyword specifies the fixed point for cell relaxation. +By default, it is the center of the box. Whatever point is +chosen will not move during the simulation. For example, if the lower +periodic boundaries pass through (0,0,0), and this point is provided +to *fixedpoint*, then the lower periodic boundaries will remain at +(0,0,0), while the upper periodic boundaries will move twice as +far. In all cases, the particle positions at each iteration are +unaffected by the chosen value, except that all particles are +displaced by the same amount, different on each iteration. + +.. note:: + + Appling an external pressure to tilt dimensions *xy*, *xz*, *yz* + can sometimes result in arbitrarily large values of the tilt factors, + i.e. a dramatically deformed simulation box. This typically indicates + that there is something badly wrong with how the simulation was + constructed. The two most common sources of this error are applying a + shear stress to a liquid system or specifying an external shear stress + tensor that exceeds the yield stress of the solid. In either case the + minimization may converge to a bogus conformation or not converge at + all. Also note that if the box shape tilts to an extreme shape, + LAMMPS will run less efficiently, due to the large volume of + communication needed to acquire ghost atoms around a processor's + irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may + also lose atoms and generate an error. + +.. note:: + + Performing a minimization with this fix is not a mathematically + well-defined minimization problem. This is because the objective + function being minimized changes if the box size/shape changes. In + practice this means the minimizer can get "stuck" before you have + reached the desired tolerance. The solution to this is to restart the + minmizer from the new adjusted box size/shape, since that creates a + new objective function valid for the new box size/shape. Repeat as + necessary until the box size/shape has reached its new equilibrium. + + + + + + +---------- + + +The *couple* keyword allows two or three of the diagonal components of +the pressure tensor to be "coupled" together. The value specified +with the keyword determines which are coupled. For example, *xz* +means the *Pxx* and *Pzz* components of the stress tensor are coupled. +*Xyz* means all 3 diagonal components are coupled. Coupling means two +things: the instantaneous stress will be computed as an average of the +corresponding diagonal components, and the coupled box dimensions will +be changed together in lockstep, meaning coupled dimensions will be +dilated or contracted by the same percentage every timestep. The +*Ptarget* values for any coupled dimensions must be identical. +*Couple xyz* can be used for a 2d simulation; the *z* dimension is +simply ignored. + + +---------- + + +The *iso*, *aniso*, and *tri* keywords are simply shortcuts that are +equivalent to specifying several other keywords together. + +The keyword *iso* means couple all 3 diagonal components together when +pressure is computed (hydrostatic pressure), and dilate/contract the +dimensions together. Using "iso Ptarget" is the same as specifying +these 4 keywords: + +.. parsed-literal:: + + x Ptarget + y Ptarget + z Ptarget + couple xyz + +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the +stress tensor as the driving forces, and the specified scalar external +pressure. Using "aniso Ptarget" is the same as specifying these 4 +keywords: + +.. parsed-literal:: + + x Ptarget + y Ptarget + z Ptarget + couple none + +The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions +are controlled independently using their individual stress components +as the driving forces, and the specified scalar pressure as the +external normal stress. Using "tri Ptarget" is the same as specifying +these 7 keywords: + +.. parsed-literal:: + + x Ptarget + y Ptarget + z Ptarget + xy 0.0 + yz 0.0 + xz 0.0 + couple none + + +---------- + + +The *vmax* keyword can be used to limit the fractional change in the +volume of the simulation box that can occur in one iteration of the +minimizer. If the pressure is not settling down during the +minimization this can be because the volume is fluctuating too much. +The specified fraction must be greater than 0.0 and should be << 1.0. +A value of 0.001 means the volume cannot change by more than 1/10 of a +percent in one iteration when *couple xyz* has been specified. For +any other case it means no linear dimension of the simulation box can +change by more than 1/10 of a percent. + + +---------- + + +With this fix, the potential energy used by the minimizer is augmented +by an additional energy provided by the fix. The overall objective +function then is: + +.. image:: Eqs/fix_box_relax1.jpg + :align: center + +where *U* is the system potential energy, *P*_t is the desired +hydrostatic pressure, *V* and *V*_0 are the system and reference +volumes, respectively. *E*_*strain* is the strain energy expression +proposed by Parrinello and Rahman :ref:`(Parrinello1981) `. +Taking derivatives of *E* w.r.t. the box dimensions, and setting these +to zero, we find that at the minimum of the objective function, the +global system stress tensor **P** will satisfy the relation: + +.. image:: Eqs/fix_box_relax2.jpg + :align: center + +where **I** is the identity matrix, **h**_0 is the box dimension tensor of +the reference cell, and **h**_0*d* is the diagonal part of +**h**_0. **S**_*t* is a symmetric stress tensor that is chosen by LAMMPS +so that the upper-triangular components of **P** equal the stress tensor +specified by the user. + +This equation only applies when the box dimensions are equal to those +of the reference dimensions. If this is not the case, then the +converged stress tensor will not equal that specified by the user. We +can resolve this problem by periodically resetting the reference +dimensions. The keyword *nreset_ref* controls how often this is done. +If this keyword is not used, or is given a value of zero, then the +reference dimensions are set to those of the initial simulation domain +and are never changed. A value of *nstep* means that every *nstep* +minimization steps, the reference dimensions are set to those of the +current simulation domain. Note that resetting the reference +dimensions changes the objective function and gradients, which +sometimes causes the minimization to fail. This can be resolved by +changing the value of *nreset*, or simply continuing the minimization +from a restart file. + +.. note:: + + As normally computed, pressure includes a kinetic- energy or + temperature-dependent component; see the :doc:`compute pressure ` command. However, atom velocities are + ignored during a minimization, and the applied pressure(s) specified + with this command are assumed to only be the virial component of the + pressure (the non-kinetic portion). Thus if atoms have a non-zero + temperature and you print the usual thermodynamic pressure, it may not + appear the system is converging to your specified pressure. The + solution for this is to either (a) zero the velocities of all atoms + before performing the minimization, or (b) make sure you are + monitoring the pressure without its kinetic component. The latter can + be done by outputting the pressure from the fix this command creates + (see below) or a pressure fix you define yourself. + +.. note:: + + Because pressure is often a very sensitive function of volume, + it can be difficult for the minimizer to equilibrate the system the + desired pressure with high precision, particularly for solids. Some + techniques that seem to help are (a) use the "min_modify line + quadratic" option when minimizing with box relaxations, (b) minimize + several times in succession if need be, to drive the pressure closer + to the target pressure, (c) relax the atom positions before relaxing + the box, and (d) relax the box to the target hydrostatic pressure + before relaxing to a target shear stress state. Also note that some + systems (e.g. liquids) will not sustain a non-hydrostatic applied + pressure, which means the minimizer will not converge. + + +---------- + + +This fix computes a temperature and pressure each timestep. The +temperature is used to compute the kinetic contribution to the +pressure, even though this is subsequently ignored by default. To do +this, the fix creates its own computes of style "temp" and "pressure", +as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp + compute fix-ID_press group-ID pressure fix-ID_temp virial + +See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is the same +as the fix group. Also note that the pressure compute does not +include a kinetic component. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its temperature and pressure calculation, as described above. Note +that as described above, if you assign a pressure compute to this fix +that includes a kinetic energy component it will affect the +minimization, most likely in an undesirable way. + +.. note:: + + If both the *temp* and *press* keywords are used in a single + thermo_modify command (or in two separate commands), then the order in + which the keywords are specified is important. Note that a :doc:`pressure compute ` defines its own temperature compute as + an argument when it is specified. The *temp* keyword will override + this (for the pressure compute being used by fix npt), but only if the + *temp* keyword comes after the *press* keyword. If the *temp* keyword + comes before the *press* keyword, then the new pressure compute + specified by the *press* keyword will be unaffected by the *temp* + setting. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +pressure-volume energy, plus the strain energy, if it exists. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +This fix is invoked during :doc:`energy minimization `, but +not for the purpose of adding a contribution to the energy or forces +being minimized. Instead it alters the simulation box geometry as +described above. + +Restrictions +"""""""""""" + + +Only dimensions that are available can be adjusted by this fix. +Non-periodic dimensions are not available. *z*, *xz*, and *yz*, are +not available for 2D simulations. *xy*, *xz*, and *yz* are only +available if the simulation domain is non-orthogonal. The +:doc:`create_box `, :doc:`read data `, and +:doc:`read_restart ` commands specify whether the +simulation box is orthogonal or non-orthogonal (triclinic) and explain +the meaning of the xy,xz,yz tilt factors. + +The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used +for 2D simulations. *scaleyz yes*, *scalexz yes*, and *scalexy yes* options +can only be used if the 2nd dimension in the keyword is periodic, +and if the tilt factor is not coupled to the barostat via keywords +*tri*, *yz*, *xz*, and *xy*. + +Related commands +"""""""""""""""" + +:doc:`fix npt `, :doc:`minimize ` + +Default +""""""" + +The keyword defaults are dilate = all, vmax = 0.0001, nreset = 0. + + +---------- + + +.. _Parrinello1981: + + + +**(Parrinello1981)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_colvars.txt b/doc/_sources/fix_colvars.txt new file mode 100644 index 0000000000..fc7e845dc7 --- /dev/null +++ b/doc/_sources/fix_colvars.txt @@ -0,0 +1,158 @@ +.. index:: fix colvars + +fix colvars command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID colvars configfile keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* colvars = style name of this fix command +* configfile = the configuration file for the colvars module +* keyword = *input* or *output* or *seed* or *tstat* +.. parsed-literal:: + + *input* arg = colvars.state file name or prefix or NULL (default: NULL) + *output* arg = output filename prefix (default: out) + *seed* arg = seed for random number generator (default: 1966) + *unwrap* arg = *yes* or *no* + use unwrapped coordinates in collective variables (default: yes) + *tstat* arg = fix id of a thermostat or NULL (default: NULL) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix mtd all colvars peptide.colvars.inp seed 2122 input peptide.colvars.state output peptide + fix abf all colvars colvars.inp tstat 1 + +Description +""""""""""" + +This fix interfaces LAMMPS to a "collective variables" or "colvars" +module library which allows to calculate potentials of mean force +(PMFs) for any set of colvars, using different sampling methods: +currently implemented are the Adaptive Biasing Force (ABF) method, +metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling +(US) via a flexible harmonic restraint bias. The colvars library is +hosted at `http://colvars.github.io/ `_ + +This documentation describes only the fix colvars command itself and +LAMMPS specific parts of the code. The full documentation of the +colvars library is available as `this supplementary PDF document `_ + +A detailed discussion of the implementation of the portable collective +variable library is in :ref:`(Fiorin) `. Additional information can +be found in :ref:`(Henin) `. + +There are some example scripts for using this package with LAMMPS in the +examples/USER/colvars directory. + + +---------- + + +The only mandatory argument to the fix is the filename to the colvars +input file that contains the input that is independent from the MD +program in which the colvars library has been integrated. + +The *group-ID* entry is ignored. The collective variable module will +always apply to the entire system and there can only be one instance +of the colvars fix at a time. The colvars fix will only communicate +the minimum information necessary and the colvars library supports +multiple, completely independent collective variables, so there is +no restriction to functionaliry by limiting the number of colvars fixes. + +The *input* keyword allows to specify a state file that would contain +the restart information required in order to continue a calculation from +a prerecorded state. Fix colvars records it state in :doc:`binary restart ` +files, so when using the :doc:`read_restart ` command, +this is usually not needed. + +The *output* keyword allows to specify the output prefix. All output +files generated will use this prefix followed by the ".colvars." and +a word like "state" or "traj". + +The *seed* keyword contains the seed for the random number generator +that will be used in the colvars module. + +The *unwrap* keyword controls whether wrapped or unwrapped coordinates +are passed to the colvars library for calculation of the collective +variables and the resulting forces. The default is *yes*, i.e. to use +the image flags to reconstruct the absolute atom positions. +Setting this to *no* will use the current local coordinates that are +wrapped back into the simulation cell at each re-neighboring instead. + +The *tstat* keyword can be either NULL or the label of a thermostating +fix that thermostats all atoms in the fix colvars group. This will be +used to provide the colvars module with the current thermostat target +temperature. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the current status of the colvars module into +:doc:`binary restart files `. This is in addition to the text +mode status file that is written by the colvars module itself and the +kind of information in both files is identical. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change from the biasing force added by the fix +to the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative energy change due to this fix. The scalar value +calculated by this fix is "extensive". + +Restrictions +"""""""""""" + + +This fix is part of the USER-COLVARS package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +There can only be one colvars fix active at a time. Since the interface +communicates only the minimum amount of information and colvars module +itself can handle an arbitrary number of collective variables, this is +not a limitation of functionality. + +Related commands +"""""""""""""""" + +:doc:`fix smd ` + +Default +""""""" + +The default options are input = NULL, output = out, seed = 1966, unwrap yes, +and tstat = NULL. + + +---------- + + +.. _Fiorin: + + + +**(Fiorin)** Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 + +.. _Henin: + + + +**(Henin)** Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, +35-47 (2010) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_deform.txt b/doc/_sources/fix_deform.txt new file mode 100644 index 0000000000..b2a35d8609 --- /dev/null +++ b/doc/_sources/fix_deform.txt @@ -0,0 +1,628 @@ +.. index:: fix deform + +fix deform command +================== + +fix deform/kk command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID deform N parameter args ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* deform = style name of this fix command +* N = perform box deformation every this many timesteps +* one or more parameter/arg pairs may be appended +.. parsed-literal:: + + parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* + *x*, *y*, *z* args = style value(s) + style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* + *final* values = lo hi + lo hi = box boundaries at end of run (distance units) + *delta* values = dlo dhi + dlo dhi = change in box boundaries at end of run (distance units) + *scale* values = factor + factor = multiplicative factor for change in box length at end of run + *vel* value = V + V = change box length at this velocity (distance/time units), + effectively an engineering strain rate + *erate* value = R + R = engineering strain rate (1/time units) + *trate* value = R + R = true strain rate (1/time units) + *volume* value = none = adjust this dim to preserve volume of system + *wiggle* values = A Tp + A = amplitude of oscillation (distance units) + Tp = period of oscillation (time units) + *variable* values = v_name1 v_name2 + v_name1 = variable with name1 for box length change as function of time + v_name2 = variable with name2 for change rate as function of time + *xy*, *xz*, *yz* args = style value + style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* + *final* value = tilt + tilt = tilt factor at end of run (distance units) + *delta* value = dtilt + dtilt = change in tilt factor at end of run (distance units) + *vel* value = V + V = change tilt factor at this velocity (distance/time units), + effectively an engineering shear strain rate + *erate* value = R + R = engineering shear strain rate (1/time units) + *trate* value = R + R = true shear strain rate (1/time units) + *wiggle* values = A Tp + A = amplitude of oscillation (distance units) + Tp = period of oscillation (time units) + *variable* values = v_name1 v_name2 + v_name1 = variable with name1 for tilt change as function of time + v_name2 = variable with name2 for change rate as function of time + +* zero or more keyword/value pairs may be appended +* keyword = *remap* or *flip* or *units* +.. parsed-literal:: + + *remap* value = *x* or *v* or *none* + x = remap coords of atoms in group into deforming box + v = remap velocities of all atoms when they cross periodic boundaries + none = no remapping of x or v + *flip* value = *yes* or *no* + allow or disallow box flips when it becomes highly skewed + *units* value = *lattice* or *box* + lattice = distances are defined in lattice units + box = distances are defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all deform 1 x final 0.0 9.0 z final 0.0 5.0 units box + fix 1 all deform 1 x trate 0.1 y volume z volume + fix 1 all deform 1 xy erate 0.001 remap v + fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0 + +Description +""""""""""" + +Change the volume and/or shape of the simulation box during a dynamics +run. Orthogonal simulation boxes have 3 adjustable parameters +(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 +adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be +adjusted independently and simultaneously by this command. This fix +can be used to perform non-equilibrium MD (NEMD) simulations of a +continuously strained system. See the :doc:`fix nvt/sllod ` and :doc:`compute temp/deform ` commands for more details. + +For the *x*, *y*, *z* parameters, the associated dimension cannot be +shrink-wrapped. For the *xy*, *yz*, *xz* parameters, the associated +2nd dimension cannot be shrink-wrapped. Dimensions not varied by this +command can be periodic or non-periodic. Dimensions corresponding to +unspecified parameters can also be controlled by a :doc:`fix npt ` or :doc:`fix nph ` command. + +The size and shape of the simulation box at the beginning of the +simulation run were either specified by the +:doc:`create_box ` or :doc:`read_data ` or +:doc:`read_restart ` command used to setup the simulation +initially if it is the first run, or they are the values from the end +of the previous run. The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands +specify whether the simulation box is orthogonal or non-orthogonal +(triclinic) and explain the meaning of the xy,xz,yz tilt factors. If +fix deform changes the xy,xz,yz tilt factors, then the simulation box +must be triclinic, even if its initial tilt factors are 0.0. + +As described below, the desired simulation box size and shape at the +end of the run are determined by the parameters of the fix deform +command. Every Nth timestep during the run, the simulation box is +expanded, contracted, or tilted to ramped values between the initial +and final values. + + +---------- + + +For the *x*, *y*, and *z* parameters, this is the meaning of their +styles and values. + +The *final*, *delta*, *scale*, *vel*, and *erate* styles all change +the specified dimension of the box via "constant displacement" which +is effectively a "constant engineering strain rate". This means the +box dimension changes linearly with time from its initial to final +value. + +For style *final*, the final lo and hi box boundaries of a dimension +are specified. The values can be in lattice or box distance units. +See the discussion of the units keyword below. + +For style *delta*, plus or minus changes in the lo/hi box boundaries +of a dimension are specified. The values can be in lattice or box +distance units. See the discussion of the units keyword below. + +For style *scale*, a multiplicative factor to apply to the box length +of a dimension is specified. For example, if the initial box length +is 10, and the factor is 1.1, then the final box length will be 11. A +factor less than 1.0 means compression. + +For style *vel*, a velocity at which the box length changes is +specified in units of distance/time. This is effectively a "constant +engineering strain rate", where rate = V/L0 and L0 is the initial box +length. The distance can be in lattice or box distance units. See +the discussion of the units keyword below. For example, if the +initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then +after 10 psec, the box length will have doubled. After 20 psec, it +will have tripled. + +The *erate* style changes a dimension of the the box at a "constant +engineering strain rate". The units of the specified strain rate are +1/time. See the :doc:`units ` command for the time units +associated with different choices of simulation units, +e.g. picoseconds for "metal" units). Tensile strain is unitless and +is defined as delta/L0, where L0 is the original box length and delta +is the change relative to the original length. The box length L as a +function of time will change as + +.. parsed-literal:: + + L(t) = L0 (1 + erate*dt) + +where dt is the elapsed time (in time units). Thus if *erate* R is +specified as 0.1 and time units are picoseconds, this means the box +length will increase by 10% of its original length every picosecond. +I.e. strain after 1 psec = 0.1, strain after 2 psec = 0.2, etc. R = +-0.01 means the box length will shrink by 1% of its original length +every picosecond. Note that for an "engineering" rate the change is +based on the original box length, so running with R = 1 for 10 +picoseconds expands the box length by a factor of 11 (strain of 10), +which is different that what the *trate* style would induce. + +The *trate* style changes a dimension of the box at a "constant true +strain rate". Note that this is not an "engineering strain rate", as +the other styles are. Rather, for a "true" rate, the rate of change +is constant, which means the box dimension changes non-linearly with +time from its initial to final value. The units of the specified +strain rate are 1/time. See the :doc:`units ` command for the +time units associated with different choices of simulation units, +e.g. picoseconds for "metal" units). Tensile strain is unitless and +is defined as delta/L0, where L0 is the original box length and delta +is the change relative to the original length. + +The box length L as a function of time will change as + +.. parsed-literal:: + + L(t) = L0 exp(trate*dt) + +where dt is the elapsed time (in time units). Thus if *trate* R is +specified as ln(1.1) and time units are picoseconds, this means the +box length will increase by 10% of its current (not original) length +every picosecond. I.e. strain after 1 psec = 0.1, strain after 2 psec += 0.21, etc. R = ln(2) or ln(3) means the box length will double or +triple every picosecond. R = ln(0.99) means the box length will +shrink by 1% of its current length every picosecond. Note that for a +"true" rate the change is continuous and based on the current length, +so running with R = ln(2) for 10 picoseconds does not expand the box +length by a factor of 11 as it would with *erate*, but by a factor of +1024 since the box length will double every picosecond. + +Note that to change the volume (or cross-sectional area) of the +simulation box at a constant rate, you can change multiple dimensions +via *erate* or *trate*. E.g. to double the box volume in a picosecond +picosecond, you could set "x erate M", "y erate M", "z erate M", with +M = pow(2,1/3) - 1 = 0.26, since if each box dimension grows by 26%, +the box volume doubles. Or you could set "x trate M", "y trate M", "z +trate M", with M = ln(1.26) = 0.231, and the box volume would double +every picosecond. + +The *volume* style changes the specified dimension in such a way that +the box volume remains constant while other box dimensions are changed +explicitly via the styles discussed above. For example, "x scale 1.1 +y scale 1.1 z volume" will shrink the z box length as the x,y box +lengths increase, to keep the volume constant (product of x,y,z +lengths). If "x scale 1.1 z volume" is specified and parameter *y* is +unspecified, then the z box length will shrink as x increases to keep +the product of x,z lengths constant. If "x scale 1.1 y volume z +volume" is specified, then both the y,z box lengths will shrink as x +increases to keep the volume constant (product of x,y,z lengths). In +this case, the y,z box lengths shrink so as to keep their relative +aspect ratio constant. + +For solids or liquids, note that when one dimension of the box is +expanded via fix deform (i.e. tensile strain), it may be physically +undesirable to hold the other 2 box lengths constant (unspecified by +fix deform) since that implies a density change. Using the *volume* +style for those 2 dimensions to keep the box volume constant may make +more physical sense, but may also not be correct for materials and +potentials whose Poisson ratio is not 0.5. An alternative is to use +:doc:`fix npt aniso ` with zero applied pressure on those 2 +dimensions, so that they respond to the tensile strain dynamically. + +The *wiggle* style oscillates the specified box length dimension +sinusoidally with the specified amplitude and period. I.e. the box +length L as a function of time is given by + +.. parsed-literal:: + + L(t) = L0 + A sin(2*pi t/Tp) + +where L0 is its initial length. If the amplitude A is a positive +number the box initially expands, then contracts, etc. If A is +negative then the box initially contracts, then expands, etc. The +amplitude can be in lattice or box distance units. See the discussion +of the units keyword below. + +The *variable* style changes the specified box length dimension by +evaluating a variable, which presumably is a function of time. The +variable with *name1* must be an :doc:`equal-style variable ` +and should calculate a change in box length in units of distance. +Note that this distance is in box units, not lattice units; see the +discussion of the *units* keyword below. The formula associated with +variable *name1* can reference the current timestep. Note that it +should return the "change" in box length, not the absolute box length. +This means it should evaluate to 0.0 when invoked on the initial +timestep of the run following the definition of fix deform. It should +evaluate to a value > 0.0 to dilate the box at future times, or a +value < 0.0 to compress the box. + +The variable *name2* must also be an :doc:`equal-style variable ` and should calculate the rate of box length +change, in units of distance/time, i.e. the time-derivative of the +*name1* variable. This quantity is used internally by LAMMPS to reset +atom velocities when they cross periodic boundaries. It is computed +internally for the other styles, but you must provide it when using an +arbitrary variable. + +Here is an example of using the *variable* style to perform the same +box deformation as the *wiggle* style formula listed above, where we +assume that the current timestep = 0. + +.. parsed-literal:: + + variable A equal 5.0 + variable Tp equal 10.0 + variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)" + variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)" + fix 2 all deform 1 x variable v_displace v_rate remap v + +For the *scale*, *vel*, *erate*, *trate*, *volume*, *wiggle*, and +*variable* styles, the box length is expanded or compressed around its +mid point. + + +---------- + + +For the *xy*, *xz*, and *yz* parameters, this is the meaning of their +styles and values. Note that changing the tilt factors of a triclinic +box does not change its volume. + +The *final*, *delta*, *vel*, and *erate* styles all change the shear +strain at a "constant engineering shear strain rate". This means the +tilt factor changes linearly with time from its initial to final +value. + +For style *final*, the final tilt factor is specified. The value +can be in lattice or box distance units. See the discussion of the +units keyword below. + +For style *delta*, a plus or minus change in the tilt factor is +specified. The value can be in lattice or box distance units. See +the discussion of the units keyword below. + +For style *vel*, a velocity at which the tilt factor changes is +specified in units of distance/time. This is effectively an +"engineering shear strain rate", where rate = V/L0 and L0 is the +initial box length perpendicular to the direction of shear. The +distance can be in lattice or box distance units. See the discussion +of the units keyword below. For example, if the initial tilt factor +is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the +tilt factor will be 15 Angstroms. After 2 psec, it will be 25 +Angstroms. + +The *erate* style changes a tilt factor at a "constant engineering +shear strain rate". The units of the specified shear strain rate are +1/time. See the :doc:`units ` command for the time units +associated with different choices of simulation units, +e.g. picoseconds for "metal" units). Shear strain is unitless and is +defined as offset/length, where length is the box length perpendicular +to the shear direction (e.g. y box length for xy deformation) and +offset is the displacement distance in the shear direction (e.g. x +direction for xy deformation) from the unstrained orientation. + +The tilt factor T as a function of time will change as + +.. parsed-literal:: + + T(t) = T0 + L0*erate*dt + +where T0 is the initial tilt factor, L0 is the original length of the +box perpendicular to the shear direction (e.g. y box length for xy +deformation), and dt is the elapsed time (in time units). Thus if +*erate* R is specified as 0.1 and time units are picoseconds, this +means the shear strain will increase by 0.1 every picosecond. I.e. if +the xy shear strain was initially 0.0, then strain after 1 psec = 0.1, +strain after 2 psec = 0.2, etc. Thus the tilt factor would be 0.0 at +time 0, 0.1*ybox at 1 psec, 0.2*ybox at 2 psec, etc, where ybox is the +original y box length. R = 1 or 2 means the tilt factor will increase +by 1 or 2 every picosecond. R = -0.01 means a decrease in shear +strain by 0.01 every picosecond. + +The *trate* style changes a tilt factor at a "constant true shear +strain rate". Note that this is not an "engineering shear strain +rate", as the other styles are. Rather, for a "true" rate, the rate +of change is constant, which means the tilt factor changes +non-linearly with time from its initial to final value. The units of +the specified shear strain rate are 1/time. See the +:doc:`units ` command for the time units associated with +different choices of simulation units, e.g. picoseconds for "metal" +units). Shear strain is unitless and is defined as offset/length, +where length is the box length perpendicular to the shear direction +(e.g. y box length for xy deformation) and offset is the displacement +distance in the shear direction (e.g. x direction for xy deformation) +from the unstrained orientation. + +The tilt factor T as a function of time will change as + +.. parsed-literal:: + + T(t) = T0 exp(trate*dt) + +where T0 is the initial tilt factor and dt is the elapsed time (in +time units). Thus if *trate* R is specified as ln(1.1) and time units +are picoseconds, this means the shear strain or tilt factor will +increase by 10% every picosecond. I.e. if the xy shear strain was +initially 0.1, then strain after 1 psec = 0.11, strain after 2 psec = +0.121, etc. R = ln(2) or ln(3) means the tilt factor will double or +triple every picosecond. R = ln(0.99) means the tilt factor will +shrink by 1% every picosecond. Note that the change is continuous, so +running with R = ln(2) for 10 picoseconds does not change the tilt +factor by a factor of 10, but by a factor of 1024 since it doubles +every picosecond. Note that the initial tilt factor must be non-zero +to use the *trate* option. + +Note that shear strain is defined as the tilt factor divided by the +perpendicular box length. The *erate* and *trate* styles control the +tilt factor, but assume the perpendicular box length remains constant. +If this is not the case (e.g. it changes due to another fix deform +parameter), then this effect on the shear strain is ignored. + +The *wiggle* style oscillates the specified tilt factor sinusoidally +with the specified amplitude and period. I.e. the tilt factor T as a +function of time is given by + +.. parsed-literal:: + + T(t) = T0 + A sin(2*pi t/Tp) + +where T0 is its initial value. If the amplitude A is a positive +number the tilt factor initially becomes more positive, then more +negative, etc. If A is negative then the tilt factor initially +becomes more negative, then more positive, etc. The amplitude can be +in lattice or box distance units. See the discussion of the units +keyword below. + +The *variable* style changes the specified tilt factor by evaluating a +variable, which presumably is a function of time. The variable with +*name1* must be an :doc:`equal-style variable ` and should +calculate a change in tilt in units of distance. Note that this +distance is in box units, not lattice units; see the discussion of the +*units* keyword below. The formula associated with variable *name1* +can reference the current timestep. Note that it should return the +"change" in tilt factor, not the absolute tilt factor. This means it +should evaluate to 0.0 when invoked on the initial timestep of the run +following the definition of fix deform. + +The variable *name2* must also be an :doc:`equal-style variable ` and should calculate the rate of tilt change, +in units of distance/time, i.e. the time-derivative of the *name1* +variable. This quantity is used internally by LAMMPS to reset atom +velocities when they cross periodic boundaries. It is computed +internally for the other styles, but you must provide it when using an +arbitrary variable. + +Here is an example of using the *variable* style to perform the same +box deformation as the *wiggle* style formula listed above, where we +assume that the current timestep = 0. + +.. parsed-literal:: + + variable A equal 5.0 + variable Tp equal 10.0 + variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)" + variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)" + fix 2 all deform 1 xy variable v_displace v_rate remap v + + +---------- + + +All of the tilt styles change the xy, xz, yz tilt factors during a +simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes +are normally bounded by half the distance of the parallel box length. +See the discussion of the *flip* keyword below, to allow this bound to +be exceeded, if desired. + +For example, if xlo = 2 and xhi = 12, then the x box length is 10 and +the xy tilt factor must be between -5 and 5. Similarly, both xz and +yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is +not a limitation, since if the maximum tilt factor is 5 (as in this +example), then configurations with tilt = ..., -15, -5, 5, 15, 25, +... are all equivalent. + +To obey this constraint and allow for large shear deformations to be +applied via the *xy*, *xz*, or *yz* parameters, the following +algorithm is used. If *prd* is the associated parallel box length (10 +in the example above), then if the tilt factor exceeds the accepted +range of -5 to 5 during the simulation, then the box is flipped to the +other limit (an equivalent box) and the simulation continues. Thus +for this example, if the initial xy tilt factor was 0.0 and "xy final +100.0" was specified, then during the simulation the xy tilt factor +would increase from 0.0 to 5.0, the box would be flipped so that the +tilt factor becomes -5.0, the tilt factor would increase from -5.0 to +5.0, the box would be flipped again, etc. The flip occurs 10 times +and the final tilt factor at the end of the simulation would be 0.0. +During each flip event, atoms are remapped into the new box in the +appropriate manner. + +The one exception to this rule is if the 1st dimension in the tilt +factor (x for xy) is non-periodic. In that case, the limits on the +tilt factor are not enforced, since flipping the box in that dimension +does not change the atom positions due to non-periodicity. In this +mode, if you tilt the system to extreme angles, the simulation will +simply become inefficient due to the highly skewed simulation box. + + +---------- + + +Each time the box size or shape is changed, the *remap* keyword +determines whether atom positions are remapped to the new box. If +*remap* is set to *x* (the default), atoms in the fix group are +remapped; otherwise they are not. Note that their velocities are not +changed, just their positions are altered. If *remap* is set to *v*, +then any atom in the fix group that crosses a periodic boundary will +have a delta added to its velocity equal to the difference in +velocities between the lo and hi boundaries. Note that this velocity +difference can include tilt components, e.g. a delta in the x velocity +when an atom crosses the y periodic boundary. If *remap* is set to +*none*, then neither of these remappings take place. + +Conceptually, setting *remap* to *x* forces the atoms to deform via an +affine transformation that exactly matches the box deformation. This +setting is typically appropriate for solids. Note that though the +atoms are effectively "moving" with the box over time, it is not due +to their having a velocity that tracks the box change, but only due to +the remapping. By contrast, setting *remap* to *v* is typically +appropriate for fluids, where you want the atoms to respond to the +change in box size/shape on their own and acquire a velocity that +matches the box change, so that their motion will naturally track the +box without explicit remapping of their coordinates. + +.. note:: + + When non-equilibrium MD (NEMD) simulations are performed using + this fix, the option "remap v" should normally be used. This is + because :doc:`fix nvt/sllod ` adjusts the atom positions + and velocities to induce a velocity profile that matches the changing + box size/shape. Thus atom coordinates should NOT be remapped by fix + deform, but velocities SHOULD be when atoms cross periodic boundaries, + since that is consistent with maintaining the velocity profile already + created by fix nvt/sllod. LAMMPS will warn you if the *remap* setting + is not consistent with fix nvt/sllod. + +.. note:: + + For non-equilibrium MD (NEMD) simulations using "remap v" it is + usually desirable that the fluid (or flowing material, e.g. granular + particles) stream with a velocity profile consistent with the + deforming box. As mentioned above, using a thermostat such as :doc:`fix nvt/sllod ` or :doc:`fix lavgevin ` + (with a bias provided by :doc:`compute temp/deform `), will typically accomplish + that. If you do not use a thermostat, then there is no driving force + pushing the atoms to flow in a manner consistent with the deforming + box. E.g. for a shearing system the box deformation velocity may vary + from 0 at the bottom to 10 at the top of the box. But the stream + velocity profile of the atoms may vary from -5 at the bottom to +5 at + the top. You can monitor these effects using the :doc:`fix ave/spatial `, :doc:`compute temp/deform `, and :doc:`compute temp/profile ` commands. One way to induce + atoms to stream consistent with the box deformation is to give them an + initial velocity profile, via the :doc:`velocity ramp ` + command, that matches the box deformation rate. This also typically + helps the system come to equilibrium more quickly, even if a + thermostat is used. + +.. note:: + + If a :doc:`fix rigid ` is defined for rigid bodies, and + *remap* is set to *x*, then the center-of-mass coordinates of rigid + bodies will be remapped to the changing simulation box. This will be + done regardless of whether atoms in the rigid bodies are in the fix + deform group or not. The velocity of the centers of mass are not + remapped even if *remap* is set to *v*, since :doc:`fix nvt/sllod ` does not currently do anything special + for rigid particles. If you wish to perform a NEMD simulation of + rigid particles, you can either thermostat them independently or + include a background fluid and thermostat the fluid via :doc:`fix nvt/sllod `. + +The *flip* keyword allows the tilt factors for a triclinic box to +exceed half the distance of the parallel box length, as discussed +above. If the *flip* value is set to *yes*, the bound is enforced by +flipping the box when it is exceeded. If the *flip* value is set to +*no*, the tilt will continue to change without flipping. Note that if +you apply large deformations, this means the box shape can tilt +dramatically LAMMPS will run less efficiently, due to the large volume +of communication needed to acquire ghost atoms around a processor's +irregular-shaped sub-domain. For extreme values of tilt, LAMMPS may +also lose atoms and generate an error. + +The *units* keyword determines the meaning of the distance units used +to define various arguments. A *box* value selects standard distance +units as defined by the :doc:`units ` command, e.g. Angstroms for +units = real or metal. A *lattice* value means the distance units are +in lattice spacings. The :doc:`lattice ` command must have +been previously used to define the lattice spacing. Note that the +units choice also affects the *vel* style parameters since it is +defined in terms of distance/time. Also note that the units keyword +does not affect the *variable* style. You should use the *xlat*, +*ylat*, *zlat* keywords of the :doc:`thermo_style ` +command if you want to include lattice spacings in a variable formula. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. + +This fix can perform deformation over multiple runs, using the *start* +and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +You cannot apply x, y, or z deformations to a dimension that is +shrink-wrapped via the :doc:`boundary ` comamnd. + +You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in +xy) that is shrink-wrapped via the :doc:`boundary ` comamnd. + +Related commands +"""""""""""""""" + +:doc:`change_box ` + +Default +""""""" + +The option defaults are remap = x, flip = yes, and units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_deposit.txt b/doc/_sources/fix_deposit.txt new file mode 100644 index 0000000000..e90855c3fc --- /dev/null +++ b/doc/_sources/fix_deposit.txt @@ -0,0 +1,293 @@ +.. index:: fix deposit + +fix deposit command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID deposit N type M seed keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* deposit = style name of this fix command +* N = # of atoms or molecules to insert +* type = atom type to assign to inserted atoms (offset for moleclue insertion) +* M = insert a single atom or molecule every M steps +* seed = random # seed (positive integer) +* one or more keyword/value pairs may be appended to args +* keyword = *region* or *id* or *global* or *local* or *near* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units* +.. parsed-literal:: + + *region* value = region-ID + region-ID = ID of region to use as insertion volume + *id* value = *max* or *next* + max = atom ID for new atom(s) is max ID of all current atoms plus one + next = atom ID for new atom(s) increments by one for every deposition + *global* values = lo hi + lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units) + *local* values = lo hi delta + lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units) + delta = lateral distance within which a neighbor is considered "nearby" (distance units) + *near* value = R + R = only insert atom/molecule if further than R from existing particles (distance units) + *attempt* value = Q + Q = attempt a single insertion up to Q times + *rate* value = V + V = z velocity (y in 2d) at which insertion volume moves (velocity units) + *vx* values = vxlo vxhi + vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units) + *vy* values = vylo vyhi + vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units) + *vz* values = vzlo vzhi + vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units) + *target* values = tx ty tz + tx,ty,tz = location of target point (distance units) + *mol* value = template-ID + template-ID = ID of molecule template specified in a separate :doc:`molecule ` command + *molfrac* values = f1 f2 ... fN + f1 to fN = relative probability of creating each of N molecules in template-ID + *rigid* value = fix-ID + fix-ID = ID of :doc:`fix rigid/small ` command + *shake* value = fix-ID + fix-ID = ID of :doc:`fix shake ` command + *units* value = *lattice* or *box* + lattice = the geometry is defined in lattice units + box = the geometry is defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box + fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8 + fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice + +Description +""""""""""" + +Insert a single atom or molecule into the simulation domain every M +timesteps until N atoms or molecules have been inserted. This is +useful for simulating deposition onto a surface. For the remainder of +this doc page, a single inserted atom or molecule is referred to as a +"particle". + +If inserted particles are individual atoms, they are assigned the +specified atom type. If they are molecules, the type of each atom in +the inserted molecule is specified in the file read by the +:doc:`molecule ` command, and those values are added to the +specified atom type. E.g. if the file specifies atom types 1,2,3, and +those are the atom types you want for inserted molecules, then specify +*type* = 0. If you specify *type* = 2, the in the inserted molecule +will have atom types 3,4,5. + +All atoms in the inserted particle are assigned to two groups: the +default group "all" and the group specified in the fix deposit command +(which can also be "all"). + +If you are computing temperature values which include inserted +particles, you will want to use the +:doc:`compute_modify ` dynamic option, which insures the +current number of atoms is used as a normalizing factor each time the +temperature is computed. + +Care must be taken that inserted particles are not too near existing +atoms, using the options described below. When inserting particles +above a surface in a non-periodic box (see the +:doc:`boundary ` command), the possibility of a particle +escaping the surface and flying upward should be considered, since the +particle may be lost or the box size may grow infinitely large. A +:doc:`fix wall/reflect ` command can be used to +prevent this behavior. Note that if a shrink-wrap boundary is used, +it is OK to insert the new particle outside the box, however the box +will immediately be expanded to include the new particle. When +simulating a sputtering experiment it is probably more realistic to +ignore those atoms using the :doc:`thermo_modify ` +command with the *lost ignore* option and a fixed +:doc:`boundary `. + +The fix deposit command must use the *region* keyword to define an +insertion volume. The specified region must have been previously +defined with a :doc:`region ` command. It must be defined with +side = *in*. + +.. note:: + + LAMMPS checks that the specified region is wholly inside the + simulation box. It can do this correctly for orthonormal simulation + boxes. However for :ref:`triclinic boxes `, it + only tests against the larger orthonormal box that bounds the tilted + simulation box. If the specified region includes volume outside the + tilted box, then an insertion will likely fail, leading to a "lost + atoms" error. Thus for triclinic boxes you should insure the + specified region is wholly inside the simulation box. + +Individual atoms are inserted, unless the *mol* keyword is used. It +specifies a *template-ID* previously defined using the +:doc:`molecule ` command, which reads files that define one or +more molecules. The coordinates, atom types, charges, etc, as well as +any bond/angle/etc and special neighbor information for the molecule +can be specified in the molecule file. See the +:doc:`molecule ` command for details. The only settings +required to be in each file are the coordinates and types of atoms in +the molecule. + +If the molecule template contains more than one molecule, the relative +probability of depositing each molecule can be specified by the +*molfrac* keyword. N relative probablities, each from 0.0 to 1.0, are +specified, where N is the number of molecules in the template. Each +time a molecule is deposited, a random number is used to sample from +the list of relative probabilities. The N values must sum to 1.0. + +If you wish to insert molecules via the *mol* keyword, that will be +treated as rigid bodies, use the *rigid* keyword, specifying as its +value the ID of a separate :doc:`fix rigid/small ` +command which also appears in your input script. + +If you wish to insert molecules via the *mol* keyword, that will have +their bonds or angles constrained via SHAKE, use the *shake* keyword, +specifying as its value the ID of a separate :doc:`fix shake ` command which also appears in your input script. + +Each timestep a particle is inserted, the coordinates for its atoms +are chosen as follows. For insertion of individual atoms, the +"position" referred to in the following description is the coordinate +of the atom. For insertion of molecule, the "position" is the +geometric center of the molecule; see the :doc:`molecule ` doc +page for details. A random rotation of the molecule around its center +point is performed, which determines the coordinates all the +individual atoms. + +A random position within the region insertion volume is generated. If +neither the *global* or *local* keyword is used, the random position +is the trial position. If the *global* keyword is used, the random +x,y values are used, but the z position of the new particle is set +above the highest current atom in the simulation by a distance +randomly chosen between lo/hi. (For a 2d simulation, this is done for +the y position.) If the *local* keyword is used, the z position is +set a distance between lo/hi above the highest current atom in the +simulation that is "nearby" the chosen x,y position. In this context, +"nearby" means the lateral distance (in x,y) between the new and old +particles is less than the *delta* setting. + +Once a trial x,y,z position has been selected, the insertion is only +performed if no current atom in the simulation is within a distance R +of any atom in the new particle, including the effect of periodic +boundary conditions if applicable. R is defined by the *near* +keyword. Note that the default value for R is 0.0, which will allow +atoms to strongly overlap if you are inserting where other atoms are +present. This distance test is performed independently for each atom +in an inserted molecule, based on the randomly rotated configuration +of the molecule. If this test fails, a new random position within the +insertion volume is chosen and another trial is made. Up to Q +attempts are made. If the particle is not successfully inserted, +LAMMPS prints a warning message. + +.. note:: + + If you are inserting finite size particles or a molecule or + rigid body consisting of finite-size particles, then you should + typically set R larger than the distance at which any inserted + particle may overlap with either a previouly inserted particle or an + existing particle. LAMMPS will issue a warning if R is smaller than + this value, based on the radii of existing and inserted particles. + +The *rate* option moves the insertion volume in the z direction (3d) +or y direction (2d). This enables particles to be inserted from a +successively higher height over time. Note that this parameter is +ignored if the *global* or *local* keywords are used, since those +options choose a z-coordinate for insertion independently. + +The vx, vy, and vz components of velocity for the inserted particle +are set using the values specified for the *vx*, *vy*, and *vz* +keywords. Note that normally, new particles should be a assigned a +negative vertical velocity so that they move towards the surface. For +molecules, the same velocity is given to every particle (no rotation +or bond vibration). + +If the *target* option is used, the velocity vector of the inserted +particle is changed so that it points from the insertion position +towards the specified target point. The magnitude of the velocity is +unchanged. This can be useful, for example, for simulating a +sputtering process. E.g. the target point can be far away, so that +all incident particles strike the surface as if they are in an +incident beam of particles at a prescribed angle. + +The *id* keyword determines how atom IDs and molecule IDs are assigned +to newly deposited particles. Molecule IDs are only assigned if +molecules are being inserted. For the *max* setting, the atom and +molecule IDs of all current atoms are checked. Atoms in the new +particle are assigned IDs starting with the current maximum plus one. +If a molecule is inserted it is assigned an ID = current maximum plus +one. This means that if particles leave the system, the new IDs may +replace the lost ones. For the *next* setting, the maximum ID of any +atom and molecule is stored at the time the fix is defined. Each time +a new particle is added, this value is incremented to assign IDs to +the new atom(s) or molecule. Thus atom and molecule IDs for deposited +particles will be consecutive even if particles leave the system over +time. + +The *units* keyword determines the meaning of the distance units used +for the other deposition parameters. A *box* value selects standard +distance units as defined by the :doc:`units ` command, +e.g. Angstroms for units = real or metal. A *lattice* value means the +distance units are in lattice spacings. The :doc:`lattice ` +command must have been previously used to define the lattice spacing. +Note that the units choice affects all the keyword values that have +units of distance or velocity. + +.. note:: + + If you are monitoring the temperature of a system where the atom + count is changing due to adding particles, you typically should use + the :doc:`compute_modify dynamic yes ` command for the + temperature compute you are using. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the deposition to :doc:`binary restart files `. This includes information about how many +particles have been depositied, the random number generator seed, the +next timestep for deposition, etc. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +None of the :doc:`fix_modify ` options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various :ref:`output commands `. No +parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The specified insertion region cannot be a "dynamic" region, as +defined by the :doc:`region ` command. + +Related commands +"""""""""""""""" + +:doc:`fix_pour `, :doc:`region ` + +Default +""""""" + +Insertions are performed for individual atoms, i.e. no *mol* setting +is defined. If the *mol* keyword is used, the default for *molfrac* +is an equal probabilities for all molecules in the template. +Additional option defaults are id = max, delta = 0.0, near = 0.0, +attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0, +and units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_drag.txt b/doc/_sources/fix_drag.txt new file mode 100644 index 0000000000..1344615d6e --- /dev/null +++ b/doc/_sources/fix_drag.txt @@ -0,0 +1,70 @@ +.. index:: fix drag + +fix drag command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID drag x y z fmag delta + +* ID, group-ID are documented in :doc:`fix ` command +* drag = style name of this fix command +* x,y,z = coord to drag atoms towards +* fmag = magnitude of force to apply to each atom (force units) +* delta = cutoff distance inside of which force is not applied (distance units) + +Examples +"""""""" + +.. parsed-literal:: + + fix center small-molecule drag 0.0 10.0 0.0 5.0 2.0 + +Description +""""""""""" + +Apply a force to each atom in a group to drag it towards the point +(x,y,z). The magnitude of the force is specified by fmag. If an atom +is closer than a distance delta to the point, then the force is not +applied. + +Any of the x,y,z values can be specified as NULL which means do not +include that dimension in the distance calculation or force +application. + +This command can be used to steer one or more atoms to a new location +in the simulation. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global 3-vector of forces, which can be accessed +by various :ref:`output commands `. This is the +total force on the group of atoms by the drag force. The vector +values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix spring `, :doc:`fix spring/self `, +:doc:`fix spring/rg `, :doc:`fix smd ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_drude.txt b/doc/_sources/fix_drude.txt new file mode 100644 index 0000000000..4cc41f7913 --- /dev/null +++ b/doc/_sources/fix_drude.txt @@ -0,0 +1,57 @@ +.. index:: fix drude + +fix drude command +================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID drude flag1 flag2 ... flagN + +* ID, group-ID are documented in :doc:`fix ` command +* drude = style name of this fix command +* flag1 flag2 ... flagN = Drude flag for each atom type (1 to N) in the system + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all drude 1 1 0 1 0 2 2 2 + fix 1 all drude C C N C N D D D + +Description +""""""""""" + +Assign each atom type in the system to be one of 3 kinds of atoms +within the Drude polarization model. This fix is designed to be +used with the :doc:`thermalized Drude oscillator model `. Polarizable models in LAMMPS +are described in :ref:`this Section `. + +The three possible types can be designated with an integer (0,1,2) +or capital letter (N,C,D): + +* 0 or N = non-polarizable atom (not part of Drude model) +* 1 or C = Drude core +* 2 or D = Drude electron + +Restrictions +"""""""""""" + + +This fix should be invoked before any other commands that implement +the Drude oscillator model, such as :doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole `. + +Related commands +"""""""""""""""" + +:doc:`fix langevin/drude `, :doc:`fix drude/transform `, :doc:`compute temp/drude `, :doc:`pair_style thole ` + +**Default:** None + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_drude_transform.txt b/doc/_sources/fix_drude_transform.txt new file mode 100644 index 0000000000..4a6a641bbc --- /dev/null +++ b/doc/_sources/fix_drude_transform.txt @@ -0,0 +1,227 @@ +.. index:: fix drude/transform/direct + +fix drude/transform/direct command +================================== + +fix drude/transform/inverse command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = *drude/transform/direct* or *drude/transform/inverse* + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 all drude/transform/direct + fix 1 all drude/transform/inverse + +Description +""""""""""" + +Transform the coordinates of Drude oscillators from real to reduced +and back for thermalizing the Drude oscillators as described in +:ref:`(Lamoureux) ` using a Nose-Hoover thermostat. This fix is +designed to be used with the :doc:`thermalized Drude oscillator model `. Polarizable models in LAMMPS are +described in :ref:`this Section `. + +Drude oscillators are a pair of atoms representing a single +polarizable atom. Ideally, the mass of Drude particles would vanish +and their positions would be determined self-consistently by iterative +minimization of the energy, the cores' positions being fixed. It is +however more efficient and it yields comparable results, if the Drude +oscillators (the motion of the Drude particle relative to the core) +are thermalized at a low temperature. In that case, the Drude +particles need a small mass. + +The thermostats act on the reduced degrees of freedom, which are +defined by the following equations. Note that in these equations +upper case denotes atomic or center of mass values and lower case +denotes Drude particle or dipole values. Primes denote the transformed +(reduced) values, while bare letters denote the original values. + +Masses: + +.. math:: + + \begin{equation} M' = M + m \end{equation} + + +.. math:: + + \begin{equation} m' = \frac {M\, m } {M'} \end{equation} + +Positions: + +.. math:: + + \begin{equation} X' = \frac {M\, X + m\, x} {M'}\end{equation} + + +.. math:: + + \begin{equation} x' = x - X \end{equation} + +Velocities: + +.. math:: + + \begin{equation} V' = \frac {M\, V + m\, v} {M'}\end{equation} + + +.. math:: + + \begin{equation} v' = v - V \end{equation} + +Forces: + +.. math:: + + \begin{equation} F' = F + f \end{equation} + + +.. math:: + + \begin{equation} f' = \frac { M\, f - m\, F} {M'}\end{equation} + +This transform conserves the total kinetic energy + +.. math:: + + \begin{equation} \frac 1 2 \, (M\, V^2\ + m\, v^2) + = \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) \end{equation} + +and the virial defined with absolute positions + +.. math:: + + \begin{equation} X\, F + x\, f = X'\, F' + x'\, f' \end{equation} + + +---------- + + +This fix requires each atom know whether it is a Drude particle or +not. You must therefore use the :doc:`fix drude ` command to +specify the Drude status of each atom type. + +.. note:: + + only the Drude core atoms need to be in the group specified for + this fix. A Drude electron will be transformed together with its core + even if it is not itself in the group. It is safe to include Drude + electrons or non-polarizable atoms in the group. The non-polarizable + atoms will simply not be transformed. + + +---------- + + +This fix does NOT perform time integration. It only transform masses, +coordinates, velocities and forces. Thus you must use separate time +integration fixes, like :doc:`fix nve ` or :doc:`fix npt ` to actually update the velocities and positions of +atoms. In order to thermalize the reduced degrees of freedom at +different temperatures, two Nose-Hoover thermostats must be defined, +acting on two distinct groups. + +.. note:: + + The *fix drude/transform/direct* command must appear before any + Nose-Hoover thermostating fixes. The *fix drude/transform/inverse* + command must appear after any Nose-Hoover thermostating fixes. + +Example: + +.. parsed-literal:: + + fix fDIRECT all drude/transform/direct + fix fNVT gCORES nvt temp 300.0 300.0 100 + fix fNVT gDRUDES nvt temp 1.0 1.0 100 + fix fINVERSE all drude/transform/inverse + compute TDRUDE all temp/drude + thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2] + +In this example, *gCORES* is the group of the atom cores and *gDRUDES* +is the group of the Drude particles (electrons). The centers of mass +of the Drude oscillators will be thermostated at 300.0 and the +internal degrees of freedom will be thermostated at 1.0. The +temperatures of cores and Drude particles, in center-of-mass and +relative coordinates, are calculated using :doc:`compute temp/drude ` + +In addition, if you want to use a barostat to simulate a system at +constant pressure, only one of the Nose-Hoover fixes must be *npt*, +the other one should be *nvt*. You must add a *compute temp/com* and a +*fix_modify* command so that the temperature of the *npt* fix be just +that of its group (the Drude cores) but the pressure be the overall +pressure *thermo_press*. + +Example: + +.. parsed-literal:: + + compute cTEMP_CORE gCORES temp/com + fix fDIRECT all drude/transform/direct + fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500 + fix_modify fNPT temp cTEMP_CORE press thermo_press + fix fNVT gDRUDES nvt temp 5.0 5.0 100 + fix fINVERSE all drude/transform/inverse + +In this example, *gCORES* is the group of the atom cores and *gDRUDES* +is the group of the Drude particles. The centers of mass of the Drude +oscillators will be thermostated at 298.0 and the internal degrees of +freedom will be thermostated at 5.0. The whole system will be +barostated at 1.0. + +In order to avoid the flying ice cube problem (irreversible transfer +of linear momentum to the center of mass of the system), you may need +to add a *fix momentum* command: + +.. parsed-literal:: + + fix fMOMENTUM all momentum 100 linear 1 1 1 + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix drude `, +:doc:`fix langevin/drude `, +:doc:`compute temp/drude `, +:doc:`pair_style thole ` + +**Default:** none + + +---------- + + +.. _Lamoureux: + + + +**(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_dt_reset.txt b/doc/_sources/fix_dt_reset.txt new file mode 100644 index 0000000000..32be807448 --- /dev/null +++ b/doc/_sources/fix_dt_reset.txt @@ -0,0 +1,103 @@ +.. index:: fix dt/reset + +fix dt/reset command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID dt/reset N Tmin Tmax Xmax keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* dt/reset = style name of this fix command +* N = recompute dt every N timesteps +* Tmin = minimum dt allowed which can be NULL (time units) +* Tmax = maximum dt allowed which can be NULL (time units) +* Xmax = maximum distance for an atom to move in one timestep (distance units) +* zero or more keyword/value pairs may be appended +* keyword = *units* + +.. parsed-literal:: + + *units* value = *lattice* or *box* + lattice = Xmax is defined in lattice units + box = Xmax is defined in simulation box units + +Examples +"""""""" + +.. parsed-literal:: + + fix 5 all dt/reset 10 1.0e-5 0.01 0.1 + fix 5 all dt/reset 10 0.01 2.0 0.2 units box + +Description +""""""""""" + +Reset the timestep size every N steps during a run, so that no atom +moves further than Xmax, based on current atom velocities and forces. +This can be useful when starting from a configuration with overlapping +atoms, where forces will be large. Or it can be useful when running +an impact simulation where one or more high-energy atoms collide with +a solid, causing a damage cascade. + +This fix overrides the timestep size setting made by the +:doc:`timestep ` command. The new timestep size *dt* is +computed in the following manner. + +For each atom, the timestep is computed that would cause it to +displace *Xmax* on the next integration step, as a function of its +current velocity and force. Since performing this calculation exactly +would require the solution to a quartic equation, a cheaper estimate +is generated. The estimate is conservative in that the atom's +displacement is guaranteed not to exceed *Xmax*, though it may be +smaller. + +Given this putative timestep for each atom, the minimum timestep value +across all atoms is computed. Then the *Tmin* and *Tmax* bounds are +applied, if specified. If one (or both) is specified as NULL, it is +not applied. + +When the :doc:`run style ` is *respa*, this fix resets the +outer loop (largest) timestep, which is the same timestep that the +:doc:`timestep ` command sets. + +Note that the cumulative simulation time (in time units), which +accounts for changes in the timestep size as a simulation proceeds, +can be accessed by the :doc:`thermo_style time ` keyword. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar stores +the last timestep on which the timestep was reset to a new value. + +The scalar value calculated by this fix is "intensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`timestep ` + +Default +""""""" + +The option defaults is units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_efield.txt b/doc/_sources/fix_efield.txt new file mode 100644 index 0000000000..4337e8d29c --- /dev/null +++ b/doc/_sources/fix_efield.txt @@ -0,0 +1,175 @@ +.. index:: fix efield + +fix efield command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID efield ex ey ez keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* efield = style name of this fix command +* ex,ey,ez = E-field component values (electric field units) +* any of ex,ey,ez can be a variable (see below) +* zero or more keyword/value pairs may be appended to args +* keyword = *region* or *energy* +.. parsed-literal:: + + *region* value = region-ID + region-ID = ID of region atoms must be in to have added force + *energy* value = v_name + v_name = variable with name that calculates the potential energy of each atom in the added E-field + + + +Examples +"""""""" + +.. parsed-literal:: + + fix kick external-field efield 1.0 0.0 0.0 + fix kick external-field efield 0.0 0.0 v_oscillate + +Description +""""""""""" + +Add a force F = qE to each charged atom in the group due to an +external electric field being applied to the system. If the system +contains point-dipoles, also add a torque on the dipoles due to the +external electric field. + +For charges, any of the 3 quantities defining the E-field components +can be specified as an equal-style or atom-style +:doc:`variable `, namely *ex*, *ey*, *ez*. If the value is a +variable, it should be specified as v_name, where name is the variable +name. In this case, the variable will be evaluated each timestep, and +its value used to determine the E-field component. + +For point-dipoles, equal-style variables can be used, but atom-style +variables are not currently supported, since they imply a spatial +gradient in the electric field which means additional terms with +gradients of the field are required for the force and torque on +dipoles. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent E-field. + +Atom-style variables can specify the same formulas as equal-style +variables but can also include per-atom values, such as atom +coordinates. Thus it is easy to specify a spatially-dependent E-field +with optional time-dependence as well. + +If the *region* keyword is used, the atom must also be in the +specified geometric :doc:`region ` in order to have force added +to it. + + +---------- + + +Adding a force or torque to atoms implies a change in their potential +energy as they move or rotate due to the applied E-field. + +For dynamics via the "run" command, this energy can be optionally +added to the system's potential energy for thermodynamic output (see +below). For energy minimization via the "minimize" command, this +energy must be added to the system's potential energy to formulate a +self-consistent minimization problem (see below). + +The *energy* keyword is not allowed if the added field is a constant +vector (ex,ey,ez), with all components defined as numeric constants +and not as variables. This is because LAMMPS can compute the energy +for each charged particle directly as E = -x dot qE = -q (x*ex + y*ey ++ z*ez), so that -Grad(E) = F. Similarly for point-dipole particles +the energy can be computed as E = -mu dot E = -(mux*ex + muy*ey + +muz*ez). + +The *energy* keyword is optional if the added force is defined with +one or more variables, and if you are performing dynamics via the +:doc:`run ` command. If the keyword is not used, LAMMPS will set +the energy to 0.0, which is typically fine for dynamics. + +The *energy* keyword is required if the added force is defined with +one or more variables, and you are performing energy minimization via +the "minimize" command for charged particles. It is not required for +point-dipoles, but a warning is issued since the minimizer in LAMMPS +does not rotate dipoles, so you should not expect to be able to +minimize the orientation of dipoles in an applied electric field. + +The *energy* keyword specifies the name of an atom-style +:doc:`variable ` which is used to compute the energy of each +atom as function of its position. Like variables used for *ex*, *ey*, +*ez*, the energy variable is specified as v_name, where name is the +variable name. + +Note that when the *energy* keyword is used during an energy +minimization, you must insure that the formula defined for the +atom-style :doc:`variable ` is consistent with the force +variable formulas, i.e. that -Grad(E) = F. For example, if the force +due to the electric field were a spring-like F = kx, then the energy +formula should be E = -0.5kx^2. If you don't do this correctly, the +minimization will not converge properly. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the potential "energy" inferred by the added force due to +the electric field to the system's potential energy as part of +:doc:`thermodynamic output `. This is a fictitious +quantity but is needed so that the :doc:`minimize ` command +can include the forces added by this fix in a consistent manner. +I.e. there is a decrease in potential energy when atoms move in the +direction of the added force due to the electric field. + +This fix computes a global scalar and a global 3-vector of forces, +which can be accessed by various :ref:`output commands `. The scalar is the potential +energy discussed above. The vector is the total force added to the +group of atoms. The scalar and vector values calculated by this fix +are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. You should not +specify force components with a variable that has time-dependence for +use with a minimizer, since the minimizer increments the timestep as +the iteration count during the minimization. + +.. note:: + + If you want the fictitious potential energy associated with the + added forces to be included in the total potential energy of the + system (the quantity being minimized), you MUST enable the + :doc:`fix_modify ` *energy* option for this fix. + +Restrictions +"""""""""""" + + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix addforce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_enforce2d.txt b/doc/_sources/fix_enforce2d.txt new file mode 100644 index 0000000000..98b0cbc4bf --- /dev/null +++ b/doc/_sources/fix_enforce2d.txt @@ -0,0 +1,80 @@ +.. index:: fix enforce2d + +fix enforce2d command +===================== + +fix enforce2d/cuda command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID enforce2d + +* ID, group-ID are documented in :doc:`fix ` command +* enforce2d = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 5 all enforce2d + +Description +""""""""""" + +Zero out the z-dimension velocity and force on each atom in the group. +This is useful when running a 2d simulation to insure that atoms do +not move from their initial z coordinate. + + +---------- + + +Styles with a *cuda* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +These accelerated styles are part of the USER-CUDA package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_eos_cv.txt b/doc/_sources/fix_eos_cv.txt new file mode 100644 index 0000000000..70e1d21e94 --- /dev/null +++ b/doc/_sources/fix_eos_cv.txt @@ -0,0 +1,74 @@ +.. index:: fix eos/cv + +fix eos/cv command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID eos/cv cv + +* ID, group-ID are documented in :doc:`fix ` command +* eos/cv = style name of this fix command +* cv = constant-volume heat capacity (energy/temperature units) + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all eos/cv 0.01 + +Description +""""""""""" + +Fix *eos/cv* applies a mesoparticle equation of state to relate the +particle internal energy (u_i) to the particle internal temperature +(dpdTheta_i). The *eos/cv* mesoparticle equation of state requires +the constant-volume heat capacity, and is defined as follows: + +.. image:: Eqs/fix_eos-cv.jpg + :align: center + +where Cv is the constant-volume heat capacity, u_cond is the internal +conductive energy, and u_mech is the internal mechanical energy. Note +that alternative definitions of the mesoparticle equation of state are +possible. + + +---------- + + +Restrictions +"""""""""""" + + +The fix *eos/cv* is only available if LAMMPS is built with the +USER-DPD package. + +Related commands +"""""""""""""""" + +:doc:`fix shardlow `, :doc:`pair dpd/fdt ` + +**Default:** none + + +---------- + + +.. _Larentzos: + + + +**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and +W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative +Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research +Laboratory, Aberdeen Proving Ground, MD (2014). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_eos_table.txt b/doc/_sources/fix_eos_table.txt new file mode 100644 index 0000000000..854409302c --- /dev/null +++ b/doc/_sources/fix_eos_table.txt @@ -0,0 +1,130 @@ +.. index:: fix eos/table + +fix eos/table command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID eos/table style file N keyword + +* ID, group-ID are documented in :doc:`fix ` command +* eos/table = style name of this fix command +* style = *linear* = method of interpolation +* file = filename containing the tabulated equation of state +* N = use N values in *linear* tables +* keyword = name of table keyword correponding to table file + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all eos/table linear eos.table 100000 KEYWORD + +Description +""""""""""" + +Fix *eos/table* applies a tabulated mesoparticle equation of state to +relate the particle internal energy (u_i) to the particle internal +temperature (dpdTheta_i). + +Fix *eos/table* creates interpolation tables of length *N* from +internal energy values listed in a file as a function of internal +temperature. + +The interpolation tables are created by fitting cubic splines to the +file values and interpolating energy values at each of *N* internal +temperatures, and vice-versa. During a simulation, these tables are +used to interpolate internal energy or temperature values as needed. +The interpolation is done with the *linear* style. + +For the *linear* style, the internal temperature is used to find 2 +surrounding table values from which an internal energy is computed by +linear interpolation, and vice-versa. + +The filename specifies a file containing tabulated internal +temperature and internal energy values. The keyword specifies a +section of the file. The format of this file is described below. + + +---------- + + +The format of a tabulated file is as follows (without the +parenthesized comments): + +.. parsed-literal:: + + # EOS TABLE (one or more comment or blank lines) + +.. parsed-literal:: + + KEYWORD (keyword is first text on line) + N 500 (N parameter) + (blank) + 1 1.00 0.000 (index, internal temperature, internal energy) + 2 1.02 0.001 + ... + 500 10.0 0.500 + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the fix command. + +The next line lists the number of table entries. The parameter "N" is +required and its value is the number of table entries that follow. +Note that this may be different than the *N* specified in the :doc:`fix eos/table ` command. Let Ntable = *N* in the fix +command, and Nfile = "N" in the tabulated file. What LAMMPS does is a +preliminary interpolation by creating splines using the Nfile +tabulated values as nodal points. It uses these to interpolate as +needed to generate energy and temperature values at Ntable different +points. The resulting tables of length Ntable are then used as +described above, when computing energy and temperature relationships. +This means that if you want the interpolation tables of length Ntable +to match exactly what is in the tabulated file (with effectively no +preliminary interpolation), you should set Ntable = Nfile. + +Following a blank line, the next N lines list the tabulated values. +On each line, the 1st value is the index from 1 to N, the 2nd value is +the internal temperature (in temperature units), the 3rd value is the +internal energy (in energy units). + +Note that the internal temperature and internal energy values must +increase from one line to the next. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds +one that matches the specified keyword. + + +---------- + + +Restrictions +"""""""""""" + + +The fix *eos/table* is only available if LAMMPS is built with the +USER-DPD package. + +The equation of state must be a monotonically increasing function. + +An exit error will occur if the internal temperature or internal +energies are not within the table cutoffs. + +Related commands +"""""""""""""""" + +:doc:`fix shardlow `, :doc:`pair dpd/fdt ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_evaporate.txt b/doc/_sources/fix_evaporate.txt new file mode 100644 index 0000000000..f9634d2be7 --- /dev/null +++ b/doc/_sources/fix_evaporate.txt @@ -0,0 +1,110 @@ +.. index:: fix evaporate + +fix evaporate command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID evaporate N M region-ID seed + +* ID, group-ID are documented in :doc:`fix ` command +* evaporate = style name of this fix command +* N = delete atoms every this many timesteps +* M = number of atoms to delete each time +* region-ID = ID of region within which to perform deletions +* seed = random number seed to use for choosing atoms to delete +* zero or more keyword/value pairs may be appended +.. parsed-literal:: + + keyword = *molecule* + *molecule* value = *no* or *yes* + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 solvent evaporate 1000 10 surface 49892 + fix 1 solvent evaporate 1000 10 surface 38277 molecule yes + +Description +""""""""""" + +Remove M atoms from the simulation every N steps. This can be used, +for example, to model evaporation of solvent particles or moleclues +(i.e. drying) of a system. Every N steps, the number of atoms in the +fix group and within the specifed region are counted. M of these are +chosen at random and deleted. If there are less than M eligible +particles, then all of them are deleted. + +If the setting for the *molecule* keyword is *no*, then only single +atoms are deleted. In this case, you should insure you do not delete +only a portion of a molecule (only some of its atoms), or LAMMPS will +soon generate an error when it tries to find those atoms. LAMMPS will +warn you if any of the atoms eligible for deletion have a non-zero +molecule ID, but does not check for this at the time of deletion. + +If the setting for the *molecule* keyword is *yes*, then when an atom +is chosen for deletion, the entire molecule it is part of is deleted. +The count of deleted atoms is incremented by the number of atoms in +the molecule, which may make it exceed *M*. If the molecule ID of the +chosen atom is 0, then it is assumed to not be part of a molecule, and +just the single atom is deleted. + +As an example, if you wish to delete 10 water molecules every *N* +steps, you should set *M* to 30. If only the water's oxygen atoms +were in the fix group, then two hydrogen atoms would be deleted when +an oxygen atom is selected for deletion, whether the hydrogens are +inside the evaporation region or not. + +Note that neighbor lists are re-built on timesteps that atoms are +removed. Thus you should not remove atoms too frequently or you will +incur overhead due to the cost of building neighbor lists. + +.. note:: + + If you are monitoring the temperature of a system where the atom + count is changing due to evaporation, you typically should use the + :doc:`compute_modify dynamic yes ` command for the + temperature compute you are using. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global scalar, which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative number of deleted atoms. The scalar value calculated by +this fix is "intensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix deposit ` + +Default +""""""" + +The option defaults are molecule = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_external.txt b/doc/_sources/fix_external.txt new file mode 100644 index 0000000000..253c357a48 --- /dev/null +++ b/doc/_sources/fix_external.txt @@ -0,0 +1,179 @@ +.. index:: fix external + +fix external command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID external mode args + +* ID, group-ID are documented in :doc:`fix ` command +* external = style name of this fix command +* mode = *pf/callback* or *pf/array* +.. parsed-literal:: + + *pf/callback* args = Ncall Napply + Ncall = make callback every Ncall steps + Napply = apply callback forces every Napply steps + *pf/array* args = Napply + Napply = apply array forces every Napply steps + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all external pf/callback 1 1 + fix 1 all external pf/callback 100 1 + fix 1 all external pf/array 10 + +Description +""""""""""" + +This fix allows external programs that are running LAMMPS through its +:ref:`library interface ` to modify certain +LAMMPS properties on specific timesteps, similar to the way other +fixes do. The external driver can be a :ref:`C/C++ or Fortran program ` or a :doc:`Python script `. + + +---------- + + +If mode is *pf/callback* then the fix will make a callback every +*Ncall* timesteps or minimization iterations to the external program. +The external program computes forces on atoms by setting values in an +array owned by the fix. The fix then adds these forces to each atom +in the group, once every *Napply* steps, similar to the way the :doc:`fix addforce ` command works. Note that if *Ncall* > +*Napply*, the force values produced by one callback will persist, and +be used multiple times to update atom forces. + +The callback function "foo" is invoked by the fix as: + +.. parsed-literal:: + + foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal); + +The arguments are as follows: + +* ptr = pointer provided by and simply passed back to external driver +* timestep = current LAMMPS timestep +* nlocal = # of atoms on this processor +* ids = list of atom IDs on this processor +* x = coordinates of atoms on this processor +* fexternal = forces to add to atoms on this processor + +Note that timestep is a "bigint" which is defined in src/lmptype.h, +typically as a 64-bit integer. + +Fexternal are the forces returned by the driver program. + +The fix has a set_callback() method which the external driver can call +to pass a pointer to its foo() function. See the +couple/lammps_quest/lmpqst.cpp file in the LAMMPS distribution for an +example of how this is done. This sample application performs +classical MD using quantum forces computed by a density functional +code `Quest `_. + +.. _quest: http://dft.sandia.gov/Quest + + + + +---------- + + +If mode is *pf/array* then the fix simply stores force values in an +array. The fix adds these forces to each atom in the group, once +every *Napply* steps, similar to the way the :doc:`fix addforce ` command works. + +The name of the public force array provided by the FixExternal +class is + +.. parsed-literal:: + + double **fexternal; + +It is allocated by the FixExternal class as an (N,3) array where N is +the number of atoms owned by a processor. The 3 corresponds to the +fx, fy, fz components of force. + +It is up to the external program to set the values in this array to +the desired quantities, as often as desired. For example, the driver +program might perform an MD run in stages of 1000 timesteps each. In +between calls to the LAMMPS :doc:`run ` command, it could retrieve +atom coordinates from LAMMPS, compute forces, set values in fexternal, +etc. + + +---------- + + +To use this fix during energy minimization, the energy corresponding +to the added forces must also be set so as to be consistent with the +added forces. Otherwise the minimization will not converge correctly. + +This can be done from the external driver by calling this public +method of the FixExternal class: + +.. parsed-literal:: + + void set_energy(double eng); + +where eng is the potential energy. Eng is an extensive quantity, +meaning it should be the sum over per-atom energies of all affected +atoms. It should also be provided in :doc:`energy units ` +consistent with the simulation. See the details below for how to +insure this energy setting is used appropriately in a minimization. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the potential "energy" set by the external driver to the +system's potential energy as part of :doc:`thermodynamic output `. This is a fictitious quantity but is +needed so that the :doc:`minimize ` command can include the +forces added by this fix in a consistent manner. I.e. there is a +decrease in potential energy when atoms move in the direction of the +added force. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +potential energy discussed above. The scalar stored by this fix +is "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +.. note:: + + If you want the fictitious potential energy associated with the + added forces to be included in the total potential energy of the + system (the quantity being minimized), you MUST enable the + :doc:`fix_modify ` *energy* option for this fix. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_freeze.txt b/doc/_sources/fix_freeze.txt new file mode 100644 index 0000000000..1ad656071e --- /dev/null +++ b/doc/_sources/fix_freeze.txt @@ -0,0 +1,99 @@ +.. index:: fix freeze + +fix freeze command +================== + +fix freeze/cuda command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID freeze + +* ID, group-ID are documented in :doc:`fix ` command +* freeze = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 2 bottom freeze + +Description +""""""""""" + +Zero out the force and torque on a granular particle. This is useful +for preventing certain particles from moving in a simulation. The +:doc:`granular pair styles ` also detect if this fix has been +defined and compute interactions between frozen and non-frozen +particles appropriately, as if the frozen particle has infinite mass. +A similar functionality for normal (point) particles can be obtained +using :doc:`fix setforce `. + + +---------- + + +Styles with a *cuda* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +These accelerated styles are part of the USER-CUDA package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global 3-vector of forces, which can be accessed +by various :ref:`output commands `. This is the +total force on the group of atoms before the forces on individual +atoms are changed by the fix. The vector values calculated by this +fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the GRANULAR package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +There can only be a single freeze fix defined. This is because other +the :doc:`granular pair styles ` treat frozen particles +differently and need to be able to reference a single group to which +this fix is applied. + +Related commands +"""""""""""""""" + +:doc:`atom_style sphere `, :doc:`fix setforce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_gcmc.txt b/doc/_sources/fix_gcmc.txt new file mode 100644 index 0000000000..435109c12a --- /dev/null +++ b/doc/_sources/fix_gcmc.txt @@ -0,0 +1,371 @@ +.. index:: fix gcmc + +fix gcmc command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID gcmc N X M type seed T mu displace keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* gcmc = style name of this fix command +* N = invoke this fix every N steps +* X = average number of GCMC exchanges to attempt every N steps +* M = average number of MC moves to attempt every N steps +* type = atom type for inserted atoms (must be 0 if mol keyword used) +* seed = random # seed (positive integer) +* T = temperature of the ideal gas reservoir (temperature units) +* mu = chemical potential of the ideal gas reservoir (energy units) +* translate = maximum Monte Carlo translation distance (length units) +* zero or more keyword/value pairs may be appended to args +.. parsed-literal:: + + keyword = *mol*, *region*, *maxangle*, *pressure*, *fugacity_coeff*, *full_energy*, *charge*, *group*, *grouptype*, *intra_energy*, or *tfac_insert* + *mol* value = template-ID + template-ID = ID of molecule template specified in a separate :doc:`molecule ` command + *shake* value = fix-ID + fix-ID = ID of :doc:`fix shake ` command + *region* value = region-ID + region-ID = ID of region where MC moves are allowed + *maxangle* value = maximum molecular rotation angle (degrees) + *pressure* value = pressure of the gas reservoir (pressure units) + *fugacity_coeff* value = fugacity coefficient of the gas reservoir (unitless) + *full_energy* = compute the entire system energy when performing MC moves + *charge* value = charge of inserted atoms (charge units) + *group* value = group-ID + group-ID = group-ID for inserted atoms (string) + *grouptype* values = type group-ID + type = atom type (int) + group-ID = group-ID for inserted atoms (string) + *intra_energy* value = intramolecular energy (energy units) + *tfac_insert* value = scale up/down temperature of inserted atoms (unitless) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01 + fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy + fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk + +Description +""""""""""" + +This fix performs grand canonical Monte Carlo (GCMC) exchanges of +atoms or molecules of the given type with an imaginary ideal gas reservoir at +the specified T and chemical potential (mu) as discussed in +:ref:`(Frenkel) `. If used with the :doc:`fix nvt ` command, +simulations in the grand canonical ensemble (muVT, constant chemical +potential, constant volume, and constant temperature) can be +performed. Specific uses include computing isotherms in microporous +materials, or computing vapor-liquid coexistence curves. + +Every N timesteps the fix attempts a number of GCMC exchanges (insertions +or deletions) of gas atoms or molecules of +the given type between the simulation cell and the imaginary +reservoir. It also attempts a number of Monte Carlo +moves (translations and molecule rotations) of gas of the given type +within the simulation cell or region. The average number of +attempted GCMC exchanges is X. The average number of attempted MC moves is M. +M should typically be chosen to be +approximately equal to the expected number of gas atoms or molecules +of the given type within the simulation cell or region, +which will result in roughly one +MC translation per atom or molecule per MC cycle. + +For MC moves of molecular gasses, rotations and translations are each +attempted with 50% probability. For MC moves of atomic gasses, +translations are attempted 100% of the time. For MC exchanges of +either molecular or atomic gasses, deletions and insertions are each +attempted with 50% probability. + +All inserted particles are always assigned to two groups: the default group +"all" and the group specified in the fix gcmc command (which can also +be "all"). In addition, particles are also added to any groups specified +by the *group* and *grouptype* keywords. +If inserted particles are individual atoms, they are +assigned the atom type given by the type argument. If they are molecules, +the type argument has no effect and must be set to zero. Instead, +the type of each atom in the inserted molecule is specified +in the file read by the :doc:`molecule ` command. + +This fix cannot be used to perform MC insertions of gas atoms or +molecules other than the exchanged type, but MC deletions, +translations, and rotations can be performed on any atom/molecule in +the fix group. All atoms in the simulation cell can be moved using +regular time integration translations, e.g. via +:doc:`fix_nvt `, resulting in a hybrid GCMC+MD simulation. A +smaller-than-usual timestep size may be needed when running such a +hybrid simulation, especially if the inserted molecules are not well +equilibrated. + +This command may optionally use the *region* keyword to define an +exchange and move volume. The specified region must have been +previously defined with a :doc:`region ` command. It must be +defined with side = *in*. Insertion attempts occur only within the +specified region. For non-rectangular regions, random trial +points are generated within the rectangular bounding box until a point is found +that lies inside the region. If no valid point is generated after 1000 trials, +no insertion is performed, but it is counted as an attempted insertion. +Move and deletion attempt candidates are selected +from gas atoms or molecules within the region. If there are no candidates, +no move or deletion is performed, but it is counted as an attempt move +or deletion. If an attempted move places the atom or molecule center-of-mass outside +the specified region, a new attempted move is generated. This process is repeated +until the atom or molecule center-of-mass is inside the specified region. + +If used with :doc:`fix_nvt `, the temperature of the imaginary +reservoir, T, should be set to be equivalent to the target temperature +used in :doc:`fix_nvt `. Otherwise, the imaginary reservoir +will not be in thermal equilibrium with the simulation cell. Also, +it is important that the temperature used by fix nvt be dynamic, +which can be achieved as follows: + +.. parsed-literal:: + + compute mdtemp mdatoms temp + compute_modify mdtemp dynamic yes + fix mdnvt mdatoms nvt temp 300.0 300.0 10.0 + fix_modify mdnvt temp mdtemp + +Note that neighbor lists are re-built every timestep that this fix is +invoked, so you should not set N to be too small. However, periodic +rebuilds are necessary in order to avoid dangerous rebuilds and missed +interactions. Specifically, avoid performing so many MC translations +per timestep that atoms can move beyond the neighbor list skin +distance. See the :doc:`neighbor ` command for details. + +When an atom or molecule is to be inserted, its +coordinates are chosen at a random position within the current +simulation cell or region, and new atom velocities are randomly chosen from +the specified temperature distribution given by T. The effective +temperature for new atom velocities can be increased or decreased +using the optional keyword *tfac_insert* (see below). Relative +coordinates for atoms in a molecule are taken from the template +molecule provided by the user. The center of mass of the molecule +is placed at the insertion point. The orientation of the molecule +is chosen at random by rotating about this point. + +Individual atoms are inserted, unless the *mol* keyword is used. It +specifies a *template-ID* previously defined using the +:doc:`molecule ` command, which reads a file that defines the +molecule. The coordinates, atom types, charges, etc, as well as any +bond/angle/etc and special neighbor information for the molecule can +be specified in the molecule file. See the :doc:`molecule ` +command for details. The only settings required to be in this file +are the coordinates and types of atoms in the molecule. + +When not using the *mol* keyword, you should ensure you do not delete +atoms that are bonded to other atoms, or LAMMPS will +soon generate an error when it tries to find bonded neighbors. LAMMPS will +warn you if any of the atoms eligible for deletion have a non-zero +molecule ID, but does not check for this at the time of deletion. + +If you wish to insert molecules via the *mol* keyword, that will have +their bonds or angles constrained via SHAKE, use the *shake* keyword, +specifying as its value the ID of a separate :doc:`fix shake ` command which also appears in your input script. + +Optionally, users may specify the maximum rotation angle for +molecular rotations using the *maxangle* keyword and specifying +the angle in degrees. Rotations are performed by generating a random +point on the unit sphere and a random rotation angle on the +range [0,maxangle). The molecule is then rotated by that angle about an +axis passing through the molecule center of mass. The axis is parallel +to the unit vector defined by the point on the unit sphere. +The same procedure is used for randomly rotating molecules when they +are inserted, except that the maximum angle is 360 degrees. + +Note that fix GCMC does not use configurational bias +MC or any other kind of sampling of intramolecular degrees of freedom. +Inserted molecules can have different orientations, but they will all +have the same intramolecular configuration, +which was specified in the molecule command input. + +For atomic gasses, inserted atoms have the specified atom type, but +deleted atoms are any atoms that have been inserted or that belong +to the user-specified fix group. For molecular gasses, exchanged +molecules use the same atom types as in the template molecule +supplied by the user. In both cases, exchanged +atoms/molecules are assigned to two groups: the default group "all" +and the group specified in the fix gcmc command (which can also be +"all"). + +The gas reservoir pressure can be specified using the *pressure* +keyword, in which case the user-specified chemical potential is +ignored. For non-ideal gas reservoirs, the user may also specify the +fugacity coefficient using the *fugacity_coeff* keyword. + +The *full_energy* option means that fix GCMC will compute the total +potential energy of the entire simulated system. The total system +energy before and after the proposed GCMC move is then used in the +Metropolis criterion to determine whether or not to accept the +proposed GCMC move. By default, this option is off, in which case +only partial energies are computed to determine the difference in +energy that would be caused by the proposed GCMC move. + +The *full_energy* option is needed for systems with complicated +potential energy calculations, including the following: + +* long-range electrostatics (kspace) +* many-body pair styles +* hybrid pair styles +* eam pair styles +* triclinic systems +* need to include potential energy contributions from other fixes + +In these cases, LAMMPS will automatically apply the *full_energy* +keyword and issue a warning message. + +When the *mol* keyword is used, the *full_energy* option also includes +the intramolecular energy of inserted and deleted molecules. If this +is not desired, the *intra_energy* keyword can be used to define an +amount of energy that is subtracted from the final energy when a molecule +is inserted, and added to the initial energy when a molecule is +deleted. For molecules that have a non-zero intramolecular energy, this +will ensure roughly the same behavior whether or not the *full_energy* +option is used. + +Inserted atoms and molecules are assigned random velocities based on the +specified temperature T. Because the relative velocity of +all atoms in the molecule is zero, this may result in inserted molecules +that are systematically too cold. In addition, the intramolecular potential +energy of the inserted molecule may cause the kinetic energy +of the molecule to quickly increase or decrease after insertion. +The *tfac_insert* keyword allows the user to counteract these effects +by changing the temperature used to assign velocities to +inserted atoms and molecules by a constant factor. For a +particular application, some experimentation may be required +to find a value of *tfac_insert* that results in inserted molecules that +equilibrate quickly to the correct temperature. + +Some fixes have an associated potential energy. Examples of such fixes +include: :doc:`efield `, :doc:`gravity `, +:doc:`addforce `, :doc:`langevin `, +:doc:`restrain `, :doc:`temp/berendsen `, +:doc:`temp/rescale `, and :doc:`wall fixes `. +For that energy to be included in the total potential energy of the +system (the quantity used when performing GCMC moves), +you MUST enable the :doc:`fix_modify ` *energy* option for +that fix. The doc pages for individual :doc:`fix ` commands +specify if this should be done. + +Use the *charge* option to insert atoms with a user-specified point +charge. Note that doing so will cause the system to become non-neutral. +LAMMPS issues a warning when using long-range electrostatics (kspace) +with non-neutral systems. See the +:doc:`compute_group_group ` documentation for more +details about simulating non-neutral systems with kspace on. + +Use of this fix typically will cause the number of atoms to fluctuate, +therefore, you will want to use the +:doc:`compute_modify ` command to insure that the +current number of atoms is used as a normalizing factor each time +temperature is computed. Here is the necessary command: + +.. parsed-literal:: + + compute_modify thermo_temp dynamic yes + +If LJ units are used, note that a value of 0.18292026 is used by this +fix as the reduced value for Planck's constant. This value was +derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 * +epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and +mass = 39.948 amu. + +The *group* keyword assigns all inserted atoms to the :doc:`group ` +of the group-ID value. The *grouptype* keyword assigns all +inserted atoms of the specified type to the :doc:`group ` +of the group-ID value. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the fix to :doc:`binary restart files `. This includes information about the random +number generator seed, the next timestep for MC exchanges, etc. See +the :doc:`read_restart ` command for info on how to +re-specify a fix in an input script that reads a restart file, so that +the operation of the fix continues in an uninterrupted fashion. + +None of the :doc:`fix_modify ` options are relevant to this +fix. + +This fix computes a global vector of length 8, which can be accessed +by various :ref:`output commands `. The vector +values are the following global cumulative quantities: + +* 1 = translation attempts +* 2 = translation successes +* 3 = insertion attempts +* 4 = insertion successes +* 5 = deletion attempts +* 6 = deletion successes +* 7 = rotation attempts +* 8 = rotation successes + +The vector values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Do not set "neigh_modify once yes" or else this fix will never be +called. Reneighboring is required. + +Can be run in parallel, but aspects of the GCMC part will not scale +well in parallel. Only usable for 3D simulations. + +Note that very lengthy simulations involving insertions/deletions of +billions of gas molecules may run out of atom or molecule IDs and +trigger an error, so it is better to run multiple shorter-duration +simulations. Likewise, very large molecules have not been tested +and may turn out to be problematic. + +Use of multiple fix gcmc commands in the same input script can be +problematic if using a template molecule. The issue is that the +user-referenced template molecule in the second fix gcmc command +may no longer exist since it might have been deleted by the first +fix gcmc command. An existing template molecule will need to be +referenced by the user for each subsequent fix gcmc command. + +Related commands +"""""""""""""""" + +:doc:`fix atom/swap `, +:doc:`fix nvt `, :doc:`neighbor `, +:doc:`fix deposit `, :doc:`fix evaporate `, +:doc:`delete_atoms ` + +Default +""""""" + +The option defaults are mol = no, maxangle = 10, full_energy = no, +except for the situations where full_energy is required, as +listed above. + + +---------- + + +.. _Frenkel: + + + +**(Frenkel)** Frenkel and Smit, Understanding Molecular Simulation, +Academic Press, London, 2002. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_gld.txt b/doc/_sources/fix_gld.txt new file mode 100644 index 0000000000..314fe1909a --- /dev/null +++ b/doc/_sources/fix_gld.txt @@ -0,0 +1,178 @@ +.. index:: fix gld + +fix gld command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* gld = style name of this fix command +* Tstart,Tstop = desired temperature at start/end of run (temperature units) +* N_k = number of terms in the Prony series representation of the memory kernel +* seed = random number seed to use for white noise (positive integer) +* series = *pprony* is presently the only available option +* c_k = the weight of the kth term in the Prony series (mass per time units) +* tau_k = the time constant of the kth term in the Prony series (time units) +* zero or more keyword/value pairs may be appended +.. parsed-literal:: + + keyword = *frozen* or *zero* + *frozen* value = *no* or *yes* + *no* = initialize extended variables using values drawn from equilibrium distribution at Tstart + *yes* = initialize extended variables to zero (i.e., from equilibrium distribution at zero temperature) + *zero* value = *no* or *yes* + *no* = do not set total random force to zero + *yes* = set total random force to zero + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all gld 1.0 1.0 2 82885 pprony 0.5 1.0 1.0 2.0 frozen yes zero yes + fix 3 rouse gld 7.355 7.355 4 48823 pprony 107.1 0.02415 186.0 0.04294 428.6 0.09661 1714 0.38643 + +Description +""""""""""" + +Applies Generalized Langevin Dynamics to a group of atoms, as +described in :ref:`(Baczewski) `. This is intended to model the +effect of an implicit solvent with a temporally non-local dissipative +force and a colored Gaussian random force, consistent with the +Fluctuation-Dissipation Theorem. The functional form of the memory +kernel associated with the temporally non-local force is constrained +to be a Prony series. + +.. note:: + + While this fix bears many similarities to :doc:`fix langevin `, it has one significant + difference. Namely, :doc:`fix gld ` performs time integration, + whereas :doc:`fix langevin ` does NOT. To this end, the + specification of another fix to perform time integration, such as :doc:`fix nve `, is NOT necessary. + +With this fix active, the force on the *j*th atom is given as + +.. image:: Eqs/fix_gld1.jpg + :align: center + +Here, the first term is representative of all conservative (pairwise, +bonded, etc) forces external to this fix, the second is the temporally +non-local dissipative force given as a Prony series, and the third is +the colored Gaussian random force. + +The Prony series form of the memory kernel is chosen to enable an +extended variable formalism, with a number of exemplary mathematical +features discussed in :ref:`(Baczewski) `. In particular, 3N_k +extended variables are added to each atom, which effect the action of +the memory kernel without having to explicitly evaluate the integral +over time in the second term of the force. This also has the benefit +of requiring the generation of uncorrelated random forces, rather than +correlated random forces as specified in the third term of the force. + +Presently, the Prony series coefficients are limited to being greater +than or equal to zero, and the time constants are limited to being +greater than zero. To this end, the value of series MUST be set to +*pprony*, for now. Future updates will allow for negative coefficients +and other representations of the memory kernel. It is with these +updates in mind that the series option was included. + +The units of the Prony series coefficients are chosen to be mass per +time to ensure that the numerical integration scheme stably approaches +the Newtonian and Langevin limits. Details of these limits, and the +associated numerical concerns are discussed in +:ref:`(Baczewski) `. + +The desired temperature at each timestep is ramped from *Tstart* to +*Tstop* over the course of the next run. + +The random # *seed* must be a positive integer. A Marsaglia random +number generator is used. Each processor uses the input seed to +generate its own unique seed and its own stream of random +numbers. Thus the dynamics of the system will not be identical on two +runs on different numbers of processors. + + +---------- + + +The keyword/value option pairs are used in the following ways. + +The keyword *frozen* can be used to specify how the extended variables +associated with the GLD memory kernel are initialized. Specifying no +(the default), the initial values are drawn at random from an +equilibrium distribution at *Tstart*, consistent with the +Fluctuation-Dissipation Theorem. Specifying yes, initializes the +extended variables to zero. + +The keyword *zero* can be used to eliminate drift due to the +thermostat. Because the random forces on different atoms are +independent, they do not sum exactly to zero. As a result, this fix +applies a small random force to the entire system, and the +center-of-mass of the system undergoes a slow random walk. If the +keyword *zero* is set to *yes*, the total random force is set exactly +to zero by subtracting off an equal part of it from each atom in the +group. As a result, the center-of-mass of a system with zero initial +momentum will not drift over time. + + +---------- + + +**Restart, run start/stop, minimize info:** + +The instantaneous values of the extended variables are written to +:doc:`binary restart files `. Because the state of the random +number generator is not saved in restart files, this means you cannot +do "exact" restarts with this fix, where the simulation continues on +the same as if no restart had taken place. However, in a statistical +sense, a restarted simulation should produce the same behavior. + +None of the :doc:`fix_modify ` options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various :ref:`output commands `. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix langevin `, :doc:`fix viscous `, +:doc:`pair_style dpd/tstat ` + +Default +""""""" + +The option defaults are frozen = no, zero = no. + + +---------- + + +.. _Baczewski: + + + +**(Baczewski)** A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_gle.txt b/doc/_sources/fix_gle.txt new file mode 100644 index 0000000000..e4b0f798fa --- /dev/null +++ b/doc/_sources/fix_gle.txt @@ -0,0 +1,171 @@ +.. index:: fix gle + +fix gle command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID id-group gle Ns Tstart Tstop seed Amatrix [noneq Cmatrix] [every stride] + +* ID, group-ID are documented in :doc:`fix ` command +* gle = style name of this fix command +* Ns = number of additional fictitious momenta +* Tstart, Tstop = temperature ramp during the run +* Amatrix = file to read the drift matrix A from +* seed = random number seed to use for generating noise (positive integer) +* zero or more keyword/value pairs may be appended +keyword = *noneq* and/or *every* + *noneq* Cmatrix = file to read the non-equilibrium covariance matrix from + *every* stride = apply the GLE once every time steps. Reduces the accuracy + of the integration of the GLE, but has *no effect* on the accuracy of equilibrium + sampling. It might change sampling properties when used together with *noneq*. + + +Examples +"""""""" + +fix 3 boundary gle 6 300 300 31415 smart.A +fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C + +Description +""""""""""" + +Apply a Generalized Langevin Equation (GLE) thermostat as described +in :ref:`(Ceriotti) `. The formalism allows one to obtain a number +of different effects ranging from efficient sampling of all +vibrational modes in the system to inexpensive (approximate) +modelling of nuclear quantum effects. Contrary to +:doc:`fix langevin `, this fix performs both +thermostatting and evolution of the Hamiltonian equations of motion, so it +should not be used together with :doc:`fix nve ` -- at least not +on the same atom groups. + +Each degree of freedom in the thermostatted group is supplemented +with Ns additional degrees of freedom s, and the equations of motion +become + +dq/dt=p/m +d(p,s)/dt=(F,0) - A(p,s) + B dW/dt + +where F is the physical force, A is the drift matrix (that generalizes +the friction in Langevin dynamics), B is the diffusion term and dW/dt +un-correlated Gaussian random forces. The A matrix couples the physical +(q,p) dynamics with that of the additional degrees of freedom, +and makes it possible to obtain effectively a history-dependent +noise and friction kernel. + +The drift matrix should be given as an external file *Afile*, +as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are +optimal for a given application and the system of choice can be +obtained from :ref:`(GLE4MD) `. + +Equilibrium sampling a temperature T is obtained by specifiying the +target value as the *Tstart* and *Tstop* arguments, so that the diffusion +matrix that gives canonical sampling for a given A is computed automatically. +However, the GLE framework also allow for non-equilibrium sampling, that +can be used for instance to model inexpensively zero-point energy +effects :ref:`(Ceriotti2) `. This is achieved specifying the +*noneq* keyword followed by the name of the file that contains the +static covariance matrix for the non-equilibrium dynamics. + +Since integrating GLE dynamics can be costly when used together with +simple potentials, one can use the *every* optional keyword to +apply the Langevin terms only once every several MD steps, in a +multiple time-step fashion. This should be used with care when doing +non-equilibrium sampling, but should have no effect on equilibrium +averages when using canonical sampling. + +The random number *seed* must be a positive integer. A Marsaglia random +number generator is used. Each processor uses the input seed to +generate its own unique seed and its own stream of random numbers. +Thus the dynamics of the system will not be identical on two runs on +different numbers of processors. + +Note also that the Generalized Langevin Dynamics scheme that is +implemented by the :doc:`fix gld ` scheme is closely related +to the present one. In fact, it should be always possible to cast the +Prony series form of the memory kernel used by GLD into an appropriate +input matrix for :doc:`fix_gle `. While the GLE scheme is more +general, the form used by :doc:`fix gld ` can be more directly +related to the representation of an implicit solvent environment. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +The instantaneous values of the extended variables are written to +:doc:`binary restart files `. Because the state of the random +number generator is not saved in restart files, this means you cannot +do "exact" restarts with this fix, where the simulation continues on +the same as if no restart had taken place. However, in a statistical +sense, a restarted simulation should produce the same behavior. +Note however that you should use a different seed each time you +restart, otherwise the same sequence of random numbers will be used +each time, which might lead to stochastic synchronization and +subtle artefacts in the sampling. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Langevin thermostatting to the +system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative energy change due to this fix. The scalar value +calculated by this fix is "extensive". + +Restrictions +"""""""""""" + + +The GLE thermostat in its current implementation should not be used +with rigid bodies, SHAKE or RATTLE. It is expected that all the +thermostatted degrees of freedom are fully flexible, and the sampled +ensemble will not be correct otherwise. + +In order to perform constant-pressure simulations please use +:doc:`fix press/berendsen `, rather than +:doc:`fix_npt `, to avoid duplicate integration of the +equations of motion. + +This fix is part of the USER-MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat `, :doc:`fix_gld ` + + +---------- + + +.. _Ceriotti: + + + +**(Ceriotti)** Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, +1170-80 (2010) + +.. _GLE4MD: + + + +**(GLE4MD)** `http://epfl-cosmo.github.io/gle4md/ `_ + +.. _Ceriotti2: + + + +**(Ceriotti2)** Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, +030603 (2009) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_gravity.txt b/doc/_sources/fix_gravity.txt new file mode 100644 index 0000000000..41050aae7c --- /dev/null +++ b/doc/_sources/fix_gravity.txt @@ -0,0 +1,158 @@ +.. index:: fix gravity + +fix gravity command +=================== + +fix gravity/cuda command +======================== + +fix gravity/omp command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group gravity magnitude style args + +* ID, group are documented in :doc:`fix ` command +* gravity = style name of this fix command +* magnitude = size of acceleration (force/mass units) +* magnitude can be a variable (see below) +* style = *chute* or *spherical* or *gradient* or *vector* +.. parsed-literal:: + + *chute* args = angle + angle = angle in +x away from -z or -y axis in 3d/2d (in degrees) + angle can be a variable (see below) + *spherical* args = phi theta + phi = azimuthal angle from +x axis (in degrees) + theta = angle from +z or +y axis in 3d/2d (in degrees) + phi or theta can be a variable (see below) + *vector* args = x y z + x y z = vector direction to apply the acceleration + x or y or z can be a variable (see below) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all gravity 1.0 chute 24.0 + fix 1 all gravity v_increase chute 24.0 + fix 1 all gravity 1.0 spherical 0.0 -180.0 + fix 1 all gravity 10.0 spherical v_phi v_theta + fix 1 all gravity 100.0 vector 1 1 0 + +Description +""""""""""" + +Impose an additional acceleration on each particle in the group. This +fix is typically used with granular systems to include a "gravity" +term acting on the macroscopic particles. More generally, it can +represent any kind of driving field, e.g. a pressure gradient inducing +a Poiseuille flow in a fluid. Note that this fix operates differently +than the :doc:`fix addforce ` command. The addforce fix +adds the same force to each atom, independent of its mass. This +command imparts the same acceleration to each atom (force/mass). + +The *magnitude* of the acceleration is specified in force/mass units. +For granular systems (LJ units) this is typically 1.0. See the +:doc:`units ` command for details. + +Style *chute* is typically used for simulations of chute flow where +the specified *angle* is the chute angle, with flow occurring in the +x +direction. For 3d systems, the tilt is away from the z axis; for 2d +systems, the tilt is away from the y axis. + +Style *spherical* allows an arbitrary 3d direction to be specified for +the acceleration vector. *Phi* and *theta* are defined in the usual +spherical coordinates. Thus for acceleration acting in the -z +direction, *theta* would be 180.0 (or -180.0). *Theta* = 90.0 and +*phi* = -90.0 would mean acceleration acts in the -y direction. For +2d systems, *phi* is ignored and *theta* is an angle in the xy plane +where *theta* = 0.0 is the y-axis. + +Style *vector* imposes an acceleration in the vector direction given +by (x,y,z). Only the direction of the vector is important; it's +length is ignored. For 2d systems, the *z* component is ignored. + +Any of the quantities *magnitude*, *angle*, *phi*, *theta*, *x*, *y*, +*z* which define the gravitational magnitude and direction, can be +specified as an equal-style :doc:`variable `. If the value is +a variable, it should be specified as v_name, where name is the +variable name. In this case, the variable will be evaluated each +timestep, and its value used to determine the quantity. You should +insure that the variable calculates a result in the approriate units, +e.g. force/mass or degrees. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent gravitational +field. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the gravitational potential energy of the system to the +system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. This scalar is the +gravitational potential energy of the particles in the defined field, +namely mass * (g dot x) for each particles, where x and mass are the +particles position and mass, and g is the gravitational field. The +scalar value calculated by this fix is "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`atom_style sphere `, :doc:`fix addforce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_heat.txt b/doc/_sources/fix_heat.txt new file mode 100644 index 0000000000..7323157ccf --- /dev/null +++ b/doc/_sources/fix_heat.txt @@ -0,0 +1,136 @@ +.. index:: fix heat + +fix heat command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID heat N eflux + +* ID, group-ID are documented in :doc:`fix ` command +* heat = style name of this fix command +* N = add/subtract heat every this many timesteps +* eflux = rate of heat addition or subtraction (energy/time units) +* eflux can be a variable (see below) +* zero or more keyword/value pairs may be appended to args +* keyword = *region* +.. parsed-literal:: + + *region* value = region-ID + region-ID = ID of region atoms must be in to have added force + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 qin heat 1 1.0 + fix 3 qin heat 10 v_flux + fix 4 qout heat 1 -1.0 region top + +Description +""""""""""" + +Add non-translational kinetic energy (heat) to a group of atoms in a +manner that conserves their aggregate momentum. Two of these fixes +can be used to establish a temperature gradient across a simulation +domain by adding heat (energy) to one group of atoms (hot reservoir) +and subtracting heat from another (cold reservoir). E.g. a simulation +sampling from the McDLT ensemble. + +If the *region* keyword is used, the atom must be in both the group +and the specified geometric :doc:`region ` in order to have +energy added or subtracted to it. If not specified, then the atoms in +the group are affected wherever they may move to. + +Heat addition/subtraction is performed every N timesteps. The *eflux* +parameter can be specified as a numeric constant or as a variable (see +below). If it is a numeric constant or equal-style variable which +evaluates to a scalar value, then the *eflux* determines the change in +aggregate energy of the entire group of atoms per unit time, e.g. in +eV/psec for :doc:`metal units `. In this case it is an +"extensive" quantity, meaning its magnitude should be scaled with the +number of atoms in the group. Note that since *eflux* has per-time +units (i.e. it is a flux), this means that a larger value of N will +add/subtract a larger amount of energy each time the fix is invoked. + +If *eflux* is specified as an atom-style variable (see below), then +the variable computes one value per atom. In this case, each value is +the energy flux for a single atom, again in units of energy per unit +time. In this case, each value is an "intensive" quantity, which need +not be scaled with the number of atoms in the group. + +As mentioned above, the *eflux* parameter can be specified as an +equal-style or atom_style :doc:`variable `. If the value is a +variable, it should be specified as v_name, where name is the variable +name. In this case, the variable will be evaluated each timestep, and +its value(s) used to determine the flux. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent flux. + +Atom-style variables can specify the same formulas as equal-style +variables but can also include per-atom values, such as atom +coordinates. Thus it is easy to specify a spatially-dependent flux +with optional time-dependence as well. + +.. note:: + + If heat is subtracted from the system too aggressively so that + the group's kinetic energy would go to zero, or any individual atom's + kinetic energy would go to zero for the case where *eflux* is an + atom-style variable, then LAMMPS will halt with an error message. + +Fix heat is different from a thermostat such as :doc:`fix nvt ` +or :doc:`fix temp/rescale ` in that energy is +added/subtracted continually. Thus if there isn't another mechanism +in place to counterbalance this effect, the entire system will heat or +cool continuously. You can use multiple heat fixes so that the net +energy change is 0.0 or use :doc:`fix viscous ` to drain +energy from the system. + +This fix does not change the coordinates of its atoms; it only scales +their velocities. Thus you must still use an integration fix +(e.g. :doc:`fix nve `) on the affected atoms. This fix should +not normally be used on atoms that have their temperature controlled +by another fix - e.g. :doc:`fix nvt ` or :doc:`fix langevin ` fix. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. This scalar is the +most recent value by which velocites were scaled. The scalar value +calculated by this fix is "intensive". If *eflux* is specified as +an atom-style variable, this fix computes the average value by which +the velocities were scaled for all of the atoms that had their +velocities scaled. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute temp `, :doc:`compute temp/region ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_imd.txt b/doc/_sources/fix_imd.txt new file mode 100644 index 0000000000..f75eea1270 --- /dev/null +++ b/doc/_sources/fix_imd.txt @@ -0,0 +1,179 @@ +.. index:: fix imd + +fix imd command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID imd trate port keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* imd = style name of this fix command +* port = port number on which the fix listens for an IMD client +* keyword = *unwrap* or *fscale* or *trate* +.. parsed-literal:: + + *unwrap* arg = *on* or *off* + off = coordinates are wrapped back into the principal unit cell (default) + on = "unwrapped" coordinates using the image flags used + *fscale* arg = factor + factor = floating point number to scale IMD forces (default: 1.0) + *trate* arg = transmission rate of coordinate data sets (default: 1) + *nowait* arg = *on* or *off* + off = LAMMPS waits to be connected to an IMD client before continuing (default) + on = LAMMPS listens for an IMD client, but continues with the run + + + +Examples +"""""""" + +.. parsed-literal:: + + fix vmd all imd 5678 + fix comm all imd 8888 trate 5 unwrap on fscale 10.0 + +Description +""""""""""" + +This fix implements the "Interactive MD" (IMD) protocol which allows +realtime visualization and manipulation of MD simulations through the +IMD protocol, as initially implemented in VMD and NAMD. Specifically +it allows LAMMPS to connect an IMD client, for example the `VMD visualization program `_, so that it can monitor the progress of the +simulation and interactively apply forces to selected atoms. + +If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD +then fix imd will use POSIX threads to spawn a IMD communication +thread on MPI rank 0 in order to offload data reading and writing +from the main execution thread and potentially lower the inferred +latencies for slow communication links. This feature has only been +tested under linux. + +There are example scripts for using this package with LAMMPS in +examples/USER/imd. Additional examples and a driver for use with the +Novint Falcon game controller as haptic device can be found at: +http://sites.google.com/site/akohlmey/software/vrpn-icms. + +The source code for this fix includes code developed by the +Theoretical and Computational Biophysics Group in the Beckman +Institute for Advanced Science and Technology at the University of +Illinois at Urbana-Champaign. We thank them for providing a software +interface that allows codes like LAMMPS to hook to `VMD `_. + +Upon initialization of the fix, it will open a communication port on +the node with MPI task 0 and wait for an incoming connection. As soon +as an IMD client is connected, the simulation will continue and the +fix will send the current coordinates of the fix's group to the IMD +client at every trate MD step. When using r-RESPA, trate applies to +the steps of the outmost RESPA level. During a run with an active IMD +connection also the IMD client can request to apply forces to selected +atoms of the fix group. + +The port number selected must be an available network port number. On +many machines, port numbers < 1024 are reserved for accounts with +system manager privilege and specific applications. If multiple imd +fixes would be active at the same time, each needs to use a different +port number. + +The *nowait* keyword controls the behavior of the fix when no IMD +client is connected. With the default setting of *off*, LAMMPS will +wait until a connection is made before continuing with the +execution. Setting *nowait* to *on* will have the LAMMPS code be ready +to connect to a client, but continue with the simulation. This can for +example be used to monitor the progress of an ongoing calculation +without the need to be permanently connected or having to download a +trajectory file. + +The *trate* keyword allows to select how often the coordinate data is +sent to the IMD client. It can also be changed on request of the IMD +client through an IMD protocol message. The *unwrap* keyword allows +to send "unwrapped" coordinates to the IMD client that undo the +wrapping back of coordinates into the principle unit cell, as done by +default in LAMMPS. The *fscale* keyword allows to apply a scaling +factor to forces transmitted by the IMD client. The IMD protocols +stipulates that forces are transferred in kcal/mol/angstrom under the +assumption that coordinates are given in angstrom. For LAMMPS runs +with different units or as a measure to tweak the forces generated by +the manipulation of the IMD client, this option allows to make +adjustments. + +To connect VMD to a listening LAMMPS simulation on the same machine +with fix imd enabled, one needs to start VMD and load a coordinate or +topology file that matches the fix group. When the VMD command +prompts appears, one types the command line: + +.. parsed-literal:: + + imd connect localhost 5678 + +This assumes that *fix imd* was started with 5678 as a port +number for the IMD protocol. + +The steps to do interactive manipulation of a running simulation in +VMD are the following: + +In the Mouse menu of the VMD Main window, select "Mouse -> Force -> +Atom". You may alternately select "Residue", or "Fragment" to apply +forces to whole residues or fragments. Your mouse can now be used to +apply forces to your simulation. Click on an atom, residue, or +fragment and drag to apply a force. Click quickly without moving the +mouse to turn the force off. You can also use a variety of 3D position +trackers to apply forces to your simulation. Game controllers or haptic +devices with force-feedback such as the Novint Falcon or Sensable +PHANTOM allow you to feel the resistance due to inertia or interactions +with neighbors that the atoms experience you are trying to move, as if +they were real objects. See the `VMD IMD Homepage `_ and the +`VRPN-ICMS Homepage `_ for more details. + +If IMD control messages are received, a line of text describing the +message and its effect will be printed to the LAMMPS output screen, if +screen output is active. + +.. _VMD: http://www.ks.uiuc.edu/Research/vmd + + + +.. _imdvmd: http://www.ks.uiuc.edu/Research/vmd/imd/ + + + +.. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms + + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +When used in combination with VMD, a topology or coordinate file has +to be loaded, which matches (in number and ordering of atoms) the +group the fix is applied to. The fix internally sorts atom IDs by +ascending integer value; in VMD (and thus the IMD protocol) those will +be assigned 0-based consecutive index numbers. + +When using multiple active IMD connections at the same time, each +needs to use a different port number. + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_indent.txt b/doc/_sources/fix_indent.txt new file mode 100644 index 0000000000..34af678901 --- /dev/null +++ b/doc/_sources/fix_indent.txt @@ -0,0 +1,223 @@ +.. index:: fix indent + +fix indent command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID indent K keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* indent = style name of this fix command +* K = force constant for indenter surface (force/distance^2 units) +* one or more keyword/value pairs may be appended +* keyword = *sphere* or *cylinder* or *plane* or *side* or *units* +.. parsed-literal:: + + *sphere* args = x y z R + x,y,z = initial position of center of indenter (distance units) + R = sphere radius of indenter (distance units) + any of x,y,z,R can be a variable (see below) + *cylinder* args = dim c1 c2 R + dim = *x* or *y* or *z* = axis of cylinder + c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) + R = cylinder radius of indenter (distance units) + any of c1,c2,R can be a variable (see below) + *plane* args = dim pos side + dim = *x* or *y* or *z* = plane perpendicular to this dimension + pos = position of plane in dimension x, y, or z (distance units) + pos can be a variable (see below) + side = *lo* or *hi* + *side* value = *in* or *out* + *in* = the indenter acts on particles inside the sphere or cylinder + *out* = the indenter acts on particles outside the sphere or cylinder + *units* value = *lattice* or *box* + lattice = the geometry is defined in lattice units + box = the geometry is defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all indent 10.0 sphere 0.0 0.0 15.0 3.0 + fix 1 all indent 10.0 sphere v_x v_y 0.0 v_radius side in + fix 2 flow indent 10.0 cylinder z 0.0 0.0 10.0 units box + +Description +""""""""""" + +Insert an indenter within a simulation box. The indenter repels all +atoms in the group that touch it, so it can be used to push into a +material or as an obstacle in a flow. Or it can be used as a +constraining wall around a simulation; see the discussion of the +*side* keyword below. + +The indenter can either be spherical or cylindrical or planar. You +must set one of those 3 keywords. + +A spherical indenter exerts a force of magnitude + +.. parsed-literal:: + + F(r) = - K (r - R)^2 + +on each atom where *K* is the specified force constant, *r* is the +distance from the atom to the center of the indenter, and *R* is the +radius of the indenter. The force is repulsive and F(r) = 0 for *r* > +*R*. + +A cylindrical indenter exerts the same force, except that *r* is the +distance from the atom to the center axis of the cylinder. The +cylinder extends infinitely along its axis. + +Spherical and cylindrical indenters account for periodic boundaries in +two ways. First, the center point of a spherical indenter (x,y,z) or +axis of a cylindrical indenter (c1,c2) is remapped back into the +simulation box, if the box is periodic in a particular dimension. +This occurs every timestep if the indenter geometry is specified with +a variable (see below), e.g. it is moving over time. Second, the +calculation of distance to the indenter center or axis accounts for +periodic boundaries. Both of these mean that an indenter can +effectively move through and straddle one or more periodic boundaries. + +A planar indenter is really an axis-aligned infinite-extent wall +exerting the same force on atoms in the system, where *R* is the +position of the plane and *r-R* is the distance from the plane. If +the *side* parameter of the plane is specified as *lo* then it will +indent from the lo end of the simulation box, meaning that atoms with +a coordinate less than the plane's current position will be pushed +towards the hi end of the box and atoms with a coordinate higher than +the plane's current position will feel no force. Vice versa if *side* +is specified as *hi*. + +Any of the 4 quantities defining a spherical indenter's geometry can +be specified as an equal-style :doc:`variable `, namely *x*, +*y*, *z*, or *R*. Similarly, for a cylindrical indenter, any of *c1*, +*c2*, or *R*, can be a variable. For a planar indenter, *pos* can be +a variable. If the value is a variable, it should be specified as +v_name, where name is the variable name. In this case, the variable +will be evaluated each timestep, and its value used to define the +indenter geometry. + +Note that equal-style variables can specify formulas with various +mathematical functions, and include :doc:`thermo_style ` +command keywords for the simulation box parameters and timestep and +elapsed time. Thus it is easy to specify indenter properties that +change as a function of time or span consecutive runs in a continuous +fashion. For the latter, see the *start* and *stop* keywords of the +:doc:`run ` command and the *elaplong* keyword of :doc:`thermo_style custom ` for details. + +For example, if a spherical indenter's x-position is specfied as v_x, +then this variable definition will keep it's center at a relative +position in the simulation box, 1/4 of the way from the left edge to +the right edge, even if the box size changes: + +.. parsed-literal:: + + variable x equal "xlo + 0.25*lx" + +Similarly, either of these variable definitions will move the indenter +from an initial position at 2.5 at a constant velocity of 5: + +.. parsed-literal:: + + variable x equal "2.5 + 5*elaplong*dt" + variable x equal vdisplace(2.5,5) + +If a spherical indenter's radius is specified as v_r, then these +variable definitions will grow the size of the indenter at a specfied +rate. + +.. parsed-literal:: + + variable r0 equal 0.0 + variable rate equal 1.0 + variable r equal "v_r0 + step*dt*v_rate" + +If the *side* keyword is specified as *out*, which is the default, +then particles outside the indenter are pushded away from its outer +surface, as described above. This only applies to spherical or +cylindrical indenters. If the *side* keyword is specified as *in*, +the action of the indenter is reversed. Particles inside the indenter +are pushed away from its inner surface. In other words, the indenter +is now a containing wall that traps the particles inside it. If the +radius shrinks over time, it will squeeze the particles. + +The *units* keyword determines the meaning of the distance units used +to define the indenter geometry. A *box* value selects standard +distance units as defined by the :doc:`units ` command, +e.g. Angstroms for units = real or metal. A *lattice* value means the +distance units are in lattice spacings. The :doc:`lattice ` +command must have been previously used to define the lattice spacing. +The (x,y,z) coords of the indenter position are scaled by the x,y,z +lattice spacings respectively. The radius of a spherical or +cylindrical indenter is scaled by the x lattice spacing. + +Note that the units keyword only affects indenter geometry parameters +specified directly with numbers, not those specified as variables. In +the latter case, you should use the *xlat*, *ylat*, *zlat* keywords of +the :doc:`thermo_style ` command if you want to include +lattice spacings in a variable formula. + +The force constant *K* is not affected by the *units* keyword. It is +always in force/distance^2 units where force and distance are defined +by the :doc:`units ` command. If you wish K to be scaled by the +lattice spacing, you can define K with a variable whose formula +contains *xlat*, *ylat*, *zlat* keywords of the +:doc:`thermo_style ` command, e.g. + +.. parsed-literal:: + + variable k equal 100.0/xlat/xlat + fix 1 all indent $k sphere ... + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy of interaction between atoms and the indenter to +the system's potential energy as part of :doc:`thermodynamic output `. The energy of each particle interacting +with the indenter is K/3 (r - R)^3. + +This fix computes a global scalar energy and a global 3-vector of +forces (on the indenter), which can be accessed by various :ref:`output commands `. The scalar and vector values +calculated by this fix are "extensive". + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. Note that if you +define the indenter geometry with a variable using a time-dependent +formula, LAMMPS uses the iteration count in the minimizer as the +timestep. But it is almost certainly a bad idea to have the indenter +change its position or size during a minimization. LAMMPS does not +check if you have done this. + +.. note:: + + If you want the atom/indenter interaction energy to be included + in the total potential energy of the system (the quantity being + minimized), you must enable the :doc:`fix_modify ` *energy* + option for this fix. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +Default +""""""" + +The option defaults are side = out and units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ipi.txt b/doc/_sources/fix_ipi.txt new file mode 100644 index 0000000000..d4786cd5ba --- /dev/null +++ b/doc/_sources/fix_ipi.txt @@ -0,0 +1,107 @@ +.. index:: fix ipi + +fix ipi command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ipi address port [unix] + +* ID, group-ID are documented in :doc:`fix ` command +* ipi = style name of this fix command +* address = internet address (FQDN or IP), or UNIX socket name +* port = port number (ignored for UNIX sockets) +* optional keyword = *unix*, if present uses a unix socket + +Examples +"""""""" + +fix 1 all ipi my.server.com 12345 +fix 1 all ipi mysocket 666 unix + +Description +""""""""""" + +This fix enables LAMMPS to be run as a client for the i-PI Python +wrapper :ref:`(IPI) ` for performing a path integral molecular dynamics +(PIMD) simulation. The philosophy behind i-PI is described in the +following publication :ref:`(IPI-CPC) `. + +A version of the i-PI package, containing only files needed for use +with LAMMPS, is provided in the tools/i-pi directory. See the +tools/i-pi/manual.pdf for an introduction to i-PI. The +examples/USER/i-pi directory contains example scripts for using i-PI +with LAMMPS. + +In brief, the path integral molecular dynamics is performed by the +Python wrapper, while the client (LAMMPS in this case) simply computes +forces and energy for each configuration. The communication between +the two components takes place using sockets, and is reduced to the +bare minimum. All the parameters of the dynamics are specified in the +input of i-PI, and all the parameters of the force field must be +specified as LAMMPS inputs, preceding the *fix ipi* command. + +The server address must be specified by the *address* argument, and +can be either the IP address, the fully-qualified name of the server, +or the name of a UNIX socket for local, faster communication. In the +case of internet sockets, the *port* argument specifies the port +number on which i-PI is listening, while the *unix* optional switch +specifies that the socket is a UNIX socket. + +Note that there is no check of data integrity, or that the atomic +configurations make sense. It is assumed that the species in the i-PI +input are listed in the same order as in the data file of LAMMPS. The +initial configuration is ignored, as it will be substituted with the +coordinates received from i-PI before forces are ever evaluated. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +There is no restart information associated with this fix, since all +the dynamical parameters are dealt with by i-PI. + +Restrictions +"""""""""""" + + +Using this fix on anything other than all atoms requires particular +care, since i-PI will know nothing on atoms that are not those whose +coordinates are transferred. However, one could use this strategy to +define an external potential acting on the atoms that are moved by +i-PI. + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. Because of +the use of UNIX domain sockets, this fix will only work in a UNIX +environment. + +Related commands +"""""""""""""""" + +:doc:`fix nve ` + + +---------- + + +.. _IPICPC: + + + +**(IPI-CPC)** Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, +1019-1026 (2014). + +.. _IPI: + + + +**(IPI)** +`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi `_ + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_langevin.txt b/doc/_sources/fix_langevin.txt new file mode 100644 index 0000000000..5c100703b9 --- /dev/null +++ b/doc/_sources/fix_langevin.txt @@ -0,0 +1,374 @@ +.. index:: fix langevin + +fix langevin command +==================== + +fix langevin/kk command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID langevin Tstart Tstop damp seed keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* langevin = style name of this fix command +* Tstart,Tstop = desired temperature at start/end of run (temperature units) +* Tstart can be a variable (see below) +* damp = damping parameter (time units) +* seed = random number seed to use for white noise (positive integer) +* zero or more keyword/value pairs may be appended +* keyword = *angmom* or *omega* or *scale* or *tally* or *zero* +.. parsed-literal:: + + *angmom* value = *no* or scale + *no* = do not thermostat rotational degrees of freedom via the angular momentum + factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below + *gjf* value = *no* or *yes* + *no* = use standard formulation + *yes* = use Gronbech-Jensen/Farago formulation + *omega* value = *no* or *yes* + *no* = do not thermostat rotational degrees of freedom via the angular velocity + *yes* = do thermostat rotational degrees of freedom via the angular velocity + *scale* values = type ratio + type = atom type (1-N) + ratio = factor by which to scale the damping coefficient + *tally* value = *no* or *yes* + *no* = do not tally the energy added/subtracted to atoms + *yes* = do tally the energy added/subtracted to atoms + *zero* value = *no* or *yes* + *no* = do not set total random force to zero + *yes* = set total random force to zero + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 boundary langevin 1.0 1.0 1000.0 699483 + fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5 + fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333 + +Description +""""""""""" + +Apply a Langevin thermostat as described in :ref:`(Schneider) ` +to a group of atoms which models an interaction with a background +implicit solvent. Used with :doc:`fix nve `, this command +performs Brownian dynamics (BD), since the total force on each atom +will have the form: + +.. parsed-literal:: + + F = Fc + Ff + Fr + Ff = - (m / damp) v + Fr is proportional to sqrt(Kb T m / (dt damp)) + +Fc is the conservative force computed via the usual inter-particle +interactions (:doc:`pair_style `, +:doc:`bond_style `, etc). + +The Ff and Fr terms are added by this fix on a per-particle basis. +See the :doc:`pair_style dpd/tstat ` command for a +thermostatting option that adds similar terms on a pairwise basis to +pairs of interacting particles. + +Ff is a frictional drag or viscous damping term proportional to the +particle's velocity. The proportionality constant for each atom is +computed as m/damp, where m is the mass of the particle and damp is +the damping factor specified by the user. + +Fr is a force due to solvent atoms at a temperature T randomly bumping +into the particle. As derived from the fluctuation/dissipation +theorem, its magnitude as shown above is proportional to sqrt(Kb T m / +dt damp), where Kb is the Boltzmann constant, T is the desired +temperature, m is the mass of the particle, dt is the timestep size, +and damp is the damping factor. Random numbers are used to randomize +the direction and magnitude of this force as described in +:ref:`(Dunweg) `, where a uniform random number is used (instead of +a Gaussian random number) for speed. + +Note that unless you use the *omega* or *angmom* keywords, the +thermostat effect of this fix is applied to only the translational +degrees of freedom for the particles, which is an important +consideration for finite-size particles, which have rotational degrees +of freedom, are being thermostatted. The translational degrees of +freedom can also have a bias velocity removed from them before +thermostatting takes place; see the description below. + +.. note:: + + Unlike the :doc:`fix nvt ` command which performs + Nose/Hoover thermostatting AND time integration, this fix does NOT + perform time integration. It only modifies forces to effect + thermostatting. Thus you must use a separate time integration fix, + like :doc:`fix nve ` to actually update the velocities and + positions of atoms using the modified forces. Likewise, this fix + should not normally be used on atoms that also have their temperature + controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix temp/rescale ` commands. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +The desired temperature at each timestep is a ramped value during the +run from *Tstart* to *Tstop*. + +*Tstart* can be specified as an equal-style or atom-style +:doc:`variable `. In this case, the *Tstop* setting is +ignored. If the value is a variable, it should be specified as +v_name, where name is the variable name. In this case, the variable +will be evaluated each timestep, and its value used to determine the +target temperature. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent temperature. + +Atom-style variables can specify the same formulas as equal-style +variables but can also include per-atom values, such as atom +coordinates. Thus it is easy to specify a spatially-dependent +temperature with optional time-dependence as well. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that remove a "bias" from the +atom velocities. E.g. removing the center-of-mass velocity from a +group of atoms or removing the x-component of velocity from the +calculation. This is not done by default, but only if the +:doc:`fix_modify ` command is used to assign a temperature +compute to this fix that includes such a bias term. See the doc pages +for individual :doc:`compute commands ` to determine which ones +include a bias. In this case, the thermostat works in the following +manner: bias is removed from each atom, thermostatting is performed on +the remaining thermal degrees of freedom, and the bias is added back +in. + +The *damp* parameter is specified in time units and determines how +rapidly the temperature is relaxed. For example, a value of 100.0 +means to relax the temperature in a timespan of (roughly) 100 time +units (tau or fmsec or psec - see the :doc:`units ` command). +The damp factor can be thought of as inversely related to the +viscosity of the solvent. I.e. a small relaxation time implies a +hi-viscosity solvent and vice versa. See the discussion about gamma +and viscosity in the documentation for the :doc:`fix viscous ` command for more details. + +The random # *seed* must be a positive integer. A Marsaglia random +number generator is used. Each processor uses the input seed to +generate its own unique seed and its own stream of random numbers. +Thus the dynamics of the system will not be identical on two runs on +different numbers of processors. + + +---------- + + +The keyword/value option pairs are used in the following ways. + +The keyword *angmom* and *omega* keywords enable thermostatting of +rotational degrees of freedom in addition to the usual translational +degrees of freedom. This can only be done for finite-size particles. + +A simulation using atom_style sphere defines an omega for finite-size +spheres. A simulation using atom_style ellipsoid defines a finite +size and shape for aspherical particles and an angular momentum. +The Langevin formulas for thermostatting the rotational degrees of +freedom are the same as those above, where force is replaced by +torque, m is replaced by the moment of inertia I, and v is replaced by +omega (which is derived from the angular momentum in the case of +aspherical particles). + +The rotational temperature of the particles can be monitored by the +:doc:`compute temp/sphere ` and :doc:`compute temp/asphere ` commands with their rotate +options. + +For the *omega* keyword there is also a scale factor of 10.0/3.0 that +is applied as a multiplier on the Ff (damping) term in the equation +above and of sqrt(10.0/3.0) as a multiplier on the Fr term. This does +not affect the thermostatting behaviour of the Langevin formalism but +insures that the randomized rotational diffusivity of spherical +particles is correct. + +For the *angmom* keyword a similar scale factor is needed which is +10.0/3.0 for spherical particles, but is anisotropic for aspherical +particles (e.g. ellipsoids). Currently LAMMPS only applies an +isotropic scale factor, and you can choose its magnitude as the +specified value of the *angmom* keyword. If your aspherical particles +are (nearly) spherical than a value of 10.0/3.0 = 3.333 is a good +choice. If they are highly aspherical, a value of 1.0 is as good a +choice as any, since the effects on rotational diffusivity of the +particles will be incorrect regardless. Note that for any reasonable +scale factor, the thermostatting effect of the *angmom* keyword on the +rotational temperature of the aspherical particles should still be +valid. + +The keyword *scale* allows the damp factor to be scaled up or down by +the specified factor for atoms of that type. This can be useful when +different atom types have different sizes or masses. It can be used +multiple times to adjust damp for several atom types. Note that +specifying a ratio of 2 increases the relaxation time which is +equivalent to the solvent's viscosity acting on particles with 1/2 the +diameter. This is the opposite effect of scale factors used by the +:doc:`fix viscous ` command, since the damp factor in fix +*langevin* is inversely related to the gamma factor in fix *viscous*. +Also note that the damping factor in fix *langevin* includes the +particle mass in Ff, unlike fix *viscous*. Thus the mass and size of +different atom types should be accounted for in the choice of ratio +values. + +The keyword *tally* enables the calculation of the cumulative energy +added/subtracted to the atoms as they are thermostatted. Effectively +it is the energy exchanged between the infinite thermal reservoir and +the particles. As described below, this energy can then be printed +out or added to the potential energy of the system to monitor energy +conservation. + +.. note:: + + this accumulated energy does NOT include kinetic energy removed + by the *zero* flag. LAMMPS will print a warning when both options are + active. + +The keyword *zero* can be used to eliminate drift due to the +thermostat. Because the random forces on different atoms are +independent, they do not sum exactly to zero. As a result, this fix +applies a small random force to the entire system, and the +center-of-mass of the system undergoes a slow random walk. If the +keyword *zero* is set to *yes*, the total random force is set exactly +to zero by subtracting off an equal part of it from each atom in the +group. As a result, the center-of-mass of a system with zero initial +momentum will not drift over time. + +The keyword *gjf* can be used to run the :ref:`Gronbech-Jensen/Farago ` time-discretization of the Langevin model. As +described in the papers cited below, the purpose of this method is to +enable longer timesteps to be used (up to the numerical stability +limit of the integrator), while still producing the correct Boltzmann +distribution of atom positions. It is implemented within LAMMPS, by +changing how the the random force is applied so that it is composed of +the average of two random forces representing half-contributions from +the previous and current time intervals. + +In common with all methods based on Verlet integration, the +discretized velocities generated by this method in conjunction with +velocity-Verlet time integration are not exactly conjugate to the +positions. As a result the temperature (computed from the discretized +velocities) will be systematically lower than the target temperature, +by a small amount which grows with the timestep. Nonetheless, the +distribution of atom positions will still be consistent with the +target temperature. + +As an example of using the *gjf* keyword, for molecules containing C-H +bonds, configurational properties generated with dt = 2.5 fs and tdamp += 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity +distribution systematically decreases with increasing timestep, the +method should not be used to generate properties that depend on the +velocity distribution, such as the velocity autocorrelation function +(VACF). In this example, the velocity distribution at dt = 2.5fs +generates an average temperature of 220 K, instead of 300 K. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a temperature :doc:`compute ` +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Langevin thermostatting to the +system's potential energy as part of :doc:`thermodynamic output `. Note that use of this option requires +setting the *tally* keyword to *yes*. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative energy change due to this fix. The scalar value +calculated by this fix is "extensive". Note that calculation of this +quantity requires setting the *tally* keyword to *yes*. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix viscous `, :doc:`fix nvt `, :doc:`pair_style dpd/tstat ` + +Default +""""""" + +The option defaults are angmom = no, omega = no, scale = 1.0 for all +types, tally = no, zero = no, gjf = no. + + +---------- + + +.. _Dunweg: + + + +**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). + +.. _Schneider: + + + +**(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978). + +.. _Gronbech-Jensen: + + + +**(Gronbech-Jensen)** Gronbech-Jensen and Farago, Mol Phys, 111, 983 +(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, +185, 524 (2014) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_langevin_drude.txt b/doc/_sources/fix_langevin_drude.txt new file mode 100644 index 0000000000..80d08c5fdd --- /dev/null +++ b/doc/_sources/fix_langevin_drude.txt @@ -0,0 +1,318 @@ +.. index:: fix langevin/drude + +fix langevin/drude command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* langevin/drude = style name of this fix command +* Tcom = desired temperature of the centers of mass (temperature units) +* damp_com = damping parameter for the thermostat on centers of mass (time units) +* seed_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer) +* Tdrude = desired temperature of the Drude oscillators (temperature units) +* damp_drude = damping parameter for the thermostat on Drude oscillators (time units) +* seed_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer) +* zero or more keyword/value pairs may be appended +* keyword = *zero* +.. parsed-literal:: + + *zero* value = *no* or *yes* + *no* = do not set total random force on centers of mass to zero + *yes* = set total random force on centers of mass to zero + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451 + fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes + +Description +""""""""""" + +Apply two Langevin thermostats as described in :ref:`(Jiang) ` for +thermalizing the reduced degrees of freedom of Drude oscillators. +This link describes how to use the :doc:`thermalized Drude oscillator model ` in LAMMPS and polarizable models in LAMMPS +are discussed in :ref:`this Section `. + +Drude oscillators are a way to simulate polarizables atoms, by +splitting them into a core and a Drude particle bound by a harmonic +bond. The thermalization works by transforming the particles degrees +of freedom by these equations. In these equations upper case denotes +atomic or center of mass values and lower case denotes Drude particle +or dipole values. Primes denote the transformed (reduced) values, +while bare letters denote the original values. + +Velocities: + +.. math:: + + \begin{equation} V' = \frac {M\, V + m\, v} {M'} \end{equation} + + +.. math:: + + \begin{equation} v' = v - V \end{equation} + +Masses: + +.. math:: + + \begin{equation} M' = M + m \end{equation} + + +.. math:: + + \begin{equation} m' = \frac {M\, m } {M'} \end{equation} + +The Langevin forces are computed as + +.. math:: + + \begin{equation} F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' \end{equation} + + +.. math:: + + \begin{equation} f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' \end{equation} + +:math:`F_r'` is a random force proportional to +:math:`\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'} {\mathrm dt\, \mathtt{damp\_com} } }`. :b:math:`f_r'` is a random force proportional to +:math:`\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'} {\mathrm dt\, \mathtt{damp\_drude} } }`. +Then the real forces acting on the particles are computed from the inverse +transform: + +.. math:: + + \begin{equation} F = \frac M {M'}\, F' - f' \end{equation} + + +.. math:: + + \begin{equation} f = \frac m {M'}\, F' + f' \end{equation} + +This fix also thermostates non-polarizable atoms in the group at +temperature *Tcom*, as if they had a massless Drude partner. The +Drude particles themselves need not be in the group. The center of +mass and the dipole are thermostated iff the core atom is in the +group. + +Note that the thermostat effect of this fix is applied to only the +translational degrees of freedom of the particles, which is an +important consideration if finite-size particles, which have +rotational degrees of freedom, are being thermostated. The +translational degrees of freedom can also have a bias velocity removed +from them before thermostating takes place; see the description below. + +.. note:: + + Like the :doc:`fix langevin ` command, this fix does + NOT perform time integration. It only modifies forces to effect + thermostating. Thus you must use a separate time integration fix, like + :doc:`fix nve ` or :doc:`fix nph ` to actually update the + velocities and positions of atoms using the modified forces. + Likewise, this fix should not normally be used on atoms that also have + their temperature controlled by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix temp/rescale ` commands. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostating. + + +---------- + + +This fix requires each atom know whether it is a Drude particle or +not. You must therefore use the :doc:`fix drude ` command to +specify the Drude status of each atom type. + +.. note:: + + only the Drude core atoms need to be in the group specified for + this fix. A Drude electron will be transformed together with its cores + even if it is not itself in the group. It is safe to include Drude + electrons or non-polarizable atoms in the group. The non-polarizable + atoms will simply be thermostatted as if they had a massless Drude + partner (electron). + +.. note:: + + Ghost atoms need to know their velocity for this fix to act + correctly. You must use the :doc:`comm_modify ` command to + enable this, e.g. + +.. parsed-literal:: + + comm_modify vel yes + + +---------- + + +*Tcom* is the target temperature of the centers of mass, which would +be used to thermostate the non-polarizable atoms. *Tdrude* is the +(normally low) target temperature of the core-Drude particle pairs +(dipoles). *Tcom* and *Tdrude* can be specified as an equal-style +:doc:`variable `. If the value is a variable, it should be +specified as v_name, where name is the variable name. In this case, +the variable will be evaluated each timestep, and its value used to +determine the target temperature. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent temperature. + +Like other fixes that perform thermostating, this fix can be used with +:doc:`compute commands ` that remove a "bias" from the atom +velocities. E.g. removing the center-of-mass velocity from a group of +atoms. This is not done by default, but only if the +:doc:`fix_modify ` command is used to assign a temperature +compute to this fix that includes such a bias term. See the doc pages +for individual :doc:`compute commands ` to determine which ones +include a bias. In this case, the thermostat works in the following +manner: bias is removed from each atom, thermostating is performed on +the remaining thermal degrees of freedom, and the bias is added back +in. NOTE: this feature has not been tested. + +Note: The temperature thermostating the core-Drude particle pairs +should be chosen low enough, so as to mimic as closely as possible the +self-consistent minimization. It must however be high enough, so that +the dipoles can follow the local electric field exerted by the +neighbouring atoms. The optimal value probably depends on the +temperature of the centers of mass and on the mass of the Drude +particles. + +*damp_com* is the characteristic time for reaching thermal equilibrium +of the centers of mass. For example, a value of 100.0 means to relax +the temperature of the centers of mass in a timespan of (roughly) 100 +time units (tau or fmsec or psec - see the :doc:`units ` +command). *damp_drude* is the characteristic time for reaching +thermal equilibrium of the dipoles. It is typically a few timesteps. + +The number *seed_com* and *seed_drude* are positive integers. They set +the seeds of the Marsaglia random number generators used for +generating the random forces on centers of mass and on the +dipoles. Each processor uses the input seed to generate its own unique +seed and its own stream of random numbers. Thus the dynamics of the +system will not be identical on two runs on different numbers of +processors. + +The keyword *zero* can be used to eliminate drift due to the +thermostat on centers of mass. Because the random forces on different +centers of mass are independent, they do not sum exactly to zero. As +a result, this fix applies a small random force to the entire system, +and the momentum of the total center of mass of the system undergoes a +slow random walk. If the keyword *zero* is set to *yes*, the total +random force on the centers of mass is set exactly to zero by +subtracting off an equal part of it from each center of mass in the +group. As a result, the total center of mass of a system with zero +initial momentum will not drift over time. + +The actual temperatures of cores and Drude particles, in +center-of-mass and relative coordinates, respectively, can be +calculated using the :doc:`compute temp/drude ` +command. + + +---------- + + +Usage example for rigid bodies in the NPT ensemble: + +.. parsed-literal:: + + comm_modify vel yes + fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes + fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500. + fix NVE DRUDES nve + compute TDRUDE all temp/drude + thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2] + +Comments: + +* Drude particles should not be in the rigid group, otherwise the Drude + oscillators will be frozen and the system will lose its + polarizability. +* *zero yes* avoids a drift of the center of mass of + the system, but is a bit slower. +* Use two different random seeds to avoid unphysical correlations. +* Temperature is controlled by the fix *langevin/drude*, so the + time-integration fixes do not thermostate. Don't forget to + time-integrate both cores and Drude particles. +* Pressure is time-integrated only once by using *nve* for Drude + particles and *nph* for atoms/cores (or vice versa). Do not use *nph* + for both. +* The temperatures of cores and Drude particles are calculated by + :doc:`compute temp/drude ` +* Contrary to the alternative thermostating using Nose-Hoover thermostat + fix *npt* and :doc:`fix drude/transform `, the + *fix_modify* command is not required here, because the fix *nph* + computes the global pressure even if its group is *ATOMS*. This is + what we want. If we thermostated *ATOMS* using *npt*, the pressure + should be the global one, but the temperature should be only that of + the cores. That's why the command *fix_modify* should be called in + that case. + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a temperature :doc:`compute ` +you have defined to this fix which will be used in its thermostating +procedure, as described above. For consistency, the group used by the +compute should include the group of this fix and the Drude particles. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix langevin `, +:doc:`fix drude `, +:doc:`fix drude/transform `, +:doc:`compute temp/drude `, +:doc:`pair_style thole ` + +Default +""""""" + +The option defaults are zero = no. + + +---------- + + +.. _Jiang: + + + +**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J +Phys Chem Lett, 2, 87-92 (2011). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_langevin_eff.txt b/doc/_sources/fix_langevin_eff.txt new file mode 100644 index 0000000000..08f95ed04f --- /dev/null +++ b/doc/_sources/fix_langevin_eff.txt @@ -0,0 +1,136 @@ +.. index:: fix langevin/eff + +fix langevin/eff command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID langevin/eff Tstart Tstop damp seed keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* langevin/eff = style name of this fix command +* Tstart,Tstop = desired temperature at start/end of run (temperature units) +* damp = damping parameter (time units) +* seed = random number seed to use for white noise (positive integer) +* zero or more keyword/value pairs may be appended +.. parsed-literal:: + + keyword = *scale* or *tally* or *zero* + *scale* values = type ratio + type = atom type (1-N) + ratio = factor by which to scale the damping coefficient + *tally* values = *no* or *yes* + *no* = do not tally the energy added/subtracted to atoms + *yes* = do tally the energy added/subtracted to atoms + +.. parsed-literal:: + + *zero* value = *no* or *yes* + *no* = do not set total random force to zero + *yes* = set total random force to zero + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 boundary langevin/eff 1.0 1.0 10.0 699483 + fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 + +Description +""""""""""" + +Apply a Langevin thermostat as described in :ref:`(Schneider) ` +to a group of nuclei and electrons in the :doc:`electron force field ` model. Used with :doc:`fix nve/eff `, +this command performs Brownian dynamics (BD), since the total force on +each atom will have the form: + +.. parsed-literal:: + + F = Fc + Ff + Fr + Ff = - (m / damp) v + Fr is proportional to sqrt(Kb T m / (dt damp)) + +Fc is the conservative force computed via the usual inter-particle +interactions (:doc:`pair_style `). + +The Ff and Fr terms are added by this fix on a per-particle basis. + +The operation of this fix is exactly like that described by the :doc:`fix langevin ` command, except that the thermostatting +is also applied to the radial electron velocity for electron +particles. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a temperature :doc:`compute ` +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Langevin thermostatting to the +system's potential energy as part of :doc:`thermodynamic output `. Note that use of this option requires +setting the *tally* keyword to *yes*. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative energy change due to this fix. The scalar value +calculated by this fix is "extensive". Note that calculation of this +quantity requires setting the *tally* keyword to *yes*. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +This fix is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix langevin ` + +Default +""""""" + +The option defaults are scale = 1.0 for all types and tally = no. + + +---------- + + +.. _Dunweg: + + + +**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991). + +.. _Schneider: + + + +**(Schneider)** Schneider and Stoll, Phys Rev B, 17, 1302 (1978). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_lb_fluid.txt b/doc/_sources/fix_lb_fluid.txt new file mode 100644 index 0000000000..f74514c9b9 --- /dev/null +++ b/doc/_sources/fix_lb_fluid.txt @@ -0,0 +1,410 @@ +.. index:: fix lb/fluid + +fix lb/fluid command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID lb/fluid nevery LBtype viscosity density keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* lb/fluid = style name of this fix command +* nevery = update the lattice-Boltzmann fluid every this many timesteps +* LBtype = 1 to use the standard finite difference LB integrator, + 2 to use the LB integrator of :ref:`Ollila et al. ` +* viscosity = the fluid viscosity (units of mass/(time*length)). +* density = the fluid density. +* zero or more keyword/value pairs may be appended +* keyword = *setArea* or *setGamma* or *scaleGamma* or *dx* or *dm* or *a0* or *noise* or *calcforce* or *trilinear* or *D3Q19* or *read_restart* or *write_restart* or *zwall_velocity* or *bodyforce* or *printfluid* +.. parsed-literal:: + + *setArea* values = type node_area + type = atom type (1-N) + node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default). + *setGamma* values = gamma + gamma = user set value for the force coupling constant. + *scaleGamma* values = type gammaFactor + type = atom type (1-N) + gammaFactor = factor to scale the *setGamma* gamma value by, for the specified atom type. + *dx* values = dx_LB = the lattice spacing. + *dm* values = dm_LB = the lattice-Boltzmann mass unit. + *a0* values = a_0_real = the square of the speed of sound in the fluid. + *noise* values = Temperature seed + Temperature = fluid temperature. + seed = random number generator seed (positive integer) + *calcforce* values = N forcegroup-ID + N = output the force and torque every N timesteps + forcegroup-ID = ID of the particle group to calculate the force and torque of + *trilinear* values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil). + *D3Q19* values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice). + *read_restart* values = restart file = name of the restart file to use to restart a fluid run. + *write_restart* values = N = write a restart file every N MD timesteps. + *zwall_velocity* values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax). + *bodyforce* values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid. + *printfluid* values = N = print the fluid density and velocity at each grid point every N timesteps. + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1 + fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873 + +Description +""""""""""" + +Implement a lattice-Boltzmann fluid on a uniform mesh covering the LAMMPS +simulation domain. The MD particles described by *group-ID* apply a velocity +dependent force to the fluid. + +The lattice-Boltzmann algorithm solves for the fluid motion governed by +the Navier Stokes equations, + +.. image:: Eqs/fix_lb_fluid_navierstokes.jpg + :align: center + +with, + +.. image:: Eqs/fix_lb_fluid_viscosity.jpg + :align: center + +where rho is the fluid density, u is the local fluid velocity, sigma +is the stress tensor, F is a local external force, and eta and Lambda +are the shear and bulk viscosities respectively. Here, we have +implemented + +.. image:: Eqs/fix_lb_fluid_stress.jpg + :align: center + +with a_0 set to 1/3 (dx/dt)^2 by default. + +The algorithm involves tracking the time evolution of a set of partial +distribution functions which evolve according to a velocity +discretized version of the Boltzmann equation, + +.. image:: Eqs/fix_lb_fluid_boltzmann.jpg + :align: center + +where the first term on the right hand side represents a single time +relaxation towards the equilibrium distribution function, and tau is a +parameter physically related to the viscosity. On a technical note, +we have implemented a 15 velocity model (D3Q15) as default; however, +the user can switch to a 19 velocity model (D3Q19) through the use of +the *D3Q19* keyword. This fix provides the user with the choice of +two algorithms to solve this equation, through the specification of +the keyword *LBtype*. If *LBtype* is set equal to 1, the standard +finite difference LB integrator is used. If *LBtype* is set equal to +2, the algorithm of :ref:`Ollila et al. ` is used. + +Physical variables are then defined in terms of moments of the distribution +functions, + +.. image:: Eqs/fix_lb_fluid_properties.jpg + :align: center + +Full details of the lattice-Boltzmann algorithm used can be found in +:ref:`Mackay et al. `. + +The fluid is coupled to the MD particles described by *group-ID* +through a velocity dependent force. The contribution to the fluid +force on a given lattice mesh site j due to MD particle alpha is +calculated as: + +.. image:: Eqs/fix_lb_fluid_fluidforce.jpg + :align: center + +where v_n is the velocity of the MD particle, u_f is the fluid +velocity interpolated to the particle location, and gamma is the force +coupling constant. Zeta is a weight assigned to the grid point, +obtained by distributing the particle to the nearest lattice sites. +For this, the user has the choice between a trilinear stencil, which +provides a support of 8 lattice sites, or the immersed boundary method +Peskin stencil, which provides a support of 64 lattice sites. While +the Peskin stencil is seen to provide more stable results, the +trilinear stencil may be better suited for simulation of objects close +to walls, due to its smaller support. Therefore, by default, the +Peskin stencil is used; however the user may switch to the trilinear +stencil by specifying the keyword, *trilinear*. + +By default, the force coupling constant, gamma, is calculated according to + +.. image:: Eqs/fix_lb_fluid_gammadefault.jpg + :align: center + +Here, m_v is the mass of the MD particle, m_u is a representative +fluid mass at the particle location, and dt_collision is a collision +time, chosen such that tau/dt_collision = 1 (see :ref:`Mackay and Denniston ` for full details). In order to calculate m_u, the +fluid density is interpolated to the MD particle location, and +multiplied by a volume, node_area*dx_lb, where node_area represents +the portion of the surface area of the composite object associated +with a given MD particle. By default, node_area is set equal to +dx_lb*dx_lb; however specific values for given atom types can be set +using the *setArea* keyword. + +The user also has the option of specifying their own value for the +force coupling constant, for all the MD particles associated with the +fix, through the use of the *setGamma* keyword. This may be useful +when modelling porous particles. See :ref:`Mackay et al. ` for a +detailed description of the method by which the user can choose an +appropriate gamma value. + +.. note:: + + while this fix applies the force of the particles on the fluid, + it does not apply the force of the fluid to the particles. When the + force coupling constant is set using the default method, there is only + one option to include this hydrodynamic force on the particles, and + that is through the use of the :doc:`lb/viscous ` fix. + This fix adds the hydrodynamic force to the total force acting on the + particles, after which any of the built-in LAMMPS integrators can be + used to integrate the particle motion. However, if the user specifies + their own value for the force coupling constant, as mentioned in + :ref:`Mackay et al. `, the built-in LAMMPS integrators may prove to + be unstable. Therefore, we have included our own integrators :doc:`fix lb/rigid/pc/sphere `, and :doc:`fix lb/pc `, to solve for the particle motion in these + cases. These integrators should not be used with the + :doc:`lb/viscous ` fix, as they add hydrodynamic forces + to the particles directly. In addition, they can not be used if the + force coupling constant has been set the default way. + +.. note:: + + if the force coupling constant is set using the default method, + and the :doc:`lb/viscous ` fix is NOT used to add the + hydrodynamic force to the total force acting on the particles, this + physically corresponds to a situation in which an infinitely massive + particle is moving through the fluid (since collisions between the + particle and the fluid do not act to change the particle's velocity). + Therefore, the user should set the mass of the particle to be + significantly larger than the mass of the fluid at the particle + location, in order to approximate an infinitely massive particle (see + the dragforce test run for an example). + + +---------- + + +Inside the fix, parameters are scaled by the lattice-Boltzmann +timestep, dt, grid spacing, dx, and mass unit, dm. dt is set equal to +(nevery*dt_MD), where dt_MD is the MD timestep. By default, dm is set +equal to 1.0, and dx is chosen so that tau/(dt) = +(3*eta*dt)/(rho*dx^2) is approximately equal to 1. However, the user +has the option of specifying their own values for dm, and dx, by using +the optional keywords *dm*, and *dx* respectively. + +.. note:: + + Care must be taken when choosing both a value for dx, and a + simulation domain size. This fix uses the same subdivision of the + simulation domain among processors as the main LAMMPS program. In + order to uniformly cover the simulation domain with lattice sites, the + lengths of the individual LAMMPS subdomains must all be evenly + divisible by dx. If the simulation domain size is cubic, with equal + lengths in all dimensions, and the default value for dx is used, this + will automatically be satisfied. + +Physical parameters describing the fluid are specified through +*viscosity*, *density*, and *a0*. If the force coupling constant is +set the default way, the surface area associated with the MD particles +is specified using the *setArea* keyword. If the user chooses to +specify a value for the force coupling constant, this is set using the +*setGamma* keyword. These parameters should all be given in terms of +the mass, distance, and time units chosen for the main LAMMPS run, as +they are scaled by the LB timestep, lattice spacing, and mass unit, +inside the fix. + + +---------- + + +The *setArea* keyword allows the user to associate a surface area with +a given atom type. For example if a spherical composite object of +radius R is represented as a spherical shell of N evenly distributed +MD particles, all of the same type, the surface area per particle +associated with that atom type should be set equal to 4*pi*R^2/N. +This keyword should only be used if the force coupling constant, +gamma, is set the default way. + +The *setGamma* keyword allows the user to specify their own value for +the force coupling constant, gamma, instead of using the default +value. + +The *scaleGamma* keyword should be used in conjunction with the +*setGamma* keyword, when the user wishes to specify different gamma +values for different atom types. This keyword allows the user to +scale the *setGamma* gamma value by a factor, gammaFactor, for a given +atom type. + +The *dx* keyword allows the user to specify a value for the LB grid +spacing. + +The *dm* keyword allows the user to specify the LB mass unit. + +If the *a0* keyword is used, the value specified is used for the +square of the speed of sound in the fluid. If this keyword is not +present, the speed of sound squared is set equal to (1/3)*(dx/dt)^2. +Setting a0 > (dx/dt)^2 is not allowed, as this may lead to +instabilities. + +If the *noise* keyword is used, followed by a a positive temperature +value, and a positive integer random number seed, a thermal +lattice-Boltzmann algorithm is used. If *LBtype* is set equal to 1 +(i.e. the standard LB integrator is chosen), the thermal LB algorithm +of :ref:`Adhikari et al. ` is used; however if *LBtype* is set +equal to 2 both the LB integrator, and thermal LB algorithm described +in :ref:`Ollila et al. ` are used. + +If the *calcforce* keyword is used, both the fluid force and torque +acting on the specified particle group are printed to the screen every +N timesteps. + +If the keyword *trilinear* is used, the trilinear stencil is used to +interpolate the particle nodes onto the fluid mesh. By default, the +immersed boundary method, Peskin stencil is used. Both of these +interpolation methods are described in :ref:`Mackay et al. `. + +If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is +used by the lattice-Boltzmann algorithm. By default, the 15 velocity +(D3Q15) lattice is used. + +If the keyword *write_restart* is used, followed by a positive +integer, N, a binary restart file is printed every N LB timesteps. +This restart file only contains information about the fluid. +Therefore, a LAMMPS restart file should also be written in order to +print out full details of the simulation. + +.. note:: + + When a large number of lattice grid points are used, the restart + files may become quite large. + +In order to restart the fluid portion of the simulation, the keyword +*read_restart* is specified, followed by the name of the binary +lb_fluid restart file to be used. + +If the *zwall_velocity* keyword is used y-velocities are assigned to +the lower and upper walls. This keyword requires the presence of +walls in the z-direction. This is set by assigning fixed boundary +conditions in the z-direction. If fixed boundary conditions are +present in the z-direction, and this keyword is not used, the walls +are assumed to be stationary. + +If the *bodyforce* keyword is used, a constant body force is added to +the fluid, defined by it's x, y and z components. + +If the *printfluid* keyword is used, followed by a positive integer, N, +the fluid densities and velocities at each lattice site are printed to the +screen every N timesteps. + + +---------- + + +For further details, as well as descriptions and results of several +test runs, see :ref:`Mackay et al. `. Please include a citation to +this paper if the lb_fluid fix is used in work contributing to +published research. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Due to the large size of the fluid data, this fix writes it's own +binary restart files, if requested, independent of the main LAMMPS +:doc:`binary restart files `; no information about *lb_fluid* +is written to the main LAMMPS :doc:`binary restart files `. + +None of the :doc:`fix_modify ` options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various :ref:`output commands <4_15>`. No +parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-LB package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix can only be used with an orthogonal simulation domain. + +Walls have only been implemented in the z-direction. Therefore, the +boundary conditions, as specified via the main LAMMPS boundary command +must be periodic for x and y, and either fixed or periodic for z. +Shrink-wrapped boundary conditions are not permitted with this fix. + +This fix must be used before any of :doc:`fix lb/viscous `, :doc:`fix lb/momentum `, :doc:`fix lb/rigid/pc/sphere `, and/ or :doc:`fix lb/pc ` , as the fluid needs to be initialized before +any of these routines try to access its properties. In addition, in +order for the hydrodynamic forces to be added to the particles, this +fix must be used in conjunction with the +:doc:`lb/viscous ` fix if the force coupling constant is +set by default, or either the :doc:`lb/viscous ` fix or +one of the :doc:`lb/rigid/pc/sphere ` or +:doc:`lb/pc ` integrators, if the user chooses to specifiy +their own value for the force coupling constant. + +Related commands +"""""""""""""""" + +:doc:`fix lb/viscous `, :doc:`fix lb/momentum `, :doc:`fix lb/rigid/pc/sphere `, :doc:`fix lb/pc ` + +Default +""""""" + +By default, the force coupling constant is set according to + +.. image:: Eqs/fix_lb_fluid_gammadefault.jpg + :align: center + +and an area of dx_lb^2 per node, used to calculate the fluid mass at +the particle node location, is assumed. + +dx is chosen such that tau/(delta t_LB) = +(3 eta dt_LB)/(rho dx_lb^2) is approximately equal to 1. +dm is set equal to 1.0. +a0 is set equal to (1/3)*(dx_lb/dt_lb)^2. +The Peskin stencil is used as the default interpolation method. +The D3Q15 lattice is used for the lattice-Boltzmann algorithm. +If walls are present, they are assumed to be stationary. + + +---------- + + +.. _Ollila: + + + +**(Ollila et al.)** Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902. + +.. _Mackay: + + + +**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. + +.. _Mackay2: + + + +**(Mackay and Denniston)** Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298. + +.. _Adhikari: + + + +**(Adhikari et al.)** Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_lb_momentum.txt b/doc/_sources/fix_lb_momentum.txt new file mode 100644 index 0000000000..beb72ba4c4 --- /dev/null +++ b/doc/_sources/fix_lb_momentum.txt @@ -0,0 +1,87 @@ +.. index:: fix lb/momentum + +fix lb/momentum command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID lb/momentum nevery keyword values ... + +* ID, group-ID are documented in the :doc:`fix ` command +* lb/momentum = style name of this fix command +* nevery = adjust the momentum every this many timesteps +* zero or more keyword/value pairs may be appended +* keyword = *linear* +.. parsed-literal:: + + *linear* values = xflag yflag zflag + xflag,yflag,zflag = 0/1 to exclude/include each dimension. + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 sphere lb/momentum + fix 1 all lb/momentum linear 1 1 0 + +Description +""""""""""" + +This fix is based on the :doc:`fix momentum ` command, and +was created to be used in place of that command, when a +lattice-Boltzmann fluid is present. + +Zero the total linear momentum of the system, including both the atoms +specified by group-ID and the lattice-Boltzmann fluid every nevery +timesteps. This is accomplished by adjusting the particle velocities +and the fluid velocities at each lattice site. + +.. note:: + + This fix only considers the linear momentum of the system. + +By default, the subtraction is performed for each dimension. This can +be changed by specifying the keyword *linear*, along with a set of +three flags set to 0/1 in order to exclude/ include the corresponding +dimension. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands <4_15>`. No parameter of this fix can be +used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +Can only be used if a lattice-Boltzmann fluid has been created via the +:doc:`fix lb/fluid ` command, and must come after this +command. + +This fix is part of the USER-LB package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix momentum `, :doc:`fix lb/fluid ` + +Default +""""""" + +Zeros the total system linear momentum in each dimension. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_lb_pc.txt b/doc/_sources/fix_lb_pc.txt new file mode 100644 index 0000000000..70012c36f1 --- /dev/null +++ b/doc/_sources/fix_lb_pc.txt @@ -0,0 +1,72 @@ +.. index:: fix lb/pc + +fix lb/pc command +================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID lb/pc + +* ID, group-ID are documented in the :doc:`fix ` command +* lb/pc = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all lb/pc + +Description +""""""""""" + +Update the positions and velocities of the individual particles +described by *group-ID*, experiencing velocity-dependent hydrodynamic +forces, using the integration algorithm described in :ref:`Mackay et al. `. This integration algorithm should only be used if a +user-specified value for the force-coupling constant used in :doc:`fix lb/fluid ` has been set; do not use this integration +algorithm if the force coupling constant has been set by default. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands <4_15>`. No parameter of this fix can be +used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-LB package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Can only be used if a lattice-Boltzmann fluid has been created via the +:doc:`fix lb/fluid ` command, and must come after this +command. + +Related commands +"""""""""""""""" + +:doc:`fix lb/fluid ` :doc:`fix lb/rigid/pc/sphere ` + +**Default:** None. + + +---------- + + +.. _Mackay: + + + +**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_lb_rigid_pc_sphere.txt b/doc/_sources/fix_lb_rigid_pc_sphere.txt new file mode 100644 index 0000000000..0763276b46 --- /dev/null +++ b/doc/_sources/fix_lb_rigid_pc_sphere.txt @@ -0,0 +1,167 @@ +.. index:: fix lb/rigid/pc/sphere + +fix lb/rigid/pc/sphere command +============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID lb/rigid/pc/sphere bodystyle args keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* lb/rigid/pc/sphere = style name of this fix command +* bodystyle = *single* or *molecule* or *group* +* *single* args = none + *molecule* args = none + *group* args = N groupID1 groupID2 ... + N = # of groups + zero or more keyword/value pairs may be appended +* keyword = *force* or *torque* or *innerNodes* +.. parsed-literal:: + + *force* values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass force is active + *torque* values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass torque is active + *innerNodes* values = innergroup-ID + innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 spheres lb/rigid/pc/sphere + fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms + +Description +""""""""""" + +This fix is based on the :doc:`fix rigid ` command, and was +created to be used in place of that fix, to integrate the equations of +motion of spherical rigid bodies when a lattice-Boltzmann fluid is +present with a user-specified value of the force-coupling constant. +The fix uses the integration algorithm described in :ref:`Mackay et al. ` to update the positions, velocities, and orientations of +a set of spherical rigid bodies experiencing velocity dependent +hydrodynamic forces. The spherical bodies are assumed to rotate as +solid, uniform density spheres, with moments of inertia calculated +using the combined sum of the masses of all the constituent particles +(which are assumed to be point particles). + + +---------- + + +By default, all of the atoms that this fix acts on experience a +hydrodynamic force due to the presence of the lattice-Boltzmann fluid. +However, the *innerNodes* keyword allows the user to specify atoms +belonging to a rigid object which do not interact with the +lattice-Boltzmann fluid (i.e. these atoms do not feel a hydrodynamic +force from the lattice-Boltzmann fluid). This can be used to +distinguish between atoms on the surface of a non-porous object, and +those on the inside. + +This feature can be used, for example, when implementing a hard sphere +interaction between two spherical objects. Instead of interactions +occurring between the particles on the surfaces of the two spheres, it +is desirable simply to place an atom at the center of each sphere, +which does not contribute to the hydrodynamic force, and have these +central atoms interact with one another. + + +---------- + + +Apart from the features described above, this fix is very similar to +the rigid fix (although it includes fewer optional arguments, and +assumes the constituent atoms are point particles); see +:doc:`fix_rigid ` for a complete documentation. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about the *rigid* and *rigid/nve* fixes are written to +:doc:`binary restart files `. + +Similar to the :doc:`fix_rigid ` command: " The rigid +fix computes a global scalar which can be accessed by various :ref:`output commands `. The scalar value calculated by +these fixes is "intensive". The scalar is the current temperature of +the collection of rigid bodies. This is averaged over all rigid +bodies and their translational and rotational degrees of freedom. The +translational energy of a rigid body is 1/2 m v^2, where m = total +mass of the body and v = the velocity of its center of mass. The +rotational energy of a rigid body is 1/2 I w^2, where I = the moment +of inertia tensor of the body and w = its angular velocity. Degrees +of freedom constrained by the *force* and *torque* keywords are +removed from this calculation." + +"All of these fixes compute a global array of values which can be +accessed by various :ref:`output commands `. +The number of rows in the array is equal to the number of rigid +bodies. The number of columns is 15. Thus for each rigid body, 15 +values are stored: the xyz coords of the center of mass (COM), the xyz +components of the COM velocity, the xyz components of the force acting +on the COM, the xyz components of the torque acting on the COM, and +the xyz image flags of the COM, which have the same meaning as image +flags for atom positions (see the "dump" command). The force and +torque values in the array are not affected by the *force* and +*torque* keywords in the fix rigid command; they reflect values before +any changes are made by those keywords. + +The ordering of the rigid bodies (by row in the array) is as follows. +For the *single* keyword there is just one rigid body. For the +*molecule* keyword, the bodies are ordered by ascending molecule ID. +For the *group* keyword, the list of group IDs determines the ordering +of bodies. + +The array values calculated by these fixes are "intensive", meaning +they are independent of the number of atoms in the simulation. + +No parameter of these fixes can be used with the *start/stop* keywords +of the :doc:`run ` command. These fixes are not invoked during +:doc:`energy minimization `. " + +Restrictions +"""""""""""" + + +This fix is part of the USER-LB package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Can only be used if a lattice-Boltzmann fluid has been created via the +:doc:`fix lb/fluid ` command, and must come after this +command. Should only be used if the force coupling constant used in +:doc:`fix lb/fluid ` has been set by the user; this +integration fix cannot be used if the force coupling constant is set +by default. + +Related commands +"""""""""""""""" + +:doc:`fix lb/fluid `, :doc:`fix lb/pc ` + +Default +""""""" + +The defaults are force * on on on, and torque * on on on. + + +---------- + + +.. _Mackay: + + + +**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_lb_viscous.txt b/doc/_sources/fix_lb_viscous.txt new file mode 100644 index 0000000000..f32fffbf60 --- /dev/null +++ b/doc/_sources/fix_lb_viscous.txt @@ -0,0 +1,107 @@ +.. index:: fix lb/viscous + +fix lb/viscous command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID lb/viscous + +* ID, group-ID are documented in :doc:`fix ` command +* lb/viscous = style name of this fix command + +Examples +"""""""" + +fix 1 flow lb/viscous + +Description +""""""""""" + +This fix is similar to the :doc:`fix viscous ` command, and +is to be used in place of that command when a lattice-Boltzmann fluid +is present, and the user wishes to integrate the particle motion using +one of the built in LAMMPS integrators. + +This fix adds a force, F = - Gamma*(velocity-fluid_velocity), to each +atom, where Gamma is the force coupling constant described in the :doc:`fix lb/fluid ` command (which applies an equal and +opposite force to the fluid). + +.. note:: + + This fix should only be used in conjunction with one of the + built in LAMMPS integrators; it should not be used with the :doc:`fix lb/pc ` or :doc:`fix lb/rigid/pc/sphere ` integrators, which + already include the hydrodynamic forces. These latter fixes should + only be used if the force coupling constant has been set by the user + (instead of using the default value); if the default force coupling + value is used, then this fix provides the only method for adding the + hydrodynamic forces to the particles. + + +---------- + + +For further details, as well as descriptions and results of several +test runs, see :ref:`Mackay et al. `. Please include a citation to +this paper if this fix is used in work contributing to published +research. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +As described in the :doc:`fix viscous ` documentation: + +"No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. This fix should only +be used with damped dynamics minimizers that allow for +non-conservative forces. See the :doc:`min_style ` command +for details." + +Restrictions +"""""""""""" + + +This fix is part of the USER-LB package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Can only be used if a lattice-Boltzmann fluid has been created via the +:doc:`fix lb/fluid ` command, and must come after this +command. + +This fix should not be used if either the :doc:`fix lb/pc ` +or :doc:`fix lb/rigid/pc/sphere ` integrator is +used. + +Related commands +"""""""""""""""" + +:doc:`fix lb/fluid `, :doc:`fix lb/pc `, :doc:`fix lb/rigid/pc/sphere ` + +**Default:** none + + +---------- + + +.. _Mackay: + + + +**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_lineforce.txt b/doc/_sources/fix_lineforce.txt new file mode 100644 index 0000000000..4894a4a7d1 --- /dev/null +++ b/doc/_sources/fix_lineforce.txt @@ -0,0 +1,60 @@ +.. index:: fix lineforce + +fix lineforce command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID lineforce x y z + +* ID, group-ID are documented in :doc:`fix ` command +* lineforce = style name of this fix command +* x y z = direction of line as a 3-vector + +Examples +"""""""" + +.. parsed-literal:: + + fix hold boundary lineforce 0.0 1.0 1.0 + +Description +""""""""""" + +Adjust the forces on each atom in the group so that only the component +of force along the linear direction specified by the vector (x,y,z) +remains. This is done by subtracting out components of force in the +plane perpendicular to the line. + +If the initial velocity of the atom is 0.0 (or along the line), then +it should continue to move along the line thereafter. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix planeforce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_meso.txt b/doc/_sources/fix_meso.txt new file mode 100644 index 0000000000..42d8658b4c --- /dev/null +++ b/doc/_sources/fix_meso.txt @@ -0,0 +1,60 @@ +.. index:: fix meso + +fix meso command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID meso + +* ID, group-ID are documented in :doc:`fix ` command +* meso = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all meso + +Description +""""""""""" + +Perform time integration to update position, velocity, internal energy +and local density for atoms in the group each timestep. This fix is +needed to time-integrate mesoscopic systems where particles carry +internal variables such as SPH or DPDE. + +See `this PDF guide `_ to using SPH in +LAMMPS. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-SPH package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +"fix meso/stationary" + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_meso_stationary.txt b/doc/_sources/fix_meso_stationary.txt new file mode 100644 index 0000000000..6fcdbcd443 --- /dev/null +++ b/doc/_sources/fix_meso_stationary.txt @@ -0,0 +1,61 @@ +.. index:: fix meso/stationary + +fix meso/stationary command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID meso/stationary + +* ID, group-ID are documented in :doc:`fix ` command +* meso = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 boundary meso/stationary + +Description +""""""""""" + +Perform time integration to update internal energy and local density, +but not position or velocity for atoms in the group each timestep. +This fix is needed for SPH simulations to correctly time-integrate +fixed boundary particles which constrain a fluid to a given region in +space. + +See `this PDF guide `_ to using SPH in +LAMMPS. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-SPH package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +"fix meso" + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_modify.txt b/doc/_sources/fix_modify.txt new file mode 100644 index 0000000000..1842785de4 --- /dev/null +++ b/doc/_sources/fix_modify.txt @@ -0,0 +1,84 @@ +.. index:: fix_modify + +fix_modify command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix_modify fix-ID keyword value ... + +* fix-ID = ID of the fix to modify +* one or more keyword/value pairs may be appended +* keyword = *temp* or *press* or *energy* +.. parsed-literal:: + + *temp* value = compute ID that calculates a temperature + *press* value = compute ID that calculates a pressure + *energy* value = *yes* or *no* + + + +Examples +"""""""" + +.. parsed-literal:: + + fix_modify 3 temp myTemp press myPress + fix_modify 1 energy yes + +Description +""""""""""" + +Modify one or more parameters of a previously defined fix. Only +specific fix styles support specific parameters. See the doc pages +for individual fix commands for info on which ones support which +fix_modify parameters. + +The *temp* keyword is used to determine how a fix computes +temperature. The specified compute ID must have been previously +defined by the user via the :doc:`compute ` command and it must +be a style of compute that calculates a temperature. All fixes that +compute temperatures define their own compute by default, as described +in their documentation. Thus this option allows the user to override +the default method for computing T. + +The *press* keyword is used to determine how a fix computes pressure. +The specified compute ID must have been previously defined by the user +via the :doc:`compute ` command and it must be a style of +compute that calculates a pressure. All fixes that compute pressures +define their own compute by default, as described in their +documentation. Thus this option allows the user to override the +default method for computing P. + +For fixes that calculate a contribution to the potential energy of the +system, the *energy* keyword will include that contribution in +thermodynamic output of potential energy. See the +:doc:`thermo_style ` command for info on how potential +energy is output. The contribution by itself can be printed by using +the keyword f_ID in the thermo_style custom command, where ID is the +fix-ID of the appropriate fix. Note that you must use this setting +for a fix if you are using it when performing an :doc:`energy minimization ` and if you want the energy and forces it +produces to be part of the optimization criteria. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix `, :doc:`compute temp `, :doc:`compute pressure `, :doc:`thermo_style ` + +Default +""""""" + +The option defaults are temp = ID defined by fix, press = ID defined +by fix, energy = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_momentum.txt b/doc/_sources/fix_momentum.txt new file mode 100644 index 0000000000..ce6d67b818 --- /dev/null +++ b/doc/_sources/fix_momentum.txt @@ -0,0 +1,89 @@ +.. index:: fix momentum + +fix momentum command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID momentum N keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* momentum = style name of this fix command +* N = adjust the momentum every this many timesteps + one or more keyword/value pairs may be appended +* keyword = *linear* or *angular* or *rescale* +.. parsed-literal:: + + *linear* values = xflag yflag zflag + xflag,yflag,zflag = 0/1 to exclude/include each dimension + *angular* values = none + +.. parsed-literal:: + + *rescale* values = none + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all momentum 1 linear 1 1 0 + fix 1 all momentum 1 linear 1 1 1 rescale + fix 1 all momentum 100 linear 1 1 1 angular + +Description +""""""""""" + +Zero the linear and/or angular momentum of the group of atoms every N +timesteps by adjusting the velocities of the atoms. One (or both) of +the *linear* or *angular* keywords must be specified. + +If the *linear* keyword is used, the linear momentum is zeroed by +subtracting the center-of-mass velocity of the group from each atom. +This does not change the relative velocity of any pair of atoms. One +or more dimensions can be excluded from this operation by setting the +corresponding flag to 0. + +If the *angular* keyword is used, the angular momentum is zeroed by +subtracting a rotational component from each atom. + +This command can be used to insure the entire collection of atoms (or +a subset of them) does not drift or rotate during the simulation due +to random perturbations (e.g. :doc:`fix langevin ` +thermostatting). + +The *rescale* keyword enables conserving the kinetic energy of the group +of atoms by rescaling the velocities after the momentum was removed. + +Note that the :doc:`velocity ` command can be used to create +initial velocities with zero aggregate linear and/or angular momentum. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix recenter `, :doc:`velocity ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_move.txt b/doc/_sources/fix_move.txt new file mode 100644 index 0000000000..103b4af3c1 --- /dev/null +++ b/doc/_sources/fix_move.txt @@ -0,0 +1,257 @@ +.. index:: fix move + +fix move command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID move style args keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* move = style name of this fix command +* style = *linear* or *wiggle* or *rotate* or *variable* +.. parsed-literal:: + + *linear* args = Vx Vy Vz + Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL + *wiggle* args = Ax Ay Az period + Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL + period = period of oscillation (time units) + *rotate* args = Px Py Pz Rx Ry Rz period + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + period = period of rotation (time units) + *variable* args = v_dx v_dy v_dz v_vx v_vy v_vz + v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL + v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL + +* zero or more keyword/value pairs may be appended +* keyword = *units* +.. parsed-literal:: + + *units* value = *box* or *lattice* + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box + fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0 + fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL + +Description +""""""""""" + +Perform updates of position and velocity for atoms in the group each +timestep using the specified settings or formulas, without regard to +forces on the atoms. This can be useful for boundary or other atoms, +whose movement can influence nearby atoms. + +.. note:: + + The atoms affected by this fix should not normally be time + integrated by other fixes (e.g. :doc:`fix nve `, :doc:`fix nvt `), since that will change their positions and + velocities twice. + +.. note:: + + As atoms move due to this fix, they will pass thru periodic + boundaries and be remapped to the other side of the simulation box, + just as they would during normal time integration (e.g. via the :doc:`fix nve ` command). It is up to you to decide whether + periodic boundaries are appropriate with the kind of atom motion you + are prescribing with this fix. + +.. note:: + + As dicsussed below, atoms are moved relative to their initial + position at the time the fix is specified. These initial coordinates + are stored by the fix in "unwrapped" form, by using the image flags + associated with each atom. See the :doc:`dump custom ` command + for a discussion of "unwrapped" coordinates. See the Atoms section of + the :doc:`read_data ` command for a discussion of image flags + and how they are set for each atom. You can reset the image flags + (e.g. to 0) before invoking this fix by using the :doc:`set image ` + command. + + +---------- + + +The *linear* style moves atoms at a constant velocity, so that their +position *X* = (x,y,z) as a function of time is given in vector +notation as + +.. parsed-literal:: + + X(t) = X0 + V * delta + +where *X0* = (x0,y0,z0) is their position at the time the fix is +specified, *V* is the specified velocity vector with components +(Vx,Vy,Vz), and *delta* is the time elapsed since the fix was +specified. This style also sets the velocity of each atom to V = +(Vx,Vy,Vz). If any of the velocity components is specified as NULL, +then the position and velocity of that component is time integrated +the same as the :doc:`fix nve ` command would perform, using +the corresponding force component on the atom. + +Note that the *linear* style is identical to using the *variable* +style with an :doc:`equal-style variable ` that uses the +vdisplace() function. E.g. + +.. parsed-literal:: + + variable V equal 10.0 + variable x equal vdisplace(0.0,$V) + fix 1 boundary move variable v_x NULL NULL v_V NULL NULL + +The *wiggle* style moves atoms in an oscillatory fashion, so that +their position *X* = (x,y,z) as a function of time is given in vector +notation as + +.. parsed-literal:: + + X(t) = X0 + A sin(omega*delta) + +where *X0* = (x0,y0,z0) is their position at the time the fix is +specified, *A* is the specified amplitude vector with components +(Ax,Ay,Az), *omega* is 2 PI / *period*, and *delta* is the time +elapsed since the fix was specified. This style also sets the +velocity of each atom to the time derivative of this expression. If +any of the amplitude components is specified as NULL, then the +position and velocity of that component is time integrated the same as +the :doc:`fix nve ` command would perform, using the +corresponding force component on the atom. + +Note that the *wiggle* style is identical to using the *variable* +style with :doc:`equal-style variables ` that use the +swiggle() and cwiggle() functions. E.g. + +.. parsed-literal:: + + variable A equal 10.0 + variable T equal 5.0 + variable omega equal 2.0*PI/$T + variable x equal swiggle(0.0,$A,$T) + variable v equal v_omega*($A-cwiggle(0.0,$A,$T)) + fix 1 boundary move variable v_x NULL NULL v_v NULL NULL + +The *rotate* style rotates atoms around a rotation axis *R* = +(Rx,Ry,Rz) that goes thru a point *P* = (Px,Py,Pz). The *period* of +the rotation is also specified. The direction of rotation for the +atoms around the rotation axis is consistent with the right-hand rule: +if your right-hand thumb points along *R*, then your fingers wrap +around the axis in the direction of rotation. + +This style also sets the velocity of each atom to (omega cross Rperp) +where omega is its angular velocity around the rotation axis and Rperp +is a perpendicular vector from the rotation axis to the atom. If the +defined :doc:`atom_style ` assigns an angular velocity or +angular moementum or orientation to each atom (:doc:`atom styles ` sphere, ellipsoid, line, tri, body), then +those properties are also updated appropriately to correspond to the +atom's motion and rotation over time. + +The *variable* style allows the position and velocity components of +each atom to be set by formulas specified via the +:doc:`variable ` command. Each of the 6 variables is +specified as an argument to the fix as v_name, where name is the +variable name that is defined elsewhere in the input script. + +Each variable must be of either the *equal* or *atom* style. +*Equal*-style variables compute a single numeric quantity, that can be +a function of the timestep as well as of other simulation values. +*Atom*-style variables compute a numeric quantity for each atom, that +can be a function per-atom quantities, such as the atom's position, as +well as of the timestep and other simulation values. Note that this +fix stores the original coordinates of each atom (see note below) so +that per-atom quantity can be used in an atom-style variable formula. +See the :doc:`variable ` command for details. + +The first 3 variables (v_dx,v_dy,v_dz) specified for the *variable* +style are used to calculate a displacement from the atom's original +position at the time the fix was specified. The second 3 variables +(v_vx,v_vy,v_vz) specified are used to compute a velocity for each +atom. + +Any of the 6 variables can be specified as NULL. If both the +displacement and velocity variables for a particular x,y,z component +are specified as NULL, then the position and velocity of that +component is time integrated the same as the :doc:`fix nve ` +command would perform, using the corresponding force component on the +atom. If only the velocity variable for a component is specified as +NULL, then the displacement variable will be used to set the position +of the atom, and its velocity component will not be changed. If only +the displacement variable for a component is specified as NULL, then +the velocity variable will be used to set the velocity of the atom, +and the position of the atom will be time integrated using that +velocity. + +The *units* keyword determines the meaning of the distance units used +to define the *linear* velocity and *wiggle* amplitude and *rotate* +origin. This setting is ignored for the *variable* style. A *box* +value selects standard units as defined by the :doc:`units ` +command, e.g. velocity in Angstroms/fmsec and amplitude and position +in Angstroms for units = real. A *lattice* value means the velocity +units are in lattice spacings per time and the amplitude and position +are in lattice spacings. The :doc:`lattice ` command must have +been previously used to define the lattice spacing. Each of these 3 +quantities may be dependent on the x,y,z dimension, since the lattice +spacings can be different in x,y,z. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the original coordinates of moving atoms to :doc:`binary restart files `, as well as the initial timestep, so that +the motion can be continuous in a restarted simulation. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +.. note:: + + Because the move positions are a function of the current + timestep and the initial timestep, you cannot reset the timestep to a + different value after reading a restart file, if you expect a fix move + command to work in an uninterrupted fashion. + +None of the :doc:`fix_modify ` options are relevant to this +fix. + +This fix produces a per-atom array which can be accessed by various +:ref:`output commands `. The number of columns +for each atom is 3, and the columns store the original unwrapped x,y,z +coords of each atom. The per-atom values can be accessed on any +timestep. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +For :doc:`rRESPA time integration `, this fix adjusts the +position and velocity of atoms on the outermost rRESPA level. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`displace_atoms ` + +**Default:** none + +The option default is units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_msst.txt b/doc/_sources/fix_msst.txt new file mode 100644 index 0000000000..1acefa46ec --- /dev/null +++ b/doc/_sources/fix_msst.txt @@ -0,0 +1,178 @@ +.. index:: fix msst + +fix msst command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID msst dir shockvel keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* msst = style name of this fix +* dir = *x* or *y* or *z* +* shockvel = shock velocity (strictly positive, distance/time units) +* zero or more keyword value pairs may be appended +* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* +.. parsed-literal:: + + *q* value = cell mass-like parameter (mass^2/distance^4 units) + *mu* value = artificial viscosity (mass/length/time units) + *p0* value = initial pressure in the shock equations (pressure units) + *v0* value = initial simulation cell volume in the shock equations (distance^3 units) + *e0* value = initial total energy (energy units) + *tscale* value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 + fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4 v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01 + +Description +""""""""""" + +This command performs the Multi-Scale Shock Technique (MSST) +integration to update positions and velocities each timestep to mimic +a compressive shock wave passing over the system. See :ref:`(Reed) ` +for a detailed description of this method. The MSST varies the cell +volume and temperature in such a way as to restrain the system to the +shock Hugoniot and the Rayleigh line. These restraints correspond to +the macroscopic conservation laws dictated by a shock +front. *shockvel* determines the steady shock velocity that will be +simulated. + +To perform a simulation, choose a value of *q* that provides volume +compression on the timescale of 100 fs to 1 ps. If the volume is not +compressing, either the shock speed is chosen to be below the material +sound speed or *p0* has been chosen inaccurately. Volume compression +at the start can be sped up by using a non-zero value of *tscale*. Use +the smallest value of *tscale* that results in compression. + +Under some special high-symmetry conditions, the pressure (volume) +and/or temperature of the system may oscillate for many cycles even +with an appropriate choice of mass-like parameter *q*. Such +oscillations have physical significance in some cases. The optional +*mu* keyword adds an artificial viscosity that helps break the system +symmetry to equilibrate to the shock Hugoniot and Rayleigh line more +rapidly in such cases. + +*tscale* is a factor between 0 and 1 that determines what fraction of +thermal kinetic energy is converted to compressive strain kinetic +energy at the start of the simulation. Setting this parameter to a +non-zero value may assist in compression at the start of simulations +where it is slow to occur. + +If keywords *e0*, *p0*,or *v0* are not supplied, these quantities will +be calculated on the first step, after the energy specified by +*tscale* is removed. The value of *e0* is not used in the dynamical +equations, but is used in calculating the deviation from the Hugoniot. + +Values of shockvel less than a critical value determined by the +material response will not have compressive solutions. This will be +reflected in lack of significant change of the volume in the MSST. + +For all pressure styles, the simulation box stays orthogonal in shape. +Parrinello-Rahman boundary conditions (tilted box) are supported by +LAMMPS, but are not implemented for MSST. + +This fix computes a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp" and "pressure", +as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp + compute fix-ID_press group-ID pressure fix-ID_temp + +See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press". The group for the new computes is "all". + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of all internal variables to :doc:`binary restart files `. See the :doc:`read_restart ` command +for info on how to re-specify a fix in an input script that reads a +restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The progress of the MSST can be monitored by printing the global +scalar and global vector quantities computed by the fix. + +The scalar is the cumulative energy change due to the fix. This is +also the energy added to the potential energy by the +:doc:`fix_modify ` *energy* command. With this command, the +thermo keyword *etotal* prints the conserved quantity of the MSST +dynamic equations. This can be used to test if the MD timestep is +sufficiently small for accurate integration of the dynamic +equations. See also :doc:`thermo_style ` command. + +The global vector contains four values in this order: + +[*dhugoniot*, *drayleigh*, *lagrangian_speed*, *lagrangian_position*] + +1. *dhugoniot* is the departure from the Hugoniot (temperature units). +2. *drayleigh* is the departure from the Rayleigh line (pressure units). +3. *lagrangian_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). +4. *lagrangian_position* is the computational cell position in the reference frame moving at the shock speed. This is usually a good estimate of distance of the computational cell behind the shock front. + +To print these quantities to the log file with descriptive column +headers, the following LAMMPS commands are suggested: + +.. parsed-literal:: + + fix msst all msst z + fix_modify msst energy yes + variable dhug equal f_msst[1] + variable dray equal f_msst[2] + variable lgr_vel equal f_msst[3] + variable lgr_pos equal f_msst[4] + thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst + +These fixes compute a global scalar and a global vector of 4 +quantities, which can be accessed by various :ref:`output commands `. The scalar values calculated +by this fix are "extensive"; the vector values are "intensive". + +Restrictions +"""""""""""" + + +This fix style is part of the SHOCK package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +All cell dimensions must be periodic. This fix can not be used with a +triclinic cell. The MSST fix has been tested only for the group-ID +all. + +Related commands +"""""""""""""""" + +:doc:`fix nphug `, :doc:`fix deform ` + +Default +""""""" + +The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0 +are calculated on the first step. + + +---------- + + +.. _Reed: + + + +**(Reed)** Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_neb.txt b/doc/_sources/fix_neb.txt new file mode 100644 index 0000000000..a3b40c24b4 --- /dev/null +++ b/doc/_sources/fix_neb.txt @@ -0,0 +1,125 @@ +.. index:: fix neb + +fix neb command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID neb Kspring + +* ID, group-ID are documented in :doc:`fix ` command +* neb = style name of this fix command +* Kspring = inter-replica spring constant (force/distance units) + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 active neb 10.0 + +Description +""""""""""" + +Add inter-replica forces to atoms in the group for a multi-replica +simulation run via the :doc:`neb ` command to perform a nudged +elastic band (NEB) calculation for transition state finding. Hi-level +explanations of NEB are given with the :doc:`neb ` command and in +:ref:`Section_howto 5 ` of the manual. The fix +neb command must be used with the "neb" command to define how +inter-replica forces are computed. + +Only the N atoms in the fix group experience inter-replica forces. +Atoms in the two end-point replicas do not experience these forces, +but those in intermediate replicas do. During the initial stage of +NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting +on the atoms of each intermediate replica I is altered, as described +in the :ref:`(Henkelman1) ` paper, to become: + +.. parsed-literal:: + + Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That + +Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the +coordinates of its neighbor replicas. That (t with a hat over it) is +the unit "tangent" vector for replica I which is a function of Ri, +Ri-1, Ri+1, and the potential energy of the 3 replicas; it points +roughly in the direction of (Ri+i - Ri-1); see the +:ref:`(Henkelman1) ` paper for details. + +The first two terms in the above equation are the component of the +interatomic forces perpendicular to the tangent vector. The last term +is a spring force between replica I and its neighbors, parallel to the +tangent vector direction with the specified spring constant *Kspring*. + +The effect of the first two terms is to push the atoms of each replica +toward the minimum energy path (MEP) of conformational states that +transition over the energy barrier. The MEP for an energy barrier is +defined as a sequence of 3N-dimensional states which cross the barrier +at its saddle point, each of which has a potential energy gradient +parallel to the MEP itself. + +The effect of the last term is to push each replica away from its two +neighbors in a direction along the MEP, so that the final set of +states are equidistant from each other. + +During the second stage of NEB, the forces on the N atoms in the +replica nearest the top of the energy barrier are altered so that it +climbs to the top of the barrier and finds the saddle point. The +forces on atoms in this replica are described in the +:ref:`(Henkelman2) ` paper, and become: + +.. parsed-literal:: + + Fi = -Grad(V) + 2 (Grad(V) dot That) That + +The inter-replica forces for the other replicas are unchanged from the +first equation. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +as invoked by the :doc:`minimize ` command via the +:doc:`neb ` command. + +Restrictions +"""""""""""" + + +This command can only be used if LAMMPS was built with the REPLICA +package. See the :ref:`Making LAMMPS ` section +for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`neb ` + +**Default:** none + +.. _Henkelman: + + + +**(Henkelman1)** Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). + +.. _Henkelman: + + + +**(Henkelman2)** Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, +9901-9904 (2000). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nh.txt b/doc/_sources/fix_nh.txt new file mode 100644 index 0000000000..6ed6b7925e --- /dev/null +++ b/doc/_sources/fix_nh.txt @@ -0,0 +1,725 @@ +.. index:: fix nvt + +fix nvt command +=============== + +fix nvt/cuda command +==================== + +fix nvt/kk command +================== + +fix nvt/omp command +=================== + +fix npt command +=============== + +fix npt/cuda command +==================== + +fix npt/intel command +===================== + +fix npt/kk command +================== + +fix npt/omp command +=================== + +fix nph command +=============== + +fix nph/kk command +================== + +fix nph/omp command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style_name keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* style_name = *nvt* or *npt* or *nph* +* one or more keyword/value pairs may be appended +.. parsed-literal:: + + keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint* or *update* + *temp* values = Tstart Tstop Tdamp + Tstart,Tstop = external temperature at start/end of run + Tdamp = temperature damping parameter (time units) + *iso* or *aniso* or *tri* values = Pstart Pstop Pdamp + Pstart,Pstop = scalar external pressure at start/end of run (pressure units) + Pdamp = pressure damping parameter (time units) + *x* or *y* or *z* or *xy* or *yz* or *xz* values = Pstart Pstop Pdamp + Pstart,Pstop = external stress tensor component at start/end of run (pressure units) + Pdamp = stress damping parameter (time units) + *couple* = *none* or *xyz* or *xy* or *yz* or *xz* + *tchain* value = N + N = length of thermostat chain (1 = single thermostat) + *pchain* values = N + N length of thermostat chain on barostat (0 = no thermostat) + *mtk* value = *yes* or *no* = add in MTK adjustment term or not + *tloop* value = M + M = number of sub-cycles to perform on thermostat + *ploop* value = M + M = number of sub-cycles to perform on barostat thermostat + *nreset* value = reset reference cell every this many timesteps + *drag* value = Df + Df = drag factor added to barostat/thermostat (0.0 = no drag) + *dilate* value = dilate-group-ID + dilate-group-ID = only dilate atoms in this group due to barostat volume changes + *scalexy* value = *yes* or *no* = scale xy with ly + *scaleyz* value = *yes* or *no* = scale yz with lz + *scalexz* value = *yes* or *no* = scale xz with lz + *flip* value = *yes* or *no* = allow or disallow box flips when it becomes highly skewed + *fixedpoint* values = x y z + x,y,z = perform barostat dilation/contraction around this point (distance units) + *update* value = *dipole* update dipole orientation (only for sphere variants) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nvt temp 300.0 300.0 100.0 + fix 1 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 + fix 2 jello npt temp 300.0 300.0 100.0 tri 5.0 5.0 1000.0 + fix 2 ice nph x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 + +Description +""""""""""" + +These commands perform time integration on Nose-Hoover style +non-Hamiltonian equations of motion which are designed to generate +positions and velocities sampled from the canonical (nvt), +isothermal-isobaric (npt), and isenthalpic (nph) ensembles. This +updates the position and velocity for atoms in the group each +timestep. + +The thermostatting and barostatting is achieved by adding some dynamic +variables which are coupled to the particle velocities +(thermostatting) and simulation domain dimensions (barostatting). In +addition to basic thermostatting and barostatting, these fixes can +also create a chain of thermostats coupled to the particle thermostat, +and another chain of thermostats coupled to the barostat +variables. The barostat can be coupled to the overall box volume, or +to individual dimensions, including the *xy*, *xz* and *yz* tilt +dimensions. The external pressure of the barostat can be specified as +either a scalar pressure (isobaric ensemble) or as components of a +symmetric stress tensor (constant stress ensemble). When used +correctly, the time-averaged temperature and stress tensor of the +particles will match the target values specified by Tstart/Tstop and +Pstart/Pstop. + +The equations of motion used are those of Shinoda et al in +:ref:`(Shinoda) `, which combine the hydrostatic equations of +Martyna, Tobias and Klein in :ref:`(Martyna) ` with the strain +energy proposed by Parrinello and Rahman in +:ref:`(Parrinello) `. The time integration schemes closely +follow the time-reversible measure-preserving Verlet and rRESPA +integrators derived by Tuckerman et al in :ref:`(Tuckerman) `. + + +---------- + + +The thermostat parameters for fix styles *nvt* and *npt* is specified +using the *temp* keyword. Other thermostat-related keywords are +*tchain*, *tloop* and *drag*, which are discussed below. + +The thermostat is applied to only the translational degrees of freedom +for the particles. The translational degrees of freedom can also have +a bias velocity removed before thermostatting takes place; see the +description below. The desired temperature at each timestep is a +ramped value during the run from *Tstart* to *Tstop*. The *Tdamp* +parameter is specified in time units and determines how rapidly the +temperature is relaxed. For example, a value of 10.0 means to relax +the temperature in a timespan of (roughly) 10 time units (e.g. tau or +fmsec or psec - see the :doc:`units ` command). The atoms in the +fix group are the only ones whose velocities and positions are updated +by the velocity/position update portion of the integration. + +.. note:: + + A Nose-Hoover thermostat will not work well for arbitrary values + of *Tdamp*. If *Tdamp* is too small, the temperature can fluctuate + wildly; if it is too large, the temperature will take a very long time + to equilibrate. A good choice for many models is a *Tdamp* of around + 100 timesteps. Note that this is NOT the same as 100 time units for + most :doc:`units ` settings. + + +---------- + + +The barostat parameters for fix styles *npt* and *nph* is specified +using one or more of the *iso*, *aniso*, *tri*, *x*, *y*, *z*, *xy*, +*xz*, *yz*, and *couple* keywords. These keywords give you the +ability to specify all 6 components of an external stress tensor, and +to couple various of these components together so that the dimensions +they represent are varied together during a constant-pressure +simulation. + +Other barostat-related keywords are *pchain*, *mtk*, *ploop*, +*nreset*, *drag*, and *dilate*, which are discussed below. + +Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z). +Triclinic (non-orthogonal) simulation boxes have 6 adjustable +dimensions (x,y,z,xy,xz,yz). The :doc:`create_box `, :doc:`read data `, and :doc:`read_restart ` commands +specify whether the simulation box is orthogonal or non-orthogonal +(triclinic) and explain the meaning of the xy,xz,yz tilt factors. + +The target pressures for each of the 6 components of the stress tensor +can be specified independently via the *x*, *y*, *z*, *xy*, *xz*, *yz* +keywords, which correspond to the 6 simulation box dimensions. For +each component, the external pressure or tensor component at each +timestep is a ramped value during the run from *Pstart* to *Pstop*. +If a target pressure is specified for a component, then the +corresponding box dimension will change during a simulation. For +example, if the *y* keyword is used, the y-box length will change. If +the *xy* keyword is used, the xy tilt factor will change. A box +dimension will not change if that component is not specified, although +you have the option to change that dimension via the :doc:`fix deform ` command. + +Note that in order to use the *xy*, *xz*, or *yz* keywords, the +simulation box must be triclinic, even if its initial tilt factors are +0.0. + +For all barostat keywords, the *Pdamp* parameter operates like the +*Tdamp* parameter, determining the time scale on which pressure is +relaxed. For example, a value of 10.0 means to relax the pressure in +a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see +the :doc:`units ` command). + +.. note:: + + A Nose-Hoover barostat will not work well for arbitrary values + of *Pdamp*. If *Pdamp* is too small, the pressure and volume can + fluctuate wildly; if it is too large, the pressure will take a very + long time to equilibrate. A good choice for many models is a *Pdamp* + of around 1000 timesteps. Note that this is NOT the same as 1000 time + units for most :doc:`units ` settings. + +Regardless of what atoms are in the fix group (the only atoms which +are time integrated), a global pressure or stress tensor is computed +for all atoms. Similarly, when the size of the simulation box is +changed, all atoms are re-scaled to new positions, unless the keyword +*dilate* is specified with a *dilate-group-ID* for a group that +represents a subset of the atoms. This can be useful, for example, to +leave the coordinates of atoms in a solid substrate unchanged and +controlling the pressure of a surrounding fluid. This option should +be used with care, since it can be unphysical to dilate some atoms and +not others, because it can introduce large, instantaneous +displacements between a pair of atoms (one dilated, one not) that are +far from the dilation origin. Also note that for atoms not in the fix +group, a separate time integration fix like :doc:`fix nve ` or +:doc:`fix nvt ` can be used on them, independent of whether they +are dilated or not. + + +---------- + + +The *couple* keyword allows two or three of the diagonal components of +the pressure tensor to be "coupled" together. The value specified +with the keyword determines which are coupled. For example, *xz* +means the *Pxx* and *Pzz* components of the stress tensor are coupled. +*Xyz* means all 3 diagonal components are coupled. Coupling means two +things: the instantaneous stress will be computed as an average of the +corresponding diagonal components, and the coupled box dimensions will +be changed together in lockstep, meaning coupled dimensions will be +dilated or contracted by the same percentage every timestep. The +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must +be identical. *Couple xyz* can be used for a 2d simulation; the *z* +dimension is simply ignored. + + +---------- + + +The *iso*, *aniso*, and *tri* keywords are simply shortcuts that are +equivalent to specifying several other keywords together. + +The keyword *iso* means couple all 3 diagonal components together when +pressure is computed (hydrostatic pressure), and dilate/contract the +dimensions together. Using "iso Pstart Pstop Pdamp" is the same as +specifying these 4 keywords: + +.. parsed-literal:: + + x Pstart Pstop Pdamp + y Pstart Pstop Pdamp + z Pstart Pstop Pdamp + couple xyz + +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the +stress tensor as the driving forces, and the specified scalar external +pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying +these 4 keywords: + +.. parsed-literal:: + + x Pstart Pstop Pdamp + y Pstart Pstop Pdamp + z Pstart Pstop Pdamp + couple none + +The keyword *tri* means *x*, *y*, *z*, *xy*, *xz*, and *yz* dimensions +are controlled independently using their individual stress components +as the driving forces, and the specified scalar pressure as the +external normal stress. Using "tri Pstart Pstop Pdamp" is the same as +specifying these 7 keywords: + +.. parsed-literal:: + + x Pstart Pstop Pdamp + y Pstart Pstop Pdamp + z Pstart Pstop Pdamp + xy 0.0 0.0 Pdamp + yz 0.0 0.0 Pdamp + xz 0.0 0.0 Pdamp + couple none + + +---------- + + +In some cases (e.g. for solids) the pressure (volume) and/or +temperature of the system can oscillate undesirably when a Nose/Hoover +barostat and thermostat is applied. The optional *drag* keyword will +damp these oscillations, although it alters the Nose/Hoover equations. +A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. +A non-zero value adds a drag term; the larger the value specified, the +greater the damping effect. Performing a short run and monitoring the +pressure and temperature is the best way to determine if the drag term +is working. Typically a value between 0.2 to 2.0 is sufficient to +damp oscillations after a few periods. Note that use of the drag +keyword will interfere with energy conservation and will also change +the distribution of positions and velocities so that they do not +correspond to the nominal NVT, NPT, or NPH ensembles. + +An alternative way to control initial oscillations is to use chain +thermostats. The keyword *tchain* determines the number of thermostats +in the particle thermostat. A value of 1 corresponds to the original +Nose-Hoover thermostat. The keyword *pchain* specifies the number of +thermostats in the chain thermostatting the barostat degrees of +freedom. A value of 0 corresponds to no thermostatting of the +barostat variables. + +The *mtk* keyword controls whether or not the correction terms due to +Martyna, Tuckerman, and Klein are included in the equations of motion +:ref:`(Martyna) `. Specifying *no* reproduces the original +Hoover barostat, whose volume probability distribution function +differs from the true NPT and NPH ensembles by a factor of 1/V. Hence +using *yes* is more correct, but in many cases the difference is +negligible. + +The keyword *tloop* can be used to improve the accuracy of integration +scheme at little extra cost. The initial and final updates of the +thermostat variables are broken up into *tloop* substeps, each of +length *dt*/*tloop*. This corresponds to using a first-order +Suzuki-Yoshida scheme :ref:`(Tuckerman) `. The keyword *ploop* +does the same thing for the barostat thermostat. + +The keyword *nreset* controls how often the reference dimensions used +to define the strain energy are reset. If this keyword is not used, +or is given a value of zero, then the reference dimensions are set to +those of the initial simulation domain and are never changed. If the +simulation domain changes significantly during the simulation, then +the final average pressure tensor will differ significantly from the +specified values of the external stress tensor. A value of *nstep* +means that every *nstep* timesteps, the reference dimensions are set +to those of the current simulation domain. + +The *scaleyz*, *scalexz*, and *scalexy* keywords control whether or +not the corresponding tilt factors are scaled with the associated box +dimensions when barostatting triclinic periodic cells. The default +values *yes* will turn on scaling, which corresponds to adjusting the +linear dimensions of the cell while preserving its shape. Choosing +*no* ensures that the tilt factors are not scaled with the box +dimensions. See below for restrictions and default values in different +situations. In older versions of LAMMPS, scaling of tilt factors was +not performed. The old behavior can be recovered by setting all three +scale keywords to *no*. + +The *flip* keyword allows the tilt factors for a triclinic box to +exceed half the distance of the parallel box length, as discussed +below. If the *flip* value is set to *yes*, the bound is enforced by +flipping the box when it is exceeded. If the *flip* value is set to +*no*, the tilt will continue to change without flipping. Note that if +applied stress induces large deformations (e.g. in a liquid), this +means the box shape can tilt dramatically and LAMMPS will run less +efficiently, due to the large volume of communication needed to +acquire ghost atoms around a processor's irregular-shaped sub-domain. +For extreme values of tilt, LAMMPS may also lose atoms and generate an +error. + +The *fixedpoint* keyword specifies the fixed point for barostat volume +changes. By default, it is the center of the box. Whatever point is +chosen will not move during the simulation. For example, if the lower +periodic boundaries pass through (0,0,0), and this point is provided +to *fixedpoint*, then the lower periodic boundaries will remain at +(0,0,0), while the upper periodic boundaries will move twice as +far. In all cases, the particle trajectories are unaffected by the +chosen value, except for a time-dependent constant translation of +positions. + +If the *update* keyword is used with the *dipole* value, then the +orientation of the dipole moment of each particle is also updated +during the time integration. This option should be used for models +where a dipole moment is assigned to finite-size particles, +e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole ` command. + + +---------- + + +.. note:: + + Using a barostat coupled to tilt dimensions *xy*, *xz*, *yz* can + sometimes result in arbitrarily large values of the tilt dimensions, + i.e. a dramatically deformed simulation box. LAMMPS allows the tilt + factors to grow a small amount beyond the normal limit of half the box + length (0.6 times the box length), and then performs a box "flip" to + an equivalent periodic cell. See the discussion of the *flip* keyword + above, to allow this bound to be exceeded, if desired. + +The flip operation is described in more detail in the doc page for +:doc:`fix deform `. Both the barostat dynamics and the atom +trajectories are unaffected by this operation. However, if a tilt +factor is incremented by a large amount (1.5 times the box length) on +a single timestep, LAMMPS can not accomodate this event and will +terminate the simulation with an error. This error typically indicates +that there is something badly wrong with how the simulation was +constructed, such as specifying values of *Pstart* that are too far +from the current stress value, or specifying a timestep that is too +large. Triclinic barostatting should be used with care. This also is +true for other barostat styles, although they tend to be more +forgiving of insults. In particular, it is important to recognize that +equilibrium liquids can not support a shear stress and that +equilibrium solids can not support shear stresses that exceed the +yield stress. + +One exception to this rule is if the 1st dimension in the tilt factor +(x for xy) is non-periodic. In that case, the limits on the tilt +factor are not enforced, since flipping the box in that dimension does +not change the atom positions due to non-periodicity. In this mode, +if you tilt the system to extreme angles, the simulation will simply +become inefficient due to the highly skewed simulation box. + +.. note:: + + Unlike the :doc:`fix temp/berendsen ` command + which performs thermostatting but NO time integration, these fixes + perform thermostatting/barostatting AND time integration. Thus you + should not use any other time integration fix, such as :doc:`fix nve ` on atoms to which this fix is applied. Likewise, + fix nvt and fix npt should not normally be used on atoms that also + have their temperature controlled by another fix - e.g. by :doc:`fix langevin ` or :doc:`fix temp/rescale ` + commands. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting and barostatting. + + +---------- + + +These fixes compute a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp" and "pressure", +as if one of these two sets of commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp + compute fix-ID_press group-ID pressure fix-ID_temp + +.. parsed-literal:: + + compute fix-ID_temp all temp + compute fix-ID_press all pressure fix-ID_temp + +See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press". For fix nvt, the group for the new computes +is the same as the fix group. For fix nph and fix npt, the group for +the new computes is "all" since pressure is computed for the entire +system. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + +Like other fixes that perform thermostatting, fix nvt and fix npt can +be used with :doc:`compute commands ` that calculate a +temperature after removing a "bias" from the atom velocities. +E.g. removing the center-of-mass velocity from a group of atoms or +only calculating temperature on the x-component of velocity or only +calculating temperature for atoms in a geometric region. This is not +done by default, but only if the :doc:`fix_modify ` command +is used to assign a temperature compute to this fix that includes such +a bias term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +These fixes can be used with either the *verlet* or *respa* +:doc:`integrators `. When using one of the barostat fixes +with *respa*, LAMMPS uses an integrator constructed +according to the following factorization of the Liouville propagator +(for two rRESPA levels): + +.. image:: Eqs/fix_nh1.jpg + :align: center + +This factorization differs somewhat from that of Tuckerman et al, in +that the barostat is only updated at the outermost rRESPA level, +whereas Tuckerman's factorization requires splitting the pressure into +pieces corresponding to the forces computed at each rRESPA level. In +theory, the latter method will exhibit better numerical stability. In +practice, because Pdamp is normally chosen to be a large multiple of +the outermost rRESPA timestep, the barostat dynamics are not the +limiting factor for numerical stability. Both factorizations are +time-reversible and can be shown to preserve the phase space measure +of the underlying non-Hamiltonian equations of motion. + +.. note:: + + This implementation has been shown to conserve linear momentum + up to machine precision under NVT dynamics. Under NPT dynamics, + for a system with zero initial total linear momentum, the total + momentum fluctuates close to zero. It may occasionally undergo brief + excursions to non-negligible values, before returning close to zero. + Over long simulations, this has the effect of causing the center-of-mass + to undergo a slow random walk. This can be mitigated by resetting + the momentum at infrequent intervals using the + :doc:`fix momentum ` command. + +.. note:: + + This implementation has been shown to conserve linear momentum + up to machine precision under NVT dynamics. Under NPT dynamics, + for a system with zero initial total linear momentum, the total + momentum fluctuates close to zero. It may occasionally undergo brief + excursions to non-negligible values, before returning close to zero. + Over long simulations, this has the effect of causing the center-of-mass + to undergo a slow random walk. This can be mitigated by resetting + the momentum at infrequent intervals using the + :doc:`fix momentum ` command. + + +---------- + + +The fix npt and fix nph commands can be used with rigid bodies or +mixtures of rigid bodies and non-rigid particles (e.g. solvent). But +there are also :doc:`fix rigid/npt ` and :doc:`fix rigid/nph ` commands, which are typically a more natural +choice. See the doc page for those commands for more discussion of +the various ways to do this. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +These fixes writes the state of all the thermostat and barostat +variables to :doc:`binary restart files `. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by these fixes. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its thermostatting or barostatting procedure, as described above. +If you do this, note that the kinetic energy derived from the compute +temperature should be consistent with the virial term computed using +all atoms for the pressure. LAMMPS will warn you if you choose to +compute temperature on a subset of atoms. + +.. note:: + + If both the *temp* and *press* keywords are used in a single + thermo_modify command (or in two separate commands), then the order in + which the keywords are specified is important. Note that a :doc:`pressure compute ` defines its own temperature compute as + an argument when it is specified. The *temp* keyword will override + this (for the pressure compute being used by fix npt), but only if the + *temp* keyword comes after the *press* keyword. If the *temp* keyword + comes before the *press* keyword, then the new pressure compute + specified by the *press* keyword will be unaffected by the *temp* + setting. + +The :doc:`fix_modify ` *energy* option is supported by these +fixes to add the energy change induced by Nose/Hoover thermostatting +and barostatting to the system's potential energy as part of +:doc:`thermodynamic output `. + +These fixes compute a global scalar and a global vector of quantities, +which can be accessed by various :ref:`output commands `. The scalar value calculated by +these fixes is "extensive"; the vector values are "intensive". + +The scalar is the cumulative energy change due to the fix. + +The vector stores internal Nose/Hoover thermostat and barostat +variables. The number and meaning of the vector values depends on +which fix is used and the settings for keywords *tchain* and *pchain*, +which specify the number of Nose/Hoover chains for the thermostat and +barostat. If no thermostatting is done, then *tchain* is 0. If no +barostatting is done, then *pchain* is 0. In the following list, +"ndof" is 0, 1, 3, or 6, and is the number of degrees of freedom in +the barostat. Its value is 0 if no barostat is used, else its value +is 6 if any off-diagonal stress tensor component is barostatted, else +its value is 1 if *couple xyz* is used or *couple xy* for a 2d +simulation, otherwise its value is 3. + +The order of values in the global vector and their meaning is as +follows. The notation means there are tchain values for eta, followed +by tchain for eta_dot, followed by ndof for omega, etc: + +* eta[tchain] = particle thermostat displacements (unitless) +* eta_dot[tchain] = particle thermostat velocities (1/time units) +* omega[ndof] = barostat displacements (unitless) +* omega_dot[ndof] = barostat velocities (1/time units) +* etap[pchain] = barostat thermostat displacements (unitless) +* etap_dot[pchain] = barostat thermostat velocities (1/time units) +* PE_eta[tchain] = potential energy of each particle thermostat displacement (energy units) +* KE_eta_dot[tchain] = kinetic energy of each particle thermostat velocity (energy units) +* PE_omega[ndof] = potential energy of each barostat displacement (energy units) +* KE_omega_dot[ndof] = kinetic energy of each barostat velocity (energy units) +* PE_etap[pchain] = potential energy of each barostat thermostat displacement (energy units) +* KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units) +* PE_strain[1] = scalar strain energy (energy units) + +These fixes can ramp their external temperature and pressure over +multiple runs, using the *start* and *stop* keywords of the +:doc:`run ` command. See the :doc:`run ` command for details of +how to do this. + +These fixes are not invoked during :doc:`energy minimization `. + + +---------- + + +Restrictions +"""""""""""" + + +*X*, *y*, *z* cannot be barostatted if the associated dimension is not +periodic. *Xy*, *xz*, and *yz* can only be barostatted if the +simulation domain is triclinic and the 2nd dimension in the keyword +(*y* dimension in *xy*) is periodic. *Z*, *xz*, and *yz*, cannot be +barostatted for 2D simulations. The :doc:`create_box `, +:doc:`read data `, and :doc:`read_restart ` +commands specify whether the simulation box is orthogonal or +non-orthogonal (triclinic) and explain the meaning of the xy,xz,yz +tilt factors. + +For the *temp* keyword, the final Tstop cannot be 0.0 since it would +make the external T = 0.0 at some timestep during the simulation which +is not allowed in the Nose/Hoover formulation. + +The *scaleyz yes* and *scalexz yes* keyword/value pairs can not be used +for 2D simulations. *scaleyz yes*, *scalexz yes*, and *scalexy yes* options +can only be used if the 2nd dimension in the keyword is periodic, +and if the tilt factor is not coupled to the barostat via keywords +*tri*, *yz*, *xz*, and *xy*. + +These fixes can be used with dynamic groups as defined by the +:doc:`group ` command. Likewise they can be used with groups to +which atoms are added or deleted over time, e.g. a deposition +simulation. However, the conservation properties of the thermostat +and barostat are defined for systems with a static set of atoms. You +may observe odd behavior if the atoms in a group vary dramatically +over time or the atom count becomes very small. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix_modify `, +:doc:`run_style ` + +Default +""""""" + +The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = +ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, +scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and +not coupled to barostat, otherwise no. + + +---------- + + +.. _Martyna: + + + +**(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). + +.. _Parrinello: + + + +**(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). + +.. _Tuckerman: + + + +**(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and +Martyna, J Phys A: Math Gen, 39, 5629 (2006). + +.. _Shinoda: + + + +**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nh_eff.txt b/doc/_sources/fix_nh_eff.txt new file mode 100644 index 0000000000..7d980e9de0 --- /dev/null +++ b/doc/_sources/fix_nh_eff.txt @@ -0,0 +1,179 @@ +.. index:: fix nvt/eff + +fix nvt/eff command +=================== + +fix npt/eff command +=================== + +fix nph/eff command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style_name keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* style_name = *nvt/eff* or *npt/eff* or *nph/eff* +.. parsed-literal:: + + one or more keyword value pairs may be appended + keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* + *temp* values = Tstart Tstop Tdamp + Tstart,Tstop = external temperature at start/end of run + Tdamp = temperature damping parameter (time units) + *iso* or *aniso* or *tri* values = Pstart Pstop Pdamp + Pstart,Pstop = scalar external pressure at start/end of run (pressure units) + Pdamp = pressure damping parameter (time units) + *x* or *y* or *z* or *xy* or *yz* or *xz* values = Pstart Pstop Pdamp + Pstart,Pstop = external stress tensor component at start/end of run (pressure units) + Pdamp = stress damping parameter (time units) + *couple* = *none* or *xyz* or *xy* or *yz* or *xz* + *tchain* value = length of thermostat chain (1 = single thermostat) + *pchain* values = length of thermostat chain on barostat (0 = no thermostat) + *mtk* value = *yes* or *no* = add in MTK adjustment term or not + *tloop* value = number of sub-cycles to perform on thermostat + *ploop* value = number of sub-cycles to perform on barostat thermostat + *nreset* value = reset reference cell every this many timesteps + *drag* value = drag factor added to barostat/thermostat (0.0 = no drag) + *dilate* value = *all* or *partial* + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nvt/eff temp 300.0 300.0 0.1 + fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0 + fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0 + fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000 + +Description +""""""""""" + +These commands perform time integration on Nose-Hoover style +non-Hamiltonian equations of motion for nuclei and electrons in the +group for the :doc:`electron force field ` model. The fixes +are designed to generate positions and velocities sampled from the +canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph) +ensembles. This is achieved by adding some dynamic variables which +are coupled to the particle velocities (thermostatting) and simulation +domain dimensions (barostatting). In addition to basic thermostatting +and barostatting, these fixes can also create a chain of thermostats +coupled to the particle thermostat, and another chain of thermostats +coupled to the barostat variables. The barostat can be coupled to the +overall box volume, or to individual dimensions, including the *xy*, +*xz* and *yz* tilt dimensions. The external pressure of the barostat +can be specified as either a scalar pressure (isobaric ensemble) or as +components of a symmetric stress tensor (constant stress ensemble). +When used correctly, the time-averaged temperature and stress tensor +of the particles will match the target values specified by +Tstart/Tstop and Pstart/Pstop. + +The operation of these fixes is exactly like that described by the +:doc:`fix nvt, npt, and nph ` commands, except that the radius +and radial velocity of electrons are also updated. Likewise the +temperature and pressure calculated by the fix, using the computes it +creates (as discussed in the :doc:`fix nvt, npt, and nph ` +doc page), are performed with computes that include the eFF contribution +to the temperature or kinetic energy from the electron radial velocity. + +.. note:: + + there are two different pressures that can be reported for eFF + when defining the pair_style (see :doc:`pair eff/cut ` to + understand these settings), one (default) that considers electrons do + not contribute radial virial components (i.e. electrons treated as + incompressible 'rigid' spheres) and one that does. The radial + electronic contributions to the virials are only tallied if the + flexible pressure option is set, and this will affect both global and + per-atom quantities. In principle, the true pressure of a system is + somewhere in between the rigid and the flexible eFF pressures, but, + for most cases, the difference between these two pressures will not be + significant over long-term averaged runs (i.e. even though the energy + partitioning changes, the total energy remains similar). + +.. note:: + + currently, there is no available option for the user to set or + create temperature distributions that include the radial electronic + degrees of freedom with the :doc:`velocity ` command, so the + the user must allow for these degrees of freedom to equilibrate + (i.e. equi-partitioning of energy) through time integration. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +See the doc page for the :doc:`fix nvt, npt, and nph ` commands +for details. + +Restrictions +"""""""""""" + + +This fix is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Other restriction discussed on the doc page for the :doc:`fix nvt, npt, and nph ` commands also apply. + +.. note:: + + The temperature for systems (regions or groups) with only + electrons and no nuclei is 0.0 (i.e. not defined) in the current + temperature calculations, a practical example would be a uniform + electron gas or a very hot plasma, where electrons remain delocalized + from the nuclei. This is because, even though electron virials are + included in the temperature calculation, these are averaged over the + nuclear degrees of freedom only. In such cases a corrective term must + be added to the pressure to get the correct kinetic contribution. + +Related commands +"""""""""""""""" + +:doc:`fix nvt `, :doc:`fix nph `, :doc:`fix npt `, +:doc:`fix_modify `, :doc:`run_style ` + +Default +""""""" + +The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = +ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none. + + +---------- + + +.. _Martyna: + + + +**(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994). + +.. _Parrinello: + + + +**(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981). + +.. _Tuckerman: + + + +**(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and +Martyna, J Phys A: Math Gen, 39, 5629 (2006). + +.. _Shinoda: + + + +**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nph_asphere.txt b/doc/_sources/fix_nph_asphere.txt new file mode 100644 index 0000000000..cf979176cc --- /dev/null +++ b/doc/_sources/fix_nph_asphere.txt @@ -0,0 +1,163 @@ +.. index:: fix nph/asphere + +fix nph/asphere command +======================= + +fix nph/asphere/omp command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nph/asphere args keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* nph/asphere = style name of this fix command +* additional barostat related keyword/value pairs from the :doc:`fix nph ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nph/asphere iso 0.0 0.0 1000.0 + fix 2 all nph/asphere x 5.0 5.0 1000.0 + fix 2 all nph/asphere x 5.0 5.0 1000.0 drag 0.2 + fix 2 water nph/asphere aniso 0.0 0.0 1000.0 dilate partial + +Description +""""""""""" + +Perform constant NPH integration to update position, velocity, +orientation, and angular velocity each timestep for aspherical or +ellipsoidal particles in the group using a Nose/Hoover pressure +barostat. P is pressure; H is enthalpy. This creates a system +trajectory consistent with the isenthalpic ensemble. + +This fix differs from the :doc:`fix nph ` command, which assumes +point particles and only updates their position and velocity. + +Additional parameters affecting the barostat are specified by keywords +and values documented with the :doc:`fix nph ` command. See, +for example, discussion of the *aniso*, and *dilate* keywords. + +The particles in the fix group are the only ones whose velocities and +positions are updated by the velocity/position update portion of the +NPH integration. + +Regardless of what particles are in the fix group, a global pressure is +computed for all particles. Similarly, when the size of the simulation +box is changed, all particles are re-scaled to new positions, unless the +keyword *dilate* is specified with a value of *partial*, in which case +only the particles in the fix group are re-scaled. The latter can be +useful for leaving the coordinates of particles in a solid substrate +unchanged and controlling the pressure of a surrounding fluid. + + +---------- + + +This fix computes a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp/asphere" and +"pressure", as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp all temp/asphere + compute fix-ID_press all pressure fix-ID_temp + +See the :doc:`compute temp/asphere ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is "all" +since pressure is computed for the entire system. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover barostatting to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix nph ` command. + +This fix can ramp its target pressure over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style ellipsoid ` +command. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical as defined by their +shape attribute. + +Related commands +"""""""""""""""" + +:doc:`fix nph `, :doc:`fix nve_asphere `, :doc:`fix nvt_asphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nph_body.txt b/doc/_sources/fix_nph_body.txt new file mode 100644 index 0000000000..ce84aa66d2 --- /dev/null +++ b/doc/_sources/fix_nph_body.txt @@ -0,0 +1,156 @@ +.. index:: fix nph/body + +fix nph/body command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nph/body args keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* nph/body = style name of this fix command +* additional barostat related keyword/value pairs from the :doc:`fix nph ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nph/body iso 0.0 0.0 1000.0 + fix 2 all nph/body x 5.0 5.0 1000.0 + fix 2 all nph/body x 5.0 5.0 1000.0 drag 0.2 + fix 2 water nph/body aniso 0.0 0.0 1000.0 dilate partial + +Description +""""""""""" + +Perform constant NPH integration to update position, velocity, +orientation, and angular velocity each timestep for body +particles in the group using a Nose/Hoover pressure +barostat. P is pressure; H is enthalpy. This creates a system +trajectory consistent with the isenthalpic ensemble. + +This fix differs from the :doc:`fix nph ` command, which assumes +point particles and only updates their position and velocity. + +Additional parameters affecting the barostat are specified by keywords +and values documented with the :doc:`fix nph ` command. See, +for example, discussion of the *aniso*, and *dilate* keywords. + +The particles in the fix group are the only ones whose velocities and +positions are updated by the velocity/position update portion of the +NPH integration. + +Regardless of what particles are in the fix group, a global pressure is +computed for all particles. Similarly, when the size of the simulation +box is changed, all particles are re-scaled to new positions, unless the +keyword *dilate* is specified with a value of *partial*, in which case +only the particles in the fix group are re-scaled. The latter can be +useful for leaving the coordinates of particles in a solid substrate +unchanged and controlling the pressure of a surrounding fluid. + + +---------- + + +This fix computes a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp/body" and +"pressure", as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp all temp/body + compute fix-ID_press all pressure fix-ID_temp + +See the :doc:`compute temp/body ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is "all" +since pressure is computed for the entire system. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover barostatting to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix nph ` command. + +This fix can ramp its target pressure over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style body ` +command. + +Related commands +"""""""""""""""" + +:doc:`fix nph `, :doc:`fix nve_body `, :doc:`fix nvt_body `, :doc:`fix npt_body `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nph_sphere.txt b/doc/_sources/fix_nph_sphere.txt new file mode 100644 index 0000000000..253cb2eb6f --- /dev/null +++ b/doc/_sources/fix_nph_sphere.txt @@ -0,0 +1,160 @@ +.. index:: fix nph/sphere + +fix nph/sphere command +====================== + +fix nph/sphere/omp command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nph/sphere args keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* nph/sphere = style name of this fix command +* additional barostat related keyword/value pairs from the :doc:`fix nph ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nph/sphere iso 0.0 0.0 1000.0 + fix 2 all nph/sphere x 5.0 5.0 1000.0 + fix 2 all nph/sphere x 5.0 5.0 1000.0 drag 0.2 + fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial + +Description +""""""""""" + +Perform constant NPH integration to update position, velocity, and +angular velocity each timestep for finite-size spherical particles in +the group using a Nose/Hoover pressure barostat. P is pressure; H is +enthalpy. This creates a system trajectory consistent with the +isenthalpic ensemble. + +This fix differs from the :doc:`fix nph ` command, which assumes +point particles and only updates their position and velocity. + +Additional parameters affecting the barostat are specified by keywords +and values documented with the :doc:`fix nph ` command. See, +for example, discussion of the *aniso*, and *dilate* keywords. + +The particles in the fix group are the only ones whose velocities and +positions are updated by the velocity/position update portion of the +NPH integration. + +Regardless of what particles are in the fix group, a global pressure is +computed for all particles. Similarly, when the size of the simulation +box is changed, all particles are re-scaled to new positions, unless the +keyword *dilate* is specified with a value of *partial*, in which case +only the particles in the fix group are re-scaled. The latter can be +useful for leaving the coordinates of particles in a solid substrate +unchanged and controlling the pressure of a surrounding fluid. + + +---------- + + +This fix computes a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp/sphere" and +"pressure", as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp all temp/sphere + compute fix-ID_press all pressure fix-ID_temp + +See the :doc:`compute temp/sphere ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is "all" +since pressure is computed for the entire system. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files `. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover barostatting to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix nph ` command. + +This fix can ramp its target pressure over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix requires that atoms store torque and angular velocity (omega) +and a radius as defined by the :doc:`atom_style sphere ` +command. + +All particles in the group must be finite-size spheres. They cannot +be point particles. + +Related commands +"""""""""""""""" + +:doc:`fix nph `, :doc:`fix nve_sphere `, :doc:`fix nvt_sphere `, :doc:`fix npt_sphere `, +:doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nphug.txt b/doc/_sources/fix_nphug.txt new file mode 100644 index 0000000000..f02bdb052c --- /dev/null +++ b/doc/_sources/fix_nphug.txt @@ -0,0 +1,258 @@ +.. index:: fix nphug + +fix nphug command +================= + +fix nphug/omp command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nphug keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +.. parsed-literal:: + + one or more keyword value pairs may be appended + keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scaleyz* or *scalexz* or *scalexy* + *temp* values = Value1 Value2 Tdamp + Value1, Value2 = Nose-Hoover target temperatures, ignored by Hugoniostat + Tdamp = temperature damping parameter (time units) + *iso* or *aniso* or *tri* values = Pstart Pstop Pdamp + Pstart,Pstop = scalar external pressures, must be equal (pressure units) + Pdamp = pressure damping parameter (time units) + *x* or *y* or *z* or *xy* or *yz* or *xz* values = Pstart Pstop Pdamp + Pstart,Pstop = external stress tensor components, must be equal (pressure units) + Pdamp = stress damping parameter (time units) + *couple* = *none* or *xyz* or *xy* or *yz* or *xz* + *tchain* value = length of thermostat chain (1 = single thermostat) + *pchain* values = length of thermostat chain on barostat (0 = no thermostat) + *mtk* value = *yes* or *no* = add in MTK adjustment term or not + *tloop* value = number of sub-cycles to perform on thermostat + *ploop* value = number of sub-cycles to perform on barostat thermostat + *nreset* value = reset reference cell every this many timesteps + *drag* value = drag factor added to barostat/thermostat (0.0 = no drag) + *dilate* value = *all* or *partial* + *scaleyz* value = *yes* or *no* = scale yz with lz + *scalexz* value = *yes* or *no* = scale xz with lz + *scalexy* value = *yes* or *no* = scale xy with ly + + + +Examples +"""""""" + +.. parsed-literal:: + + fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 + fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 + +Description +""""""""""" + +This command is a variant of the Nose-Hoover +:doc:`fix npt ` fix style. +It performs time integration of the Hugoniostat equations +of motion developed by Ravelo et al. :ref:`(Ravelo) `. +These equations compress the system to a state with average +axial stress or pressure equal to the specified target value +and that satisfies the Rankine-Hugoniot (RH) +jump conditions for steady shocks. + +The compression can be performed +either +hydrostatically (using keyword *iso*, *aniso*, or *tri*) or uniaxially +(using keywords *x*, *y*, or *z*). In the hydrostatic case, +the cell dimensions change dynamically so that the average axial stress +in all three directions converges towards the specified target value. +In the uniaxial case, the chosen cell dimension changes dynamically +so that the average +axial stress in that direction converges towards the target value. The +other two cell dimensions are kept fixed (zero lateral strain). + +This leads to the following additional restrictions on the keywords: + +* One and only one of the following keywords should be used: *iso*, *aniso*, *tri*, *x*, *y*, *z* +* The specified initial and final target pressures must be the same. +* The keywords *xy*, *xz*, *yz* may not be used. +* The only admissible value for the couple keyword is *xyz*, which has the same effect as keyword *iso* +* The *temp* keyword must be used to specify the time constant for kinetic energy relaxation, but initial and final target temperature values are ignored. + +Essentially, a Hugoniostat simulation is an NPT simulation in which the +user-specified target temperature is replaced with a time-dependent +target temperature Tt obtained from the following equation: + +.. image:: Eqs/fix_nphug.jpg + :align: center + +where T and Tt are the instantaneous and target temperatures, +P and P0 are the instantaneous and reference pressures or axial stresses, +depending on whether hydrostatic or uniaxial compression is being +performed, V and V0 are the instantaneous and reference volumes, +E and E0 are the instantaneous and reference internal energy (potential +plus kinetic), Ndof is the number of degrees of freedom used in the +definition of temperature, and kB is the Boltzmann constant. Delta is the +negative deviation of the instantaneous temperature from the target temperature. +When the system reaches a stable equilibrium, the value of Delta should +fluctuate about zero. + +The values of E0, V0, and P0 are the instantaneous values at the start of +the simulation. These can be overridden using the fix_modify keywords *e0*, +*v0*, and *p0* described below. + + +---------- + + +.. note:: + + Unlike the :doc:`fix temp/berendsen ` command + which performs thermostatting but NO time integration, this fix + performs thermostatting/barostatting AND time integration. Thus you + should not use any other time integration fix, such as :doc:`fix nve ` on atoms to which this fix is applied. Likewise, + this fix should not be used on atoms that have their temperature + controlled by another fix - e.g. by :doc:`fix langevin ` or :doc:`fix temp/rescale ` commands. + + +---------- + + +This fix computes a temperature and pressure at each timestep. To do +this, the fix creates its own computes of style "temp" and "pressure", +as if one of these two sets of commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp + compute fix-ID_press group-ID pressure fix-ID_temp + +.. parsed-literal:: + + compute fix-ID_temp all temp + compute fix-ID_press all pressure fix-ID_temp + +See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press". The group for +the new computes is "all" since pressure is computed for the entire +system. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the values of E0, V0, and P0, as well as the +state of all the thermostat and barostat +variables to :doc:`binary restart files `. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The :doc:`fix_modify ` *e0*, *v0* and *p0* keywords +can be used to define the values of E0, V0, and P0. Note the +the values for *e0* and *v0* are extensive, and so must correspond +to the total energy and volume of the entire system, not energy and +volume per atom. If any of these quantities are not specified, then the +instantaneous value in the system at the start of the simulation is used. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by these fixes. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its thermostatting or barostatting procedure, as described above. +If you do this, note that the kinetic energy derived from the compute +temperature should be consistent with the virial term computed using +all atoms for the pressure. LAMMPS will warn you if you choose to +compute temperature on a subset of atoms. + +The :doc:`fix_modify ` *energy* option is supported by these +fixes to add the energy change induced by Nose/Hoover thermostatting +and barostatting to the system's potential energy as part of +:doc:`thermodynamic output `. Either way, this energy is *not* +included in the definition of internal energy E when calculating the value +of Delta in the above equation. + +These fixes compute a global scalar and a global vector of quantities, +which can be accessed by various :ref:`output commands `. The scalar value calculated by +these fixes is "extensive"; the vector values are "intensive". + +The scalar is the cumulative energy change due to the fix. + +The vector stores three quantities unique to this fix (Delta, Us, and up), +followed by all the internal Nose/Hoover thermostat and barostat +variables defined for :doc:`fix_style npt `. Delta is the deviation +of the temperature from the target temperature, given by the above equation. +Us and up are the shock and particle velocity corresponding to a steady +shock calculated from the RH conditions. They have units of distance/time. + +Restrictions +"""""""""""" + + +This fix style is part of the SHOCK package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +All the usual restrictions for :doc:`fix_style npt ` apply, +plus the additional ones mentioned above. + +Related commands +"""""""""""""""" + +:doc:`fix msst `, :doc:`fix npt `, :doc:`fix_modify ` + +Default +""""""" + +The keyword defaults are the same as those for :doc:`fix npt ` + + +---------- + + +.. _Ravelo: + + + +**(Ravelo)** Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_npt_asphere.txt b/doc/_sources/fix_npt_asphere.txt new file mode 100644 index 0000000000..a679232af1 --- /dev/null +++ b/doc/_sources/fix_npt_asphere.txt @@ -0,0 +1,188 @@ +.. index:: fix npt/asphere + +fix npt/asphere command +======================= + +fix npt/asphere/omp command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID npt/asphere keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* npt/asphere = style name of this fix command +* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 + fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 + fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 + fix 2 water npt/asphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial + +Description +""""""""""" + +Perform constant NPT integration to update position, velocity, +orientation, and angular velocity each timestep for aspherical or +ellipsoidal particles in the group using a Nose/Hoover temperature +thermostat and Nose/Hoover pressure barostat. P is pressure; T is +temperature. This creates a system trajectory consistent with the +isothermal-isobaric ensemble. + +This fix differs from the :doc:`fix npt ` command, which +assumes point particles and only updates their position and velocity. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the aspherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +Additional parameters affecting the thermostat and barostat are +specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. + +The particles in the fix group are the only ones whose velocities and +positions are updated by the velocity/position update portion of the +NPT integration. + +Regardless of what particles are in the fix group, a global pressure is +computed for all particles. Similarly, when the size of the simulation +box is changed, all particles are re-scaled to new positions, unless the +keyword *dilate* is specified with a value of *partial*, in which case +only the particles in the fix group are re-scaled. The latter can be +useful for leaving the coordinates of particles in a solid substrate +unchanged and controlling the pressure of a surrounding fluid. + + +---------- + + +This fix computes a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp/asphere" and +"pressure", as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp all temp/asphere + compute fix-ID_press all pressure fix-ID_temp + +See the :doc:`compute temp/asphere ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is "all" +since pressure is computed for the entire system. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover thermostat and barostat +to :doc:`binary restart files `. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting and +barostatting to the system's potential energy as part of +:doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix npt ` command. + +This fix can ramp its target temperature and pressure over multiple +runs, using the *start* and *stop* keywords of the :doc:`run ` +command. See the :doc:`run ` command for details of how to do +this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style ellipsoid ` +command. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical as defined by their +shape attribute. + +Related commands +"""""""""""""""" + +:doc:`fix npt `, :doc:`fix nve_asphere `, :doc:`fix nvt_asphere `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_npt_body.txt b/doc/_sources/fix_npt_body.txt new file mode 100644 index 0000000000..b791d2a939 --- /dev/null +++ b/doc/_sources/fix_npt_body.txt @@ -0,0 +1,181 @@ +.. index:: fix npt/body + +fix npt/body command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID npt/body keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* npt/body = style name of this fix command +* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all npt/body temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 + fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 + fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 + fix 2 water npt/body temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial + +Description +""""""""""" + +Perform constant NPT integration to update position, velocity, +orientation, and angular velocity each timestep for body +particles in the group using a Nose/Hoover temperature +thermostat and Nose/Hoover pressure barostat. P is pressure; T is +temperature. This creates a system trajectory consistent with the +isothermal-isobaric ensemble. + +This fix differs from the :doc:`fix npt ` command, which +assumes point particles and only updates their position and velocity. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the body particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +Additional parameters affecting the thermostat and barostat are +specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. + +The particles in the fix group are the only ones whose velocities and +positions are updated by the velocity/position update portion of the +NPT integration. + +Regardless of what particles are in the fix group, a global pressure is +computed for all particles. Similarly, when the size of the simulation +box is changed, all particles are re-scaled to new positions, unless the +keyword *dilate* is specified with a value of *partial*, in which case +only the particles in the fix group are re-scaled. The latter can be +useful for leaving the coordinates of particles in a solid substrate +unchanged and controlling the pressure of a surrounding fluid. + + +---------- + + +This fix computes a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp/body" and +"pressure", as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp all temp/body + compute fix-ID_press all pressure fix-ID_temp + +See the :doc:`compute temp/body ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is "all" +since pressure is computed for the entire system. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover thermostat and barostat +to :doc:`binary restart files `. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting and +barostatting to the system's potential energy as part of +:doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix npt ` command. + +This fix can ramp its target temperature and pressure over multiple +runs, using the *start* and *stop* keywords of the :doc:`run ` +command. See the :doc:`run ` command for details of how to do +this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style body ` +command. + +Related commands +"""""""""""""""" + +:doc:`fix npt `, :doc:`fix nve_body `, :doc:`fix nvt_body `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_npt_sphere.txt b/doc/_sources/fix_npt_sphere.txt new file mode 100644 index 0000000000..b3268beb52 --- /dev/null +++ b/doc/_sources/fix_npt_sphere.txt @@ -0,0 +1,183 @@ +.. index:: fix npt/sphere + +fix npt/sphere command +====================== + +fix npt/sphere/omp command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID npt/sphere keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* npt/sphere = style name of this fix command +* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 + fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 + fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2 + fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial + +Description +""""""""""" + +Perform constant NPT integration to update position, velocity, and +angular velocity each timestep for finite-sizex spherical particles in +the group using a Nose/Hoover temperature thermostat and Nose/Hoover +pressure barostat. P is pressure; T is temperature. This creates a +system trajectory consistent with the isothermal-isobaric ensemble. + +This fix differs from the :doc:`fix npt ` command, which +assumes point particles and only updates their position and velocity. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the spherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +Additional parameters affecting the thermostat and barostat are +specified by keywords and values documented with the :doc:`fix npt ` command. See, for example, discussion of the *temp*, +*iso*, *aniso*, and *dilate* keywords. + +The particles in the fix group are the only ones whose velocities and +positions are updated by the velocity/position update portion of the +NPT integration. + +Regardless of what particles are in the fix group, a global pressure is +computed for all particles. Similarly, when the size of the simulation +box is changed, all particles are re-scaled to new positions, unless the +keyword *dilate* is specified with a value of *partial*, in which case +only the particles in the fix group are re-scaled. The latter can be +useful for leaving the coordinates of particles in a solid substrate +unchanged and controlling the pressure of a surrounding fluid. + + +---------- + + +This fix computes a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp/sphere" and +"pressure", as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp all temp/sphere + compute fix-ID_press all pressure fix-ID_temp + +See the :doc:`compute temp/sphere ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is "all" +since pressure is computed for the entire system. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover thermostat and barostat +to :doc:`binary restart files `. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its thermostatting or barostatting procedure. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting and +barostatting to the system's potential energy as part of +:doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix npt ` command. + +This fix can ramp its target temperature and pressure over multiple +runs, using the *start* and *stop* keywords of the :doc:`run ` +command. See the :doc:`run ` command for details of how to do +this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix requires that atoms store torque and angular velocity (omega) +and a radius as defined by the :doc:`atom_style sphere ` +command. + +All particles in the group must be finite-size spheres. They cannot +be point particles. + +Related commands +"""""""""""""""" + +:doc:`fix npt `, :doc:`fix nve_sphere `, :doc:`fix nvt_sphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve.txt b/doc/_sources/fix_nve.txt new file mode 100644 index 0000000000..3ea8025d1b --- /dev/null +++ b/doc/_sources/fix_nve.txt @@ -0,0 +1,93 @@ +.. index:: fix nve + +fix nve command +=============== + +fix nve/cuda command +==================== + +fix nve/intel command +===================== + +fix nve/kk command +================== + +fix nve/omp command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve + +* ID, group-ID are documented in :doc:`fix ` command +* nve = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve + +Description +""""""""""" + +Perform constant NVE integration to update position and velocity for +atoms in the group each timestep. V is volume; E is energy. This +creates a system trajectory consistent with the microcanonical +ensemble. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix nvt `, :doc:`fix npt ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_asphere.txt b/doc/_sources/fix_nve_asphere.txt new file mode 100644 index 0000000000..6c796f8e7a --- /dev/null +++ b/doc/_sources/fix_nve_asphere.txt @@ -0,0 +1,98 @@ +.. index:: fix nve/asphere + +fix nve/asphere command +======================= + +fix nve/asphere/intel command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve/asphere + +* ID, group-ID are documented in :doc:`fix ` command +* nve/asphere = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve/asphere + +Description +""""""""""" + +Perform constant NVE integration to update position, velocity, +orientation, and angular velocity for aspherical particles in the +group each timestep. V is volume; E is energy. This creates a system +trajectory consistent with the microcanonical ensemble. + +This fix differs from the :doc:`fix nve ` command, which +assumes point particles and only updates their position and velocity. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style ellipsoid ` +command. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical as defined by their +shape attribute. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nve/sphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_asphere_noforce.txt b/doc/_sources/fix_nve_asphere_noforce.txt new file mode 100644 index 0000000000..a5a5b1e762 --- /dev/null +++ b/doc/_sources/fix_nve_asphere_noforce.txt @@ -0,0 +1,72 @@ +.. index:: fix nve/asphere/noforce + +fix nve/asphere/noforce command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve/asphere/noforce + +* ID, group-ID are documented in :doc:`fix ` command +* nve/asphere/noforce = style name of this fix command + +Examples +"""""""" + +fix 1 all nve/asphere/noforce + +Description +""""""""""" + +Perform updates of position and orientation, but not velocity or +angular momentum for atoms in the group each timestep. In other +words, the force and torque on the atoms is ignored and their velocity +and angular momentum are not updated. The atom velocities and +angularm momenta are used to update their positions and orientation. + +This is useful as an implicit time integrator for Fast Lubrication +Dynamics, since the velocity and angular momentum are updated by the +`pair_style lubricuteU `_ command. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style ellipsoid ` +command. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical as defined by their +shape attribute. + +Related commands +"""""""""""""""" + +:doc:`fix nve/noforce `, :doc:`fix nve/asphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_body.txt b/doc/_sources/fix_nve_body.txt new file mode 100644 index 0000000000..1dae9fb8ae --- /dev/null +++ b/doc/_sources/fix_nve_body.txt @@ -0,0 +1,68 @@ +.. index:: fix nve/body + +fix nve/body command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve/body + +* ID, group-ID are documented in :doc:`fix ` command +* nve/body = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve/body + +Description +""""""""""" + +Perform constant NVE integration to update position, velocity, +orientation, and angular velocity for body particles in the group each +timestep. V is volume; E is energy. This creates a system trajectory +consistent with the microcanonical ensemble. See :ref:`Section_howto 14 ` of the manual and the :doc:`body ` +doc page for more details on using body particles. + +This fix differs from the :doc:`fix nve ` command, which +assumes point particles and only updates their position and velocity. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style body ` +command. + +All particles in the group must be body particles. They cannot be +point particles. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nve/sphere `, :doc:`fix nve/asphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_eff.txt b/doc/_sources/fix_nve_eff.txt new file mode 100644 index 0000000000..3bb827d4d7 --- /dev/null +++ b/doc/_sources/fix_nve_eff.txt @@ -0,0 +1,59 @@ +.. index:: fix nve/eff + +fix nve/eff command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve/eff + +* ID, group-ID are documented in :doc:`fix ` command +* nve/eff = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve/eff + +Description +""""""""""" + +Perform constant NVE integration to update position and velocity for +nuclei and electrons in the group for the :doc:`electron force field ` model. V is volume; E is energy. This creates a +system trajectory consistent with the microcanonical ensemble. + +The operation of this fix is exactly like that described by the :doc:`fix nve ` command, except that the radius and radial velocity +of electrons are also updated. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nvt/eff `, :doc:`fix npt/eff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_limit.txt b/doc/_sources/fix_nve_limit.txt new file mode 100644 index 0000000000..849e16af2e --- /dev/null +++ b/doc/_sources/fix_nve_limit.txt @@ -0,0 +1,97 @@ +.. index:: fix nve/limit + +fix nve/limit command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve/limit xmax + +* ID, group-ID are documented in :doc:`fix ` command +* nve = style name of this fix command +* xmax = maximum distance an atom can move in one timestep (distance units) + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve/limit 0.1 + +Description +""""""""""" + +Perform constant NVE updates of position and velocity for atoms in the +group each timestep. A limit is imposed on the maximum distance an +atom can move in one timestep. This is useful when starting a +simulation with a configuration containing highly overlapped atoms. +Normally this would generate huge forces which would blow atoms out of +the simulation box, causing LAMMPS to stop with an error. + +Using this fix can overcome that problem. Forces on atoms must still +be computable (which typically means 2 atoms must have a separation +distance > 0.0). But large velocities generated by large forces are +reset to a value that corresponds to a displacement of length *xmax* +in a single timestep. *Xmax* is specified in distance units; see the +:doc:`units ` command for details. The value of *xmax* should be +consistent with the neighbor skin distance and the frequency of +neighbor list re-building, so that pairwise interactions are not +missed on successive timesteps as atoms move. See the +:doc:`neighbor ` and :doc:`neigh_modify ` commands +for details. + +Note that if a velocity reset occurs the integrator will not conserve +energy. On steps where no velocity resets occur, this integrator is +exactly like the :doc:`fix nve ` command. Since forces are +unaltered, pressures computed by thermodynamic output will still be +very large for overlapped configurations. + +.. note:: + + You should not use :doc:`fix shake ` in conjunction + with this fix. That is because fix shake applies contraint forces + based on the predicted postitions of atoms after the next timestep. + It has no way of knowing the timestep may change due to this fix, + which will cause the constraint forces to be invalid. A better + strategy is to turn off fix shake when performing initial dynamics + that need this fix, then turn fix shake on when doing normal dynamics + with a fixed-size timestep. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +count of how many updates of atom's velocity/position were limited by +the maximum distance criterion. This should be roughly the number of +atoms so affected, except that updates occur at both the beginning and +end of a timestep in a velocity Verlet timestepping algorithm. This +is a cumulative quantity for the current run, but is re-initialized to +zero each time a run is performed. The scalar value calculated by +this fix is "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nve/noforce `, +:doc:`pair_style soft ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_line.txt b/doc/_sources/fix_nve_line.txt new file mode 100644 index 0000000000..576cc1a673 --- /dev/null +++ b/doc/_sources/fix_nve_line.txt @@ -0,0 +1,65 @@ +.. index:: fix nve/line + +fix nve/line command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve/line + +* ID, group-ID are documented in :doc:`fix ` command +* nve/line = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve/line + +Description +""""""""""" + +Perform constant NVE integration to update position, velocity, +orientation, and angular velocity for line segment particles in the +group each timestep. V is volume; E is energy. This creates a system +trajectory consistent with the microcanonical ensemble. See +:doc:`Section_howto 14 ` of the manual for an overview of +using line segment particles. + +This fix differs from the :doc:`fix nve ` command, which +assumes point particles and only updates their position and velocity. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that particles be line segments as defined by the +:doc:`atom_style line ` command. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nve/asphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_noforce.txt b/doc/_sources/fix_nve_noforce.txt new file mode 100644 index 0000000000..84e3c54553 --- /dev/null +++ b/doc/_sources/fix_nve_noforce.txt @@ -0,0 +1,63 @@ +.. index:: fix nve/noforce + +fix nve/noforce command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve + +* ID, group-ID are documented in :doc:`fix ` command +* nve/noforce = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 wall nve/noforce + +Description +""""""""""" + +Perform updates of position, but not velocity for atoms in the group +each timestep. In other words, the force on the atoms is ignored and +their velocity is not updated. The atom velocities are used to update +their positions. + +This can be useful for wall atoms, when you set their velocities, and +want the wall to move (or stay stationary) in a prescribed fashion. + +This can also be accomplished via the :doc:`fix setforce ` +command, but with fix nve/noforce, the forces on the wall atoms are +unchanged, and can thus be printed by the :doc:`dump ` command or +queried with an equal-style :doc:`variable ` that uses the +fcm() group function to compute the total force on the group of atoms. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix nve ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_sphere.txt b/doc/_sources/fix_nve_sphere.txt new file mode 100644 index 0000000000..72d77ef1b4 --- /dev/null +++ b/doc/_sources/fix_nve_sphere.txt @@ -0,0 +1,111 @@ +.. index:: fix nve/sphere + +fix nve/sphere command +====================== + +fix nve/sphere/omp command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve/sphere + +* ID, group-ID are documented in :doc:`fix ` command +* nve/sphere = style name of this fix command +* zero or more keyword/value pairs may be appended +* keyword = *update* +.. parsed-literal:: + + *update* value = *dipole* + dipole = update orientation of dipole moment during integration + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve/sphere + fix 1 all nve/sphere update dipole + +Description +""""""""""" + +Perform constant NVE integration to update position, velocity, and +angular velocity for finite-size spherical particles in the group each +timestep. V is volume; E is energy. This creates a system trajectory +consistent with the microcanonical ensemble. + +This fix differs from the :doc:`fix nve ` command, which +assumes point particles and only updates their position and velocity. + +If the *update* keyword is used with the *dipole* value, then the +orientation of the dipole moment of each particle is also updated +during the time integration. This option should be used for models +where a dipole moment is assigned to finite-size particles, +e.g. spheroids via use of the :doc:`atom_style hybrid sphere dipole ` command. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix requires that atoms store torque and angular velocity (omega) +and a radius as defined by the :doc:`atom_style sphere ` +command. If the *dipole* keyword is used, then they must also store a +dipole moment as defined by the :doc:`atom_style dipole ` +command. + +All particles in the group must be finite-size spheres. They cannot +be point particles. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nve/asphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nve_tri.txt b/doc/_sources/fix_nve_tri.txt new file mode 100644 index 0000000000..44ad68ae29 --- /dev/null +++ b/doc/_sources/fix_nve_tri.txt @@ -0,0 +1,65 @@ +.. index:: fix nve/tri + +fix nve/tri command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nve/tri + +* ID, group-ID are documented in :doc:`fix ` command +* nve/tri = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve/tri + +Description +""""""""""" + +Perform constant NVE integration to update position, velocity, +orientation, and angular momentum for triangular particles in the +group each timestep. V is volume; E is energy. This creates a system +trajectory consistent with the microcanonical ensemble. See +:doc:`Section_howto 14 ` of the manual for an overview of +using triangular particles. + +This fix differs from the :doc:`fix nve ` command, which +assumes point particles and only updates their position and velocity. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that particles be triangles as defined by the +:doc:`atom_style tri ` command. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nve/asphere ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nvt_asphere.txt b/doc/_sources/fix_nvt_asphere.txt new file mode 100644 index 0000000000..c340033ed8 --- /dev/null +++ b/doc/_sources/fix_nvt_asphere.txt @@ -0,0 +1,162 @@ +.. index:: fix nvt/asphere + +fix nvt/asphere command +======================= + +fix nvt/asphere/omp command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nvt/asphere keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* nvt/asphere = style name of this fix command +* additional thermostat related keyword/value pairs from the :doc:`fix nvt ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nvt/asphere temp 300.0 300.0 100.0 + fix 1 all nvt/asphere temp 300.0 300.0 100.0 drag 0.2 + +Description +""""""""""" + +Perform constant NVT integration to update position, velocity, +orientation, and angular velocity each timestep for aspherical or +ellipsoidal particles in the group using a Nose/Hoover temperature +thermostat. V is volume; T is temperature. This creates a system +trajectory consistent with the canonical ensemble. + +This fix differs from the :doc:`fix nvt ` command, which +assumes point particles and only updates their position and velocity. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the aspherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +Additional parameters affecting the thermostat are specified by +keywords and values documented with the :doc:`fix nvt ` +command. See, for example, discussion of the *temp* and *drag* +keywords. + +This fix computes a temperature each timestep. To do this, the fix +creates its own compute of style "temp/asphere", as if this command +had been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp/asphere + +See the :doc:`compute temp/asphere ` command for +details. Note that the ID of the new compute is the fix-ID + +underscore + "temp", and the group for the new compute is the same as +the fix group. + +Note that this is NOT the compute used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp*. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* will have no +effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a :doc:`compute ` you have +defined to this fix which will be used in its thermostatting +procedure. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix nvt ` command. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the ASPHERE package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style ellipsoid ` +command. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical as defined by their +shape attribute. + +Related commands +"""""""""""""""" + +:doc:`fix nvt `, :doc:`fix nve_asphere `, :doc:`fix npt_asphere `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nvt_body.txt b/doc/_sources/fix_nvt_body.txt new file mode 100644 index 0000000000..43289ffe26 --- /dev/null +++ b/doc/_sources/fix_nvt_body.txt @@ -0,0 +1,155 @@ +.. index:: fix nvt/body + +fix nvt/body command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nvt/body keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* nvt/body = style name of this fix command +* additional thermostat related keyword/value pairs from the :doc:`fix nvt ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nvt/body temp 300.0 300.0 100.0 + fix 1 all nvt/body temp 300.0 300.0 100.0 drag 0.2 + +Description +""""""""""" + +Perform constant NVT integration to update position, velocity, +orientation, and angular velocity each timestep for body +particles in the group using a Nose/Hoover temperature +thermostat. V is volume; T is temperature. This creates a system +trajectory consistent with the canonical ensemble. + +This fix differs from the :doc:`fix nvt ` command, which +assumes point particles and only updates their position and velocity. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the body particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +Additional parameters affecting the thermostat are specified by +keywords and values documented with the :doc:`fix nvt ` +command. See, for example, discussion of the *temp* and *drag* +keywords. + +This fix computes a temperature each timestep. To do this, the fix +creates its own compute of style "temp/body", as if this command +had been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp/body + +See the :doc:`compute temp/body ` command for +details. Note that the ID of the new compute is the fix-ID + +underscore + "temp", and the group for the new compute is the same as +the fix group. + +Note that this is NOT the compute used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp*. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* will have no +effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a :doc:`compute ` you have +defined to this fix which will be used in its thermostatting +procedure. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix nvt ` command. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires that atoms store torque and angular momementum and a +quaternion as defined by the :doc:`atom_style body ` +command. + +Related commands +"""""""""""""""" + +:doc:`fix nvt `, :doc:`fix nve_body `, :doc:`fix npt_body `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nvt_sllod.txt b/doc/_sources/fix_nvt_sllod.txt new file mode 100644 index 0000000000..8165a02df3 --- /dev/null +++ b/doc/_sources/fix_nvt_sllod.txt @@ -0,0 +1,197 @@ +.. index:: fix nvt/sllod + +fix nvt/sllod command +===================== + +fix nvt/sllod/omp command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nvt/sllod keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* nvt/sllod = style name of this fix command +* additional thermostat related keyword/value pairs from the :doc:`fix nvt ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nvt/sllod temp 300.0 300.0 100.0 + fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2 + +Description +""""""""""" + +Perform constant NVT integration to update positions and velocities +each timestep for atoms in the group using a Nose/Hoover temperature +thermostat. V is volume; T is temperature. This creates a system +trajectory consistent with the canonical ensemble. + +This thermostat is used for a simulation box that is changing size +and/or shape, for example in a non-equilibrium MD (NEMD) simulation. +The size/shape change is induced by use of the :doc:`fix deform ` command, so each point in the simulation box +can be thought of as having a "streaming" velocity. This +position-dependent streaming velocity is subtracted from each atom's +actual velocity to yield a thermal velocity which is used for +temperature computation and thermostatting. For example, if the box +is being sheared in x, relative to y, then points at the bottom of the +box (low y) have a small x velocity, while points at the top of the +box (hi y) have a large x velocity. These velocities do not +contribute to the thermal "temperature" of the atom. + +.. note:: + + :doc:`Fix deform ` has an option for remapping either + atom coordinates or velocities to the changing simulation box. To use + fix nvt/sllod, fix deform should NOT remap atom positions, because fix + nvt/sllod adjusts the atom positions and velocities to create a + velocity profile that matches the changing box size/shape. Fix deform + SHOULD remap atom velocities when atoms cross periodic boundaries + since that is consistent with maintaining the velocity profile created + by fix nvt/sllod. LAMMPS will give an error if this setting is not + consistent. + +The SLLOD equations of motion, originally proposed by Hoover and Ladd +(see :ref:`(Evans and Morriss) `), were proven to be equivalent to +Newton's equations of motion for shear flow by :ref:`(Evans and Morriss) `. They were later shown to generate the desired +velocity gradient and the correct production of work by stresses for +all forms of homogeneous flow by :ref:`(Daivis and Todd) `. As +implemented in LAMMPS, they are coupled to a Nose/Hoover chain +thermostat in a velocity Verlet formulation, closely following the +implementation used for the :doc:`fix nvt ` command. + +Additional parameters affecting the thermostat are specified by +keywords and values documented with the :doc:`fix nvt ` +command. See, for example, discussion of the *temp* and *drag* +keywords. + +This fix computes a temperature each timestep. To do this, the fix +creates its own compute of style "temp/deform", as if this command had +been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp/deform + +See the :doc:`compute temp/deform ` command for +details. Note that the ID of the new compute is the fix-ID + +underscore + "temp", and the group for the new compute is the same as +the fix group. + +Note that this is NOT the compute used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp*. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* will have no +effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a :doc:`compute ` you have +defined to this fix which will be used in its thermostatting +procedure. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix nvt ` command. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix works best without Nose-Hoover chain thermostats, i.e. using +tchain = 1. Setting tchain to larger values can result in poor +equilibration. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, +:doc:`fix_modify `, :doc:`compute temp/deform ` + +Default +""""""" + +Same as :doc:`fix nvt `, except tchain = 1. + + +---------- + + +.. _Evans: + + + +**(Evans and Morriss)** Evans and Morriss, Phys Rev A, 30, 1528 (1984). + +.. _Daivis: + + + +**(Daivis and Todd)** Daivis and Todd, J Chem Phys, 124, 194103 (2006). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nvt_sllod_eff.txt b/doc/_sources/fix_nvt_sllod_eff.txt new file mode 100644 index 0000000000..c22198ba7d --- /dev/null +++ b/doc/_sources/fix_nvt_sllod_eff.txt @@ -0,0 +1,102 @@ +.. index:: fix nvt/sllod/eff + +fix nvt/sllod/eff command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nvt/sllod/eff keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* nvt/sllod/eff = style name of this fix command +* additional thermostat related keyword/value pairs from the :doc:`fix nvt/eff ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 + fix 1 all nvt/sllod/eff temp 300.0 300.0 0.1 drag 0.2 + +Description +""""""""""" + +Perform constant NVT integration to update positions and velocities +each timestep for nuclei and electrons in the group for the :doc:`electron force field ` model, using a Nose/Hoover temperature +thermostat. V is volume; T is temperature. This creates a system +trajectory consistent with the canonical ensemble. + +The operation of this fix is exactly like that described by the :doc:`fix nvt/sllod ` command, except that the radius and +radial velocity of electrons are also updated and thermostatted. +Likewise the temperature calculated by the fix, using the compute it +creates (as discussed in the :doc:`fix nvt, npt, and nph ` doc +page), is performed with a :doc:`compute temp/deform/eff ` commmand that includes +the eFF contribution to the temperature from the electron radial +velocity. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a :doc:`compute ` you have +defined to this fix which will be used in its thermostatting +procedure. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix nvt/eff ` command. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix works best without Nose-Hoover chain thermostats, i.e. using +tchain = 1. Setting tchain to larger values can result in poor +equilibration. + +Related commands +"""""""""""""""" + +:doc:`fix nve/eff `, :doc:`fix nvt/eff `, :doc:`fix langevin/eff `, :doc:`fix nvt/sllod `, :doc:`fix_modify `, :doc:`compute temp/deform/eff ` + +Default +""""""" + +Same as :doc:`fix nvt/eff `, except tchain = 1. + + +---------- + + +.. _Tuckerman: + + + +**(Tuckerman)** Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, +106, 5615 (1997). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_nvt_sphere.txt b/doc/_sources/fix_nvt_sphere.txt new file mode 100644 index 0000000000..5575c04ee7 --- /dev/null +++ b/doc/_sources/fix_nvt_sphere.txt @@ -0,0 +1,158 @@ +.. index:: fix nvt/sphere + +fix nvt/sphere command +====================== + +fix nvt/sphere/omp command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID nvt/sphere keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* nvt/sphere = style name of this fix command +* additional thermostat related keyword/value pairs from the :doc:`fix nvt ` command can be appended + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nvt/sphere temp 300.0 300.0 100.0 + fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2 + +Description +""""""""""" + +Perform constant NVT integration to update position, velocity, and +angular velocity each timestep for finite-size spherical particles in +the group using a Nose/Hoover temperature thermostat. V is volume; T +is temperature. This creates a system trajectory consistent with the +canonical ensemble. + +This fix differs from the :doc:`fix nvt ` command, which +assumes point particles and only updates their position and velocity. + +The thermostat is applied to both the translational and rotational +degrees of freedom for the spherical particles, assuming a compute is +used which calculates a temperature that includes the rotational +degrees of freedom (see below). The translational degrees of freedom +can also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +Additional parameters affecting the thermostat are specified by +keywords and values documented with the :doc:`fix nvt ` +command. See, for example, discussion of the *temp* and *drag* +keywords. + +This fix computes a temperature each timestep. To do this, the fix +creates its own compute of style "temp/sphere", as if this command +had been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp/sphere + +See the :doc:`compute temp/sphere ` command for +details. Note that the ID of the new compute is the fix-ID + +underscore + "temp", and the group for the new compute is the same as +the fix group. + +Note that this is NOT the compute used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp*. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* will have no +effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files `. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a :doc:`compute ` you have +defined to this fix which will be used in its thermostatting +procedure. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change induced by Nose/Hoover thermostatting to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes the same global scalar and global vector of +quantities as does the :doc:`fix nvt ` command. + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix requires that atoms store torque and angular velocity (omega) +and a radius as defined by the :doc:`atom_style sphere ` +command. + +All particles in the group must be finite-size spheres. They cannot +be point particles. + +Related commands +"""""""""""""""" + +:doc:`fix nvt `, :doc:`fix nve_sphere `, :doc:`fix nvt_asphere `, :doc:`fix npt_sphere `, :doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_oneway.txt b/doc/_sources/fix_oneway.txt new file mode 100644 index 0000000000..8a3285e6d9 --- /dev/null +++ b/doc/_sources/fix_oneway.txt @@ -0,0 +1,72 @@ +.. index:: fix oneway + +fix oneway command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID oneway N region-ID direction + +* ID, group-ID are documented in :doc:`fix ` command +* oneway = style name of this fix command +* N = apply this fix every this many timesteps +* region-ID = ID of region where fix is active +* direction = *x* or *-x* or *y* or *-y* or *z* or *-z* = coordinate and direction of the oneway constraint + + +Examples +"""""""" + +.. parsed-literal:: + + fix ions oneway 10 semi -x + fix all oneway 1 left -z + fix all oneway 1 right z + +Description +""""""""""" + +Enforce that particles in the group and in a given region can only +move in one direction. This is done by reversing a particle's +velocity component, if it has the wrong sign in the specified +dimension. The effect is that the particle moves in one direction +only. + +This can be used, for example, as a simple model of a semi-permeable +membrane, or as an implementation of Maxwell's demon. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix wall/reflect ` command + +**Default:** none + + +---------- + + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_orient_fcc.txt b/doc/_sources/fix_orient_fcc.txt new file mode 100644 index 0000000000..fa6a63a45b --- /dev/null +++ b/doc/_sources/fix_orient_fcc.txt @@ -0,0 +1,201 @@ +.. index:: fix orient/fcc + +fix orient/fcc command +====================== + +.. parsed-literal:: + + fix ID group-ID orient/fcc nstats dir alat dE cutlo cuthi file0 file1 + +* ID, group-ID are documented in :doc:`fix ` command +* nstats = print stats every this many steps, 0 = never +* dir = 0/1 for which crystal is used as reference +* alat = fcc cubic lattice constant (distance units) +* dE = energy added to each atom (energy units) +* cutlo,cuthi = values between 0.0 and 1.0, cutlo < cuthi +* file0,file1 = files that specify orientation of each grain + +Examples +"""""""" + +.. parsed-literal:: + + fix gb all orient/fcc 0 1 4.032008 0.001 0.25 0.75 xi.vec chi.vec + +Description +""""""""""" + +The fix applies an orientation-dependent force to atoms near a planar +grain boundary which can be used to induce grain boundary migration +(in the direction perpendicular to the grain boundary plane). The +motivation and explanation of this force and its application are +described in :ref:`(Janssens) `. The force is only applied to +atoms in the fix group. + +The basic idea is that atoms in one grain (on one side of the +boundary) have a potential energy dE added to them. Atoms in the +other grain have 0.0 potential energy added. Atoms near the boundary +(whose neighbor environment is intermediate between the two grain +orientations) have an energy between 0.0 and dE added. This creates +an effective driving force to reduce the potential energy of atoms +near the boundary by pushing them towards one of the grain +orientations. For dir = 1 and dE > 0, the boundary will thus move so +that the grain described by file0 grows and the grain described by +file1 shrinks. Thus this fix is designed for simulations of two-grain +systems, either with one grain boundary and free surfaces parallel to +the boundary, or a system with periodic boundary conditions and two +equal and opposite grain boundaries. In either case, the entire +system can displace during the simulation, and such motion should be +accounted for in measuring the grain boundary velocity. + +The potential energy added to atom I is given by these formulas + +.. image:: Eqs/fix_orient_fcc.jpg + :align: center + +which are fully explained in :ref:`(Janssens) `. The order +parameter Xi for atom I in equation (1) is a sum over the 12 nearest +neighbors of atom I. Rj is the vector from atom I to its neighbor J, +and RIj is a vector in the reference (perfect) crystal. That is, if +dir = 0/1, then RIj is a vector to an atom coord from file 0/1. +Equation (2) gives the expected value of the order parameter XiIJ in +the other grain. Hi and lo cutoffs are defined in equations (3) and +(4), using the input parameters *cutlo* and *cuthi* as thresholds to +avoid adding grain boundary energy when the deviation in the order +parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a +perfect crystal). The added potential energy Ui for atom I is given +in equation (6) where it is interpolated between 0 and dE using the +two threshold Xi values and the Wi value of equation (5). + +The derivative of this energy expression gives the force on each atom +which thus depends on the orientation of its neighbors relative to the +2 grain orientations. Only atoms near the grain boundary feel a net +force which tends to drive them to one of the two grain orientations. + +In equation (1), the reference vector used for each neighbor is the +reference vector closest to the actual neighbor position. This means +it is possible two different neighbors will use the same reference +vector. In such cases, the atom in question is far from a perfect +orientation and will likely receive the full dE addition, so the +effect of duplicate reference vector usage is small. + +The *dir* parameter determines which grain wants to grow at the +expense of the other. A value of 0 means the first grain will shrink; +a value of 1 means it will grow. This assumes that *dE* is positive. +The reverse will be true if *dE* is negative. + +The *alat* parameter is the cubic lattice constant for the fcc +material and is only used to compute a cutoff distance of 1.57 * alat +/ sqrt(2) for finding the 12 nearest neighbors of each atom (which +should be valid for an fcc crystal). A longer/shorter cutoff can be +imposed by adjusting *alat*. If a particular atom has less than 12 +neighbors within the cutoff, the order parameter of equation (1) is +effectively multiplied by 12 divided by the actual number of neighbors +within the cutoff. + +The *dE* parameter is the maximum amount of additional energy added to +each atom in the grain which wants to shrink. + +The *cutlo* and *cuthi* parameters are used to reduce the force added +to bulk atoms in each grain far away from the boundary. An atom in +the bulk surrounded by neighbors at the ideal grain orientation would +compute an order parameter of 0 or 1 and have no force added. +However, thermal vibrations in the solid will cause the order +parameters to be greater than 0 or less than 1. The cutoff parameters +mask this effect, allowing forces to only be added to atoms with +order-parameters between the cutoff values. + +*File0* and *file1* are filenames for the two grains which each +contain 6 vectors (6 lines with 3 values per line) which specify the +grain orientations. Each vector is a displacement from a central atom +(0,0,0) to a nearest neighbor atom in an fcc lattice at the proper +orientation. The vector lengths should all be identical since an fcc +lattice has a coordination number of 12. Only 6 are listed due to +symmetry, so the list must include one from each pair of +equal-and-opposite neighbors. A pair of orientation files for a +Sigma=5 tilt boundary are show below. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the potential energy of atom interactions with the grain +boundary driving force to the system's potential energy as part of +:doc:`thermodynamic output `. + +This fix calculates a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +potential energy change due to this fix. The scalar value calculated +by this fix is "extensive". + +This fix also calculates a per-atom array which can be accessed by +various :ref:`output commands `. The array +stores the order parameter Xi and normalized order parameter (0 to 1) +for each atom. The per-atom values can be accessed on any timestep. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix should only be used with fcc lattices. + +Related commands +"""""""""""""""" + +:doc:`fix_modify ` + +**Default:** none + + +---------- + + +.. _Janssens: + + + +**(Janssens)** Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature +Materials, 5, 124-127 (2006). + + +---------- + + +For illustration purposes, here are example files that specify a +Sigma=5 <100> tilt boundary. This is for a lattice constant of 3.5706 +Angs. + +file0: + +.. parsed-literal:: + + 0.798410432046075 1.785300000000000 1.596820864092150 + -0.798410432046075 1.785300000000000 -1.596820864092150 + 2.395231296138225 0.000000000000000 0.798410432046075 + 0.798410432046075 0.000000000000000 -2.395231296138225 + 1.596820864092150 1.785300000000000 -0.798410432046075 + 1.596820864092150 -1.785300000000000 -0.798410432046075 + +file1: + +.. parsed-literal:: + + -0.798410432046075 1.785300000000000 1.596820864092150 + 0.798410432046075 1.785300000000000 -1.596820864092150 + 0.798410432046075 0.000000000000000 2.395231296138225 + 2.395231296138225 0.000000000000000 -0.798410432046075 + 1.596820864092150 1.785300000000000 0.798410432046075 + 1.596820864092150 -1.785300000000000 0.798410432046075 + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_phonon.txt b/doc/_sources/fix_phonon.txt new file mode 100644 index 0000000000..e0a59b1fb6 --- /dev/null +++ b/doc/_sources/fix_phonon.txt @@ -0,0 +1,231 @@ +.. index:: fix phonon + +fix phonon command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* phonon = style name of this fix command +* N = measure the Green's function every this many timesteps +* Noutput = output the dynamical matrix every this many measurements +* Nwait = wait this many timesteps before measuring +* map_file = *file* or *GAMMA* +.. parsed-literal:: + + *file* is the file that contains the mapping info between atom ID and the lattice indices. + +.. parsed-literal:: + + *GAMMA* flags to treate the whole simulation box as a unit cell, so that the mapping + info can be generated internally. In this case, dynamical matrix at only the gamma-point + will/can be evaluated. + +* prefix = prefix for output files +* one or none keyword/value pairs may be appended +* keyword = *sysdim* or *nasr* +.. parsed-literal:: + + *sysdim* value = d + d = dimension of the system, usually the same as the MD model dimension + *nasr* value = n + n = number of iterations to enforce the acoustic sum rule + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all phonon 20 5000 200000 map.in LJ1D sysdim 1 + fix 1 all phonon 20 5000 200000 map.in EAM3D + fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 + +Description +""""""""""" + +Calculate the dynamical matrix from molecular dynamics simulations +based on fluctuation-dissipation theory for a group of atoms. + +Consider a crystal with *N* unit cells in three dimensions labelled *l += (l1,l2,l3)* where *li* +are integers. Each unit cell is defined by three linearly independent +vectors **a**1, **a**2, **a**3 forming a +parallelipiped, containing *K* basis atoms labelled *k*. + +Based on fluctuation-dissipation theory, the force constant +coefficients of the system in reciprocal space are given by +(:ref:`Campañá ` , :ref:`Kong `) +
      Φkα,k'β(q) = +kBT +G-1kα,k'β(q),
      + +where **G** is the Green's functions coefficients given by + +.. raw:: html + +
      Gkα,k'β(q) = + <ukα(q)•uk'β*(q)>,
      + +where <...> denotes the ensemble average, and +
      **u**kα(q) = ∑l +ulkα exp(i**qr**l)
      + +is the α component of the atomic displacement for the *k*th atom +in the unit cell in reciprocal space at **q**. In practice, the Green's +functions coefficients can also be measured according to the following +formula, + +.. raw:: html + +
      Gkα,k'β(q) = + <Rkα(q)•R*k'β(q)> + - <R>kα(q)•<R>*k'β(q), +
      + +where **R** is the instantaneous positions of atoms, and <**R**> is the +averaged atomic positions. It gives essentially the same results as +the displacement method and is easier to implement in an MD code. + +Once the force constant matrix is known, the dynamical matrix **D** can +then be obtained by + +.. raw:: html + +
      Dkα, k'β(q) = (mkmk')-1/2 Φkα,k'β(q)
      + +whose eigenvalues are exactly the phonon frequencies at **q**. + +This fix uses positions of atoms in the specified group and calculates +two-point correlations. To achieve this. the positions of the atoms +are examined every *Nevery* steps and are Fourier-transformed into +reciprocal space, where the averaging process and correlation +computation is then done. After every *Noutput* measurements, the +matrix **G**(**q**) is calculated and inverted to obtain the elastic +stiffness coefficients. The dynamical matrices are then constructed +and written to *prefix*.bin.timestep files in binary format and to the +file *prefix*.log for each wavevector **q**. + +A detailed description of this method can be found in +(:ref:`Kong2011 `). + +The *sysdim* keyword is optional. If specified with a value smaller +than the dimensionality of the LAMMPS simulation, its value is used +for the dynamical matrix calculation. For example, using LAMMPS ot +model a 2D or 3D system, the phonon dispersion of a 1D atomic chain +can be computed using *sysdim* = 1. + +The *nasr* keyword is optional. An iterative procedure is employed to +enforce the acoustic sum rule on Φ at Γ, and the number +provided by keyword *nasr* gives the total number of iterations. For a +system whose unit cell has only one atom, *nasr* = 1 is sufficient; +for other systems, *nasr* = 10 is typically sufficient. + +The *map_file* contains the mapping information between the lattice +indices and the atom IDs, which tells the code which atom sits at +which lattice point; the lattice indices start from 0. An auxiliary +code, `latgen `_, can be employed to +generate the compatible map file for various crystals. + +In case one simulates an aperiodic system, where the whole simulation box +is treated as a unit cell, one can set *map_file* as *GAMMA*, so that the mapping +info will be generated internally and a file is not needed. In this case, the +dynamical matrix at only the gamma-point will/can be evaluated. Please keep in +mind that fix-phonon is designed for cyrstals, it will be inefficient and +even degrade the performance of lammps in case the unit cell is too large. + +The calculated dynamical matrix elements are written out in +:doc:`energy/distance^2/mass ` units. The coordinates for *q* +points in the log file is in the units of the basis vectors of the +corresponding reciprocal lattice. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to change the temperature compute from thermo_temp +to the one that reflects the true temperature of atoms in the group. + +No global scalar or vector or per-atom quantities are stored by this +fix for access by various :ref:`output commands <4_15>`. + +Instead, this fix outputs its initialization information (including +mapping information) and the calculated dynamical matrices to the file +*prefix*.log, with the specified *prefix*. The dynamical matrices are +also written to files *prefix*.bin.timestep in binary format. These +can be read by the post-processing tool in tools/phonon to compute the +phonon density of states and/or phonon dispersion curves. + +No parameter of this fix can be used with the *start/stop* keywords +of the :doc:`run ` command. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix assumes a crystalline system with periodical lattice. The +temperature of the system should not exceed the melting temperature to +keep the system in its solid state. + +This fix is part of the USER-PHONON package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix requires LAMMPS be built with an FFT library. See the +:ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`compute msd ` + +Default +""""""" + +The option defaults are sysdim = the same dimemsion as specified by +the `dimension `_ command, and nasr = 20. + + +---------- + + +.. _Campana: + + + +**(Campañá)** C. Campañá and +M. H. Müser, *Practical Green's function approach to the +simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) `_ + +.. _Kong: + + + +**(Kong)** L.T. Kong, G. Bartels, C. Campañá, +C. Denniston, and Martin H. Müser, *Implementation of Green's +function molecular dynamics: An extension to LAMMPS*, `Computer Physics Communications [180](6):1004-1010 (2009). `_ + +L.T. Kong, C. Denniston, and Martin H. Müser, +*An improved version of the Green's function molecular dynamics +method*, `Computer Physics Communications [182](2):540-541 (2011). `_ + +.. _Kong2011: + + + +**(Kong2011)** L.T. Kong, *Phonon dispersion measured directly from +molecular dynamics simulations*, `Computer Physics Communications [182](10):2201-2207, (2011). `_ + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_pimd.txt b/doc/_sources/fix_pimd.txt new file mode 100644 index 0000000000..4b3bc718bd --- /dev/null +++ b/doc/_sources/fix_pimd.txt @@ -0,0 +1,222 @@ +.. index:: fix pimd + +fix pimd command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID pimd keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* pimd = style name of this fix command +* zero or more keyword/value pairs may be appended +* keyword = *method* or *fmass* or *sp* or *temp* or *nhc* +.. parsed-literal:: + + *method* value = *pimd* or *nmpimd* or *cmd* + *fmass* value = scaling factor on mass + *sp* value = scaling factor on Planck constant + *temp* value = temperature (temperarate units) + *nhc* value = Nc = number of chains in Nose-Hoover thermostat + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all pimd method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4 + +Description +""""""""""" + +This command performs quantum molecular dynamics simulations based on +the Feynman path integral to include effects of tunneling and +zero-point motion. In this formalism, the isomorphism of a quantum +partition function for the original system to a classical partition +function for a ring-polymer system is exploited, to efficiently sample +configurations from the canonical ensemble :ref:`(Feynman) `. +The classical partition function and its components are given +by the following equations: + +.. image:: Eqs/fix_pimd.jpg + :align: center + +The interested user is referred to any of the numerous references on +this methodology, but briefly, each quantum particle in a path +integral simulation is represented by a ring-polymer of P quasi-beads, +labeled from 1 to P. During the simulation, each quasi-bead interacts +with beads on the other ring-polymers with the same imaginary time +index (the second term in the effective potential above). The +quasi-beads also interact with the two neighboring quasi-beads through +the spring potential in imaginary-time space (first term in effective +potential). To sample the canonical ensemble, a Nose-Hoover massive +chain thermostat is applied :ref:`(Tuckerman) `. With the +massive chain algorithm, a chain of NH thermostats is coupled to each +degree of freedom for each quasi-bead. The keyword *temp* sets the +target temperature for the system and the keyword *nhc* sets the +number *Nc* of thermostats in each chain. For example, for a +simulation of N particles with P beads in each ring-polymer, the total +number of NH thermostats would be 3 x N x P x Nc. + +.. note:: + + This fix implements a complete velocity-verlet integrator + combined with NH massive chain thermostat, so no other time + integration fix should be used. + +The *method* keyword determines what style of PIMD is performed. A +value of *pimd* is standard PIMD. A value of *nmpimd* is for +normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics +(CMD). The difference between the styles is as follows. + +In standard PIMD, the value used for a bead's fictitious mass is +arbitrary. A common choice is to use Mi = m/P, which results in the +mass of the entire ring-polymer being equal to the real quantum +particle. But it can be difficult to efficiently integrate the +equations of motion for the stiff harmonic interactions in the ring +polymers. + +A useful way to resolve this issue is to integrate the equations of +motion in a normal mode representation, using Normal Mode +Path-Integral Molecular Dynamics (NMPIMD) :ref:`(Cao1) `. In NMPIMD, +the NH chains are attached to each normal mode of the ring-polymer and +the fictitious mass of each mode is chosen as Mk = the eigenvalue of +the Kth normal mode for k > 0. The k = 0 mode, referred to as the +zero-frequency mode or centroid, corresponds to overall translation of +the ring-polymer and is assigned the mass of the real particle. + +Motion of the centroid can be effectively uncoupled from the other +normal modes by scaling the fictitious masses to achieve a partial +adiabatic separation. This is called a Centroid Molecular Dynamics +(CMD) approximation :ref:`(Cao2) `. The time-evolution (and resulting +dynamics) of the quantum particles can be used to obtain centroid time +correlation functions, which can be further used to obtain the true +quantum correlation function for the original system. The CMD method +also uses normal modes to evolve the system, except only the k > 0 +modes are thermostatted, not the centroid degrees of freedom. + +The keyword *fmass* sets a further scaling factor for the fictitious +masses of beads, which can be used for the Partial Adiabatic CMD +:ref:`(Hone) `, or to be set as P, which results in the fictitious +masses to be equal to the real particle masses. + +The keyword *sp* is a scaling factor on Planck's constant, which can +be useful for debugging or other purposes. The default value of 1.0 +is appropriate for most situations. + +The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme +as described in :ref:`(Calhoun) `. In LAMMPS this is done by using +:ref:`multi-replica feature ` in LAMMPS, where +each quasi-particle system is stored and simulated on a separate +partition of processors. The following diagram illustrates this +approach. The original system with 2 ring polymers is shown in red. +Since each ring has 4 quasi-beads (imaginary time slices), there are 4 +replicas of the system, each running on one of the 4 partitions of +processors. Each replica (shown in green) owns one quasi-bead in each +ring. + +.. image:: JPG/pimd.jpg + :align: center + +To run a PIMD simulation with M quasi-beads in each ring polymer using +N MPI tasks for each partition's domain-decomposition, you would use P += MxN processors (cores) and run the simulation as follows: + +.. parsed-literal:: + + mpirun -np P lmp_mpi -partition MxN -in script + +Note that in the LAMMPS input script for a multi-partition simulation, +it is often very useful to define a :doc:`uloop-style variable ` such as + +.. parsed-literal:: + + variable ibead uloop M pad + +where M is the number of quasi-beads (partitions) used in the +calculation. The uloop variable can then be used to manage I/O +related tasks for each of the partitions, e.g. + +.. parsed-literal:: + + dump dcd all dcd 10 system_${ibead}.dcd + restart 1000 system_${ibead}.restart1 system_${ibead}.restart2 + read_restart system_${ibead}.restart2 + +Restrictions +"""""""""""" + + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +A PIMD simulation can be initialized with a single data file read via +the :doc:`read_data ` command. However, this means all +quasi-beads in a ring polymer will have identical positions and +velocities, resulting in identical trajectories for all quasi-beads. +To avoid this, users can simply initialize velocities with different +random number seeds assigned to each partition, as defined by the +uloop variable, e.g. + +.. parsed-literal:: + + velocity all create 300.0 1234${ibead} rot yes dist gaussian + +Default +""""""" + +The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0, +and nhc = 2. + + +---------- + + +.. _Feynman: + + + +**(Feynman)** R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and +Path Integrals, McGraw-Hill, New York (1965). + +.. _Tuckerman: + + + +**(Tuckerman)** M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993). + +.. _Cao1: + + + +**(Cao1)** J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993). + +.. _Cao2: + + + +**(Cao2)** J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994). + +.. _Hone: + + + +**(Hone)** T. Hone, P. Rossky, G. Voth, J Chem Phys, 124, +154103 (2006). + +.. _Calhoun: + + + +**(Calhoun)** A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, +415 (1996). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_planeforce.txt b/doc/_sources/fix_planeforce.txt new file mode 100644 index 0000000000..71672b51bd --- /dev/null +++ b/doc/_sources/fix_planeforce.txt @@ -0,0 +1,60 @@ +.. index:: fix planeforce + +fix planeforce command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID planeforce x y z + +* ID, group-ID are documented in :doc:`fix ` command +* planeforce = style name of this fix command +* x y z = 3-vector that is normal to the plane + +Examples +"""""""" + +.. parsed-literal:: + + fix hold boundary planeforce 1.0 0.0 0.0 + +Description +""""""""""" + +Adjust the forces on each atom in the group so that only the +components of force in the plane specified by the normal vector +(x,y,z) remain. This is done by subtracting out the component of +force perpendicular to the plane. + +If the initial velocity of the atom is 0.0 (or in the plane), then it +should continue to move in the plane thereafter. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix lineforce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_poems.txt b/doc/_sources/fix_poems.txt new file mode 100644 index 0000000000..13e5635ecc --- /dev/null +++ b/doc/_sources/fix_poems.txt @@ -0,0 +1,149 @@ +fix poems +========= + +Syntax: + +.. parsed-literal:: + + fix ID group-ID poems keyword values + +* ID, group-ID are documented in :doc:`fix ` command +* poems = style name of this fix command +* keyword = *group* or *file* or *molecule* +.. parsed-literal:: + + *group* values = list of group IDs + *molecule* values = none + *file* values = filename + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 fluid poems group clump1 clump2 clump3 + fix 3 fluid poems file cluster.list + +Description +""""""""""" + +Treats one or more sets of atoms as coupled rigid bodies. This means +that each timestep the total force and torque on each rigid body is +computed and the coordinates and velocities of the atoms are updated +so that the collection of bodies move as a coupled set. This can be +useful for treating a large biomolecule as a collection of connected, +coarse-grained particles. + +The coupling, associated motion constraints, and time integration is +performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS) `_ which computes the +constrained rigid-body motion of articulated (jointed) multibody +systems :ref:`(Anderson) `. POEMS was written and is distributed +by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, +and other members of his group at Rensselaer Polytechnic Institute +(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For +copyright information on POEMS and other details, please refer to the +documents in the poems directory distributed with LAMMPS. + +.. _poems: http://www.rpi.edu/~anderk5/lab + + + +This fix updates the positions and velocities of the rigid atoms with +a constant-energy time integration, so you should not update the same +atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). + +Each body must have a non-degenerate inertia tensor, which means if +must contain at least 3 non-collinear atoms. Which atoms are in which +bodies can be defined via several options. + +For option *group*, each of the listed groups is treated as a rigid +body. Note that only atoms that are also in the fix group are +included in each rigid body. + +For option *molecule*, each set of atoms in the group with a different +molecule ID is treated as a rigid body. + +For option *file*, sets of atoms are read from the specified file and +each set is treated as a rigid body. Each line of the file specifies +a rigid body in the following format: + +ID type atom1-ID atom2-ID atom3-ID ... + +ID as an integer from 1 to M (the number of rigid bodies). Type is +any integer; it is not used by the fix poems command. The remaining +arguments are IDs of atoms in the rigid body, each typically from 1 to +N (the number of atoms in the system). Only atoms that are also in +the fix group are included in each rigid body. Blank lines and lines +that begin with '#' are skipped. + +A connection between a pair of rigid bodies is inferred if one atom is +common to both bodies. The POEMS solver treats that atom as a +spherical joint with 3 degrees of freedom. Currently, a collection of +bodies can only be connected by joints as a linear chain. The entire +collection of rigid bodies can represent one or more chains. Other +connection topologies (tree, ring) are not allowed, but will be added +later. Note that if no joints exist, it is more efficient to use the +:doc:`fix rigid ` command to simulate the system. + +When the poems fix is defined, it will print out statistics on the +total # of clusters, bodies, joints, atoms involved. A cluster in +this context means a set of rigid bodies connected by joints. + +For computational efficiency, you should turn off pairwise and bond +interactions within each rigid body, as they no longer contribute to +the motion. The "neigh_modify exclude" and "delete_bonds" commands +can be used to do this if each rigid body is a group. + +For computational efficiency, you should only define one fix poems +which includes all the desired rigid bodies. LAMMPS will allow +multiple poems fixes to be defined, but it is more expensive. + +The degrees-of-freedom removed by coupled rigid bodies are accounted +for in temperature and pressure computations. Similarly, the rigid +body contribution to the pressure virial is also accounted for. The +latter is only correct if forces within the bodies have been turned +off, and there is only a single fix poems defined. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the POEMS package. It is only enabled if LAMMPS +was built with that package, which also requires the POEMS library be +built and linked with LAMMPS. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix rigid `, :doc:`delete_bonds `, +:doc:`neigh_modify ` exclude + +**Default:** none + + +---------- + + +.. _Anderson: + + + +**(Anderson)** Anderson, Mukherjee, Critchley, Ziegler, and Lipton +"POEMS: Parallelizable Open-source Efficient Multibody Software ", +Engineering With Computers (2006). (`link to paper `_) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_pour.txt b/doc/_sources/fix_pour.txt new file mode 100644 index 0000000000..1251dfcbbb --- /dev/null +++ b/doc/_sources/fix_pour.txt @@ -0,0 +1,281 @@ +.. index:: fix pour + +fix pour command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID pour N type seed keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* pour = style name of this fix command +* N = # of particles to insert +* type = atom type to assign to inserted particles (offset for molecule insertion) +* seed = random # seed (positive integer) +* one or more keyword/value pairs may be appended to args +* keyword = *region* or *diam* or *vol* or *rate* or *dens* or *vel* or *mol* or *rigid* or *shake* or *ignore* +.. parsed-literal:: + + *region* value = region-ID + region-ID = ID of region to use as insertion volume + *diam* values = dstyle args + dstyle = *one* or *range* or *poly* + *one* args = D + D = single diameter for inserted particles (distance units) + *range* args = Dlo Dhi + Dlo,Dhi = range of diameters for inserted particles (distance units) + *poly* args = Npoly D1 P1 D2 P2 ... + Npoly = # of (D,P) pairs + D1,D2,... = diameter for subset of inserted particles (distance units) + P1,P2,... = percentage of inserted particles with this diameter (0-1) + *id* values = idflag + idflag = *max* or *next* = how to choose IDs for inserted particles and molecules + *vol* values = fraction Nattempt + fraction = desired volume fraction for filling insertion volume + Nattempt = max # of insertion attempts per particle + *rate* value = V + V = z velocity (3d) or y velocity (2d) at which + insertion volume moves (velocity units) + *dens* values = Rholo Rhohi + Rholo,Rhohi = range of densities for inserted particles (mass/volume units) + *vel* values (3d) = vxlo vxhi vylo vyhi vz + *vel* values (2d) = vxlo vxhi vy + vxlo,vxhi = range of x velocities for inserted particles (velocity units) + vylo,vyhi = range of y velocities for inserted particles (velocity units) + vz = z velocity (3d) assigned to inserted particles (velocity units) + vy = y velocity (2d) assigned to inserted particles (velocity units) + *mol* value = template-ID + template-ID = ID of molecule template specified in a separate :doc:`molecule ` command + *molfrac* values = f1 f2 ... fN + f1 to fN = relative probability of creating each of N molecules in template-ID + *rigid* value = fix-ID + fix-ID = ID of :doc:`fix rigid/small ` command + *shake* value = fix-ID + fix-ID = ID of :doc:`fix shake ` command + *ignore* value = none + skip any line or triangle particles when detecting possible + overlaps with inserted particles + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 all pour 1000 2 29494 region myblock + fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam range 0.9 1.1 + fix 2 all pour 10000 1 19985583 region disk diam poly 2 0.7 0.4 1.5 0.6 + fix ins all pour 500 1 4767548 vol 0.8 10 region slab mol object rigid myRigid + +Description +""""""""""" + +Insert finite-size particles or molecules into the simulation box +every few timesteps within a specified region until N particles or +molecules have been inserted. This is typically used to model the +pouring of granular particles into a container under the influence of +gravity. For the remainder of this doc page, a single inserted atom +or molecule is referred to as a "particle". + +If inserted particles are individual atoms, they are assigned the +specified atom type. If they are molecules, the type of each atom in +the inserted molecule is specified in the file read by the +:doc:`molecule ` command, and those values are added to the +specified atom type. E.g. if the file specifies atom types 1,2,3, and +those are the atom types you want for inserted molecules, then specify +*type* = 0. If you specify *type* = 2, the in the inserted molecule +will have atom types 3,4,5. + +All atoms in the inserted particle are assigned to two groups: the +default group "all" and the group specified in the fix pour command +(which can also be "all"). + +This command must use the *region* keyword to define an insertion +volume. The specified region must have been previously defined with a +:doc:`region ` command. It must be of type *block* or a z-axis +*cylinder* and must be defined with side = *in*. The cylinder style +of region can only be used with 3d simulations. + +Individual atoms are inserted, unless the *mol* keyword is used. It +specifies a *template-ID* previously defined using the +:doc:`molecule ` command, which reads a file that defines the +molecule. The coordinates, atom types, center-of-mass, moments of +inertia, etc, as well as any bond/angle/etc and special neighbor +information for the molecule can be specified in the molecule file. +See the :doc:`molecule ` command for details. The only +settings required to be in this file are the coordinates and types of +atoms in the molecule. + +If the molecule template contains more than one molecule, the relative +probability of depositing each molecule can be specified by the +*molfrac* keyword. N relative probablities, each from 0.0 to 1.0, are +specified, where N is the number of molecules in the template. Each +time a molecule is inserted, a random number is used to sample from +the list of relative probabilities. The N values must sum to 1.0. + +If you wish to insert molecules via the *mol* keyword, that will be +treated as rigid bodies, use the *rigid* keyword, specifying as its +value the ID of a separate :doc:`fix rigid/small ` +command which also appears in your input script. + +If you wish to insert molecules via the *mol* keyword, that will have +their bonds or angles constrained via SHAKE, use the *shake* keyword, +specifying as its value the ID of a separate :doc:`fix shake ` command which also appears in your input script. + +Each timestep particles are inserted, they are placed randomly inside +the insertion volume so as to mimic a stream of poured particles. If +they are molecules they are also oriented randomly. Each atom in the +particle is tested for overlaps with existing particles, including +effects due to periodic boundary conditions if applicable. If an +overlap is detected, another random insertion attempt is made; see the +*vol* keyword discussion below. The larger the volume of the +insertion region, the more particles that can be inserted at any one +timestep. Particles are inserted again after enough time has elapsed +that the previously inserted particles fall out of the insertion +volume under the influence of gravity. Insertions continue every so +many timesteps until the desired # of particles has been inserted. + +.. note:: + + If you are monitoring the temperature of a system where the + particle count is changing due to adding particles, you typically + should use the :doc:`compute_modify dynamic yes ` + command for the temperature compute you are using. + + +---------- + + +All other keywords are optional with defaults as shown below. + +The *diam* option is only used when inserting atoms and specifes the +diameters of inserted particles. There are 3 styles: *one*, *range*, +or *poly*. For *one*, all particles will have diameter *D*. For +*range*, the diameter of each particle will be chosen randomly and +uniformly between the specified *Dlo* and *Dhi* bounds. For *poly*, a +series of *Npoly* diameters is specified. For each diameter a +percentage value from 0.0 to 1.0 is also specified. The *Npoly* +percentages must sum to 1.0. For the example shown above with "diam 2 +0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7 +or 1.5. 40% of the particles will be small; 60% will be large. + +Note that for molecule insertion, the diameters of individual atoms in +the molecule can be specified in the file read by the +:doc:`molecule ` command. If not specified, the diameter of +each atom in the molecule has a default diameter of 1.0. + +The *id* option has two settings which are used to determine the atom +or molecule IDs to assign to inserted particles/molecules. In both +cases a check is done of the current system to find the maximum +current atom and molecule ID of any existing particle. Newly inserted +particles and molecules are assigned IDs that increment those max +values. For the *max* setting, which is the default, this check is +done at every insertion step, which allows for particles to leave the +system, and their IDs to potentially be re-used. For the *next* +setting this check is done only once when the fix is specified, which +can be more efficient if you are sure particles will not be added in +some other way. + +The *vol* option specifies what volume fraction of the insertion +volume will be filled with particles. For particles with a size +specified by the *diam range* keyword, they are assumed to all be of +maximum diamter *Dhi* for purposes of computing their contribution to +the volume fraction. + +The higher the volume fraction value, the more particles are inserted +each timestep. Since inserted particles cannot overlap, the maximum +volume fraction should be no higher than about 0.6. Each timestep +particles are inserted, LAMMPS will make up to a total of M tries to +insert the new particles without overlaps, where M = # of inserted +particles * Nattempt. If LAMMPS is unsuccessful at completing all +insertions, it prints a warning. + +The *dens* and *vel* options enable inserted particles to have a range +of densities or xy velocities. The specific values for a particular +inserted particle will be chosen randomly and uniformly between the +specified bounds. Internally, the density value for a particle is +converted to a mass, based on the radius (volume) of the particle. +The *vz* or *vy* value for option *vel* assigns a z-velocity (3d) or +y-velocity (2d) to each inserted particle. + +The *rate* option moves the insertion volume in the z direction (3d) +or y direction (2d). This enables pouring particles from a +successively higher height over time. + +The *ignore* option is useful when running a simulation that used line +segment (2d) or triangle (3d) particles, typically to define +boundaries for spherical granular particles to interact with. See the +:doc:`atom_style line or tri ` command for details. Lines +and triangles store their size, and if the size is large it may +overlap (in a spherical sense) with the insertion region, even if the +line/triangle is oriented such that there is no actual overlap. This +can prevent particles from being inserted. The *ignore* keyword +causes the overlap check to skip any line or triangle particles. +Obviously you should only use it if there is in fact no overlap of the +line or triangle particles with the insertion region. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. This means you must be careful when restarting a +pouring simulation, when the restart file was written in the middle of +the pouring operation. Specifically, you should use a new fix pour +command in the input script for the restarted simulation that +continues the operation. You will need to adjust the arguments of the +original fix pour command to do this. + +Also note that because the state of the random number generator is not +saved in restart files, you cannot do "exact" restarts with this fix, +where the simulation continues on the same as if no restart had taken +place. However, in a statistical sense, a restarted simulation should +produce the same behavior if you adjust the fix pour parameters +appropriately. + +None of the :doc:`fix_modify ` options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various :ref:`output commands `. No +parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the GRANULAR package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +For 3d simulations, a gravity fix in the -z direction must be defined +for use in conjunction with this fix. For 2d simulations, gravity +must be defined in the -y direction. + +The specified insertion region cannot be a "dynamic" region, as +defined by the :doc:`region ` command. + +Related commands +"""""""""""""""" + +:doc:`fix_deposit `, :doc:`fix_gravity `, +:doc:`region ` + +Default +""""""" + +Insertions are performed for individual particles, i.e. no *mol* +setting is defined. If the *mol* keyword is used, the default for +*molfrac* is an equal probabilities for all molecules in the template. +Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol = +0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0 (for 3d), vel = 0.0 0.0 0.0 +(for 2d), and id = max. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_press_berendsen.txt b/doc/_sources/fix_press_berendsen.txt new file mode 100644 index 0000000000..3eb456210f --- /dev/null +++ b/doc/_sources/fix_press_berendsen.txt @@ -0,0 +1,248 @@ +.. index:: fix press/berendsen + +fix press/berendsen command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID press/berendsen keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* press/berendsen = style name of this fix command +.. parsed-literal:: + + one or more keyword value pairs may be appended + keyword = *iso* or *aniso* or *x* or *y* or *z* or *couple* or *dilate* or *modulus* + *iso* or *aniso* values = Pstart Pstop Pdamp + Pstart,Pstop = scalar external pressure at start/end of run (pressure units) + Pdamp = pressure damping parameter (time units) + *x* or *y* or *z* values = Pstart Pstop Pdamp + Pstart,Pstop = external stress tensor component at start/end of run (pressure units) + Pdamp = stress damping parameter (time units) + *couple* = *none* or *xyz* or *xy* or *yz* or *xz* + *modulus* value = bulk modulus of system (pressure units) + *dilate* value = *all* or *partial* + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all press/berendsen iso 0.0 0.0 1000.0 + fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial + +Description +""""""""""" + +Reset the pressure of the system by using a Berendsen barostat +:ref:`(Berendsen) `, which rescales the system volume and +(optionally) the atoms coordinates within the simulation box every +timestep. + +Regardless of what atoms are in the fix group, a global pressure is +computed for all atoms. Similarly, when the size of the simulation +box is changed, all atoms are re-scaled to new positions, unless the +keyword *dilate* is specified with a value of *partial*, in which case +only the atoms in the fix group are re-scaled. The latter can be +useful for leaving the coordinates of atoms in a solid substrate +unchanged and controlling the pressure of a surrounding fluid. + +.. note:: + + Unlike the :doc:`fix npt ` or :doc:`fix nph ` + commands which perform Nose/Hoover barostatting AND time integration, + this fix does NOT perform time integration. It only modifies the box + size and atom coordinates to effect barostatting. Thus you must use a + separate time integration fix, like :doc:`fix nve ` or :doc:`fix nvt ` to actually update the positions and velocities of + atoms. This fix can be used in conjunction with thermostatting fixes + to control the temperature, such as :doc:`fix nvt ` or :doc:`fix langevin ` or :doc:`fix temp/berendsen `. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting and barostatting. + + +---------- + + +The barostat is specified using one or more of the *iso*, *aniso*, +*x*, *y*, *z*, and *couple* keywords. These keywords give you the +ability to specify the 3 diagonal components of an external stress +tensor, and to couple various of these components together so that the +dimensions they represent are varied together during a +constant-pressure simulation. Unlike the :doc:`fix npt ` and +:doc:`fix nph ` commands, this fix cannot be used with triclinic +(non-orthogonal) simulation boxes to control all 6 components of the +general pressure tensor. + +The target pressures for each of the 3 diagonal components of the +stress tensor can be specified independently via the *x*, *y*, *z*, +keywords, which correspond to the 3 simulation box dimensions. For +each component, the external pressure or tensor component at each +timestep is a ramped value during the run from *Pstart* to *Pstop*. +If a target pressure is specified for a component, then the +corresponding box dimension will change during a simulation. For +example, if the *y* keyword is used, the y-box length will change. A +box dimension will not change if that component is not specified, +although you have the option to change that dimension via the :doc:`fix deform ` command. + +For all barostat keywords, the *Pdamp* parameter determines the time +scale on which pressure is relaxed. For example, a value of 1000.0 +means to relax the pressure in a timespan of (roughly) 1000 time units +(tau or fmsec or psec - see the :doc:`units ` command). + +.. note:: + + The relaxation time is actually also a function of the bulk + modulus of the system (inverse of isothermal compressibility). The + bulk modulus has units of pressure and is the amount of pressure that + would need to be applied (isotropically) to reduce the volume of the + system by a factor of 2 (assuming the bulk modulus was a constant, + independent of density, which it's not). The bulk modulus can be set + via the keyword *modulus*. The *Pdamp* parameter is effectively + multiplied by the bulk modulus, so if the pressure is relaxing faster + than expected or desired, increasing the bulk modulus has the same + effect as increasing *Pdamp*. The converse is also true. LAMMPS does + not attempt to guess a correct value of the bulk modulus; it just uses + 10.0 as a default value which gives reasonable relaxation for a + Lennard-Jones liquid, but will be way off for other materials and way + too small for solids. Thus you should experiment to find appropriate + values of *Pdamp* and/or the *modulus* when using this fix. + + +---------- + + +The *couple* keyword allows two or three of the diagonal components of +the pressure tensor to be "coupled" together. The value specified +with the keyword determines which are coupled. For example, *xz* +means the *Pxx* and *Pzz* components of the stress tensor are coupled. +*Xyz* means all 3 diagonal components are coupled. Coupling means two +things: the instantaneous stress will be computed as an average of the +corresponding diagonal components, and the coupled box dimensions will +be changed together in lockstep, meaning coupled dimensions will be +dilated or contracted by the same percentage every timestep. The +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must +be identical. *Couple xyz* can be used for a 2d simulation; the *z* +dimension is simply ignored. + + +---------- + + +The *iso* and *aniso* keywords are simply shortcuts that are +equivalent to specifying several other keywords together. + +The keyword *iso* means couple all 3 diagonal components together when +pressure is computed (hydrostatic pressure), and dilate/contract the +dimensions together. Using "iso Pstart Pstop Pdamp" is the same as +specifying these 4 keywords: + +.. parsed-literal:: + + x Pstart Pstop Pdamp + y Pstart Pstop Pdamp + z Pstart Pstop Pdamp + couple xyz + +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the +stress tensor as the driving forces, and the specified scalar external +pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying +these 4 keywords: + +.. parsed-literal:: + + x Pstart Pstop Pdamp + y Pstart Pstop Pdamp + z Pstart Pstop Pdamp + couple none + + +---------- + + +This fix computes a temperature and pressure each timestep. To do +this, the fix creates its own computes of style "temp" and "pressure", +as if these commands had been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp + compute fix-ID_press group-ID pressure fix-ID_temp + +See the :doc:`compute temp ` and :doc:`compute pressure ` commands for details. Note that the +IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID ++ underscore + "press", and the group for the new computes is the same +as the fix group. + +Note that these are NOT the computes used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp* +and *thermo_press*. This means you can change the attributes of this +fix's temperature or pressure via the +:doc:`compute_modify ` command or print this temperature +or pressure during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* or +*thermo_press* will have no effect on this fix. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by this fix. You can use them to assign a +:doc:`compute ` you have defined to this fix which will be used +in its temperature and pressure calculations. If you do this, note +that the kinetic energy derived from the compute temperature should be +consistent with the virial term computed using all atoms for the +pressure. LAMMPS will warn you if you choose to compute temperature +on a subset of atoms. + +No global or per-atom quantities are stored by this fix for access by +various :ref:`output commands `. + +This fix can ramp its target pressure over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +Any dimension being adjusted by this fix must be periodic. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nph `, :doc:`fix npt `, :doc:`fix temp/berendsen `, +:doc:`fix_modify ` + +Default +""""""" + +The keyword defaults are dilate = all, modulus = 10.0 in units of +pressure for whatever :doc:`units ` are defined. + + +---------- + + +.. _Berendsen: + + + +**(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem +Phys, 81, 3684 (1984). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_print.txt b/doc/_sources/fix_print.txt new file mode 100644 index 0000000000..01a999d013 --- /dev/null +++ b/doc/_sources/fix_print.txt @@ -0,0 +1,105 @@ +.. index:: fix print + +fix print command +================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID print N string keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* print = style name of this fix command +* N = print every N steps +* string = text string to print with optional variable names +* zero or more keyword/value pairs may be appended +* keyword = *file* or *append* or *screen* or *title* +.. parsed-literal:: + + *file* value = filename + *append* value = filename + *screen* value = *yes* or *no* + *title* value = string + string = text to print as 1st line of output file + + + +Examples +"""""""" + +.. parsed-literal:: + + fix extra all print 100 "Coords of marker atom = $x $y $z" + fix extra all print 100 "Coords of marker atom = $x $y $z" file coord.txt + +Description +""""""""""" + +Print a text string every N steps during a simulation run. This can +be used for diagnostic purposes or as a debugging tool to monitor some +quantity during a run. The text string must be a single argument, so +it should be enclosed in double quotes if it is more than one word. +If it contains variables it must be enclosed in double quotes to +insure they are not evaluated when the input script line is read, but +will instead be evaluated each time the string is printed. + +The specified group-ID is ignored by this fix. + +See the :doc:`variable ` command for a description of *equal* +style variables which are the most useful ones to use with the fix +print command, since they are evaluated afresh each timestep that the +fix print line is output. Equal-style variables calculate formulas +involving mathematical operations, atom properties, group properties, +thermodynamic properties, global values calculated by a +:doc:`compute ` or :doc:`fix `, or references to other +:doc:`variables `. + +If the *file* or *append* keyword is used, a filename is specified to +which the output generated by this fix will be written. If *file* is +used, then the filename is overwritten if it already exists. If +*append* is used, then the filename is appended to if it already +exists, or created if it does not exist. + +If the *screen* keyword is used, output by this fix to the screen and +logfile can be turned on or off as desired. + +The *title* keyword allow specification of the string that will be +printed as the first line of the output file, assuming the *file* +keyword was used. By default, the title line is as follows: + +.. parsed-literal:: + + # Fix print output for fix ID + +where ID is replaced with the fix-ID. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`variable `, :doc:`print ` + +Default +""""""" + +The option defaults are no file output, screen = yes, and title string +as described above. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_property_atom.txt b/doc/_sources/fix_property_atom.txt new file mode 100644 index 0000000000..c491a26b02 --- /dev/null +++ b/doc/_sources/fix_property_atom.txt @@ -0,0 +1,243 @@ +.. index:: fix property/atom + +fix property/atom command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID property/atom vec1 vec2 ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* property/atom = style name of this fix command +* vec1,vec2,... = *mol* or *q* or *i_name* or *d_name* +.. parsed-literal:: + + *mol* = molecule IDs + *q* = charge + *i_name* = new integer vector referenced by name + *d_name* = new floating-point vector referenced by name + +* zero of more keyword/value pairs may be appended +* keyword = *ghost* +.. parsed-literal:: + + *ghost* value = *no* or *yes* for whether ghost atom info in communicated + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all property/atom mol + fix 1 all property/atom i_myflag1 i_myflag2 + fix 1 all property/atom d_sx d_sy d_sz + +Description +""""""""""" + +Create one or more additional per-atom vectors to store information +about atoms and to use during a simulation. The specified *group-ID* +is ignored by this fix. + +The atom style used for a simulation defines a set of per-atom +properties, as explained on the :doc:`atom_style ` and +:doc:`read_data ` doc pages. The latter command allows these +properties to be defined for each atom in the system when a data file +is read. This fix will augment the set of properties with new custom +ones. + +This can be useful in at least two scenarios. + +If the atom style does not define molecule IDs or per-atom charge, +they can be added using the *mol* or *q* keywords. This can be +useful, e.g, to define "molecules" to use as rigid bodies with the +:doc:`fix rigid ` command, or just to carry around an extra +flag with the atoms (stored as a molecule ID). An alternative is to +use an atom style that does define molecule IDs or charge or to use a +hybrid atom style that combines two styles to allow for molecule IDs +or charge, but that has 2 practical drawbacks. First it typically +necessitates changing the format of the data file. And it may define +additional properties that aren't needed such as bond lists, which has +some overhead when there are no bonds. + +In the future, we may add additional per-atom properties similar to +*mol* or *q*, which "turn-on" specific properties defined by some atom +styles, so they can be used by atom styles that don't define them. + +More generally, the *i_name* and *d_name* vectors allow one or more +new custom per-atom properties to be defined. Each name must be +unique and can use alphanumeric or underscore characters. These +vectors can store whatever values you decide are useful in your +simulation. As explained below there are several ways to initialize +and access and output these values, both via input script commands and +in new code that you add to LAMMPS. + +This is effectively a simple way to add per-atom properties to a model +without needing to write code for a new :doc:`atom style ` +that defines the properties. Note however that implementing a new +atom style allows new atom properties to be more tightly and +seamlessly integrated with the rest of the code. + +The new atom properties encode values that migrate with atoms to new +processors and are written to restart files. If you want the new +properties to also be defined for ghost atoms, then use the *ghost* +keyword with a value of *yes*. This will invoke extra communication +when ghost atoms are created (at every re-neighboring) to insure the +new properties are also defined for the ghost atoms. + +.. note:: + + If you use this command with the *mol* or *charge* vectors than + you most likely want to set *ghost* yes, since these properties are + stored with ghost atoms if you use an :doc:`atom_style ` + that defines them, and many LAMMPS operations that use molecule IDs or + charge, such as neighbor lists and pair styles, will expect ghost + atoms to have these valuse. LAMMPS will issue a warning it you define + those vectors but do not set *ghost* yes. + +.. note:: + + The properties for ghost atoms are not updated every timestep, + but only once every few steps when neighbor lists are re-built. Thus + the *ghost* keyword is suitable for static properties, like molecule + IDs, but not for dynamic properties that change every step. For the + latter, the code you add to LAMMPS to change the properties will also + need to communicate their new values to/from ghost atoms, an operation + that can be invoked from within a :doc:`pair style ` or + :doc:`fix ` or :doc:`compute ` that you write. + + +---------- + + +This fix is one of a small number that can be defined in an input +script before the simulation box is created or atoms are defined. +This is so it can be used with the :doc:`read_data ` command +as described below. + +Per-atom properties that are defined by the :doc:`atom style ` are initialized when atoms are created, e.g. by +the :doc:`read_data ` or :doc:`create_atoms ` +commands. The per-atom properaties defined by this fix are not. So +you need to initialize them explicitly. This can be done by the +:doc:`read_data ` command, using its *fix* keyword and +passing it the fix-ID of this fix. + +Thus these commands: + +.. parsed-literal:: + + fix prop all property/atom mol d_flag + read_data data.txt fix prop NULL Molecules + +would allow a data file to have a section like this: + +.. parsed-literal:: + + Molecules + +.. parsed-literal:: + + 1 4 1.5 + 2 4 3.0 + 3 10 1.0 + 4 10 1.0 + 5 10 1.0 + ... + N 763 4.5 + +where N is the number of atoms, and the first field on each line is +the atom-ID, followed by a molecule-ID and a floating point value that +will be stored in a new property called "flag". Note that the list of +per-atom properties can be in any order. + +Another way of initializing the new properties is via the +:doc:`set ` command. For example, if you wanted molecules +defined for every set of 10 atoms, based on their atom-IDs, +these commands could be used: + +.. parsed-literal:: + + fix prop all property/atom mol + variable cluster atom ((id-1)/10)+1 + set id * mol v_cluster + +The :doc:`atom-style variable ` will create values for atoms +with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the +:doc:`set ` commands assigns them to the molecule ID for each atom, +they will be truncated to an integer value, so atoms 31-40 will all be +assigned a molecule ID of 4. + +Note that :doc:`atomfile-style variables ` can also be used in +place of atom-style variables, which means in this case that the +molecule IDs could be read-in from a separate file and assinged by the +:doc:`set ` command. This allows you to initialize new per-atom +properties in a completely general fashion. + + +---------- + + +For new atom properties specified as *i_name* or *d_name*, the +:doc:`compute property/atom ` command can access +their values. This means that the values can be output via the :doc:`dump custom ` command, accessed by fixes like :doc:`fix ave/atom `, accessed by other computes like :doc:`compute reduce `, or used in `atom-style variables `_. + +For example, these commands will output two new properties to a custom +dump file: + +.. parsed-literal:: + + fix prop all property/atom i_flag1 d_flag2 + compute 1 all property/atom i_flag1 d_flag2 + dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2] + + +---------- + + +If you wish to add new :doc:`pair styles `, +:doc:`fixes `, or :doc:`computes ` that use the per-atom +properties defined by this fix, see :ref:`Section modify ` of the manual which has some details +on how the properties can be accessed from added classes. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a +simulation is restarted. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`read_data `, :doc:`set `, :doc:`compute property/atom ` + +Default +""""""" + +The default keyword values are ghost = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_qbmsst.txt b/doc/_sources/fix_qbmsst.txt new file mode 100644 index 0000000000..e63c6218fa --- /dev/null +++ b/doc/_sources/fix_qbmsst.txt @@ -0,0 +1,253 @@ +.. index:: fix qbmsst + +fix qbmsst command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID qbmsst dir shockvel keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* qbmsst = style name of this fix +* dir = *x* or *y* or *z* +* shockvel = shock velocity (strictly positive, velocity units) +* zero or more keyword/value pairs may be appended +* keyword = *q* or *mu* or *p0* or *v0* or *e0* or *tscale* or *damp* or *seed*or *f_max* or *N_f* or *eta* or *beta* or *T_init* +.. parsed-literal:: + + *q* value = cell mass-like parameter (mass^2/distance^4 units) + *mu* value = artificial viscosity (mass/distance/time units) + *p0* value = initial pressure in the shock equations (pressure units) + *v0* value = initial simulation cell volume in the shock equations (distance^3 units) + *e0* value = initial total energy (energy units) + *tscale* value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) + *damp* value = damping parameter (time units) inverse of friction γ + *seed* value = random number seed (positive integer) + *f_max* value = upper cutoff frequency of the vibration spectrum (1/time units) + *N_f* value = number of frequency bins (positive integer) + *eta* value = coupling constant between the shock system and the quantum thermal bath (positive unitless) + *beta* value = the quantum temperature is updated every beta time steps (positive integer) + *T_init* value = quantum temperature for the initial state (temperature units) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units) + fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) + +Two example input scripts are given, including shocked alpha quartz +and shocked liquid methane. The input script first equilibrate an +initial state with the quantum thermal bath at the target temperature +and then apply the qbmsst to simulate shock compression with quantum +nuclear correction. The following two figures plot related quantities +for shocked alpha quartz. + +.. image:: JPG/qbmsst_init.jpg + :align: center + +Figure 1. Classical temperature Tcl = ∑ +mivi2/3NkB vs. time +for coupling the alpha quartz initial state with the quantum thermal +bath at target quantum temperature Tqm = 300 K. The +NpH ensemble is used for time integration while QTB provides the +colored random force. Tcl converges at the timescale +of *damp* which is set to be 1 ps. + +.. image:: JPG/qbmsst_shock.jpg + :align: center + +Figure 2. Quantum temperature and pressure vs. time for simulating +shocked alpha quartz with the QBMSST. The shock propagates along the z +direction. Restart of the QBMSST command is demonstrated in the +example input script. Thermodynamic quantities stay continuous before +and after the restart. + +Description +""""""""""" + +This command performs the Quantum-Bath coupled Multi-Scale Shock +Technique (QBMSST) integration. See :ref:`(Qi) ` for a detailed +description of this method. The QBMSST provides description of the +thermodynamics and kinetics of shock processes while incorporating +quantum nuclear effects. The *shockvel* setting determines the steady +shock velocity that will be simulated along direction *dir*. + +Quantum nuclear effects :doc:`(fix qtb) ` can be crucial +especially when the temperature of the initial state is below the +classical limit or there is a great change in the zero point energies +between the initial and final states. Theoretical post processing +quantum corrections of shock compressed water and methane have been +reported as much as 30% of the temperatures :ref:`(Goldman) `. A +self-consistent method that couples the shock to a quantum thermal +bath described by a colored noise Langevin thermostat has been +developed by Qi et al :ref:`(Qi) ` and applied to shocked methane. The +onset of chemistry is reported to be at a pressure on the shock +Hugoniot that is 40% lower than observed with classical molecular +dynamics. + +It is highly recommended that the system be already in an equilibrium +state with a quantum thermal bath at temperature of *T_init*. The fix +command :doc:`fix qtb ` at constant temperature *T_init* could +be used before applying this command to introduce self-consistent +quantum nuclear effects into the initial state. + +The parameters *q*, *mu*, *e0*, *p0*, *v0* and *tscale* are described +in the command :doc:`fix msst `. The values of *e0*, *p0*, or +*v0* will be calculated on the first step if not specified. The +parameter of *damp*, *f_max*, and *N_f* are described in the command +:doc:`fix qtb `. + +The fix qbmsst command couples the shock system to a quantum thermal +bath with a rate that is proportional to the change of the total +energy of the shock system, etot - etot0. +Here etot consists of both the system energy and a thermal +term, see :ref:`(Qi) `, and etot0 = *e0* is the +initial total energy. + +The *eta* (η) parameter is a unitless coupling constant +between the shock system and the quantum thermal bath. A small *eta* +value cannot adjust the quantum temperature fast enough during the +temperature ramping period of shock compression while large *eta* +leads to big temperature oscillation. A value of *eta* between 0.3 and +1 is usually appropriate for simulating most systems under shock +compression. We observe that different values of *eta* lead to almost +the same final thermodynamic state behind the shock, as expected. + +The quantum temperature is updated every *beta* (β) steps +with an integration time interval *beta* times longer than the +simulation time step. In that case, etot is taken as its +average over the past *beta* steps. The temperature of the quantum +thermal bath Tqm changes dynamically according to +the following equation where Δt is the MD time step and +γ is the friction constant which is equal to the inverse +of the *damp* parameter. + +.. raw:: html + +
      dTqm/dt = + γη∑βl = + 1[etot(t-lΔt)-etot0]/3βNkB +
      + +The parameter *T_init* is the initial temperature of the quantum +thermal bath and the system before shock loading. + +For all pressure styles, the simulation box stays orthorhombic in +shape. Parrinello-Rahman boundary conditions (tilted box) are +supported by LAMMPS, but are not implemented for QBMSST. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Because the state of the random number generator is not written to +:doc:`binary restart files `, this fix cannot be restarted +"exactly" in an uninterrupted fashion. However, in a statistical +sense, a restarted simulation should produce similar behaviors of the +system as if it is not interrupted. To achieve such a restart, one +should write explicitly the same value for *q*, *mu*, *damp*, *f_max*, +*N_f*, *eta*, and *beta* and set *tscale* = 0 if the system is +compressed during the first run. + +The progress of the QBMSST can be monitored by printing the global +scalar and global vector quantities computed by the fix. The global +vector contains five values in this order: + +[*dhugoniot*, *drayleigh*, *lagrangian_speed*, *lagrangian_position*, +*quantum_temperature*] + +1. *dhugoniot* is the departure from the Hugoniot (temperature units). +2. *drayleigh* is the departure from the Rayleigh line (pressure units). +3. *lagrangian_speed* is the laboratory-frame Lagrangian speed (particle velocity) of the computational cell (velocity units). +4. *lagrangian_position* is the computational cell position in the reference frame moving at the shock speed. This is the distance of the computational cell behind the shock front. +5. *quantum_temperature* is the temperature of the quantum thermal bath Tqm. + +To print these quantities to the log file with descriptive column +headers, the following LAMMPS commands are suggested. Here the +:doc:`fix_modify ` energy command is also enabled to allow +the thermo keyword *etotal* to print the quantity etot. See +also the :doc:`thermo_style ` command. + +.. parsed-literal:: + + fix fix_id all msst z + fix_modify fix_id energy yes + variable dhug equal f_fix_id[1] + variable dray equal f_fix_id[2] + variable lgr_vel equal f_fix_id[3] + variable lgr_pos equal f_fix_id[4] + variable T_qm equal f_fix_id[5] + thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id + +The global scalar under the entry f_fix_id is the quantity of thermo +energy as an extra part of etot. This global scalar and the +vector of 5 quantities can be accessed by various :ref:`output commands `. It is worth noting that the +temp keyword under the :doc:`thermo_style ` command print +the instantaneous classical temperature Tcl as +described in the command :doc:`fix qtb `. + + +---------- + + +Restrictions +"""""""""""" + + +This fix style is part of the USER-QTB package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +All cell dimensions must be periodic. This fix can not be used with a +triclinic cell. The QBMSST fix has been tested only for the group-ID +all. + + +---------- + + +Related commands +"""""""""""""""" + +:doc:`fix qtb `, :doc:`fix msst ` + + +---------- + + +Default +""""""" + +The keyword defaults are q = 10, mu = 0, tscale = 0.01, damp = 1, seed += 880302, f_max = 200.0, N_f = 100, eta = 1.0, beta = 100, and +T_init=300.0. e0, p0, and v0 are calculated on the first step. + + +---------- + + +.. _Goldman: + + + +**(Goldman)** Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009) + +.. _Qi: + + + +**(Qi)** Qi and Reed, J. Phys. Chem. A 116, 10451 (2012). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_qeq.txt b/doc/_sources/fix_qeq.txt new file mode 100644 index 0000000000..b28a407c5f --- /dev/null +++ b/doc/_sources/fix_qeq.txt @@ -0,0 +1,259 @@ +.. index:: fix qeq/point + +fix qeq/point command +===================== + +fix qeq/shielded command +======================== + +fix qeq/slater command +====================== + +fix qeq/dynamic command +======================= + +fix qeq/fire command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/dynamic* or *qeq/fire* +* Nevery = perform charge equilibration every this many steps +* cutoff = global cutoff for charge-charge interactions (distance unit) +* tolerance = precision to which charges will be equilibrated +* maxiter = maximum iterations to perform charge equilibration +* qfile = a filename with QEq parameters +* zero or more keyword/value pairs may be appended +* keyword = *alpha* or *qdamp* or *qstep* +.. parsed-literal:: + + *alpha* value = Slater type orbital exponent (qeq/slater only) + *qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only) + *qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1 + fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2 + fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2 + fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq + fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1 + +Description +""""""""""" + +Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) ` (also known +as the matrix inversion method) and in :ref:`(Rick and Stuart) ` (also +known as the extended Lagrangian method) based on the +electronegativity equilization principle. + +These fixes can be used with any :doc:`pair style ` in +LAMMPS, so long as per-atom charges are defined. The most typical +use-case is in conjunction with a :doc:`pair style ` that +performs charge equilibration periodically (e.g. every timestep), such +as the ReaxFF or Streitz-Mintmire potential. +But these fixes can also be used with +potentials that normally assume per-atom charges are fixed, e.g. a +:doc:`Buckingham ` or :doc:`LJ/Coulombic ` potential. + +Because the charge equilibration calculation is effectively +independent of the pair style, these fixes can also be used to perform +a one-time assignment of charges to atoms. For example, you could +define the QEq fix, perform a zero-timestep run via the :doc:`run ` +command without any pair style defined which would set per-atom +charges (based on the current atom configuration), then remove the fix +via the :doc:`unfix ` command before performing further dynamics. + +.. note:: + + Computing and using charge values different from published + values defined for a fixed-charge potential like Buckingham or CHARMM + or AMBER, can have a strong effect on energies and forces, and + produces a different model than the published versions. + +.. note:: + + The :doc:`fix qeq/comb ` command must still be used + to perform charge equliibration with the :doc:`COMB potential `. The :doc:`fix qeq/reax ` + command can be used to perform charge equilibration with the :doc:`ReaxFF force field `, although fix qeq/shielded yields the + same results as fix qeq/reax if *Nevery*, *cutoff*, and *tolerance* + are the same. Eventually the fix qeq/reax command will be deprecated. + +The QEq method minimizes the electrostatic energy of the system (or +equalizes the derivative of energy with respect to charge of all the +atoms) by adjusting the partial charge on individual atoms based on +interactions with their neighbors within *cutoff*. It reqires a few +parameters, in *metal* units, for each atom type which provided in a +file specified by *qfile*. The file has the following format + +.. parsed-literal:: + + 1 chi eta gamma zeta qcore + 2 chi eta gamma zeta qcore + ... + Ntype chi eta gamma zeta qcore + +There is one line per atom type with the following parameters. +Only a subset of the parameters is used by each QEq style as descibed +below, thus the others can be set to 0.0 if desired. + +* *chi* = electronegativity in energy units +* *eta* = self-Coulomb potential in energy units +* *gamma* = shielded Coulomb constant defined by :ref:`ReaxFF force field ` in distance units +* *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire ` potential in reverse distance units +* *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential ` potential in charge units + +The *qeq/point* style describes partial charges on atoms as point +charges. Interaction between a pair of charged particles is 1/r, +which is the simplest description of the interaction between charges. +Only the *chi* and *eta* parameters from the *qfile* file are used. +Note that Coulomb catastrophe can occur if repulsion between the pair +of charged particles is too weak. This style solves partial charges +on atoms via the matrix inversion method. A tolerance of 1.0e-6 is +usually a good number. + +The *qeq/shielded* style describes partial charges on atoms also as +point charges, but uses a shielded Coulomb potential to describe the +interaction between a pair of charged particles. Interaction through +the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field ` paper. The shielding accounts for charge overlap +between charged particles at small separation. This style is the same +as :doc:`fix qeq/reax `, and can be used with :doc:`pair_style reax/c `. Only the *chi*, *eta*, and *gamma* +parameters from the *qfile* file are used. This style solves partial +charges on atoms via the matrix inversion method. A tolerance of +1.0e-6 is usually a good number. + +The *qeq/slater* style describes partial charges on atoms as spherical +charge densities centered around atoms via the Slater 1*s* orbital, so +that the interaction between a pair of charged particles is the +product of two Slater 1*s* orbitals. The expression for the Slater +1*s* orbital is given under equation (6) of the +:ref:`Streitz-Mintmire ` paper. Only the *chi*, *eta*, *zeta*, and +*qcore* parameters from the *qfile* file are used. This style solves +partial charges on atoms via the matrix inversion method. A tolerance +of 1.0e-6 is usually a good number. Keyword *alpha* can be used to +change the Slater type orbital exponent. + +The *qeq/dynamic* style describes partial charges on atoms as point +charges that interact through 1/r, but the extended Lagrangian method +is used to solve partial charges on atoms. Only the *chi* and *eta* +parameters from the *qfile* file are used. Note that Coulomb +catastrophe can occur if repulsion between the pair of charged +particles is too weak. A tolerance of 1.0e-3 is usually a good +number. Keyword *qdamp* can be used to change the damping factor, while +keyword *qstep* can be used to change the time step size. + +The :ref:`*qeq/fire* ` style describes the same charge model and charge +solver as the *qeq/dynamic* style, but employs a FIRE minimization +algorithm to solve for equilibrium charges. +Keyword *qdamp* can be used to change the damping factor, while +keyword *qstep* can be used to change the time step size. + +Note that *qeq/point*, *qeq/shielded*, and *qeq/slater* describe +different charge models, whereas the matrix inversion method and the +extended Lagrangian method (*qeq/dynamic* and *qeq/fire*) are +different solvers. + +Note that *qeq/point*, *qeq/dynamic* and *qeq/fire* styles all describe +charges as point charges that interact through 1/r relationship, but +solve partial charges on atoms using different solvers. These three +styles should yield comparable results if +the QEq parameters and *Nevery*, *cutoff*, and *tolerance* are the +same. Style *qeq/point* is typically faster, *qeq/dynamic* scales +better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*. + +.. note:: + + To avoid the evaluation of the derivative of charge with respect + to position, which is typically ill-defined, the system should have a + zero net charge. + +.. note:: + + Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is + non-trivial. Charges on atoms are not guaranteed to equilibrate with + arbitrary choices of these parameters. We do not develop these QEq + paramters. See the examples/qeq directory for some examples. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about these fixes is written to :doc:`binary restart files `. No global scalar or vector or per-atom +quantities are stored by these fixes for access by various :ref:`output commands `. No parameter of these fixes +can be used with the *start/stop* keywords of the :doc:`run ` +command. + +Thexe fixes are invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +These fixes are part of the QEQ package. They are only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix qeq/reax `, :doc:`fix qeq/comb ` + +**Default:** none + + +---------- + + +.. _Rappe: + + + +**(Rappe and Goddard)** A. K. Rappe and W. A. Goddard III, J Physical +Chemistry, 95, 3358-3363 (1991). + +.. _Nakano: + + + +**(Nakano)** A. Nakano, Computer Physics Communications, 104, 59-69 (1997). + +.. _Rick: + + + +**(Rick and Stuart)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics +101, 16141 (1994). + +.. _Streitz: + + + +**(Streitz-Mintmire)** F. H. Streitz, J. W. Mintmire, Physical Review B, 50, +16, 11996 (1994) + +.. _vanDuin: + + + +**(ReaxFF)** A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J +Physical Chemistry, 105, 9396-9049 (2001) + +.. _Shan: + + + +**(QEq/Fire)** T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_qeq_comb.txt b/doc/_sources/fix_qeq_comb.txt new file mode 100644 index 0000000000..319e40b0e5 --- /dev/null +++ b/doc/_sources/fix_qeq_comb.txt @@ -0,0 +1,160 @@ +.. index:: fix qeq/comb + +fix qeq/comb command +==================== + +fix qeq/comb/omp command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID qeq/comb Nevery precision keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* qeq/comb = style name of this fix command +* Nevery = perform charge equilibration every this many steps +* precision = convergence criterion for charge equilibration +* zero or more keyword/value pairs may be appended +* keyword = *file* +.. parsed-literal:: + + *file* value = filename + filename = name of file to write QEQ equilibration info to + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 surface qeq/comb 10 0.0001 + +Description +""""""""""" + +Perform charge equilibration (QeQ) in conjunction with the COMB +(Charge-Optimized Many-Body) potential as described in +:ref:`(COMB_1) ` and :ref:`(COMB_2) `. It performs the charge +equilibration portion of the calculation using the so-called QEq +method, whereby the charge on each atom is adjusted to minimize the +energy of the system. This fix can only be used with the COMB +potential; see the :doc:`fix qeq/reax ` command for a QeQ +calculation that can be used with any potential. + +Only charges on the atoms in the specified group are equilibrated. +The fix relies on the pair style (COMB in this case) to calculate the +per-atom electronegativity (effective force on the charges). An +electronegativity equalization calculation (or QEq) is performed in an +interative fashion, which in parallel requires communication at each +iteration for processors to exchange charge information about nearby +atoms with each other. See :ref:`Rappe_and_Goddard ` and +:ref:`Rick_and_Stuart ` for details. + +During a run, charge equilibration is peformed every *Nevery* time +steps. Charge equilibration is also always enforced on the first step +of each run. The *precision* argument controls the tolerance for the +difference in electronegativity for all atoms during charge +equilibration. *Precision* is a trade-off between the cost of +performing charge equilibration (more iterations) and accuracy. + +If the *file* keyword is used, then information about each +equilibration calculation is written to the specifed file. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix produces a per-atom vector which can be accessed by various +:ref:`output commands `. The vector stores the +gradient of the charge on each atom. The per-atom values be accessed +on any timestep. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +This fix can be invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix command currently only supports :doc:`pair style *comb* `. + +Related commands +"""""""""""""""" + +:doc:`pair_style comb ` + +Default +""""""" + +No file output is performed. + + +---------- + + +.. _COMB_1: + + + +**(COMB_1)** J. Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007), + +.. _COMB_2: + + + +**(COMB_2)** T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, S. R. +Phillpot, Phys Rev B, 81, 125328 (2010). + +.. _Rappe_and_Goddard: + + + +**(Rappe_and_Goddard)** A. K. Rappe, W. A. Goddard, J Phys Chem 95, 3358 +(1991). + +.. _Rick_and_Stuart: + + + +**(Rick_and_Stuart)** S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys +101, 16141 (1994). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_qeq_reax.txt b/doc/_sources/fix_qeq_reax.txt new file mode 100644 index 0000000000..e150aff964 --- /dev/null +++ b/doc/_sources/fix_qeq_reax.txt @@ -0,0 +1,117 @@ +.. index:: fix qeq/reax + +fix qeq/reax command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params + +* ID, group-ID are documented in :doc:`fix ` command +* qeq/reax = style name of this fix command +* Nevery = perform QEq every this many steps +* cutlo,cuthi = lo and hi cutoff for Taper radius +* tolerance = precision to which charges will be equilibrated +* params = reax/c or a filename + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c + fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq + +Description +""""""""""" + +Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) `. It is +typically used in conjunction with the ReaxFF force field model as +implemented in the :doc:`pair_style reax/c ` command, but +it can be used with any potential in LAMMPS, so long as it defines and +uses charges on each atom. The :doc:`fix qeq/comb ` +command should be used to perform charge equliibration with the :doc:`COMB potential `. For more technical details about the +charge equilibration performed by fix qeq/reax, see the +:ref:`(Aktulga) ` paper. + +The QEq method minimizes the electrostatic energy of the system by +adjusting the partial charge on individual atoms based on interactions +with their neighbors. It reqires some parameters for each atom type. +If the *params* setting above is the word "reax/c", then these are +extracted from the :doc:`pair_style reax/c ` command and +the ReaxFF force field file it reads in. If a file name is specified +for *params*, then the parameters are taken from the specified file +and the file must contain one line for each atom type. The latter +form must be used when performing QeQ with a non-ReaxFF potential. +Each line should be formatted as follows: + +.. parsed-literal:: + + itype chi eta gamma + +where *itype* is the atom type from 1 to Ntypes, *chi* denotes the +electronegativity in eV, *eta* denotes the self-Coulomb +potential in eV, and *gamma* denotes the valence orbital +exponent. Note that these 3 quantities are also in the ReaxFF +potential file, except that eta is defined here as twice the eta value +in the ReaxFF file. Note that unlike the rest of LAMMPS, the units +of this fix are hard-coded to be A, eV, and electronic charge. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. No global scalar or vector or per-atom +quantities are stored by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. + +This fix is invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-REAXC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix does not correctly handle interactions +involving multiple periodic images of the same atom. Hence, it should not +be used for periodic cell dimensions less than 10 angstroms. + +Related commands +"""""""""""""""" + +:doc:`pair_style reax/c ` + +**Default:** none + + +---------- + + +.. _Rappe: + + + +**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95, +3358-3363 (1991). + +.. _Nakano: + + + +**(Nakano)** Nakano, Computer Physics Communications, 104, 59-69 (1997). + +.. _Aktulga: + + + +(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, +245-259 (2012). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_qmmm.txt b/doc/_sources/fix_qmmm.txt new file mode 100644 index 0000000000..dbee374df0 --- /dev/null +++ b/doc/_sources/fix_qmmm.txt @@ -0,0 +1,73 @@ +.. index:: fix qmmm + +fix qmmm command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID qmmm + +* ID, group-ID are documented in :doc:`fix ` command +* qmmm = style name of this fix command + +Examples +"""""""" + +fix 1 qmol qmmm + +Description +""""""""""" + +This fix provides functionality to enable a quantum +mechanics/molecular mechanice (QM/MM) coupling of LAMMPS to a quantum +mechanical code. The current implementation only supports an ONIOM +style mechanical coupling to the `Quantum ESPRESSO `_ plane +wave DFT package. Electrostatic coupling is in preparation and the +interface has been written in a manner that coupling to other QM codes +should be possible without changes to LAMMPS itself. + +.. _espresso: http://www.quantum-espresso.org + + + +The interface code for this is in the lib/qmmm directory of the LAMMPS +distribution and is being made available at this early stage of +development in order to encourage contributions for interfaces to +other QM codes. This will allow the LAMMPS side of the implementation +to be adapted if necessary before being finalized. + +Details about how to use this fix are currently documented in the +description of the QM/MM interface code itself in lib/qmmm/README. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-QMMM package. It is only enabled if +LAMMPS was built with that package. It also requires building a +library provided with LAMMPS. See the :ref:`Making LAMMPS ` section for more info. + +The fix is only functional when LAMMPS is built as a library and +linked with a compatible QM program and a QM/MM frontend into a QM/MM +executable. See the lib/qmmm/README file for details. + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_qtb.txt b/doc/_sources/fix_qtb.txt new file mode 100644 index 0000000000..42c5cea1fc --- /dev/null +++ b/doc/_sources/fix_qtb.txt @@ -0,0 +1,215 @@ +.. index:: fix qtb + +fix qtb command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID qtb keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* qtb = style name of this fix +* zero or more keyword/value pairs may be appended +* keyword = *temp* or *damp* or *seed* or *f_max* or *N_f* +.. parsed-literal:: + + *temp* value = target quantum temperature (temperature units) + *damp* value = damping parameter (time units) inverse of friction &gamma; + *seed* value = random number seed (positive integer) + *f_max* value = upper cutoff frequency of the vibration spectrum (1/time units) + *N_f* value = number of frequency bins (positive integer) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve + fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units) + fix 2 all nph iso 1.01325 1.01325 1 + fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units) + +Description +""""""""""" + +This command performs the quantum thermal bath scheme proposed by +:ref:`(Dammak) ` to include self-consistent quantum nuclear effects, +when used in conjunction with the :doc:`fix nve ` or :doc:`fix nph ` commands. + +Classical molecular dynamics simulation does not include any quantum +nuclear effect. Quantum treatment of the vibrational modes will +introduce zero point energy into the system, alter the energy power +spectrum and bias the heat capacity from the classical limit. Missing +all the quantum nuclear effects, classical MD cannot model systems at +temperatures lower than their classical limits. This effect is +especially important for materials with a large population of hydrogen +atoms and thus higher classical limits. + +The equation of motion implemented by this command follows a Langevin +form: + +.. raw:: html + +
      miai = fi + + Ri - + miγvi.
      + +Here mi, ai, fi +, Ri, γ and vi +represent mass, acceleration, force exerted by all other atoms, random +force, frictional coefficient (the inverse of damping parameter damp), +and velocity. The random force Ri is "colored" so +that any vibrational mode with frequency ω will have a +temperature-sensitive energy θ(ω,T) which +resembles the energy expectation for a quantum harmonic oscillator +with the same natural frequency: + +.. raw:: html + +
      θ(ω,T) = + ℏω/2 + + ℏω[exp(ℏω/kBT)-1]-1 +
      + +To efficiently generate the random forces, we employ the method +of :ref:`(Barrat) `, that circumvents the need to generate all +random forces for all times before the simulation. The memory +requirement of this approach is less demanding and independent +of the simulation duration. Since the total random force Rtot +does not necessarily vanish for a finite number of atoms, +Ri is replaced by Ri - Rtot/Ntot +to avoid collective motion of the system. + +The *temp* parameter sets the target quantum temperature. LAMMPS will +still have an output temperature in its thermo style. That is the +instantaneous classical temperature Tcl derived from +the atom velocities at thermal equilibrium. A non-zero +Tcl will be present even when the quantum +temperature approaches zero. This is associated with zero-point energy +at low temperatures. + +.. raw:: html + +
      Tcl = ∑ + mivi2/3NkB +
      + +The *damp* parameter is specified in time units, and it equals the +inverse of the frictional coefficient γ. γ +should be as small as possible but slightly larger than the timescale +of anharmonic coupling in the system which is about 10 ps to 100 +ps. When γ is too large, it gives an energy spectrum that +differs from the desired Bose-Einstein spectrum. When γ +is too small, the quantum thermal bath coupling to the system will be +less significant than anharmonic effects, reducing to a classical +limit. We find that setting γ between 5 THz and 1 THz +could be appropriate depending on the system. + +The random number *seed* is a positive integer used to initiate a +Marsaglia random number generator. Each processor uses the input seed +to generate its own unique seed and its own stream of random +numbers. Thus the dynamics of the system will not be identical on two +runs on different numbers of processors. + +The *f_max* parameter truncate the noise frequency domain so that +vibrational modes with frequencies higher than *f_max* will not be +modulated. If we denote Δt as the time interval for the +MD integration, *f_max* is always reset by the code to make +α = (int)(2*f_max*Δt)-1 a +positive integer and print out relative information. An appropriate +value for the cutoff frequency *f_max* would be around 2~3 +fD, where fD is the Debye +frequency. + +The *N_f* parameter is the frequency grid size, the number of points +from 0 to *f_max* in the frequency domain that will be +sampled. 3×2 *N_f* per-atom random numbers are required +in the random force generation and there could be as many atoms as in +the whole simulation that can migrate into every individual +processor. A larger *N_f* provides a more accurate sampling of the +spectrum while consumes more memory. With fixed *f_max* and +γ, *N_f* should be big enough to converge the classical +temperature Tcl as a function of target quantum bath +temperature. Memory usage per processor could be from 10 to 100 +Mbytes. + +.. note:: + + Unlike the :doc:`fix nvt ` command which performs + Nose/Hoover thermostatting AND time integration, this fix does NOT + perform time integration. It only modifies forces to a colored + thermostat. Thus you must use a separate time integration fix, like + :doc:`fix nve ` or :doc:`fix nph ` to actually update the + velocities and positions of atoms (as shown in the + examples). Likewise, this fix should not normally be used with other + fixes or commands that also specify system temperatures , e.g. :doc:`fix nvt ` and :doc:`fix temp/rescale `. + + +---------- + + +**Restart, fix_modify, output, run start/stop, minimizie info:** + +No information about this fix is written to :doc:`binary restart files `. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix. However, in a statistical sense, a restarted +simulation should produce similar behaviors of the system. + +This fix is not invoked during :doc:`energy minimization `. + + +---------- + + +Restrictions +"""""""""""" + + +This fix style is part of the USER-QTB package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + + +---------- + + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nph `, :doc:`fix langevin `, :doc:`fix qbmsst ` + + +---------- + + +Default +""""""" + +The keyword defaults are temp = 300, damp = 1, seed = 880302, +f_max=200.0 and N_f = 100. + + +---------- + + +.. _Dammak: + + + +**(Dammak)** Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev +Lett, 103, 190601 (2009). + +.. _Barrat: + + + +**(Barrat)** Barrat and Rodney, J. Stat. Phys, 144, 679 (2011). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_reax_bonds.txt b/doc/_sources/fix_reax_bonds.txt new file mode 100644 index 0000000000..a3c5a53794 --- /dev/null +++ b/doc/_sources/fix_reax_bonds.txt @@ -0,0 +1,76 @@ +.. index:: fix reax/bonds + +fix reax/bonds command +====================== + +fix reax/c/bonds command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID reax/bonds Nevery filename + +* ID, group-ID are documented in :doc:`fix ` command +* reax/bonds = style name of this fix command +* Nevery = output interval in timesteps +* filename = name of output file + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all reax/bonds 100 bonds.tatb + fix 1 all reax/c/bonds 100 bonds.reaxc + +Description +""""""""""" + +Write out the bond information computed by the ReaxFF potential +specified by :doc:`pair_style reax ` or :doc:`pair_style reax/c ` in the exact same format as the original +stand-alone ReaxFF code of Adri van Duin. The bond information is +written to *filename* on timesteps that are multiples of *Nevery*, +including timestep 0. For time-averaged chemical species analysis, +please see the :doc:`fix species ` command. + +The format of the output file should be self-explantory. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +The fix reax/bonds command requires that the :doc:`pair_style reax ` be invoked. This fix is part of the REAX +package. It is only enabled if LAMMPS was built with that package, +which also requires the REAX library be built and linked with LAMMPS. +The fix reax/c/bonds command requires that the :doc:`pair_style reax/c ` be invoked. This fix is part of the +USER-REAXC package. It is only enabled if LAMMPS was built with that +package. See the :ref:`Making LAMMPS ` section +for more info. + +Related commands +"""""""""""""""" + +:doc:`pair_style reax `, :doc:`pair_style reax/c `, :doc:`fix reax/c/species ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_reaxc_species.txt b/doc/_sources/fix_reaxc_species.txt new file mode 100644 index 0000000000..41b7605feb --- /dev/null +++ b/doc/_sources/fix_reaxc_species.txt @@ -0,0 +1,166 @@ +.. index:: fix reax/c/species + +fix reax/c/species command +========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* reax/c/species = style name of this command +* Nevery = sample bond-order every this many timesteps +* Nrepeat = # of bond-order samples used for calculating averages +* Nfreq = calculate average bond-order every this many timesteps +* filename = name of output file +* zero or more keyword/value pairs may be appended +* keyword = *cutoff* or *element* or *position* +.. parsed-literal:: + + *cutoff* value = I J Cutoff + I, J = atom types + Cutoff = Bond-order cutoff value for this pair of atom types + *element* value = Element1, Element2, ... + *position* value = posfreq filepos + posfreq = write position files every this many timestep + filepos = name of position output file + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all reax/c/species 10 10 100 species.out + fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55 + fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos + +Description +""""""""""" + +Write out the chemical species information computed by the ReaxFF +potential specified by :doc:`pair_style reax/c `. +Bond-order values (either averaged or instantaneous, depending on +value of *Nrepeat*) are used to determine chemical bonds. Every +*Nfreq* timesteps, chemical species information is written to +*filename* as a two line output. The first line is a header +containing labels. The second line consists of the following: +timestep, total number of molecules, total number of distinct species, +number of molecules of each species. In this context, "species" means +a unique molecule. The chemical formula of each species is given in +the first line. + +Optional keyword *cutoff* can be assigned to change the minimum +bond-order values used in identifying chemical bonds between pairs of +atoms. Bond-order cutoffs should be carefully chosen, as bond-order +cutoffs that are too small may include too many bonds (which will +result in an error), while cutoffs that are too large will result in +fragmented molecules. The default cutoff of 0.3 usually gives good +results. + +The optional keyword *element* can be used to specify the chemical +symbol printed for each LAMMPS atom type. The number of symbols must +match the number of LAMMPS atom types and each symbol must consist of +1 or 2 alphanumeric characters. Normally, these symbols should be +chosen to match the chemical identity of each LAMMPS atom type, as +specified using the :doc:`reax/c pair_coeff ` command and +the ReaxFF force field file. + +The optional keyword *position* writes center-of-mass positions of +each identified molecules to file *filepos* every *posfreq* timesteps. +The first line contains information on timestep, total number of +molecules, total number of distinct species, and box dimensions. The +second line is a header containing labels. From the third line +downward, each molecule writes a line of output containing the +following information: molecule ID, number of atoms in this molecule, +chemical formula, total charge, and center-of-mass xyz positions of +this molecule. The xyz positions are in fractional coordinates +relative to the box dimensions. + +For the keyword *position*, the *filepos* is the name of the output +file. It can contain the wildcard character "*". If the "*" +character appears in *filepos*, then one file per snapshot is written +at *posfreq* and the "*" character is replaced with the timestep +value. For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc. + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the bond-order values are sampled to get the average bond +order. The species analysis is performed using the average bond-order +on timesteps that are a multiple of *Nfreq*. The average is over +*Nrepeat* bond-order samples, computed in the preceding portion of the +simulation every *Nevery* timesteps. *Nfreq* must be a multiple of +*Nevery* and *Nevery* must be non-zero even if *Nrepeat* is 1. +Also, the timesteps +contributing to the average bond-order cannot overlap, +i.e. Nrepeat*Nevery can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order +values on timesteps 90,92,94,96,98,100 will be used to compute the +average bond-order for the species analysis output on timestep 100. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes both a global vector of length 2 and a per-atom +vector, either of which can be accessed by various :ref:`output commands `. The values in the global +vector are "intensive". + +The 2 values in the global vector are as follows: + +* 1 = total number of molecules +* 2 = total number of distinct species + +The per-atom vector stores the molecule ID for each atom as identified +by the fix. If an atom is not in a molecule, its ID will be 0. +For atoms in the same molecule, the molecule ID for all of them +will be the same and will be equal to the smallest atom ID of +any atom in the molecule. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +The fix species currently only works with +:doc:`pair_style reax/c ` and it requires that the :doc:`pair_style reax/c ` be invoked. This fix is part of the +USER-REAXC package. It is only enabled if LAMMPS was built with that +package. See the :ref:`Making LAMMPS ` section +for more info. + +It should be possible to extend it to other reactive pair_styles (such as +:doc:`rebo `, :doc:`airebo `, +:doc:`comb `, and :doc:`bop `), but this has not yet been done. + +Related commands +"""""""""""""""" + +:doc:`pair_style reax/c `, :doc:`fix reax/bonds ` + +Default +""""""" + +The default values for bond-order cutoffs are 0.3 for all I-J pairs. The +default element symbols are C, H, O, N. Position files are not written +by default. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_recenter.txt b/doc/_sources/fix_recenter.txt new file mode 100644 index 0000000000..5ab5fd46c8 --- /dev/null +++ b/doc/_sources/fix_recenter.txt @@ -0,0 +1,141 @@ +.. index:: fix recenter + +fix recenter command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID recenter x y z keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* recenter = style name of this fix command +* x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below) +* zero or more keyword/value pairs may be appended +* keyword = *shift* or *units* +.. parsed-literal:: + + *shift* value = group-ID + group-ID = group of atoms whose coords are shifted + *units* value = *box* or *lattice* or *fraction* + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all recenter 0.0 0.5 0.0 + fix 1 all recenter INIT INIT NULL + fix 1 all recenter INIT 0.0 0.0 units box + +Description +""""""""""" + +Constrain the center-of-mass position of a group of atoms by adjusting +the coordinates of the atoms every timestep. This is simply a small +shift that does not alter the dynamics of the system or change the +relative coordinates of any pair of atoms in the group. This can be +used to insure the entire collection of atoms (or a portion of them) +do not drift during the simulation due to random perturbations +(e.g. :doc:`fix langevin ` thermostatting). + +Distance units for the x,y,z values are determined by the setting of +the *units* keyword, as discussed below. One or more x,y,z values can +also be specified as NULL, which means exclude that dimension from +this operation. Or it can be specified as INIT which means to +constrain the center-of-mass to its initial value at the beginning of +the run. + +The center-of-mass (COM) is computed for the group specified by the +fix. If the current COM is different than the specified x,y,z, then a +group of atoms has their coordinates shifted by the difference. By +default the shifted group is also the group specified by the fix. A +different group can be shifted by using the *shift* keyword. For +example, the COM could be computed on a protein to keep it in the +center of the simulation box. But the entire system (protein + water) +could be shifted. + +If the *units* keyword is set to *box*, then the distance units of +x,y,z are defined by the :doc:`units ` command - e.g. Angstroms +for *real* units. A *lattice* value means the distance units are in +lattice spacings. The :doc:`lattice ` command must have been +previously used to define the lattice spacing. A *fraction* value +means a fractional distance between the lo/hi box boundaries, e.g. 0.5 += middle of the box. The default is to use lattice units. + +Note that the :doc:`velocity ` command can be used to create +velocities with zero aggregate linear and/or angular momentum. + +.. note:: + + This fix performs its operations at the same point in the + timestep as other time integration fixes, such as :doc:`fix nve `, :doc:`fix nvt `, or :doc:`fix npt `. + Thus fix recenter should normally be the last such fix specified in + the input script, since the adjustments it makes to atom coordinates + should come after the changes made by time integration. LAMMPS will + warn you if your fixes are not ordered this way. + +.. note:: + + If you use this fix on a small group of atoms (e.g. a molecule + in solvent) without using the *shift* keyword to adjust the positions + of all atoms in the system, then the results can be unpredictable. + For example, if the molecule is pushed in one direction by the + solvent, its velocity will increase. But its coordinates will be + recentered, meaning it is pushed back towards the force. Thus over + time, the velocity and temperature of the molecule could become very + large (though it won't appear to be moving due to the recentering). + If you are thermostatting the entire system, then the solvent would be + cooled to compensate. A better solution for this simulation scenario + is to use the :doc:`fix spring ` command to tether the + molecule in place. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +distance the group is moved by fix recenter. + +This fix also computes global 3-vector which can be accessed by +various :ref:`output commands `. The 3 +quantities in the vector are xyz components of displacement applied to +the group of atoms by the fix. + +The scalar and vector values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix should not be used with an x,y,z setting that causes a large +shift in the system on the 1st timestep, due to the requested COM +being very different from the initial COM. This could cause atoms to +be lost, especially in parallel. Instead, use the +:doc:`displace_atoms ` command, which can be used to +move atoms a large distance. + +Related commands +"""""""""""""""" + +:doc:`fix momentum `, :doc:`velocity ` + +Default +""""""" + +The option defaults are shift = fix group-ID, and units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_restrain.txt b/doc/_sources/fix_restrain.txt new file mode 100644 index 0000000000..003cb9786d --- /dev/null +++ b/doc/_sources/fix_restrain.txt @@ -0,0 +1,209 @@ +.. index:: fix restrain + +fix restrain command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID restrain keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* restrain = style name of this fix command +* one or more keyword/arg pairs may be appended +* keyword = *bond* or *angle* or *dihedral* +.. parsed-literal:: + + *bond* args = atom1 atom2 Kstart Kstop r0 + atom1,atom2 = IDs of 2 atoms in bond + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + r0 = equilibrium bond distance (distance units) + *angle* args = atom1 atom2 atom3 Kstart Kstop theta0 + atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + theta0 = equilibrium angle theta (degrees) + *dihedral* args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 + atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order + Kstart,Kstop = restraint coefficients at start/end of run (energy units) + phi0 = equilibrium dihedral angle phi (degrees) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 + fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0 + fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0 + fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 + +Description +""""""""""" + +Restrain the motion of the specified sets of atoms by making them part +of a bond or angle or dihedral interaction whose strength can vary +over time during a simulation. This is functionally equivalent to +creating a bond or angle or dihedral for the same atoms in a data +file, as specified by the :doc:`read_data ` command, albeit +with a time-varying pre-factor coefficient. For the purpose of +forcefield parameter-fitting or mapping a molecular potential energy +surface, this fix reduces the hassle and risk associated with +modifying data files. In other words, use this fix to temporarily +force a molecule to adopt a particular conformation. To create a +permanent bond or angle or dihedral, you should modify the data file. + +The group-ID specified by this fix is ignored. + +The second example above applies a restraint to hold the dihedral +angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant +restraint coefficient. The fourth example applies similar restraints +to multiple dihedral angles using a restraint coefficient that +increases from 0.0 to 2000.0 over the course of the run. + +.. note:: + + Adding a force to atoms implies a change in their potential + energy as they move due to the applied force field. For dynamics via + the :doc:`run ` command, this energy can be added to the system's + potential energy for thermodynamic output (see below). For energy + minimization via the :doc:`minimize ` command, this energy + must be added to the system's potential energy to formulate a + self-consistent minimization problem (see below). + +In order for a restraint to be effective, the restraint force must +typically be significantly larger than the forces associated with +conventional forcefield terms. If the restraint is applied during a +dynamics run (as opposed to during an energy minimization), a large +restraint coefficient can significantly reduce the stable timestep +size, especially if the atoms are initially far from the preferred +conformation. You may need to experiment to determine what value of K +works best for a given application. + +For the case of finding a minimum energy structure for a single +molecule with particular restratins (e.g. for fitting forcefield +parameters or constructing a potential energy surface), commands such +as the following may be useful: + +.. parsed-literal:: + + # minimize molecule energy with restraints + velocity all create 600.0 8675309 mom yes rot yes dist gaussian + fix NVE all nve + fix TFIX all langevin 600.0 0.0 100 24601 + fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 ${angle1} dihedral 3 1 2 9 0.0 5000.0 ${angle2} + fix_modify REST energy yes + run 10000 + fix TFIX all langevin 0.0 0.0 100 24601 + fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 ${angle1} dihedral 3 1 2 9 5000.0 5000.0 ${angle2} + fix_modify REST energy yes + run 10000 + # sanity check for convergence + minimize 1e-6 1e-9 1000 100000 + # report unrestrained energies + unfix REST + run 0 + + +---------- + + +The *bond* keyword applies a bond restraint to the specified atoms +using the same functional form used by the :doc:`bond_style harmonic ` command. The potential associated with +the restraint is + +.. image:: Eqs/bond_harmonic.jpg + :align: center + +with the following coefficients: + +* K (energy/distance^2) +* r0 (distance) + +K and r0 are specified with the fix. Note that the usual 1/2 factor +is included in K. + + +---------- + + +The *angle* keyword applies an angle restraint to the specified atoms +using the same functional form used by the :doc:`angle_style harmonic ` command. The potential associated with +the restraint is + +.. image:: Eqs/angle_harmonic.jpg + :align: center + +with the following coefficients: + +* K (energy/radian^2) +* theta0 (degrees) + +K and theta0 are specified with the fix. Note that the usual 1/2 +factor is included in K. + + +---------- + + +The *dihedral* keyword applies a dihedral restraint to the specified +atoms using a simplified form of the function used by the +:doc:`dihedral_style charmm ` command. The potential +associated with the restraint is + +.. image:: Eqs/dihedral_charmm.jpg + :align: center + +with the following coefficients: + +* K (energy) +* n = 1 +* d (degrees) = phi0 + 180 + +K and phi0 are specified with the fix. Note that the value of n is +hard-wired to 1. Also note that the energy will be a minimum when the +current dihedral angle phi is equal to phi0. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the potential energy associated with this fix to the +system's potential energy as part of :doc:`thermodynamic output `. + +.. note:: + + If you want the fictitious potential energy associated with the + added forces to be included in the total potential energy of the + system (the quantity being minimized), you MUST enable the + :doc:`fix_modify ` *energy* option for this fix. + +This fix computes a global scalar, which can be accessed by various +:ref:`output commands `. The scalar is the +potential energy for all the restraints as discussed above. The scalar +value calculated by this fix is "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_rigid.txt b/doc/_sources/fix_rigid.txt new file mode 100644 index 0000000000..a0284c8d54 --- /dev/null +++ b/doc/_sources/fix_rigid.txt @@ -0,0 +1,871 @@ +.. index:: fix rigid + +fix rigid command +================= + +fix rigid/nve command +===================== + +fix rigid/nvt command +===================== + +fix rigid/npt command +===================== + +fix rigid/nph command +===================== + +fix rigid/small command +======================= + +fix rigid/nve/small command +=========================== + +fix rigid/nvt/small command +=========================== + +fix rigid/npt/small command +=========================== + +fix rigid/nph/small command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style bodystyle args keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = *rigid* or *rigid/nve* or *rigid/nvt* or *rigid/npt* or *rigid/nph* or *rigid/small* or *rigid/nve/small* or *rigid/nvt/small* or *rigid/npt/small* or *rigid/nph/small* +* bodystyle = *single* or *molecule* or *group* +.. parsed-literal:: + + *single* args = none + *molecule* args = none + *group* args = N groupID1 groupID2 ... + N = # of groups + groupID1, groupID2, ... = list of N group IDs + +* zero or more keyword/value pairs may be appended +* keyword = *langevin* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* +.. parsed-literal:: + + *langevin* values = Tstart Tstop Tperiod seed + Tstart,Tstop = desired temperature at start/stop of run (temperature units) + Tdamp = temperature damping parameter (time units) + seed = random number seed to use for white noise (positive integer) + *temp* values = Tstart Tstop Tdamp + Tstart,Tstop = desired temperature at start/stop of run (temperature units) + Tdamp = temperature damping parameter (time units) + *iso* or *aniso* values = Pstart Pstop Pdamp + Pstart,Pstop = scalar external pressure at start/end of run (pressure units) + Pdamp = pressure damping parameter (time units) + *x* or *y* or *z* values = Pstart Pstop Pdamp + Pstart,Pstop = external stress tensor component at start/end of run (pressure units) + Pdamp = stress damping parameter (time units) + *couple* = *none* or *xyz* or *xy* or *yz* or *xz* + *tparam* values = Tchain Titer Torder + Tchain = length of Nose/Hoover thermostat chain + Titer = number of thermostat iterations performed + Torder = 3 or 5 = Yoshida-Suzuki integration parameters + *pchain* values = Pchain + Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat + *dilate* value = dilate-group-ID + dilate-group-ID = only dilate atoms in this group due to barostat volume changes + *force* values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass force is active + *torque* values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass torque is active + *infile* filename + filename = file with per-body values of mass, center-of-mass, moments of inertia + *mol* value = template-ID + template-ID = ID of molecule template specified in a separate :doc:`molecule ` command + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 clump rigid single + fix 1 clump rigid/small molecule + fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984 + fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 + fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on + fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984 + fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off + fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0 + fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz + fix 1 water rigid/nph molecule iso 0.5 0.5 1.0 + fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 + +Description +""""""""""" + +Treat one or more sets of atoms as independent rigid bodies. This +means that each timestep the total force and torque on each rigid body +is computed as the sum of the forces and torques on its constituent +particles. The coordinates, velocities, and orientations of the atoms +in each body are then updated so that the body moves and rotates as a +single entity. + +Examples of large rigid bodies are a colloidal particle, or portions +of a biomolecule such as a protein. + +Example of small rigid bodies are patchy nanoparticles, such as those +modeled in :ref:`this paper ` by Sharon Glotzer's group, clumps of +granular particles, lipid molecules consiting of one or more point +dipoles connected to other spheroids or ellipsoids, irregular +particles built from line segments (2d) or triangles (3d), and +coarse-grain models of nano or colloidal particles consisting of a +small number of constituent particles. Note that the :doc:`fix shake ` command can also be used to rigidify small +molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats +the constituent atoms as point masses. + +These fixes also update the positions and velocities of the atoms in +each rigid body via time integration, in the NVE, NVT, NPT, or NPH +ensemble, as described below. + +There are two main variants of this fix, fix rigid and fix +rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two +variants, as their style names indicate. + +.. note:: + + Not all of the *bodystyle* options and keyword/value options are + available for both the *rigid* and *rigid/small* variants. See + details below. + +The *rigid* variant is typically the best choice for a system with a +small number of large rigid bodies, each of which can extend across +the domain of many processors. It operates by creating a single +global list of rigid bodies, which all processors contribute to. +MPI_Allreduce operations are performed each timestep to sum the +contributions from each processor to the force and torque on all the +bodies. This operation will not scale well in parallel if large +numbers of rigid bodies are simulated. + +The *rigid/small* variant is typically best for a system with a large +number of small rigid bodies. Each body is assigned to the atom +closest to the geometrical center of the body. The fix operates using +local lists of rigid bodies owned by each processor and information is +exchanged and summed via local communication between neighboring +processors when ghost atom info is accumlated. + +.. note:: + + To use *rigid/small* the ghost atom cutoff must be large enough + to span the distance between the atom that owns the body and every + other atom in the body. This distance value is printed out when the + rigid bodies are defined. If the :doc:`pair_style ` cutoff + plus neighbor skin does not span this distance, then you should use + the :doc:`comm_modify cutoff ` command with a setting + epsilon larger than the distance. + +Which of the two variants is faster for a particular problem is hard +to predict. The best way to decide is to perform a short test run. +Both variants should give identical numerical answers for short runs. +Long runs should give statistically similar results, but round-off +differences may accumulate to produce divergent trajectories. + +.. note:: + + You should not update the atoms in rigid bodies via other + time-integration fixes (e.g. :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix npt `), or you will be integrating + their motion more than once each timestep. When performing a hybrid + simulation with some atoms in rigid bodies, and some not, a separate + time integration fix like :doc:`fix nve ` or :doc:`fix nvt ` should be used for the non-rigid particles. + +.. note:: + + These fixes are overkill if you simply want to hold a collection + of atoms stationary or have them move with a constant velocity. A + simpler way to hold atoms stationary is to not include those atoms in + your time integration fix. E.g. use "fix 1 mobile nve" instead of + "fix 1 all nve", where "mobile" is the group of atoms that you want to + move. You can move atoms with a constant velocity by assigning them + an initial velocity (via the :doc:`velocity ` command), + setting the force on them to 0.0 (via the :doc:`fix setforce ` command), and integrating them as usual + (e.g. via the :doc:`fix nve ` command). + +.. note:: + + The aggregate properties of each rigid body are calculated one + time at the start of the first simulation run after this fix is + specified. The properties include the position and velocity of the + center-of-mass of the body, its moments of inertia, and its angular + momentum. This is done using the properties of the constituent atoms + of the body at that point in time (or see the *infile* keyword + option). Thereafter, changing properties of individual atoms in the + body will have no effect on a rigid body's dynamics, unless they + effect the :doc:`pair_style ` interactions that individual + particles are part of. For example, you might think you could + displace the atoms in a body or add a large velocity to each atom in a + body to make it move in a desired direction before a 2nd run is + performed, using the :doc:`set ` or + :doc:`displace_atoms ` or :doc:`velocity ` + command. But these commands will not affect the internal attributes + of the body, and the position and velocity or individual atoms in the + body will be reset when time integration starts. + + +---------- + + +Each rigid body must have two or more atoms. An atom can belong to at +most one rigid body. Which atoms are in which bodies can be defined +via several options. + +.. note:: + + With fix rigid/small, which requires bodystyle *molecule*, you + can define a system that has no rigid bodies initially. This is + useful when you are using the *mol* keyword in conjunction with + another fix that is adding rigid bodies on-the-fly, such as :doc:`fix deposit ` or :doc:`fix pour `. + +For bodystyle *single* the entire fix group of atoms is treated as one +rigid body. This option is only allowed for fix rigid and its +sub-styles. + +For bodystyle *molecule*, each set of atoms in the fix group with a +different molecule ID is treated as a rigid body. This option is +allowed for fix rigid and fix rigid/small, and their sub-styles. Note +that atoms with a molecule ID = 0 will be treated as a single rigid +body. For a system with atomic solvent (typically this is atoms with +molecule ID = 0) surrounding rigid bodies, this may not be what you +want. Thus you should be careful to use a fix group that only +includes atoms you want to be part of rigid bodies. + +For bodystyle *group*, each of the listed groups is treated as a +separate rigid body. Only atoms that are also in the fix group are +included in each rigid body. This option is only allowed for fix +rigid and its sub-styles. + +.. note:: + + To compute the initial center-of-mass position and other + properties of each rigid body, the image flags for each atom in the + body are used to "unwrap" the atom coordinates. Thus you must insure + that these image flags are consistent so that the unwrapping creates a + valid rigid body (one where the atoms are close together), + particularly if the atoms in a single rigid body straddle a periodic + boundary. This means the input data file or restart file must define + the image flags for each atom consistently or that you have used the + :doc:`set ` command to specify them correctly. If a dimension is + non-periodic then the image flag of each atom must be 0 in that + dimension, else an error is generated. + +The *force* and *torque* keywords discussed next are only allowed for +fix rigid and its sub-styles. + +By default, each rigid body is acted on by other atoms which induce an +external force and torque on its center of mass, causing it to +translate and rotate. Components of the external center-of-mass force +and torque can be turned off by the *force* and *torque* keywords. +This may be useful if you wish a body to rotate but not translate, or +vice versa, or if you wish it to rotate or translate continuously +unaffected by interactions with other particles. Note that if you +expect a rigid body not to move or rotate by using these keywords, you +must insure its initial center-of-mass translational or angular +velocity is 0.0. Otherwise the initial translational or angular +momentum the body has will persist. + +An xflag, yflag, or zflag set to *off* means turn off the component of +force of torque in that dimension. A setting of *on* means turn on +the component, which is the default. Which rigid body(s) the settings +apply to is determined by the first argument of the *force* and +*torque* keywords. It can be an integer M from 1 to Nbody, where +Nbody is the number of rigid bodies defined. A wild-card asterisk can +be used in place of, or in conjunction with, the M argument to set the +flags for multiple rigid bodies. This takes the form "*" or "*n" or +"n*" or "m*n". If N = the number of rigid bodies, then an asterisk +with no numeric values means all bodies from 1 to N. A leading +asterisk means all bodies from 1 to n (inclusive). A trailing +asterisk means all bodies from n to N (inclusive). A middle asterisk +means all types from m to n (inclusive). Note that you can use the +*force* or *torque* keywords as many times as you like. If a +particular rigid body has its component flags set multiple times, the +settings from the final keyword are used. + +.. note:: + + For computational efficiency, you may wish to turn off pairwise + and bond interactions within each rigid body, as they no longer + contribute to the motion. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` + commands are used to do this. If the rigid bodies have strongly + overalapping atoms, you may need to turn off these interactions to + avoid numerical problems due to large equal/opposite intra-body forces + swamping the contribution of small inter-body forces. + +For computational efficiency, you should typically define one fix +rigid or fix rigid/small command which includes all the desired rigid +bodies. LAMMPS will allow multiple rigid fixes to be defined, but it +is more expensive. + + +---------- + + +The constituent particles within a rigid body can be point particles +(the default in LAMMPS) or finite-size particles, such as spheres or +ellipsoids or line segments or triangles. See the :doc:`atom_style sphere and ellipsoid and line and tri ` commands for more +details on these kinds of particles. Finite-size particles contribute +differently to the moment of inertia of a rigid body than do point +particles. Finite-size particles can also experience torque (e.g. due +to :doc:`frictional granular interactions `) and have an +orientation. These contributions are accounted for by these fixes. + +Forces between particles within a body do not contribute to the +external force or torque on the body. Thus for computational +efficiency, you may wish to turn off pairwise and bond interactions +between particles within each rigid body. The :doc:`neigh_modify exclude ` and :doc:`delete_bonds ` +commands are used to do this. For finite-size particles this also +means the particles can be highly overlapped when creating the rigid +body. + + +---------- + + +The *rigid* and *rigid/small* and *rigid/nve* styles perform constant +NVE time integration. The only difference is that the *rigid* and +*rigid/small* styles use an integration technique based on Richardson +iterations. The *rigid/nve* style uses the methods described in the +paper by :ref:`Miller `, which are thought to provide better energy +conservation than an iterative approach. + +The *rigid/nvt* and *rigid/nvt/small* styles performs constant NVT +integration using a Nose/Hoover thermostat with chains as described +originally in :ref:`(Hoover) ` and :ref:`(Martyna) `, which +thermostats both the translational and rotational degrees of freedom +of the rigid bodies. The rigid-body algorithm used by *rigid/nvt* +is described in the paper by :ref:`Kamberaj `. + +The *rigid/npt* and *rigid/nph* (and their /small counterparts) styles +perform constant NPT or NPH integration using a Nose/Hoover barostat +with chains. For the NPT case, the same Nose/Hoover thermostat is also +used as with *rigid/nvt*. + +The barostat parameters are specified using one or more of the *iso*, +*aniso*, *x*, *y*, *z* and *couple* keywords. These keywords give you +the ability to specify 3 diagonal components of the external stress +tensor, and to couple these components together so that the dimensions +they represent are varied together during a constant-pressure +simulation. The effects of these keywords are similar to those +defined in :doc:`fix npt/nph ` + +.. note:: + + Currently the *rigid/npt* and *rigid/nph* (and their /small + counterparts) styles do not support triclinic (non-orthongonal) boxes. + +The target pressures for each of the 6 components of the stress tensor +can be specified independently via the *x*, *y*, *z* keywords, which +correspond to the 3 simulation box dimensions. For each component, +the external pressure or tensor component at each timestep is a ramped +value during the run from *Pstart* to *Pstop*. If a target pressure is +specified for a component, then the corresponding box dimension will +change during a simulation. For example, if the *y* keyword is used, +the y-box length will change. A box dimension will not change if that +component is not specified, although you have the option to change +that dimension via the :doc:`fix deform ` command. + +For all barostat keywords, the *Pdamp* parameter operates like the +*Tdamp* parameter, determining the time scale on which pressure is +relaxed. For example, a value of 10.0 means to relax the pressure in +a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see +the :doc:`units ` command). + +Regardless of what atoms are in the fix group (the only atoms which +are time integrated), a global pressure or stress tensor is computed +for all atoms. Similarly, when the size of the simulation box is +changed, all atoms are re-scaled to new positions, unless the keyword +*dilate* is specified with a *dilate-group-ID* for a group that +represents a subset of the atoms. This can be useful, for example, to +leave the coordinates of atoms in a solid substrate unchanged and +controlling the pressure of a surrounding fluid. Another example is a +system consisting of rigid bodies and point particles where the +barostat is only coupled with the rigid bodies. This option should be +used with care, since it can be unphysical to dilate some atoms and +not others, because it can introduce large, instantaneous +displacements between a pair of atoms (one dilated, one not) that are +far from the dilation origin. + +The *couple* keyword allows two or three of the diagonal components of +the pressure tensor to be "coupled" together. The value specified +with the keyword determines which are coupled. For example, *xz* +means the *Pxx* and *Pzz* components of the stress tensor are coupled. +*Xyz* means all 3 diagonal components are coupled. Coupling means two +things: the instantaneous stress will be computed as an average of the +corresponding diagonal components, and the coupled box dimensions will +be changed together in lockstep, meaning coupled dimensions will be +dilated or contracted by the same percentage every timestep. The +*Pstart*, *Pstop*, *Pdamp* parameters for any coupled dimensions must +be identical. *Couple xyz* can be used for a 2d simulation; the *z* +dimension is simply ignored. + +The *iso* and *aniso* keywords are simply shortcuts that are +equivalent to specifying several other keywords together. + +The keyword *iso* means couple all 3 diagonal components together when +pressure is computed (hydrostatic pressure), and dilate/contract the +dimensions together. Using "iso Pstart Pstop Pdamp" is the same as +specifying these 4 keywords: + +.. parsed-literal:: + + x Pstart Pstop Pdamp + y Pstart Pstop Pdamp + z Pstart Pstop Pdamp + couple xyz + +The keyword *aniso* means *x*, *y*, and *z* dimensions are controlled +independently using the *Pxx*, *Pyy*, and *Pzz* components of the +stress tensor as the driving forces, and the specified scalar external +pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying +these 4 keywords: + +.. parsed-literal:: + + x Pstart Pstop Pdamp + y Pstart Pstop Pdamp + z Pstart Pstop Pdamp + couple none + + +---------- + + +The keyword/value option pairs are used in the following ways. + +The *langevin* and *temp* and *tparam* keywords perform thermostatting +of the rigid bodies, altering both their translational and rotational +degrees of freedom. What is meant by "temperature" of a collection of +rigid bodies and how it can be monitored via the fix output is +discussed below. + +The *langevin* keyword applies a Langevin thermostat to the constant +NVE time integration performed by either the *rigid* or *rigid/small* +or *rigid/nve* styles. It cannot be used with the *rigid/nvt* style. +The desired temperature at each timestep is a ramped value during the +run from *Tstart* to *Tstop*. The *Tdamp* parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +:doc:`units ` command). The random # *seed* must be a positive +integer. + +The way that Langevin thermostatting operates is explained on the :doc:`fix langevin ` doc page. If you wish to simply viscously +damp the rotational motion without thermostatting, you can set +*Tstart* and *Tstop* to 0.0, which means only the viscous drag term in +the Langevin thermostat will be applied. See the discussion on the +:doc:`fix viscous ` doc page for details. + +.. note:: + + When the *langevin* keyword is used with fix rigid versus fix + rigid/small, different dynamics will result for parallel runs. This + is because of the way random numbers are used in the two cases. The + dynamics for the two cases should be statistically similar, but will + not be identical, even for a single timestep. + +The *temp* and *tparam* keywords apply a Nose/Hoover thermostat to the +NVT time integration performed by the *rigid/nvt* style. They cannot +be used with the *rigid* or *rigid/small* or *rigid/nve* styles. The +desired temperature at each timestep is a ramped value during the run +from *Tstart* to *Tstop*. The *Tdamp* parameter is specified in time +units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +:doc:`units ` command). + +Nose/Hoover chains are used in conjunction with this thermostat. The +*tparam* keyword can optionally be used to change the chain settings +used. *Tchain* is the number of thermostats in the Nose Hoover chain. +This value, along with *Tdamp* can be varied to dampen undesirable +oscillations in temperature that can occur in a simulation. As a rule +of thumb, increasing the chain length should lead to smaller +oscillations. The keyword *pchain* specifies the number of +thermostats in the chain thermostatting the barostat degrees of +freedom. + +.. note:: + + There are alternate ways to thermostat a system of rigid bodies. + You can use :doc:`fix langevin ` to treat the individual + particles in the rigid bodies as effectively immersed in an implicit + solvent, e.g. a Brownian dynamics model. For hybrid systems with both + rigid bodies and solvent particles, you can thermostat only the + solvent particles that surround one or more rigid bodies by + appropriate choice of groups in the compute and fix commands for + temperature and thermostatting. The solvent interactions with the + rigid bodies should then effectively thermostat the rigid body + temperature as well without use of the Langevin or Nose/Hoover options + associated with the fix rigid commands. + + +---------- + + +The *mol* keyword can only be used with fix rigid/small. It must be +used when other commands, such as :doc:`fix deposit ` or +:doc:`fix pour `, add rigid bodies on-the-fly during a +simulation. You specify a *template-ID* previously defined using the +:doc:`molecule ` command, which reads a file that defines the +molecule. You must use the same *template-ID* that the other fix +which is adding rigid bodies uses. The coordinates, atom types, atom +diameters, center-of-mass, and moments of inertia can be specified in +the molecule file. See the :doc:`molecule ` command for +details. The only settings required to be in this file are the +coordinates and types of atoms in the molecule, in which case the +molecule command calculates the other quantities itself. + +Note that these other fixes create new rigid bodies, in addition to +those defined initially by this fix via the *bodystyle* setting. + +Also note that when using the *mol* keyword, extra restart information +about all rigid bodies is written out whenever a restart file is +written out. See the NOTE in the next section for details. + + +---------- + + +The *infile* keyword allows a file of rigid body attributes to be read +in from a file, rather then having LAMMPS compute them. There are 5 +such attributes: the total mass of the rigid body, its center-of-mass +position, its 6 moments of inertia, its center-of-mass velocity, and +the 3 image flags of the center-of-mass position. For rigid bodies +consisting of point particles or non-overlapping finite-size +particles, LAMMPS can compute these values accurately. However, for +rigid bodies consisting of finite-size particles which overlap each +other, LAMMPS will ignore the overlaps when computing these 4 +attributes. The amount of error this induces depends on the amount of +overlap. To avoid this issue, the values can be pre-computed +(e.g. using Monte Carlo integration). + +The format of the file is as follows. Note that the file does not +have to list attributes for every rigid body integrated by fix rigid. +Only bodies which the file specifies will have their computed +attributes overridden. The file can contain initial blank lines or +comment lines starting with "#" which are ignored. The first +non-blank, non-comment line should list N = the number of lines to +follow. The N successive lines contain the following information: + +.. parsed-literal:: + + ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm + ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm + ... + IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm + +The rigid body IDs are all positive integers. For the *single* +bodystyle, only an ID of 1 can be used. For the *group* bodystyle, +IDs from 1 to Ng can be used where Ng is the number of specified +groups. For the *molecule* bodystyle, use the molecule ID for the +atoms in a specific rigid body as the rigid body ID. + +The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are +self-explanatory. The center-of-mass should be consistent with what +is calculated for the position of the rigid body with all its atoms +unwrapped by their respective image flags. If this produces a +center-of-mass that is outside the simulation box, LAMMPS wraps it +back into the box. + +The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the +values consistent with the current orientation of the rigid body +around its center of mass. The values are with respect to the +simulation box XYZ axes, not with respect to the prinicpal axes of the +rigid body itself. LAMMPS performs the latter calculation internally. + +The (vxcm,vycm,vzcm) values are the velocity of the center of mass. +The (lx,ly,lz) values are the angular momentum of the body. The +(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you +wish the body to have no initial motion. + +The (ixcm,iycm,izcm) values are the image flags of the center of mass +of the body. For periodic dimensions, they specify which image of the +simulation box the body is considered to be in. An image of 0 means +it is inside the box as defined. A value of 2 means add 2 box lengths +to get the true value. A value of -1 means subtract 1 box length to +get the true value. LAMMPS updates these flags as the rigid bodies +cross periodic boundaries during the simulation. + +.. note:: + + If you use the *infile* or *mol* keywords and write restart + files during a simulation, then each time a restart file is written, + the fix also write an auxiliary restart file with the name + rfile.rigid, where "rfile" is the name of the restart file, + e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary + file is in the same format described above. Thus it can be used in a + new input script that restarts the run and re-specifies a rigid fix + using an *infile* keyword and the appropriate filename. Note that the + auxiliary file will contain one line for every rigid body, even if the + original file only listed a subset of the rigid bodies. + + +---------- + + +If you use a :doc:`temperature compute ` with a group that +includes particles in rigid bodies, the degrees-of-freedom removed by +each rigid body are accounted for in the temperature (and pressure) +computation, but only if the temperature group includes all the +particles in a particular rigid body. + +A 3d rigid body has 6 degrees of freedom (3 translational, 3 +rotational), except for a collection of point particles lying on a +straight line, which has only 5, e.g a dimer. A 2d rigid body has 3 +degrees of freedom (2 translational, 1 rotational). + +.. note:: + + You may wish to explicitly subtract additional + degrees-of-freedom if you use the *force* and *torque* keywords to + eliminate certain motions of one or more rigid bodies. LAMMPS does + not do this automatically. + +The rigid body contribution to the pressure of the system (virial) is +also accounted for by this fix. + + +---------- + + +If your simlulation is a hybrid model with a mixture of rigid bodies +and non-rigid particles (e.g. solvent) there are several ways these +rigid fixes can be used in tandem with :doc:`fix nve `, :doc:`fix nvt `, :doc:`fix npt `, and :doc:`fix nph `. + +If you wish to perform NVE dynamics (no thermostatting or +barostatting), use fix rigid or fix rigid/nve to integrate the rigid +bodies, and :doc:`fix nve ` to integrate the non-rigid +particles. + +If you wish to perform NVT dynamics (thermostatting, but no +barostatting), you can use fix rigid/nvt for the rigid bodies, and any +thermostatting fix for the non-rigid particles (:doc:`fix nvt `, +:doc:`fix langevin `, :doc:`fix temp/berendsen `). You can also use fix rigid +or fix rigid/nve for the rigid bodies and thermostat them using :doc:`fix langevin ` on the group that contains all the +particles in the rigid bodies. The net force added by :doc:`fix langevin ` to each rigid body effectively thermostats +its translational center-of-mass motion. Not sure how well it does at +thermostatting its rotational motion. + +If you with to perform NPT or NPH dynamics (barostatting), you cannot +use both :doc:`fix npt ` and fix rigid/npt (or the nph +variants). This is because there can only be one fix which monitors +the global pressure and changes the simulation box dimensions. So you +have 3 choices: + +* Use fix rigid/npt for the rigid bodies. Use the *dilate* all option + so that it will dilate the positions of the non-rigid particles as + well. Use :doc:`fix nvt ` (or any other thermostat) for the + non-rigid particles. +* Use :doc:`fix npt ` for the group of non-rigid particles. Use + the *dilate* all option so that it will dilate the center-of-mass + positions of the rigid bodies as well. Use fix rigid/nvt for the + rigid bodies. +* Use :doc:`fix press/berendsen ` to compute the + pressure and change the box dimensions. Use fix rigid/nvt for the + rigid bodies. Use `fix nvt `_ (or any other thermostat) for + the non-rigid particles. +In all case, the rigid bodies and non-rigid particles both contribute +to the global pressure and the box is scaled the same by any of the +barostatting fixes. + +You could even use the 2nd and 3rd options for a non-hybrid simulation +consisting of only rigid bodies, assuming you give :doc:`fix npt ` an empty group, though it's an odd thing to do. The +barostatting fixes (:doc:`fix npt ` and :doc:`fix press/berensen `) will monitor the pressure +and change the box dimensions, but not time integrate any particles. +The integration of the rigid bodies will be performed by fix +rigid/nvt. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about the *rigid* and *rigid/small* and *rigid/nve* +fixes are written to :doc:`binary restart files `. The +exception is if the *infile* or *mol* keyword is used, in which case +an auxiliary file is written out with rigid body information each time +a restart file is written, as explained above for the *infile* +keyword. For style *rigid/nvt* the state of the Nose/Hoover +thermostat is written to :doc:`binary restart files `. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The :doc:`fix_modify ` *energy* option is supported by the +rigid/nvt fix to add the energy change induced by the thermostatting +to the system's potential energy as part of :doc:`thermodynamic output `. + +The :doc:`fix_modify ` *temp* and *press* options are +supported by the rigid/npt and rigid/nph fixes to change the computes used +to calculate the instantaneous pressure tensor. Note that the rigid/nvt fix +does not use any external compute to compute instantaneous temperature. + +The *rigid* and *rigid/small* and *rigid/nve* fixes compute a global +scalar which can be accessed by various :ref:`output commands `. The scalar value calculated by +these fixes is "intensive". The scalar is the current temperature of +the collection of rigid bodies. This is averaged over all rigid +bodies and their translational and rotational degrees of freedom. The +translational energy of a rigid body is 1/2 m v^2, where m = total +mass of the body and v = the velocity of its center of mass. The +rotational energy of a rigid body is 1/2 I w^2, where I = the moment +of inertia tensor of the body and w = its angular velocity. Degrees +of freedom constrained by the *force* and *torque* keywords are +removed from this calculation, but only for the *rigid* and +*rigid/nve* fixes. + +The *rigid/nvt*, *rigid/npt*, and *rigid/nph* fixes compute a global +scalar which can be accessed by various :ref:`output commands `. The scalar value calculated by +these fixes is "extensive". The scalar is the cumulative energy +change due to the thermostatting and barostatting the fix performs. + +All of the *rigid* fixes except *rigid/small* compute a global array +of values which can be accessed by various :ref:`output commands `. The number of rows in the +array is equal to the number of rigid bodies. The number of columns +is 15. Thus for each rigid body, 15 values are stored: the xyz coords +of the center of mass (COM), the xyz components of the COM velocity, +the xyz components of the force acting on the COM, the xyz components +of the torque acting on the COM, and the xyz image flags of the COM. + +The center of mass (COM) for each body is similar to unwrapped +coordinates written to a dump file. It will always be inside (or +slightly outside) the simulation box. The image flags have the same +meaning as image flags for atom positions (see the "dump" command). +This means you can calculate the unwrapped COM by applying the image +flags to the COM, the same as when unwrapped coordinates are written +to a dump file. + +The force and torque values in the array are not affected by the +*force* and *torque* keywords in the fix rigid command; they reflect +values before any changes are made by those keywords. + +The ordering of the rigid bodies (by row in the array) is as follows. +For the *single* keyword there is just one rigid body. For the +*molecule* keyword, the bodies are ordered by ascending molecule ID. +For the *group* keyword, the list of group IDs determines the ordering +of bodies. + +The array values calculated by these fixes are "intensive", meaning +they are independent of the number of atoms in the simulation. + +No parameter of these fixes can be used with the *start/stop* keywords +of the :doc:`run ` command. These fixes are not invoked during +:doc:`energy minimization `. + + +---------- + + +Restrictions +"""""""""""" + + +These fixes are all part of the RIGID package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Assigning a temperature via the :doc:`velocity create ` +command to a system with :doc:`rigid bodies ` may not have +the desired outcome for two reasons. First, the velocity command can +be invoked before the rigid-body fix is invoked or initialized and the +number of adjusted degrees of freedom (DOFs) is known. Thus it is not +possible to compute the target temperature correctly. Second, the +assigned velocities may be partially canceled when constraints are +first enforced, leading to a different temperature than desired. A +workaround for this is to perform a :doc:`run 0 ` command, which +insures all DOFs are accounted for properly, and then rescale the +temperature to the desired value before performing a simulation. For +example: + +.. parsed-literal:: + + velocity all create 300.0 12345 + run 0 # temperature may not be 300K + velocity all scale 300.0 # now it should be + +Related commands +"""""""""""""""" + +:doc:`delete_bonds `, :doc:`neigh_modify ` +exclude, :doc:`fix shake ` + +Default +""""""" + +The option defaults are force * on on on and torque * on on on, +meaning all rigid bodies are acted on by center-of-mass force and +torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3. + + +---------- + + +.. _Hoover: + + + +**(Hoover)** Hoover, Phys Rev A, 31, 1695 (1985). + +.. _Kamberaj: + + + +**(Kamberaj)** Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005). + +.. _Martyna: + + + +**(Martyna)** Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992); +Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117. + +.. _Miller: + + + +**(Miller)** Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, +J Chem Phys, 116, 8649 (2002). + +.. _Zhang: + + + +**(Zhang)** Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_saed_vtk.txt b/doc/_sources/fix_saed_vtk.txt new file mode 100644 index 0000000000..4d99c78dd8 --- /dev/null +++ b/doc/_sources/fix_saed_vtk.txt @@ -0,0 +1,217 @@ +.. index:: fix saed/vtk + +fix saed/vtk command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ... + +* ID, group-ID are documented in :doc:`fix ` command +* saed/vtk = style name of this fix command +* Nevery = use input values every this many timesteps +* Nrepeat = # of times to use input values for calculating averages +* Nfreq = calculate averages every this many timesteps +* c_ID = saed compute ID +.. parsed-literal:: + + keyword = *file* or *ave* or *start* or *file* or *overwrite*:l + *ave* args = *one* or *running* or *window M* + one = output a new average value every Nfreq steps + running = output cumulative average of all previous Nfreq steps + window M = output average of M most recent Nfreq steps + *start* args = Nstart + Nstart = start averaging on this timestep + *file* arg = filename + filename = name of file to output time averages to + *overwrite* arg = none = overwrite output file with only latest output + + + +Examples +"""""""" + +.. parsed-literal:: + + compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 + compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo + +.. parsed-literal:: + + fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed + fix saed/vtk 1 1 1 c_2 file Ni_000.saed + +Description +""""""""""" + +Time average computed intensities from `compute_saed `_ and +write output to a file in the 3rd generation vtk image data format for +visualization directly in parallelized visualization software packages +like ParaView and VisIt. Note that if no time averaging is done, this +command can be used as a convenient way to simply output diffraction +intensities at a single snapshot. + +To produce output in the image data vtk format ghost data is added +outside the *Kmax* range assigned in the compute saed. The ghost data is +assigned a value of -1 and can be removed setting a minimum isovolume +of 0 within the vizualiziton software. SAED images can be created by +visualizing a spherical slice of the data that is centered at +R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda. + +The group specified within this command is ignored. However, note that +specified values may represent calculations performed by saed computes +which store their own "group" definitions. + +Fix saed/vtk is designed to work only with `compute_saed `_ +values, e.g. + +.. parsed-literal:: + + compute 3 top saed 0.0251 Al O + fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed + + +---------- + + +The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what +timesteps the input values will be used in order to contribute to the +average. The final averaged quantities are generated on timesteps +that are a multiple of *Nfreq*. The average is over *Nrepeat* +quantities, computed in the preceding portion of the simulation every +*Nevery* timesteps. *Nfreq* must be a multiple of *Nevery* and +*Nevery* must be non-zero even if *Nrepeat* is 1. +Also, the timesteps +contributing to the average value cannot overlap, +i.e. Nrepeat*Nevery can not exceed Nfreq. + +For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on +timesteps 90,92,94,96,98,100 will be used to compute the final average +on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on +timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time +averaging is done; values are simply generated on timesteps +100,200,etc. + + +---------- + + +The output for fix ave/time/saed is a file writen with the 3rd generation +vtk image data formatting. The filename assigned by the *file* keyword is +appended with _N.vtk where N is an index (0,1,2...) to account for multiple +diffraction intensity outputs. + +By default the header contains the following information (with example data): + +.. parsed-literal:: + + # vtk DataFile Version 3.0 c_SAED + Image data set + ASCII + DATASET STRUCTURED_POINTS + DIMENSIONS 337 219 209 + ASPECT_RATIO 0.00507953 0.00785161 0.00821458 + ORIGIN -0.853361 -0.855826 -0.854316 + POINT_DATA 15424827 + SCALARS intensity float + LOOKUP_TABLE default + ...data + +In this example, kspace is sampled across a 337 x 219 x 209 point mesh +where the mesh spacing is approximately 0.005, 0.007, and 0.008 +inv(length) units in the k1, k2, and k3 directions, respectively. +The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that +the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are +sampled in total. + + +---------- + + +Additional optional keywords also affect the operation of this fix. + +The *ave* keyword determines how the values produced every *Nfreq* +steps are averaged with values produced on previous steps that were +multiples of *Nfreq*, before they are accessed by another output +command or written to a file. + +If the *ave* setting is *one*, then the values produced on timesteps +that are multiples of *Nfreq* are independent of each other; they are +output as-is without further averaging. + +If the *ave* setting is *running*, then the values produced on +timesteps that are multiples of *Nfreq* are summed and averaged in a +cumulative sense before being output. Each output value is thus the +average of the value produced on that timestep with all preceding +values. This running average begins when the fix is defined; it can +only be restarted by deleting the fix via the :doc:`unfix ` +command, or by re-defining the fix by re-specifying it. + +If the *ave* setting is *window*, then the values produced on +timesteps that are multiples of *Nfreq* are summed and averaged within +a moving "window" of time, so that the last M values are used to +produce the output. E.g. if M = 3 and Nfreq = 1000, then the output +on step 10000 will be the average of the individual values on steps +8000,9000,10000. Outputs on early steps will average over less than M +values if they are not available. + +The *start* keyword specifies what timestep averaging will begin on. +The default is step 0. Often input values can be 0.0 at time 0, so +setting *start* to a larger value can avoid including a 0.0 in a +running or windowed average. + +The *file* keyword allows a filename to be specified. Every *Nfreq* +steps, the vector of saed intensity data is written to a new file using +the 3rd generation vtk format. The base of each file is assigned by +the *file* keyword and this string is appended with _N.vtk where N is +an index (0,1,2...) to account for situations with multiple diffraction +intensity outputs. + +The *overwrite* keyword will continuously overwrite the output file +with the latest output, so that it only contains one timestep worth of +output. This option can only be used with the *ave running* setting. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +The attributes for fix_saed_vtk must match the values assigned in the +associated :doc:`compute_saed ` command. + +Related commands +"""""""""""""""" + +:doc:`compute_saed ` + +Default +""""""" + +The option defaults are ave = one, start = 0, no file output. + + +---------- + + +.. _Coleman: + + + +**(Coleman)** Coleman, Spearot, Capolungo, MSMSE, 21, 055020 +(2013). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_setforce.txt b/doc/_sources/fix_setforce.txt new file mode 100644 index 0000000000..3eddd85502 --- /dev/null +++ b/doc/_sources/fix_setforce.txt @@ -0,0 +1,140 @@ +.. index:: fix setforce + +fix setforce command +==================== + +fix setforce/cuda command +========================= + +fix setforce/kk command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID setforce fx fy fz keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* setforce = style name of this fix command +* fx,fy,fz = force component values +* any of fx,fy,fz can be a variable (see below) +* zero or more keyword/value pairs may be appended to args +* keyword = *region* +.. parsed-literal:: + + *region* value = region-ID + region-ID = ID of region atoms must be in to have added force + + + +Examples +"""""""" + +.. parsed-literal:: + + fix freeze indenter setforce 0.0 0.0 0.0 + fix 2 edge setforce NULL 0.0 0.0 + fix 2 edge setforce NULL 0.0 v_oscillate + +Description +""""""""""" + +Set each component of force on each atom in the group to the specified +values fx,fy,fz. This erases all previously computed forces on the +atom, though additional fixes could add new forces. This command can +be used to freeze certain atoms in the simulation by zeroing their +force, either for running dynamics or performing an energy +minimization. For dynamics, this assumes their initial velocity is +also zero. + +Any of the fx,fy,fz values can be specified as NULL which means do not +alter the force component in that dimension. + +Any of the 3 quantities defining the force components can be specified +as an equal-style or atom-style :doc:`variable `, namely *fx*, +*fy*, *fz*. If the value is a variable, it should be specified as +v_name, where name is the variable name. In this case, the variable +will be evaluated each timestep, and its value used to determine the +force component. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent force field. + +Atom-style variables can specify the same formulas as equal-style +variables but can also include per-atom values, such as atom +coordinates. Thus it is easy to specify a spatially-dependent force +field with optional time-dependence as well. + +If the *region* keyword is used, the atom must also be in the +specified geometric :doc:`region ` in order to have force added +to it. + + +---------- + + +Styles with a *cuda* or *kk* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +The region keyword is also supported by Kokkos, but a Kokkos-enabled +region must be used. See the region :doc:`region ` command for more +information. + +These accelerated styles are part of the USER-CUDA or Kokkos package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global 3-vector of forces, which can be accessed +by various :ref:`output commands `. This is the +total force on the group of atoms before the forces on individual +atoms are changed by the fix. The vector values calculated by this +fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command, but you cannot set +forces to any value besides zero when performing a minimization. Use +the :doc:`fix addforce ` command if you want to apply a +non-zero force to atoms during a minimization. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix addforce `, :doc:`fix aveforce ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_shake.txt b/doc/_sources/fix_shake.txt new file mode 100644 index 0000000000..5dba355484 --- /dev/null +++ b/doc/_sources/fix_shake.txt @@ -0,0 +1,262 @@ +.. index:: fix shake + +fix shake command +================= + +fix shake/cuda command +====================== + +fix rattle command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style tol iter N constraint values ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = shake or rattle = style name of this fix command +* tol = accuracy tolerance of SHAKE solution +* iter = max # of iterations in each SHAKE solution +* N = print SHAKE statistics every this many timesteps (0 = never) +* one or more constraint/value pairs are appended +* constraint = *b* or *a* or *t* or *m* +.. parsed-literal:: + + *b* values = one or more bond types + *a* values = one or more angle types + *t* values = one or more atom types + *m* value = one or more mass values + +* zero or more keyword/value pairs may be appended +* keyword = *mol* +.. parsed-literal:: + + *mol* value = template-ID + template-ID = ID of molecule template specified in a separate :doc:`molecule ` command + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 sub shake 0.0001 20 10 b 4 19 a 3 5 2 + fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 + fix 1 sub shake 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol + fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 + fix 1 sub rattle 0.0001 20 10 t 5 6 m 1.0 a 31 mol myMol + +Description +""""""""""" + +Apply bond and angle constraints to specified bonds and angles in the +simulation by either the SHAKE or RATTLE algorithms. This typically +enables a longer timestep. + +**SHAKE vs RATTLE:** + +The SHAKE algorithm was invented for schemes such as standard Verlet +timesteppnig, where only the coordinates are integrated and the +velocities are approximated as finite differences to the trajectories +(:ref:`Ryckaert et al. (1977) `). If the velocities are +integrated explicitly, as with velocity Verlet which is what LAMMPS +uses as an integration method, a second set of constraining forces is +required in order to eliminate velocity components along the bonds +(:ref:`Andersen (1983) `). + +In order to formulate individual constraints for SHAKE and RATTLE, +focus on a single molecule whose bonds are constrained. Let Ri and Vi +be the position and velocity of atom *i* at time *n*, for +*i*=1,...,*N*, where *N* is the number of sites of our reference +molecule. The distance vector between sites *i* and *j* is given by + +.. image:: Eqs/fix_rattle_rij.jpg + :align: center + +The constraints can then be formulated as + +.. image:: Eqs/fix_rattle_constraints.jpg + :align: center + +The SHAKE algorithm satisfies the first condition, i.e. the sites at +time *n+1* will have the desired separations Dij immediately after the +coordinates are integrated. If we also enforce the second condition, +the velocity components along the bonds will vanish. RATTLE satisfies +both conditions. As implemented in LAMMPS, fix rattle uses fix shake +for satisfying the coordinate constraints. Therefore the settings and +optional keywords are the same for both fixes, and all the information +below about SHAKE is also relevant for RATTLE. + +**SHAKE:** + +Each timestep the specified bonds and angles are reset to their +equilibrium lengths and angular values via the SHAKE algorithm +(:ref:`Ryckaert et al. (1977) `). This is done by applying an +additional constraint force so that the new positions preserve the +desired atom separations. The equations for the additional force are +solved via an iterative method that typically converges to an accurate +solution in a few iterations. The desired tolerance (e.g. 1.0e-4 = 1 +part in 10000) and maximum # of iterations are specified as arguments. +Setting the N argument will print statistics to the screen and log +file about regarding the lengths of bonds and angles that are being +constrained. Small delta values mean SHAKE is doing a good job. + +In LAMMPS, only small clusters of atoms can be constrained. This is +so the constraint calculation for a cluster can be performed by a +single processor, to enable good parallel performance. A cluster is +defined as a central atom connected to others in the cluster by +constrained bonds. LAMMPS allows for the following kinds of clusters +to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or +one central atom bonded to 2 others and the angle between the 3 atoms +also constrained. This means water molecules or CH2 or CH3 groups may +be constrained, but not all the C-C backbone bonds of a long polymer +chain. + +The *b* constraint lists bond types that will be constrained. The *t* +constraint lists atom types. All bonds connected to an atom of the +specified type will be constrained. The *m* constraint lists atom +masses. All bonds connected to atoms of the specified masses will be +constrained (within a fudge factor of MASSDELTA specified in +fix_shake.cpp). The *a* constraint lists angle types. If both bonds +in the angle are constrained then the angle will also be constrained +if its type is in the list. + +For all constraints, a particular bond is only constrained if both +atoms in the bond are in the group specified with the SHAKE fix. + +The degrees-of-freedom removed by SHAKE bonds and angles are accounted +for in temperature and pressure computations. Similarly, the SHAKE +contribution to the pressure of the system (virial) is also accounted +for. + +.. note:: + + This command works by using the current forces on atoms to + caculate an additional constraint force which when added will leave + the atoms in positions that satisfy the SHAKE constraints (e.g. bond + length) after the next time integration step. If you define fixes + (e.g. :doc:`fix efield `) that add additional force to the + atoms after fix shake operates, then this fix will not take them into + account and the time integration will typically not satisfy the SHAKE + constraints. The solution for this is to make sure that fix shake is + defined in your input script after any other fixes which add or change + forces (to atoms that fix shake operates on). + + +---------- + + +The *mol* keyword should be used when other commands, such as :doc:`fix deposit ` or :doc:`fix pour `, add molecules +on-the-fly during a simulation, and you wish to contrain the new +molecules via SHAKE. You specify a *template-ID* previously defined +using the :doc:`molecule ` command, which reads a file that +defines the molecule. You must use the same *template-ID* that the +command adding molecules uses. The coordinates, atom types, special +bond restrictions, and SHAKE info can be specified in the molecule +file. See the :doc:`molecule ` command for details. The only +settings required to be in this file (by this command) are the SHAKE +info of atoms in the molecule. + + +---------- + + +Styles with a *cuda* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +These accelerated styles are part of the USER-CUDA package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +**RATTLE:** + +The velocity constraints lead to a linear system of equations which +can be solved analytically. The implementation of the algorithm in +LAMMPS closely follows (:ref:`Andersen (1983) `). + +.. note:: + + The fix rattle command modifies forces and velocities and thus + should be defined after all other integration fixes in your input + script. If you define other fixes that modify velocities or forces + after fix rattle operates, then fix rattle will not take them into + account and the overall time integration will typically not satisfy + the RATTLE constraints. You can check whether the constraints work + correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp + to 1 and recompiling LAMMPS. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to these fixes. No global or per-atom quantities are +stored by these fixes for access by various :ref:`output commands `. No parameter of these fixes +can be used with the *start/stop* keywords of the :doc:`run ` +command. These fixes are not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +These fixes are part of the RIGID package. They are only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +For computational efficiency, there can only be one shake or rattle +fix defined in a simulation. + +If you use a tolerance that is too large or a max-iteration count that +is too small, the constraints will not be enforced very strongly, +which can lead to poor energy conservation. You can test for this in +your system by running a constant NVE simulation with a particular set +of SHAKE parameters and monitoring the energy versus time. + +SHAKE or RATTLE should not be used to contrain an angle at 180 degrees +(e.g. linear CO2 molecule). This causes numeric difficulties. + +**Related commands:** none + +**Default:** none + + +---------- + + +.. _Ryckaert: + + + +**(Ryckaert)** J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, +J of Comp Phys, 23, 327-341 (1977). + +.. _Andersen: + + + +**(Andersen)** H. Andersen, J of Comp Phys, 52, 24-34 (1983). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_shardlow.txt b/doc/_sources/fix_shardlow.txt new file mode 100644 index 0000000000..560aaf5fa4 --- /dev/null +++ b/doc/_sources/fix_shardlow.txt @@ -0,0 +1,115 @@ +.. index:: fix shardlow + +fix shardlow command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID shardlow + +* ID, group-ID are documented in :doc:`fix ` command +* shardlow = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all shardlow + +Description +""""""""""" + +Specifies that the Shardlow splitting algorithm (SSA) is to be used to +integrate the DPD equations of motion. The SSA splits the integration +into a stochastic and deterministic integration step. The fix +*shardlow* performs the stochastic integration step and must be used +in conjunction with a deterministic integrator (e.g. :doc:`fix nve ` or :doc:`fix nph `). The stochastic +integration of the dissipative and random forces is performed prior to +the deterministic integration of the conservative force. Further +details regarding the method are provided in :ref:`(Lisal) ` and +:ref:`(Larentzos) `. + +The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt ` or :doc:`pair_style dpd/fdt/energy ` command to properly initialize the +fluctuation-dissipation theorem parameter(s) sigma (and kappa, if +necessary). + +Note that numerous variants of DPD can be specified by choosing an +appropriate combination of the integrator and :doc:`pair_style dpd/fdt ` command. DPD under isothermal conditions can +be specified by using fix *shardlow*, fix *nve* and pair_style +*dpd/fdt*. DPD under isoenergetic conditions can be specified by +using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*. DPD +under isobaric conditions can be specified by using fix shardlow, fix +*nph* and pair_style *dpd/fdt*. DPD under isoenthalpic conditions can +be specified by using fix shardlow, fix *nph* and pair_style +*dpd/fdt/energy*. Examples of each DPD variant are provided in the +examples/USER/dpd directory. + + +---------- + + +Restrictions +"""""""""""" + + +This fix is only available if LAMMPS is built with the USER-DPD +package. See the :ref:`Making LAMMPS ` section +for more info. + +This fix is currently limited to orthogonal simulation cell +geometries. + +This fix must be used with an additional fix that specifies time +integration, e.g. :doc:`fix nve ` or :doc:`fix nph `. + +The Shardlow splitting algorithm requires the sizes of the sub-domain +lengths to be larger than twice the cutoff+skin. Generally, the +domain decomposition is dependant on the number of processors +requested. + +Related commands +"""""""""""""""" + +:doc:`pair_style dpd/fdt `, :doc:`fix eos/cv ` + +**Default:** none + + +---------- + + +.. _Lisal: + + + +**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative +particle dynamics as isothermal, isobaric, isoenergetic, and +isoenthalpic conditions using Shardlow-like splitting algorithms.", +J. Chem. Phys., 135, 204105 (2011). + +.. _Larentzos: + + + +**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and +W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic +Dissipative Particle Dynamics Using Shardlow-Like Splitting +Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014). + +.. _Larentzos: + + + +**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and +W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative +Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research +Laboratory, Aberdeen Proving Ground, MD (2014). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_smd.txt b/doc/_sources/fix_smd.txt new file mode 100644 index 0000000000..62d215a648 --- /dev/null +++ b/doc/_sources/fix_smd.txt @@ -0,0 +1,168 @@ +.. index:: fix smd + +fix smd command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID smd type values keyword values + +* ID, group-ID are documented in :doc:`fix ` command +* smd = style name of this fix command +* mode = *cvel* or *cfor* to select constant velocity or constant force SMD +.. parsed-literal:: + + *cvel* values = K vel + K = spring constant (force/distance units) + vel = velocity of pulling (distance/time units) + *cfor* values = force + force = pulling force (force units) + +* keyword = *tether* or *couple* +.. parsed-literal:: + + *tether* values = x y z R0 + x,y,z = point to which spring is tethered + R0 = distance of end of spring from tether point (distance units) + *couple* values = group-ID2 x y z R0 + group-ID2 = 2nd group to couple to fix group with a spring + x,y,z = direction of spring, automatically computed with 'auto' + R0 = distance of end of spring (distance units) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0 + fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0 + fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0 + fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0 + +Description +""""""""""" + +This fix implements several options of steered MD (SMD) as reviewed in +:ref:`(Izrailev) `, which allows to induce conformational changes +in systems and to compute the potential of mean force (PMF) along the +assumed reaction coordinate :ref:`(Park) ` based on Jarzynski's +equality :ref:`(Jarzynski) `. This fix borrows a lot from :doc:`fix spring ` and :doc:`fix setforce `. + +You can apply a moving spring force to a group of atoms (*tether* +style) or between two groups of atoms (*couple* style). The spring +can then be used in either constant velocity (*cvel*) mode or in +constant force (*cfor*) mode to induce transitions in your systems. +When running in *tether* style, you may need some way to fix some +other part of the system (e.g. via :doc:`fix spring/self `) + +The *tether* style attaches a spring between a point at a distance of +R0 away from a fixed point *x,y,z* and the center of mass of the fix +group of atoms. A restoring force of magnitude K (R - R0) Mi / M is +applied to each atom in the group where *K* is the spring constant, Mi +is the mass of the atom, and M is the total mass of all atoms in the +group. Note that *K* thus represents the total force on the group of +atoms, not a per-atom force. + +In *cvel* mode the distance R is incremented or decremented +monotonously according to the pulling (or pushing) velocity. +In *cfor* mode a constant force is added and the actual distance +in direction of the spring is recorded. + +The *couple* style links two groups of atoms together. The first +group is the fix group; the second is specified by group-ID2. The +groups are coupled together by a spring that is at equilibrium when +the two groups are displaced by a vector in direction *x,y,z* with +respect to each other and at a distance R0 from that displacement. +Note that *x,y,z* only provides a direction and will be internally +normalized. But since it represents the *absolute* displacement of +group-ID2 relative to the fix group, (1,1,0) is a different spring +than (-1,-1,0). For each vector component, the displacement can be +described with the *auto* parameter. In this case the direction is +recomputed in every step, which can be useful for steering a local +process where the whole object undergoes some other change. When the +relative positions and distance between the two groups are not in +equilibrium, the same spring force described above is applied to atoms +in each of the two groups. + +For both the *tether* and *couple* styles, any of the x,y,z values can +be specified as NULL which means do not include that dimension in the +distance calculation or force application. + +For constant velocity pulling (*cvel* mode), the running integral +over the pulling force in direction of the spring is recorded and +can then later be used to compute the potential of mean force (PMF) +by averaging over multiple independent trajectories along the same +pulling path. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +The fix stores the direction of the spring, current pulling target +distance and the running PMF to :doc:`binary restart files `. +See the :doc:`read_restart ` command for info on how to +re-specify a fix in an input script that reads a restart file, so that +the operation of the fix continues in an uninterrupted fashion. + +None of the :doc:`fix_modify ` options are relevant to this +fix. + +This fix computes a vector list of 7 quantities, which can be accessed +by various :ref:`output commands `. The +quantities in the vector are in this order: the x-, y-, and +z-component of the pulling force, the total force in direction of the +pull, the equilibrium distance of the spring, the distance between the +two reference points, and finally the accumulated PMF (the sum of +pulling forces times displacement). + +The force is the total force on the group of atoms by the spring. In +the case of the *couple* style, it is the force on the fix group +(group-ID) or the negative of the force on the 2nd group (group-ID2). +The vector values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix drag `, :doc:`fix spring `, +:doc:`fix spring/self `, +:doc:`fix spring/rg ` + +**Default:** none + + +---------- + + +.. _Israilev: + + + +**(Izrailev)** Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, +Wriggers, Schulten. Computational Molecular Dynamics: Challenges, +Methods, Ideas, volume 4 of Lecture Notes in Computational Science and +Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998. + +**(Park)** +Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004) + +**(Jarzynski)** +Jarzynski, Phys. Rev. Lett. 78, 2690 (1997) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_smd_adjust_dt.txt b/doc/_sources/fix_smd_adjust_dt.txt new file mode 100644 index 0000000000..0bcb34a4b8 --- /dev/null +++ b/doc/_sources/fix_smd_adjust_dt.txt @@ -0,0 +1,68 @@ +.. index:: fix smd/adjust_dt + +fix smd/adjust_dt command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID smd/adjust_dt arg + +* ID, group-ID are documented in :doc:`fix ` command +* smd/adjust_dt = style name of this fix command +* arg = *s_fact* +.. parsed-literal:: + + *s_fact* = safety factor + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all smd/adjust_dt 0.1 + +Description +""""""""""" + +The fix calculates a new stable time increment for use with the SMD time integrators. + +The stable time increment is based on multiple conditions. For the SPH pair styles, a +CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of +sound cannot propagate further than a typical spacing between particles within a single time step to ensure +no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a +stable maximum time step. + +This fix inquires the minimum stable time increment across all particles contained in the group for which this +fix is defined. An additional safety factor *s_fact* is applied to the time increment. + +See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Currently, no part of USER-SMD supports restarting nor minimization. + +Restrictions +"""""""""""" + + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` +section for more info. + +Related commands +"""""""""""""""" + +:doc:`smd/tlsph_dt ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_smd_integrate_tlsph.txt b/doc/_sources/fix_smd_integrate_tlsph.txt new file mode 100644 index 0000000000..56f5382444 --- /dev/null +++ b/doc/_sources/fix_smd_integrate_tlsph.txt @@ -0,0 +1,66 @@ +.. index:: fix smd/integrate_tlsph + +fix smd/integrate_tlsph command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID smd/integrate_tlsph keyword values + +* ID, group-ID are documented in :doc:`fix ` command +* smd/integrate_tlsph = style name of this fix command +* zero or more keyword/value pairs may be appended + +* keyword = *limit_velocity* +.. parsed-literal:: + + *limit_velocity* value = max_vel + max_vel = maximum allowed velocity + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all smd/integrate_tlsph + fix 1 all smd/integrate_tlsph limit_velocity 1000 + +Description +""""""""""" + +The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style. + +See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. + +The *limit_velocity* keyword will control the velocity, scaling the norm of +the velocity vector to max_vel in case it exceeds this velocity limit. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. + +Restrictions +"""""""""""" + + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` +section for more info. + +Related commands +"""""""""""""""" + +:doc:`smd/integrate_ulsph ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_smd_integrate_ulsph.txt b/doc/_sources/fix_smd_integrate_ulsph.txt new file mode 100644 index 0000000000..979422706d --- /dev/null +++ b/doc/_sources/fix_smd_integrate_ulsph.txt @@ -0,0 +1,71 @@ +.. index:: fix smd/integrate_ulsph + +fix smd/integrate_ulsph command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID smd/integrate_ulsph keyword + +* ID, group-ID are documented in :doc:`fix ` command +* smd/integrate_ulsph = style name of this fix command +* zero or more keyword/value pairs may be appended + +keyword = adjust_radius or limit_velocity + +adjust_radius values = adjust_radius_factor min_nn max_nn + adjust_radius_factor = factor which scale the smooth/kernel radius + min_nn = minimum number of neighbors + max_nn = maximum number of neighbors +limit_velocity values = max_velocity + max_velocity = maximum allowed velocity. + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 + +.. parsed-literal:: + + fix 1 all smd/integrate_ulsph limit_velocity 1000 + +Description +""""""""""" + +The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style. +See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. + +The *adjust_radius* keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains +within the interval *min_nn* to *max_nn*. The parameter *adjust_radius_factor* determines the amount of adjustment per timestep. Typical values are +*adjust_radius_factor*=1.02, *min_nn*=15, and *max_nn*=20. + +The *limit_velocity* keyword will control the velocity, scaling the norm of +the velocity vector to max_vel in case it exceeds this velocity limit. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. + +Restrictions +"""""""""""" + + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` +section for more info. + +Related commands +"""""""""""""""" + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_smd_move_triangulated_surface.txt b/doc/_sources/fix_smd_move_triangulated_surface.txt new file mode 100644 index 0000000000..411b7c1d6b --- /dev/null +++ b/doc/_sources/fix_smd_move_triangulated_surface.txt @@ -0,0 +1,86 @@ +.. index:: fix smd/move_tri_surf + +fix smd/move_tri_surf command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID smd/move_tri_surf keyword + +* ID, group-ID are documented in :doc:`fix ` command +* smd/move_tri_surf keyword = style name of this fix command +* keyword = **LINEAR* or **WIGGLE* or **ROTATE* +.. parsed-literal:: + + **LINEAR* args = Vx Vy Vz + Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL + **WIGGLE* args = Vx Vy Vz max_travel + vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL + max_travel = wiggle amplitude + **ROTATE* args = Px Py Pz Rx Ry Rz period + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + period = period of rotation (time units) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 tool smd/move_tri_surf *LINEAR 20 20 10 + fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10 + fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 + +Description +""""""""""" + +This fix applies only to rigid surfaces read from .STL files via fix :doc:`smd/wall_surface ` . +It updates position and velocity for the particles in the group each timestep without regard to forces on the particles. +The rigid surfaces can thus be moved along simple trajectories during the simulation. + +The **LINEAR* style moves particles with the specified constant velocity +vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle +to V = (Vx,Vy,Vz). + +The **WIGGLE* style moves particles in an oscillatory fashion. +Particles are moved along (vx, vy, vz) with constant velocity until a +displacement of max_travel is reached. Then, the velocity vector is +reversed. This process is repeated. + +The **ROTATE* style rotates particles around a rotation axis R = (Rx,Ry,Rz) that +goes through a point P = (Px,Py,Pz). The period of the rotation is also +specified. This style also sets the velocity of each particle to (omega cross +Rperp) where omega is its angular velocity around the rotation axis and +Rperp is a perpendicular vector from the rotation axis to the particle. + +See `this PDF guide `_ to using Smooth Mach Dynamics in LAMMPS. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. + +Restrictions +"""""""""""" + + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` +section for more info. + +Related commands +"""""""""""""""" + +:doc:`smd/triangle_mesh_vertices `, :doc:`smd/wall_surface ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_smd_setvel.txt b/doc/_sources/fix_smd_setvel.txt new file mode 100644 index 0000000000..702e63c308 --- /dev/null +++ b/doc/_sources/fix_smd_setvel.txt @@ -0,0 +1,99 @@ +.. index:: fix smd/setvel + +fix smd/setvel command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID smd/setvel vx vy vz keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* smd/setvel = style name of this fix command +* vx,vy,vz = velocity component values +* any of vx,vy,vz can be a variable (see below) +* zero or more keyword/value pairs may be appended to args +* keyword = *region* +.. parsed-literal:: + + *region* value = region-ID + region-ID = ID of region particles must be in to have their velocities set + + + +Examples +"""""""" + +.. parsed-literal:: + + fix top_velocity top_group setvel 1.0 0.0 0.0 + +Description +""""""""""" + +Set each component of velocity on each particle in the group to the specified +values vx,vy,vz, regardless of the forces acting on the particle. This command can +be used to impose velocity boundary conditions. + +Any of the vx,vy,vz values can be specified as NULL which means do not +alter the velocity component in that dimension. + +This fix is indented to be used together with a time integration fix. + +Any of the 3 quantities defining the velocity components can be specified +as an equal-style or atom-style :doc:`variable `, namely *vx*, +*vy*, *vz*. If the value is a variable, it should be specified as +v_name, where name is the variable name. In this case, the variable +will be evaluated each timestep, and its value used to determine the +force component. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent velocity field. + +Atom-style variables can specify the same formulas as equal-style +variables but can also include per-atom values, such as atom +coordinates. Thus it is easy to specify a spatially-dependent velocity +field with optional time-dependence as well. + +If the *region* keyword is used, the particle must also be in the +specified geometric :doc:`region ` in order to have its velocity set by this command. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Currently, no part of USER-SMD supports restarting nor minimization +None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global 3-vector of forces, which can be accessed +by various :ref:`output commands `. This is the +total force on the group of atoms. The vector values calculated by this +fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +Restrictions +"""""""""""" + + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` +section for more info. + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_smd_tlsph_reference_configuration.txt b/doc/_sources/fix_smd_tlsph_reference_configuration.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/doc/_sources/fix_smd_wall_surface.txt b/doc/_sources/fix_smd_wall_surface.txt new file mode 100644 index 0000000000..05a742b256 --- /dev/null +++ b/doc/_sources/fix_smd_wall_surface.txt @@ -0,0 +1,71 @@ +.. index:: fix smd/wall_surface + +fix smd/wall_surface command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID smd/wall_surface arg type mol-ID + +* ID, group-ID are documented in :doc:`fix ` command +* smd/wall_surface = style name of this fix command +* arg = *file* +.. parsed-literal:: + + *file* = file name of a triangular mesh in stl format + +* type = particle type to be given to the new particles created by this fix +* mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) + + +Examples +"""""""" + +.. parsed-literal:: + + fix stl_surf all smd/wall_surface tool.stl 2 65535 + +Description +""""""""""" + +This fix creates reads a traingulated surface from a file in .STL format. +For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions. +The radius of the new particle is that of the minimum circle which encompasses the triangle vertices. + +The triangulated surface can be used as a complex rigid wall via the :doc:`smd/tri_surface ` pair style. +It is possible to move the triangulated surface via the :doc:`smd/move_tri_surf ` fix style. + +Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles +in the system. See the "funnel_flow" example in the USER-SMD examples directory. + +See `this PDF guide `_ to use Smooth Mach Dynamics in LAMMPS. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs. + +Restrictions +"""""""""""" + + +This fix is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` +section for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535. + +Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file. + +Related commands +"""""""""""""""" + +:doc:`smd/triangle_mesh_vertices `, :doc:`smd/move_tri_surf `, :doc:`smd/tri_surface ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_spring.txt b/doc/_sources/fix_spring.txt new file mode 100644 index 0000000000..c6ab8d71a0 --- /dev/null +++ b/doc/_sources/fix_spring.txt @@ -0,0 +1,159 @@ +.. index:: fix spring + +fix spring command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID spring keyword values + +* ID, group-ID are documented in :doc:`fix ` command +* spring = style name of this fix command +* keyword = *tether* or *couple* +.. parsed-literal:: + + *tether* values = K x y z R0 + K = spring constant (force/distance units) + x,y,z = point to which spring is tethered + R0 = equilibrium distance from tether point (distance units) + *couple* values = group-ID2 K x y z R0 + group-ID2 = 2nd group to couple to fix group with a spring + K = spring constant (force/distance units) + x,y,z = direction of spring + R0 = equilibrium distance of spring (distance units) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix pull ligand spring tether 50.0 0.0 0.0 0.0 0.0 + fix pull ligand spring tether 50.0 0.0 0.0 0.0 5.0 + fix pull ligand spring tether 50.0 NULL NULL 2.0 3.0 + fix 5 bilayer1 spring couple bilayer2 100.0 NULL NULL 10.0 0.0 + fix longitudinal pore spring couple ion 100.0 NULL NULL -20.0 0.0 + fix radial pore spring couple ion 100.0 0.0 0.0 NULL 5.0 + +Description +""""""""""" + +Apply a spring force to a group of atoms or between two groups of +atoms. This is useful for applying an umbrella force to a small +molecule or lightly tethering a large group of atoms (e.g. all the +solvent or a large molecule) to the center of the simulation box so +that it doesn't wander away over the course of a long simulation. It +can also be used to hold the centers of mass of two groups of atoms at +a given distance or orientation with respect to each other. + +The *tether* style attaches a spring between a fixed point *x,y,z* and +the center of mass of the fix group of atoms. The equilibrium +position of the spring is R0. At each timestep the distance R from +the center of mass of the group of atoms to the tethering point is +computed, taking account of wrap-around in a periodic simulation box. +A restoring force of magnitude K (R - R0) Mi / M is applied to each +atom in the group where *K* is the spring constant, Mi is the mass of +the atom, and M is the total mass of all atoms in the group. Note +that *K* thus represents the total force on the group of atoms, not a +per-atom force. + +The *couple* style links two groups of atoms together. The first +group is the fix group; the second is specified by group-ID2. The +groups are coupled together by a spring that is at equilibrium when +the two groups are displaced by a vector *x,y,z* with respect to each +other and at a distance R0 from that displacement. Note that *x,y,z* +is the equilibrium displacement of group-ID2 relative to the fix +group. Thus (1,1,0) is a different spring than (-1,-1,0). When the +relative positions and distance between the two groups are not in +equilibrium, the same spring force described above is applied to atoms +in each of the two groups. + +For both the *tether* and *couple* styles, any of the x,y,z values can +be specified as NULL which means do not include that dimension in the +distance calculation or force application. + +The first example above pulls the ligand towards the point (0,0,0). +The second example holds the ligand near the surface of a sphere of +radius 5 around the point (0,0,0). The third example holds the ligand +a distance 3 away from the z=2 plane (on either side). + +The fourth example holds 2 bilayers a distance 10 apart in z. For the +last two examples, imagine a pore (a slab of atoms with a cylindrical +hole cut out) oriented with the pore axis along z, and an ion moving +within the pore. The fifth example holds the ion a distance of -20 +below the z = 0 center plane of the pore (umbrella sampling). The +last example holds the ion a distance 5 away from the pore axis +(assuming the center-of-mass of the pore in x,y is the pore axis). + +.. note:: + + The center of mass of a group of atoms is calculated in + "unwrapped" coordinates using atom image flags, which means that the + group can straddle a periodic boundary. See the :doc:`dump ` doc + page for a discussion of unwrapped coordinates. It also means that a + spring connecting two groups or a group and the tether point can cross + a periodic boundary and its length be calculated correctly. One + exception is for rigid bodies, which should not be used with the fix + spring command, if the rigid body will cross a periodic boundary. + This is because image flags for rigid bodies are used in a different + way, as explained on the :doc:`fix rigid ` doc page. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy stored in the spring to the system's potential +energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +spring energy = 0.5 * K * r^2. + +This fix also computes global 4-vector which can be accessed by +various :ref:`output commands `. The first 3 +quantities in the vector are xyz components of the total force added +to the group of atoms by the spring. In the case of the *couple* +style, it is the force on the fix group (group-ID) or the negative of +the force on the 2nd group (group-ID2). The 4th quantity in the +vector is the magnitude of the force added by the spring, as a +positive value if (r-R0) > 0 and a negative value if (r-R0) < 0. This +sign convention can be useful when using the spring force to compute a +potential of mean force (PMF). + +The scalar and vector values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +.. note:: + + If you want the spring energy to be included in the total + potential energy of the system (the quantity being minimized), you + MUST enable the :doc:`fix_modify ` *energy* option for this + fix. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix drag `, :doc:`fix spring/self `, +:doc:`fix spring/rg `, :doc:`fix smd ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_spring_rg.txt b/doc/_sources/fix_spring_rg.txt new file mode 100644 index 0000000000..92ffe8aa82 --- /dev/null +++ b/doc/_sources/fix_spring_rg.txt @@ -0,0 +1,79 @@ +.. index:: fix spring/rg + +fix spring/rg command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID spring/rg K RG0 + +* ID, group-ID are documented in :doc:`fix ` command +* spring/rg = style name of this fix command +* K = harmonic force constant (force/distance units) +* RG0 = target radius of gyration to constrain to (distance units) + +.. parsed-literal:: + + if RG0 = NULL, use the current RG as the target value + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 protein spring/rg 5.0 10.0 + fix 2 micelle spring/rg 5.0 NULL + +Description +""""""""""" + +Apply a harmonic restraining force to atoms in the group to affect +their central moment about the center of mass (radius of gyration). +This fix is useful to encourage a protein or polymer to fold/unfold +and also when sampling along the radius of gyration as a reaction +coordinate (i.e. for protein folding). + +The radius of gyration is defined as RG in the first formula. The +energy of the constraint and associated force on each atom is given by +the second and third formulas, when the group is at a different RG +than the target value RG0. + +.. image:: Eqs/fix_spring_rg.jpg + :align: center + +The (xi - center-of-mass) term is computed taking into account +periodic boundary conditions, m_i is the mass of the atom, and M is +the mass of the entire group. Note that K is thus a force constant +for the aggregate force on the group of atoms, not a per-atom force. + +If RG0 is specified as NULL, then the RG of the group is computed at +the time the fix is specified, and that value is used as the target. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix spring `, :doc:`fix spring/self ` +:doc:`fix drag `, :doc:`fix smd ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_spring_self.txt b/doc/_sources/fix_spring_self.txt new file mode 100644 index 0000000000..6eaebfa6c8 --- /dev/null +++ b/doc/_sources/fix_spring_self.txt @@ -0,0 +1,91 @@ +.. index:: fix spring/self + +fix spring/self command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID spring/self K dir + +* ID, group-ID are documented in :doc:`fix ` command +* spring/self = style name of this fix command +* K = spring constant (force/distance units) +* dir = xyz, xy, xz, yz, x, y, or z (optional, default: xyz) + +Examples +"""""""" + +.. parsed-literal:: + + fix tether boundary-atoms spring/self 10.0 + fix zrest move spring/self 10.0 z + +Description +""""""""""" + +Apply a spring force independently to each atom in the group to tether +it to its initial position. The initial position for each atom is its +location at the time the fix command was issued. At each timestep, +the magnitude of the force on each atom is -Kr, where r is the +displacement of the atom from its current position to its initial +position. The distance r correctly takes into account any crossings +of periodic boundary by the atom since it was in its intitial +position. + +With the (optional) dir flag, one can select in which direction the +spring force is applied. By default, the restraint is applied in all +directions, but it can be limited to the xy-, xz-, yz-plane and the +x-, y-, or z-direction, thus restraining the atoms to a line or a +plane, respectively. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the original coordinates of tethered atoms to :doc:`binary restart files `, so that the spring effect will be the +same in a restarted simulation. See the +:doc:`read_restart ` command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy stored in the per-atom springs to the system's +potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is an +energy which is the sum of the spring energy for each atom, where the +per-atom energy is 0.5 * K * r^2. The scalar value calculated by this +fix is "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +.. note:: + + If you want the per-atom spring energy to be included in the + total potential energy of the system (the quantity being minimized), + you MUST enable the :doc:`fix_modify ` *energy* option for + this fix. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix drag `, :doc:`fix spring `, +:doc:`fix smd `, :doc:`fix spring/rg ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_srd.txt b/doc/_sources/fix_srd.txt new file mode 100644 index 0000000000..b8d97f6e51 --- /dev/null +++ b/doc/_sources/fix_srd.txt @@ -0,0 +1,429 @@ +.. index:: fix srd + +fix srd command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID srd N groupbig-ID Tsrd hgrid seed keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* srd = style name of this fix command +* N = reset SRD particle velocities every this many timesteps +* groupbig-ID = ID of group of large particles that SRDs interact with +* Tsrd = temperature of SRD particles (temperature units) +* hgrid = grid spacing for SRD grouping (distance units) +* seed = random # seed (positive integer) + +* zero or more keyword/value pairs may be appended +* keyword = *lamda* or *collision* or *overlap* or *inside* or *exact* or *radius* or *bounce* or *search* or *cubic* or *shift* or *tstat* or *rescale* +.. parsed-literal:: + + *lamda* value = mean free path of SRD particles (distance units) + *collision* value = *noslip* or *slip* = collision model + *overlap* value = *yes* or *no* = whether big particles may overlap + *inside* value = *error* or *warn* or *ignore* = how SRD particles which end up inside a big particle are treated + *exact* value = *yes* or *no* + *radius* value = rfactor = scale collision radius by this factor + *bounce* value = Nbounce = max # of collisions an SRD particle can undergo in one timestep + *search* value = sgrid = grid spacing for collision partner searching (distance units) + *cubic* values = style tolerance + style = *error* or *warn* + tolerance = fractional difference allowed (0 <= tol <= 1) + *shift* values = flag shiftseed + flag = *yes* or *no* or *possible* = SRD bin shifting for better statistics + *yes* = perform bin shifting each time SRD velocities are rescaled + *no* = no shifting + *possible* = shift depending on mean free path and bin size + shiftseed = random # seed (positive integer) + *tstat* value = *yes* or *no* = thermostat SRD particles or not + *rescale* value = *yes* or *no* or *rotate* or *collide* = rescaling of SRD velocities + *yes* = rescale during velocity rotation and collisions + *no* = no rescaling + *rotate* = rescale during velocity rotation, but not collisions + *collide* = rescale during collisions, but not velocity rotation + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 srd srd 10 big 1.0 0.25 482984 + fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5 + +Description +""""""""""" + +Treat a group of partilces as stochastic rotation dynamics (SRD) +particles that serve as a background solvent when interacting with big +(colloidal) particles in groupbig-ID. The SRD formalism is described +in :ref:`(Hecht) `. The key idea behind using SRD particles as a +cheap coarse-grained solvent is that SRD particles do not interact +with each other, but only with the solute particles, which in LAMMPS +can be spheroids, ellipsoids, or line segments, or triangles, or rigid +bodies containing multiple spherioids or ellipsoids or line segments +or triangles. The collision and rotation properties of the model +imbue the SRD particles with fluid-like properties, including an +effective viscosity. Thus simulations with large solute particles can +be run more quickly, to measure solute propoerties like diffusivity +and viscosity in a background fluid. The usual LAMMPS fixes for such +simulations, such as :doc:`fix deform `, :doc:`fix viscosity `, and :doc:`fix nvt/sllod `, +can be used in conjunction with the SRD model. + +For more details on how the SRD model is implemented in LAMMPS, :ref:`this paper ` describes the implementation and usage of pure SRD +fluids. :ref:`This paper `, which is nearly complete, describes +the implementation and usage of mixture systems (solute particles in +an SRD fluid). See the examples/srd directory for sample input +scripts using SRD particles in both settings. + +This fix does 2 things: + +(1) It advects the SRD particles, performing collisions between SRD +and big particles or walls every timestep, imparting force and torque +to the big particles. Collisions also change the position and +velocity of SRD particles. + +(2) It resets the velocity distribution of SRD particles via random +rotations every N timesteps. + +SRD particles have a mass, temperature, characteristic timestep +dt_SRD, and mean free path between collisions (lamda). The +fundamental equation relating these 4 quantities is + +.. parsed-literal:: + + lamda = dt_SRD * sqrt(Kboltz * Tsrd / mass) + +The mass of SRD particles is set by the :doc:`mass ` command +elsewhere in the input script. The SRD timestep dt_SRD is N times the +step dt defined by the :doc:`timestep ` command. Big +particles move in the normal way via a time integration :doc:`fix ` +with a short timestep dt. SRD particles advect with a large timestep +dt_SRD >= dt. + +If the *lamda* keyword is not specified, the the SRD temperature +*Tsrd* is used in the above formula to compute lamda. If the *lamda* +keyword is specified, then the *Tsrd* setting is ignored and the above +equation is used to compute the SRD temperature. + +The characteristic length scale for the SRD fluid is set by *hgrid* +which is used to bin SRD particles for purposes of resetting their +velocities. Normally hgrid is set to be 1/4 of the big particle +diameter or smaller, to adequately resolve fluid properties around the +big particles. + +Lamda cannot be smaller than 0.6 * hgrid, else an error is generated +(unless the *shift* keyword is used, see below). The velocities of +SRD particles are bounded by Vmax, which is set so that an SRD +particle will not advect further than Dmax = 4*lamda in dt_SRD. This +means that roughly speaking, Dmax should not be larger than a big +particle diameter, else SRDs may pass thru big particles without +colliding. A warning is generated if this is the case. + +Collisions between SRD particles and big particles or walls are +modeled as a lightweight SRD point particle hitting a heavy big +particle of given diameter or a wall at a point on its surface and +bouncing off with a new velocity. The collision changes the momentum +of the SRD particle. It imparts a force and torque to the big +particle. It imparts a force to a wall. Static or moving SRD walls +are setup via the :doc:`fix wall/srd ` command. For the +remainder of this doc page, a collision of an SRD particle with a wall +can be viewed as a collision with a big particle of infinite radius +and mass. + +The *collision* keyword sets the style of collisions. The *slip* +style means that the tangential component of the SRD particle momentum +is preserved. Thus a force is imparted to a big particle, but no +torque. The normal component of the new SRD velocity is sampled from +a Gaussian distribution at temperature *Tsrd*. + +For the *noslip* style, both the normal and tangential components of +the new SRD velocity are sampled from a Gaussian distribution at +temperature *Tsrd*. Additionally, a new tangential direction for the +SRD velocity is chosen randomly. This collision style imparts torque +to a big particle. Thus a time integrator :doc:`fix ` that rotates +the big particles appropriately should be used. + + +---------- + + +The *overlap* keyword should be set to *yes* if two (or more) big +particles can ever overlap. This depends on the pair potential +interaction used for big-big interactions, or could be the case if +multiple big particles are held together as rigid bodies via the :doc:`fix rigid ` command. If the *overlap* keyword is *no* and +big particles do in fact overlap, then SRD/big collisions can generate +an error if an SRD ends up inside two (or more) big particles at once. +How this error is treated is determined by the *inside* keyword. +Running with *overlap* set to *no* allows for faster collision +checking, so it should only be set to *yes* if needed. + +The *inside* keyword determines how a collision is treated if the +computation determines that the timestep started with the SRD particle +already inside a big particle. If the setting is *error* then this +generates an error message and LAMMPS stops. If the setting is *warn* +then this generates a warning message and the code continues. If the +setting is *ignore* then no message is generated. One of the output +quantities logged by the fix (see below) tallies the number of such +events, so it can be monitored. Note that once an SRD particle is +inside a big particle, it may remain there for several steps until it +drifts outside the big particle. + +The *exact* keyword determines how accurately collisions are computed. +A setting of *yes* computes the time and position of each collision as +SRD and big particles move together. A setting of *no* estimates the +position of each collision based on the end-of-timestep positions of +the SRD and big particle. If *overlap* is set to yes, the setting of +the *exact* keyword is ignored since time-accurate collisions are +needed. + +The *radius* keyword scales the effective size of big particles. If +big particles will overlap as they undergo dynamics, then this keyword +can be used to scale down their effective collision radius by an +amount *rfactor*, so that SRD particle will only collide with one big +particle at a time. For example, in a Lennard-Jones system at a +temperature of 1.0 (in reduced LJ units), the minimum separation +bewteen two big particles is as small as about 0.88 sigma. Thus an +*rfactor* value of 0.85 should prevent dual collisions. + +The *bounce* keyword can be used to limit the maximum number of +collisions an SRD particle undergoes in a single timestep as it +bounces between nearby big particles. Note that if the limit is +reached, the SRD can be left inside a big particle. A setting of 0 is +the same as no limit. + + +---------- + + +There are 2 kinds of bins created and maintained when running an SRD +simulation. The first are "SRD bins" which are used to bin SRD +particles and reset their velocities, as discussed above. The second +are "search bins" which are used to identify SRD/big particle +collisions. + +The *search* keyword can be used to choose a search bin size for +identifying SRD/big particle collisions. The default is to use the +*hgrid* parameter for SRD bins as the search bin size. Choosing a +smaller or large value may be more efficient, depending on the +problem. But, in a statistical sense, it should not change the +simulation results. + +The *cubic* keyword can be used to generate an error or warning when +the bin size chosen by LAMMPS creates SRD bins that are non-cubic or +different than the requested value of *hgrid* by a specified +*tolerance*. Note that using non-cubic SRD bins can lead to +undetermined behavior when rotating the velocities of SRD particles, +hence LAMMPS tries to protect you from this problem. + +LAMMPS attempts to set the SRD bin size to exactly *hgrid*. However, +there must be an integer number of bins in each dimension of the +simulation box. Thus the actual bin size will depend on the size and +shape of the overall simulation box. The actual bin size is printed +as part of the SRD output when a simulation begins. + +If the actual bin size in non-cubic by an amount exceeding the +tolerance, an error or warning is printed, depending on the style of +the *cubic* keyword. Likewise, if the actual bin size differs from +the requested *hgrid* value by an amount exceeding the tolerance, then +an error or warning is printed. The *tolerance* is a fractional +difference. E.g. a tolerance setting of 0.01 on the shape means that +if the ratio of any 2 bin dimensions exceeds (1 +/- tolerance) then an +error or warning is generated. Similarly, if the ratio of any bin +dimension with *hgrid* exceeds (1 +/- tolerance), then an error or +warning is generated. + +.. note:: + + The fix srd command can be used with simluations the size and/or + shape of the simulation box changes. This can be due to non-periodic + boundary conditions or the use of fixes such as the :doc:`fix deform ` or :doc:`fix wall/srd ` commands + to impose a shear on an SRD fluid or an interaction with an external + wall. If the box size changes then the size of SRD bins must be + recalculated every reneighboring. This is not necessary if only the + box shape changes. This re-binning is always done so as to fit an + integer number of bins in the current box dimension, whether it be a + fixed, shrink-wrapped, or periodic boundary, as set by the + :doc:`boundary ` command. If the box size or shape changes, + then the size of the search bins must be recalculated avery + reneighboring. Note that changing the SRD bin size may alter the + properties of the SRD fluid, such as its viscosity. + +The *shift* keyword determines whether the coordinates of SRD +particles are randomly shifted when binned for purposes of rotating +their velocities. When no shifting is performed, SRD particles are +binned and the velocity distribution of the set of SRD particles in +each bin is adjusted via a rotation operator. This is a statistically +valid operation if SRD particles move sufficiently far between +successive rotations. This is determined by their mean-free path +lamda. If lamda is less than 0.6 of the SRD bin size, then shifting +is required. A shift means that all of the SRD particles are shifted +by a vector whose coordinates are chosen randomly in the range [-1/2 +bin size, 1/2 bin size]. Note that all particles are shifted by the +same vector. The specified random number *shiftseed* is used to +generate these vectors. This operation sufficiently randomizes which +SRD particles are in the same bin, even if lamda is small. + +If the *shift* flag is set to *no*, then no shifting is performed, but +bin data will be communicated if bins overlap processor boundaries. +An error will be generated if lamda < 0.6 of the SRD bin size. If the +*shift* flag is set to *possible*, then shifting is performed only if +lamda < 0.6 of the SRD bin size. A warning is generated to let you +know this is occurring. If the *shift* flag is set to *yes* then +shifting is performed regardless of the magnitude of lamda. Note that +the *shiftseed* is not used if the *shift* flag is set to *no*, but +must still be specified. + +Note that shifting of SRD coordinates requires extra communication, +hence it should not normally be enabled unless required. + +The *tstat* keyword will thermostat the SRD particles to the specified +*Tsrd*. This is done every N timesteps, during the velocity rotation +operation, by rescaling the thermal velocity of particles in each SRD +bin to the desired temperature. If there is a streaming velocity +associated with the system, e.g. due to use of the :doc:`fix deform ` command to perform a simulation undergoing +shear, then that is also accounted for. The mean velocity of each bin +of SRD particles is set to the position-dependent streaming velocity, +based on the coordinates of the center of the SRD bin. Note that +collisions of SRD particles with big particles or walls has a +thermostatting effect on the colliding particles, so it may not be +necessary to thermostat the SRD particles on a bin by bin basis in +that case. Also note that for streaming simulations, if no +thermostatting is performed (the default), then it may take a long +time for the SRD fluid to come to equilibrium with a velocity profile +that matches the simulation box deformation. + +The *rescale* keyword enables rescaling of an SRD particle's velocity +if it would travel more than 4 mean-free paths in an SRD timestep. If +an SRD particle exceeds this velocity it is possible it will be lost +when migrating to other processors or that collisions with big +particles will be missed, either of which will generate errors. Thus +the safest mode is to run with rescaling enabled. However rescaling +removes kinetic energy from the system (the particle's velocity is +reduced). The latter will not typically be a problem if +thermostatting is enabled via the *tstat* keyword or if SRD collisions +with big particles or walls effectively thermostat the system. If you +wish to turn off rescaling (on is the default), e.g. for a pure SRD +system with no thermostatting so that the temperature does not decline +over time, the *rescale* keyword can be used. The *no* value turns +rescaling off during collisions and the per-bin velocity rotation +operation. The *collide* and *rotate* values turn it on for +one of the operations and off for the other. + + +---------- + + +.. note:: + + This fix is normally used for simulations with a huge number of + SRD particles relative to the number of big particles, e.g. 100 to 1. + In this scenario, computations that involve only big particles + (neighbor list creation, communication, time integration) can slow + down dramatically due to the large number of background SRD particles. + +Three other input script commands will largely overcome this effect, +speeding up an SRD simulation by a significant amount. These are the +:doc:`atom_modify first `, :doc:`neigh_modify include `, and :doc:`comm_modify group ` +commands. Each takes a group-ID as an argument, which in this case +should be the group-ID of the big solute particles. + +Additionally, when a :doc:`pair_style ` for big/big particle +interactions is specified, the :doc:`pair_coeff ` command +should be used to turn off big/SRD interactions, e.g. by setting their +epsilon or cutoff length to 0.0. + +The "delete_atoms overlap" command may be useful in setting up an SRD +simulation to insure there are no initial overlaps between big and SRD +particles. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix tabulates several SRD statistics which are stored in a vector +of length 12, which can be accessed by various :ref:`output commands `. The vector values calculated +by this fix are "intensive", meaning they do not scale with the size +of the simulation. Technically, the first 8 do scale with the size of +the simulation, but treating them as intensive means they are not +scaled when printed as part of thermodyanmic output. + +These are the 12 quantities. All are values for the current timestep, +except for quantity 5 and the last three, each of which are +cummulative quantities since the beginning of the run. + +* (1) # of SRD/big collision checks performed +* (2) # of SRDs which had a collision +* (3) # of SRD/big colllisions (including multiple bounces) +* (4) # of SRD particles inside a big particle +* (5) # of SRD particles whose velocity was rescaled to be < Vmax +* (6) # of bins for collision searching +* (7) # of bins for SRD velocity rotation +* (8) # of bins in which SRD temperature was computed +* (9) SRD temperature +* (10) # of SRD particles which have undergone max # of bounces +* (11) max # of bounces any SRD particle has had in a single step +* (12) # of reneighborings due to SRD particles moving too far + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This command can only be used if LAMMPS was built with the SRD +package. See the :ref:`Making LAMMPS ` section +for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`fix wall/srd ` + +Default +""""""" + +The option defaults are lamda inferred from Tsrd, collision = noslip, +overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0, +search = hgrid, cubic = error 0.01, shift = no, tstat = no, and +rescale = yes. + + +---------- + + +.. _Hecht: + + + +**(Hecht)** Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005). + +.. _Petersen: + + + +**(Petersen)** Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J +Chem Phys, 132, 174106 (2010). + +.. _Lechman: + + + +**(Lechman)** Lechman, et al, in preparation (2010). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_store_force.txt b/doc/_sources/fix_store_force.txt new file mode 100644 index 0000000000..f86d7b123f --- /dev/null +++ b/doc/_sources/fix_store_force.txt @@ -0,0 +1,80 @@ +.. index:: fix store/force + +fix store/force command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID store/force + +* ID, group-ID are documented in :doc:`fix ` command +* store/force = style name of this fix command + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all store/force + +Description +""""""""""" + +Store the forces on atoms in the group at the point during each +timestep when the fix is invoked, as described below. This is useful +for storing forces before constraints or other boundary conditions are +computed which modify the forces, so that unmodified forces can be +:doc:`written to a dump file ` or accessed by other :ref:`output commands ` that use per-atom quantities. + +This fix is invoked at the point in the velocity-Verlet timestepping +immediately after :doc:`pair `, :doc:`bond `, +:doc:`angle `, :doc:`dihedral `, +:doc:`improper `, and :doc:`long-range ` +forces have been calculated. It is the point in the timestep when +various fixes that compute constraint forces are calculated and +potentially modify the force on each atom. Examples of such fixes are +:doc:`fix shake `, :doc:`fix wall `, and :doc:`fix indent `. + +.. note:: + + The order in which various fixes are applied which operate at + the same point during the timestep, is the same as the order they are + specified in the input script. Thus normally, if you want to store + per-atom forces due to force field interactions, before constraints + are applied, you should list this fix first within that set of fixes, + i.e. before other fixes that apply constraints. However, if you wish + to include certain constraints (e.g. fix shake) in the stored force, + then it could be specified after some fixes and before others. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix produces a per-atom array which can be accessed by various +:ref:`output commands `. The number of columns +for each atom is 3, and the columns store the x,y,z forces on each +atom. The per-atom values be accessed on any timestep. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix store_state ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_store_state.txt b/doc/_sources/fix_store_state.txt new file mode 100644 index 0000000000..b062d6fa13 --- /dev/null +++ b/doc/_sources/fix_store_state.txt @@ -0,0 +1,145 @@ +.. index:: fix store/state + +fix store/state command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID store/state N input1 input2 ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* store/state = style name of this fix command +* N = store atom attributes every N steps, N = 0 for initial store only +* input = one or more atom attributes +.. parsed-literal:: + + possible attributes = id, mol, type, mass, + x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz, + vx, vy, vz, fx, fy, fz, + q, mux, muy, muz, mu, + radius, diameter, omegax, omegay, omegaz, + angmomx, angmomy, angmomz, tqx, tqy, tqz, + c_ID, c_ID[N], f_ID, f_ID[N], v_name, + d_name, i_name + +.. parsed-literal:: + + id = atom ID + mol = molecule ID + type = atom type + mass = atom mass + x,y,z = unscaled atom coordinates + xs,ys,zs = scaled atom coordinates + xu,yu,zu = unwrapped atom coordinates + xsu,ysu,zsu = scaled unwrapped atom coordinates + ix,iy,iz = box image that the atom is in + vx,vy,vz = atom velocities + fx,fy,fz = forces on atoms + q = atom charge + mux,muy,muz = orientation of dipolar atom + mu = magnitued of dipole moment of atom + radius,diameter = radius.diameter of spherical particle + omegax,omegay,omegaz = angular velocity of spherical particle + angmomx,angmomy,angmomz = angular momentum of aspherical particle + tqx,tqy,tqz = torque on finite-size particles + c_ID = per-atom vector calculated by a compute with ID + c_ID[I] = Ith column of per-atom array calculated by a compute with ID + f_ID = per-atom vector calculated by a fix with ID + f_ID[I] = Ith column of per-atom array calculated by a fix with ID + v_name = per-atom vector calculated by an atom-style variable with name + d_name = per-atom floating point vector name, managed by fix property/atom + i_name = per-atom integer vector name, managed by fix property/atom + +* zero or more keyword/value pairs may be appended +* keyword = *com* +.. parsed-literal:: + + *com* value = *yes* or *no* + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all store/state 0 x y z + fix 1 all store/state 0 xu yu zu com yes + fix 2 all store/state 1000 vx vy vz + +Description +""""""""""" + +Define a fix that stores attributes for each atom in the group at the +time the fix is defined. If *N* is 0, then the values are never +updated, so this is a way of archiving an atom attribute at a given +time for future use in a calculation or output. See the discussion of +:ref:`output commands ` that take fixes as +inputs. + +If *N* is not zero, then the attributes will be updated every *N* +steps. + +.. note:: + + Actually, only atom attributes specified by keywords like *xu* + or *vy* or *radius* are initially stored immediately at the point in + your input script when the fix is defined. Attributes specified by a + compute, fix, or variable are not initially stored until the first run + following the fix definition begins. This is because calculating + those attributes may require quantities that are not defined in + between runs. + +The list of possible attributes is the same as that used by the :doc:`dump custom ` command, which describes their meaning. + +If the *com* keyword is set to *yes* then the *xu*, *yu*, and *zu* +inputs store the position of each atom relative to the center-of-mass +of the group of atoms, instead of storing the absolute position. + +The requested values are stored in a per-atom vector or array as +discussed below. Zeroes are stored for atoms not in the specified +group. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the per-atom values it stores to :doc:`binary restart files `, so that the values can be restored when a +simulation is restarted. See the :doc:`read_restart ` +command for info on how to re-specify a fix in an input script that +reads a restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +None of the :doc:`fix_modify ` options are relevant to this +fix. + +If a single input is specified, this fix produces a per-atom vector. +If multiple inputs are specified, a per-atom array is produced where +the number of columns for each atom is the number of inputs. These +can be accessed by various :ref:`output commands `. The per-atom values be +accessed on any timestep. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`dump custom `, :doc:`compute property/atom `, +:doc:`fix property/atom `, :doc:`variable ` + +Default +""""""" + +The option default is com = no. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_temp_berendsen.txt b/doc/_sources/fix_temp_berendsen.txt new file mode 100644 index 0000000000..d0e7b14061 --- /dev/null +++ b/doc/_sources/fix_temp_berendsen.txt @@ -0,0 +1,199 @@ +.. index:: fix temp/berendsen + +fix temp/berendsen command +========================== + +fix temp/berendsen/cuda command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID temp/berendsen Tstart Tstop Tdamp + +* ID, group-ID are documented in :doc:`fix ` command +* temp/berendsen = style name of this fix command +* Tstart,Tstop = desired temperature at start/end of run +.. parsed-literal:: + + Tstart can be a variable (see below) + +* Tdamp = temperature damping parameter (time units) +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all temp/berendsen 300.0 300.0 100.0 + +Description +""""""""""" + +Reset the temperature of a group of atoms by using a Berendsen +thermostat :ref:`(Berendsen) `, which rescales their velocities +every timestep. + +The thermostat is applied to only the translational degrees of freedom +for the particles, which is an important consideration for finite-size +particles which have rotational degrees of freedom are being +thermostatted with this fix. The translational degrees of freedom can +also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +The desired temperature at each timestep is a ramped value during the +run from *Tstart* to *Tstop*. The *Tdamp* parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +:doc:`units ` command). + +*Tstart* can be specified as an equal-style :doc:`variable `. +In this case, the *Tstop* setting is ignored. If the value is a +variable, it should be specified as v_name, where name is the variable +name. In this case, the variable will be evaluated each timestep, and +its value used to determine the target temperature. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent temperature. + +.. note:: + + Unlike the :doc:`fix nvt ` command which performs + Nose/Hoover thermostatting AND time integration, this fix does NOT + perform time integration. It only modifies velocities to effect + thermostatting. Thus you must use a separate time integration fix, + like :doc:`fix nve ` to actually update the positions of atoms + using the modified velocities. Likewise, this fix should not normally + be used on atoms that also have their temperature controlled by + another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +This fix computes a temperature each timestep. To do this, the fix +creates its own compute of style "temp", as if this command had been +issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp + +See the :doc:`compute temp ` command for details. Note +that the ID of the new compute is the fix-ID + underscore + "temp", +and the group for the new compute is the same as the fix group. + +Note that this is NOT the compute used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp*. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* will have no +effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +These accelerated styles are part of the USER-CUDA package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a temperature :doc:`compute ` +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change implied by a velocity rescaling to the +system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative energy change due to this fix. The scalar value +calculated by this fix is "extensive". + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix can be used with dynamic groups as defined by the +:doc:`group ` command. Likewise it can be used with groups to +which atoms are added or deleted over time, e.g. a deposition +simulation. However, the conservation properties of the thermostat +and barostat are defined for systems with a static set of atoms. You +may observe odd behavior if the atoms in a group vary dramatically +over time or the atom count becomes very small. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, +:doc:`fix_modify `, :doc:`compute temp `, +:doc:`fix press/berendsen ` + +**Default:** none + + +---------- + + +.. _Berendsen: + + + +**(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem +Phys, 81, 3684 (1984). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_temp_csvr.txt b/doc/_sources/fix_temp_csvr.txt new file mode 100644 index 0000000000..290e240d82 --- /dev/null +++ b/doc/_sources/fix_temp_csvr.txt @@ -0,0 +1,197 @@ +.. index:: fix temp/csvr + +fix temp/csvr command +===================== + +fix temp/csld command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID temp/csvr Tstart Tstop Tdamp seed + +.. parsed-literal:: + + fix ID group-ID temp/csld Tstart Tstop Tdamp seed + +* ID, group-ID are documented in :doc:`fix ` command +* temp/csvr or temp/csld = style name of this fix command +* Tstart,Tstop = desired temperature at start/end of run +.. parsed-literal:: + + Tstart can be a variable (see below) + +* Tdamp = temperature damping parameter (time units) +* seed = random number seed to use for white noise (positive integer) +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all temp/csvr 300.0 300.0 100.0 54324 + +.. parsed-literal:: + + fix 1 all temp/csld 100.0 300.0 10.0 123321 + +Description +""""""""""" + +Adjust the temperature with a canonical sampling thermostat that uses +global velocity rescaling with Hamiltonian dynamics (*temp/csvr*) +:ref:`(Bussi1) `, or Langevin dynamics (*temp/csld*) +:ref:`(Bussi2) `. In the case of *temp/csvr* the thermostat is +similar to the empirical Berendsen thermostat in +:doc:`temp/berendsen `, but chooses the actual +scaling factor from a suitably chosen (gaussian) distribution rather +than having it determined from the time constant directly. In the case +of *temp/csld* the velocities are updated to a linear combination of +the current velocities with a gaussian distribution of velocities at +the desired temperature. Both termostats are applied every timestep. + +The thermostat is applied to only the translational degrees of freedom +for the particles, which is an important consideration for finite-size +particles which have rotational degrees of freedom are being +thermostatted with these fixes. The translational degrees of freedom +can also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +The desired temperature at each timestep is a ramped value during the +run from *Tstart* to *Tstop*. The *Tdamp* parameter is specified in +time units and determines how rapidly the temperature is relaxed. For +example, a value of 100.0 means to relax the temperature in a timespan +of (roughly) 100 time units (tau or fmsec or psec - see the +:doc:`units ` command). + +*Tstart* can be specified as an equal-style :doc:`variable `. +In this case, the *Tstop* setting is ignored. If the value is a +variable, it should be specified as v_name, where name is the variable +name. In this case, the variable will be evaluated each timestep, and +its value used to determine the target temperature. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent temperature. + +.. note:: + + Unlike the :doc:`fix nvt ` command which performs + Nose/Hoover thermostatting AND time integration, these fixes do NOT + perform time integration. They only modify velocities to effect + thermostatting. Thus you must use a separate time integration fix, + like :doc:`fix nve ` to actually update the positions of atoms + using the modified velocities. Likewise, these fixes should not + normally be used on atoms that also have their temperature controlled + by another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +These fixes compute a temperature each timestep. To do this, the fix +creates its own compute of style "temp", as if this command had been +issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp + +See the :doc:`compute temp ` command for details. Note +that the ID of the new compute is the fix-ID + underscore + "temp", +and the group for the new compute is the same as the fix group. + +Note that this is NOT the compute used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp*. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* will have no +effect on this fix. + +Like other fixes that perform thermostatting, these fixes can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about these fixes are written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *temp* option is supported by these +fixes. You can use it to assign a temperature :doc:`compute ` +you have defined to these fixes which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +these fixes and by the compute should be the same. + +These fixes can ramp its target temperature over multiple runs, using +the *start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +These fixes are not invoked during :doc:`energy minimization `. + +These fixes compute a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative energy change due to the fix. The scalar value +calculated by this fix is "extensive". + +Restrictions +"""""""""""" + + +These fixes are not compatible with :doc:`fix shake `. + +The fix can be used with dynamic groups as defined by the +:doc:`group ` command. Likewise it can be used with groups to +which atoms are added or deleted over time, e.g. a deposition +simulation. However, the conservation properties of the thermostat +and barostat are defined for systems with a static set of atoms. You +may observe odd behavior if the atoms in a group vary dramatically +over time or the atom count becomes very small. + +Related commands +"""""""""""""""" + +:doc:`fix nve `, :doc:`fix nvt `, :doc:`fix temp/rescale `, :doc:`fix langevin `, +:doc:`fix_modify `, :doc:`compute temp `, +:doc:`fix temp/berendsen ` + +**Default:** none + + +---------- + + +.. _Bussi1: + + + +.. _Bussi2: + +**(Bussi1)** Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007) + + +**(Bussi2)** Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007) + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_temp_rescale.txt b/doc/_sources/fix_temp_rescale.txt new file mode 100644 index 0000000000..66bdf2ffea --- /dev/null +++ b/doc/_sources/fix_temp_rescale.txt @@ -0,0 +1,189 @@ +.. index:: fix temp/rescale + +fix temp/rescale command +======================== + +fix temp/rescale/cuda command +============================= + +fix temp/rescale/limit/cuda command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID temp/rescale N Tstart Tstop window fraction + +* ID, group-ID are documented in :doc:`fix ` command +* temp/rescale = style name of this fix command +* N = perform rescaling every N steps +* Tstart,Tstop = desired temperature at start/end of run (temperature units) +.. parsed-literal:: + + Tstart can be a variable (see below) + +* window = only rescale if temperature is outside this window (temperature units) +* fraction = rescale to target temperature by this fraction +Examples +"""""""" + +.. parsed-literal:: + + fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5 + fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 + fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 + +Description +""""""""""" + +Reset the temperature of a group of atoms by explicitly rescaling +their velocities. + +The rescaling is applied to only the translational degrees of freedom +for the particles, which is an important consideration if finite-size +particles which have rotational degrees of freedom are being +thermostatted with this fix. The translational degrees of freedom can +also have a bias velocity removed from them before thermostatting +takes place; see the description below. + +Rescaling is performed every N timesteps. The target temperature is a +ramped value between the *Tstart* and *Tstop* temperatures at the +beginning and end of the run. + +*Tstart* can be specified as an equal-style :doc:`variable `. +In this case, the *Tstop* setting is ignored. If the value is a +variable, it should be specified as v_name, where name is the variable +name. In this case, the variable will be evaluated each timestep, and +its value used to determine the target temperature. + +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent temperature. + +Rescaling is only performed if the difference between the current and +desired temperatures is greater than the *window* value. The amount +of rescaling that is applied is a *fraction* (from 0.0 to 1.0) of the +difference between the actual and desired temperature. E.g. if +*fraction* = 1.0, the temperature is reset to exactly the desired +value. + +.. note:: + + Unlike the :doc:`fix nvt ` command which performs + Nose/Hoover thermostatting AND time integration, this fix does NOT + perform time integration. It only modifies velocities to effect + thermostatting. Thus you must use a separate time integration fix, + like :doc:`fix nve ` to actually update the positions of atoms + using the modified velocities. Likewise, this fix should not normally + be used on atoms that also have their temperature controlled by + another fix - e.g. by :doc:`fix nvt ` or :doc:`fix langevin ` commands. + +See :ref:`this howto section ` of the manual for +a discussion of different ways to compute temperature and perform +thermostatting. + +This fix computes a temperature each timestep. To do this, the fix +creates its own compute of style "temp", as if one of this command had +been issued: + +.. parsed-literal:: + + compute fix-ID_temp group-ID temp + +See the :doc:`compute temp ` for details. Note that the +ID of the new compute is the fix-ID + underscore + "temp", and the +group for the new compute is the same as the fix group. + +Note that this is NOT the compute used by thermodynamic output (see +the :doc:`thermo_style ` command) with ID = *thermo_temp*. +This means you can change the attributes of this fix's temperature +(e.g. its degrees-of-freedom) via the +:doc:`compute_modify ` command or print this temperature +during thermodynamic output via the :doc:`thermo_style custom ` command using the appropriate compute-ID. +It also means that changing attributes of *thermo_temp* will have no +effect on this fix. + +Like other fixes that perform thermostatting, this fix can be used +with :doc:`compute commands ` that calculate a temperature +after removing a "bias" from the atom velocities. E.g. removing the +center-of-mass velocity from a group of atoms or only calculating +temperature on the x-component of velocity or only calculating +temperature for atoms in a geometric region. This is not done by +default, but only if the :doc:`fix_modify ` command is used +to assign a temperature compute to this fix that includes such a bias +term. See the doc pages for individual :doc:`compute commands ` to determine which ones include a bias. In +this case, the thermostat works in the following manner: the current +temperature is calculated taking the bias into account, bias is +removed from each atom, thermostatting is performed on the remaining +thermal degrees of freedom, and the bias is added back in. + + +---------- + + +Styles with a *cuda* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +These accelerated styles are part of the USER-CUDA package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a temperature :doc:`compute ` +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change implied by a velocity rescaling to the +system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative energy change due to this fix. The scalar value +calculated by this fix is "extensive". + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix langevin `, :doc:`fix nvt `, +:doc:`fix_modify ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_temp_rescale_eff.txt b/doc/_sources/fix_temp_rescale_eff.txt new file mode 100644 index 0000000000..bc7aff88b1 --- /dev/null +++ b/doc/_sources/fix_temp_rescale_eff.txt @@ -0,0 +1,82 @@ +.. index:: fix temp/rescale/eff + +fix temp/rescale/eff command +============================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID temp/rescale/eff N Tstart Tstop window fraction + +* ID, group-ID are documented in :doc:`fix ` command +* temp/rescale/eff = style name of this fix command +* N = perform rescaling every N steps +* Tstart,Tstop = desired temperature at start/end of run (temperature units) +* window = only rescale if temperature is outside this window (temperature units) +* fraction = rescale to target temperature by this fraction + +Examples +"""""""" + +.. parsed-literal:: + + fix 3 flow temp/rescale/eff 10 1.0 100.0 0.02 1.0 + +Description +""""""""""" + +Reset the temperature of a group of nuclei and electrons in the +:doc:`electron force field ` model by explicitly rescaling +their velocities. + +The operation of this fix is exactly like that described by the :doc:`fix temp/rescale ` command, except that the rescaling +is also applied to the radial electron velocity for electron +particles. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *temp* option is supported by this +fix. You can use it to assign a temperature :doc:`compute ` +you have defined to this fix which will be used in its thermostatting +procedure, as described above. For consistency, the group used by +this fix and by the compute should be the same. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy change implied by a velocity rescaling to the +system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative energy change due to this fix. The scalar value +calculated by this fix is "extensive". + +This fix can ramp its target temperature over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the USER-EFF package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`fix langevin/eff `, :doc:`fix nvt/eff `, :doc:`fix_modify `, +:doc:`fix_temp_rescale `, + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_tfmc.txt b/doc/_sources/fix_tfmc.txt new file mode 100644 index 0000000000..fc14a677ca --- /dev/null +++ b/doc/_sources/fix_tfmc.txt @@ -0,0 +1,178 @@ +.. index:: fix tfmc + +fix tfmc command +================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID tfmc Delta Temp seed keyword value + +* ID, group-ID are documented in :doc:`fix ` command +* tfmc = style name of this fix command +* Delta = maximal displacement length (distance units) +* Temp = imposed temperature of the system +* seed = random number seed (positive integer) +* zero or more keyword/arg pairs may be appended +* keyword = *com* or *rot* +.. parsed-literal:: + + *com* args = xflag yflag zflag + xflag,yflag,zflag = 0/1 to exclude/include each dimension + *rot* args = none + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all tfmc 0.1 1000.0 159345 + fix 1 all tfmc 0.05 600.0 658943 com 1 1 0 + fix 1 all tfmc 0.1 750.0 387068 com 1 1 1 rot + +Description +""""""""""" + +Perform uniform-acceptance force-bias Monte Carlo (fbMC) simulations, +using the time-stamped force-bias Monte Carlo (tfMC) algorithm +described in :ref:`(Mees) ` and :ref:`(Bal) `. + +One successful use case of force-bias Monte Carlo methods is that they +can be used to extend the time scale of atomistic simulations, in +particular when long time scale relaxation effects must be considered; +some interesting examples are given in the review by :ref:`(Neyts) `. +An example of a typical use case would be the modelling of chemical +vapour deposition (CVD) processes on a surface, in which impacts by +gas-phase species can be performed using MD, but subsequent relaxation +of the surface is too slow to be done using MD only. Using tfMC can +allow for a much faster relaxation of the surface, so that higher +fluxes can be used, effectively extending the time scale of the +simulation. (Such an alternating simulation approach could be set up +using a :doc:`loop `.) + +The initial version of tfMC algorithm in :ref:`(Mees) ` contained an +estimation of the effective time scale of such a simulation, but it +was later shown that the speed-up one can gain from a tfMC simulation +is system- and process-dependent, ranging from none to several orders +of magnitude. In general, solid-state processes such as +(re)crystallisation or growth can be accelerated by up to two or three +orders of magnitude, whereas diffusion in the liquid phase is not +accelerated at all. The observed pseudodynamics when using the tfMC +method is not the actual dynamics one would obtain using MD, but the +relative importance of processes can match the actual relative +dynamics of the system quite well, provided *Delta* is chosen with +care. Thus, the system's equilibrium is reached faster than in MD, +along a path that is generally roughly similar to a typical MD +simulation (but not necessarily so). See :ref:`(Bal) ` for details. + +Each step, all atoms in the selected group are displaced using the +stochastic tfMC algorithm, which is designed to sample the canonical +(NVT) ensemble at the temperature *Temp*. Although tfMC is a Monte +Carlo algorithm and thus strictly speaking does not perform time +integration, it is similar in the sense that it uses the forces on all +atoms in order to update their positions. Therefore, it is implemented +as a time integration fix, and no other fixes of this type (such as +:doc:`fix nve `) should be used at the same time. Because +velocities do not play a role in this kind of Monte Carlo simulations, +instantaneous temperatures as calculated by :doc:`temperature computes ` or :doc:`thermodynamic output ` have no meaning: the only relevant +temperature is the sampling temperature *Temp*. Similarly, performing +tfMC simulations does not require setting a :doc:`timestep ` +and the :doc:`simulated time ` as calculated by LAMMPS is +meaningless. + +The critical parameter determining the success of a tfMC simulation is +*Delta*, the maximal displacement length of the lightest element in +the system: the larger it is, the longer the effective time scale of +the simulation will be (there is an approximately quadratic +dependence). However, *Delta* must also be chosen sufficiently small +in order to comply with detailed balance; in general values between 5 +and 10 % of the nearest neighbor distance are found to be a good +choice. For a more extensive discussion with specific examples, please +refer to :ref:`(Bal) `, which also describes how the code calculates +element-specific maximal displacements from *Delta*, based on the +fourth root of their mass. + +Because of the uncorrelated movements of the atoms, the center-of-mass +of the fix group will not necessarily be stationary, just like its +orientation. When the *com* keyword is used, all atom positions will +be shifted (after every tfMC iteration) in order to fix the position +of the center-of-mass along the included directions, by setting the +corresponding flag to 1. The *rot* keyword does the same for the +rotational component of the tfMC displacements after every iteration. + +.. note:: + + the *com* and *rot* keywords should not be used if an external + force is acting on the specified fix group, along the included + directions. This can be either a true external force (e.g. through + :doc:`fix wall `) or forces due to the interaction with atoms + not included in the fix group. This is because in such cases, + translations or rotations of the fix group could be induced by these + external forces, and removing them will lead to a violation of + detailed balance. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +None of the :doc:`fix_modify ` options are relevant to this +fix. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MC package. It is only enabled if LAMMPS was +built with that package. See the :ref:`Making LAMMPS ` section for more info. + +This fix is not compatible with :doc:`fix shake `. + +Related commands +"""""""""""""""" + +:doc:`fix gcmc `, :doc:`fix nvt ` + +Default +""""""" + +The option default is com = 0 0 0 + + +---------- + + +.. _Bal: + + + +**(Bal)** K. M Bal and E. C. Neyts, J. Chem. Phys. 141, 204104 (2014). + +.. _Mees: + + + +**(Mees)** M. J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and +A. Stesmans, Phys. Rev. B 85, 134301 (2012). + +.. _Neyts: + + + +**(Neyts)** E. C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 +(2013). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_thermal_conductivity.txt b/doc/_sources/fix_thermal_conductivity.txt new file mode 100644 index 0000000000..b5f68af2df --- /dev/null +++ b/doc/_sources/fix_thermal_conductivity.txt @@ -0,0 +1,184 @@ +.. index:: fix thermal/conductivity + +fix thermal/conductivity command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID thermal/conductivity N edim Nbin keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* thermal/conductivity = style name of this fix command +* N = perform kinetic energy exchange every N steps +* edim = *x* or *y* or *z* = direction of kinetic energy transfer +* Nbin = # of layers in edim direction (must be even number) +* zero or more keyword/value pairs may be appended +* keyword = *swap* +.. parsed-literal:: + + *swap* value = Nswap = number of swaps to perform every N steps + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all thermal/conductivity 100 z 20 + fix 1 all thermal/conductivity 50 z 20 swap 2 + +Description +""""""""""" + +Use the Muller-Plathe algorithm described in :ref:`this paper ` to exchange kinetic energy between two particles +in different regions of the simulation box every N steps. This +induces a temperature gradient in the system. As described below this +enables the thermal conductivity of a material to be calculated. This +algorithm is sometimes called a reverse non-equilibrium MD (reverse +NEMD) approach to computing thermal conductivity. This is because the +usual NEMD approach is to impose a temperature gradient on the system +and measure the response as the resulting heat flux. In the +Muller-Plathe method, the heat flux is imposed, and the temperature +gradient is the system's response. + +See the :doc:`compute heat/flux ` command for details +on how to compute thermal conductivity in an alternate way, via the +Green-Kubo formalism. + +The simulation box is divided into *Nbin* layers in the *edim* +direction, where the layer 1 is at the low end of that dimension and +the layer *Nbin* is at the high end. Every N steps, Nswap pairs of +atoms are chosen in the following manner. Only atoms in the fix group +are considered. The hottest Nswap atoms in layer 1 are selected. +Similarly, the coldest Nswap atoms in the "middle" layer (see below) +are selected. The two sets of Nswap atoms are paired up and their +velocities are exchanged. This effectively swaps their kinetic +energies, assuming their masses are the same. If the masses are +different, an exchange of velocities relative to center of mass motion +of the 2 atoms is performed, to conserve kinetic energy. Over time, +this induces a temperature gradient in the system which can be +measured using commands such as the following, which writes the +temperature profile (assuming z = edim) to the file tmp.profile: + +.. parsed-literal:: + + compute ke all ke/atom + variable temp atom c_ke/1.5 + fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp & + file tmp.profile units reduced + +Note that by default, Nswap = 1, though this can be changed by the +optional *swap* keyword. Setting this parameter appropriately, in +conjunction with the swap rate N, allows the heat flux to be adjusted +across a wide range of values, and the kinetic energy to be exchanged +in large chunks or more smoothly. + +The "middle" layer for velocity swapping is defined as the *Nbin*/2 + +1 layer. Thus if *Nbin* = 20, the two swapping layers are 1 and 11. +This should lead to a symmetric temperature profile since the two +layers are separated by the same distance in both directions in a +periodic sense. This is why *Nbin* is restricted to being an even +number. + +As described below, the total kinetic energy transferred by these +swaps is computed by the fix and can be output. Dividing this +quantity by time and the cross-sectional area of the simulation box +yields a heat flux. The ratio of heat flux to the slope of the +temperature profile is proportional to the thermal conductivity of the +fluid, in appropriate units. See the :ref:`Muller-Plathe paper ` for details. + +.. note:: + + If your system is periodic in the direction of the heat flux, + then the flux is going in 2 directions. This means the effective heat + flux in one direction is reduced by a factor of 2. You will see this + in the equations for thermal conductivity (kappa) in the Muller-Plathe + paper. LAMMPS is simply tallying kinetic energy which does not + account for whether or not your system is periodic; you must use the + value appropriately to yield a kappa for your system. + +.. note:: + + After equilibration, if the temperature gradient you observe is + not linear, then you are likely swapping energy too frequently and are + not in a regime of linear response. In this case you cannot + accurately infer a thermal conductivity and should try increasing the + Nevery parameter. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative kinetic energy transferred between the bottom and middle +of the simulation box (in the *edim* direction) is stored as a scalar +quantity by this fix. This quantity is zeroed when the fix is defined +and accumlates thereafter, once every N steps. The units of the +quantity are energy; see the :doc:`units ` command for details. +The scalar value calculated by this fix is "intensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Swaps conserve both momentum and kinetic energy, even if the masses of +the swapped atoms are not equal. Thus you should not need to +thermostat the system. If you do use a thermostat, you may want to +apply it only to the non-swapped dimensions (other than *vdim*). + +LAMMPS does not check, but you should not use this fix to swap the +kinetic energy of atoms that are in constrained molecules, e.g. via +:doc:`fix shake ` or :doc:`fix rigid `. This is +because application of the constraints will alter the amount of +transferred momentum. You should, however, be able to use flexible +molecules. See the :ref:`Zhang paper ` for a discussion and results +of this idea. + +When running a simulation with large, massive particles or molecules +in a background solvent, you may want to only exchange kinetic energy +bewteen solvent particles. + +Related commands +"""""""""""""""" + +:doc:`fix ave/spatial `, :doc:`fix viscosity `, :doc:`compute heat/flux ` + +Default +""""""" + +The option defaults are swap = 1. + + +---------- + + +.. _Muller-Plathe: + + + +**(Muller-Plathe)** Muller-Plathe, J Chem Phys, 106, 6082 (1997). + +.. _Zhang: + + + +**(Zhang)** Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, +109, 15060-15067 (2005). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ti_rs.txt b/doc/_sources/fix_ti_rs.txt new file mode 100644 index 0000000000..204ab6e503 --- /dev/null +++ b/doc/_sources/fix_ti_rs.txt @@ -0,0 +1,172 @@ +.. index:: fix ti/rs + +fix ti/rs command +================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* ti/rs = style name of this fix command +* lambda_initial/lambda_final = initial/final values of the coupling parameter +* t_switch/t_equil = number of steps of the switching/equilibration procedure +* keyword = *function* +.. parsed-literal:: + + *function* value = function-ID + function-ID = ID of the switching function (1, 2 or 3) + + + +**Example:** + +.. parsed-literal:: + + fix ref all ti/rs 50.0 2000 1000 + fix vf vacancy ti/rs 10.0 70000 50000 function 2 + +Description +""""""""""" + +This fix allows you to compute the free energy temperature dependence +by performing a thermodynamic integration procedure known as +Reversible Scaling :ref:`(de Koning99, ` :ref:`de Koning00a) `. The thermodynamic integration is performed +using the nonequilibrium method of Adiabatic Switching +:ref:`(Watanabe, ` :ref:`de Koning96) `. + +The forces on the atoms are dynamically scaled during the simulation, +the rescaling is done in the following manner: + +.. image:: Eqs/fix_ti_rs_force.jpg + :align: center + +where F_int is the total force on the atoms due to the interatomic +potential and lambda is the coupling parameter of the thermodynamic +integration. + +The fix acts as follows: during the first *t_equil* steps after the +fix is defined the value of lambda is *lambda_initial* , this is the +period to equilibrate the system in the lambda = *lambda_initial* +state. After this the value of lambda changes continuously from +*lambda_initial* to *lambda_final* according to the function defined +using the keyword *function* (described below), this is done in +*t_switch* steps. Then comes the second equilibration period of +*t_equil* to equilibrate the system in the lambda = *lambda_final* +state. After that the switching back to the lambda = *lambda_initial* +state is done using *t_switch* timesteps and following the same +switching function. After this period the value of lambda is kept +equal to *lambda_initial* indefinitely or until a :doc:`unfix ` +erase the fix. + +The description of thermodynamic integration in both directions is +done in :ref:`de Koning00b `, the main reason is to try to +eliminate the dissipated heat due to the nonequilibrium process. + +The *function* keyword allows the use of three different switching +rates. The option *1* results in a constant rescaling where the lambda +parameter changes at a constant rate during the switching time +according to the switching function + +.. image:: Eqs/fix_ti_rs_function_1.jpg + :align: center + +where tau is the scaled time variable t/t_switch. This switching +function has the characteristic that the temperature scaling is faster +at temperatures closer to the final temperature of the procedure. The +option number *2* performs the switching at a rate defined by the +following switching function + +.. image:: Eqs/fix_ti_rs_function_2.jpg + :align: center + +This switching function has the characteristic that the temperature +scaling occurs at a constant rate during all the procedure. The option +number *3* performs the switching at a rate defined by the following +switching function + +.. image:: Eqs/fix_ti_rs_function_3.jpg + :align: center + +This switching function has the characteristic that the temperature +scaling is faster at temperatures closer to the initial temperature of +the procedure. + +An example script using this command is provided in the +examples/USER/misc/ti directory. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +This fix computes a global vector quantitie which can be accessed by +various :ref:`output commands `. The vector has +2 positions, the first one is the coupling parameter lambda and the +second one is the time derivative of lambda. The scalar and vector +values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +Related commands +"""""""""""""""" + +:doc:`fix ti/spring ` + +Restrictions +"""""""""""" + + +This command is part of the USER-MISC package. It is only enabled if +LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +Default +""""""" + +The keyword default is function = 1. + + +---------- + + +.. _deKoning99: + + + +**(de Koning 99)** M. de Koning, A. Antonelli and S. Yip, Phys Rev Lett, 83, 3973 (1999). + +.. _Watanabe: + + + +**(Watanabe)** M. Watanabe and W. P. Reinhardt, Phys Rev Lett, 65, 3301 (1990). + +.. _deKoning96: + + + +**(de Koning 96)** M. de Koning and A. Antonelli, Phys Rev E, 53, 465 (1996). + +.. _deKoning00a: + + + +**(de Koning 00a)** M. de Koning, A. Antonelli and S. Yip, J Chem Phys, 115, 11025 (2000). + +.. _deKoning00b: + + + +**(de Koning 00b)** M. de Koning et al., Computing in Science & Engineering, 2, 88 (2000). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ti_spring.txt b/doc/_sources/fix_ti_spring.txt new file mode 100644 index 0000000000..704172b3f4 --- /dev/null +++ b/doc/_sources/fix_ti_spring.txt @@ -0,0 +1,189 @@ +.. index:: fix ti/spring + +fix ti/spring command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ti/spring K t_switch t_equil keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* ti/spring = style name of this fix command +* K = spring constant (force/distance units) +* t_switch/t_equil = number of steps of the switching/equilibration procedure +* zero or more keyword/value pairs may be appended to args +* keyword = *function* +.. parsed-literal:: + + *function* value = function-ID + function-ID = ID of the switching function (1 or 2) + + + +**Example:** + +.. parsed-literal:: + + fix ref all ti/spring 50.0 2000 1000 function 2 + +Description +""""""""""" + +This fix allows you to compute the free energy of solids by performing +a thermodynamic integration between the solid of interest and an +Einstein crystal :ref:`(Frenkel) `. The thermodynamic integration +is performed using the nonequilibrium method of Adiabatic Switching +:ref:`(Watanabe, ` :ref:`de Koning96) `. + +A spring force is applied independently to each atom in the group to +tether it to its initial position. The initial position for each atom +is its location at the time the fix command was issued. More details +about the springs are available in :doc:`fix spring/self `. The forces on the atoms are +dynamically scaled during the simulation, the rescaling is done in the +following manner: + +.. image:: Eqs/fix_ti_spring_force.jpg + :align: center + +where F_harm is the force due to the springs, F_solid is the total +force on the atoms due to the interatomic potential and lambda is the +coupling parameter of the thermodynamic integration. + +The fix acts as follows: during the first *t_equil* steps after the +fix is defined the value of lambda is zero, this is the period to +equilibrate the system in the lambda = 0 state. After this the value +of lambda changes continuously from 0 to 1 according to the function +defined using the keyword *function* (described below), this is done +in *t_switch* steps. Then comes the second equilibration period of +*t_equil* to equilibrate the system in the lambda = 1 state. After +that the switching back to the lambda = 0 state is made using +*t_switch* timesteps and following the same switching function. After +this period the value of lambda is kept equal to zero and the fix has +no action in the dynamics of the system anymore. + +The description of thermodynamic integration in both directions is +done in :ref:`de Koning97 `, the main reason is to try to +eliminate the dissipated heat due to the nonequilibrium process. + +The *function* keyword allows the use of two different switching +rates, the option *1* results in a constant rescaling where the lambda +parameter changes at a constant rate during the switching time +according to the switching function + +.. image:: Eqs/fix_ti_spring_function_1.jpg + :align: center + +where tau is the scaled time variable t/t_switch. The option number +*2* performs the switching at a rate defined by the following +switching function + +.. image:: Eqs/fix_ti_spring_function_2.jpg + :align: center + +This function has zero slope as lambda approaches its extreme values +(0 and 1), according to (:ref:`de Koning96) ` this results in +smaller fluctuations on the integral to be computed on the +thermodynamic integration. + +.. note:: + + It is importante to keep the center of mass fixed during the + thermodynamic integration, a non-zero total velocity will result in + divergencies during the integration due to the fact that the atoms are + 'attatched' to its equilibrium positions by the Einstein + crystal. Check the option *zero* of `fix langevin `_ + and :doc:`velocity `. The use of the Nose-Hoover thermostat + (:doc:`fix nvt `) is NOT recommended due to its well documented + issues with the canonical sampling of harmonic degrees of freedom + (notice that the *chain* option will NOT solve this problem). The + Langevin thermostat (`fix langevin `_) works fine. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the original coordinates of tethered atoms to :doc:`binary restart files `, so that the spring effect will be the +same in a restarted simulation. See the :doc:`read restart ` command for info on how to re-specify a fix +in an input script that reads a restart file, so that the operation of +the fix continues in an uninterrupted fashion. + +The :doc:`fix modify ` *energy* option is supported by this +fix to add the energy stored in the per-atom springs to the system's +potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar and a global vector quantities which +can be accessed by various :ref:`output commands `. The scalar is an energy which +is the sum of the spring energy for each atom, where the per-atom +energy is 0.5 * K * r^2. The vector has 2 positions, the first one is +the coupling parameter lambda and the second one is the time +derivative of lambda. The scalar and vector values calculated by this +fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +.. note:: + + If you want the per-atom spring energy to be included in the + total potential energy of the system (the quantity being minimized), + you MUST enable the :doc:`fix modify ` *energy* option for + this fix. + +An example script using this command is provided in the +examples/USER/misc/ti directory. + +Related commands +"""""""""""""""" + +:doc:`fix spring `, :doc:`fix ti/rs ` + +Restrictions +"""""""""""" + + +This command is part of the USER-MISC package. It is only enabled if +LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +Default +""""""" + +The keyword default is function = 1. + + +---------- + + +.. _Frenkel: + + + +**(Frenkel)** Daan Frenkel and Anthony J. C. Ladd, J. Chem. Phys. 81, 3188 +(1984). + +.. _Watanabe: + + + +**(Watanabe)** M. Watanabe and W. P. Reinhardt, Phys Rev Lett, 65, 3301 (1990). + +.. _deKoning96: + + + +**(de Koning 96)** M. de Koning and A. Antonelli, Phys Rev E, 53, 465 (1996). + +.. _deKoning97: + + + +**(de Koning 97)** M. de Koning and A. Antonelli, Phys Rev B, 55, 735 (1997). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_tmd.txt b/doc/_sources/fix_tmd.txt new file mode 100644 index 0000000000..a6da5810e0 --- /dev/null +++ b/doc/_sources/fix_tmd.txt @@ -0,0 +1,148 @@ +.. index:: fix tmd + +fix tmd command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID tmd rho_final file1 N file2 + +* ID, group-ID are documented in :doc:`fix ` command +* tmd = style name of this fix command +* rho_final = desired value of rho at the end of the run (distance units) +* file1 = filename to read target structure from +* N = dump TMD statistics every this many timesteps, 0 = no dump +* file2 = filename to write TMD statistics to (only needed if N > 0) + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all nve + fix 2 tmdatoms tmd 1.0 target_file 100 tmd_dump_file + +Description +""""""""""" + +Perform targeted molecular dynamics (TMD) on a group of atoms. A +holonomic constraint is used to force the atoms to move towards (or +away from) the target configuration. The parameter "rho" is +monotonically decreased (or increased) from its initial value to +rho_final at the end of the run. + +Rho has distance units and is a measure of the root-mean-squared +distance (RMSD) between the current configuration of the atoms in the +group and the target coordinates listed in file1. Thus a value of +rho_final = 0.0 means move the atoms all the way to the final +structure during the course of the run. + +The target file1 can be ASCII text or a gzipped text file (detected by +a .gz suffix). The format of the target file1 is as follows: + +.. parsed-literal:: + + 0.0 25.0 xlo xhi + 0.0 25.0 ylo yhi + 0.0 25.0 zlo zhi + 125 24.97311 1.69005 23.46956 0 0 -1 + 126 1.94691 2.79640 1.92799 1 0 0 + 127 0.15906 3.46099 0.79121 1 0 0 + ... + +The first 3 lines may or may not be needed, depending on the format of +the atoms to follow. If image flags are included with the atoms, the +1st 3 lo/hi lines must appear in the file. If image flags are not +included, the 1st 3 lines should not appear. The 3 lines contain the +simulation box dimensions for the atom coordinates, in the same format +as in a LAMMPS data file (see the :doc:`read_data ` command). + +The remaining lines each contain an atom ID and its target x,y,z +coordinates. The atom lines (all or none of them) can optionally be +followed by 3 integer values: nx,ny,nz. For periodic dimensions, they +specify which image of the box the atom is considered to be in, i.e. a +value of N (positive or negative) means add N times the box length to +the coordinate to get the true value. + +The atom lines can be listed in any order, but every atom in the group +must be listed in the file. Atoms not in the fix group may also be +listed; they will be ignored. + +TMD statistics are written to file2 every N timesteps, unless N is +specified as 0, which means no statistics. + +The atoms in the fix tmd group should be integrated (via a fix nve, +nvt, npt) along with other atoms in the system. + +Restarts can be used with a fix tmd command. For example, imagine a +10000 timestep run with a rho_initial = 11 and a rho_final = 1. If a +restart file was written after 2000 time steps, then the configuration +in the file would have a rho value of 9. A new 8000 time step run +could be performed with the same rho_final = 1 to complete the +conformational change at the same transition rate. Note that for +restarted runs, the name of the TMD statistics file should be changed +to prevent it being overwritten. + +For more information about TMD, see :ref:`(Schlitter1) ` and +:ref:`(Schlitter2) `. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. + +This fix can ramp its rho parameter over multiple runs, using the +*start* and *stop* keywords of the :doc:`run ` command. See the +:doc:`run ` command for details of how to do this. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +All TMD fixes must be listed in the input script after all integrator +fixes (nve, nvt, npt) are applied. This ensures that atoms are moved +before their positions are corrected to comply with the constraint. + +Atoms that have a TMD fix applied should not be part of a group to +which a SHAKE fix is applied. This is because LAMMPS assumes there +are not multiple competing holonomic constraints applied to the same +atoms. + +To read gzipped target files, you must compile LAMMPS with the +-DLAMMPS_GZIP option - see the :ref:`Making LAMMPS ` section of the documentation. + +**Related commands:** none + +**Default:** none + + +---------- + + +.. _Schlitter1: + + + +**(Schlitter1)** Schlitter, Swegat, Mulders, "Distance-type reaction +coordinates for modelling activated processes", J Molecular Modeling, +7, 171-177 (2001). + +.. _Schlitter2: + + + +**(Schlitter2)** Schlitter and Klahn, "The free energy of a reaction +coordinate at multiple constraints: a concise formulation", Molecular +Physics, 101, 3439-3443 (2003). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_ttm.txt b/doc/_sources/fix_ttm.txt new file mode 100644 index 0000000000..a22456551c --- /dev/null +++ b/doc/_sources/fix_ttm.txt @@ -0,0 +1,379 @@ +.. index:: fix ttm + +fix ttm command +=============== + +fix ttm/mod command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile + fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile + +* ID, group-ID are documented in :doc:`fix ` command +* style = *ttm* or *ttm_mod* +* seed = random number seed to use for white noise (positive integer) +* remaining arguments for fix ttm: +.. parsed-literal:: + + C_e = electronic specific heat (energy/(electron*temperature) units) + rho_e = electronic density (electrons/volume units) + kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) + gamma_p = friction coefficient due to electron-ion interactions (mass/time units) + gamma_s = friction coefficient due to electronic stopping (mass/time units) + v_0 = electronic stopping critical velocity (velocity units) + Nx = number of thermal solve grid points in the x-direction (positive integer) + Ny = number of thermal solve grid points in the y-direction (positive integer) + Nz = number of thermal solve grid points in the z-direction (positive integer) + T_infile = filename to read initial electronic temperature from + N = dump TTM temperatures every this many timesteps, 0 = no dump + T_outfile = filename to write TTM temperatures to (only needed if N > 0) + +* remaining arguments for fix ttm/mod: +.. parsed-literal:: + + init_file = file with the parameters to TTM + Nx = number of thermal solve grid points in the x-direction (positive integer) + Ny = number of thermal solve grid points in the y-direction (positive integer) + Nz = number of thermal solve grid points in the z-direction (positive integer) + T_infile = filename to read initial electronic temperature from + N = dump TTM temperatures every this many timesteps, 0 = no dump + T_outfile = filename to write TTM temperatures to (only needed if N > 0) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out + fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out + fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out + +Description +""""""""""" + +Use a two-temperature model (TTM) to represent heat transfer through +and between electronic and atomic subsystems. LAMMPS models the +atomic subsystem as usual with a molecular dynamics model and the +classical force field specified by the user, but the electronic +subsystem is modeled as a continuum, or a background "gas", on a +regular grid. Energy can be transferred spatially within the grid +representing the electrons. Energy can also be transferred between +the electronic and the atomic subsystems. The algorithm underlying +this fix was derived by D. M. Duffy and A. M. Rutherford and is +discussed in two J Physics: Condensed Matter papers: :ref:`(Duffy) ` +and :ref:`(Rutherford) `. They used this algorithm in cascade +simulations where a primary knock-on atom (PKA) was initialized with a +high velocity to simulate a radiation event. + +The description in this sub-section applies to both fix ttm and fix +ttm/mod. Fix ttm/mod adds options to account for external heat +sources (e.g. at a surface) and for specifying parameters that allow +the electronic heat capacity to depend strongly on electronic +temperature. It is more expensive computationally than fix ttm +because it treats the thermal diffusion equation as non-linear. More +details on fix ttm/mod are given below. + +Heat transfer between the electronic and atomic subsystems is carried +out via an inhomogeneous Langevin thermostat. This thermostat differs +from the regular Langevin thermostat (:doc:`fix langevin `) in three important ways. First, the +Langevin thermostat is applied uniformly to all atoms in the +user-specified group for a single target temperature, whereas the TTM +fix applies Langevin thermostatting locally to atoms within the +volumes represented by the user-specified grid points with a target +temperature specific to that grid point. Second, the Langevin +thermostat couples the temperature of the atoms to an infinite heat +reservoir, whereas the heat reservoir for fix TTM is finite and +represents the local electrons. Third, the TTM fix allows users to +specify not just one friction coefficient, but rather two independent +friction coefficients: one for the electron-ion interactions +(*gamma_p*), and one for electron stopping (*gamma_s*). + +When the friction coefficient due to electron stopping, *gamma_s*, is +non-zero, electron stopping effects are included for atoms moving +faster than the electron stopping critical velocity, *v_0*. For +further details about this algorithm, see :ref:`(Duffy) ` and +:ref:`(Rutherford) `. + +Energy transport within the electronic subsystem is solved according +to the heat diffusion equation with added source terms for heat +transfer between the subsystems: + +.. image:: Eqs/fix_ttm.jpg + :align: center + +where C_e is the specific heat, rho_e is the density, kappa_e is the +thermal conductivity, T is temperature, the "e" and "a" subscripts +represent electronic and atomic subsystems respectively, g_p is the +coupling constant for the electron-ion interaction, and g_s is the +electron stopping coupling parameter. C_e, rho_e, and kappa_e are +specified as parameters to the fix. The other quantities are derived. +The form of the heat diffusion equation used here is almost the same +as that in equation 6 of :ref:`(Duffy) `, with the exception that the +electronic density is explicitly reprensented, rather than being part +of the the specific heat parameter. + +Currently, fix ttm assumes that none of the user-supplied parameters +will vary with temperature. Note that :ref:`(Duffy) ` used a tanh() +functional form for the temperature dependence of the electronic +specific heat, but ignored temperature dependencies of any of the +other parameters. See more discussion below for fix ttm/mod. + +These fixes require use of periodic boundary conditions and a 3D +simulation. Periodic boundary conditions are also used in the heat +equation solve for the electronic subsystem. This varies from the +approach of :ref:`(Rutherford) ` where the atomic subsystem was +embedded within a larger continuum representation of the electronic +subsystem. + +The initial electronic temperature input file, *T_infile*, is a text +file LAMMPS reads in with no header and with four numeric columns +(ix,iy,iz,Temp) and with a number of rows equal to the number of +user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are node +indices from 0 to nxnodes-1, etc. For example, the initial electronic +temperatures on a 1 by 2 by 3 grid could be specified in a *T_infile* +as follows: + +.. parsed-literal:: + + 0 0 0 1.0 + 0 0 1 1.0 + 0 0 2 1.0 + 0 1 0 2.0 + 0 1 1 2.0 + 0 1 2 2.0 + +where the electronic temperatures along the y=0 plane have been set to +1.0, and the electronic temperatures along the y=1 plane have been set +to 2.0. The order of lines in this file is no important. If all the +nodal values are not specified, LAMMPS will generate an error. + +The temperature output file, *T_oufile*, is created and written by +this fix. Temperatures for both the electronic and atomic subsystems +at every node and every N timesteps are output. If N is specified as +zero, no output is generated, and no output filename is needed. The +format of the output is as follows. One long line is written every +output timestep. The timestep itself is given in the first column. +The next Nx*Ny*Nz columns contain the temperatures for the atomic +subsystem, and the final Nx*Ny*Nz columns contain the temperatures for +the electronic subsystem. The ordering of the Nx*Ny*Nz columns is +with the z index varing fastest, y the next fastest, and x the +slowest. + +These fixes do not change the coordinates of their atoms; they only +scales their velocities. Thus a time integration fix (e.g. :doc:`fix nve `) should still be used to time integrate the affected +atoms. The fixes should not normally be used on atoms that have their +temperature controlled by another fix - e.g. :doc:`fix nvt ` or +:doc:`fix langevin `. + +.. note:: + + The current implementations of these fixes create a copy of the + electron grid that overlays the entire simulation domain, for each + processor. Values on the grid are summed across all processors. Thus + you should insure that this grid is not too large, else your + simulation could incur high memory and communication costs. + + +---------- + + +**Additional details for fix ttm/mod** + +Fix ttm/mod uses the heat diffusion equation with possible external +heat sources (e.g. laser heating in ablation simulations): + +.. image:: Eqs/fix_ttm_mod.jpg + :align: center + +where theta is the Heaviside step function, I_0 is the (absorbed) +laser pulse intensity for ablation simulations, l_skin is the depth +of skin-layer, and all other designations have the same meaning as in +the former equation. The duration of the pulse is set by the parameter +*tau* in the *init_file*. + +Fix ttm/mod also allows users to specify the dependencies of C_e and +kappa_e on the electronic temperature. The specific heat is expressed +as + +.. image:: Eqs/fix_ttm_ce.jpg + :align: center + +where *X* = T_e/1000, and the thermal conductivity is defined as +kappa_e = D_e*rho_e*C_e, where D_e is the thermal diffusion +coefficient. + +Electronic pressure effects are included in the TTM model to account +for the blast force acting on ions because of electronic pressure +gradient (see :ref:`(Chen) `, :ref:`(Norman) `). The total force +acting on an ion is: + +.. image:: Eqs/fix_ttm_blast.jpg + :align: center + +where F_langevin is a force from Langevin thermostat simulating +electron-phonon coupling, and nabla P_e/n_ion is the electron blast +force. + +The electronic pressure is taken to be P_e = B*rho_e*C_e*T_e + +The current fix ttm/mod implementation allows TTM simulations with a +vacuum. The vacuum region is defined as the grid cells with zero +electronic temperature. The numerical scheme does not allow energy +exchange with such cells. Since the material can expand to previously +unoccupied region in some simulations, the vacuum border can be +allowed to move. It is controlled by the *surface_movement* parameter +in the *init_file*. If it is set to 1, then "vacuum" cells can be +changed to "electron-filled" cells with the temperature *T_e_min* if +atoms move into them (currently only implemented for the case of +1-dimensional motion of flat surface normal to the X axis). The +initial borders of vacuum can be set in the *init_file* via *lsurface* +and *rsurface* parameters. In this case, electronic pressure gradient +is calculated as + +.. image:: Eqs/fix_ttm_blast1.jpg + :align: center + +where lambda is the electron mean free path (see :ref:`(Norman) `, +:ref:`(Pisarev) `) + +The fix ttm/mod parameter file *init_file* has the following syntax/ +Every line with the odd number is considered as a comment and +ignored. The lines with the even numbers are treated as follows: + +.. parsed-literal:: + + a_0, energy/(temperature*electron) units + a_1, energy/(temperature^2*electron) units + a_2, energy/(temperature^3*electron) units + a_3, energy/(temperature^4*electron) units + a_4, energy/(temperature^5*electron) units + C_0, energy/(temperature*electron) units + A, 1/temperature units + rho_e, electrons/volume units + D_e, length^2/time units + gamma_p, mass/time units + gamma_s, mass/time units + v_0, length/time units + I_0, energy/(time*length^2) units + lsurface, electron grid units (positive integer) + rsurface, electron grid units (positive integer) + l_skin, length units + tau, time units + B, dimensionless + lambda, length units + n_ion, ions/volume units + surface_movement: 0 to disable tracking of surface motion, 1 to enable + T_e_min, temperature units + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +These fixes write the state of the electronic subsystem and the energy +exchange between the subsystems to :doc:`binary restart files `. See the :doc:`read_restart ` command +for info on how to re-specify a fix in an input script that reads a +restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +Because the state of the random number generator is not saved in the +restart files, this means you cannot do "exact" restarts with this +fix, where the simulation continues on the same as if no restart had +taken place. However, in a statistical sense, a restarted simulation +should produce the same behavior. + +None of the :doc:`fix_modify ` options are relevant to these +fixes. + +Both fixes compute 2 output quantities stored in a vector of length 2, +which can be accessed by various :ref:`output commands `. The first quantity is the +total energy of the electronic subsystem. The second quantity is the +energy transferred from the electronic to the atomic subsystem on that +timestep. Note that the velocity verlet integrator applies the fix ttm +forces to the atomic subsystem as two half-step velocity updates: one +on the current timestep and one on the subsequent timestep. +Consequently, the change in the atomic subsystem energy is lagged by +half a timestep relative to the change in the electronic subsystem +energy. As a result of this, users may notice slight fluctuations in +the sum of the atomic and electronic subsystem energies reported at +the end of the timestep. + +The vector values calculated are "extensive". + +No parameter of the fixes can be used with the *start/stop* keywords +of the :doc:`run ` command. The fixes are not invoked during +:doc:`energy minimization `. + +Restrictions +"""""""""""" + + +Fix *ttm* is part of the MISC package. It is only enabled if LAMMPS +was built with that package. Fix *ttm/mod* is part of the USER-MISC +package. It is only enabled if LAMMPS was built with that package. +See the :ref:`Making LAMMPS ` section for more +info. + +These fixes can only be used for 3d simulations and orthogonal +simlulation boxes. You must also use periodic +:doc:`boundary ` conditions. + +Related commands +"""""""""""""""" + +:doc:`fix langevin `, :doc:`fix dt/reset ` + +**Default:** none + + +---------- + + +.. _Duffy: + + + +**(Duffy)** D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, +016207-016218 (2007). + +.. _Rutherford: + + + +**(Rutherford)** A M Rutherford and D M Duffy, J. Phys.: +Condens. Matter, 19, 496201-496210 (2007). + +.. _Chen: + + + +**(Chen)** J Chen, D Tzou and J Beraun, Int. J. Heat +Mass Transfer, 49, 307-316 (2006). + +.. _Norman: + + + +**(Norman)** G E Norman, S V Starikov, V V Stegailov et al., Contrib. +Plasma Phys., 53, 129-139 (2013). + +.. _Pisarev: + + + +**(Pisarev)** V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, +475401 (2014). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_tune_kspace.txt b/doc/_sources/fix_tune_kspace.txt new file mode 100644 index 0000000000..61d862afbe --- /dev/null +++ b/doc/_sources/fix_tune_kspace.txt @@ -0,0 +1,108 @@ +.. index:: fix tune/kspace + +fix tune/kspace command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID tune/kspace N + +* ID, group-ID are documented in :doc:`fix ` command +* tune/kspace = style name of this fix command +* N = invoke this fix every N steps + + +Examples +"""""""" + +.. parsed-literal:: + + fix 2 all tune/kspace 100 + +Description +""""""""""" + +This fix tests each kspace style (Ewald, PPPM, and MSM), and +automatically selects the fastest style to use for the remainder +of the run. If the fastest style is Ewald or PPPM, the fix also +adjusts the coulomb cutoff towards optimal speed. Future versions +of this fix will automatically select other kspace parameters +to use for maximum simulation speed. The kspace parameters may +include the style, cutoff, grid points in each direction, order, +Ewald parameter, MSM parallelization cut-point, MPI tasks to use, etc. + +The rationale for this fix is to provide the user with +as-fast-as-possible simulations that include long-range electrostatics +(kspace) while meeting the user-prescribed accuracy requirement. A +simple heuristic could never capture the optimal combination of +parameters for every possible run-time scenario. But by performing +short tests of various kspace parameter sets, this fix allows +parameters to be tailored specifically to the user's machine, MPI +ranks, use of threading or accelerators, the simulated system, and the +simulation details. In addition, it is possible that parameters could +be evolved with the simulation on-the-fly, which is useful for systems +that are dynamically evolving (e.g. changes in box size/shape or +number of particles). + +When this fix is invoked, LAMMPS will perform short timed tests of +various parameter sets to determine the optimal parameters. Tests are +performed on-the-fly, with a new test initialized every N steps. N should +be chosen large enough so that adequate CPU time lapses between tests, +thereby providing statistically significant timings. But N should not be +chosen to be so large that an unfortunate parameter set test takes an +inordinate amount of wall time to complete. An N of 100 for most problems +seems reasonable. Once an optimal parameter set is found, that set is +used for the remainder of the run. + +This fix uses heristics to guide it's selection of parameter sets to test, +but the actual timed results will be used to decide which set to use in the +simulation. + +It is not necessary to discard trajectories produced using sub-optimal +parameter sets, or a mix of various parameter sets, since the user-prescribed +accuracy will have been maintained throughout. However, some users may prefer +to use this fix only to discover the optimal parameter set for a given setup +that can then be used on subsequent production runs. + +This fix starts with kspace parameters that are set by the user with the +:doc:`kspace_style ` and :doc:`kspace_modify ` +commands. The prescribed accuracy will be maintained by this fix throughout +the simulation. + +None of the :doc:`fix_modify ` options are relevant to this +fix. + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the KSPACE package. It is only enabled if LAMMPS was +built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Do not set "neigh_modify once yes" or else this fix will never be +called. Reneighboring is required. + +Related commands +"""""""""""""""" + +:doc:`kspace_style `, :doc:`boundary ` +:doc:`kspace_modify `, :doc:`pair_style lj/cut/coul/long `, :doc:`pair_style lj/charmm/coul/long `, :doc:`pair_style lj/long `, :doc:`pair_style lj/long/coul/long `, +:doc:`pair_style buck/coul/long ` + +Default +""""""" + + +---------- + + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_vector.txt b/doc/_sources/fix_vector.txt new file mode 100644 index 0000000000..51c4d51798 --- /dev/null +++ b/doc/_sources/fix_vector.txt @@ -0,0 +1,176 @@ +.. index:: fix vector + +fix vector command +================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID vector Nevery value1 value2 ... + +* ID, group-ID are documented in :doc:`fix ` command +* vector = style name of this fix command +* Nevery = use input values every this many timesteps +* one or more input values can be listed +* value = c_ID, c_ID[N], f_ID, f_ID[N], v_name +.. parsed-literal:: + + c_ID = global scalar calculated by a compute with ID + c_ID[I] = Ith component of global vector calculated by a compute with ID + f_ID = global scalar calculated by a fix with ID + f_ID[I] = Ith component of global vector calculated by a fix with ID + v_name = global value calculated by an equal-style variable with name + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all vector 100 c_myTemp + fix 1 all vector 5 c_myTemp v_integral + +Description +""""""""""" + +Use one or more global values as inputs every few timesteps, and +simply store them. For a single specified value, the values are +stored as a global vector of growing length. For multiple specified +values, they are stored as rows in a global array, whose number of +rows is growing. The resulting vector or array can be used by other +:ref:`output commands `. + +One way to to use this command is to accumulate a vector that is +time-integrated using the :doc:`variable trap() ` function. +For example the velocity auto-correlation function (VACF) can be +time-integrated, to yield a diffusion coefficient, as follows: + +.. parsed-literal:: + + compute 2 all vacf + fix 5 all vector 1 c_2[4] + variable diff equal dt*trap(f_5) + thermo_style custom step v_diff + +The group specified with this command is ignored. However, note that +specified values may represent calculations performed by computes and +fixes which store their own "group" definitions. + +Each listed value can be the result of a :doc:`compute ` or +:doc:`fix ` or the evaluation of an equal-style +:doc:`variable `. In each case, the compute, fix, or variable +must produce a global quantity, not a per-atom or local quantity. +And the global quantity must be a scalar, not a vector or array. + +:doc:`Computes ` that produce global quantities are those which +do not have the word *atom* in their style name. Only a few +:doc:`fixes ` produce global quantities. See the doc pages for +individual fixes for info on which ones produce such values. +:doc:`Variables ` of style *equal* are the only ones that can +be used with this fix. Variables of style *atom* cannot be used, +since they produce per-atom values. + +The *Nevery* argument specifies on what timesteps the input values +will be used in order to be stored. Only timesteps that are a +multiple of *Nevery*, including timestep 0, will contribute values. + +Note that if you perform multiple runs, using the "pre no" option of +the :doc:`run ` command to avoid initialization on subsequent runs, +then you need to use the *stop* keyword with the first :doc:`run ` +command with a timestep value that encompasses all the runs. This is +so that the vector or array stored by this fix can be allocated to a +sufficient size. + + +---------- + + +If a value begins with "c_", a compute ID must follow which has been +previously defined in the input script. If no bracketed term is +appended, the global scalar calculated by the compute is used. If a +bracketed term is appended, the Ith element of the global vector +calculated by the compute is used. + +Note that there is a :doc:`compute reduce ` command +which can sum per-atom quantities into a global scalar or vector which +can thus be accessed by fix vector. Or it can be a compute defined +not in your input script, but by :doc:`thermodynamic output ` or other fixes such as :doc:`fix nvt ` +or :doc:`fix temp/rescale `. See the doc pages for +these commands which give the IDs of these computes. Users can also +write code for their own compute styles and :doc:`add them to LAMMPS `. + +If a value begins with "f_", a fix ID must follow which has been +previously defined in the input script. If no bracketed term is +appended, the global scalar calculated by the fix is used. If a +bracketed term is appended, the Ith element of the global vector +calculated by the fix is used. + +Note that some fixes only produce their values on certain timesteps, +which must be compatible with *Nevery*, else an error will result. +Users can also write code for their own fix styles and :doc:`add them to LAMMPS `. + +If a value begins with "v_", a variable name must follow which has +been previously defined in the input script. Only equal-style +variables can be referenced. See the :doc:`variable ` command +for details. Note that variables of style *equal* define a formula +which can reference individual atom properties or thermodynamic +keywords, or they can invoke other computes, fixes, or variables when +they are evaluated, so this is a very general means of specifying +quantities to be stored by fix vector. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix produces a global vector or global array which can be +accessed by various :ref:`output commands `. +The values can only be accessed on timesteps that are multiples of +*Nevery*. + +A vector is produced if only a single input value is specified. +An array is produced if multiple input values are specified. +The length of the vector or the number of rows in the array grows +by 1 every *Nevery* timesteps. + +If the fix prouduces a vector, then the entire vector will be either +"intensive" or "extensive", depending on whether the values stored in +the vector are "intensive" or "extensive". If the fix produces an +array, then all elements in the array must be the same, either +"intensive" or "extensive". If a compute or fix provides the value +stored, then the compute or fix determines whether the value is +intensive or extensive; see the doc page for that compute or fix for +further info. Values produced by a variable are treated as intensive. + +This fix can allocate storage for stored values accumulated over +multiple runs, using the *start* and *stop* keywords of the +:doc:`run ` command. See the :doc:`run ` command for details of +how to do this. If using the :doc:`run pre no ` command option, +this is required to allow the fix to allocate sufficient storage for +stored values. + +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`compute `, :doc:`variable ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_viscosity.txt b/doc/_sources/fix_viscosity.txt new file mode 100644 index 0000000000..9ca28b4996 --- /dev/null +++ b/doc/_sources/fix_viscosity.txt @@ -0,0 +1,188 @@ +.. index:: fix viscosity + +fix viscosity command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID viscosity N vdim pdim Nbin keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* viscosity = style name of this fix command +* N = perform momentum exchange every N steps +* vdim = *x* or *y* or *z* = which momentum component to exchange +* pdim = *x* or *y* or *z* = direction of momentum transfer +* Nbin = # of layers in pdim direction (must be even number) +* zero or more keyword/value pairs may be appended +* keyword = *swap* or *target* +.. parsed-literal:: + + *swap* value = Nswap = number of swaps to perform every N steps + *vtarget* value = V or INF = target velocity of swap partners (velocity units) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all viscosity 100 x z 20 + fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5 + +Description +""""""""""" + +Use the Muller-Plathe algorithm described in :ref:`this paper ` to exchange momenta between two particles in +different regions of the simulation box every N steps. This induces a +shear velocity profile in the system. As described below this enables +a viscosity of the fluid to be calculated. This algorithm is +sometimes called a reverse non-equilibrium MD (reverse NEMD) approach +to computing viscosity. This is because the usual NEMD approach is to +impose a shear velocity profile on the system and measure the response +via an off-diagonal component of the stress tensor, which is +proportional to the momentum flux. In the Muller-Plathe method, the +momentum flux is imposed, and the shear velocity profile is the +system's response. + +The simulation box is divided into *Nbin* layers in the *pdim* +direction, where the layer 1 is at the low end of that dimension and +the layer *Nbin* is at the high end. Every N steps, Nswap pairs of +atoms are chosen in the following manner. Only atoms in the fix group +are considered. Nswap atoms in layer 1 with positive velocity +components in the *vdim* direction closest to the target value *V* are +selected. Similarly, Nswap atoms in the "middle" layer (see below) with +negative velocity components in the *vdim* direction closest to the +negative of the target value *V* are selected. The two sets of Nswap +atoms are paired up and their *vdim* momenta components are swapped +within each pair. This resets their velocities, typically in opposite +directions. Over time, this induces a shear velocity profile in the +system which can be measured using commands such as the following, +which writes the profile to the file tmp.profile: + +.. parsed-literal:: + + fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx & + file tmp.profile units reduced + +Note that by default, Nswap = 1 and vtarget = INF, though this can be +changed by the optional *swap* and *vtarget* keywords. When vtarget = +INF, one or more atoms with the most positive and negative velocity +components are selected. Setting these parameters appropriately, in +conjunction with the swap rate N, allows the momentum flux rate to be +adjusted across a wide range of values, and the momenta to be +exchanged in large chunks or more smoothly. + +The "middle" layer for momenta swapping is defined as the *Nbin*/2 + 1 +layer. Thus if *Nbin* = 20, the two swapping layers are 1 and 11. +This should lead to a symmetric velocity profile since the two layers +are separated by the same distance in both directions in a periodic +sense. This is why *Nbin* is restricted to being an even number. + +As described below, the total momentum transferred by these velocity +swaps is computed by the fix and can be output. Dividing this +quantity by time and the cross-sectional area of the simulation box +yields a momentum flux. The ratio of momentum flux to the slope of +the shear velocity profile is proportional to the viscosity of the +fluid, in appropriate units. See the :ref:`Muller-Plathe paper ` for details. + +.. note:: + + If your system is periodic in the direction of the momentum + flux, then the flux is going in 2 directions. This means the + effective momentum flux in one direction is reduced by a factor of 2. + You will see this in the equations for viscosity in the Muller-Plathe + paper. LAMMPS is simply tallying momentum which does not account for + whether or not your system is periodic; you must use the value + appropriately to yield a viscosity for your system. + +.. note:: + + After equilibration, if the velocity profile you observe is not + linear, then you are likely swapping momentum too frequently and are + not in a regime of linear response. In this case you cannot + accurately infer a viscosity and should try increasing the Nevery + parameter. + +An alternative method for calculating a viscosity is to run a NEMD +simulation, as described in :ref:`Section_howto 13 ` of the manual. NEMD simulations +deform the simmulation box via the :doc:`fix deform ` +command. Thus they cannot be run on a charged system using a :doc:`PPPM solver ` since PPPM does not currently support +non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; +thus it does not suffer from this limitation. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global scalar which can be accessed by various +:ref:`output commands `. The scalar is the +cummulative momentum transferred between the bottom and middle of the +simulation box (in the *pdim* direction) is stored as a scalar +quantity by this fix. This quantity is zeroed when the fix is defined +and accumlates thereafter, once every N steps. The units of the +quantity are momentum = mass*velocity. The scalar value calculated by +this fix is "intensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Swaps conserve both momentum and kinetic energy, even if the masses of +the swapped atoms are not equal. Thus you should not need to +thermostat the system. If you do use a thermostat, you may want to +apply it only to the non-swapped dimensions (other than *vdim*). + +LAMMPS does not check, but you should not use this fix to swap +velocities of atoms that are in constrained molecules, e.g. via :doc:`fix shake ` or :doc:`fix rigid `. This is because +application of the constraints will alter the amount of transferred +momentum. You should, however, be able to use flexible molecules. +See the :ref:`Maginn paper ` for an example of using this algorithm +in a computation of alcohol molecule properties. + +When running a simulation with large, massive particles or molecules +in a background solvent, you may want to only exchange momenta bewteen +solvent particles. + +Related commands +"""""""""""""""" + +:doc:`fix ave/spatial `, :doc:`fix thermal/conductivity ` + +Default +""""""" + +The option defaults are swap = 1 and vtarget = INF. + + +---------- + + +.. _Muller-Plathe: + + + +**(Muller-Plathe)** Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999). + +.. _Maginn: + + + +**(Maginn)** Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, +260, 218-231 (2007). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_viscous.txt b/doc/_sources/fix_viscous.txt new file mode 100644 index 0000000000..44e36b2f37 --- /dev/null +++ b/doc/_sources/fix_viscous.txt @@ -0,0 +1,139 @@ +.. index:: fix viscous + +fix viscous command +=================== + +fix viscous/cuda command +======================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID viscous gamma keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* viscous = style name of this fix command +* gamma = damping coefficient (force/velocity units) +* zero or more keyword/value pairs may be appended +.. parsed-literal:: + + keyword = *scale* + *scale* values = type ratio + type = atom type (1-N) + ratio = factor to scale the damping coefficient by + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 flow viscous 0.1 + fix 1 damp viscous 0.5 scale 3 2.5 + +Description +""""""""""" + +Add a viscous damping force to atoms in the group that is proportional +to the velocity of the atom. The added force can be thought of as a +frictional interaction with implicit solvent, i.e. the no-slip Stokes +drag on a spherical particle. In granular simulations this can be +useful for draining the kinetic energy from the system in a controlled +fashion. If used without additional thermostatting (to add kinetic +energy to the system), it has the effect of slowly (or rapidly) +freezing the system; hence it can also be used as a simple energy +minimization technique. + +The damping force F is given by F = - gamma * velocity. The larger +the coefficient, the faster the kinetic energy is reduced. If the +optional keyword *scale* is used, gamma can scaled up or down by the +specified factor for atoms of that type. It can be used multiple +times to adjust gamma for several atom types. + +.. note:: + + You should specify gamma in force/velocity units. This is not + the same as mass/time units, at least for some of the LAMMPS + :doc:`units ` options like "real" or "metal" that are not + self-consistent. + +In a Brownian dynamics context, gamma = Kb T / D, where Kb = +Boltzmann's constant, T = temperature, and D = particle diffusion +coefficient. D can be written as Kb T / (3 pi eta d), where eta = +dynamic viscosity of the frictional fluid and d = diameter of +particle. This means gamma = 3 pi eta d, and thus is proportional to +the viscosity of the fluid and the particle diameter. + +In the current implementation, rather than have the user specify a +viscosity, gamma is specified directly in force/velocity units. If +needed, gamma can be adjusted for atoms of different sizes +(i.e. sigma) by using the *scale* keyword. + +Note that Brownian dynamics models also typically include a randomized +force term to thermostat the system at a chosen temperature. The :doc:`fix langevin ` command does this. It has the same +viscous damping term as fix viscous and adds a random force to each +atom. The random force term is proportional to the sqrt of the chosen +thermostatting temperature. Thus if you use fix langevin with a +target T = 0, its random force term is zero, and you are essentially +performing the same operation as fix viscous. Also note that the +gamma of fix viscous is related to the damping parameter of :doc:`fix langevin `, however the former is specified in units +of force/velocity and the latter in units of time, so that it can more +easily be used as a thermostat. + + +---------- + + +Styles with a *cuda* suffix are functionally the same as the +corresponding style without the suffix. They have been optimized to +run faster, depending on your available hardware, as discussed in +:doc:`Section_accelerate ` of the manual. The +accelerated styles take the same arguments and should produce the same +results, except for round-off and precision issues. + +These accelerated styles are part of the USER-CUDA package. They are +only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. This fix should only +be used with damped dynamics minimizers that allow for +non-conservative forces. See the :doc:`min_style ` command +for details. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix langevin ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_wall.txt b/doc/_sources/fix_wall.txt new file mode 100644 index 0000000000..b074d0e894 --- /dev/null +++ b/doc/_sources/fix_wall.txt @@ -0,0 +1,345 @@ +.. index:: fix wall/lj93 + +fix wall/lj93 command +===================== + +fix wall/lj126 command +====================== + +fix wall/lj1043 command +======================= + +fix wall/colloid command +======================== + +fix wall/harmonic command +========================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID style face args ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* style = *wall/lj93* or *wall/lj126* or *wall/lj1043* or *wall/colloid* or *wall/harmonic* +* one or more face/arg pairs may be appended +* face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* +.. parsed-literal:: + + args = coord epsilon sigma cutoff + coord = position of wall = EDGE or constant or variable + EDGE = current lo or hi edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = :doc:`equal-style variable ` like v_x or v_wiggle + epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) + epsilon can be a variable (see below) + sigma = size factor for wall-particle interaction (distance units) + sigma can be a variable (see below) + cutoff = distance from wall at which wall-particle interaction is cut off (distance units) + +* zero or more keyword/value pairs may be appended +* keyword = *units* or *fld* +.. parsed-literal:: + + *units* value = *lattice* or *box* + *lattice* = the wall position is defined in lattice units + *box* = the wall position is defined in simulation box units + *fld* value = *yes* or *no* + *yes* = invoke the wall constraint to be compatible with implicit FLD + *no* = invoke the wall constraint in the normal way + *pbc* value = *yes* or *no* + *yes* = allow periodic boundary in a wall dimension + *no* = require non-perioidic boundaries in any wall dimension + + + +Examples +"""""""" + +.. parsed-literal:: + + fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box + fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 + fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 + fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 + +Description +""""""""""" + +Bound the simulation domain on one or more of its faces with a flat +wall that interacts with the atoms in the group by generating a force +on the atom in a direction perpendicular to the wall. The energy of +wall-particle interactions depends on the style. + +For style *wall/lj93*, the energy E is given by the 9/3 potential: + +.. image:: Eqs/fix_wall_lj93.jpg + :align: center + +For style *wall/lj126*, the energy E is given by the 12/6 potential: + +.. image:: Eqs/pair_lj.jpg + :align: center + +For style *wall/lj1043*, the energy E is given by the 10/4/3 potential: + +.. image:: Eqs/fix_wall_lj1043.jpg + :align: center + +For style *wall/colloid*, the energy E is given by an integrated form +of the :doc:`pair_style colloid ` potential: + +.. image:: Eqs/fix_wall_colloid.jpg + :align: center + +For style *wall/harmonic*, the energy E is given by a harmonic spring +potential: + +.. image:: Eqs/fix_wall_harmonic.jpg + :align: center + +In all cases, *r* is the distance from the particle to the wall at +position *coord*, and Rc is the *cutoff* distance at which the +particle and wall no longer interact. The energy of the wall +potential is shifted so that the wall-particle interaction energy is +0.0 at the cutoff distance. + +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*. A *lo* face interacts with +particles near the lower side of the simulation box in that dimension. +A *hi* face interacts with particles near the upper side of the +simulation box in that dimension. + +The position of each wall can be specified in one of 3 ways: as the +EDGE of the simulation box, as a constant value, or as a variable. If +EDGE is used, then the corresponding boundary of the current +simulation box is used. If a numeric constant is specified then the +wall is placed at that position in the appropriate dimension (x, y, or +z). In both the EDGE and constant cases, the wall will never move. +If the wall position is a variable, it should be specified as v_name, +where name is an :doc:`equal-style variable ` name. In this +case the variable is evaluated each timestep and the result becomes +the current position of the reflecting wall. Equal-style variables +can specify formulas with various mathematical functions, and include +:doc:`thermo_style ` command keywords for the simulation +box parameters and timestep and elapsed time. Thus it is easy to +specify a time-dependent wall position. See examples below. + +For the *wall/lj93* and *wall/lj126* and *wall/lj1043* styles, +*epsilon* and *sigma* are the usual Lennard-Jones parameters, which +determine the strength and size of the particle as it interacts with +the wall. Epsilon has energy units. Note that this *epsilon* and +*sigma* may be different than any *epsilon* or *sigma* values defined +for a pair style that computes particle-particle interactions. + +The *wall/lj93* interaction is derived by integrating over a 3d +half-lattice of Lennard-Jones 12/6 particles. The *wall/lj126* +interaction is effectively a harder, more repulsive wall interaction. +The *wall/lj1043* interaction is yet a different form of wall +interaction, described in Magda et al in :ref:`(Magda) `. + +For the *wall/colloid* style, *R* is the radius of the colloid +particle, *D* is the distance from the surface of the colloid particle +to the wall (r-R), and *sigma* is the size of a constituent LJ +particle inside the colloid particle and wall. Note that the cutoff +distance Rc in this case is the distance from the colloid particle +center to the wall. The prefactor *epsilon* can be thought of as an +effective Hamaker constant with energy units for the strength of the +colloid-wall interaction. More specifically, the *epsilon* pre-factor += 4 * pi^2 * rho_wall * rho_colloid * epsilon * sigma^6, where epsilon +and sigma are the LJ parameters for the constituent LJ +particles. Rho_wall and rho_colloid are the number density of the +constituent particles, in the wall and colloid respectively, in units +of 1/volume. + +The *wall/colloid* interaction is derived by integrating over +constituent LJ particles of size *sigma* within the colloid particle +and a 3d half-lattice of Lennard-Jones 12/6 particles of size *sigma* +in the wall. As mentioned in the preceeding paragraph, the density of +particles in the wall and colloid can be different, as specified by +the *epsilon* pre-factor. + +For the *wall/harmonic* style, *epsilon* is effectively the spring +constant K, and has units (energy/distance^2). The input parameter +*sigma* is ignored. The minimum energy position of the harmonic +spring is at the *cutoff*. This is a repulsive-only spring since the +interaction is truncated at the *cutoff* + +For any wall, the *epsilon* and/or *sigma* parameter can be specified +as an :doc:`equal-style variable `, in which case it should be +specified as v_name, where name is the variable name. As with a +variable wall position, the variable is evaluated each timestep and +the result becomes the current epsilon or sigma of the wall. +Equal-style variables can specify formulas with various mathematical +functions, and include :doc:`thermo_style ` command +keywords for the simulation box parameters and timestep and elapsed +time. Thus it is easy to specify a time-dependent wall interaction. + +.. note:: + + For all of the styles, you must insure that r is always > 0 for + all particles in the group, or LAMMPS will generate an error. This + means you cannot start your simulation with particles at the wall + position *coord* (r = 0) or with particles on the wrong side of the + wall (r < 0). For the *wall/lj93* and *wall/lj126* styles, the energy + of the wall/particle interaction (and hence the force on the particle) + blows up as r -> 0. The *wall/colloid* style is even more + restrictive, since the energy blows up as D = r-R -> 0. This means + the finite-size particles of radius R must be a distance larger than R + from the wall position *coord*. The *harmonic* style is a softer + potential and does not blow up as r -> 0, but you must use a large + enough *epsilon* that particles always reamin on the correct side of + the wall (r > 0). + +The *units* keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant or +variable is used. It is not relevant when EDGE is used to specify a +face position. In the variable case, the variable is assumed to +produce a value compatible with the *units* setting you specify. + +A *box* value selects standard distance units as defined by the +:doc:`units ` command, e.g. Angstroms for units = real or metal. +A *lattice* value means the distance units are in lattice spacings. +The :doc:`lattice ` command must have been previously used to +define the lattice spacings. + +The *fld* keyword can be used with a *yes* setting to invoke the wall +constraint before pairwise interactions are computed. This allows an +implicit FLD model using :doc:`pair_style lubricateU ` +to include the wall force in its calculations. If the setting is +*no*, wall forces are imposed after pairwise interactions, in the +usual manner. + +The *pbc* keyword can be used with a *yes* setting to allow walls to +be specified in a periodic dimension. See the +:doc:`boundary ` command for options on simulation box +boundaries. The default for *pbc* is *no*, which means the system +must be non-periodic when using a wall. But you may wish to use a +periodic box. E.g. to allow some particles to interact with the wall +via the fix group-ID, and others to pass through it and wrap around a +periodic box. In this case you should insure that the wall if +sufficiently far enough away from the box boundary. If you do not, +then particles may interact with both the wall and with periodic +images on the other side of the box, which is probably not what you +want. + + +---------- + + +Here are examples of variable definitions that move the wall position +in a time-dependent fashion using equal-style +:doc:`variables `. The wall interaction parameters (epsilon, +sigma) could be varied with additional variable definitions. + +.. parsed-literal:: + + variable ramp equal ramp(0,10) + fix 1 all wall xlo v_ramp 1.0 1.0 2.5 + +.. parsed-literal:: + + variable linear equal vdisplace(0,20) + fix 1 all wall xlo v_linear 1.0 1.0 2.5 + +.. parsed-literal:: + + variable wiggle equal swiggle(0.0,5.0,3.0) + fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 + +.. parsed-literal:: + + variable wiggle equal cwiggle(0.0,5.0,3.0) + fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 + +The ramp(lo,hi) function adjusts the wall position linearly from lo to +hi over the course of a run. The vdisplace(c0,velocity) function does +something similar using the equation position = c0 + velocity*delta, +where delta is the elapsed time. + +The swiggle(c0,A,period) function causes the wall position to +oscillate sinusoidally according to this equation, where omega = 2 PI +/ period: + +.. parsed-literal:: + + position = c0 + A sin(omega*delta) + +The cwiggle(c0,A,period) function causes the wall position to +oscillate sinusoidally according to this equation, which will have an +initial wall velocity of 0.0, and thus may impose a gentler +perturbation on the particles: + +.. parsed-literal:: + + position = c0 + A (1 - cos(omega*delta)) + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy of interaction between atoms and each wall to +the system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar energy and a global vector of +forces, which can be accessed by various :ref:`output commands `. Note that the scalar energy is +the sum of interactions with all defined walls. If you want the +energy on a per-wall basis, you need to use multiple fix wall +commands. The length of the vector is equal to the number of walls +defined by the fix. Each vector value is the normal force on a +specific wall. Note that an outward force on a wall will be a +negative value for *lo* walls and a positive value for *hi* walls. +The scalar and vector values calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +.. note:: + + If you want the atom/wall interaction energy to be included in + the total potential energy of the system (the quantity being + minimized), you MUST enable the :doc:`fix_modify ` *energy* + option for this fix. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix wall/reflect `, +:doc:`fix wall/gran `, +:doc:`fix wall/region ` + +Default +""""""" + +The option defaults units = lattice, fld = no, and pbc = no. + + +---------- + + +.. _Magda: + + + +**(Magda)** Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985); +erratum in JCP 84, 2901 (1986). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_wall_gran.txt b/doc/_sources/fix_wall_gran.txt new file mode 100644 index 0000000000..c62eb60421 --- /dev/null +++ b/doc/_sources/fix_wall_gran.txt @@ -0,0 +1,175 @@ +.. index:: fix wall/gran + +fix wall/gran command +===================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID wall/gran Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ... + +* ID, group-ID are documented in :doc:`fix ` command +* wall/gran = style name of this fix command +* Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) +* Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) +* gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) +* gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) +* xmu = static yield criterion (unitless value between 0.0 and 1.0e4) +* dampflag = 0 or 1 if tangential damping force is excluded or included +* wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder* +* args = list of arguments for a particular style +.. parsed-literal:: + + *xplane* or *yplane* or *zplane* args = lo hi + lo,hi = position of lower and upper plane (distance units), either can be NULL) + *zcylinder* args = radius + radius = cylinder radius (distance units) + +* zero or more keyword/value pairs may be appended to args +* keyword = *wiggle* or *shear* +.. parsed-literal:: + + *wiggle* values = dim amplitude period + dim = *x* or *y* or *z* + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) + *shear* values = dim vshear + dim = *x* or *y* or *z* + vshear = magnitude of shear velocity (velocity units) + + + +Examples +"""""""" + +.. parsed-literal:: + + fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0 + fix 1 all wall/gran 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL + fix 2 all wall/gran 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 + +Description +""""""""""" + +Bound the simulation domain of a granular system with a frictional +wall. All particles in the group interact with the wall when they are +close enough to touch it. + +The first set of parameters (Kn, Kt, gamma_n, gamma_t, xmu, and +dampflag) have the same meaning as those specified with the +:doc:`pair_style granular ` force fields. This means a NULL +can be used for either Kt or gamma_t as described on that page. If a +NULL is used for Kt, then a default value is used where Kt = 2/7 Kn. +If a NULL is used for gamma_t, then a default value is used where +gamma_t = 1/2 gamma_n. + +The nature of the wall/particle interactions are determined by which +pair_style is used in your input script: *hooke*, *hooke/history*, or +*hertz/history*. The equation for the force between the wall and +particles touching it is the same as the corresponding equation on the +:doc:`pair_style granular ` doc page, in the limit of one of +the two particles going to infinite radius and mass (flat wall). +I.e. delta = radius - r = overlap of particle with wall, m_eff = mass +of particle, and sqrt(RiRj/Ri+Rj) becomes sqrt(radius of particle). +The units for Kn, Kt, gamma_n, and gamma_t are as described on that +doc page. The meaning of xmu and dampflag are also as described on +that page. Note that you can choose different values for these 6 +wall/particle coefficients than for particle/particle interactions, if +you wish your wall to interact differently with the particles, e.g. if +the wall is a different material. + +.. note:: + + As discussed on the doc page for :doc:`pair_style granular `, versions of LAMMPS before 9Jan09 used a + different equation for Hertzian interactions. This means Hertizian + wall/particle interactions have also changed. They now include a + sqrt(radius) term which was not present before. Also the previous + versions used Kn and Kt from the pairwise interaction and hardwired + dampflag to 1, rather than letting them be specified directly. This + means you can set the values of the wall/particle coefficients + appropriately in the current code to reproduce the results of a + prevoius Hertzian monodisperse calculation. For example, for the + common case of a monodisperse system with particles of diameter 1, Kn, + Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were + previously. + +The *wallstyle* can be planar or cylindrical. The 3 planar options +specify a pair of walls in a dimension. Wall positions are given by +*lo* and *hi*. Either of the values can be specified as NULL if a +single wall is desired. For a *zcylinder* wallstyle, the cylinder's +axis is at x = y = 0.0, and the radius of the cylinder is specified. + +Optionally, the wall can be moving, if the *wiggle* or *shear* +keywords are appended. Both keywords cannot be used together. + +For the *wiggle* keyword, the wall oscillates sinusoidally, similar to +the oscillations of particles which can be specified by the +:doc:`fix_move ` command. This is useful in packing +simulations of granular particles. The arguments to the *wiggle* +keyword specify a dimension for the motion, as well as it's +*amplitude* and *period*. Note that if the dimension is in the plane +of the wall, this is effectively a shearing motion. If the dimension +is perpendicular to the wall, it is more of a shaking motion. A +*zcylinder* wall can only be wiggled in the z dimension. + +Each timestep, the position of a wiggled wall in the appropriate *dim* +is set according to this equation: + +.. parsed-literal:: + + position = coord + A - A cos (omega * delta) + +where *coord* is the specified initial position of the wall, *A* is +the *amplitude*, *omega* is 2 PI / *period*, and *delta* is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression. + +For the *shear* keyword, the wall moves continuously in the specified +dimension with velocity *vshear*. The dimension must be tangential to +walls with a planar *wallstyle*, e.g. in the *y* or *z* directions for +an *xplane* wall. For *zcylinder* walls, a dimension of *z* means the +cylinder is moving in the z-direction along it's axis. A dimension of +*x* or *y* means the cylinder is spinning around the z-axis, either in +the clockwise direction for *vshear* > 0 or counter-clockwise for +*vshear* < 0. In this case, *vshear* is the tangential velocity of +the wall at whatever *radius* has been defined. + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +This fix writes the shear friction state of atoms interacting with the +wall to :doc:`binary restart files `, so that a simulation can +continue correctly if granular potentials with shear "history" effects +are being used. See the :doc:`read_restart ` command for +info on how to re-specify a fix in an input script that reads a +restart file, so that the operation of the fix continues in an +uninterrupted fashion. + +None of the :doc:`fix_modify ` options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various :ref:`output commands `. No +parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix is part of the GRANULAR package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Any dimension (xyz) that has a granular wall must be non-periodic. + +Related commands +"""""""""""""""" + +:doc:`fix_move `, :doc:`pair_style granular ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_wall_piston.txt b/doc/_sources/fix_wall_piston.txt new file mode 100644 index 0000000000..68d3f99737 --- /dev/null +++ b/doc/_sources/fix_wall_piston.txt @@ -0,0 +1,133 @@ +.. index:: fix wall/piston + +fix wall/piston command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID wall/piston face ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* wall/piston = style name of this fix command +* face = *zlo* +* zero or more keyword/value pairs may be appended +* keyword = *pos* or *vel* or *ramp* or *units* +.. parsed-literal:: + + *pos* args = z + z = z coordinate at which the piston begins (distance units) + *vel* args = vz + vz = final velocity of the piston (velocity units) + *ramp* = use a linear velocity ramp from 0 to vz + *temp* args = target damp seed extent + target = target velocity for region immediately ahead of the piston + damp = damping paramter (time units) + seed = random number seed for langevin kicks + extent = extent of thermostated region (distance units) + *units* value = *lattice* or *box* + *lattice* = the wall position is defined in lattice units + *box* = the wall position is defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + fix xwalls all wall/piston zlo + fix walls all wall/piston zlo pos 1.0 vel 10.0 units box + fix top all wall/piston zlo vel 10.0 ramp + +Description +""""""""""" + +Bound the simulation with a moving wall which reflect particles in the +specified group and drive the system with an effective infinite-mass +piston capable of driving shock waves. + +A momentum mirror technique is used, which means that if an atom (or +the wall) moves such that an atom is outside the wall on a timestep by +a distance delta (e.g. due to :doc:`fix nve `), then it is put +back inside the face by the same delta, and the velocity relative to +the moving wall is flipped in z. For instance, a stationary particle +hit with a piston wall with velocity vz, will end the timestep with a +velocity of 2*vz. + +Currently the *face* keyword can only be *zlo*. This creates a piston +moving in the positive z direction. Particles with z coordinate less +than the wall position are reflected to a z coordinate greater than +the wall position. If the piston velocity is vpz and the particle +velocity before reflection is vzi, the particle velocity after +reflection is -vzi + 2*vpz. + +The initial position of the wall can be specified by the *pos* keyword. + +The final velocity of the wall can be specified by the *vel* keyword + +The *ramp* keyword will cause the wall/piston to adjust the velocity +linearly from zero velocity to *vel* over the course of the run. If +the *ramp* keyword is omitted then the wall/piston moves at a constant +velocity defined by *vel*. + +The *temp* keyword will cause the region immediately in front of the +wall/piston to be thermostated with a Langevin thermostat. This +region moves with the piston. The damping and kicking are measured in +the reference frame of the piston. So, a temperature of zero would +mean all particles were moving at exactly the speed of the +wall/piston. + +The *units* keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant is used. + +A *box* value selects standard distance units as defined by the +:doc:`units ` command, e.g. Angstroms for units = real or metal. +A *lattice* value means the distance units are in lattice spacings. +The :doc:`lattice ` command must have been previously used to +define the lattice spacings. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +This fix style is part of the SHOCK package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +The face that has the wall/piston must be boundary type 's' +(shrink-wrapped). The opposing face can be +any boundary type other than periodic. + +A wall/piston should not be used with rigid bodies such as those +defined by a "fix rigid" command. This is because the wall/piston +displaces atoms directly rather than exerting a force on them. + +Related commands +"""""""""""""""" + +:doc:`fix wall/reflect ` command, :doc:`fix append/atoms ` command + +Default +""""""" + +The keyword defaults are pos = 0, vel = 0, units = lattice. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_wall_reflect.txt b/doc/_sources/fix_wall_reflect.txt new file mode 100644 index 0000000000..b361985354 --- /dev/null +++ b/doc/_sources/fix_wall_reflect.txt @@ -0,0 +1,220 @@ +.. index:: fix wall/reflect + +fix wall/reflect command +======================== + +fix wall/reflect/kk command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID wall/reflect face arg ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* wall/reflect = style name of this fix command +* one or more face/arg pairs may be appended +* face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* +.. parsed-literal:: + + *xlo*,*ylo*,*zlo* arg = EDGE or constant or variable + EDGE = current lo edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = :doc:`equal-style variable ` like v_x or v_wiggle + *xhi*,*yhi*,*zhi* arg = EDGE or constant or variable + EDGE = current hi edge of simulation box + constant = number like 50.0 or 100.3 (distance units) + variable = :doc:`equal-style variable ` like v_x or v_wiggle + +* zero or more keyword/value pairs may be appended +* keyword = *units* +.. parsed-literal:: + + *units* value = *lattice* or *box* + *lattice* = the wall position is defined in lattice units + *box* = the wall position is defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + fix xwalls all wall/reflect xlo EDGE xhi EDGE + fix walls all wall/reflect xlo 0.0 ylo 10.0 units box + fix top all wall/reflect zhi v_pressdown + +Description +""""""""""" + +Bound the simulation with one or more walls which reflect particles +in the specified group when they attempt to move thru them. + +Reflection means that if an atom moves outside the wall on a timestep +by a distance delta (e.g. due to :doc:`fix nve `), then it is +put back inside the face by the same delta, and the sign of the +corresponding component of its velocity is flipped. + +When used in conjunction with :doc:`fix nve ` and :doc:`run_style verlet `, the resultant time-integration algorithm is +equivalent to the primitive splitting algorithm (PSA) described by +:ref:`Bond `. Because each reflection event divides +the corresponding timestep asymmetrically, energy conservation is only +satisfied to O(dt), rather than to O(dt^2) as it would be for +velocity-Verlet integration without reflective walls. + +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*. A *lo* face reflects particles +that move to a coordinate less than the wall position, back in the +*hi* direction. A *hi* face reflects particles that move to a +coordinate higher than the wall position, back in the *lo* direction. + +The position of each wall can be specified in one of 3 ways: as the +EDGE of the simulation box, as a constant value, or as a variable. If +EDGE is used, then the corresponding boundary of the current +simulation box is used. If a numeric constant is specified then the +wall is placed at that position in the appropriate dimension (x, y, or +z). In both the EDGE and constant cases, the wall will never move. +If the wall position is a variable, it should be specified as v_name, +where name is an :doc:`equal-style variable ` name. In this +case the variable is evaluated each timestep and the result becomes +the current position of the reflecting wall. Equal-style variables +can specify formulas with various mathematical functions, and include +:doc:`thermo_style ` command keywords for the simulation +box parameters and timestep and elapsed time. Thus it is easy to +specify a time-dependent wall position. + +The *units* keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant or +variable is used. It is not relevant when EDGE is used to specify a +face position. In the variable case, the variable is assumed to +produce a value compatible with the *units* setting you specify. + +A *box* value selects standard distance units as defined by the +:doc:`units ` command, e.g. Angstroms for units = real or metal. +A *lattice* value means the distance units are in lattice spacings. +The :doc:`lattice ` command must have been previously used to +define the lattice spacings. + + +---------- + + +Here are examples of variable definitions that move the wall position +in a time-dependent fashion using equal-style +:doc:`variables `. + +.. parsed-literal:: + + variable ramp equal ramp(0,10) + fix 1 all wall/reflect xlo v_ramp + +.. parsed-literal:: + + variable linear equal vdisplace(0,20) + fix 1 all wall/reflect xlo v_linear + +.. parsed-literal:: + + variable wiggle equal swiggle(0.0,5.0,3.0) + fix 1 all wall/reflect xlo v_wiggle + +.. parsed-literal:: + + variable wiggle equal cwiggle(0.0,5.0,3.0) + fix 1 all wall/reflect xlo v_wiggle + +The ramp(lo,hi) function adjusts the wall position linearly from lo to +hi over the course of a run. The vdisplace(c0,velocity) function does +something similar using the equation position = c0 + velocity*delta, +where delta is the elapsed time. + +The swiggle(c0,A,period) function causes the wall position to +oscillate sinusoidally according to this equation, where omega = 2 PI +/ period: + +.. parsed-literal:: + + position = c0 + A sin(omega*delta) + +The cwiggle(c0,A,period) function causes the wall position to +oscillate sinusoidally according to this equation, which will have an +initial wall velocity of 0.0, and thus may impose a gentler +perturbation on the particles: + +.. parsed-literal:: + + position = c0 + A (1 - cos(omega*delta)) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. No global or per-atom quantities are stored +by this fix for access by various :ref:`output commands `. No parameter of this fix can +be used with the *start/stop* keywords of the :doc:`run ` command. +This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +Any dimension (xyz) that has a reflecting wall must be non-periodic. + +A reflecting wall should not be used with rigid bodies such as those +defined by a "fix rigid" command. This is because the wall/reflect +displaces atoms directly rather than exerts a force on them. For +rigid bodies, use a soft wall instead, such as :doc:`fix wall/lj93 `. LAMMPS will flag the use of a rigid +fix with fix wall/reflect with a warning, but will not generate an +error. + +Related commands +"""""""""""""""" + +:doc:`fix wall/lj93 `, :doc:`fix oneway ` + +**Default:** none + + +---------- + + +.. _Bond: + + + +**(Bond)** Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_wall_region.txt b/doc/_sources/fix_wall_region.txt new file mode 100644 index 0000000000..12d418b06b --- /dev/null +++ b/doc/_sources/fix_wall_region.txt @@ -0,0 +1,227 @@ +.. index:: fix wall/region + +fix wall/region command +======================= + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID wall/region region-ID style epsilon sigma cutoff + +* ID, group-ID are documented in :doc:`fix ` command +* wall/region = style name of this fix command +* region-ID = region whose boundary will act as wall +* style = *lj93* or *lj126* or *colloid* or *harmonic* +* epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units) +* sigma = size factor for wall-particle interaction (distance units) +* cutoff = distance from wall at which wall-particle interaction is cut off (distance units) + +Examples +"""""""" + +.. parsed-literal:: + + fix wall all wall/region mySphere lj93 1.0 1.0 2.5 + +Description +""""""""""" + +Treat the surface of the geometric region defined by the *region-ID* +as a bounding wall which interacts with nearby particles according to +the specified style. The distance between a particle and the surface +is the distance to the nearest point on the surface and the force the +wall exerts on the particle is along the direction between that point +and the particle, which is the direction normal to the surface at that +point. Note that if the region surface is comprised of multiple +"faces", then each face can exert a force on the particle if it is +close enough. E.g. for :doc:`region_style block `, a particle +in the interior, near a corner of the block, could feel wall forces +from 1, 2, or 3 faces of the block. + +Regions are defined using the :doc:`region ` command. Note that +the region volume can be interior or exterior to the bounding surface, +which will determine in which direction the surface interacts with +particles, i.e. the direction of the surface normal. Regions can +either be primitive shapes (block, sphere, cylinder, etc) or +combinations of primitive shapes specified via the *union* or +*intersect* region styles. These latter styles can be used to +construct particle containers with complex shapes. Regions can also +change over time via the :doc:`region ` command keywords (move) +and *rotate*. If such a region is used with this fix, then the of +region surface will move over time in the corresponding manner. + +.. note:: + + As discussed on the :doc:`region ` command doc page, + regions in LAMMPS do not get wrapped across periodic boundaries. It + is up to you to insure that periodic or non-periodic boundaries are + specified appropriately via the :doc:`boundary ` command when + using a region as a wall that bounds particle motion. This also means + that if you embed a region in your simulation box and want it to + repulse particles from its surface (using the "side out" option in the + :doc:`region ` command), that its repulsive force will not be + felt across a periodic boundary. + +.. note:: + + For primitive regions with sharp corners and/or edges (e.g. a + block or cylinder), wall/particle forces are computed accurately for + both interior and exterior regions. For *union* and *intersect* + regions, additional sharp corners and edges may be present due to the + intersection of the surfaces of 2 or more primitive volumes. These + corners and edges can be of two types: concave or convex. Concave + points/edges are like the corners of a cube as seen by particles in + the interior of a cube. Wall/particle forces around these features + are computed correctly. Convex points/edges are like the corners of a + cube as seen by particles exterior to the cube, i.e. the points jut + into the volume where particles are present. LAMMPS does NOT compute + the location of these convex points directly, and hence wall/particle + forces in the cutoff volume around these points suffer from + inaccuracies. The basic problem is that the outward normal of the + surface is not continuous at these points. This can cause particles + to feel no force (they don't "see" the wall) when in one location, + then move a distance epsilon, and suddenly feel a large force because + they now "see" the wall. In a worst-case scenario, this can blow + particles out of the simulation box. Thus, as a general rule you + should not use the fix wall/region command with *union* or + *interesect* regions that have convex points or edges. + +.. note:: + + Similarly, you should not define *union* or *intersert* regions + for use with this command that share a common face, even if the face + is smooth. E.g. two regions of style block in a *union* region, where + the two blocks have the same face. This is because LAMMPS discards + points that are part of multiple sub-regions when calculating + wall/particle interactions, to avoid double-counting the interaction. + Having two coincident faces could cause the face to become invisible + to the particles. The solution is to make the two faces differ by + epsilon in their position. + +The energy of wall-particle interactions depends on the specified +style. + +For style *lj93*, the energy E is given by the 9/3 potential: + +.. image:: Eqs/fix_wall_lj93.jpg + :align: center + +For style *lj126*, the energy E is given by the 12/6 potential: + +.. image:: Eqs/pair_lj.jpg + :align: center + +For style *colloid*, the energy E is given by an integrated form of +the :doc:`pair_style colloid ` potential: + +.. image:: Eqs/fix_wall_colloid.jpg + :align: center + +For style *wall/harmonic*, the energy E is given by a harmonic spring +potential: + +.. image:: Eqs/fix_wall_harmonic.jpg + :align: center + +In all cases, *r* is the distance from the particle to the region +surface, and Rc is the *cutoff* distance at which the particle and +surface no longer interact. The energy of the wall potential is +shifted so that the wall-particle interaction energy is 0.0 at the +cutoff distance. + +For the *lj93* and *lj126* styles, *epsilon* and *sigma* are the usual +Lennard-Jones parameters, which determine the strength and size of the +particle as it interacts with the wall. Epsilon has energy units. +Note that this *epsilon* and *sigma* may be different than any +*epsilon* or *sigma* values defined for a pair style that computes +particle-particle interactions. + +The *lj93* interaction is derived by integrating over a 3d +half-lattice of Lennard-Jones 12/6 particles. The *lj126* interaction +is effectively a harder, more repulsive wall interaction. + +For the *colloid* style, *epsilon* is effectively a Hamaker constant +with energy units for the colloid-wall interaction, *R* is the radius +of the colloid particle, *D* is the distance from the surface of the +colloid particle to the wall (r-R), and *sigma* is the size of a +constituent LJ particle inside the colloid particle. Note that the +cutoff distance Rc in this case is the distance from the colloid +particle center to the wall. + +The *colloid* interaction is derived by integrating over constituent +LJ particles of size *sigma* within the colloid particle and a 3d +half-lattice of Lennard-Jones 12/6 particles of size *sigma* in the +wall. + +For the *wall/harmonic* style, *epsilon* is effectively the spring +constant K, and has units (energy/distance^2). The input parameter +*sigma* is ignored. The minimum energy position of the harmonic +spring is at the *cutoff*. This is a repulsive-only spring since the +interaction is truncated at the *cutoff* + +.. note:: + + For all of the styles, you must insure that r is always > 0 for + all particles in the group, or LAMMPS will generate an error. This + means you cannot start your simulation with particles on the region + surface (r = 0) or with particles on the wrong side of the region + surface (r < 0). For the *wall/lj93* and *wall/lj126* styles, the + energy of the wall/particle interaction (and hence the force on the + particle) blows up as r -> 0. The *wall/colloid* style is even more + restrictive, since the energy blows up as D = r-R -> 0. This means + the finite-size particles of radius R must be a distance larger than R + from the region surface. The *harmonic* style is a softer potential + and does not blow up as r -> 0, but you must use a large enough + *epsilon* that particles always reamin on the correct side of the + region surface (r > 0). + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. + +The :doc:`fix_modify ` *energy* option is supported by this +fix to add the energy of interaction between atoms and the wall to the +system's potential energy as part of :doc:`thermodynamic output `. + +This fix computes a global scalar energy and a global 3-length vector +of forces, which can be accessed by various :ref:`output commands `. The scalar energy is the sum +of energy interactions for all particles interacting with the wall +represented by the region surface. The 3 vector quantities are the +x,y,z components of the total force acting on the wall due to the +particles. The scalar and vector values calculated by this fix are +"extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. + +The forces due to this fix are imposed during an energy minimization, +invoked by the :doc:`minimize ` command. + +.. note:: + + If you want the atom/wall interaction energy to be included in + the total potential energy of the system (the quantity being + minimized), you MUST enable the :doc:`fix_modify ` *energy* + option for this fix. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`fix wall/lj93 `, +:doc:`fix wall/lj126 `, +:doc:`fix wall/colloid `, +:doc:`fix wall/gran ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/fix_wall_srd.txt b/doc/_sources/fix_wall_srd.txt new file mode 100644 index 0000000000..9bf28e02a1 --- /dev/null +++ b/doc/_sources/fix_wall_srd.txt @@ -0,0 +1,225 @@ +.. index:: fix wall/srd + +fix wall/srd command +==================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID wall/srd face arg ... keyword value ... + +* ID, group-ID are documented in :doc:`fix ` command +* wall/srd = style name of this fix command +* one or more face/arg pairs may be appended +* face = *xlo* or *xhi* or *ylo* or *yhi* or *zlo* or *zhi* +.. parsed-literal:: + + *xlo*,*ylo*,*zlo* arg = EDGE or constant or variable + EDGE = current lo edge of simulation box + constant = number like 0.0 or -30.0 (distance units) + variable = :doc:`equal-style variable ` like v_x or v_wiggle + *xhi*,*yhi*,*zhi* arg = EDGE or constant or variable + EDGE = current hi edge of simulation box + constant = number like 50.0 or 100.3 (distance units) + variable = :doc:`equal-style variable ` like v_x or v_wiggle + +* zero or more keyword/value pairs may be appended +* keyword = *units* +.. parsed-literal:: + + *units* value = *lattice* or *box* + *lattice* = the wall position is defined in lattice units + *box* = the wall position is defined in simulation box units + + + +Examples +"""""""" + +.. parsed-literal:: + + fix xwalls all wall/srd xlo EDGE xhi EDGE + fix walls all wall/srd xlo 0.0 ylo 10.0 units box + fix top all wall/srd zhi v_pressdown + +Description +""""""""""" + +Bound the simulation with one or more walls which interact with +stochastic reaction dynamics (SRD) particles as slip (smooth) or +no-slip (rough) flat surfaces. The wall interaction is actually +invoked via the :doc:`fix srd ` command, only on the group of +SRD particles it defines, so the group setting for the fix wall/srd +command is ignored. + +A particle/wall collision occurs if an SRD particle moves outside the +wall on a timestep. This alters the position and velocity of the SRD +particle and imparts a force to the wall. + +The *collision* and *Tsrd* settings specified via the :doc:`fix srd ` command affect the SRD/wall collisions. A *slip* +setting for the *collision* keyword means that the tangential +component of the SRD particle momentum is preserved. Thus only a +normal force is imparted to the wall. The normal component of the new +SRD velocity is sampled from a Gaussian distribution at temperature +*Tsrd*. + +For a *noslip* setting of the *collision* keyword, both the normal and +tangential components of the new SRD velocity are sampled from a +Gaussian distribution at temperature *Tsrd*. Additionally, a new +tangential direction for the SRD velocity is chosen randomly. This +collision style imparts both a normal and tangential force to the +wall. + +Up to 6 walls or faces can be specified in a single command: *xlo*, +*xhi*, *ylo*, *yhi*, *zlo*, *zhi*. A *lo* face reflects particles +that move to a coordinate less than the wall position, back in the +*hi* direction. A *hi* face reflects particles that move to a +coordinate higher than the wall position, back in the *lo* direction. + +The position of each wall can be specified in one of 3 ways: as the +EDGE of the simulation box, as a constant value, or as a variable. If +EDGE is used, then the corresponding boundary of the current +simulation box is used. If a numeric constant is specified then the +wall is placed at that position in the appropriate dimension (x, y, or +z). In both the EDGE and constant cases, the wall will never move. +If the wall position is a variable, it should be specified as v_name, +where name is an :doc:`equal-style variable ` name. In this +case the variable is evaluated each timestep and the result becomes +the current position of the reflecting wall. Equal-style variables +can specify formulas with various mathematical functions, and include +:doc:`thermo_style ` command keywords for the simulation +box parameters and timestep and elapsed time. Thus it is easy to +specify a time-dependent wall position. + +.. note:: + + Because the trajectory of the SRD particle is tracked as it + collides with the wall, you must insure that r = distance of the + particle from the wall, is always > 0 for SRD particles, or LAMMPS + will generate an error. This means you cannot start your simulation + with SRD particles at the wall position *coord* (r = 0) or with + particles on the wrong side of the wall (r < 0). + +.. note:: + + If you have 2 or more walls that come together at an edge or + corner (e.g. walls in the x and y dimensions), then be sure to set the + *overlap* keyword to *yes* in the :doc:`fix srd ` command, + since the walls effectively overlap when SRD particles collide with + them. LAMMPS will issue a warning if you do not do this. + +.. note:: + + The walls of this fix only interact with SRD particles, as + defined by the :doc:`fix srd ` command. If you are simulating + a mixture containing other kinds of particles, then you should + typically use :doc:`another wall command ` to act on the other + particles. Since SRD particles will be colliding both with the walls + and the other particles, it is important to insure that the other + particle's finite extent does not overlap an SRD wall. If you do not + do this, you may generate errors when SRD particles end up "inside" + another particle or a wall at the beginning of a collision step. + +The *units* keyword determines the meaning of the distance units used +to define a wall position, but only when a numeric constant is used. +It is not relevant when EDGE or a variable is used to specify a face +position. + +A *box* value selects standard distance units as defined by the +:doc:`units ` command, e.g. Angstroms for units = real or metal. +A *lattice* value means the distance units are in lattice spacings. +The :doc:`lattice ` command must have been previously used to +define the lattice spacings. + + +---------- + + +Here are examples of variable definitions that move the wall position +in a time-dependent fashion using equal-style +:doc:`variables `. + +.. parsed-literal:: + + variable ramp equal ramp(0,10) + fix 1 all wall/srd xlo v_ramp + +.. parsed-literal:: + + variable linear equal vdisplace(0,20) + fix 1 all wall/srd xlo v_linear + +.. parsed-literal:: + + variable wiggle equal swiggle(0.0,5.0,3.0) + fix 1 all wall/srd xlo v_wiggle + +.. parsed-literal:: + + variable wiggle equal cwiggle(0.0,5.0,3.0) + fix 1 all wall/srd xlo v_wiggle + +The ramp(lo,hi) function adjusts the wall position linearly from lo to +hi over the course of a run. The displace(c0,velocity) function does +something similar using the equation position = c0 + velocity*delta, +where delta is the elapsed time. + +The swiggle(c0,A,period) function causes the wall position to +oscillate sinusoidally according to this equation, where omega = 2 PI +/ period: + +.. parsed-literal:: + + position = c0 + A sin(omega*delta) + +The cwiggle(c0,A,period) function causes the wall position to +oscillate sinusoidally according to this equation, which will have an +initial wall velocity of 0.0, and thus may impose a gentler +perturbation on the particles: + +.. parsed-literal:: + + position = c0 + A (1 - cos(omega*delta)) + + +---------- + + +Restart, fix_modify, output, run start/stop, minimize info +"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options +are relevant to this fix. + +This fix computes a global array of values which can be accessed by +various :ref:`output commands `. The number of +rows in the array is equal to the number of walls defined by the fix. +The number of columns is 3, for the x,y,z components of force on each +wall. + +Note that an outward normal force on a wall will be a negative value +for *lo* walls and a positive value for *hi* walls. The array values +calculated by this fix are "extensive". + +No parameter of this fix can be used with the *start/stop* keywords of +the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. + +Restrictions +"""""""""""" + + +Any dimension (xyz) that has an SRD wall must be non-periodic. + +Related commands +"""""""""""""""" + +:doc:`fix srd ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/group.txt b/doc/_sources/group.txt new file mode 100644 index 0000000000..9bd92c3a97 --- /dev/null +++ b/doc/_sources/group.txt @@ -0,0 +1,315 @@ +.. index:: group + +group command +============= + +Syntax +"""""" + +.. parsed-literal:: + + group ID style args + +* ID = user-defined name of the group +* style = *delete* or *region* or *type* or *id* or *molecule* or *variable* or *include* or *subtract* or *union* or *intersect* or *dynamic* or *static* +.. parsed-literal:: + + *delete* = no args + *clear* = no args + *region* args = region-ID + *type* or *id* or *molecule* + args = list of one or more atom types, atom IDs, or molecule IDs + any entry in list can be a sequence formatted as A:B or A:B:C where + A = starting index, B = ending index, + C = increment between indices, 1 if not specified + args = logical value + logical = "<" or "<=" or ">" or ">=" or "==" or "!=" + value = an atom type or atom ID or molecule ID (depending on *style*) + args = logical value1 value2 + logical = "<>" + value1,value2 = atom types or atom IDs or molecule IDs (depending on *style*) + *variable* args = variable-name + *include* args = molecule + molecule = add atoms to group with same molecule ID as atoms already in group + *subtract* args = two or more group IDs + *union* args = one or more group IDs + *intersect* args = two or more group IDs + *dynamic* args = parent-ID keyword value ... + one or more keyword/value pairs may be appended + keyword = *region* or *var* or *every* + *region* value = region-ID + *var* value = name of variable + *every* value = N = update group every this many timesteps + *static* = no args + + + +Examples +"""""""" + +.. parsed-literal:: + + group edge region regstrip + group water type 3 4 + group sub id 10 25 50 + group sub id 10 25 50 500:1000 + group sub id 100:10000:10 + group sub id <= 150 + group polyA molecule <> 50 250 + group hienergy variable eng + group hienergy include molecule + group boundary subtract all a2 a3 + group boundary union lower upper + group boundary intersect upper flow + group boundary delete + group mine dynamic all region myRegion every 100 + +Description +""""""""""" + +Identify a collection of atoms as belonging to a group. The group ID +can then be used in other commands such as :doc:`fix `, +:doc:`compute `, :doc:`dump `, or :doc:`velocity ` +to act on those atoms together. + +If the group ID already exists, the group command adds the specified +atoms to the group. + +.. note:: + + By default groups are static, meaning the atoms are permanently + assigned to the group. For example, if the *region* style is used to + assign atoms to a group, the atoms will remain in the group even if + they later move out of the region. As explained below, the *dynamic* + style can be used to make a group dynamic so that a periodic + determination is made as to which atoms are in the group. Since many + LAMMPS commands operate on groups of atoms, you should think carefully + about whether making a group dynamic makes sense for your model. + +A group with the ID *all* is predefined. All atoms belong to this +group. This group cannot be deleted, or made dynamic. + +The *delete* style removes the named group and un-assigns all atoms +that were assigned to that group. Since there is a restriction (see +below) that no more than 32 groups can be defined at any time, the +*delete* style allows you to remove groups that are no longer needed, +so that more can be specified. You cannot delete a group if it has +been used to define a current :doc:`fix ` or :doc:`compute ` +or :doc:`dump `. + +The *clear* style un-assigns all atoms that were assigned to that +group. This may be dangerous to do during a simulation run, +e.g. using the :doc:`run every ` command if a fix or compute or +other operation expects the atoms in the group to remain constant, but +LAMMPS does not check for this. + +The *region* style puts all atoms in the region volume into the group. +Note that this is a static one-time assignment. The atoms remain +assigned (or not assigned) to the group even in they later move out of +the region volume. + +The *type*, *id*, and *molecule* styles put all atoms with the +specified atom types, atom IDs, or molecule IDs into the group. These +3 styles can use arguments specified in one of two formats. + +The first format is a list of values (types or IDs). For example, the +2nd command in the examples above puts all atoms of type 3 or 4 into +the group named *water*. Each entry in the list can be a +colon-separated sequence A:B or A:B:C, as in two of the examples +above. A "sequence" generates a sequence of values (types or IDs), +with an optional increment. The first example with 500:1000 has the +default increment of 1 and would add all atom IDs from 500 to 1000 +(inclusive) to the group sub, along with 10,25,50 since they also +appear in the list of values. The second example with 100:10000:10 +uses an increment of 10 and would thus would add atoms IDs +100,110,120, ... 9990,10000 to the group sub. + +The second format is a *logical* followed by one or two values (type +or ID). The 7 valid logicals are listed above. All the logicals +except <> take a single argument. The 3rd example above adds all +atoms with IDs from 1 to 150 to the group named *sub*. The logical <> +means "between" and takes 2 arguments. The 4th example above adds all +atoms belonging to molecules with IDs from 50 to 250 (inclusive) to +the group named polyA. + +The *variable* style evaluates a variable to determine which atoms to +add to the group. It must be an :doc:`atom-style variable ` +previously defined in the input script. If the variable evaluates +to a non-zero value for a particular atom, then that atom is added +to the specified group. + +Atom-style variables can specify formulas that include thermodynamic +quantities, per-atom values such as atom coordinates, or per-atom +quantities calculated by computes, fixes, or other variables. They +can also include Boolean logic where 2 numeric values are compared to +yield a 1 or 0 (effectively a true or false). Thus using the +*variable* style, is a general way to flag specific atoms to include +or exclude from a group. + +For example, these lines define a variable "eatom" that calculates the +potential energy of each atom and includes it in the group if its +potential energy is above the threshhold value -3.0. + +.. parsed-literal:: + + compute 1 all pe/atom + compute 2 all reduce sum c_1 + thermo_style custom step temp pe c_2 + run 0 + +.. parsed-literal:: + + variable eatom atom "c_1 > -3.0" + group hienergy variable eatom + +Note that these lines + +.. parsed-literal:: + + compute 2 all reduce sum c_1 + thermo_style custom step temp pe c_2 + run 0 + +are necessary to insure that the "eatom" variable is current when the +group command invokes it. Because the eatom variable computes the +per-atom energy via the pe/atom compute, it will only be current if a +run has been performed which evaluated pairwise energies, and the +pe/atom compute was actually invoked during the run. Printing the +thermodyanmic info for compute 2 insures that this is the case, since +it sums the pe/atom compute values (in the reduce compute) to output +them to the screen. See the "Variable Accuracy" section of the +:doc:`variable ` doc page for more details on insuring that +variables are current when they are evaluated between runs. + +The *include* style with its arg *molecule* adds atoms to a group that +have the same molecule ID as atoms already in the group. The molecule +ID = 0 is ignored in this operation, since it is assumed to flag +isolated atoms that are not part of molecules. An example of where +this operation is useful is if the *region* style has been used +previously to add atoms to a group that are within a geometric region. +If molecules straddle the region boundary, then atoms outside the +region that are part of molecules with atoms inside the region will +not be in the group. Using the group command a 2nd time with *include +molecule* will add those atoms that are outside the region to the +group. + +.. note:: + + The *include molecule* operation is relatively expensive in a + parallel sense. This is because it requires communication of relevant + molecule IDs between all the processors and each processor to loop + over its atoms once per processor, to compare its atoms to the list of + molecule IDs from every other processor. Hence it scales as N, rather + than N/P as most of the group operations do, where N is the number of + atoms, and P is the number of processors. + +The *subtract* style takes a list of two or more existing group names +as arguments. All atoms that belong to the 1st group, but not to any +of the other groups are added to the specified group. + +The *union* style takes a list of one or more existing group names as +arguments. All atoms that belong to any of the listed groups are +added to the specified group. + +The *intersect* style takes a list of two or more existing group names +as arguments. Atoms that belong to every one of the listed groups are +added to the specified group. + + +---------- + + +The *dynamic* style flags an existing or new group as dynamic. This +means atoms will be (re)assigned to the group periodically as a +simulation runs. This is in contrast to static groups where atoms are +permanently assigned to the group. The way the assignment occurs is +as follows. Only atoms in the group specified as the parent group via +the parent-ID are assigned to the dynamic group before the following +conditions are applied. If the *region* keyword is used, atoms not in +the specified region are removed from the dynamic group. If the *var* +keyword is used, the variable name must be an atom-style or +atomfile-style variable. The variable is evaluated and atoms whose +per-atom values are 0.0, are removed from the dynamic group. + +The assignment of atoms to a dynamic group is done at the beginning of +each run and on every timestep that is a multiple of *N*, which is the +argument for the *every* keyword (N = 1 is the default). For an +energy minimization, via the :doc:`minimize ` command, an +assignement is made at the beginning of the minimization, but not +during the iterations of the minimizer. + +The point in the timestep at which atoms are assigned to a dynamic +group is after the initial stage of velocity Verlet time integration +has been performed, and before neighbor lists or forces are computed. +This is the point in the timestep where atom positions have just +changed due to the time integration, so the region criterion should be +accurate, if applied. + +.. note:: + + If the *region* keyword is used to determine what atoms are in + the dynamic group, atoms can move outside of the simulation box + between reneighboring events. Thus if you want to include all atoms + on the left side of the simulation box, you probably want to set the + left boundary of the region to be outside the simulation box by some + reasonable amount (e.g. up to the cutoff of the potential), else they + may be excluded from the dynamic region. + +Here is an example of using a dynamic group to shrink the set of atoms +being integrated by using a spherical region with a variable radius +(shrinking from 18 to 5 over the course of the run). This could be +used to model a quench of the system, freezing atoms outside the +shrinking sphere, then converting the remaining atoms to a static +group and running further. + +.. parsed-literal:: + + variable nsteps equal 5000 + variable rad equal 18-(step/v_nsteps)*(18-5) + region ss sphere 20 20 0 v_rad + group mobile dynamic all region ss + fix 1 mobile nve + run ${nsteps} + group mobile static + run ${nsteps} + +.. note:: + + All fixes and computes take a group ID as an argument, but they + do not all allow for use of a dynamic group. If you get an error + message that this is not allowed, but feel that it should be for the + fix or compute in question, then please post your reasoning to the + LAMMPS mail list and we can change it. + +The *static* style removes the setting for a dynamic group, converting +it to a static group (the default). The atoms in the static group are +those currently in the dynamic group. + + +---------- + + +Restrictions +"""""""""""" + + +There can be no more than 32 groups defined at one time, including +"all". + +The parent group of a dynamic group cannot itself be a dynamic group. + +Related commands +"""""""""""""""" + +:doc:`dump `, :doc:`fix `, :doc:`region `, +:doc:`velocity ` + +Default +""""""" + +All atoms belong to the "all" group. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/group2ndx.txt b/doc/_sources/group2ndx.txt new file mode 100644 index 0000000000..b3eaa834ef --- /dev/null +++ b/doc/_sources/group2ndx.txt @@ -0,0 +1,62 @@ +.. index:: group2ndx + +group2ndx command +================= + +Syntax +"""""" + +.. parsed-literal:: + + group2ndx file group-ID ... + +* file = name of index file to write out +* zero or more group IDs may be appended + + +Examples +"""""""" + +.. parsed-literal:: + + group2ndx allindex.ndx + group2ndx someindex.ndx upper lower mobile + +Description +""""""""""" + +Write a Gromacs style index file in text format that associates atom IDs +with the corresponding group definitions. This index file can be used +with in combination with Gromacs analysis tools or to import group +definitions into the :doc:`fix colvars ` input file. + +Without specifying any group IDs, all groups will be written to the index +file. When specifying group IDs, only those groups will be written to the +index file. In order to follow the Gromacs conventions, the group *all* +will be renamed to *System* in the index file. + + +---------- + + +Restrictions +"""""""""""" + + +This command requires that atoms have atom IDs, since this is the +information that is written to the index file. + +This fix is part of the USER-COLVARS package. It is only enabled if +LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. + +Related commands +"""""""""""""""" + +:doc:`group `, :doc:`dump `, :doc:`fix colvars ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/if.txt b/doc/_sources/if.txt new file mode 100644 index 0000000000..f33ec99841 --- /dev/null +++ b/doc/_sources/if.txt @@ -0,0 +1,214 @@ +.. index:: if + +if command +========== + +Syntax +"""""" + +.. parsed-literal:: + + if boolean then t1 t2 ... elif boolean f1 f2 ... elif boolean f1 f2 ... else e1 e2 ... + +* boolean = a Boolean expression evaluated as TRUE or FALSE (see below) +* then = required word +* t1,t2,...,tN = one or more LAMMPS commands to execute if condition is met, each enclosed in quotes +* elif = optional word, can appear multiple times +* f1,f2,...,fN = one or more LAMMPS commands to execute if elif condition is met, each enclosed in quotes (optional arguments) +* else = optional argument +* e1,e2,...,eN = one or more LAMMPS commands to execute if no condition is met, each enclosed in quotes (optional arguments) + +Examples +"""""""" + +.. parsed-literal:: + + if "${steps} > 1000" then quit + if "${myString} == a10" then quit + if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y" + if "(${eng} > 0.0) || ($n < 1000)" then & + "timestep 0.005" & + elif $n<10000 & + "timestep 0.01" & + else & + "timestep 0.02" & + "print 'Max step reached'" + if "${eng} > ${eng_previous}" then "jump file1" else "jump file2" + +Description +""""""""""" + +This command provides an if-then-else capability within an input +script. A Boolean expression is evaluted and the result is TRUE or +FALSE. Note that as in the examples above, the expression can contain +variables, as defined by the :doc:`variable ` command, which +will be evaluated as part of the expression. Thus a user-defined +formula that reflects the current state of the simulation can be used +to issue one or more new commands. + +If the result of the Boolean expression is TRUE, then one or more +commands (t1, t2, ..., tN) are executed. If it is FALSE, then Boolean +expressions associated with successive elif keywords are evaluated +until one is found to be true, in which case its commands (f1, f2, +..., fN) are executed. If no Boolean expression is TRUE, then the +commands associated with the else keyword, namely (e1, e2, ..., eN), +are executed. The elif and else keywords and their associated +commands are optional. If they aren't specified and the initial +Boolean expression is FALSE, then no commands are executed. + +The syntax for Boolean expressions is described below. + +Each command (t1, f1, e1, etc) can be any valid LAMMPS input script +command, except an :doc:`include ` command, which is not +allowed. If the command is more than one word, it must enclosed in +quotes, so it will be treated as a single argument, as in the examples +above. + +.. note:: + + If a command itself requires a quoted argument (e.g. a + :doc:`print ` command), then double and single quotes can be used + and nested in the usual manner, as in the examples above and below. + See :ref:`Section_commands 2 ` of the manual for + more details on using quotes in arguments. Only one of level of + nesting is allowed, but that should be sufficient for most use cases. + +Note that by using the line continuation character "&", the if command +can be spread across many lines, though it is still a single command: + +.. parsed-literal:: + + if "$a < $b" then & + "print 'Minimum value = $a'" & + "run 1000" & + else & + 'print "Minimum value = $b"' & + "minimize 0.001 0.001 1000 10000" + +Note that if one of the commands to execute is :doc:`quit `, as in +the first example above, then executing the command will cause LAMMPS +to halt. + +Note that by jumping to a label in the same input script, the if +command can be used to break out of a loop. See the :doc:`variable delete ` command for info on how to delete the associated +loop variable, so that it can be re-used later in the input script. + +Here is an example of a loop which checks every 1000 steps if the +system temperature has reached a certain value, and if so, breaks out +of the loop to finish the run. Note that any variable could be +checked, so long as it is current on the timestep when the run +completes. As explained on the :doc:`variable ` doc page, +this can be insured by includig the variable in thermodynamic output. + +.. parsed-literal:: + + variable myTemp equal temp + label loop + variable a loop 1000 + run 1000 + if "${myTemp} < 300.0" then "jump SELF break" + next a + jump SELF loop + label break + print "ALL DONE" + +Here is an example of a double loop which uses the if and +:doc:`jump ` commands to break out of the inner loop when a +condition is met, then continues iterating thru the outer loop. + +.. parsed-literal:: + + label loopa + variable a loop 5 + label loopb + variable b loop 5 + print "A,B = $a,$b" + run 10000 + if "$b > 2" then "jump SELF break" + next b + jump in.script loopb + label break + variable b delete + next a + jump SELF loopa + + +---------- + + +The Boolean expressions for the if and elif keywords have a C-like +syntax. Note that each expression is a single argument within the if +command. Thus if you want to include spaces in the expression for +clarity, you must enclose the entire expression in quotes. + +An expression is built out of numbers (which start with a digit or +period or minus sign) or strings (which start with a letter and can +contain alphanumeric characters or underscores): + +.. parsed-literal:: + + 0.2, 100, 1.0e20, -15.4, etc + InP, myString, a123, ab_23_cd, etc + +and Boolean operators: + +.. parsed-literal:: + + A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A || B, !A + +Each A and B is a number or string or a variable reference like $a or +${abc}, or A or B can be another Boolean expression. + +If a variable is used it can produce a number when evaluated, like an +:doc:`equal-style variable `. Or it can produce a string, +like an :doc:`index-style variable `. For an individual +Boolean operator, A and B must both be numbers or must both be +strings. You cannot compare a number to a string. + +Expressions are evaluated left to right and have the usual C-style +precedence: the unary logical NOT operator "!" has the highest +precedence, the 4 relational operators "<", "<=", ">", and ">=" are +next; the two remaining relational operators "==" and "!=" are next; +then the logical AND operator "&&"; and finally the logical OR +operator "||" has the lowest precedence. Parenthesis can be used to +group one or more portions of an expression and/or enforce a different +order of evaluation than what would occur with the default precedence. + +When the 6 relational operators (first 6 in list above) compare 2 +numbers, they return either a 1.0 or 0.0 depending on whether the +relationship between A and B is TRUE or FALSE. When the 6 relational +operators compare 2 strings, they also return a 1.0 or 0.0 for TRUE or +FALSE, but the comparison is done by the C function strcmp(). + +When the 3 logical operators (last 3 in list above) compare 2 numbers, +they also return either a 1.0 or 0.0 depending on whether the +relationship between A and B is TRUE or FALSE (or just A). The +logical AND operator will return 1.0 if both its arguments are +non-zero, else it returns 0.0. The logical OR operator will return +1.0 if either of its arguments is non-zero, else it returns 0.0. The +logical NOT operator returns 1.0 if its argument is 0.0, else it +returns 0.0. The 3 logical operators can only be used to operate on +numbers, not on strings. + +The overall Boolean expression produces a TRUE result if the result is +non-zero. If the result is zero, the expression result is FALSE. + + +---------- + + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`variable `, :doc:`print ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_class2.txt b/doc/_sources/improper_class2.txt new file mode 100644 index 0000000000..d57d7f50b3 --- /dev/null +++ b/doc/_sources/improper_class2.txt @@ -0,0 +1,144 @@ +.. index:: improper_style class2 + +improper_style class2 command +============================= + +improper_style class2/omp command +================================= + +Syntax +"""""" + +.. parsed-literal:: + + improper_style class2 + +Examples +"""""""" + +.. parsed-literal:: + + improper_style class2 + improper_coeff 1 100.0 0 + improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 + +Description +""""""""""" + +The *class2* improper style uses the potential + +.. image:: Eqs/improper_class2.jpg + :align: center + +where Ei is the improper term and Eaa is an angle-angle term. The 3 X +terms in Ei are an average over 3 out-of-plane angles. + +The 4 atoms in an improper quadruplet (listed in the data file read by +the :doc:`read_data ` command) are ordered I,J,K,L. X_IJKL +refers to the angle between the plane of I,J,K and the plane of J,K,L, +and the bond JK lies in both planes. Similarly for X_KJLI and X_LJIK. +Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X +terms. Thus J (the 2nd atom in the quadruplet) is the atom of +symmetry in the 3 X angles. + +The subscripts on the various theta's refer to different combinations +of 3 atoms (I,J,K,L) used to form a particular angle. E.g. Theta_IJL +is the angle formed by atoms I,J,L with J in the middle. Theta1, +theta2, theta3 are the equilibrium positions of those angles. Again, +atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the +theta angles, since it is always the center atom. + +Since atom J is the atom of symmetry, normally the bonds J-I, J-K, J-L +would exist for an improper to be defined between the 4 atoms, but +this is not required. + +See :ref:`(Sun) ` for a description of the COMPASS class2 force field. + +Coefficients for the Ei and Eaa formulas must be defined for each +improper type via the :doc:`improper_coeff ` command as +in the example above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands. + +These are the 2 coefficients for the Ei formula: + +* K (energy/radian^2) +* X0 (degrees) + +X0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + +For the Eaa formula, each line in a +:doc:`improper_coeff ` command in the input script lists +7 coefficients, the first of which is "aa" to indicate they are +AngleAngle coefficients. In a data file, these coefficients should be +listed under a "AngleAngle Coeffs" heading and you must leave out the +"aa", i.e. only list 6 coefficients after the improper type. + +* aa +* M1 (energy/distance) +* M2 (energy/distance) +* M3 (energy/distance) +* theta1 (degrees) +* theta2 (degrees) +* theta3 (degrees) + +The theta values are specified in degrees, but LAMMPS converts them to +radians internally; hence the units of M are in energy/radian^2. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This improper style can only be used if LAMMPS was built with the +CLASS2 package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +**Default:** none + + +---------- + + +.. _Sun: + + + +**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_coeff.txt b/doc/_sources/improper_coeff.txt new file mode 100644 index 0000000000..1e73907789 --- /dev/null +++ b/doc/_sources/improper_coeff.txt @@ -0,0 +1,115 @@ +.. index:: improper_coeff + +improper_coeff command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + improper_coeff N args + +* N = improper type (see asterisk form below) +* args = coefficients for one or more improper types + +Examples +"""""""" + +.. parsed-literal:: + + improper_coeff 1 300.0 0.0 + improper_coeff * 80.2 -1 2 + improper_coeff *4 80.2 -1 2 + +Description +""""""""""" + +Specify the improper force field coefficients for one or more improper +types. The number and meaning of the coefficients depends on the +improper style. Improper coefficients can also be set in the data +file read by the :doc:`read_data ` command or in a restart +file. + +N can be specified in one of two ways. An explicit numeric value can +be used, as in the 1st example above. Or a wild-card asterisk can be +used to set the coefficients for multiple improper types. This takes +the form "*" or "*n" or "n*" or "m*n". If N = the number of improper +types, then an asterisk with no numeric values means all types from 1 +to N. A leading asterisk means all types from 1 to n (inclusive). A +trailing asterisk means all types from n to N (inclusive). A middle +asterisk means all types from m to n (inclusive). + +Note that using an improper_coeff command can override a previous +setting for the same improper type. For example, these commands set +the coeffs for all improper types, then overwrite the coeffs for just +improper type 2: + +.. parsed-literal:: + + improper_coeff * 300.0 0.0 + improper_coeff 2 50.0 0.0 + +A line in a data file that specifies improper coefficients uses the +exact same format as the arguments of the improper_coeff command in an +input script, except that wild-card asterisks should not be used since +coefficients for all N types must be listed in the file. For example, +under the "Improper Coeffs" section of a data file, the line that +corresponds to the 1st example above would be listed as + +.. parsed-literal:: + + 1 300.0 0.0 + +The :doc:`improper_style class2 ` is an exception to +this rule, in that an additional argument is used in the input script +to allow specification of the cross-term coefficients. See its doc +page for details. + + +---------- + + +Here is an alphabetic list of improper styles defined in LAMMPS. Click on +the style to display the formula it computes and coefficients +specified by the associated :doc:`improper_coeff ` command. + +Note that there are also additional improper styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the improper section of +:ref:`this page `. + +* :doc:`improper_style none ` - turn off improper interactions +* :doc:`improper_style hybrid ` - define multiple styles of improper interactions + +* :doc:`improper_style class2 ` - COMPASS (class 2) improper +* :doc:`improper_style cvff ` - CVFF improper +* :doc:`improper_style harmonic ` - harmonic improper +* :doc:`improper_style umbrella ` - DREIDING improper + + +---------- + + +Restrictions +"""""""""""" + + +This command must come after the simulation box is defined by a +:doc:`read_data `, :doc:`read_restart `, or +:doc:`create_box ` command. + +An improper style must be defined before any improper coefficients are +set, either in the input script or in a data file. + +Related commands +"""""""""""""""" + +:doc:`improper_style ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_cossq.txt b/doc/_sources/improper_cossq.txt new file mode 100644 index 0000000000..c456838aa9 --- /dev/null +++ b/doc/_sources/improper_cossq.txt @@ -0,0 +1,104 @@ +.. index:: improper_style cossq + +improper_style cossq command +============================ + +improper_style cossq/omp command +================================ + +Syntax +"""""" + +.. parsed-literal:: + + improper_style cossq + +Examples +"""""""" + +.. parsed-literal:: + + improper_style cossq + improper_coeff 1 4.0 0.0 + +Description +""""""""""" + +The *cossq* improper style uses the potential + +.. image:: Eqs/improper_cossq.jpg + :align: center + +where x is the improper angle, x0 is its equilibrium value, and K is a +prefactor. + +If the 4 atoms in an improper quadruplet (listed in the data file read +by the :doc:`read_data ` command) are ordered I,J,K,L then X +is the angle between the plane of I,J,K and the plane of J,K,L. +Alternatively, you can think of atoms J,K,L as being in a plane, and +atom I above the plane, and X as a measure of how far out-of-plane I +is with respect to the other 3 atoms. + +Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an +improper to be defined between the 4 atoms. + +The following coefficients must be defined for each improper type via +the :doc:`improper_coeff ` command as in the example +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* K (energy/radian^2) +* X0 (degrees) + +X0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This improper style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_cvff.txt b/doc/_sources/improper_cvff.txt new file mode 100644 index 0000000000..3ceb182b55 --- /dev/null +++ b/doc/_sources/improper_cvff.txt @@ -0,0 +1,100 @@ +.. index:: improper_style cvff + +improper_style cvff command +=========================== + +improper_style cvff/omp command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + improper_style cvff + +Examples +"""""""" + +.. parsed-literal:: + + improper_style cvff + improper_coeff 1 80.0 -1 4 + +Description +""""""""""" + +The *cvff* improper style uses the potential + +.. image:: Eqs/improper_cvff.jpg + :align: center + +where phi is the improper dihedral angle. + +If the 4 atoms in an improper quadruplet (listed in the data file read +by the :doc:`read_data ` command) are ordered I,J,K,L then +the improper dihedral angle is between the plane of I,J,K and the +plane of J,K,L. Note that because this is effectively a dihedral +angle, the formula for this improper style is the same as for +:doc:`dihedral_style harmonic `. + +Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an +improper to be defined between the 4 atoms. + +The following coefficients must be defined for each improper type via +the :doc:`improper_coeff ` command as in the example +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* K (energy) +* d (+1 or -1) +* n (0,1,2,3,4,6) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This improper style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_distance.txt b/doc/_sources/improper_distance.txt new file mode 100644 index 0000000000..125b1f82c0 --- /dev/null +++ b/doc/_sources/improper_distance.txt @@ -0,0 +1,70 @@ +.. index:: improper_style distance + +improper_style distance command +=============================== + +Syntax +"""""" + +improper_style distance + +Examples +"""""""" + +.. parsed-literal:: + + improper_style distance + improper_coeff 1 80.0 100.0 + +Description +""""""""""" + +The *distance* improper style uses the potential + +.. image:: Eqs/improper_dist-1.jpg + :align: center + +where d is the distance between the central atom and the plane formed +by the other three atoms. If the 4 atoms in an improper quadruplet +(listed in the data file read by the :doc:`read_data ` +command) are ordered I,J,K,L then the I-atom is assumed to be the +central atom. + +.. image:: JPG/improper_distance.jpg + :align: center + +Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an +improper to be defined between the 4 atoms. + +The following coefficients must be defined for each improper type via +the improper_coeff command as in the example above, or in the data +file or restart files read by the read_data or read_restart commands: + +* K_2 (energy/distance^2) +* K_4 (energy/distance^4) + + +---------- + + +Restrictions +"""""""""""" + + +This improper style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_fourier.txt b/doc/_sources/improper_fourier.txt new file mode 100644 index 0000000000..c77b9fd133 --- /dev/null +++ b/doc/_sources/improper_fourier.txt @@ -0,0 +1,97 @@ +.. index:: improper_style fourier + +improper_style fourier command +============================== + +improper_style fourier/omp command +================================== + +Syntax +"""""" + +.. parsed-literal:: + + improper_style fourier + +Examples +"""""""" + +.. parsed-literal:: + + improper_style fourier + improper_coeff 1 100.0 180.0 + +Description +""""""""""" + +The *fourier* improper style uses the following potential: + +.. image:: Eqs/improper_fourier.jpg + :align: center + +where K is the force constant and omega is the angle between the IL +axis and the IJK plane: + +.. image:: Eqs/umbrella.jpg + :align: center + +If all parameter (see bellow) is not zero, the all the three possible angles will taken in account. + +The following coefficients must be defined for each improper type via +the :doc:`improper_coeff ` command as in the example +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* K (energy) +* C0 (real) +* C1 (real) +* C2 (real) +* all (integer >= 0) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This angle style can only be used if LAMMPS was built with the +USER_MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_harmonic.txt b/doc/_sources/improper_harmonic.txt new file mode 100644 index 0000000000..29a52bce79 --- /dev/null +++ b/doc/_sources/improper_harmonic.txt @@ -0,0 +1,109 @@ +.. index:: improper_style harmonic + +improper_style harmonic command +=============================== + +improper_style harmonic/intel command +===================================== + +improper_style harmonic/kk command +================================== + +improper_style harmonic/omp command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + improper_style harmonic + +Examples +"""""""" + +.. parsed-literal:: + + improper_style harmonic + improper_coeff 1 100.0 0 + +Description +""""""""""" + +The *harmonic* improper style uses the potential + +.. image:: Eqs/improper_harmonic.jpg + :align: center + +where X is the improper angle, X0 is its equilibrium value, and K is a +prefactor. Note that the usual 1/2 factor is included in K. + +If the 4 atoms in an improper quadruplet (listed in the data file read +by the :doc:`read_data ` command) are ordered I,J,K,L then X +is the angle between the plane of I,J,K and the plane of J,K,L. +Alternatively, you can think of atoms J,K,L as being in a plane, and +atom I above the plane, and X as a measure of how far out-of-plane I +is with respect to the other 3 atoms. + +Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an +improper to be defined between the 4 atoms. + +The following coefficients must be defined for each improper type via +the :doc:`improper_coeff ` command as in the example +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* K (energy/radian^2) +* X0 (degrees) + +X0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This improper style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_hybrid.txt b/doc/_sources/improper_hybrid.txt new file mode 100644 index 0000000000..728a46bfd2 --- /dev/null +++ b/doc/_sources/improper_hybrid.txt @@ -0,0 +1,80 @@ +.. index:: improper_style hybrid + +improper_style hybrid command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + improper_style hybrid style1 style2 ... + +* style1,style2 = list of one or more improper styles + +Examples +"""""""" + +.. parsed-literal:: + + improper_style hybrid harmonic helix + improper_coeff 1 harmonic 120.0 30 + improper_coeff 2 cvff 20.0 -1 2 + +Description +""""""""""" + +The *hybrid* style enables the use of multiple improper styles in one +simulation. An improper style is assigned to each improper type. For +example, impropers in a polymer flow (of improper type 1) could be +computed with a *harmonic* potential and impropers in the wall +boundary (of improper type 2) could be computed with a *cvff* +potential. The assignment of improper type to style is made via the +:doc:`improper_coeff ` command or in the data file. + +In the improper_coeff command, the first coefficient sets the improper +style and the remaining coefficients are those appropriate to that +style. In the example above, the 2 improper_coeff commands would set +impropers of improper type 1 to be computed with a *harmonic* +potential with coefficients 120.0, 30 for K, X0. Improper type 2 +would be computed with a *cvff* potential with coefficients 20.0, -1, +2 for K, d, n. + +If the improper *class2* potential is one of the hybrid styles, it +requires additional AngleAngle coefficients be specified in the data +file. These lines must also have an additional "class2" argument +added after the improper type. For improper types which are assigned +to other hybrid styles, use the style name (e.g. "harmonic") +appropriate to that style. The AngleAngle coeffs for that improper +type will then be ignored. + +An improper style of *none* can be specified as the 2nd argument to +the improper_coeff command, if you desire to turn off certain improper +types. + + +---------- + + +Restrictions +"""""""""""" + + +This improper style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Unlike other improper styles, the hybrid improper style does not store +improper coefficient info for individual sub-styles in a :doc:`binary restart files `. Thus when retarting a simulation from a +restart file, you need to re-specify improper_coeff commands. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_none.txt b/doc/_sources/improper_none.txt new file mode 100644 index 0000000000..68ef034d38 --- /dev/null +++ b/doc/_sources/improper_none.txt @@ -0,0 +1,38 @@ +.. index:: improper_style none + +improper_style none command +=========================== + +Syntax +"""""" + +.. parsed-literal:: + + improper_style none + +Examples +"""""""" + +.. parsed-literal:: + + improper_style none + +Description +""""""""""" + +Using an improper style of none means improper forces are not +computed, even if quadruplets of improper atoms were listed in the +data file read by the :doc:`read_data ` command. + +Restrictions +"""""""""""" + none + +**Related commands:** none + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_ring.txt b/doc/_sources/improper_ring.txt new file mode 100644 index 0000000000..665836a62e --- /dev/null +++ b/doc/_sources/improper_ring.txt @@ -0,0 +1,113 @@ +.. index:: improper_style ring + +improper_style ring command +=========================== + +improper_style ring/omp command +=============================== + +Syntax +"""""" + +.. parsed-literal:: + + improper_style ring + +Examples +"""""""" + +.. parsed-literal:: + + improper_style ring + improper_coeff 1 8000 70.5 + +Description +""""""""""" + +The *ring* improper style uses the potential + +.. image:: Eqs/improper_ring.jpg + :align: center + +where K is a prefactor, theta is the angle formed by the atoms +specified by (i,j,k,l) indices and theta0 its equilibrium value. + +If the 4 atoms in an improper quadruplet (listed in the data file read +by the :doc:`read_data ` command) are ordered i,j,k,l then +theta_*ijl* is the angle between atoms i,j and l, theta_*ijk* is the +angle between atoms i,j and k, theta_*kjl* is the angle between atoms +j,k, and l. + +The "ring" improper style implements the improper potential introduced +by Destree et al., in Equation (9) of :ref:`(Destree) `. This +potential does not affect small amplitude vibrations but is used in an +ad-hoc way to prevent the onset of accidentially large amplitude +fluctuations leading to the occurrence of a planar conformation of the +three bonds i-j, j-k and j-l, an intermediate conformation toward the +chiral inversion of a methine carbon. In the "Impropers" section of +data file four atoms: i, j, k and l are specified with i,j and l lying +on the backbone of the chain and k specifying the chirality of j. + +The following coefficients must be defined for each improper type via +the :doc:`improper_coeff ` command as in the example +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* K (energy/radian^2) +* theta0 (degrees) + +theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This improper style can only be used if LAMMPS was built with the +USER-MISC package. See the :ref:`Making LAMMPS ` +section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +.. _Destree: + + + +**(Destree)** M. Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, +J Chem Phys, 112, 9632 (2000). + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_style.txt b/doc/_sources/improper_style.txt new file mode 100644 index 0000000000..89cfd8d9b0 --- /dev/null +++ b/doc/_sources/improper_style.txt @@ -0,0 +1,112 @@ +.. index:: improper_style + +improper_style command +====================== + +Syntax +"""""" + +.. parsed-literal:: + + improper_style style + +* style = *none* or *hybrid* or *class2* or *cvff* or *harmonic* + +Examples +"""""""" + +.. parsed-literal:: + + improper_style harmonic + improper_style cvff + improper_style hybrid cvff harmonic + +Description +""""""""""" + +Set the formula(s) LAMMPS uses to compute improper interactions +between quadruplets of atoms, which remain in force for the duration +of the simulation. The list of improper quadruplets is read in by a +:doc:`read_data ` or :doc:`read_restart ` command +from a data or restart file. Note that the ordering of the 4 atoms in +an improper quadruplet determines the the definition of the improper +angle used in the formula for each style. See the doc pages of +individual styles for details. + +Hybrid models where impropers are computed using different improper +potentials can be setup using the *hybrid* improper style. + +The coefficients associated with an improper style can be specified in +a data or restart file or via the :doc:`improper_coeff ` +command. + +All improper potentials store their coefficient data in binary restart +files which means improper_style and +:doc:`improper_coeff ` commands do not need to be +re-specified in an input script that restarts a simulation. See the +:doc:`read_restart ` command for details on how to do +this. The one exception is that improper_style *hybrid* only stores +the list of sub-styles in the restart file; improper coefficients need +to be re-specified. + +.. note:: + + When both an improper and pair style is defined, the + :doc:`special_bonds ` command often needs to be used to + turn off (or weight) the pairwise interaction that would otherwise + exist between a group of 4 bonded atoms. + + +---------- + + +Here is an alphabetic list of improper styles defined in LAMMPS. +Click on the style to display the formula it computes and coefficients +specified by the associated :doc:`improper_coeff ` +command. + +Note that there are also additional improper styles submitted by users +which are included in the LAMMPS distribution. The list of these with +links to the individual styles are given in the improper section of +:ref:`this page `. + +* :doc:`improper_style none ` - turn off improper interactions +* :doc:`improper_style hybrid ` - define multiple styles of improper interactions + +* :doc:`improper_style class2 ` - COMPASS (class 2) improper +* :doc:`improper_style cvff ` - CVFF improper +* :doc:`improper_style harmonic ` - harmonic improper +* :doc:`improper_style umbrella ` - DREIDING improper + + +---------- + + +Restrictions +"""""""""""" + + +Improper styles can only be set for atom_style choices that allow +impropers to be defined. + +Most improper styles are part of the MOLECULE package. They are only +enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info on packages. +The doc pages for individual improper potentials tell if it is part of +a package. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +Default +""""""" + +.. parsed-literal:: + + improper_style none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/improper_umbrella.txt b/doc/_sources/improper_umbrella.txt new file mode 100644 index 0000000000..ace10272da --- /dev/null +++ b/doc/_sources/improper_umbrella.txt @@ -0,0 +1,110 @@ +.. index:: improper_style umbrella + +improper_style umbrella command +=============================== + +improper_style umbrella/omp command +=================================== + +Syntax +"""""" + +.. parsed-literal:: + + improper_style umbrella + +Examples +"""""""" + +.. parsed-literal:: + + improper_style umbrella + improper_coeff 1 100.0 180.0 + +Description +""""""""""" + +The *umbrella* improper style uses the following potential, which is +commonly referred to as a classic inversion and used in the +:ref:`DREIDING ` force field: + +.. image:: Eqs/improper_umbrella.jpg + :align: center + +where K is the force constant and omega is the angle between the IL +axis and the IJK plane: + +.. image:: Eqs/umbrella.jpg + :align: center + +If omega0 = 0 the potential term has a minimum for the planar +structure. Otherwise it has two minima at +/- omega0, with a barrier +in between. + +See :ref:`(Mayo) ` for a description of the DREIDING force field. + +The following coefficients must be defined for each improper type via +the :doc:`improper_coeff ` command as in the example +above, or in the data file or restart files read by the +:doc:`read_data ` or :doc:`read_restart ` +commands: + +* K (energy) +* omega0 (degrees) + + +---------- + + +Styles with a *cuda*, *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed in :doc:`Section_accelerate ` +of the manual. The accelerated styles take the same arguments and +should produce the same results, except for round-off and precision +issues. + +These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL, +KOKKOS, USER-OMP and OPT packages, respectively. They are only +enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS ` section for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :ref:`-suffix command-line switch ` when you invoke LAMMPS, or you can +use the :doc:`suffix ` command in your input script. + +See :doc:`Section_accelerate ` of the manual for +more instructions on how to use the accelerated styles effectively. + + +---------- + + +Restrictions +"""""""""""" + + +This improper style can only be used if LAMMPS was built with the +MOLECULE package (which it is by default). See the :ref:`Making LAMMPS ` section for more info on packages. + +Related commands +"""""""""""""""" + +:doc:`improper_coeff ` + +**Default:** none + + +---------- + + +.. _Mayo: + + + +**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990), + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/include.txt b/doc/_sources/include.txt new file mode 100644 index 0000000000..9dce22029b --- /dev/null +++ b/doc/_sources/include.txt @@ -0,0 +1,50 @@ +.. index:: include + +include command +=============== + +Syntax +"""""" + +.. parsed-literal:: + + include file + +* file = filename of new input script to switch to + +Examples +"""""""" + +.. parsed-literal:: + + include newfile + include in.run2 + +Description +""""""""""" + +This command opens a new input script file and begins reading LAMMPS +commands from that file. When the new file is finished, the original +file is returned to. Include files can be nested as deeply as +desired. If input script A includes script B, and B includes A, then +LAMMPS could run for a long time. + +If the filename is a variable (see the :doc:`variable ` +command), different processor partitions can run different input +scripts. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`variable `, :doc:`jump ` + +**Default:** none + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/info.txt b/doc/_sources/info.txt new file mode 100644 index 0000000000..edbce761e5 --- /dev/null +++ b/doc/_sources/info.txt @@ -0,0 +1,97 @@ +.. index:: info + +info command +============ + +Syntax +"""""" + +.. parsed-literal:: + + info args + +args = one or more of the following keywords: *out*, *all*, *system*, *communication*, *computes*, *dumps*, *fixes*, *groups*, *regions*, *variables*, *time*, or *configuration* + *out* values = *screen*, *log*, *append* filename, *overwrite* filename:ul + +Examples +"""""""" + +.. parsed-literal:: + + info system + info groups computes variables + info all out log + info all out append info.txt + +Description +""""""""""" + +Print out information about the current internal state of the running +LAMMPS process. This can be helpful when debugging or validating +complex input scripts. Several output categories are available and +one or more output category may be requested. + +The *out* flag controls where the output is sent. It can only be sent +to one target. By default this is the screen, if it is active. The +*log* argument selects the log file instead. With the *append* and +*overwrite* option, followed by a filename, the output is written +to that file, which is either appended to or overwritten, respectively. + +The *all* flag activates printing all categories listed below. + +The *system* category prints a general system overview listing. This +includes the unit style, atom style, number of atoms, bonds, angles, +dihedrals, and impropers and the number of the respective types, box +dimensions and properties, force computing styles and more. + +The *communication* category prints a variety of information about +communication and parallelization: the MPI library version level, +the number of MPI ranks and OpenMP threads, the communication style +and layout, the processor grid dimensions, ghost atom communication +mode, cutoff, and related settings. + +The *computes* category prints a list of all currently defined +computes, their IDs and styles and groups they operate on. + +The *dumps* category prints a list of all currently active dumps, +their IDs, styles, filenames, groups, and dump frequencies. + +The *fixes* category prints a list of all currently defined fixes, +their IDs and styles and groups they operate on. + +The *groups* category prints a list of all currently defined groups. + +The *regions* category prints a list of all currently defined regions, +their IDs and styles and whether "inside" or "outside" atoms are +selected. + +The *variables* category prints a list of all currently defined +variables, their names, styles, definition and last computed value, if +available. + +The *time* category prints the accumulated CPU and wall time for the +process that writes output (usually MPI rank 0). + +The *configuration* command prints some information about the LAMMPS +version and architection and OS it is run on. Where supported, also +information about the memory consumption provided by the OS is +reported. + +Restrictions +"""""""""""" + none + +Related commands +"""""""""""""""" + +:doc:`print ` + +Default +""""""" + +The *out* option has the default *screen*. + + +.. _lws: http://lammps.sandia.gov +.. _ld: Manual.html +.. _lc: Section_commands.html#comm diff --git a/doc/_sources/jump.txt b/doc/_sources/jump.txt new file mode 100644 index 0000000000..6009093528 --- /dev/null +++ b/doc/_sources/jump.txt @@ -0,0 +1,156 @@ +.. index:: jump + +jump command +============ + +Syntax +"""""" + +.. parsed-literal:: + + jump file label + +* file = filename of new input script to switch to +* label = optional label within file to jump to + +Examples +"""""""" + +.. parsed-literal:: + + jump newfile + jump in.run2 runloop + jump SELF runloop + +Description +""""""""""" + +This command closes the current input script file, opens the file with +the specified name, and begins reading LAMMPS commands from that file. +Unlike the :doc:`include ` command, the original file is not +returned to, although by using multiple jump commands it is possible +to chain from file to file or back to the original file. + +If the word "SELF" is used for the filename, then the current input +script is re-opened and read again. + +.. note:: + + The SELF option is not guaranteed to work when the current input + script is being read through stdin (standard input), e.g. + +.. parsed-literal:: + + lmp_g++ < in.script + +since the SELF option invokes the C-library rewind() call, which may +not be supported for stdin on some systems or by some MPI +implementations. This can be worked around by using the :ref:`-in command-line argument `, e.g. + +.. parsed-literal:: + + lmp_g++ -in in.script + +or by using the :ref:`-var command-line argument ` to pass the script name as a +variable to the input script. In the latter case, a +:doc:`variable ` called "fname" could be used in place of +SELF, e.g. + +.. parsed-literal:: + + lmp_g++ -var fname in.script < in.script + +The 2nd argument to the jump command is optional. If specified, it is +treated as a label and the new file is scanned (without executing +commands) until the label is found, and commands are executed from +that point forward. This can be used to loop over a portion of the +input script, as in this example. These commands perform 10 runs, +each of 10000 steps, and create 10 dump files named file.1, file.2, +etc. The :doc:`next ` command is used to exit the loop after 10 +iterations. When the "a" variable has been incremented for the tenth +time, it will cause the next jump command to be skipped. + +.. parsed-literal:: + + variable a loop 10 + label loop + dump 1 all atom 100 file.$a + run 10000 + undump 1 + next a + jump in.lj loop + +If the jump *file* argument is a variable, the jump command can be +used to cause different processor partitions to run different input +scripts. In this example, LAMMPS is run on 40 processors, with 4 +partitions of 10 procs each. An in.file containing the example +variable and jump command will cause each partition to run a different +simulation. + +.. parsed-literal:: + + mpirun -np 40 lmp_ibm -partition 4x10 -in in.file + +.. parsed-literal:: + + variable f world script.1 script.2 script.3 script.4 + jump $f + +Here is an example of a loop which checks every 1000 steps if the +system temperature has reached a certain value, and if so, breaks out +of the loop to finish the run. Note that any variable could be +checked, so long as it is current on the timestep when the run +completes. As explained on the :doc:`variable ` doc page, +this can be insured by includig the variable in thermodynamic output. + +.. parsed-literal:: + + variable myTemp equal temp + label loop + variable a loop 1000 + run 1000 + if "${myTemp} < 300.0" then "jump SELF break" + next a + jump SELF loop + label break + print "ALL DONE" + +Here is an example of a double loop which uses the if and +:doc:`jump ` commands to break out of the inner loop when a +condition is met, then continues iterating thru the outer loop. + +.. parsed-literal:: + + label loopa + variable a loop 5 + label loopb + variable b loop 5 + print "A,B = $a,$b" + run 10000 + if "$b > 2" then "jump SELF break" + next b + jump in.script loopb + label break + variable b delete + next a + jump SELF loopa + +Restrictions +"""""""""""" + + +If you jump to a file and it does not contain the specified label, +LAMMPS will come to the end of the file and exit. + +Related commands +"""""""""""""""" + +:doc:`variable `, :doc:`include `, :doc:`label       - + + + + + - + - + - + - + - + - + - + - + - + - + - + @@ -300,6 +310,9 @@ Gaussians with a specified position and bandwidth or uncertainty in position, which is represented by the eradius = electron size.

      For the peri style, the particles are spherical and each stores a per-particle mass and volume.

      +

      The dpd style is for dissipative particle dynamics (DPD) particles +which store the particle internal temperature (dpdTheta), internal +conductive energy (uCond) and internal mechanical energy (uMech).

      The meso style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv).

      @@ -399,16 +412,21 @@ more instructions on how to use the accelerated styles effectively.

      Restrictions

      This command cannot be used after the simulation box is defined by a read_data or create_box command.

      +

      Many of the styles listed above are only enabled if LAMMPS was built +with a specific package, as listed below. See the Making LAMMPS section for more info.

      The angle, bond, full, molecular, and template styles are -part of the MOLECULE package. The line and tri styles are part -of the ASPHERE pacakge. The body style is part of the BODY package. -The dipole style is part of the DIPOLE package. The peri style is -part of the PERI package for Peridynamics. The electron style is -part of the USER-EFF package for electronic force fields. The meso style is part of the USER-SPH -package for smoothed particle hydrodyanmics (SPH). See this PDF guide to using SPH in LAMMPS. The -wavepacket style is part of the USER-AWPMD package for the -antisymmetrized wave packet MD method. They are -only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

      +part of the MOLECULE package.

      +

      The line and tri styles are part of the ASPHERE pacakge.

      +

      The body style is part of the BODY package.

      +

      The dipole style is part of the DIPOLE package.

      +

      The peri style is part of the PERI package for Peridynamics.

      +

      The electron style is part of the USER-EFF package for electronic force fields.

      +

      The dpd style is part of the USER-DPD package for dissipative +particle dynamics (DPD).

      +

      The meso style is part of the USER-SPH package for smoothed particle +hydrodyanmics (SPH). See this PDF guide to using SPH in LAMMPS.

      +

      The wavepacket style is part of the USER-AWPMD package for the +antisymmetrized wave packet MD method.

      - + - - + + + + - + - + - + - + - + - + - - + + - + - + - + - + - +
      charge and dipole moment system with dipolar particles
      electron
      dpdinternal temperature and internal energiesDPD particles
      electron charge and spin and eradius electronic force field
      ellipsoid
      ellipsoid shape, quaternion, angular momentum aspherical particles
      full
      full molecular + charge bio-molecules
      line
      line end points, angular velocity rigid bodies
      meso
      meso rho, e, cv SPH particles
      molecular
      molecular bonds, angles, dihedrals, impropers uncharged molecules
      peri
      peri mass, volume mesocopic Peridynamic models
      smd
      smd volume, kernel diameter, contact radius, mass solid and fluid SPH particles
      sphere
      sphere diameter, mass, angular velocity granular models
      template
      template template index, template atom small molecules with fixed topology
      tri
      tri corner points, angular momentum rigid bodies
      wavepacket
      wavepacket charge, spin, eradius, etag, cs_re, cs_im AWPMD
      compute pressure
      -
      compute property/atom
      @@ -1018,6 +1026,14 @@ +
      fix eos/cv +
      + + +
      fix eos/table +
      + +
      fix evaporate
      @@ -1312,6 +1328,10 @@ +
      fix shardlow +
      + +
      fix smd
      @@ -1724,6 +1744,14 @@ +
      pair_style dpd/conservative +
      + + +
      pair_style dpd/fdt +
      + +
      pair_style dsmc
      @@ -1827,12 +1855,12 @@
      pair_style lj/sf
      +
      pair_style lj/smooth
      -
      pair_style lj/smooth/linear
      diff --git a/doc/package.html b/doc/package.html index 4d8a3b19df..f79f993d3f 100644 --- a/doc/package.html +++ b/doc/package.html @@ -695,7 +695,7 @@ support. These settings are made automatically if the “-sf intel” not used, you must invoke the package intel command in your input script or or via the “-pk intel” command-line switch.

      For the KOKKOS package, the option defaults neigh = full, newton = -off, binsize = 0.0, and comm = host. These settings are made +off, binsize = 0.0, and comm = device. These settings are made automatically by the required “-k on” command-line switch. You can change them bu using the package kokkos command in your input script or via the “-pk kokkos” command-line switch.

      diff --git a/doc/pair_body_rounded_polygon.html b/doc/pair_body_rounded_polygon.html new file mode 100644 index 0000000000..e48ea1bf47 --- /dev/null +++ b/doc/pair_body_rounded_polygon.html @@ -0,0 +1,280 @@ + + + + + + + + + + + pair_style body/rounded/polygon command — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      + + + + +
      + + + + + + +
      +
      +
      + +
      + +
      +
      +
      + +
      +

      pair_style body/rounded/polygon command

      +
      +

      Syntax

      +
      pair_style body/rounded/polygon cutoff_global cutoff_inner delta_ua c_n
+
      +
      +
        +
      • cutoff_global = global cutoff for COM interactions (distance units)
        • +
      • cutoff_inner = cutoff for vertex-vertex and vertex-edge interactions (distance units)
        • +
      • delta_ua = characteristic contact length (distance units)
        • +
      • c_n = normal friction coefficient (energy time/distance^2)
        • +
      +
      +
      +

      Examples

      +
      pair_style body/rounded/polygon 6.0 0.5 0.5 0.1
+pair_coeff 1 1 1.0 100.0 12.0
+
      +
      +
      +
      +

      Description

      +

      Style body/rounded/polygon implements the pairwise body/body +interactions between 2D convex polygons, as described +in Fraige. This pair style is designed for use with +the “rounded/polygon” body style, which is specified as +an argument to the “atom-style body/rounded/polygon” command. +See the body doc page for more details about the body +styles LAMMPS supports.

      +

      The “rounded/polygon” style treats a body particle as a discrete +element model (DEM) polygon composed of N vertices. +The coordinates of a body particle are its center-of-mass (COM). +The initial position of the vertices are specified the data file. +The current implementation follows the multiple contact points model as +described in Fraige, but neglects and the contact history +the tangential contact forces for now.

      +

      The parameters delta_ua and c_n are the characteristic contact length +and the normal friction coefficient, respectively. See Eqs. (1) and (5) +in Fraige for more details.

      +

      For style body/rounded/polygon, the following coefficients +must be defined for each pair of atoms types via the pair_coeff +command as in the examples above:

      +
        +
      • sigma = vertex rounded diameter (distance units)
        • +
      • k_n = normal repulsion strength (energy/distance^2)
        • +
      • k_na = normal attraction strength (energy/distance^2)
        • +
      • cutoff = cutoff for COM interactions (distance units)
        • +
      +

      The last parameter is optional. If not specified, the global +cutoff specified in the pair_style command is used.

      +

      Note that the current implementation assumes that the edge length +of the polygons (L) should be at least twice greater than +the vertex rounded radius (sigma) so as to distinguish vertex-vertex from +vertex-edge contacts.

      +
      +

      Note

      +

      Because this pair style requires the body velocities to compute +the friction component of the forces, users should specify +comm_modify vel yes in the input script with this pair style.

      +
      +
      +

      Mixing, shift, table, tail correction, restart, rRESPA info:

      +

      For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of this pair style can be mixed. The +default mix value is geometric. See the “pair_modify” command for +details.

      +

      This pair style does not support the pair_modify +shift, table, and tail options.

      +

      This pair style does not write its information to binary restart files.

      +

      This pair style can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords.

      +
      +
      +
      +

      Restrictions

      +

      This style is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the Making LAMMPS section for more info.

      +

      Defining particles to be bodies so they participate in body/body or +body/particle interactions requires the use of the atom_style body command.

      +
      + +
      + + +
      +
      +
      + + +
      + +
      +

      + © Copyright 2013 Sandia Corporation. +

      +
      + Built with Sphinx using a theme provided by Read the Docs. + +
      + +
      +
      + +
      + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_body_rounded_polygon.txt b/doc/pair_body_rounded_polygon.txt new file mode 100644 index 0000000000..966b14fce4 --- /dev/null +++ b/doc/pair_body_rounded_polygon.txt @@ -0,0 +1,107 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style body/rounded/polygon command :h3 + +[Syntax:] + +pair_style body/rounded/polygon cutoff_global cutoff_inner delta_ua c_n :pre + +cutoff_global = global cutoff for COM interactions (distance units) +cutoff_inner = cutoff for vertex-vertex and vertex-edge interactions (distance units) +delta_ua = characteristic contact length (distance units) +c_n = normal friction coefficient (energy time/distance^2) :ul + +[Examples:] + +pair_style body/rounded/polygon 6.0 0.5 0.5 0.1 +pair_coeff 1 1 1.0 100.0 12.0 :pre + +[Description:] + +Style {body/rounded/polygon} implements the pairwise body/body +interactions between 2D convex polygons, as described +in "Fraige"_#Fraige. This pair style is designed for use with +the "rounded/polygon" body style, which is specified as +an argument to the "atom-style body/rounded/polygon" command. +See the "body"_body.html doc page for more details about the body +styles LAMMPS supports. + +The "rounded/polygon" style treats a body particle as a discrete +element model (DEM) polygon composed of N vertices. +The coordinates of a body particle are its center-of-mass (COM). +The initial position of the vertices are specified the data file. +The current implementation follows the multiple contact points model as +described in "Fraige"_#Fraige, but neglects and the contact history +the tangential contact forces for now. + +The parameters {delta_ua} and {c_n} are the characteristic contact length +and the normal friction coefficient, respectively. See Eqs. (1) and (5) +in "Fraige"_#Fraige for more details. + +For style {body/rounded/polygon}, the following coefficients +must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html +command as in the examples above: + +sigma = vertex rounded diameter (distance units) +k_n = normal repulsion strength (energy/distance^2) +k_na = normal attraction strength (energy/distance^2) +cutoff = cutoff for COM interactions (distance units) :ul + +The last parameter is optional. If not specified, the global +cutoff specified in the pair_style command is used. + +Note that the current implementation assumes that the edge length +of the polygons (L) should be at least twice greater than +the vertex rounded radius (sigma) so as to distinguish vertex-vertex from +vertex-edge contacts. + +NOTE: Because this pair style requires the body velocities to compute +the friction component of the forces, users should specify +{comm_modify vel yes} in the input script with this pair style. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +For atom type pairs I,J and I != J, the epsilon and sigma coefficients +and cutoff distance for all of this pair style can be mixed. The +default mix value is {geometric}. See the "pair_modify" command for +details. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +This style is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. + +Defining particles to be bodies so they participate in body/body or +body/particle interactions requires the use of the "atom_style +body"_atom_style.html command. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:link(Fraige) +[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, +Particuology, 6, 455 (2008). diff --git a/doc/pair_dpd_conservative.html b/doc/pair_dpd_conservative.html new file mode 100644 index 0000000000..3c72a6a929 --- /dev/null +++ b/doc/pair_dpd_conservative.html @@ -0,0 +1,252 @@ + + + + + + + + + + + pair_style dpd/conservative command — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      + + + + +
      + + + + + + +
      +
      +
      + +
      + +
      +
      +
      + +
      +

      pair_style dpd/conservative command

      +
      +

      Syntax

      +
      pair_style dpd/conservative cutoff
+
      +
      +
        +
      • cutoff = global cutoff for DPD interactions (distance units)
        • +
      +
      +
      +

      Examples

      +
      pair_style dpd/conservative 2.5
+pair_coeff * * 3.0 2.5
+pair_coeff 1 1 3.0
+
      +
      +
      +
      +

      Description

      +

      Style dpd/conservative computes the conservative force for +dissipative particle dynamics (DPD). The conservative force on atom I +due to atom J is given by

      +_images/pair_dpd_conservative.jpg +

      where the weighting factor, omega_ij, varies between 0 and 1, and is +chosen to have the following functional form:

      +_images/pair_dpd_omega.jpg +

      where Rij is a unit vector in the direction Ri - Rj, and Rc is the +cutoff. Note that alternative definitions of the weighting function +exist, but would have to be implemented as a separate pair style +command.

      +

      Style dpd/conservative differs from the other dpd styles in that the +dissipative and random forces are not computed within the pair style.

      +

      For style dpd/conservative, the pairwise energy is due only to the +conservative force term Fc, and is shifted to be zero at the cutoff +distance Rc. The pairwise virial is calculated using only the +conservative term.

      +

      Style dpd/conservative requires the following coefficients to be +defined for each pair of atoms types via the +pair_coeff command as in the examples above, or in +the data file or restart files read by the read_data +or read_restart commands:

      +
        +
      • A (force units)
        • +
      • cutoff (distance units)
        • +
      +

      The last coefficient is optional. If not specified, the global DPD +cutoff is used.

      +
      +
      +
      +

      Restrictions

      +

      The pair style dpd/conservative is only available if LAMMPS is built +with the USER-DPD package.

      +
      + +
      + + +
      +
      +
      + + +
      + +
      +

      + © Copyright 2013 Sandia Corporation. +

      +
      + Built with Sphinx using a theme provided by Read the Docs. + +
      + +
      +
      + +
      + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_dpd_conservative.txt b/doc/pair_dpd_conservative.txt new file mode 100644 index 0000000000..41e279a83d --- /dev/null +++ b/doc/pair_dpd_conservative.txt @@ -0,0 +1,72 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style dpd/conservative command :h3 + +[Syntax:] + +pair_style dpd/conservative cutoff :pre + +cutoff = global cutoff for DPD interactions (distance units) :ul + +[Examples:] + +pair_style dpd/conservative 2.5 +pair_coeff * * 3.0 2.5 +pair_coeff 1 1 3.0 :pre + +[Description:] + +Style {dpd/conservative} computes the conservative force for +dissipative particle dynamics (DPD). The conservative force on atom I +due to atom J is given by + +:c,image(Eqs/pair_dpd_conservative.jpg) + +where the weighting factor, omega_ij, varies between 0 and 1, and is +chosen to have the following functional form: + +:c,image(Eqs/pair_dpd_omega.jpg) + +where Rij is a unit vector in the direction Ri - Rj, and Rc is the +cutoff. Note that alternative definitions of the weighting function +exist, but would have to be implemented as a separate pair style +command. + +Style {dpd/conservative} differs from the other dpd styles in that the +dissipative and random forces are not computed within the pair style. + +For style {dpd/conservative}, the pairwise energy is due only to the +conservative force term Fc, and is shifted to be zero at the cutoff +distance Rc. The pairwise virial is calculated using only the +conservative term. + +Style {dpd/conservative} requires the following coefficients to be +defined for each pair of atoms types via the +"pair_coeff"_pair_coeff.html command as in the examples above, or in +the data file or restart files read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands: + +A (force units) +cutoff (distance units) :ul + +The last coefficient is optional. If not specified, the global DPD +cutoff is used. + +:line + +[Restrictions:] + +The pair style {dpd/conservative} is only available if LAMMPS is built +with the USER-DPD package. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "pair_dpd"_pair_dpd.html + +[Default:] none diff --git a/doc/pair_dpd_fdt.html b/doc/pair_dpd_fdt.html new file mode 100644 index 0000000000..319def9f26 --- /dev/null +++ b/doc/pair_dpd_fdt.html @@ -0,0 +1,313 @@ + + + + + + + + + + + pair_style dpd/fdt command — LAMMPS documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      + + + + +
      + + + + + + +
      +
      +
      + +
      + +
      +
      +
      + +
      +

      pair_style dpd/fdt command

      +
      +
      +

      pair_style dpd/fdt/energy command

      +
      +

      Syntax

      +
      pair_style style args
+
      +
      +
        +
      • style = dpd/fdt or dpd/fdt/energy
        • +
      • args = list of arguments for a particular style
        • +
      +
      +dpd/fdt args = T cutoff seed
+  T = temperature (temperature units)
+  cutoff = global cutoff for DPD interactions (distance units)
+  seed = random # seed (positive integer)
+dpd/fdt/energy args = cutoff seed
+  cutoff = global cutoff for DPD interactions (distance units)
+  seed = random # seed (positive integer)
+
      +
      +
      +

      Examples

      +
      pair_style dpd/fdt 300.0 2.5 34387
+pair_coeff * * 3.0 1.0 2.5
+
      +
      +
      pair_style dpd/fdt/energy 2.5 34387
+pair_coeff * * 3.0 1.0 0.1 2.5
+
      +
      +
      +
      +

      Description

      +

      Styles dpd/fdt and dpd/fdt/energy set the fluctuation-dissipation +theorem parameters and compute the conservative force for dissipative +particle dynamics (DPD). The conservative force on atom I due to atom +J is given by

      +_images/pair_dpd_conservative.jpg +

      where the weighting factor, omega_ij, varies between 0 and 1, and is +chosen to have the following functional form:

      +_images/pair_dpd_omega.jpg +

      where Rij is a unit vector in the direction Ri - Rj, and Rc is the +cutoff. Note that alternative definitions of the weighting function +exist, but would have to be implemented as a separate pair style +command.

      +

      These pair style differ from the other dpd styles in that the +dissipative and random forces are not computed within the pair style. +This style can be combined with the fix shardlow +to perform the stochastic integration of the dissipative and random +forces through the Shardlow splitting algorithm approach.

      +

      The pairwise energy associated with styles dpd/fdt and +dpd/fdt/energy is only due to the conservative force term Fc, and is +shifted to be zero at the cutoff distance Rc. The pairwise virial is +calculated using only the conservative term.

      +

      For style dpd/fdt, the fluctuation-dissipation theorem defines gamma +to be set equal to sigma*sigma/(2 T), where T is the set point +temperature specified as a pair style parameter in the above examples. +This style can be combined with fix shardlow to +perform DPD simulations under isothermal and isobaric conditions (see +(Lisal)). The following coefficients must be defined for +each pair of atoms types via the pair_coeff command +as in the examples above, or in the data file or restart files read by +the read_data or read_restart +commands:

      +
        +
      • A (force units)
        • +
      • sigma (force*time^(1/2) units)
        • +
      • cutoff (distance units)
        • +
      +

      The last coefficient is optional. If not specified, the global DPD +cutoff is used.

      +

      For style dpd/fdt/energy, the fluctuation-dissipation theorem +defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where +dpdTheta is the average internal temperature for the pair. +Furthermore, the fluctuation-dissipation defines alpha*alpha to be set +equal to 2*kB*kappa, where kappa is the mesoparticle thermal +conductivity parameter. This style can be combined with fix shardlow to perform DPD simulations under +isoenergetic and isoenthalpic conditions (see (Lisal)). The +following coefficients must be defined for each pair of atoms types +via the pair_coeff command as in the examples above, +or in the data file or restart files read by the +read_data or read_restart +commands:

      +
        +
      • A (force units)
        • +
      • sigma (force*time^(1/2) units)
        • +
      • kappa (1/time units)
        • +
      • cutoff (distance units)
        • +
      +

      The last coefficient is optional. If not specified, the global DPD +cutoff is used.

      +

      For style dpd/fdt/energy, the particle internal temperature is +related to the particle internal energy through a mesoparticle +equation of state. Thus, an an additional fix eos must be +specified.

      +
      +
      +
      +

      Restrictions

      +

      Pair styles dpd/fdt and dpd/fdt/energy are only available if +LAMMPS is built with the USER-DPD package.

      +

      Pair styles dpd/fdt and dpd/fdt/energy require use of the +communicate vel yes option so that velocites are +stored by ghost atoms.

      +

      Pair style dpd/fdt/energy requires atom_style dpd +to be used in order to properly account for the particle internal +energies and temperatures.

      +
      + +
      + + +
      +
      +
      + + +
      + +
      +

      + © Copyright 2013 Sandia Corporation. +

      +
      + Built with Sphinx using a theme provided by Read the Docs. + +
      + +
      +
      + +
      + +
      + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/doc/pair_dpd_fdt.txt b/doc/pair_dpd_fdt.txt new file mode 100644 index 0000000000..ac31e82e30 --- /dev/null +++ b/doc/pair_dpd_fdt.txt @@ -0,0 +1,136 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style dpd/fdt command :h3 +pair_style dpd/fdt/energy command :h3 + +[Syntax:] + +pair_style style args :pre + +style = {dpd/fdt} or {dpd/fdt/energy} +args = list of arguments for a particular style :ul + {dpd/fdt} args = T cutoff seed + T = temperature (temperature units) + cutoff = global cutoff for DPD interactions (distance units) + seed = random # seed (positive integer) + {dpd/fdt/energy} args = cutoff seed + cutoff = global cutoff for DPD interactions (distance units) + seed = random # seed (positive integer) :pre + +[Examples:] + +pair_style dpd/fdt 300.0 2.5 34387 +pair_coeff * * 3.0 1.0 2.5 :pre + +pair_style dpd/fdt/energy 2.5 34387 +pair_coeff * * 3.0 1.0 0.1 2.5 :pre + +[Description:] + +Styles {dpd/fdt} and {dpd/fdt/energy} set the fluctuation-dissipation +theorem parameters and compute the conservative force for dissipative +particle dynamics (DPD). The conservative force on atom I due to atom +J is given by + +:c,image(Eqs/pair_dpd_conservative.jpg) + +where the weighting factor, omega_ij, varies between 0 and 1, and is +chosen to have the following functional form: + +:c,image(Eqs/pair_dpd_omega.jpg) + +where Rij is a unit vector in the direction Ri - Rj, and Rc is the +cutoff. Note that alternative definitions of the weighting function +exist, but would have to be implemented as a separate pair style +command. + +These pair style differ from the other dpd styles in that the +dissipative and random forces are not computed within the pair style. +This style can be combined with the "fix shardlow"_fix_shardlow.html +to perform the stochastic integration of the dissipative and random +forces through the Shardlow splitting algorithm approach. + +The pairwise energy associated with styles {dpd/fdt} and +{dpd/fdt/energy} is only due to the conservative force term Fc, and is +shifted to be zero at the cutoff distance Rc. The pairwise virial is +calculated using only the conservative term. + +For style {dpd/fdt}, the fluctuation-dissipation theorem defines gamma +to be set equal to sigma*sigma/(2 T), where T is the set point +temperature specified as a pair style parameter in the above examples. +This style can be combined with "fix shardlow"_fix_shardlow.html to +perform DPD simulations under isothermal and isobaric conditions (see +"(Lisal)"_#Lisal). The following coefficients must be defined for +each pair of atoms types via the "pair_coeff"_pair_coeff.html command +as in the examples above, or in the data file or restart files read by +the "read_data"_read_data.html or "read_restart"_read_restart.html +commands: + +A (force units) +sigma (force*time^(1/2) units) +cutoff (distance units) :ul + +The last coefficient is optional. If not specified, the global DPD +cutoff is used. + +For style {dpd/fdt/energy}, the fluctuation-dissipation theorem +defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where +dpdTheta is the average internal temperature for the pair. +Furthermore, the fluctuation-dissipation defines alpha*alpha to be set +equal to 2*kB*kappa, where kappa is the mesoparticle thermal +conductivity parameter. This style can be combined with "fix +shardlow"_fix_shardlow.html to perform DPD simulations under +isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal). The +following coefficients must be defined for each pair of atoms types +via the "pair_coeff"_pair_coeff.html command as in the examples above, +or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html +commands: + +A (force units) +sigma (force*time^(1/2) units) +kappa (1/time units) +cutoff (distance units) :ul + +The last coefficient is optional. If not specified, the global DPD +cutoff is used. + +For style {dpd/fdt/energy}, the particle internal temperature is +related to the particle internal energy through a mesoparticle +equation of state. Thus, an an additional "fix eos"_fix.html must be +specified. + +:line + +[Restrictions:] + +Pair styles {dpd/fdt} and {dpd/fdt/energy} are only available if +LAMMPS is built with the USER-DPD package. + +Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the +"communicate vel yes"_communicate.html option so that velocites are +stored by ghost atoms. + +Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html +to be used in order to properly account for the particle internal +energies and temperatures. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "fix shardlow"_fix_shardlow.html + +[Default:] none + +:line + +:link(Lisal) +[(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative +particle dynamics as isothermal, isobaric, isoenergetic, and +isoenthalpic conditions using Shardlow-like splitting algorithms.", +J. Chem. Phys., 135, 204105 (2011). diff --git a/doc/read_data.html b/doc/read_data.html index f3ec32e439..5d81d3bcc1 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -631,74 +631,78 @@ of analysis.

      dipole atom-ID atom-type q x y z mux muy muz
      electron
      dpdatom-ID atom-type theta x y z
      electron atom-ID atom-type q spin eradius x y z
      ellipsoid
      ellipsoid atom-ID atom-type ellipsoidflag density x y z
      full
      full atom-ID molecule-ID atom-type q x y z
      line
      line atom-ID molecule-ID atom-type lineflag density x y z
      meso
      meso atom-ID atom-type rho e cv x y z
      molecular
      molecular atom-ID molecule-ID atom-type x y z
      peri
      peri atom-ID atom-type volume density x y z
      smdatom-ID atom-type molecule volume mass kernel_radius contact_radius x y z
      smdatom-ID atom-type molecule volume mass kernel-radius contact-radius x y z
      sphere
      sphere atom-ID atom-type diameter density x y z
      template
      template atom-ID molecule-ID template-index template-atom atom-type x y z
      tri
      tri atom-ID molecule-ID atom-type triangleflag density x y z
      wavepacket
      wavepacket atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
      hybrid
      hybrid atom-ID atom-type x y z sub-style1 sub-style2 ...
      -

      The keywords have these meanings:

      +

      The per-atom values have these meanings and units, listed alphabetically:

      • atom-ID = integer ID of atom
        • -
      • molecule-ID = integer ID of molecule the atom belongs to
      • atom-type = type of atom (1-Ntype)
        • -
      • q = charge on atom (charge units)
        • -
      • diameter = diameter of spherical atom (distance units)
        • -
      • ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
        • -
      • lineflag = 1 for line segment particles, 0 for point particles
        • -
      • triangleflag = 1 for triangular particles, 0 for point particles
      • bodyflag = 1 for body particles, 0 for point particles
        • -
      • template-index = which molecule within the molecule template the atom is part of
        • -
      • template-atom = which atom within a template molecule the atom is
        • -
      • density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
        • -
      • mass = mass of particle (mass units)
        • -
      • volume = volume of particle (distance^3 units)
        • -
      • x,y,z = coordinates of atom
        • -
      • mux,muy,muz = components of dipole moment of atom (dipole units)
        • -
      • rho = density (need units) for SPH particles
        • -
      • e = energy (need units) for SPH particles
        • +
      • contact-radius = ??? (distance units)
        • +
      • cs_re,cs_im = real/imaginary parts of wavepacket coefficients
      • cv = heat capacity (need units) for SPH particles
        • -
      • spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
        • +
      • density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
        • +
      • diameter = diameter of spherical atom (distance units)
        • +
      • e = energy (need units) for SPH particles
        • +
      • ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
      • eradius = electron radius (or fixed-core radius)
      • etag = integer ID of electron that each wavepacket belongs to
        • -
      • cs_re,cs_im = real/imaginary parts of wavepacket coefficients
        • -
      • kernel_radius = ??? (distance units)
        • -
      • contact_radius = ??? (distance units)
        • +
      • kernel-radius = ??? (distance units)
        • +
      • lineflag = 1 for line segment particles, 0 for point or spherical particles
        • +
      • mass = mass of particle (mass units)
        • +
      • molecule-ID = integer ID of molecule the atom belongs to
        • +
      • mux,muy,muz = components of dipole moment of atom (dipole units)
        • +
      • q = charge on atom (charge units)
        • +
      • rho = density (need units) for SPH particles
        • +
      • spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
        • +
      • template-atom = which atom within a template molecule the atom is
        • +
      • template-index = which molecule within the molecule template the atom is part of
        • +
      • theta = internal temperature of a DPD particle
        • +
      • triangleflag = 1 for triangular particles, 0 for point or sperhical particles
        • +
      • volume = volume of Peridynamic particle (distance^3 units)
        • +
      • x,y,z = coordinates of atom (distance units)

      The units for these quantities depend on the unit style; see the units command for details.

      diff --git a/doc/read_data.txt b/doc/read_data.txt index d15fa2b835..37c082accf 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -527,6 +527,7 @@ body: atom-ID atom-type bodyflag mass x y z bond: atom-ID molecule-ID atom-type x y z charge: atom-ID atom-type q x y z dipole: atom-ID atom-type q x y z mux muy muz +dpd: atom-ID atom-type theta x y z electron: atom-ID atom-type q spin eradius x y z ellipsoid: atom-ID atom-type ellipsoidflag density x y z full: atom-ID molecule-ID atom-type q x y z @@ -534,40 +535,41 @@ line: atom-ID molecule-ID atom-type lineflag density x y z meso: atom-ID atom-type rho e cv x y z molecular: atom-ID molecule-ID atom-type x y z peri: atom-ID atom-type volume density x y z -smd: atom-ID atom-type molecule volume mass kernel_radius contact_radius x y z +smd: atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z sphere: atom-ID atom-type diameter density x y z template: atom-ID molecule-ID template-index template-atom atom-type x y z tri: atom-ID molecule-ID atom-type triangleflag density x y z wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:) -The keywords have these meanings: +The per-atom values have these meanings and units, listed alphabetically: atom-ID = integer ID of atom -molecule-ID = integer ID of molecule the atom belongs to atom-type = type of atom (1-Ntype) -q = charge on atom (charge units) -diameter = diameter of spherical atom (distance units) -ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles -lineflag = 1 for line segment particles, 0 for point particles -triangleflag = 1 for triangular particles, 0 for point particles bodyflag = 1 for body particles, 0 for point particles -template-index = which molecule within the molecule template the atom is part of -template-atom = which atom within a template molecule the atom is -density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) -mass = mass of particle (mass units) -volume = volume of particle (distance^3 units) -x,y,z = coordinates of atom -mux,muy,muz = components of dipole moment of atom (dipole units) -rho = density (need units) for SPH particles -e = energy (need units) for SPH particles +contact-radius = ??? (distance units) +cs_re,cs_im = real/imaginary parts of wavepacket coefficients cv = heat capacity (need units) for SPH particles -spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) +density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) +diameter = diameter of spherical atom (distance units) +e = energy (need units) for SPH particles +ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles eradius = electron radius (or fixed-core radius) etag = integer ID of electron that each wavepacket belongs to -cs_re,cs_im = real/imaginary parts of wavepacket coefficients -kernel_radius = ??? (distance units) -contact_radius = ??? (distance units) :ul +kernel-radius = ??? (distance units) +lineflag = 1 for line segment particles, 0 for point or spherical particles +mass = mass of particle (mass units) +molecule-ID = integer ID of molecule the atom belongs to +mux,muy,muz = components of dipole moment of atom (dipole units) +q = charge on atom (charge units) +rho = density (need units) for SPH particles +spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP) +template-atom = which atom within a template molecule the atom is +template-index = which molecule within the molecule template the atom is part of +theta = internal temperature of a DPD particle +triangleflag = 1 for triangular particles, 0 for point or sperhical particles +volume = volume of Peridynamic particle (distance^3 units) +x,y,z = coordinates of atom (distance units) :ul The units for these quantities depend on the unit style; see the "units"_units.html command for details. diff --git a/doc/searchindex.js b/doc/searchindex.js index 4cd7603b1e..a79054cb4f 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6,278,299,300,312,326,336,349,355,361,362,363,365,366,367,370,395,416,417,424,466,467,469,471,472,474,477,479],affin:[16,17,18,220,370,386],afil:233,aforement:18,afresh:[287,477,495],afshar:391,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,146,147,148,149,150,151,152,155,156,157,158,160,161,168,169,171,172,175,176,181,190,191,192,193,194,195,197,198,199,203,204,206,207,214,215,216,217,218,220,224,231,242,243,244,245,246,251,252,253,255,261,262,263,269,274,275,276,278,281,285,289,297,299,302,310,315,317,318,319,321,322,323,324,325,329,331,333,337,340,341,347,354,360,361,363,364,366,368,369,370,371,372,377,384,386,393,394,395,396,402,403,404,415,416,417,419,420,421,422,426,430,432,433,440,441,451,453,454,455,458,464,466,468,469,470,471,472,474,475,477,479,481,483,486,487,490,494,495,496,497,498,499],afterrun:477,afterward:3,afterword:41,ag1:167,ag2:167,again:[6,11,12,16,17,62,142,148,154,162,191,194,220,235,285,340,354,365,416,417,464,466,467,469,471,476,483,485,495,497],against:[11,12,13,64,221,365,432,433],aggreg:[6,12,65,68,69,79,93,110,117,235,251,297,299,312,464,496],aggress:[235,483],agilio:[9,13],agre:[3,8,188,363,372,404,433],agreement:[5,7],ahd:401,ahead:333,aidan:[0,5,7,9,13,358],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:193,akohlmei:[7,9,13,195,236],aktulga:[7,9,292,433],al2o3:440,al2o3_001:[120,300],al3:167,ala:[242,440],alain:9,alat:[280,419],alb:[430,453,455],albeit:298,albert:9,alchem:[87,162],alcohol:329,alcu:[371,377],alcu_eam:430,alderton:390,alejandr:[255,256],alessandro:13,algebra:422,algorithm:[0,1,6,7,8,9,41,61,194,203,214,217,220,242,244,245,269,282,290,299,302,321,322,326,329,334,361,362,363,367,370,395,417,422,437,439,464,466,483],alia:[12,16],alias:[1,356],aliceblu:194,align:[6,12,29,41,71,170,188,210,214,237,358,469,472,490],alkali:395,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,161,162,163,164,165,166,167,168,169,170,171,172,174,176,181,187,188,191,192,193,194,195,197,198,199,200,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,248,250,251,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,275,276,277,278,279,280,281,282,284,285,286,287,288,289,290,291,292,294,295,296,297,298,299,300,301,302,303,304,305,306,310,311,313,314,315,316,317,318,321,322,323,324,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,345,350,353,354,355,356,357,358,360,363,364,365,366,367,369,370,371,372,373,375,376,377,378,380,381,382,383,384,386,387,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,486,487,488,490,494,495,496,497,498,499],allen:[29,87,390,398],allentildeslei:87,allign:3,allindex:338,alloc:[3,5,6,8,9,11,12,60,229,328,364,366,370,428,433,469,477],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,92,108,110,144,146,147,148,161,166,167,168,170,176,187,188,191,193,194,195,197,198,200,202,203,204,206,207,208,209,210,211,212,214,216,217,218,219,220,221,225,226,229,231,232,233,234,236,239,242,245,246,250,252,255,256,280,284,285,286,287,288,289,293,299,300,302,303,305,306,310,314,321,322,323,324,326,327,328,329,330,331,337,339,341,350,355,356,358,363,364,365,366,369,370,373,377,378,379,380,381,382,387,393,395,399,400,401,402,407,411,416,417,422,424,430,433,434,437,439,440,449,459,461,464,467,469,471,472,473,474,475,476,479,481,482,483,486,487,495,496],almost:[2,3,12,60,237,289,326,356,367,370,449],alo:387,alon:[6,7,217,295,432,433,467],alond:13,along:[6,8,9,12,29,40,71,87,120,166,167,168,190,191,193,206,217,237,242,243,247,252,254,289,299,302,303,307,311,312,321,325,326,332,335,337,358,361,362,363,365,387,390,399,402,405,407,411,419,432,433,452,469,472,479,480,495],alonso:[420,421],alpha:[6,12,51,198,242,281,289,290,294,363,371,374,378,387,391,393,394,396,401,406,407,419,425,429,454,456,487,490],alpha_:[],alpha_c:415,alpha_i:441,alpha_ialpha_j:[],alpha_lj:415,alphabet:[2,3,22,37,44,55,63,176,187,197,341,350,364,384,450,469],alphanumer:[3,63,197,288,296,339,364,495],alreadi:[3,7,8,9,12,16,17,18,42,168,169,171,192,202,206,210,211,214,216,220,246,287,289,314,337,364,365,391,400,402,409,417,449,459,462,465,469,470,474,479,495],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,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008:[432,433],chi:[93,157,190,280,290,292,396,398,496],chiefli:431,child:8,chip:[7,12,17,18,370,482],chipot:219,chiral:349,chmod:[11,12],cho:419,chocol:[7,194],choic:[3,6,12,15,16,18,40,41,54,87,143,146,147,161,172,188,206,210,211,214,217,220,221,233,239,242,253,255,282,290,299,321,350,356,361,362,365,367,370,402,415,424,428,469,478,479,482,483,489,490,494],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,119,158,159,193,215,216,217,218,221,228,239,242,253,255,257,258,259,260,261,262,263,285,286,314,318,332,355,356,362,459,464,466,478,484],chose:[453,455],chosen:[2,3,6,12,17,142,168,171,180,188,193,199,204,218,221,228,231,232,240,242,253,255,260,282,285,296,314,318,321,322,327,329,330,336,356,357,362,370,395,399,406,409,435,453,464,478,483,490],chri:166,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,94,105,107,116,148,163,165,206],chute:[4,10,234],ciccotti:302,cieplak:[6,174,481],cii:207,cij:207,circl:[42,71,310],circular:[3,6,146,189],circumst:18,circumv:[92,108,294],citat:[],cite:[3,7,8,12,239,440],ckio:2,cko:2,cl1:167,clarendon:[29,390],clarifi:[7,453,455],clariti:339,clark:427,class2:[],classic:[0,3,5,6,7,8,9,229,282,289,294,326,351,395],classifi:[9,450,458],claus:467,clean:[6,12,14,15,17,477],cleanli:[468,498],clear:[],clearli:7,clebsch:142,clermont:[9,13],clever:473,click:[2,11,22,37,44,55,168,176,187,193,236,341,350,365,384,450],client:[236,238],climb:[254,365,483],clinic:[7,13],clo:[157,190,496],clock:[12,464,483],clockwis:332,close:[3,6,11,12,13,39,41,67,71,143,171,191,216,217,218,233,240,242,255,276,299,302,332,335,354,356,359,361,362,365,370,372,377,387,388,405,419,424,436,438,455,473,479,490,492],closer:[3,41,118,166,190,191,214,218,222,323,365],closest:[216,280,299,329,398,434,449,459],cloud:[440,490],clovertown:18,clsuter:72,clump1:[284,299],clump2:[284,299],clump3:[284,299],clump:299,cluster:[],clutter:[3,9],cmap:469,cmatrix:233,cmax:419,cmd:[11,12,282,480],cmdarg:11,cmin:419,cmm:[],cmoput:135,cn1:207,cn2:207,cna:[],cnn:207,cnr:[9,13],cnt:[402,473],co2:[40,167,302,364],coars:[7,9,29,36,40,54,180,284,299,314,400,435,481],coarser:[356,495],coarsest:142,code:[],coeff:[3,7,8,12,21,22,33,44,50,174,175,176,181,340,341,347,384,402,406,424,437,439,442,469],coeffcient:469,coeffici:[],coefficienct:391,coefficient0:393,coefficient1:393,coeffieci:[6,374,405],coeffincientn:393,coexist:[9,231,395],cohes:[6,396,419],coincid:[124,335,382,416,417,464],colberg:192,cold:[6,153,231,235,366,490],coldest:322,coleman8:9,coleman:[9,120,167,300],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,94,99,105,107,116,148,156,163,165,168,191,194,206,219,245,251,284,294,297,299,337,355,364,366,385,469,476,482,488,499],collid:[225,314,336],colliex:167,collinear:[3,284],collis:[3,242,314,332,336,392,399,462],colllis:314,colloid:[],colombo:39,colon:[195,337,470],color1:194,color2:194,color:[3,9,41,191,193,194,214,232,289,294],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,94,105,107,108,110,112,115,116,117,118,119,121,142,143,148,156,163,165,166,167,188,191,194,197,205,206,207,209,210,211,212,245,252,253,289,299,315,316,326,336,397,401,432,433,470,484,486,495],columnar:166,colvar:[],colvarmodul:12,com:[],comamnd:220,comand:217,comannd:370,comb3:[],comb:[],comb_1:291,comb_2:291,combiant:388,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,93,104,110,117,146,147,161,191,193,203,209,236,245,255,282,288,318,327,335,338,340,355,356,358,362,370,385,387,388,395,396,402,414,415,441,451,453,455,458,461,472,477,482,490,495],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,192,236,238,239,356,365,370,391,424,429,452,471],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,174,188,191,240,299,326,364,365,371,393,394,396,406,419,426,433,440,441,451,452,453,454,455,458,466,467,469,490,495],commerci:7,commmand:[3,6,12,59,109,277,405,463,464,466,483,498],common:[],commonli:[3,6,12,17,25,57,59,106,108,170,191,193,195,351,400,409,441,453,455,469,472,481],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,166,171,172,193,194,214,215,216,218,219,220,236,238,242,244,245,246,255,281,288,290,291,292,299,314,326,337,353,355,366,367,368,370,392,428,466,467,478,479,495,497,499],communc:355,comp:[7,192,238,239,302,356,365,395,424,429,434,448,452,454],compact:[63,197,384,450],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,112,120,151,167,176,187,194,224,290,337,339,355,356,363,365,419,440,464,483,484,490,494],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,175,176,187,340,341,350,383,450],compat:[3,5,7,8,9,11,12,13,17,18,41,71,119,121,179,191,195,199,205,206,207,209,210,211,212,214,281,293,318,321,328,331,334,355,370,403,422,424,452,466,467,495],compens:[6,215,216,297,366,395],compet:325,competit:356,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,166,191,192,193,195,236,325,356,370,422,469,470,474,495],compl:17,complain:[12,17],complement:419,complementari:[7,387,407],complet:[3,6,9,11,12,15,41,59,71,194,210,214,219,245,282,285,288,314,325,327,339,354,365,370,396,437,439,457,464,469,474,477,481,483,486,490,495],complex:[6,8,11,12,13,25,40,42,62,92,108,142,144,156,168,169,242,310,335,353,365,395,422,452,467,469,472,495],compli:[321,325],complic:[6,7,9,12,13,204,231,467],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,92,94,95,98,105,106,107,108,109,110,111,112,114,115,119,129,132,133,134,135,138,139,140,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,163,164,165,190,191,193,194,200,201,205,206,207,208,209,210,211,212,213,217,218,220,221,226,229,234,238,239,242,245,247,251,252,254,255,256,260,261,262,263,274,275,276,278,279,281,282,283,286,297,299,301,302,303,307,308,311,314,317,318,319,321,328,329,334,335,336,355,358,362,363,364,365,370,376,391,395,399,416,417,437,439,440,441,469,470,479,487,495,496],componenet:6,composit:[6,204,242,393],compound:[386,395,396,458],compres:[71,116,206],compress:[],compris:[40,335,434,457],compton:[120,167],comptu:3,compuat:356,comput:[],computation:[3,6,215,216,326,377],computational:490,compute_arrai:8,compute_fep:[199,415],compute_group_group:231,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,300],compute_scalar:8,compute_temp:8,compute_ti:199,compute_vector:8,compute_xrd:167,concaten:[2,3,498],concav:335,concentr:[71,393],concept:[6,148,158,206,478],conceptu:[3,6,71,156,218,220,365,387,402,419,474],concern:[6,73,87,192,232],concetr:71,concis:[11,325],conclud:12,concret:8,concurr:[9,16,356,495],conden:[326,453,455],condens:[6,150,326,372,389,393,407,458],condit:[],conducit:6,conduct:[],cone:472,confer:422,confid:[3,483],config:[12,191,466],configfil:219,configur:[1,2,6,12,15,17,38,59,124,170,188,190,191,193,197,218,219,220,221,225,231,238,239,269,282,290,325,353,363,365,372,377,394,419,422,451,453,455,458,464,469,471,472,483],confin:[469,483],conflict:[3,12,40,424,467],conform:[3,6,13,59,217,218,254,298,303,325,349,365,395,481],confus:[3,458],conjuct:391,conjug:[7,8,239,362,395,432,433],conjunct:[6,7,71,86,87,116,151,156,162,168,172,194,198,199,239,242,246,269,285,286,290,291,292,294,299,314,322,329,334,355,356,365,378,380,384,387,391,395,401,407,424,427,435,456,469,472,476,490,499],connect:[3,6,87,153,171,217,236,284,299,302,311,365,388,399,449,455,466,467,473,490],conput:3,consecut:[3,11,12,39,71,168,194,198,199,221,236,237,387,407,411,464,470,472],consequ:[1,6,204,326,406,483],conserv:[3,29,197,204,217,224,225,232,235,239,241,242,246,251,253,255,269,299,302,317,318,322,329,330,334,365,390,391,399,413,440,478,483],consid:[6,9,70,71,78,87,117,150,153,154,171,191,194,198,199,205,207,210,214,216,217,221,243,256,281,299,321,322,325,326,329,356,384,395,402,433,434,440,449,464,465,467,470,471,472,474,477,479,487,490,495],consider:[6,8,239,240,317,318,319,370,478],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,148,151,153,168,180,190,195,200,201,206,220,221,224,226,229,232,239,240,241,252,255,257,258,259,260,261,262,263,264,265,267,268,269,270,272,273,274,275,276,277,278,286,289,294,296,298,299,317,318,319,320,330,355,356,358,364,365,370,372,377,379,385,387,395,398,402,405,416,417,419,422,424,434,437,439,440,452,459,467,469,470,471,472,473,474,481,490,495],consistent_fe_initi:203,consit:299,constant:[],constitu:[3,6,245,299,331,335,385,434],constitut:[437,439],constrain:[3,6,8,145,146,147,148,149,151,154,155,156,157,158,160,161,197,206,221,231,232,237,245,249,284,285,297,299,302,312,322,329,363,364,395,474,481,490],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,167,218,255,281,298,335,366,370,390,422,424,449,451,452,472,473,488,495],constructor:[8,11],consult:433,consum:[1,294,428,495],consumpt:353,contact:[],contact_stiff:[436,438],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,148,156,166,167,168,170,174,176,187,188,191,193,194,195,197,198,199,203,205,206,207,209,210,211,212,214,219,221,226,233,237,238,239,242,253,269,280,281,284,285,287,289,292,296,299,300,304,314,321,325,326,335,336,339,354,356,364,365,368,369,371,372,373,377,386,387,390,393,394,395,402,403,419,422,426,430,431,432,433,441,451,452,453,454,455,456,458,464,465,466,467,469,470,471,472,474,476,478,481,483,486,487,490,495,497,499],content:[12,18,433,485,487],context:[3,6,8,12,17,118,119,194,215,216,221,284,296,330,362,461,469,476,485,494,495,496],contibut:70,contigu:466,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,164,194,197,198,199,204,206,207,208,209,210,211,212,214,217,218,219,220,221,231,232,233,235,236,237,239,240,241,247,252,253,255,257,258,259,260,261,262,263,274,275,276,277,278,283,285,288,289,299,300,303,313,314,316,323,324,326,332,335,339,354,369,370,377,391,392,409,412,432,433,434,437,439,454,464,467,469,471,472,477,483,486,487,495,497],continuum:[6,7,9,203,326,437,439],contour_integr:203,contract:[59,218,220,255,286,299],contradictori:3,contrain:302,contraint:269,contrari:[233,240],contrast:[1,6,42,55,64,150,153,220,337,437,439,461,498],contrib:326,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,199,204,205,206,207,209,210,211,212,218,231,239,242,245,246,250,256,276,277,284,285,293,296,299,300,302,328,355,363,365,373,391,392,393,395,402,416,417,422,424,432,433,440,481,487,490],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,177,191,193,197,203,204,214,218,219,220,235,236,239,240,255,257,258,259,260,261,262,263,286,291,299,305,306,317,318,319,326,330,353,355,367,395,398,422,432,433,436,438,451,455,464,466,478,484,485],control_typ:203,controlfil:433,convect:91,conveni:[6,12,29,191,195,212,300,358,441,495],convent:[3,8,9,29,179,186,187,194,298,311,338,393,395,495],converg:[3,6,41,88,191,193,195,200,214,217,218,226,229,260,289,291,294,298,302,361,362,363,365,386,387,407,440,464,476,483],convers:[3,8,142,193,194,204,207,286,355,387,388,389,395,407,411,415,427,467,483,494],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,168,175,191,193,194,212,253,285,337,340,342,346,349,358,365,371,393,422,453,455,462,467,469,470,471,476,486,490,494,495,497,499],convex:[42,335,376],convinc:[7,12],cook:9,cooki:7,cool:[7,158,235,297],cooordin:191,cooper:[5,7],coord123:116,coord1:[3,116,206,210,211],coord2:[3,116,206,210,211],coord3:[3,116,206,210,211],coord:[],coordb:440,coordbb:440,coordiat:363,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,151,157,163,165,166,168,172,190,191,192,193,194,195,197,200,205,206,209,210,211,214,215,216,217,218,219,220,221,224,226,227,229,231,234,235,236,237,238,239,240,252,254,255,257,258,259,261,262,263,276,279,280,281,284,285,286,296,297,299,301,302,303,308,311,312,313,314,316,324,325,326,333,334,336,337,358,363,364,365,370,371,372,375,376,394,440,464,469,470,471,472,474,477,479,483,490,495,496],coordn:[116,206],coorind:[],copi:[0,3,4,8,11,12,15,17,40,121,193,326,365,384,432,467],copper:462,coproccesor:16,coprocessor:[1,4,7,9,16,17,370,482],coproprocessor:17,copy_arrai:8,copyright:[7,8,284],coral:194,core:[],core_shel:150,coreshel:[6,9,380,387,389],cornel:[6,174,481],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,193,335,336,358,457,469],cornflowerblu:194,cornsilk:194,corpor:16,corr:386,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,150,155,162,193,220,231,233,239,255,256,276,284,286,289,325,331,335,355,365,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,469,484,487,490],correction_max_iter:203,correctli:[3,8,9,11,17,71,81,103,104,105,145,146,147,149,151,153,154,155,156,157,160,161,164,191,194,200,221,226,229,240,249,255,256,292,299,302,311,313,332,335,365,366,370,389,417,422,466,467,469,479,494,496],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,155,162,166,167,174,175,176,177,178,179,180,182,183,185,186,188,190,191,193,194,198,199,200,206,208,209,210,211,213,216,218,220,227,229,230,234,239,242,243,251,252,253,255,257,258,259,260,261,262,263,264,265,269,272,274,275,276,278,281,282,286,291,299,301,302,317,319,321,330,331,332,334,335,336,338,340,341,342,343,345,346,349,351,356,360,362,364,365,371,372,374,378,379,380,381,382,383,384,385,386,387,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,424,425,426,427,429,430,432,433,434,435,440,441,442,451,452,453,454,455,458,460,461,462,464,466,467,469,470,472,482,483,484,486,487,490,495],correspondingli:[416,417,478],cosin:[],cosineshift:27,cosmo:[233,238],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,167,193,194,206,210,211,214,215,216,228,255,291,326,355,356,368,387,407,411,422,424,451,466,478],costheta0:[451,453,455,458],costheta:430,costli:[11,88,233,366],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,148,158,163,165,181,191,193,194,198,199,206,207,210,214,220,229,238,288,289,290,294,297,299,301,314,315,321,325,326,327,331,335,337,339,347,352,354,361,363,366,370,373,397,401,402,405,432,433,465,466,467,469,471,473,476,477,485,490,495,496],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,169,173,290,292,327,355,356,363,370,378,380,381,382,383,386,387,388,389,390,395,399,400,402,407,411,415,418,424,427,432,433,435,440,450,455,456,458,461,474,481,487,490,494],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,156,166,172,200,201,204,206,209,210,211,213,214,221,226,228,231,237,255,269,285,302,317,318,335,356,363,364,365,367,370,397,401,424,487,495],counter:[332,464,475,477,483],counteract:231,counterbal:235,counterbalanc:29,counterpart:[191,299,464],counterproduct:18,coupl:[],courant:304,cours:[3,8,128,130,162,191,198,199,232,298,311,325,331,333,334,336,337,356,416,442,466,469,482,490,495,497],courtesi:358,cov:440,coval:[6,29,395,419,440,490],covari:233,cover:[6,71,188,194,203,242,395,457],coverag:[71,210],cpc:238,cpp:[1,3,6,8,9,11,12,13,87,191,198,199,229,302],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,194,208,224,240,327,353,356,370,384,450,464,482,483,486,487,488,495],cpuremain:487,cr2:167,cr3:167,crack:[4,366],crada:[5,7],crai:[5,7,13,18,191],crash:[3,12,366,490],craympi:370,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:203,create_faceset:203,create_group:192,create_nodeset:203,createatom:[],creation:[],crimson:194,critchlei:284,criteria:[3,118,169,193,194,215,216,217,250,363,429,457,471,474,495],criterion:[12,41,123,168,171,204,214,217,231,269,291,304,332,337,363,365,386,395,399,440,474,483,484],criterioni:483,critic:[6,48,49,253,321,326,363],crmax:71,crmin:71,cross:[3,12,22,71,89,146,166,176,191,193,205,210,216,220,252,254,276,299,307,311,313,322,329,341,358,365,382,391,392,393,400,401,402,407,409,411,430,435,437,439,453,455,462,469,473,479,497],crossov:1,crossterm:469,crozier:[0,7,13],crucial:289,crystal:[4,6,13,73,108,280,281,324,358,366,473,487,490],crystallin:[6,104,281,358,454,490],crystallis:321,crystallogr:[120,167],crystallograph:[358,487],crystallographi:[120,167,358],cs1:167,cs_chunk:6,cs_im:[40,469],cs_re:[40,469],csanyi:[142,431,441],cscl:419,csequ:6,csh:[11,12,384],cshrc:[11,12],csic:[394,451,453,455,458],csinfo:6,csisi:[394,451,453,455,458],csld:[],cst:393,cstherm:6,cstyle:466,csvr:[],ctcm:[371,393],ctemp_cor:224,cterm:303,ctr:9,ctype:11,cu1:167,cu2:167,cu3au:419,cube:[6,41,166,171,214,224,335,358,490],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:377,cummul:[3,6,212,215,216,217,219,228,233,239,241,314,317,318,319,320,322,329,401,487],cumul:[6,204,206,209,210,211,225,231,239,253,255,260,269,299,300,365],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,148,156,158,164,166,169,172,190,191,192,193,194,195,198,199,203,206,210,211,212,214,215,216,217,218,219,220,221,225,226,229,231,233,236,237,239,245,252,255,256,261,262,263,269,274,275,276,278,284,285,290,291,293,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,317,318,319,325,326,329,330,331,332,333,334,336,337,339,353,354,355,356,359,360,362,363,364,365,370,376,377,384,386,390,393,395,396,399,402,403,406,416,417,419,420,421,424,430,432,433,436,437,438,439,442,453,455,456,459,464,465,466,467,469,470,471,472,473,475,476,477,479,481,483,484,486,487,495,496,497,498,499],curv:[6,168,231,281],curvatur:[398,434,462],custom:[],cut0:467,cut1:478,cut2:478,cut:[],cuthi:[280,292],cutinn:[379,416,417],cutlo:[280,292],cutmax:430,cutoff1:[383,390,407,411,415,418,427,435],cutoff2:[378,380,381,383,389,390,407,411,415,418,427,435],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,166,169,171,172,216,217,222,280,289,290,292,294,296,299,314,327,331,335,337,353,355,356,363,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,467,471,474,478,490,495],cutoff_glob:376,cutoff_inn:376,cutoffa:394,cutoffc:394,cuu3:393,cval:167,cvd:321,cvel:303,cvff:[],cwiggl:[3,252,331,334,336,495],cyan:[2,193,194],cycl:[3,231,253,255,256,260],cyclic:[3,188],cygwin:12,cylind:[3,4,71,193,206,237,285,332,335,472],cylindr:[6,237,311,332],cypress:370,cyrot:377,cyrstal:281,d3q15:242,d3q19:242,d_double_doubl:15,d_e:326,d_flag2:288,d_flag:288,d_name:[115,191,288,316,479],d_single_doubl:15,d_single_singl:15,d_sx:288,d_sy:288,d_sz:288,daan:324,dai:12,daili:12,daivi:276,damag:[],dammak:294,damp:[3,6,197,202,239,240,241,246,255,256,260,286,289,290,294,299,317,318,330,332,333,362,363,365,378,380,382,387,390,395,399,407,415,427,435,450,456,483,490],damp_com:240,damp_drud:240,dampen:[299,490],dampflag:[332,399],dan:17,danger:[3,12,231,337,391,487],dangl:171,daniel:9,darden:[356,390],darkblu:194,darkcyan:194,darken:193,darkgoldenrod:194,darkgrai:194,darkgreen:194,darkkhaki:194,darkmagenta:194,darkolivegreen:194,darkorang:194,darkorchid:194,darkr:194,darksalmon:194,darkseagreen:194,darkslateblu:194,darkslategrai:194,darkturquois:194,darkviolet:194,dasgupta:290,dash:[399,486],dat:[6,91,188,203,465],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,300],dataset:300,datatyp:3,date:[0,6,12,13,190,432,433,495],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,191,207],davenport:418,davi:331,david:[9,19,355,356,453,455],daw:[393,430],dbg:14,dcd:[3,6,7,191,192,193,194,195,282,470,474],ddim:190,deactiv:415,dealt:238,debug:[6,7,11,12,13,14,17,120,124,167,168,282,287,353,355,370,403,424,459,467,468,476,479,486,495],deby:[],decai:[92,387,462],decid:[3,6,12,16,71,252,288,299,327,484],decipher:358,declar:192,declin:314,decod:193,decompos:[87,441],decomposit:[3,5,7,18,62,203,282],decoupl:[6,490],decreas:[3,191,200,201,208,217,220,226,229,231,239,325,355],decrement:303,deepli:352,deeppink:194,deepskyblu:194,def:[12,13,467],defaul:61,defect:[6,70,166,422],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,174,175,176,177,178,179,180,182,183,185,186,187,188,189,190,191,192,193,194,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,220,221,224,225,226,229,230,231,234,237,238,239,240,241,242,250,252,254,255,256,257,258,259,260,261,262,263,265,266,267,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,290,292,297,299,300,301,302,304,308,312,314,316,317,318,319,320,322,323,324,326,328,329,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,349,350,351,353,355,356,358,360,362,363,364,365,366,367,368,369,370,372,373,374,375,376,378,379,380,381,382,383,384,385,387,388,390,391,392,394,395,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,422,423,424,425,426,427,429,430,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,466,467,469,470,472,473,474,475,478,479,480,481,483,484,486,487,490,491,492,493,494,495,496],definit:[2,3,6,8,12,13,78,80,118,142,194,206,207,208,209,210,211,212,220,237,260,300,316,328,331,334,336,338,350,353,364,373,377,385,395,405,430,437,439,441,457,467,469,471,478,480,494,495],defint:487,deform:[],deg2theta:167,deg:490,degener:[3,284],degrad:[8,18,281,356,478],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,167,168,174,175,178,179,186,188,190,193,206,217,224,231,233,234,239,240,245,255,256,260,261,262,263,274,275,276,278,282,284,298,299,302,317,318,319,324,340,342,346,349,351,363,390,393,401,479,487,490,496],degress:[148,206],del:483,delai:[3,6,12,366,392,487],deleg:402,delet:[2,3,7,8,12,54,57,60,63,166,171,172,197,206,207,209,210,211,212,215,217,228,231,255,300,317,318,337,339,354,364,366,369,424,449,469,470,471,472,480,481,486,491,493,495,496],delete_atom:[],delete_bond:[],delete_el:203,deli:190,delimit:[467,495],deloc:[256,395,440],delr:419,delt_lo:483,delta:[],delta_1:377,delta_3:377,delta_7:377,delta_conf:3,delta_ij:[419,430],delta_mu:3,delta_pi:377,delta_r:430,delta_sigma:377,delta_ua:376,delx:190,delz:190,dem:376,demand:294,demo:11,demon:279,demonstr:[289,419],den:285,dendrim:401,denniston:[9,242,244,245,246,281],denomin:[7,173],denot:[120,224,240,281,292,294,387,400,402,433,437,439],dens:[71,217,395],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,154,166,168,198,199,203,206,210,211,214,220,229,242,245,248,249,281,285,286,290,326,331,358,360,364,371,377,393,419,420,421,430,434,440,444,446,447,448,469,478,479,487,494],density_continu:439,density_summ:439,depart:[0,7],departur:[253,289],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,151,155,156,162,168,169,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,193,194,197,198,199,200,201,204,206,208,209,210,212,213,214,216,218,220,226,227,230,233,234,235,237,239,240,242,244,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,280,291,294,296,299,301,302,308,314,317,318,319,321,323,325,326,328,330,331,334,335,336,337,339,340,341,342,343,345,346,349,351,356,358,363,364,366,367,368,370,371,372,374,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,393,394,395,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,419,420,422,423,425,426,427,429,430,432,433,434,435,440,441,442,450,451,452,453,454,455,456,458,460,461,462,464,466,469,471,472,475,479,481,483,486,487,489,495,496],dependend:6,depflag:12,dephas:[464,483],depos:221,deposit:[],deprec:[290,432],depth:[51,146,193,326,398,434],dequidt:9,der:[87,109,385,386,415,432,433,461,490],deriv:[6,7,8,9,38,56,63,87,142,162,188,207,218,220,231,239,252,255,257,258,259,260,261,262,263,280,286,290,294,323,324,326,331,332,335,362,364,372,377,385,390,395,396,400,409,413,414,419,422,432,433,450,452,461,490],derjagin:461,derlet:280,descend:194,descent:[7,362],descib:[40,193,290],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,148,152,153,156,159,161,162,166,167,168,170,171,180,185,188,191,192,197,198,199,206,207,208,209,210,211,212,214,217,218,219,220,221,223,224,232,233,236,237,238,239,240,241,242,244,245,246,250,254,255,256,260,268,277,280,282,287,288,289,290,291,292,299,303,311,314,315,316,317,318,319,320,321,322,323,324,329,331,332,334,339,355,356,358,361,362,363,364,365,369,372,373,375,376,378,379,380,382,383,384,385,386,387,390,393,395,396,398,399,400,402,405,407,408,409,410,411,412,413,414,415,416,417,418,419,422,423,429,430,431,432,433,434,435,440,441,442,449,450,451,452,453,454,455,456,458,460,461,462,464,466,467,469,470,471,472,473,479,482,483,486,495,496,497],descript:[],descriptor:[142,191,403],deserno:356,design:[0,3,6,7,8,9,11,13,14,15,17,120,150,153,167,203,217,223,224,255,256,280,281,300,321,326,373,374,375,376,379,382,387,389,395,415,416,417,420,421,430,433,452,478],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,150,168,181,190,206,212,218,220,229,231,232,239,240,241,245,255,276,284,285,286,287,290,294,299,302,314,317,318,319,320,325,332,347,352,355,356,358,361,363,364,365,391,393,401,416,417,451,453,455,465,466,467,469,473,478,483,484,486,487,495,496,497],desk:7,desktop:[4,6,7,10,12,193],despit:490,destabil:377,destre:349,destroi:[11,39,215,216],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,148,151,161,162,163,165,168,169,172,173,176,187,190,191,193,194,197,198,199,203,206,207,208,209,210,212,214,216,217,218,219,220,221,229,231,232,233,234,236,237,239,241,242,246,252,253,254,255,256,257,258,259,260,261,262,263,267,269,274,275,276,277,278,281,284,285,286,288,289,291,292,293,299,302,314,317,318,319,320,321,322,324,325,326,327,328,329,330,337,339,341,350,355,356,359,363,364,366,367,370,371,372,373,375,376,377,379,381,382,383,384,385,386,387,390,391,395,396,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,417,418,419,423,424,429,432,433,434,440,441,442,450,457,460,461,467,469,470,471,472,474,475,478,479,481,484,487,488,495,496,499],detect:[2,3,12,42,61,63,86,92,230,285,325,365,386,401,406,464,466,469,480,483,495],determ:370,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,156,157,166,167,168,190,191,193,194,195,196,200,201,202,205,206,207,208,209,210,211,212,213,214,218,220,221,224,226,231,234,235,237,239,240,245,250,252,253,255,261,262,263,274,275,276,278,280,282,285,286,289,296,297,298,299,300,301,304,306,308,314,317,318,319,321,327,328,331,332,333,334,335,336,337,350,355,356,358,364,366,367,370,372,373,381,386,390,392,393,397,399,402,403,411,419,422,424,433,434,440,449,452,456,461,466,469,470,472,474,476,479,483,485,486,488,494,495,496],detil:110,devan:[9,435],devanathan:455,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,236,260,284,289,290,293,372,377,395,421,422,440,458,471],devemi:9,deviat:[253,260,280,397],deviator:9,devic:[1,3,12,15,17,236,370],device_typ:370,devin:[291,386],devis:421,dfactor:193,dff:490,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,356],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,293,422],dhi:[59,190,220,285],dhug:[253,289],dhugoniot:[253,289],dia:419,diagnost:[],diagon:[3,6,83,142,143,144,218,255,286,299,329,437,439],diagonalstyl:441,diagram:[41,120,167,187,214,282],diallo:401,diam:[193,194,285,364],diamet:[3,6,40,42,115,168,191,193,194,198,199,239,285,299,314,316,330,332,364,376,385,398,399,409,434,457,461,469,470,479],diamond:[358,395,419],diamter:[40,285],dick:6,dicsuss:252,dictat:[204,253],did:[3,12,363,391,392,393,399,424,453,455,477],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,164,328,355],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,149,151,154,155,156,157,158,160,161,162,168,169,171,176,187,188,190,191,193,194,197,199,202,204,206,209,214,215,216,217,218,219,220,224,230,231,232,233,234,235,236,239,240,242,252,255,256,257,258,259,261,262,263,265,267,270,272,273,274,275,278,280,282,284,286,289,290,291,294,297,299,302,303,311,312,314,317,318,319,322,323,324,326,329,330,331,332,335,339,340,350,352,354,355,356,358,359,361,362,364,365,367,368,369,370,371,372,377,381,382,384,385,386,391,393,395,398,399,400,402,405,407,408,410,411,418,419,420,421,423,424,426,430,432,433,434,435,436,437,439,440,441,442,450,451,452,453,455,457,458,461,463,464,466,467,469,471,472,473,474,477,478,479,481,483,484,486,487,488,490,494,495,496,497],differenti:[1,3,6,29,188,355,387,430,454],difficult:[218,282,370,401,478],difficulti:[92,108,302,432],diffract:[],diffus:[],digit:[2,3,194,339,422],dih_table1:188,dih_table2:188,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:216,dihydrid:395,dij:302,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,149,150,151,154,155,156,157,158,160,168,190,210,220,237,332,358,419,472,494,495,496],dimdim:495,dimems:281,dimens:[],dimensinon:71,dimension:[3,39,92,114,120,142,145,148,149,150,151,154,155,156,157,158,160,167,189,206,210,254,281,326,358,361,365,430,469,479],dimensionless:[106,123,124,126,129,131,133,138,142,326,356,441,461],dimentionless:137,dimer:[6,299,419],dimgrai:194,dimstr:[41,214],dinola:[286,317],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,191,316,490],dir1:480,dir2:480,dir:[1,3,4,8,9,11,12,253,280,289,313,430,432,433,467,480,495],dirac:142,direc:430,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,191,192,193,200,226,233,237,242,281,300,318,330,332,333,334,335,358,362,370,371,372,378,380,381,387,390,393,395,407,411,424,427,435,449,467,479,480,481,487,495],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,195,219,238,284,290,293,310,314,323,324,365,369,371,372,377,384,386,387,393,394,396,403,404,415,419,420,421,422,426,430,431,432,433,440,441,451,453,454,455,458,467,469,470,471,480,495],disabl:[3,12,16,326,406,467,482,495],disadvantag:[6,214],disallow:[191,220,255],disappear:471,discard:[2,3,41,71,208,210,214,327,335,466,471,472],discontinu:[9,188,363,413],discourag:419,discov:[13,327],discret:[6,8,40,42,193,194,239,242,376],discuss:[],disk:[6,84,85,92,161,189,221,231,285,467],disloc:[70,422],disord:[39,70,422],disp:[],dispar:434,disperion:[390,411],dispers:[3,6,7,9,166,281,355,356,381,390,411,416,424,433,452,458],displac:[],displace_atom:[],displace_box:59,displacemet:472,displai:[11,13,22,37,44,55,176,187,191,193,341,350,384,450],dispters:3,disregard:422,dissip:[6,232,239,281,323,324,379,391,399,416,417,450],dissolut:215,dist:[6,69,91,110,119,191,282,298,392,449,464,496],distanc:[],distinct:[6,224,296,355,434],distinguish:[6,86,142,245,376,395,468],distort:[166,371],distrbut:371,distribut:[],distro:[113,384,429,430],ditto:[8,12,14,15,16,17,18,42,117,216,462,467],div:8,divd:119,diverg:[3,12,39,299,324,471,490,497],divid:[3,6,16,41,91,114,119,128,130,143,165,166,176,187,194,206,207,209,214,220,280,322,329,334,355,363,365,396,433,440,458,478,486,495],divis:[6,242,377,405,415,466,487,495],dl_poli:[6,7],dlambda:162,dlammps_async_imd:236,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,193],dlammps_gzip:[3,12,191,193,325,469,470,474],dlammps_jpeg:[3,12,193],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,193],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,191],dlen:479,dlmp_intel_offload:[12,16],dlo:[59,190,220,285],dlopen:6,dlvo:[7,385,461],dm_lb:242,dmax:[314,361],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,148,161,163,165,168,169,170,176,187,190,191,192,193,194,195,197,198,199,204,205,206,207,208,209,210,211,212,221,231,239,240,250,255,256,261,262,263,267,274,275,276,277,278,285,288,299,311,314,317,318,319,328,332,335,337,339,341,350,354,363,364,365,370,371,372,375,376,384,386,387,393,394,396,401,402,404,405,419,420,421,424,426,429,430,431,441,450,451,453,455,457,458,467,469,470,471,472,474,477,478,479,486,487,495,496,497,498],docuement:434,dodd:[42,376],dodgerblu:194,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,148,150,151,156,158,162,167,168,169,170,172,174,176,181,187,188,190,191,192,193,194,197,203,204,206,210,213,214,216,217,218,220,224,226,228,231,232,235,237,239,240,242,245,251,255,256,257,258,259,261,262,263,274,275,276,277,278,286,287,288,292,294,297,299,314,317,319,321,322,326,329,330,331,334,335,336,337,342,343,344,346,347,349,354,355,356,357,358,364,365,366,371,372,373,374,375,376,377,379,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,402,403,404,405,406,409,410,412,413,414,416,417,419,420,421,422,424,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,465,466,467,469,470,471,472,473,476,477,479,480,481,482,483,486,487,490,495,499],doegenomestolif:7,doesn:[3,7,8,12,168,191,204,210,211,311,364,366,370,372,386,394,404,432,433,451,453,454,455,458,469,471],dof:[3,8,114,146,147,148,161,206,299,496],dof_per_atom:[148,206],dof_per_chunk:[148,206],doff:[364,469],doi:[6,219],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,157,167,170,190,192,193,194,197,204,214,218,220,221,235,238,242,255,256,282,294,299,326,331,332,355,356,365,370,392,424,464,466,469,473,486],domin:[1,395,483],don:[0,8,11,12,13,118,171,200,226,240,288,335,419,440,467,469],donadio:318,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,162,165,168,171,188,191,193,194,203,204,206,208,209,210,211,212,214,215,216,217,218,220,221,229,231,236,237,239,240,247,255,261,262,263,274,275,276,278,279,281,282,283,285,2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,208,209,212,213,214,218,220,221,226,231,232,234,235,237,239,240,242,245,246,252,253,260,271,280,282,285,287,289,290,291,294,296,298,299,301,303,308,310,317,318,319,322,323,324,326,328,329,331,334,336,337,339,354,358,363,365,366,367,369,370,386,391,397,398,401,405,416,422,423,430,432,433,434,436,437,438,440,441,442,452,457,458,462,465,466,467,469,471,472,476,477,480,483,485,487,495,496],equat:[3,6,7,8,9,91,108,114,120,167,176,187,197,218,224,225,233,239,240,242,245,253,254,255,256,260,276,280,282,289,290,294,302,314,322,326,329,331,332,334,336,349,355,356,385,390,391,395,396,399,404,416,417,419,424,434,437,439,444,445,447,448,462,490],equi:256,equidist:254,equil:[3,290,359,476,499],equilater:479,equilibr:[3,4,5,6,7,9,59,91,168,197,204,207,217,218,231,253,255,256,276,277,289,290,291,292,322,323,324,329,386,387,432,433,465,479],equilibria:329,equilibribum:[215,216],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,151,152,175,177,218,220,231,232,233,240,242,255,260,276,289,290,294,298,302,303,311,314,321,322,324,329,340,342,346,349,386,419,426,440,490],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:203,equival:[6,12,13,29,59,61,126,127,135,140,166,170,194,209,212,218,220,231,239,255,276,286,298,299,334,391,395,440,453,455,469,472,477,478,487,490],equlibrium:6,equliibr:[290,292],er3:167,eradiu:[40,115,395,469],eras:[301,323],erat:[220,417],erc:387,erfc:[387,407,424],erforc:115,erg:494,erhart:[204,393,453,455],ermscal:373,ernst:9,eror:3,eros:419,erose_form:419,erot:[],errata:[453,455],erratum:331,erron:3,error:[],erta:399,ervel:[115,469],escap:[221,490],especi:[8,11,16,156,168,197,204,214,231,289,294,297,298,370,466],espresso:[9,293],essenti:[8,11,12,27,88,130,149,150,151,154,155,156,157,158,160,177,207,260,281,330,356,372,387,407,455,474,487],essex:29,establish:[87,235],estim:[1,3,6,10,12,38,41,56,91,143,203,214,225,253,314,321,355,356,361,424,433,452,483,487],esu:494,esub:419,eta:[6,242,255,289,290,292,330,394,396,398,430,454,458,494],eta_dot:255,eta_ij:430,eta_ji:396,etag:[40,469],etail:487,etap:255,etap_dot:255,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,148,149,150,151,152,154,155,156,157,158,160,162,168,170,171,172,181,191,193,194,197,198,203,204,205,206,209,210,211,212,215,216,220,221,229,231,232,239,255,285,296,300,326,327,335,339,354,355,363,364,365,366,368,393,394,402,415,417,422,428,432,433,451,453,455,458,464,467,469,470,471,476,478,479,483,485,486,487,488,490,494,495,497,499],ethernet:18,etol:[363,365,464,483],etot0:289,etot:[6,95,97,98,112,143,154,194,224,240,253,289,486,487],eu2:167,eu3:167,euler:[363,365],eulerian:203,euqat:443,europhi:242,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,148,158,166,168,190,191,193,194,198,199,200,201,203,205,206,207,208,209,210,211,212,213,220,226,232,234,235,237,238,239,240,281,287,290,301,304,308,317,318,319,328,331,334,336,337,339,355,356,361,363,370,422,424,430,436,438,440,452,464,465,467,471,472,474,476,477,478,479,483,485,487,495,496],evalut:[339,467],evan:[156,276],evanseck:[6,20,174,382,481],evapor:[],evaul:[8,363],evdwl:[109,432,433,487],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,166,169,170,184,188,191,194,197,198,199,204,205,206,209,210,211,212,214,215,216,218,220,221,224,237,240,253,255,256,281,285,294,296,299,300,310,314,322,326,329,331,335,337,348,355,361,363,365,370,375,395,396,399,402,405,424,434,458,459,469,470,472,474,475,476,478,479,481,484,486,487,488,490,499],evenli:[3,41,143,188,214,242,405,459],event:[],eventu:[3,6,12,15,170,290,483],ever:[54,56,238,314],evera:[385,398,434,450],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,156,171,191,192,193,194,195,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,225,228,229,231,233,235,236,237,242,243,251,255,256,260,279,280,281,285,286,287,288,289,290,291,292,294,296,297,299,300,302,303,314,316,317,318,319,320,321,322,325,326,327,328,329,337,339,354,356,365,366,367,370,391,392,402,415,432,433,440,446,463,464,465,469,471,473,474,476,477,478,483,484,485,487,495,499],everyth:[8,109],everywher:[118,409],eviri:395,evolut:[233,242,282,464],evolv:[242,282,327],ewald:[2,3,5,6,7,8,12,88,112,120,143,327,355,356,363,378,380,381,387,390,395,407,411,427,435,450,452],ewald_disp:390,ewalddisp:3,exact:[22,41,44,71,124,162,171,176,214,217,232,233,239,240,241,285,294,295,314,326,341,355,384,471,476,483,495,497,499],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,91,118,146,152,159,168,188,198,199,209,214,220,225,232,239,240,241,256,268,269,277,281,289,314,319,320,333,370,384,391,393,399,402,416,424,452,471,472,479,483,495],exager:490,examin:[6,8,9,17,217,281],examp:[467,495],exampl:[],exce:[3,6,16,17,18,41,58,71,170,205,206,209,210,211,212,214,218,220,225,228,255,281,296,300,305,306,314,363,370,469,495],exceed:[3,41,59,214,220,255,314,477],excel:395,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,168,172,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,194,197,200,206,207,209,213,214,218,220,227,230,231,234,237,239,241,255,256,257,258,259,260,261,262,263,264,265,268,269,272,274,275,276,277,278,282,291,292,299,301,302,311,314,317,319,320,326,330,334,337,339,340,341,342,343,345,346,349,350,351,355,356,358,360,364,365,366,368,369,370,371,372,374,378,379,380,381,382,383,384,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,417,420,425,426,427,429,432,433,434,435,442,450,451,452,453,454,455,458,460,461,462,464,466,467,469,471,472,474,477,478,479,480,481,483,487,490,494,495,496,498],excess:[208,395],exchang:[2,3,6,8,9,61,62,197,203,204,231,239,291,299,322,326,329,355,370,395,484],exchange:355,excit:[9,395],exclud:[3,6,9,12,16,17,63,71,114,142,148,155,156,172,191,206,210,215,216,243,251,284,297,299,321,332,337,363,364,366,379,399,402,405,416,417,424,449,481],exclus:[1,3,9,12,16,87,370,386,422,424,478,488],excurs:[255,464],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,169,193,236,293,339,354,357,369,465,467,477,480,483,495],exempl:440,exemplari:232,exemplifi:395,exert:[6,237,240,294,333,334,335,356],exhaust:[203,369,495],exhibit:[92,255,362,395,478],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,168,169,187,192,193,194,197,202,213,216,218,221,231,284,285,287,337,340,342,343,344,346,350,359,364,370,402,432,449,459,465,467,469,470,471,480,481,482,495,496,497],exit:[2,3,11,12,41,57,191,214,354,369,467,468,477,486,495],exlanatori:3,exp:[],expand:[],expans:[12,142,191,480,495],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,149,160,166,188,214,226,231,233,252,280,286,288,289,294,299,337,356,366,384,419,422,424,464,467,469,471,474,478,483,495],expens:[6,10,71,194,280,284,299,326,337,355,356,366,370,467],experi:[6,13,15,17,213,221,236,245,254,286,298,299,361,365,391,424,478,483],experienc:[6,12,244,245],experiment:[231,355,370,483],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,148,156,188,191,193,194,197,206,207,212,214,216,218,220,255,280,288,299,311,337,339,354,355,358,364,365,369,375,393,405,440,442,457,467,470,471,474,476,479,490,495,499],explan:[3,6,59,115,142,191,206,254,280,402,463,466,467,469,478],explanatori:[3,8,119,191,205,206,209,210,211,299,364,466,495],explantori:[3,295],explic:423,explicit:[6,9,11,22,44,77,87,115,118,162,176,198,199,220,305,306,341,360,372,373,377,382,384,393,395,406,416,456,463,466,470,473],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,155,158,166,168,174,175,177,178,179,180,182,183,185,186,188,191,194,200,210,213,220,227,230,232,234,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,288,289,291,299,301,302,317,319,320,326,330,334,340,342,343,345,346,349,351,364,370,371,372,374,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,396,397,398,399,400,401,402,406,407,408,409,410,411,412,413,414,415,416,420,422,424,425,426,427,429,434,435,442,443,444,445,446,447,448,450,451,452,453,454,455,456,458,460,461,462,469,471,472,478,479,481,482,488,490],explictli:[16,482],exploit:[9,15,17,282],explor:[120,167],expon:[3,290,292,393,398,401,415,423,435],exponenti:[87,430,451,458,462,483,495],expos:11,exposit:[203,391,392],express:[6,142,154,168,198,199,218,252,280,290,326,332,339,377,393,395,409,419,440,441,450,495],expressiont:377,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,197,200,201,204,212,213,219,222,226,229,230,231,233,234,235,237,239,241,253,255,260,269,280,281,297,298,299,301,303,308,311,313,317,318,319,320,321,323,324,326,328,331,335,336,398,419,422,433,434,441,486,487],extent:[1,3,41,42,45,57,71,166,170,191,202,210,214,237,333,336,355,358,372,436,438,452,466,469,472],exterior:[3,6,166,335],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,147,149,151,154,155,156,157,158,160,161,167,168,169,170,174,194,209,214,216,255,287,288,289,299,314,363,364,367,368,390,399,402,405,419,424,466,467,469,472,481,490,495],extract:[3,6,11,13,36,63,87,109,117,119,121,198,199,292,365,387,396,419,441,467,474,486],extract_atom:11,extract_comput:[11,467],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,193,208,218,220,255,324,395,454,490],extrema:415,extrins:203,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[164,328],f_a:[453,454,455],f_ave:119,f_c:454,f_f:455,f_fix_id:289,f_harm:324,f_i:[29,430],f_id:[6,71,119,121,191,197,205,206,207,208,209,210,211,212,250,316,328,487,495],f_ij:430,f_indent:212,f_int:323,f_j:29,f_jj:91,f_k:430,f_langevin:326,f_max:[289,294],f_msst:253,f_r:[240,453,454,455],f_sigma:377,f_solid:324,f_ss:6,f_temp:[],face:[3,6,57,59,71,156,166,170,202,210,211,331,333,334,335,336,358,398,419,434,469,472],face_threshold:166,facet:166,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,233,285,314,324,399,440,481],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,162,167,170,174,185,190,191,193,194,198,199,207,214,218,220,221,231,236,239,241,242,253,255,256,260,282,286,290,298,302,304,306,314,318,322,329,330,331,335,346,356,358,364,370,372,373,377,378,380,382,387,388,389,391,395,399,402,406,407,419,422,424,426,427,433,435,442,451,456,466,469,472,473,478,481,483,484,487,490,494,495],factori:[3,467],factoriz:355,fail:[3,11,12,59,172,218,221,355,363,365,389,433,467],failur:[123,437,468,495],fairli:[11,424,478,483],faken:73,falcon:236,fall:[3,6,194,209,285,467,495],fals:[86,337,339,440,495],fame:8,famili:[458,466],familiar:[0,11],fan:430,far:[3,6,12,17,57,59,61,86,191,194,195,214,215,216,218,221,255,280,298,299,314,331,342,346,361,365,366,457,467,469,474,487],farago:239,farrel:[453,455],farther:191,fashion:[6,8,41,71,168,194,197,198,199,204,210,214,216,221,231,233,237,252,253,255,257,258,259,260,261,262,263,271,274,275,276,277,278,288,289,291,299,303,307,313,316,324,326,330,331,332,334,336,365,402,416,472,481,495,498],fasolino:404,fast:[6,7,9,12,13,17,39,191,266,289,327,355,356,379,416,417,422,450,452,471,476,478,487,496,499],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,155,174,175,177,178,179,180,182,183,185,186,188,191,194,200,213,214,220,227,230,234,238,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,286,290,291,299,301,302,314,317,319,321,323,326,330,334,340,342,343,345,346,349,351,355,356,367,368,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,393,394,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,420,425,426,427,429,434,435,442,450,451,452,453,454,455,458,460,461,462,464,472,478,482,490],fastest:[1,6,14,17,156,210,326,327,370,466],fatal:[3,486],fault:[70,433],faulti:12,fava:398,favor:217,favorit:7,fbmc:321,fcc:[],fcm:[271,495],fdirect:224,fdotr:403,fdti:87,fe2:167,fe3:167,fe_md_boundari:203,featu:8,featur:[],fecr:393,feedback:[7,236],feel:[7,236,237,245,280,335,337,365,424],felling:421,felt:335,femtosecond:494,fene:[],fennel:[387,407],fep:[],ferguson:[6,174,481],fermi:[1,12,15,154,370,455],fermion:[9,395],fernando:418,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,195,205,206,207,209,210,211,212,240,255,285,288,290,302,328,355,363,364,365,372,440,466,469,474,478,480,488,495,497],fewer:[1,3,11,15,16,61,245,478],fewest:3,fextern:229,feynman:282,fff:467,ffield:[386,396,432,433,440],ffmpeg:[3,12,193],ffplai:193,fft:[1,3,7,12,14,15,88,111,112,143,281,355,356,478],fft_inc:[12,356],fft_lib:12,fft_path:12,fftbench:[355,488],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:449,fictiti:[6,200,201,226,229,233,282,298,387,407,411,449],field1:[470,474],field2:470,field:[],fifth:[311,426],figur:[1,3,8,11,12,289,466,467],fij:390,file0:280,file1:[11,13,280,325,339,364,474,476,480],file2:[11,13,325,339,364,474,476,480],file:[],file_from:192,filen:364,filenam:[3,12,13,38,41,56,188,191,193,194,195,203,206,207,208,209,210,211,212,214,219,280,284,287,290,291,292,295,296,299,300,325,326,352,353,354,364,365,371,372,377,387,393,394,396,404,419,420,421,426,430,431,432,433,440,441,451,452,453,454,455,458,465,466,467,470,471,476,480,487,495,497,498,499],filennam:476,filep:[3,191,194,471,476,499],filepo:296,fill:[7,9,168,193,285,326,358,366,377,422,433,472],filter:[194,203],final_integr:8,final_integrate_respa:8,finchham:[6,150,389],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,171,188,195,204,217,218,228,231,254,280,285,286,294,298,361,363,365,366,387,402,407,411,419,440,450,452,490,495],find_custom:8,fine:[16,17,172,200,226,324,366,370,495],finer:[142,168,495],finest:355,finger:[168,190,252,472],finish:[6,11,41,214,339,352,354,355,367,369,370,457,474,495,496],finit:[],finni:[7,393,450],finvers:224,fiorin:[9,219],fire:[],firebrick:194,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,153,156,162,164,166,167,169,170,171,175,188,191,192,193,194,195,197,198,206,207,209,210,211,212,214,217,220,231,232,237,242,252,253,254,255,280,282,287,288,289,291,296,299,302,303,311,312,314,315,316,323,324,325,326,328,332,337,339,340,347,358,363,364,365,366,369,370,371,372,375,377,378,380,382,384,386,387,393,395,396,399,400,402,403,404,405,406,407,411,416,417,419,421,422,424,426,430,432,433,440,441,449,451,452,453,454,455,458,462,464,465,466,467,469,470,471,474,476,478,481,482,483,486,487,490,495,496,497,499],fischer:[6,9,19,20,174,382,481],fit:[3,6,9,12,38,56,188,298,314,372,377,404,419,424,445,452,454,477,495],five:[73,154,289,364,377,420,469,483],fix:[],fix_adapt:[162,199,415],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,204,285],fix_evapor:204,fix_flux:203,fix_gcmc:[204,364],fix_gl:233,fix_gld:233,fix_grav:285,fix_id:[3,218,253,255,257,258,259,260,261,262,263,286,289],fix_modifi:[],fix_mov:[190,332],fix_nh:8,fix_npt:233,fix_nvt:[204,231],fix_poem:[3,6],fix_pour:[3,221],fix_qbmsst:9,fix_qeq:[3,386],fix_rattl:302,fix_reax_bond:432,fix_rigid:[245,375],fix_saed_vtk:300,fix_setforc:8,fix_shak:302,fix_srd:3,fix_styl:260,fix_temp_rescal:320,fixedpoint:[218,255],fixextern:229,fixid:203,fji:390,flag1:[223,368],flag2:[223,368],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,163,167,171,191,193,194,195,212,217,219,223,236,239,243,245,251,252,281,288,299,311,313,314,321,325,334,337,353,356,364,368,369,370,372,401,406,419,422,449,464,466,467,469,470,471,473,474,475,479,495],flag_buck:381,flag_coul:[381,390,411],flag_lj:[390,411],flagfld:[379,416,417],flaghi:[3,379,416,417],flaglog:[379,416,417],flagn:223,flagvf:[379,416,417],flat:[6,326,331,332,336],flavor:[2,7,12],fld:[9,331,379,416,417],flen:373,flex_press:373,flexibl:[3,6,8,169,193,206,210,219,233,256,322,329,395,454,487],flip:[3,6,220,255,333,334],floor:495,flop:12,floralwhit:194,flow:[],fluctuat:[6,64,87,218,231,232,239,242,255,260,280,281,324,326,349],fluid:[],fluid_veloc:246,flush:[3,194,486],flux:[],flv:193,fly:[7,9,12,41,193,197,203,208,221,224,299,302,327,377,422,487,490],fmackai:9,fmag:222,fmass:282,fmax:[363,487],fmomentum:224,fmsec:[2,194,239,240,252,255,286,299,317,318,478,489,494,496],fname:354,fno:[12,16],fnorm:[363,487],fnpt:224,fnvt:224,foce:402,fock:373,focu:302,fogarti:[9,292,433],foil:[142,280,441],fold:[312,478],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,148,154,156,161,164,166,168,169,174,177,178,179,180,182,183,185,186,188,191,192,193,194,197,203,204,205,206,207,208,209,210,211,212,214,219,220,221,224,225,229,231,232,233,236,238,239,240,242,245,253,255,260,261,262,263,274,275,276,278,281,282,284,287,288,289,290,292,294,296,298,299,300,302,316,317,318,319,322,323,324,325,326,328,329,337,338,342,343,344,345,346,349,351,353,358,360,363,364,365,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,429,430,431,432,433,434,435,437,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,466,467,469,470,472,474,476,477,478,481,483,484,485,490,495,496,498],foo:[4,8,11,12,191,193,229,467,480,495],foot:6,footprint:[12,370],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:245,forcefield:[298,401],forcegroup:242,forcezero:361,ford:390,forestgreen:194,forev:71,forget:[240,490],forgiv:255,fork:[12,191],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,162,163,172,176,194,197,198,199,216,232,233,239,241,245,252,276,281,292,294,298,299,326,331,335,340,341,344,349,360,362,364,365,372,373,377,384,393,395,397,401,402,406,418,419,421,422,426,427,430,432,433,434,440,441,442,450,452,453,454,455,461,463,466,467,469,474,479,486,490,495],formal:[6,78,80,91,232,233,239,255,282,314,322,440],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,176,188,191,192,193,194,195,206,209,210,211,212,214,216,281,284,288,290,292,295,299,300,310,325,326,337,338,341,360,364,365,371,372,377,384,393,396,406,419,421,431,432,433,435,441,452,458,459,466,467,469,470,471,474,485,486,487,495,497],former:[6,12,16,39,41,194,214,326,330,377,379,475,481,495],formerli:[7,13],formul:[1,40,64,143,200,226,239,255,276,290,292,298,302,325,355,372,377,393,395,398,419,429],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,167,168,173,175,176,187,190,191,198,199,200,201,206,207,208,209,212,213,220,226,234,235,237,239,240,252,280,281,287,296,301,308,312,314,317,318,319,328,331,334,336,337,339,340,341,343,350,358,364,372,373,375,377,382,383,384,385,390,391,393,394,398,399,400,401,403,406,407,409,410,411,413,414,416,417,419,423,424,425,434,435,442,450,451,453,454,455,458,460,461,465,469,472,479,486,487,494,495,496],forth:[1,6,11,12,13,14,15,369,467,472,476],fortran:[3,6,9,11,12,13,229,393,402,419,432,433],fortun:8,forward:[3,8,87,354,365,370],foster:[377,429,430],foul:171,found:[3,6,9,12,73,162,191,217,219,231,236,242,281,321,327,339,354,366,384,387,390,464,470,471,486],four:[6,11,54,81,104,105,142,164,253,326,349,364,365,422,464],fourier:[],fourth:[6,106,298,311,321,382,426,440],fox:[6,120,174,448,481],fphi:[38,56,452],fpic:12,fplo:[38,56,452],fprime:452,fqdn:238,fqq:390,frac:[],fraction:[1,3,6,8,12,16,39,41,80,111,143,171,190,193,194,204,215,216,217,218,253,285,289,296,297,314,319,320,358,365,370,377,379,399,416,417,474,479],fragment:[42,236,296],fraig:[42,376],frame:[83,142,194,203,253,289,333,398],framer:[193,194],framework:[5,233,371,441],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,162,199,280,314,323,324,325,326,362,365,373,395,415,422,430,461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recomput:[103,130,172,225,303,392,481],reconstruct:[3,219,440],record:[195,219,303],recov:[218,255],rectangl:[41,214,358],rectangular:[7,41,62,170,214,231,358,469,471,473],rectilinear:[120,167],rector:53,recurs:[41,214,377,457],recust:41,recv:466,red:[2,10,193,194,217,282],redefin:[3,471,477,495],redirect:12,redo:12,reduc:[],reduct:[18,19,119,120,167,253,289,355],redund:396,ree:445,reed:[253,289],rees:[7,9,13],ref:[323,324,362],refactor:6,refer:[],referenc:[3,6,12,63,68,71,116,191,197,207,212,231,288,328,356,387,401,426,434,467,487,495],reflect:[],reformat:7,refresh:203,reg:472,regard:[6,59,252,302,307,429,433],regardless:[15,71,168,171,190,209,210,220,239,255,257,258,259,261,262,263,286,299,308,314,370,466,472,479],regim:[6,322,329,388,478],region:[],region_spher:8,region_styl:335,regist:[8,118,144,310,432,433],regoin:6,regress:495,regspher:168,regstrip:337,regul:6,regular:[1,3,9,41,62,88,166,170,191,193,204,214,231,326,356,388,405,466,469,471,473],reigon:495,reinhardt:[323,324],reject:[168,217,432,484],rel:[1,6,14,27,36,41,59,71,92,104,124,132,142,146,150,151,153,168,177,194,197,204,210,214,220,221,224,231,237,240,251,252,276,280,285,294,296,297,303,311,314,316,321,322,326,333,337,355,356,363,395,398,399,416,417,419,434,461,470,478,483,487,490,496],relat:[],relatic:[],relationship:[6,290,339,355,440,461,490,495],relax:[],releas:[0,5,7,8,13,215],relect:[3,424],reles:42,relev:[2,6,12,41,78,80,113,130,168,172,194,198,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,220,221,222,225,227,228,230,231,232,235,236,242,243,244,246,247,248,249,251,252,254,264,265,266,267,268,269,270,271,272,273,279,283,284,285,287,288,291,293,295,296,297,300,301,302,303,308,312,314,315,316,321,322,325,326,327,328,329,330,331,332,333,334,336,337,355,363,373,374,379,385,387,388,390,391,392,395,397,398,399,400,401,406,408,409,410,412,413,414,416,417,424,425,429,434,442,449,452,460,461,462,466,482,496],reli:[3,12,291,395,433,462,469,479],reloc:12,remain:[7,12,33,37,41,50,55,59,71,87,105,148,149,150,151,155,156,157,158,160,171,181,187,188,191,198,199,204,206,207,210,211,218,220,239,240,247,255,256,261,262,263,274,275,276,278,283,284,306,314,317,318,319,325,326,337,339,347,350,364,377,395,402,415,422,424,450,464,469,470,474,479,481,483,487,490,495,496],remaina:377,remaind:[168,191,221,285,314,327,455,469],remap:[3,6,12,59,61,71,151,168,190,210,220,237,252,276,355,469,470,471],remedi:[6,490],rememb:2,remov:[2,3,6,8,9,13,54,71,72,77,92,108,116,118,142,146,147,148,149,150,151,155,156,157,158,160,161,168,171,172,197,206,210,215,228,239,240,245,251,253,255,261,262,263,274,275,276,278,284,290,299,300,302,314,317,318,319,321,337,355,365,390,417,422,469,472,480,481,495,496],remove_bia:8,remove_bias_al:8,remove_molecul:203,remove_sourc:203,remove_speci:203,ren:167,renam:[12,338,480],render:[12,13,191,193,194],rendon:[255,256],reneighbor:[3,8,12,39,57,71,210,214,231,314,327,337,391,486,487],renssela:284,renumb:71,reorder:[3,12,39,466],repeat:[2,6,193,194,210,217,218,231,307,358,377,453,455,457,464,483],repeatedli:2,repel:237,repes:191,replac:[2,3,6,11,12,41,63,89,90,119,145,146,147,148,149,150,151,154,155,156,157,158,160,161,191,193,194,195,206,207,209,210,211,212,214,217,221,239,260,287,294,296,387,409,470,471,476,477,487,495,496,497,499],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,403,431,432,433],reprens:326,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,90,115,118,180,188,191,193,206,207,208,209,210,211,212,218,224,232,234,239,242,255,282,284,286,294,299,300,303,311,326,328,335,356,365,371,377,398,405,415,416,417,419,420,421,427,430,432,433,456,457,464,466,469,479,481,484,490,495,497],represent:[3,6,8,9,57,59,136,170,191,232,233,282,326,377,395,398,422,434,469,472,490],reprocess:474,reproduc:[3,255,332,387,393,399],repul:419,repuls:[6,7,9,36,40,45,46,110,237,290,331,332,335,372,376,377,385,387,391,395,399,401,415,419,423,440,449,455,458,461,462,479],reqir:[290,292],request:[3,6,8,12,41,104,171,188,191,236,242,297,314,316,353,355,424,432,433,464,474,479,483,495,496,497],requir:[],rerun:[],rescal:[],research:[5,7,242,246,422,464,483],resembl:294,reserv:[12,236,490],reservoir:[91,231,235,239,326],reset:[],reset_atomic_reference_posit:203,reset_dt:8,reset_target:8,reset_tim:203,reset_timestep:[],resid:13,residu:236,residue1:366,resist:[6,236],resolut:[208,440,452],resolv:[218,282,314,417],resort:3,resourc:[7,371,393],respa:[3,16,225,236,255,368,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,425,427,429,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,457,458,460,461,462,477,478,489,495],respecifi:422,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,87,89,97,98,111,114,120,124,145,150,153,155,162,166,167,174,175,177,178,179,180,182,183,185,186,188,193,194,210,211,216,217,218,22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ai:454,sall:[9,440],salmon:194,salt:[388,397,419,469],salter:440,same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,57,59,62,63,65,69,71,72,77,79,81,82,84,85,87,88,89,90,91,92,93,95,98,104,105,106,108,110,111,112,114,115,117,118,119,142,143,144,145,146,147,148,149,150,151,154,155,156,157,158,160,161,162,164,166,168,169,170,171,172,174,175,176,177,178,179,180,181,182,183,185,186,188,189,190,191,192,193,194,197,198,199,200,203,204,206,209,210,211,212,213,214,215,216,217,218,220,221,225,226,227,230,231,232,233,234,235,236,237,238,239,240,241,242,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,277,278,280,281,282,284,285,286,289,290,291,292,294,295,296,297,298,299,301,302,303,308,311,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,332,333,334,335,337,339,340,341,342,343,345,346,349,351,355,356,358,359,360,364,365,366,367,368,369,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,406,407,408,409,410,411,412,413,414,415,416,417,419,420,423,424,425,426,427,429,430,434,435,440,442,449,450,451,452,453,454,455,458,460,461,462,464,466,467,469,470,471,472,474,477,478,479,480,481,482,483,487,490,494,495,496,498],sampl:[1,2,4,6,9,10,11,12,14,91,104,146,147,161,166,190,193,206,207,210,211,219,221,229,231,233,235,255,256,282,285,294,296,300,311,312,314,318,321,324,336,366,377,392,469,483],sample_frequ:203,san:429,sandia:[0,5,7,9,13,14,17,70,113,396,419,429],sandybrown:194,saniti:[298,366],satellit:[6,150],satifsi:495,satisfi:[3,12,73,120,142,167,218,242,260,302,334,363,366,399,483],satur:388,save:[6,8,12,19,40,59,188,193,208,217,232,233,239,240,241,285,294,326,356,366,368,377,471,474,481],sb3:167,sb5:167,sc3:167,scalabl:[],scalar:[],scale:[0,1,3,4,5,6,9,10,13,18,40,59,63,71,72,91,115,118,119,142,154,162,188,190,191,193,194,197,198,199,203,204,207,218,220,231,235,236,237,239,241,242,253,255,257,258,259,260,261,262,263,282,286,289,290,299,305,306,314,316,318,321,323,324,326,330,337,355,356,358,364,367,371,372,373,388,392,395,399,402,416,417,419,422,429,436,438,456,470,472,474,478,481,483,486,487,495,496],scale_factor:[436,438],scalegamma:242,scalexi:[3,218,255,260],scalexz:[218,255,260],scaleyz:[218,255,260],scan:[194,216,354,470],scatter:[11,120,167],scatter_atom:11,scatter_coord:11,scenario:[6,40,61,217,288,297,314,327,335,366,473,474,478,486],scf:490,schaik:415,schedul:464,schell:454,schemat:217,scheme:[6,9,18,232,233,255,282,294,302,326,355,456],schlitter1:325,schlitter2:325,schlitter:325,schmid:391,schneider:[239,241],schoen:355,schr:490,schroding:395,schroeder:[108,490],schulten:[240,303,356,490],schunk:314,schwen:9,sci:[73,334,386,421,430,440],scienc:[8,203,217,236,303,323,393,420,440,454],scientif:[142,393],scm:11,scratch:[12,41,214],screen:[],screenshot:11,scripe:11,script:[],scripta:67,scsl:12,sdk:[],sea:11,seagreen:194,seamlessli:288,search:[0,2,3,8,12,92,108,169,171,194,195,314,361,362,363,365,367,464,470,471,483,495],seashel:194,sec:[12,489,494],second:[1,3,6,9,10,11,12,16,54,57,59,61,71,88,91,104,106,108,114,135,136,140,143,144,156,162,166,167,169,170,171,190,191,194,197,198,206,207,209,210,211,212,217,231,232,237,252,254,282,296,298,299,302,303,311,312,314,323,324,326,337,355,358,362,363,365,366,370,375,377,378,380,381,386,387,393,395,396,399,400,402,405,406,409,419,424,426,440,451,454,455,456,458,462,464,465,466,467,469,471,476,478,482,483,487,490,494,495,496,497,499],second_mo:440,secondari:[3,180],sectinn:498,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,63,64,65,66,67,68,69,71,74,75,78,79,80,81,83,86,87,88,89,90,91,93,94,97,98,99,100,101,102,104,105,106,107,109,110,111,113,114,115,116,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,167,169,174,175,176,177,178,179,180,181,182,183,185,186,187,188,190,191,192,193,195,197,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,223,224,226,227,228,230,231,232,233,234,236,238,239,240,241,242,243,244,245,246,248,249,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,289,290,291,292,293,294,295,296,299,301,302,303,304,305,306,307,308,310,314,317,318,319,320,321,322,323,324,325,326,327,329,330,332,333,334,337,338,340,341,342,343,344,345,346,347,349,350,351,356,357,358,360,364,365,367,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":215,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,148,156,157,161,167,168,171,173,187,189,190,191,193,194,195,196,198,199,200,202,203,204,206,210,211,212,215,216,218,219,220,221,225,228,231,232,237,239,240,241,242,243,245,250,253,255,256,260,276,277,281,282,285,286,287,288,289,291,294,296,297,299,300,314,316,321,322,323,324,327,329,331,333,337,350,353,355,356,358,359,361,362,364,366,367,368,370,373,377,379,395,416,417,422,424,432,433,449,450,464,465,466,469,470,472,474,476,477,478,481,483,485,486,487,488,489,494,496,497,498],"function":495,"long":[208,378,380,381,382,383,387,389,390,407,411,415,427,435],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[198,199],addforc:200,addit:[12,13],addtorqu:201,adiabat:6,adjust_dt:304,adp:371,airebo:372,alloi:393,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:202,arrai:6,aspher:[6,82,146,257,261,265,266,274],atc:[9,203],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,166,202,204,205,288,495],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:213,awpmd:[9,373],balanc:[41,214],barostat:6,basal:67,beck:374,berendsen:[286,317],between:6,binary2txt:13,bodi:[6,8,42,68,147,258,262,267,275,375,376],bond:[8,13,69,215,216,217,295],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:377,born:[378,389],boundari:[7,57],box:[6,58,218],brownian:379,buck:[380,381,389,418],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,174,382,415],chunk:[6,66,71,75,90,94,105,107,116,148,163,165,206],citat:7,class2:[21,43,175,340,383],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[331,385,461],colvar:[9,13,219],com:[74,75,149],comb3:386,comb:[291,386],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,495],compute_modifi:103,condit:7,conduct:[6,322],constant:6,constraint:7,contact:[76,122],contact_radiu:[],coord:77,core:6,correl:[207,208],cosin:[23,24,25,26,27,28,177],cossq:342,coul:[378,380,381,382,383,387,388,389,400,407,411,415,427,435],coupl:6,creat:216,create_atom:168,create_bond:169,create_box:170,createatom:13,creation:7,csld:318,csvr:318,cubic:409,cuda:[9,14,111,114,145,155,200,213,227,230,234,255,264,301,302,317,319,330,378,380,382,383,393,399,400,407,408,410,413,425,451,453],custom:8,cut:[49,373,380,383,387,390,395,397,407,408,415,423,427],cvff:343,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[387,407],dec:[],defgrad:129,deform:[151,152,220],delete_atom:171,delete_bond:172,delta:24,deposit:221,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36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:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,195,196,201,208,209,211,212,213,214,217,218,219,220,222,223,233,239,241,243,249,256,260,261,262,263,265,266,267,273,278,279,280,282,303,304,317,331,341,354,360,366,367,368,370,371,372,375,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,222,375,391],afil:237,aforement:18,afresh:[291,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,199,200,201,205,206,208,209,216,217,218,219,220,222,226,235,246,247,248,249,250,255,256,257,259,265,266,267,273,278,279,280,282,285,289,293,301,303,306,315,320,322,323,324,326,327,328,329,330,334,336,338,342,345,346,352,359,365,366,368,369,371,373,374,375,376,377,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,196,222,239,289,345,359,370,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,223,370,439,440],aggreg:[6,12,65,68,69,79,95,112,119,239,255,301,303,317,471,503],aggress:[239,490],agilio:[9,13],agre:[3,8,190,368,377,411,440],agreement:[5,7],ahd:408,ahead:338,aidan:[0,5,7,9,13,363],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:195,akohlmei:[7,9,13,197,240],aktulga:[7,9,296,440],al2o3:447,al2o3_001:[122,304],al3:169,ala:[246,447],alain:9,alat:[284,426],alb:[437,460,462],albeit:302,albert:9,alchem:[89,164],alcohol:334,alcu:[376,382],alcu_eam:437,alderton:395,alejandr:[259,260],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,196,205,216,219,222,246,248,249,273,286,294,303,306,307,326,327,331,334,339,366,367,368,372,375,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,361],aliceblu:196,align:[6,12,29,41,71,172,190,212,216,241,363,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,252,254,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,315,316,318,319,320,321,322,323,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,350,355,358,359,360,361,362,363,365,368,369,370,371,372,374,375,376,377,378,380,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:343,alloc:[3,5,6,8,9,11,12,60,233,333,369,371,375,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,195,196,197,199,200,202,204,205,206,208,209,210,211,212,213,214,216,218,219,220,221,222,223,227,228,233,235,236,237,238,240,243,246,249,250,254,256,259,260,284,288,289,290,291,292,293,297,303,304,306,308,310,311,315,319,326,327,328,329,331,332,333,334,335,336,342,344,346,355,360,361,363,368,369,370,371,374,375,378,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,241,293,331,361,372,375,456],alo:392,alon:[6,7,219,299,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,195,208,219,241,246,247,251,256,258,293,303,306,308,312,316,317,326,330,331,337,340,342,363,366,367,368,370,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,200,246,285,293,294,298,368,376,379,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,199,346,355,369,389,457,476],alphanumer:[3,63,199,292,300,344,369,502],alreadi:[3,7,8,9,12,16,17,18,4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rashev:400,bare:[226,242,244],barost:[226,497],barostat:[],barostt:6,barr:391,barrat:298,barrett:67,barrier:[3,4,6,258,356,370,391,404,490],bartel:285,bartok2010:448,bartok2013:448,bartok:[9,144,438,448],bartok_2010:438,bartok_phd:438,bary:501,barycent:315,basal:[],base:[3,4,6,8,9,11,12,13,14,15,20,63,64,71,78,89,93,106,115,122,150,152,169,170,172,193,194,195,196,199,205,212,213,216,217,218,222,223,227,235,240,243,247,249,273,285,286,289,292,294,296,303,304,308,309,319,326,361,375,377,379,382,396,402,405,408,409,410,412,414,423,427,428,434,436,437,447,458,461,462,465,471,473,476,477,478,480,483,486,487,490,491,494,501,502,503,506],bash:389,bashford:[6,20,176,387,488],basi:[3,6,12,40,144,150,170,204,243,245,285,319,336,363,412,486,502],basic:[6,7,8,12,17,41,117,145,195,196,205,216,259,260,284,340,376,378,429,470,478,497],basin:[88,370,471,490],bask:[400,426,437],bath:[9,293,298],batom1:[69,119,121,193,196],batom2:[69,119,121,193,196],bayli:[6,176,488],bb13:177,bcc:[3,4,7,64,70,73,363,426,428],bcolor:[3,195,196],bdiam:[3,195,196],be2:169,bead:[5,7,10,13,40,45,46,162,203,219,286,456],beam:223,bear:[6,236],becau:13,becaus:[0,1,3,6,8,12,16,17,18,40,41,42,59,64,71,72,77,94,110,120,132,144,150,155,160,170,171,172,176,193,194,195,196,197,202,208,216,217,218,219,220,222,228,234,235,236,237,242,243,244,245,256,259,260,273,280,289,293,294,298,303,316,321,326,327,330,331,334,338,339,340,341,342,348,360,366,368,370,371,374,375,381,387,389,392,394,396,402,403,405,406,407,408,409,413,422,423,424,426,431,441,456,457,463,464,473,474,476,478,479,480,483,485,486,488,490,497,502,503,504,506],beck:[],becker:[376,400],beckman:240,becom:[1,2,3,6,7,8,18,39,41,54,57,59,71,172,193,195,196,216,217,218,219,222,235,237,246,258,259,300,301,322,323,336,337,339,340,341,360,361,366,370,377,390,392,400,402,405,414,431,437,441,458,465,468,476,477,479,486,502],been:[1,2,3,6,7,8,9,11,12,13,16,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,45,46,47,48,49,51,53,54,56,57,59,60,63,65,69,71,89,113,116,117,118,119,121,123,147,148,149,150,151,152,153,157,158,159,160,162,163,171,172,173,174,176,177,179,180,181,182,184,185,187,188,190,192,193,195,196,197,202,204,206,207,208,209,211,212,213,214,215,216,219,220,221,222,223,229,234,235,238,240,241,243,244,246,247,248,249,250,254,256,257,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,288,289,290,293,295,297,300,301,303,305,306,315,320,322,323,324,331,332,333,335,336,337,338,339,341,342,345,347,348,350,351,354,356,359,360,361,368,371,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,428,429,432,433,434,436,439,440,441,442,449,456,458,459,460,461,462,464,465,467,468,469,471,473,474,476,477,478,479,480,482,486,490,493,494,502,503,504,505],befor:[1,2,3,6,8,9,12,14,17,22,29,39,40,41,44,59,66,71,74,75,81,91,92,96,106,107,108,109,118,150,153,158,159,165,170,171,173,174,178,191,192,196,200,201,202,203,204,206,208,211,212,213,214,215,216,220,225,226,234,235,240,242,243,244,246,249,256,259,265,266,267,278,279,282,285,292,293,294,297,298,303,304,305,320,322,323,324,330,336,337,338,342,346,365,366,368,370,375,403,406,422,426,429,457,466,471,473,474,477,478,479,480,481,483,484,486,490,493,494,497,502,503,504,505,506],began:[5,12],begin:[3,8,12,38,39,56,71,121,123,171,190,192,193,196,200,201,205,207,208,209,211,212,213,214,216,222,231,273,288,301,304,319,321,324,333,338,341,342,357,359,360,361,362,364,367,369,370,371,374,375,400,429,431,437,444,446,447,449,456,459,469,471,476,483,490,492,494,501,502,504],behalf:3,behav:[3,27,179,367,368],behavior:[3,174,190,193,195,197,219,220,223,235,236,237,240,243,244,245,259,289,293,298,319,322,323,331,367,382,402,426,469,470,478,482,502,504],behaviour:[6,243],behind:[8,242,257,293,319,360],beig:196,belak:7,believ:11,bellott:[6,20,176,387,488],bellow:350,belong:[2,3,40,71,124,173,206,208,212,235,249,303,342,369,443,476],below:[1,2,3,5,6,8,9,11,12,15,16,17,22,38,39,40,41,42,44,54,56,59,60,63,65,68,69,71,77,79,93,95,116,117,120,121,122,144,145,150,156,158,164,168,169,170,173,174,176,178,189,190,192,193,195,196,199,200,202,203,205,208,209,210,211,212,213,215,216,218,219,220,222,223,228,231,233,235,238,239,241,243,244,249,256,257,259,264,265,266,267,278,279,282,284,289,292,293,294,301,302,303,305,306,313,316,319,320,321,322,323,324,327,328,329,331,334,336,337,342,344,346,358,360,363,365,366,368,369,370,372,375,376,377,378,382,383,384,387,388,389,390,392,395,400,402,403,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,442,448,449,456,457,459,464,465,467,468,469,470,471,474,476,477,478,479,481,483,484,486,488,489,490,492,493,494,496,497,502,503,506],bench:[1,6,11,12],benchmark:[1,7,10,11,12,13,14,15,16,17,18,41,216,360,489],beneath:223,benedict:429,benefici:[61,372],benefit:[1,236,485],bennet:89,beowulf:7,berardi:[405,441],beraun:331,berendsen:[],berensen:303,berkelei:168,berkowitz:360,berlin:[7,9,308],bern:[3,286,2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,compass:[7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[3,29,199,206,219,226,227,236,239,243,245,246,250,255,257,259,273,303,306,307,322,323,327,334,335,339,370,395,396,406,420,447,485,490],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,404,408,409,412,439,440,472,473,474,476,478,480,483,484,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,404,408,431,494,502],counter:[337,471,482,484,490],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,471],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,423,449,473,476,489,497,502,504],courtesi:363,cov:447,coval:[6,29,402,426,447,497],covari:237,cover:[6,71,190,196,205,246,402,464],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,497],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,436,464,478,481,502],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,480,494,497],crystallin:[6,106,285,363,461,497],crystallis:326,crystallogr:[122,169],crystallograph:[363,494],crystallographi:[122,169,363],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[376,400],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,216,226,340,363,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,408,494],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,235,285],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[284,296],cutinn:[384,423,424],cutlo:[284,296],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:381,cutoff_inn:381,cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,502],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,479],cylindr:[6,241,316,337],cypress:375,cyrot:382,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,486],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:244,damp_drud:244,dampen:[303,497],dampflag:[337,406],dan:17,danger:[3,12,235,342,396,494],dangl:173,daniel:9,darden:[361,395],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:3,delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459,485],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,2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43,244,246,249,257,258,259,260,264,280,284,286,293,294,298,306,307,319,327,331,334,336,337,339,341,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,11,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[231,307],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,11,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,195,196,197,214,219,221,225,240,243,247,249,255,256,285,292,303,316,318,319,326,330,339,342,358,361,369,373,374,375,377,408,413,426,429,456,471,473,474,476,477,478,480,481,482,486,502],flag_buck:386,flag_coul:[386,395,418],flag_lj:[395,418],flagfld:[384,423,424],flaghi:[3,384,423,424],flaglog:[384,423,424],flagn:225,flagvf:[384,423,424],flat:[6,331,336,337,341],flavor:[2,7,12],fld:[9,336,384,423,424],flen:378,flex_press:378,flexibl:[3,6,8,171,195,208,212,221,237,260,327,334,402,461,494],flip:[3,6,222,259,338,339],floor:502,flop:12,floralwhit:196,flow:[],fluctuat:[6,64,89,220,235,236,243,246,259,264,284,285,307,329,331,354,398],fluid:[],fluid_veloc:250,flush:[3,196,493],flux:[],flv:195,fly:[7,9,12,41,195,199,205,210,223,226,303,306,332,382,429,494,497],fmackai:9,fmag:224,fmass:286,fmax:[368,494],fmomentum:226,fmsec:[2,196,243,244,256,259,290,303,322,323,485,496,501,503],fname:359,fno:[12,16],fnorm:[368,494],fnpt:226,fnvt:226,foce:409,fock:378,focu:306,fogarti:[9,296,440],foil:[144,284,448],fold:[317,485],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,40,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,82,93,94,99,100,110,117,120,121,123,144,145,148,149,150,156,158,163,166,168,170,171,176,179,180,181,182,184,185,187,188,190,193,194,195,196,199,205,206,207,208,209,210,211,212,213,214,216,221,222,223,226,227,230,231,233,235,236,237,240,242,243,244,246,249,257,259,264,265,266,267,278,279,280,282,285,286,288,291,292,293,294,296,298,300,302,303,304,306,321,322,323,324,327,328,329,330,331,333,334,342,343,347,348,349,350,351,354,356,358,363,365,368,369,370,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,473,474,476,477,479,481,483,484,485,488,490,491,492,497,502,503,505],foo:[4,8,11,12,193,195,233,474,487,502],foot:6,footprint:[12,375],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:249,forcefield:[302,408],forcegroup:246,forcezero:366,ford:395,forestgreen:196,forev:71,forget:[244,497],forgiv:259,fork:[12,193],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,89,91,92,94,96,106,107,109,120,144,145,164,165,174,178,196,199,200,201,218,236,237,243,245,249,256,280,285,296,298,302,303,331,336,340,345,346,349,354,365,367,369,370,377,378,382,389,397,398,400,402,404,408,409,413,425,426,428,429,433,434,437,439,440,441,447,448,449,457,459,460,461,462,468,470,473,474,476,481,486,493,497,502],formal:[6,78,80,93,236,237,243,259,286,319,327,447],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,178,190,193,194,195,196,197,208,211,212,213,214,216,218,231,285,288,292,294,296,299,303,304,315,330,331,342,343,346,365,369,370,376,377,382,389,400,403,413,426,428,438,439,440,442,448,459,465,466,473,474,476,477,478,481,492,493,494,502,504],former:[6,12,16,39,41,196,216,331,335,382,384,482,488,502],formerli:[7,13],formul:[1,40,64,145,202,228,243,259,280,294,296,302,306,330,360,377,382,400,402,405,426,436],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,89,91,92,93,97,99,100,109,116,122,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,169,170,175,177,178,189,192,193,200,201,202,203,208,209,210,211,214,215,222,228,238,239,241,243,244,256,284,285,291,300,305,313,317,319,322,323,324,333,336,339,341,342,344,345,346,348,355,363,369,377,378,380,382,387,388,389,390,395,396,400,401,405,406,407,408,410,413,414,416,417,418,420,421,423,424,426,430,431,432,441,442,449,457,458,460,461,462,465,467,468,472,476,479,486,493,494,501,502,503],forth:[1,6,11,12,13,14,15,374,474,479,483],fortran:[3,6,9,11,12,13,233,400,409,426,439,440],fortun:8,forward:[3,8,89,359,370,375],foster:[382,436,437],foul:173,found:[3,6,9,12,73,164,193,219,221,235,240,246,285,326,332,344,359,371,389,392,395,471,477,478,493],four:[6,11,54,81,106,107,144,166,257,331,354,369,370,429,471],fourier:[],fourth:[6,108,302,316,326,387,433,447],fox:[6,122,176,455,488],fphi:[38,56,459],fpic:12,fplo:[38,56,459],fprime:459,fqdn:242,fqq:395,frac:[],fraction:[1,3,6,8,12,16,39,41,80,113,145,173,192,195,196,206,217,218,219,220,257,289,293,300,301,319,324,325,363,370,375,382,384,406,423,424,481,486],fragment:[42,240,300],fraig:[42,381],frame:[85,144,196,205,257,293,338,405],framer:[195,196],framework:[5,237,376,448],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,89,164,201,284,319,328,329,330,331,367,370,378,402,422,429,437,468,473],freedom:[3,6,8,97,99,100,102,104,105,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,208,219,226,235,237,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,303,306,322,323,324,329,368,395,494,497,503],freeli:[0,6,7,12,148,149,163,168,195],freez:[],frenkel:[235,329],freq:204,frequenc:[3,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465],input1:[65,68,69,79,95,112,117,118,119,121,123,321],input2:[65,68,69,79,95,112,117,118,119,121,123,321],input:[],input_doubl:3,inquir:309,insensit:12,insert:[3,5,7,8,12,59,170,199,223,235,241,289,360,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,196,207,212,213,223,224,232,235,241,246,249,289,303,319,336,338,339,340,341,342,358,363,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[246,395,446],instal:[],instanc:[6,11,200,221,237,338,404,409,431,437,474,497],instantan:[6,63,219,220,236,237,259,264,285,290,293,298,300,303,326,482,494],instanti:[6,11,12,205,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,201,208,211,212,213,214,216,220,221,235,243,246,249,250,285,291,301,303,321,339,358,360,361,364,371,375,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,240,288],instruct:[],insuffici:[3,6,12],insult:259,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,195,196,202,217,218,223,228,229,232,233,235,238,243,255,291,292,301,303,319,331,336,340,341,342,344,359,369,371,375,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,195,196,206,208,212,213,217,218,219,223,225,233,235,236,237,240,243,244,245,246,285,288,289,292,293,298,303,319,321,323,326,330,331,350,360,363,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,210,236,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,199,208,209,211,212,213,214,216,217,218,219,227,232,239,249,257,259,264,300,303,304,319,327,331,333,334,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,219,243,245,258,295,303,360,370,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,199,200,201,217,218,219,234,235,240,241,243,245,249,273,284,286,288,289,294,296,302,303,310,311,319,320,326,331,335,336,337,340,341,346,347,348,349,351,355,360,361,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,258,328,329,376,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:340,interest:[1,5,7,8,9,11,13,71,169,286,326,329,361,401,424,439,440,474,502],interf:375,interfac:[],interfer:[12,259,377],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,340,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,195,258,284,354,370,474,475,484,488],intermix:471,intermolecular:377,intern:[],internal_element_set:205,internal_quadratur:205,internet:242,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,195,196,205,231,246,284,360,361,370,382,431,440,453,459,460],interpret:[2,6,11,195,211,406,449,471,474,490,502],interrupt:293,intersect:[3,6,122,196,340,342,479],intersert:340,interspers:368,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,194,209,243,259,293,298,299,311,447,453,471,490,502],intestieti:122,intial:[6,375,377],intiial:[41,481],intiti:[3,318],intra:303,intra_energi:235,intramolecular:[29,235],introduc:[6,9,94,110,195,259,293,298,303,354,360,376,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:363,inv:[122,169,304],invalid:[3,12,71,91,173,273,370,423,424,478],invari:[110,137,142,144],invent:306,invers:[],invert:[1,6,174,285],invis:340,invoc:[168,219,375,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,227,228,229,232,233,234,235,236,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,294,295,296,297,298,299,300,301,303,304,305,306,308,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,347,348,350,351,354,356,359,360,361,362,363,3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01,302,303,305,306,308,316,318,319,320,322,323,324,325,327,328,329,330,331,333,334,335,336,337,339,340,341,342,344,345,347,348,350,351,352,354,356,359,360,361,363,365,367,368,369,370,371,374,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,426,427,428,429,431,432,433,434,435,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,465,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,506],young:[406,443,445],your:[0,1,2,3,4,5,6,7,8,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,59,61,111,113,116,120,147,148,149,153,157,163,168,170,171,172,173,174,176,177,179,180,181,182,184,185,187,188,190,192,193,194,195,202,205,209,211,214,215,217,218,219,220,222,223,229,234,235,238,240,243,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,289,292,295,301,303,305,306,308,321,322,324,327,331,333,334,335,336,337,339,340,341,342,345,347,348,350,351,354,356,361,363,369,370,371,374,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,399,400,401,403,404,405,406,407,408,409,410,411,414,415,416,417,418,419,420,421,422,423,426,427,428,429,431,432,433,434,436,437,439,440,441,442,449,456,458,459,460,461,462,465,467,468,469,470,473,474,476,478,479,480,483,484,485,486,487,488,489,493,494,501,502,504,506],yourself:[6,8,12,13,220,369],yplane:337,ypo:170,ysu:[3,193,321,477],yuan:9,yukawa:[],yukawa_1_1:466,yxz:473,yzx:473,z_i:[402,462,469],z_j:[462,469],z_meam:426,zachari:13,zannoni:405,zbl:[],zblcut:462,zblcutinn:448,zblcutout:448,zblexpscal:462,zblz:448,zcm:303,zcylind:337,zepeda:206,zero:[3,4,6,9,11,12,26,27,39,41,48,49,59,61,63,66,71,72,75,89,90,92,94,96,105,106,107,108,109,110,112,113,114,116,117,118,119,120,121,122,125,144,145,148,149,150,151,158,159,162,163,165,167,168,169,170,172,173,174,176,179,188,190,192,193,195,196,199,200,201,202,204,206,207,208,209,210,211,212,213,214,215,216,217,218,220,222,227,228,229,232,234,235,236,237,239,243,244,245,246,247,249,255,256,257,259,264,273,276,286,291,292,293,294,295,298,300,301,303,304,305,306,310,311,313,319,321,326,327,329,331,334,335,336,337,338,339,341,342,343,344,350,363,366,368,369,370,371,375,378,382,383,385,386,387,390,392,395,396,397,398,402,405,407,408,409,410,414,416,418,419,422,424,425,426,429,431,436,440,441,442,447,456,459,463,465,469,471,472,473,476,477,479,481,483,484,485,486,490,491,494,497,502,503,504,506],zeta:[3,246,294,403],zfactor:195,zflag:[157,158,247,249,255,303,326],zhang:[303,327,406],zhi:[3,6,172,193,204,330,336,339,341,476,479,494],zhi_bound:[6,193],zhou:[13,382,403,437,460,462],zhu:455,ziegenhain:13,ziegler:[288,426,457,462,469],zimmerman2004:205,zimmerman2010:205,zimmerman:[9,70,205,382],zlat:[222,241,494],zlib:193,zlim:447,zlo:[3,6,172,193,204,330,336,338,339,341,476,479,494],zlo_bound:[6,193],zmax:[204,246,502],zmin:[246,502],zn2:169,zone:[122,304],zoom:[3,193,195,196],zorig:71,zplane:337,zr4:169,zrest:318,zsu:[3,193,321,477],zwall:336,zwall_veloc:246,zxy:473,zybin:440,zyx:473},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313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\ No newline at end of file diff --git a/doc/set.html b/doc/set.html index 488d95d16e..ce138011f6 100644 --- a/doc/set.html +++ b/doc/set.html @@ -135,7 +135,7 @@
    • style = atom or type or mol or group or region
    • ID = atom ID range or type range or mol ID range or group ID or region ID
    • one or more keyword/value pairs may be appended
      • -
    • keyword = type or type/fraction or mol or x or y or z or charge or dipole or dipole/random or quat or quat/random or diameter or shape or length or tri or theta or theta/random or angmom or omega or mass or density or volume or image or bond or angle or dihedral or improper or meso/e or meso/cv or meso/rho or smd/contact/radius or smd/mass/density or i_name or d_name
      • +
    • keyword = type or type/fraction or mol or x or y or z or charge or dipole or dipole/random or quat or quat/random or diameter or shape or length or tri or theta or theta/random or angmom or omega or mass or density or volume or image or bond or angle or dihedral or improper or meso/e or meso/cv or meso/rho or smd/contact/radius or smd/mass/density or dpd/theta or i_name or d_name
     type value = atom type
@@ -205,6 +205,7 @@
   value can be an atom-style variable (see below)
 smd/mass/density = set particle mass based on volume by providing a mass density
   value can be an atom-style variable (see below)
+dpd/theta value = internal temperature of DPD particles (temperature units)
 i_name value = value for custom integer vector with name
 d_name value = value for custom floating-point vector with name
    @@ -462,6 +463,8 @@ prevent different individual physical bodies from penetrating each other. Note that the SPH smoothing kernel diameter used for computing long range, nonlocal interactions, is set using the diameter keyword.

    +

    Keyword dpd/theta sets the internal temperature of a DPD particle +as defined by the USER-DPD package.

    Keywords i_name and d_name refer to custom integer and floating-point properties that have been added to each atom via the fix property/atom command. When that command diff --git a/doc/set.txt b/doc/set.txt index d5d0d973c1..184e147d11 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -23,7 +23,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {mass} or {density} or {volume} or {image} or \ {bond} or {angle} or {dihedral} or {improper} or \ {meso/e} or {meso/cv} or {meso/rho} or \ - {smd/contact/radius} or {smd/mass/density} or \ + {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \ {i_name} or {d_name} :l {type} value = atom type value can be an atom-style variable (see below) @@ -92,6 +92,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ value can be an atom-style variable (see below) {smd/mass/density} = set particle mass based on volume by providing a mass density value can be an atom-style variable (see below) + {dpd/theta} value = internal temperature of DPD particles (temperature units) {i_name} value = value for custom integer vector with name {d_name} value = value for custom floating-point vector with name :pre :ule @@ -389,6 +390,9 @@ other. Note that the SPH smoothing kernel diameter used for computing long range, nonlocal interactions, is set using the {diameter} keyword. +Keyword {dpd/theta} sets the internal temperature of a DPD particle +as defined by the USER-DPD package. + Keywords {i_name} and {d_name} refer to custom integer and floating-point properties that have been added to each atom via the "fix property/atom"_fix_property_atom.html command. When that command diff --git a/examples/USER/dpd/README b/examples/USER/dpd/README new file mode 100644 index 0000000000..7c8c2b2e69 --- /dev/null +++ b/examples/USER/dpd/README @@ -0,0 +1,8 @@ +This directory contains input files for DPD simulations under +isothermal, isoenergetic, isobaric and isoenthalpic conditions. All +the DPD scenarios use the Shardlow splitting algorithm to integrate +the equations of motion. The compute dpd command is used in the +isoenergetic and isenthalpic case to demonstrate how one can access +the particle internal energies. + + diff --git a/examples/USER/dpd/dpd-shardlow/data.dpd b/examples/USER/dpd/dpd-shardlow/data.dpd new file mode 100644 index 0000000000..77119ec9c9 --- /dev/null +++ b/examples/USER/dpd/dpd-shardlow/data.dpd @@ -0,0 +1,2018 @@ +LAMMPS data file via write_data, version 11 Jul 2013, timestep = 10000 + +1000 atoms +1 atom types + +-5.3687390278320350e+00 6.1461796331020025e+01 xlo xhi +-4.6558041136200217e+00 5.3234209917616923e+01 ylo yhi +-6.5611825409372848e+00 4.6247227792940926e+01 zlo zhi + +Masses + +1 222.12 + +Atoms + +808 1 3.1126920919683769e+00 2.2216331538625722e+00 -4.0778149745654719e+00 0 0 1 +835 1 -3.3072771004072274e+00 2.1002775288305759e+00 -4.0956694061705790e+00 1 0 1 +196 1 -2.1205146614627246e-01 3.1832997315315215e-01 1.1057163354986859e+00 1 1 0 +997 1 -3.6389056715160084e-01 -3.8629439649272719e+00 -4.3438569614718308e+00 1 1 1 +803 1 9.8431765184872795e+00 2.3728199420784817e+00 -4.0288647001488815e+00 0 0 1 +164 1 1.3006433358066118e+01 3.4716458984576981e-02 1.4047635682945758e+00 0 1 0 +167 1 6.5583146636692859e+00 1.0798584505249131e-01 1.2958581805539762e+00 0 1 0 +962 1 6.4097972328072714e+00 -3.6083107126788727e+00 -3.9071764500839774e+00 0 1 1 +965 1 1.3021960426960327e+01 -3.7102862184212890e+00 -3.6615116640139505e+00 0 1 1 +816 1 1.6423301459333743e+01 2.1547212880684015e+00 -3.9039489182038816e+00 0 0 1 +175 1 1.9664019024592918e+01 5.2856627409220813e-02 1.3448643652446224e+00 0 1 0 +970 1 1.9882169102864921e+01 -3.8609552996521659e+00 -3.7750404150870152e+00 0 1 1 +811 1 2.3249670823888149e+01 2.2350540652536841e+00 -3.8994862383868849e+00 0 0 1 +172 1 2.6421026886093102e+01 1.6144488007316227e-01 1.3309299134412029e+00 0 1 0 +973 1 2.6503327089466190e+01 -3.5346104113939969e+00 -3.9086580761736522e+00 0 1 1 +824 1 3.0046156133052676e+01 2.2963983564968720e+00 -3.9159487504011521e+00 0 0 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-6.1648277376311866e-01 +990 -4.2268440978917821e-01 -9.8793472469058341e-01 -8.7679427588397063e-01 +948 -8.8136275334031566e-01 1.7544044778981864e+00 -1.4599148312301717e+00 +959 8.6871759097478907e-01 4.9533084350552470e-01 -1.7773072955689229e-01 +800 1.0017998424230110e+00 2.2271183277218118e+00 1.8965047672514926e-01 +993 4.1735392872951978e-02 9.1268647255630830e-01 1.7919156690459288e+00 diff --git a/examples/USER/dpd/dpd-shardlow/in.dpd-shardlow b/examples/USER/dpd/dpd-shardlow/in.dpd-shardlow new file mode 100644 index 0000000000..3f9db47e67 --- /dev/null +++ b/examples/USER/dpd/dpd-shardlow/in.dpd-shardlow @@ -0,0 +1,27 @@ +# Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme +log log.dpd +boundary p p p + +units metal +atom_style atomic # Can be either dpd or atomic +read_data data.dpd + +comm_modify mode single vel yes +mass 1 100.0 + +pair_style dpd/fdt 300.0 10.0 234324 +pair_coeff 1 1 0.075 0.022 10.0 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no once no + +timestep 0.001 + +thermo 1 +thermo_style custom step temp pe ke etotal +thermo_modify format float %15.10f + +fix 1 all shardlow +fix 2 all nve + +run 100 \ No newline at end of file diff --git a/examples/USER/dpd/dpd-shardlow/log.reference b/examples/USER/dpd/dpd-shardlow/log.reference new file mode 100644 index 0000000000..12f8f70014 --- /dev/null +++ b/examples/USER/dpd/dpd-shardlow/log.reference @@ -0,0 +1,173 @@ +LAMMPS (7 Dec 2015) +# Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme +boundary p p p + +units metal +atom_style atomic # Can be either dpd or atomic +read_data data.dpd + orthogonal box = (-5.36874 -4.6558 -6.56118) to (61.4618 53.2342 46.2472) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + reading velocities ... + 1000 velocities + +comm_modify mode single vel yes +mass 1 100.0 + +pair_style dpd/fdt 300.0 10.0 234324 +pair_coeff 1 1 0.075 0.022 10.0 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no once no + +timestep 0.001 + +thermo 1 +thermo_style custom step temp pe ke etotal +thermo_modify format float %15.10f + +fix 1 all shardlow +fix 2 all nve + +run 100 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6 -> bins = 12 10 9 +Memory usage per processor = 2.04518 Mbytes +Step Temp PotEng KinEng TotEng + 0 128.6667660382 263.2538386154 16.6148533499 279.8686919654 + 1 128.8781761686 263.2538784644 16.6421529271 279.8960313916 + 2 129.0263870902 263.2539595162 16.6612915346 279.9152510508 + 3 129.0944237374 263.2540669039 16.6700771671 279.9241440710 + 4 129.1614377649 263.2542208758 16.6787307477 279.9329516235 + 5 129.5099128271 263.2544124900 16.7237296409 279.9781421309 + 6 129.4373659799 263.2546219015 16.7143616023 279.9689835038 + 7 129.5468806805 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263.4544359567 18.5216688552 281.9761048118 +Loop time of 0.802761 on 1 procs for 100 steps with 1000 atoms + +Performance: 10.763 ns/day, 2.230 hours/ns, 124.570 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.083614 | 0.083614 | 0.083614 | 0.0 | 10.42 +Neigh | 0.31261 | 0.31261 | 0.31261 | 0.0 | 38.94 +Comm | 0.012618 | 0.012618 | 0.012618 | 0.0 | 1.57 +Output | 0.0033751 | 0.0033751 | 0.0033751 | 0.0 | 0.42 +Modify | 0.38911 | 0.38911 | 0.38911 | 0.0 | 48.47 +Other | | 0.001439 | | | 0.18 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1728 ave 1728 max 1728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18783 ave 18783 max 18783 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18783 +Ave neighs/atom = 18.783 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/dpd/dpde-shardlow/data.dpde b/examples/USER/dpd/dpde-shardlow/data.dpde new file mode 100644 index 0000000000..b18b5795e8 --- /dev/null +++ b/examples/USER/dpd/dpde-shardlow/data.dpde @@ -0,0 +1,2018 @@ +LAMMPS data file via write_data, version 11 Jul 2013, timestep = 10000 + +1000 atoms +1 atom types + +-5.3687390278320350e+00 6.1461796331020025e+01 xlo xhi +-4.6558041136200217e+00 5.3234209917616923e+01 ylo yhi +-6.5611825409372848e+00 4.6247227792940926e+01 zlo zhi + +Masses + +1 222.12 + +Atoms + +808 1 3.0000000000000000e+02 3.1126920919683769e+00 2.2216331538625722e+00 -4.0778149745654719e+00 0 0 1 +835 1 3.0000000000000000e+02 -3.3072771004072274e+00 2.1002775288305759e+00 -4.0956694061705790e+00 1 0 1 +196 1 3.0000000000000000e+02 -2.1205146614627246e-01 3.1832997315315215e-01 1.1057163354986859e+00 1 1 0 +997 1 3.0000000000000000e+02 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isoenergetic conditions using the VV-SSA integration scheme +log log.dpde +boundary p p p + +units metal # ev, ps +atom_style dpd +read_data data.dpde + +comm_modify mode single vel yes +mass 1 100.0 + +pair_style dpd/fdt/energy 10.0 245455 +pair_coeff 1 1 0.075 0.022 3.2E-5 10.00 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no once no + +timestep 0.001 + +compute dpdU all dpd +variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2] + +thermo 1 +thermo_style custom step temp pe ke v_totEnergy +thermo_modify format float %15.10f + +fix 1 all shardlow +fix 2 all nve +fix 3 all eos/cv 0.0005 + +run 100 diff --git a/examples/USER/dpd/dpde-shardlow/log.reference b/examples/USER/dpd/dpde-shardlow/log.reference new file mode 100644 index 0000000000..2c4269def7 --- /dev/null +++ b/examples/USER/dpd/dpde-shardlow/log.reference @@ -0,0 +1,177 @@ +LAMMPS (7 Dec 2015) +# Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme +boundary p p p + +units metal # ev, ps +atom_style dpd +read_data data.dpde + orthogonal box = (-5.36874 -4.6558 -6.56118) to (61.4618 53.2342 46.2472) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + reading velocities ... + 1000 velocities + +comm_modify mode single vel yes +mass 1 100.0 + +pair_style dpd/fdt/energy 10.0 245455 +pair_coeff 1 1 0.075 0.022 3.2E-5 10.00 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no once no + +timestep 0.001 + +compute dpdU all dpd +variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2] + +thermo 1 +thermo_style custom step temp pe ke v_totEnergy +thermo_modify format float %15.10f + +fix 1 all shardlow +fix 2 all nve +fix 3 all eos/cv 0.0005 + +run 100 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6 -> bins = 12 10 9 +Memory usage per processor = 3.33107 Mbytes +Step Temp PotEng KinEng totEnerg + 0 128.6667660382 263.2538386154 16.6148533499 429.8686919654 + 1 128.9849917287 263.2538898270 16.6559461149 429.8686919651 + 2 128.8333822604 263.2539770413 16.6363686501 429.8686919650 + 3 128.7339619634 263.2541060527 16.6235304192 429.8686919618 + 4 129.0775205811 263.2542863822 16.6678944475 429.8686919618 + 5 129.4306564211 263.2545145142 16.7134951910 429.8686919618 + 6 129.4114326993 263.2547749062 16.7110128148 429.8686919619 + 7 129.3005442814 263.2550718076 16.6966936953 429.8686919620 + 8 129.3692785510 263.2554082313 16.7055694123 429.8686919600 + 9 129.2906385442 263.2557915576 16.6954145587 429.8686919569 + 10 129.4374487159 263.2562107913 16.7143722861 429.8686919571 + 11 129.8074096259 263.2566619501 16.7621456657 429.8686919573 + 12 129.5775408090 263.2571482272 16.7324625020 429.8686919571 + 13 129.6608210294 263.2576775975 16.7432165506 429.8686919575 + 14 129.9636716679 263.2582382637 16.7823239215 429.8686919579 + 15 130.1728562587 263.2588485908 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139.9518374325 263.4333392965 18.0721046047 429.8686921820 + 94 139.9391743335 263.4371869424 18.0704694076 429.8686921863 + 95 139.8447896149 263.4410731790 18.0582814253 429.8686921964 + 96 140.0697631915 263.4449843697 18.0873324623 429.8686922001 + 97 140.3594611923 263.4489471179 18.1247414215 429.8686922046 + 98 140.8455519472 263.4529407598 18.1875107508 429.8686922091 + 99 140.8172402178 263.4569615862 18.1838548322 429.8686922137 + 100 140.7185453082 263.4610092311 18.1711102712 429.8686922182 +Loop time of 0.844031 on 1 procs for 100 steps with 1000 atoms + +Performance: 10.237 ns/day, 2.345 hours/ns, 118.479 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.071503 | 0.071503 | 0.071503 | 0.0 | 8.47 +Neigh | 0.26602 | 0.26602 | 0.26602 | 0.0 | 31.52 +Comm | 0.013571 | 0.013571 | 0.013571 | 0.0 | 1.61 +Output | 0.0046957 | 0.0046957 | 0.0046957 | 0.0 | 0.56 +Modify | 0.48701 | 0.48701 | 0.48701 | 0.0 | 57.70 +Other | | 0.001228 | | | 0.15 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1726 ave 1726 max 1726 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18773 ave 18773 max 18773 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18773 +Ave neighs/atom = 18.773 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/dpd/dpdh-shardlow/data.dpdh b/examples/USER/dpd/dpdh-shardlow/data.dpdh new file mode 100644 index 0000000000..b7d2a6760f --- /dev/null +++ b/examples/USER/dpd/dpdh-shardlow/data.dpdh @@ -0,0 +1,20266 @@ + + + + 10125 atoms + +1 atom types + + -64.50000000000000 64.50000000000000 xlo xhi + -64.50000000000000 64.50000000000000 ylo yhi + -64.50000000000000 64.50000000000000 zlo zhi + +Atoms + + 1 1 300.0 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Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme +log log.dpdh +boundary p p p + +units metal # ev, ps +atom_style dpd +read_data data.dpdh + +comm_modify mode single vel yes +mass 1 100.0 + +pair_style dpd/fdt/energy 10.0 234324 +pair_coeff 1 1 0.075 0.022 3.2E-5 10.0 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no once no + +timestep 0.001 + +compute dpdU all dpd +variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol + +thermo 1 +thermo_style custom step temp press vol pe ke v_totEnergy cella cellb cellc +thermo_modify format float %15.10f + +fix 1 all shardlow +fix 0 all nph iso 0.0 0.0 1000.0 +fix 2 all eos/cv 0.0005 + +run 100 \ No newline at end of file diff --git a/examples/USER/dpd/dpdh-shardlow/log.reference b/examples/USER/dpd/dpdh-shardlow/log.reference new file mode 100644 index 0000000000..5a4ae28db0 --- /dev/null +++ b/examples/USER/dpd/dpdh-shardlow/log.reference @@ -0,0 +1,177 @@ +LAMMPS (7 Dec 2015) +# Input File for DPD fluid under isenthalpic conditions using the VV-SSA integration scheme +boundary p p p + +units metal # ev, ps +atom_style dpd +read_data data.dpdh + orthogonal box = (-64.5 -64.5 -64.5) to (64.5 64.5 64.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10125 atoms + reading velocities ... + 10125 velocities + +comm_modify mode single vel yes +mass 1 100.0 + +pair_style dpd/fdt/energy 10.0 234324 +pair_coeff 1 1 0.075 0.022 3.2E-5 10.0 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no once no + +timestep 0.001 + +compute dpdU all dpd +variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol + +thermo 1 +thermo_style custom step temp press vol pe ke v_totEnergy cella cellb cellc +thermo_modify format float %15.10f + +fix 1 all shardlow +fix 0 all nph iso 0.0 0.0 1000.0 +fix 2 all eos/cv 0.0005 + +run 100 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6 -> bins = 22 22 22 +Memory usage per processor = 6.99064 Mbytes +Step Temp Press Volume PotEng KinEng totEnerg Cella Cellb Cellc + 0 239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740 313.3218455755 6048176597.3066043854 129.0000000000 129.0000000000 129.0000000000 + 1 239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632 313.3869004818 6048257397.9450139999 129.0000000012 129.0000000012 129.0000000012 + 2 239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907 313.5010849268 6048391577.0431976318 129.0000000047 129.0000000047 129.0000000047 + 3 239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058 313.6306241122 6048541946.5712041855 129.0000000105 129.0000000105 129.0000000105 + 4 239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043 313.4653942786 6048377030.7404508591 129.0000000186 129.0000000186 129.0000000186 + 5 239.6512678169 2817.6153097076 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2146689.5364683764 2638.4801107361 321.2703568219 6056176929.0169973373 129.0000107459 129.0000107459 129.0000107459 + 97 245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061 321.1595231342 6056028008.1910085678 129.0000109710 129.0000109710 129.0000109710 + 98 245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390 321.1536874797 6055991214.3494358063 129.0000111984 129.0000111984 129.0000111984 + 99 245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546 321.2074270397 6056018909.4481058121 129.0000114282 129.0000114282 129.0000114282 + 100 245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051 321.5958367642 6056403111.1006603241 129.0000116603 129.0000116603 129.0000116603 +Loop time of 4.26657 on 1 procs for 100 steps with 10125 atoms + +Performance: 2.025 ns/day, 11.852 hours/ns, 23.438 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.40111 | 0.40111 | 0.40111 | 0.0 | 9.40 +Neigh | 1.4039 | 1.4039 | 1.4039 | 0.0 | 32.90 +Comm | 0.040107 | 0.040107 | 0.040107 | 0.0 | 0.94 +Output | 0.012053 | 0.012053 | 0.012053 | 0.0 | 0.28 +Modify | 2.4038 | 2.4038 | 2.4038 | 0.0 | 56.34 +Other | | 0.005648 | | | 0.13 + +Nlocal: 10125 ave 10125 max 10125 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 6703 ave 6703 max 6703 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 166831 ave 166831 max 166831 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 166831 +Ave neighs/atom = 16.4771 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/USER/dpd/dpdp-shardlow/data.dpd b/examples/USER/dpd/dpdp-shardlow/data.dpd new file mode 100644 index 0000000000..77119ec9c9 --- /dev/null +++ b/examples/USER/dpd/dpdp-shardlow/data.dpd @@ -0,0 +1,2018 @@ +LAMMPS data file via write_data, version 11 Jul 2013, timestep = 10000 + +1000 atoms +1 atom types + +-5.3687390278320350e+00 6.1461796331020025e+01 xlo xhi +-4.6558041136200217e+00 5.3234209917616923e+01 ylo yhi +-6.5611825409372848e+00 4.6247227792940926e+01 zlo zhi + +Masses + +1 222.12 + +Atoms + +808 1 3.1126920919683769e+00 2.2216331538625722e+00 -4.0778149745654719e+00 0 0 1 +835 1 -3.3072771004072274e+00 2.1002775288305759e+00 -4.0956694061705790e+00 1 0 1 +196 1 -2.1205146614627246e-01 3.1832997315315215e-01 1.1057163354986859e+00 1 1 0 +997 1 -3.6389056715160084e-01 -3.8629439649272719e+00 -4.3438569614718308e+00 1 1 1 +803 1 9.8431765184872795e+00 2.3728199420784817e+00 -4.0288647001488815e+00 0 0 1 +164 1 1.3006433358066118e+01 3.4716458984576981e-02 1.4047635682945758e+00 0 1 0 +167 1 6.5583146636692859e+00 1.0798584505249131e-01 1.2958581805539762e+00 0 1 0 +962 1 6.4097972328072714e+00 -3.6083107126788727e+00 -3.9071764500839774e+00 0 1 1 +965 1 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1.7919156690459288e+00 diff --git a/examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow b/examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow new file mode 100644 index 0000000000..7f64d40312 --- /dev/null +++ b/examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow @@ -0,0 +1,27 @@ +# Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme +log log.dpdp +boundary p p p + +units metal +atom_style atomic # Can be either dpd or atomic +read_data data.dpd + +comm_modify mode single vel yes +mass 1 100.0 + +pair_style dpd/fdt 300.0 10.0 234324 +pair_coeff 1 1 0.075 0.022 10.0 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no once no + +timestep 0.001 + +thermo 1 +thermo_style custom step temp press vol pe ke etotal enthalpy cella cellb cellc +thermo_modify format float %15.10f + +fix 1 all shardlow +fix 0 all nph iso 0.0 0.0 1000.0 + +run 100 \ No newline at end of file diff --git a/examples/USER/dpd/dpdp-shardlow/log.reference b/examples/USER/dpd/dpdp-shardlow/log.reference new file mode 100644 index 0000000000..9cb6f0c53e --- /dev/null +++ b/examples/USER/dpd/dpdp-shardlow/log.reference @@ -0,0 +1,173 @@ +LAMMPS (7 Dec 2015) +# Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme +boundary p p p + +units metal +atom_style atomic # Can be either dpd or atomic +read_data data.dpd + orthogonal box = (-5.36874 -4.6558 -6.56118) to (61.4618 53.2342 46.2472) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1000 atoms + reading velocities ... + 1000 velocities + +comm_modify mode single vel yes +mass 1 100.0 + +pair_style dpd/fdt 300.0 10.0 234324 +pair_coeff 1 1 0.075 0.022 10.0 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no once no + +timestep 0.001 + +thermo 1 +thermo_style custom step temp press vol pe ke etotal enthalpy cella cellb cellc +thermo_modify format float %15.10f + +fix 1 all shardlow +fix 0 all nph iso 0.0 0.0 1000.0 + +run 100 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6 -> bins = 12 10 9 +Memory usage per processor = 2.04518 Mbytes +Step Temp Press Volume PotEng KinEng TotEng Enthalpy Cella Cellb Cellc + 0 128.6667660382 3065.7908751302 204306.2673181506 263.2538386154 16.6148533499 279.8686919654 670.8120681014 66.8305353589 57.8900140312 52.8084103339 + 1 128.8781761640 3065.9340218365 204306.2673289568 263.2538784443 16.6421529266 279.8960313709 670.8576613026 66.8305353600 57.8900140323 52.8084103348 + 2 129.0263870719 3066.0331169958 204306.2673613764 263.2539594358 16.6612915322 279.9152509680 670.8895173736 66.8305353636 57.8900140353 52.8084103376 + 3 129.0944236964 3066.0775853577 204306.2674154095 263.2540667231 16.6700771618 279.9241438848 670.9040809083 66.8305353695 57.8900140404 52.8084103423 + 4 129.1614376919 3066.1201695887 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140.0251352305 3069.7614239791 204306.3382596381 263.3837812869 18.0815696143 281.4653509011 672.9151792214 66.8305430941 57.8900207316 52.8084164461 + 82 140.4343345655 3069.9447540285 204306.3400223668 263.3870704597 18.1344098865 281.5214803462 672.9946899248 66.8305432863 57.8900208981 52.8084165980 + 83 140.8339491089 3070.1205252103 204306.3418067376 263.3904045656 18.1860124661 281.5764170317 673.0720440188 66.8305434808 57.8900210667 52.8084167517 + 84 141.2138258327 3070.2828678237 204306.3436127516 263.3937910919 18.2350662835 281.6288573754 673.1451894287 66.8305436777 57.8900212372 52.8084169073 + 85 141.4316065757 3070.3348892447 204306.3454404097 263.3972231992 18.2631885036 281.6604117028 673.1833809261 66.8305438770 57.8900214099 52.8084170648 + 86 141.6165004814 3070.3639126512 204306.3472897122 263.4006984023 18.2870640172 281.6877624195 673.2144361936 66.8305440787 57.8900215845 52.8084172241 + 87 141.7511192071 3070.3578486993 204306.3491606590 263.4042216826 18.3044474524 281.7086691350 673.2345732314 66.8305442827 57.8900217612 52.8084173853 + 88 141.8992247234 3070.3595802006 204306.3510532502 263.4077909549 18.3235724488 281.7313634037 673.2574919246 66.8305444890 57.8900219400 52.8084175484 + 89 142.0700970483 3070.3750740931 204306.3529674859 263.4114074261 18.3456373433 281.7570447694 673.2851527089 66.8305446978 57.8900221208 52.8084177133 + 90 141.8940825299 3070.1552595577 204306.3549033655 263.4150659370 18.3229084328 281.7379743697 673.2380557076 66.8305449088 57.8900223036 52.8084178801 + 91 141.9603474040 3070.0979256101 204306.3568608879 263.4187731305 18.3314652746 281.7502384052 673.2430123833 66.8305451223 57.8900224885 52.8084180488 + 92 142.2257467272 3070.1741170513 204306.3588400532 263.4225144876 18.3657365240 281.7882510116 673.2907445632 66.8305453381 57.8900226755 52.8084182193 + 93 142.5512734406 3070.2900234935 204306.3608408622 263.4263001648 18.4077720766 281.8340722414 673.3513497860 66.8305455562 57.8900228644 52.8084183917 + 94 142.6487617290 3070.2508281658 204306.3628633148 263.4301422965 18.4203608255 281.8505031221 673.3627864321 66.8305457768 57.8900230555 52.8084185659 + 95 142.7997358153 3070.2465681156 204306.3649074110 263.4340465006 18.4398562429 281.8739027435 673.3856467375 66.8305459996 57.8900232485 52.8084187421 + 96 143.4667389211 3070.5895488558 204306.3669731522 263.4380042392 18.5259869441 281.9639911833 673.5194753590 66.8305462249 57.8900234436 52.8084189200 + 97 143.4616118167 3070.4774890551 204306.3690605390 263.4420072006 18.5253248766 281.9673320772 673.5085306100 66.8305464525 57.8900236408 52.8084190999 + 98 143.3138195521 3070.2680530999 204306.3711695705 263.4460419232 18.5062403307 281.9522822539 673.4667779706 66.8305466824 57.8900238400 52.8084192816 + 99 143.5996384267 3070.3502690101 204306.3733002463 263.4501213575 18.5431483749 281.9932697324 673.5182535421 66.8305469148 57.8900240412 52.8084194652 + 100 143.4332465710 3070.1261458307 204306.3754525657 263.4542352328 18.5216620473 281.9758972802 673.4723054704 66.8305471495 57.8900242445 52.8084196506 +Loop time of 0.77396 on 1 procs for 100 steps with 1000 atoms + +Performance: 11.163 ns/day, 2.150 hours/ns, 129.206 timesteps/s +99.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.081886 | 0.081886 | 0.081886 | 0.0 | 10.58 +Neigh | 0.29547 | 0.29547 | 0.29547 | 0.0 | 38.18 +Comm | 0.012082 | 0.012082 | 0.012082 | 0.0 | 1.56 +Output | 0.0047195 | 0.0047195 | 0.0047195 | 0.0 | 0.61 +Modify | 0.37794 | 0.37794 | 0.37794 | 0.0 | 48.83 +Other | | 0.001861 | | | 0.24 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1728 ave 1728 max 1728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 18783 ave 18783 max 18783 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 18783 +Ave neighs/atom = 18.783 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/src/Makefile b/src/Makefile index f9fe676cea..cda8355751 100644 --- a/src/Makefile +++ b/src/Makefile @@ -47,7 +47,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole fld gpu \ voronoi xtc PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \ - user-diffraction user-drude user-eff user-fep user-h5md \ + user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-mgpt \ user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \ user-quip user-reaxc user-smd user-smtbq user-sph user-tally diff --git a/src/USER-DPD/README b/src/USER-DPD/README new file mode 100644 index 0000000000..1626375c4b --- /dev/null +++ b/src/USER-DPD/README @@ -0,0 +1,35 @@ +This package implements the dissipative particle dynamics (DPD) method +under isothermal, isoenergetic, isobaric and isenthalpic conditions. +The DPD equations of motion are integrated through the Shardlow +splitting algorithm. + +Currently, the package has the following features: + +* A new DPD atom style for tracking the DPD particle internal energies + and internal temperature + +* Compute commands for accessing the DPD particle internal energies + and internal temperature + +* "fix eos" commands for relating the DPD internal energy to the DPD + internal temperature through a coarse-grained particle + equation-of-state + +* "fix shardlow" command for integrating the stochastic ODEs + +* Pair styles for modeling a DPD fluid + +* Commands for setting the particle internal temperature + +See the doc pages for "atom style dpd", "compute dpd" and "compute +dpd/atom", "fix eos/cv" and "fix eos/table", "fix shardlow", "pair +dpd/conservative" and "pair dpd/fdt" and "pair dpd/fdt/energy" +commands to get started. At the bottom of the doc page are many links +to additional documentation contained in the doc/USER/dpd directory. + +There are example scripts for using this package in examples/USER/dpd. + +The primary people who created this package are James Larentzos +(james.p.larentzos.civ at mail.mil), Timothy Mattox (Timothy.Mattox at +engilitycorp.com) and John Brennan (john.k.brennan.civ at mail.mil). +Contact them directly if you have questions. diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp new file mode 100644 index 0000000000..7f48293389 --- /dev/null +++ b/src/USER-DPD/atom_vec_dpd.cpp @@ -0,0 +1,871 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#include +#include "atom_vec_dpd.h" +#include "atom.h" +#include "comm.h" +#include "domain.h" +#include "modify.h" +#include "fix.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +AtomVecDPD::AtomVecDPD(LAMMPS *lmp) : AtomVec(lmp) +{ + molecular = 0; + mass_type = 1; + + comm_x_only = comm_f_only = 0; // we communicate not only x forward but also dpdTheta + size_forward = 6; // 3 + dpdTheta + uCond + uMech + size_reverse = 3; // 3 + size_border = 9; // 6 + dpdTheta + uCond + uMech + size_velocity = 3; + size_data_atom = 6; // we read id + type + dpdTheta + x + y + z + size_data_vel = 4; + xcol_data = 4; // 1=id 2=type 3=dpdTheta 4=x + + atom->dpd_flag = 1; +} + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n +------------------------------------------------------------------------- */ + +void AtomVecDPD::grow(int n) +{ + if (n == 0) grow_nmax(); + else nmax = n; + atom->nmax = nmax; + if (nmax < 0) + error->one(FLERR,"Per-processor system is too big"); + + tag = memory->grow(atom->tag,nmax,"atom:tag"); + type = memory->grow(atom->type,nmax,"atom:type"); + mask = memory->grow(atom->mask,nmax,"atom:mask"); + image = memory->grow(atom->image,nmax,"atom:image"); + x = memory->grow(atom->x,nmax,3,"atom:x"); + v = memory->grow(atom->v,nmax,3,"atom:v"); + f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); + + dpdTheta = memory->grow(atom->dpdTheta, nmax, "atom:dpdTheta"); + uCond = memory->grow(atom->uCond,nmax,"atom:uCond"); + uMech = memory->grow(atom->uMech,nmax,"atom:uMech"); + duCond = memory->grow(atom->duCond,nmax,"atom:duCond"); + duMech = memory->grow(atom->duMech,nmax,"atom:duMech"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs +------------------------------------------------------------------------- */ + +void AtomVecDPD::grow_reset() +{ + tag = atom->tag; type = atom->type; + mask = atom->mask; image = atom->image; + x = atom->x; v = atom->v; f = atom->f; + dpdTheta = atom->dpdTheta; + uCond = atom->uCond; + uMech = atom->uMech; + duCond = atom->duCond; + duMech = atom->duMech; +} + +/* ---------------------------------------------------------------------- + copy atom I info to atom J +------------------------------------------------------------------------- */ + +void AtomVecDPD::copy(int i, int j, int delflag) +{ + tag[j] = tag[i]; + type[j] = type[i]; + mask[j] = mask[i]; + image[j] = image[i]; + x[j][0] = x[i][0]; + x[j][1] = x[i][1]; + x[j][2] = x[i][2]; + v[j][0] = v[i][0]; + v[j][1] = v[i][1]; + v[j][2] = v[i][2]; + dpdTheta[j] = dpdTheta[i]; + uCond[j] = uCond[i]; + uMech[j] = uMech[i]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::pack_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::pack_comm_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecDPD::unpack_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + dpdTheta[i] = buf[m++]; + uCond[i] = buf[m++]; + uMech[i] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecDPD::unpack_comm_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + dpdTheta[i] = buf[m++]; + uCond[i] = buf[m++]; + uMech[i] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::pack_reverse(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = f[i][0]; + buf[m++] = f[i][1]; + buf[m++] = f[i][2]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecDPD::unpack_reverse(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + f[j][0] += buf[m++]; + f[j][1] += buf[m++]; + f[j][2] += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::pack_border(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::pack_border_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::pack_comm_hybrid(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::pack_border_hybrid(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = dpdTheta[j]; + buf[m++] = uCond[j]; + buf[m++] = uMech[j]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecDPD::unpack_border(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + dpdTheta[i] = buf[m++]; + uCond[i] = buf[m++]; + uMech[i] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecDPD::unpack_border_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + dpdTheta[i] = buf[m++]; + uCond[i] = buf[m++]; + uMech[i] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::unpack_comm_hybrid(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + dpdTheta[i] = buf[m++]; + uCond[i] = buf[m++]; + uMech[i] = buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::unpack_border_hybrid(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + dpdTheta[i] = buf[m++]; + uCond[i] = buf[m++]; + uMech[i] = buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- + pack data for atom I for sending to another proc + xyz must be 1st 3 values, so comm::exchange() can test on them +------------------------------------------------------------------------- */ + +int AtomVecDPD::pack_exchange(int i, double *buf) +{ + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = dpdTheta[i]; + buf[m++] = uCond[i]; + buf[m++] = uMech[i]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecDPD::unpack_exchange(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + dpdTheta[nlocal] = buf[m++]; + uCond[nlocal] = buf[m++]; + uMech[nlocal] = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> + unpack_exchange(nlocal,&buf[m]); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes +------------------------------------------------------------------------- */ + +int AtomVecDPD::size_restart() +{ + int i; + + int nlocal = atom->nlocal; + int n = 14 * nlocal; // 11 + dpdTheta + uCond + uMech + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive +------------------------------------------------------------------------- */ + +int AtomVecDPD::pack_restart(int i, double *buf) +{ + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = dpdTheta[i]; + buf[m++] = uCond[i]; + buf[m++] = uMech[i]; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities +------------------------------------------------------------------------- */ + +int AtomVecDPD::unpack_restart(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); + } + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + dpdTheta[nlocal] = buf[m++]; + uCond[nlocal] = buf[m++]; + uMech[nlocal] = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults +------------------------------------------------------------------------- */ + +void AtomVecDPD::create_atom(int itype, double *coord) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = 0; + type[nlocal] = itype; + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + mask[nlocal] = 1; + image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + dpdTheta[nlocal] = 0.0; + uCond[nlocal] = 0.0; + uMech[nlocal] = 0.0; + duCond[nlocal] = 0.0; + duMech[nlocal] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities +------------------------------------------------------------------------- */ + +void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = ATOTAGINT(values[0]); + type[nlocal] = atoi(values[1]); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + dpdTheta[nlocal] = atof(values[2]); + if (dpdTheta[nlocal] <= 0) + error->one(FLERR,"Internal temperature in Atoms section of date file must be > zero"); + + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + + image[nlocal] = imagetmp; + + mask[nlocal] = 1; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + uCond[nlocal] = 0.0; + uMech[nlocal] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Atoms section of data file + initialize other atom quantities for this sub-style +------------------------------------------------------------------------- */ + +int AtomVecDPD::data_atom_hybrid(int nlocal, char **values) +{ + dpdTheta[nlocal] = atof(values[0]); + + return 1; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecDPD::pack_data(double **buf) +{ + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(tag[i]).d; + buf[i][1] = ubuf(type[i]).d; + buf[i][2] = dpdTheta[i]; + buf[i][3] = x[i][0]; + buf[i][4] = x[i][1]; + buf[i][5] = x[i][2]; + buf[i][6] = ubuf((image[i] & IMGMASK) - IMGMAX).d; + buf[i][7] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; + buf[i][8] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid atom info for data file +------------------------------------------------------------------------- */ + +int AtomVecDPD::pack_data_hybrid(int i, double *buf) +{ + buf[0] = dpdTheta[i]; + return 1; +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecDPD::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", + (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, + buf[i][2],buf[i][3],buf[i][4],buf[i][5], + (int) ubuf(buf[i][6]).i,(int) ubuf(buf[i][7]).i, + (int) ubuf(buf[i][8]).i); +} + +/* ---------------------------------------------------------------------- + write hybrid atom info to data file +------------------------------------------------------------------------- */ + +int AtomVecDPD::write_data_hybrid(FILE *fp, double *buf) +{ + fprintf(fp," %-1.16e",buf[0]); + return 1; +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory +------------------------------------------------------------------------- */ + +bigint AtomVecDPD::memory_usage() +{ + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); + if (atom->memcheck("type")) bytes += memory->usage(type,nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); + if (atom->memcheck("image")) bytes += memory->usage(image,nmax); + if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); + if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); + if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3); + if (atom->memcheck("dpdTheta")) bytes += memory->usage(dpdTheta,nmax); + if (atom->memcheck("uCond")) bytes += memory->usage(uCond,nmax); + if (atom->memcheck("uMech")) bytes += memory->usage(uMech,nmax); + if (atom->memcheck("duCond")) bytes += memory->usage(duCond,nmax); + if (atom->memcheck("duMech")) bytes += memory->usage(duMech,nmax); + + return bytes; +} diff --git a/src/USER-DPD/atom_vec_dpd.h b/src/USER-DPD/atom_vec_dpd.h new file mode 100644 index 0000000000..0f5c348f5c --- /dev/null +++ b/src/USER-DPD/atom_vec_dpd.h @@ -0,0 +1,95 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(dpd,AtomVecDPD) + +#else + +#ifndef LMP_ATOM_VEC_DPD_H +#define LMP_ATOM_VEC_DPD_H + +#include "atom_vec.h" + +namespace LAMMPS_NS { + +class AtomVecDPD : public AtomVec { + public: + AtomVecDPD(class LAMMPS *); + virtual ~AtomVecDPD() {} + void grow(int); + void grow_reset(); + void copy(int, int, int); + virtual int pack_comm(int, int *, double *, int, int *); + virtual int pack_comm_vel(int, int *, double *, int, int *); + int pack_comm_hybrid(int, int *, double *); + virtual void unpack_comm(int, int, double *); + virtual void unpack_comm_vel(int, int, double *); + int unpack_comm_hybrid(int, int, double *); + int pack_reverse(int, int, double *); + void unpack_reverse(int, int *, double *); + virtual int pack_border(int, int *, double *, int, int *); + virtual int pack_border_vel(int, int *, double *, int, int *); + int pack_border_hybrid(int, int *, double *); + virtual void unpack_border(int, int, double *); + virtual void unpack_border_vel(int, int, double *); + int unpack_border_hybrid(int, int, double *); + virtual int pack_exchange(int, double *); + virtual int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + int data_atom_hybrid(int, char **); + void pack_data(double **); + int pack_data_hybrid(int, double *); + void write_data(FILE *, int, double **); + int write_data_hybrid(FILE *, double *); + bigint memory_usage(); + double *uCond,*uMech,*dpdTheta; + double *duCond,*duMech; + + protected: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Per-processor system is too big + +The number of owned atoms plus ghost atoms on a single +processor must fit in 32-bit integer. + +E: Invalid atom type in Atoms section of data file + +Atom types must range from 1 to specified # of types. + +E: Internal temperature in Atoms section of data file must be > zero + +All internal temperatures must be > zero + +*/ diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp new file mode 100644 index 0000000000..a1299ca28a --- /dev/null +++ b/src/USER-DPD/compute_dpd.cpp @@ -0,0 +1,88 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#include +#include "compute_dpd.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "domain.h" +#include "group.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeDpd::ComputeDpd(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute dpd command"); + + vector_flag = 1; + size_vector = 5; + extvector = 0; + + vector = new double[size_vector]; + + if (atom->dpd_flag != 1) error->all(FLERR,"compute dpd requires atom_style with internal temperature and energies (e.g. dpd)"); +} + +/* ---------------------------------------------------------------------- */ + +ComputeDpd::~ComputeDpd() +{ + + delete [] vector; + +} + +/* ---------------------------------------------------------------------- */ + +void ComputeDpd::compute_vector() +{ + invoked_vector = update->ntimestep; + + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *dpdTheta = atom->dpdTheta; + int nlocal = atom->nlocal; + int *mask = atom->mask; + int natoms; + + dpdU = new double[size_vector]; + + for (int i = 0; i < size_vector; i++) dpdU[i] = double(0.0); + + for (int i = 0; i < nlocal; i++){ + if (mask[i] & groupbit){ + dpdU[0] += uCond[i]; + dpdU[1] += uMech[i]; + dpdU[2] += uCond[i] + uMech[i]; + dpdU[3] += 1.0 / dpdTheta[i]; + dpdU[4]++; + } + } + + MPI_Allreduce(dpdU,vector,size_vector,MPI_DOUBLE,MPI_SUM,world); + + natoms = vector[4]; + vector[3] = natoms / vector[3]; + + delete [] dpdU; + +} diff --git a/src/USER-DPD/compute_dpd.h b/src/USER-DPD/compute_dpd.h new file mode 100644 index 0000000000..022beb68b3 --- /dev/null +++ b/src/USER-DPD/compute_dpd.h @@ -0,0 +1,60 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(dpd,ComputeDpd) + +#else + +#ifndef LMP_COMPUTE_DPD_H +#define LMP_COMPUTE_DPD_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeDpd : public Compute { + public: + ComputeDpd(class LAMMPS *, int, char **); + ~ComputeDpd(); + void init() {} + void compute_vector(); + + private: + double *dpdU; + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: compute dpd requires atom_style with internal temperature and energies (e.g. dpd) + +Self-explanatory. + +*/ diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp new file mode 100644 index 0000000000..52f2abc68f --- /dev/null +++ b/src/USER-DPD/compute_dpd_atom.cpp @@ -0,0 +1,107 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#include "math.h" +#include +#include +#include "compute_dpd_atom.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "domain.h" +#include "group.h" +#include "memory.h" +#include "error.h" +#include "comm.h" + +#include + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +ComputeDpdAtom::ComputeDpdAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal compute dpd/atom command"); + + peratom_flag = 1; + size_peratom_cols = 3; + + nmax = 0; + dpdAtom = NULL; + + if (atom->dpd_flag != 1) error->all(FLERR,"compute dpd requires atom_style with internal temperature and energies (e.g. dpd)"); +} + +/* ---------------------------------------------------------------------- */ + +ComputeDpdAtom::~ComputeDpdAtom() +{ + memory->destroy(dpdAtom); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeDpdAtom::init() +{ + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"dpd/atom") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute dpd/atom command"); +} + +/* ---------------------------------------------------------------------- + gather compute vector data from other nodes +------------------------------------------------------------------------- */ + +void ComputeDpdAtom::compute_peratom() +{ + + invoked_peratom = update->ntimestep; + + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *dpdTheta = atom->dpdTheta; + int nlocal = atom->nlocal; + int *mask = atom->mask; + if (nlocal > nmax) { + memory->destroy(dpdAtom); + nmax = atom->nmax; + memory->create(dpdAtom,nmax,size_peratom_cols,"dpd/atom:dpdAtom"); + array_atom = dpdAtom; + } + + for (int i = 0; i < nlocal; i++){ + if (mask[i] & groupbit){ + dpdAtom[i][0] = uCond[i]; + dpdAtom[i][1] = uMech[i]; + dpdAtom[i][2] = dpdTheta[i]; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double ComputeDpdAtom::memory_usage() +{ + double bytes = size_peratom_cols * nmax * sizeof(double); + return bytes; +} diff --git a/src/USER-DPD/compute_dpd_atom.h b/src/USER-DPD/compute_dpd_atom.h new file mode 100644 index 0000000000..771b01510e --- /dev/null +++ b/src/USER-DPD/compute_dpd_atom.h @@ -0,0 +1,65 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(dpd/atom,ComputeDpdAtom) + +#else + +#ifndef LMP_COMPUTE_DPD_ATOM_H +#define LMP_COMPUTE_DPD_ATOM_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeDpdAtom : public Compute { + public: + ComputeDpdAtom(class LAMMPS *, int, char **); + ~ComputeDpdAtom(); + void init(); + void compute_peratom(); + double memory_usage(); + + private: + int nmax; + double **dpdAtom; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: compute dpd requires atom_style with internal temperature and energies (e.g. dpd) + +Self-explanatory + +W: More than one compute dpd/atom command + +Self-explanatory + +*/ diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp new file mode 100644 index 0000000000..7207a80a95 --- /dev/null +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -0,0 +1,108 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_eos_cv.h" +#include "atom.h" +#include "error.h" +#include "force.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixEOScv::FixEOScv(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (narg != 4) error->all(FLERR,"Illegal fix eos/cv command"); + cvEOS = force->numeric(FLERR,arg[3]); + if(cvEOS <= double(0.0)) error->all(FLERR,"EOS cv must be > 0.0"); + + restart_peratom = 1; + nevery = 1; +} + +/* ---------------------------------------------------------------------- */ + +int FixEOScv::setmask() +{ + int mask = 0; + mask |= POST_INTEGRATE; + mask |= END_OF_STEP; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixEOScv::init() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *dpdTheta = atom->dpdTheta; + + if(this->restart_reset){ + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + dpdTheta[i] = (uCond[i]+uMech[i])/cvEOS; + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + uCond[i] = double(0.5)*cvEOS*dpdTheta[i]; + uMech[i] = double(0.5)*cvEOS*dpdTheta[i]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixEOScv::post_integrate() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *dpdTheta = atom->dpdTheta; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + dpdTheta[i] = (uCond[i]+uMech[i])/cvEOS; + if(dpdTheta[i] <= double(0.0)) + error->one(FLERR,"Internal temperature < zero"); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixEOScv::end_of_step() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *dpdTheta = atom->dpdTheta; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + dpdTheta[i] = (uCond[i]+uMech[i])/cvEOS; + if(dpdTheta[i] <= double(0.0)) + error->one(FLERR,"Internal temperature < zero"); + } +} diff --git a/src/USER-DPD/fix_eos_cv.h b/src/USER-DPD/fix_eos_cv.h new file mode 100644 index 0000000000..ab59275ec8 --- /dev/null +++ b/src/USER-DPD/fix_eos_cv.h @@ -0,0 +1,65 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(eos/cv,FixEOScv) + +#else + +#ifndef LMP_FIX_EOS_CV_H +#define LMP_FIX_EOS_CV_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixEOScv : public Fix { + public: + FixEOScv(class LAMMPS *, int, char **); + virtual ~FixEOScv() {} + int setmask(); + virtual void init(); + virtual void post_integrate(); + virtual void end_of_step(); + + protected: + double cvEOS; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: EOS cv must be > 0.0 + +The constant volume heat capacity must be larger than zero. + +E: Internal temperature < zero + +Self-explanatory. EOS may not be valid under current simulation conditions. + +*/ diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp new file mode 100644 index 0000000000..85aa20ee98 --- /dev/null +++ b/src/USER-DPD/fix_eos_table.cpp @@ -0,0 +1,433 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_eos_table.h" +#include "atom.h" +#include "error.h" +#include "force.h" +#include "memory.h" + +#define MAXLINE 1024 + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixEOStable::FixEOStable(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (narg != 7) error->all(FLERR,"Illegal fix eos/table command"); + restart_peratom = 1; + nevery = 1; + + if (strcmp(arg[3],"linear") == 0) tabstyle = LINEAR; + else error->all(FLERR,"Unknown table style in fix eos/table"); + + tablength = force->inumeric(FLERR,arg[5]); + if (tablength < 2) error->all(FLERR,"Illegal number of eos/table entries"); + + ntables = 0; + tables = NULL; + int me; + MPI_Comm_rank(world,&me); + tables = (Table *) + memory->srealloc(tables,(ntables+2)*sizeof(Table),"eos:tables"); + Table *tb = &tables[ntables]; + Table *tb2 = &tables[ntables+1]; + null_table(tb); + null_table(tb2); + if (me == 0) read_table(tb,tb2,arg[4],arg[6]); + bcast_table(tb); + bcast_table(tb2); + + // error check on table parameters + + if (tb->ninput <= 1) error->one(FLERR,"Invalid eos/table length"); + + tb->lo = tb->rfile[0]; + tb->hi = tb->rfile[tb->ninput-1]; + if (tb->lo >= tb->hi) error->all(FLERR,"eos/table values are not increasing"); + + if (tb2->ninput <= 1) error->one(FLERR,"Invalid eos/table length"); + + tb2->lo = tb2->rfile[0]; + tb2->hi = tb2->rfile[tb2->ninput-1]; + if (tb2->lo >= tb2->hi) error->all(FLERR,"eos/table values are not increasing"); + + // spline read-in and compute r,e,f vectors within table + + spline_table(tb); + compute_table(tb); + spline_table(tb2); + compute_table(tb2); + ntables++; +} + +/* ---------------------------------------------------------------------- */ + +FixEOStable::~FixEOStable() +{ + for (int m = 0; m < 2*ntables; m++) free_table(&tables[m]); + memory->sfree(tables); +} + +/* ---------------------------------------------------------------------- */ + +int FixEOStable::setmask() +{ + int mask = 0; + mask |= POST_INTEGRATE; + mask |= END_OF_STEP; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStable::init() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *dpdTheta = atom->dpdTheta; + double tmp; + + if(this->restart_reset){ + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]); + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + energy_lookup(dpdTheta[i],tmp); + uCond[i] = tmp / double(2.0); + uMech[i] = tmp / double(2.0); + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStable::post_integrate() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *dpdTheta = atom->dpdTheta; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]); + if(dpdTheta[i] <= double(0.0)) + error->one(FLERR,"Internal temperature < zero"); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStable::end_of_step() +{ + int nlocal = atom->nlocal; + int *mask = atom->mask; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *dpdTheta = atom->dpdTheta; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]); + if(dpdTheta[i] <= double(0.0)) + error->one(FLERR,"Internal temperature < zero"); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStable::null_table(Table *tb) +{ + tb->rfile = tb->efile = NULL; + tb->e2file = NULL; + tb->r = tb->e = tb->de = NULL; + tb->e2 = NULL; +} + +/* ---------------------------------------------------------------------- */ + +void FixEOStable::free_table(Table *tb) +{ + memory->destroy(tb->rfile); + memory->destroy(tb->efile); + memory->destroy(tb->e2file); + + memory->destroy(tb->r); + memory->destroy(tb->e); + memory->destroy(tb->de); + memory->destroy(tb->e2); +} + +/* ---------------------------------------------------------------------- + read table file, only called by proc 0 +------------------------------------------------------------------------- */ + +void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword) +{ + char line[MAXLINE]; + + // open file + + FILE *fp = fopen(file,"r"); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open file %s",file); + error->one(FLERR,str); + } + + // loop until section found with matching keyword + + while (1) { + if (fgets(line,MAXLINE,fp) == NULL) + error->one(FLERR,"Did not find keyword in table file"); + if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line + if (line[0] == '#') continue; // comment + char *word = strtok(line," \t\n\r"); + if (strcmp(word,keyword) == 0) break; // matching keyword + fgets(line,MAXLINE,fp); // no match, skip section + param_extract(tb,tb2,line); + fgets(line,MAXLINE,fp); + for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + } + + // read args on 2nd line of section + // allocate table arrays for file values + + fgets(line,MAXLINE,fp); + param_extract(tb,tb2,line); + memory->create(tb->rfile,tb->ninput,"eos:rfile"); + memory->create(tb->efile,tb->ninput,"eos:efile"); + memory->create(tb2->rfile,tb2->ninput,"eos:rfile2"); + memory->create(tb2->efile,tb2->ninput,"eos:efile2"); + + // read r,e table values from file + + int itmp; + fgets(line,MAXLINE,fp); + for (int i = 0; i < tb->ninput; i++) { + fgets(line,MAXLINE,fp); + sscanf(line,"%d %lg %lg",&itmp,&tb->rfile[i],&tb->efile[i]); + sscanf(line,"%d %lg %lg",&itmp,&tb2->efile[i],&tb2->rfile[i]); + } + + fclose(fp); +} + +/* ---------------------------------------------------------------------- + build spline representation of e,f over entire range of read-in table + this function sets these values in e2file +------------------------------------------------------------------------- */ + +void FixEOStable::spline_table(Table *tb) +{ + memory->create(tb->e2file,tb->ninput,"eos:e2file"); +} + +/* ---------------------------------------------------------------------- + compute r,e,f vectors from splined values +------------------------------------------------------------------------- */ + +void FixEOStable::compute_table(Table *tb) +{ + // delta = table spacing for N-1 bins + int tlm1 = tablength-1; + + tb->delta = (tb->hi - tb->lo)/ tlm1; + tb->invdelta = 1.0/tb->delta; + tb->deltasq6 = tb->delta*tb->delta / 6.0; + + // N-1 evenly spaced bins in r from min to max + // r,e = value at lower edge of bin + // de values = delta values of e,f + // r,e are N in length so de arrays can compute difference + + memory->create(tb->r,tablength,"eos:r"); + memory->create(tb->e,tablength,"eos:e"); + memory->create(tb->de,tlm1,"eos:de"); + memory->create(tb->e2,tablength,"eos:e2"); + + double a; + for (int i = 0; i < tablength; i++) { + a = tb->lo + i*tb->delta; + tb->r[i] = a; + tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,a); + } + + for (int i = 0; i < tlm1; i++) { + tb->de[i] = tb->e[i+1] - tb->e[i]; + } +} + +/* ---------------------------------------------------------------------- + extract attributes from parameter line in table section + format of line: N value + N is required, other params are optional +------------------------------------------------------------------------- */ + +void FixEOStable::param_extract(Table *tb, Table *tb2, char *line) +{ + tb->ninput = 0; + tb2->ninput = 0; + + char *word = strtok(line," \t\n\r\f"); + while (word) { + if (strcmp(word,"N") == 0) { + word = strtok(NULL," \t\n\r\f"); + tb->ninput = atoi(word); + tb2->ninput = atoi(word); + } else { + error->one(FLERR,"Invalid keyword in fix eos/table parameters"); + } + word = strtok(NULL," \t\n\r\f"); + } + + if (tb->ninput == 0) error->one(FLERR,"fix eos/table parameters did not set N"); + if (tb2->ninput == 0) error->one(FLERR,"fix eos/table parameters did not set N"); +} + +/* ---------------------------------------------------------------------- + broadcast read-in table info from proc 0 to other procs + this function communicates these values in Table: + ninput,rfile,efile +------------------------------------------------------------------------- */ + +void FixEOStable::bcast_table(Table *tb) +{ + MPI_Bcast(&tb->ninput,1,MPI_INT,0,world); + + int me; + MPI_Comm_rank(world,&me); + if (me > 0) { + memory->create(tb->rfile,tb->ninput,"eos:rfile"); + memory->create(tb->efile,tb->ninput,"eos:efile"); + } + + MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world); + MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world); +} + +/* ---------------------------------------------------------------------- + spline and splint routines modified from Numerical Recipes +------------------------------------------------------------------------- */ + +void FixEOStable::spline(double *x, double *y, int n, + double yp1, double ypn, double *y2) +{ + int i,k; + double p,qn,sig,un; + double *u = new double[n]; + + if (yp1 > 0.99e30) y2[0] = u[0] = 0.0; + else { + y2[0] = -0.5; + u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1); + } + for (i = 1; i < n-1; i++) { + sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]); + p = sig*y2[i-1] + 2.0; + y2[i] = (sig-1.0) / p; + u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]); + u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p; + } + if (ypn > 0.99e30) qn = un = 0.0; + else { + qn = 0.5; + un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2])); + } + y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0); + for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k]; + + delete [] u; +} + +/* ---------------------------------------------------------------------- */ + +double FixEOStable::splint(double *xa, double *ya, double *y2a, int n, double x) +{ + int klo,khi,k; + double h,b,a,y; + + klo = 0; + khi = n-1; + while (khi-klo > 1) { + k = (khi+klo) >> 1; + if (xa[k] > x) khi = k; + else klo = k; + } + h = xa[khi]-xa[klo]; + a = (xa[khi]-x) / h; + b = (x-xa[klo]) / h; + y = a*ya[klo] + b*ya[khi] + + ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0; + return y; +} + +/* ---------------------------------------------------------------------- + calculate internal energy u at temperature t + insure t is between min/max +------------------------------------------------------------------------- */ + +void FixEOStable::energy_lookup(double t, double &u) +{ + int itable; + double fraction,a,b; + + Table *tb = &tables[0]; + if(t < tb->lo || t > tb->hi){ + printf("Temperature=%lf TableMin=%lf TableMax=%lf\n",t,tb->lo,tb->hi); + error->one(FLERR,"Temperature is not within table cutoffs"); + } + + if (tabstyle == LINEAR) { + itable = static_cast ((t - tb->lo) * tb->invdelta); + fraction = (t - tb->r[itable]) * tb->invdelta; + u = tb->e[itable] + fraction*tb->de[itable]; + } +} +/* ---------------------------------------------------------------------- + calculate temperature t at energy u + insure u is between min/max +------------------------------------------------------------------------- */ + +void FixEOStable::temperature_lookup(double u, double &t) +{ + int itable; + double fraction,a,b; + + Table *tb = &tables[1]; + if(u < tb->lo || u > tb->hi){ + printf("Energy=%lf TableMin=%lf TableMax=%lf\n",u,tb->lo,tb->hi); + error->one(FLERR,"Energy is not within table cutoffs"); + } + + if (tabstyle == LINEAR) { + itable = static_cast ((u - tb->lo) * tb->invdelta); + fraction = (u - tb->r[itable]) * tb->invdelta; + t = tb->e[itable] + fraction*tb->de[itable]; + } +} diff --git a/src/USER-DPD/fix_eos_table.h b/src/USER-DPD/fix_eos_table.h new file mode 100644 index 0000000000..b508ce3f39 --- /dev/null +++ b/src/USER-DPD/fix_eos_table.h @@ -0,0 +1,130 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(eos/table,FixEOStable) + +#else + +#ifndef LMP_FIX_EOS_TABLE_H +#define LMP_FIX_EOS_TABLE_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixEOStable : public Fix { + public: + FixEOStable(class LAMMPS *, int, char **); + virtual ~FixEOStable(); + int setmask(); + virtual void init(); + virtual void post_integrate(); + virtual void end_of_step(); + void energy_lookup(double, double &); + void temperature_lookup(double, double &); + + protected: + enum{LINEAR}; + + int tabstyle,tablength; + struct Table { + int ninput; + double lo,hi; + double *rfile,*efile; + double *e2file; + double delta,invdelta,deltasq6; + double *r,*e,*de,*e2; + }; + int ntables; + Table *tables; + + void allocate(); + void null_table(Table *); + void free_table(Table *); + void read_table(Table *, Table *, char *, char *); + void bcast_table(Table *); + void spline_table(Table *); + void compute_table(Table *); + + void param_extract(Table *, Table *, char *); + void spline(double *, double *, int, double, double, double *); + double splint(double *, double *, double *, int, double); + + }; +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Unknown table style in fix eos/table + +Style of table is invalid for use with fix eos/table command. + +E: Illegal number of eos/table entries + +There must be at least 2 table entries. + +E: Invalid eos/table length + +Length of read-in fix eos/table is invalid + +E: eos/table values are not increasing + +The EOS must be a monotonically, increasing function + +E: Internal temperature < zero + +Self-explanatory. EOS may not be valid under current simulation conditions. + +E: Cannot open file %s + +The specified file cannot be opened. Check that the path and name are +correct. + +E: Did not find keyword in table file + +Keyword used in fix eos/table command was not found in table file. + +E: Invalid keyword in fix eos/table parameters + +Keyword used in list of table parameters is not recognized. + +E: fix eos/table parameters did not set N + +List of fix eos/table parameters must include N setting. + +E: Temperature is not within table cutoffs + +The internal temperature does not lie with the minimum +and maximum temperature cutoffs of the table + +E: Energy is not within table cutoffs + +The internal energy does not lie with the minimum +and maximum energy cutoffs of the table + +*/ diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp new file mode 100644 index 0000000000..8dd6e4e2e7 --- /dev/null +++ b/src/USER-DPD/fix_shardlow.cpp @@ -0,0 +1,568 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: + James Larentzos and Timothy I. Mattox (Engility Corporation) + + Martin Lisal (Institute of Chemical Process Fundamentals + of the Czech Academy of Sciences and J. E. Purkinje University) + + John Brennan, Joshua Moore and William Mattson (Army Research Lab) + + Please cite the related publications: + J. P. Larentzos, J. K. Brennan, J. D. Moore, M. Lisal, W. D. Mattson, + "Parallel implementation of isothermal and isoenergetic Dissipative + Particle Dynamics using Shardlow-like splitting algorithms", + Computer Physics Communications, 2014, 185, pp 1987--1998. + + M. Lisal, J. K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics + at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using + Shardlow-like splitting algorithms", Journal of Chemical Physics, 2011, + 135, 204105. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_shardlow.h" +#include "atom.h" +#include "force.h" +#include "update.h" +#include "respa.h" +#include "error.h" +#include +#include "atom_vec.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "random_mars.h" +#include "memory.h" +#include "domain.h" +#include "modify.h" +#include "pair_dpd_fdt.h" +#include "pair_dpd_fdt_energy.h" +#include "pair.h" +#include "citeme.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define EPSILON 1.0e-10 + +static const char cite_fix_shardlow[] = + "fix shardlow command:\n\n" + "@Article{Larentzos14,\n" + " author = {J. P. Larentzos, J. K. Brennan, J. D. Moore, M. Lisal, W. D. Mattson},\n" + " title = {Parallel implementation of isothermal and isoenergetic Dissipative Particle Dynamics using Shardlow-like splitting algorithms},\n" + " journal = {Computer Physics Communications},\n" + " year = 2014,\n" + " volume = 185\n" + " pages = {1987--1998}\n" + "}\n\n" + "@Article{Lisal11,\n" + " author = {M. Lisal, J. K. Brennan, J. Bonet Avalos},\n" + " title = {Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms},\n" + " journal = {Journal of Chemical Physics},\n" + " year = 2011,\n" + " volume = 135\n" + " pages = {204105}\n" + "}\n\n"; + +/* ---------------------------------------------------------------------- */ + +FixShardlow::FixShardlow(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (lmp->citeme) lmp->citeme->add(cite_fix_shardlow); + + if (narg != 3) error->all(FLERR,"Illegal fix shardlow command"); + + pairDPD = NULL; + pairDPDE = NULL; + pairDPD = (PairDPDfdt *) force->pair_match("dpd/fdt",1); + pairDPDE = (PairDPDfdtEnergy *) force->pair_match("dpd/fdt/energy",1); + + if(pairDPDE){ + comm_forward = 10; + comm_reverse = 5; + } else { + comm_forward = 6; + comm_reverse = 3; + } + + if(pairDPD == NULL && pairDPDE == NULL) + error->all(FLERR,"Must use pair_style dpd/fdt or dpd/fdt/energy with fix shardlow"); + + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"nve") == 0 || strcmp(modify->fix[i]->style,"nph") == 0) + error->all(FLERR,"A deterministic integrator must be specified after fix shardlow in input file (e.g. fix nve or fix nph)."); +} + +/* ---------------------------------------------------------------------- */ + +int FixShardlow::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= PRE_NEIGHBOR; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixShardlow::init_list(int id, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void FixShardlow::setup(int vflag) +{ + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"nvt") == 0 || strcmp(modify->fix[i]->style,"npt") == 0) + error->all(FLERR,"Cannot use constant temperature integration routines with DPD."); +} + +/* ---------------------------------------------------------------------- */ + +void FixShardlow::setup_pre_force(int vflag) +{ + neighbor->build_one(list); +} + +/* ---------------------------------------------------------------------- + Perform the stochastic integration and Shardlow update + Allow for both per-type and per-atom mass + + NOTE: only implemented for orthogonal boxes, not triclinic +------------------------------------------------------------------------- */ + +void FixShardlow::initial_integrate(int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + double xtmp,ytmp,ztmp,delx,dely,delz; + double vxtmp,vytmp,vztmp,delvx,delvy,delvz; + double rsq,r,rinv; + double dot,wd,wr,randnum,factor_dpd,factor_dpd1; + double dpx,dpy,dpz; + double denom, mu_ij; + + double **x = atom->x; + double **v = atom->v; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int nlocal = atom->nlocal; + int nghost = atom->nghost; + int nall = nlocal + nghost; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double randPair; + + double *uCond = atom->uCond; + double *uMech = atom->uMech; + double *duCond = atom->duCond; + double *duMech = atom->duMech; + double *dpdTheta = atom->dpdTheta; + double kappa_ij, alpha_ij, theta_ij, gamma_ij, sigma_ij, u_ij; + double vxi, vyi, vzi, vxj, vyj, vzj; + double vx0i, vy0i, vz0i, vx0j, vy0j, vz0j; + double dot1, dot2, dot3, dot4; + double mass_i, mass_j; + double massinv_i, massinv_j; + double cut, cut2; + + const double dt = update->dt; + const double dtsqrt = sqrt(dt); + + // NOTE: this logic is specific to orthogonal boxes, not triclinic + + // Enforce the constraint that ghosts must be contained in the nearest sub-domains + double bbx = domain->subhi[0] - domain->sublo[0]; + double bby = domain->subhi[1] - domain->sublo[1]; + double bbz = domain->subhi[2] - domain->sublo[2]; + + double rcut = double(2.0)*neighbor->cutneighmax; + + if (domain->triclinic) + error->all(FLERR,"Fix shardlow does not yet support triclinic geometries"); + + if(rcut >= bbx || rcut >= bby || rcut>= bbz ) + error->all(FLERR,"Shardlow algorithm requires sub-domain length > 2*(rcut+skin). Either reduce the number of processors requested, or change the cutoff/skin\n"); + + // Allocate memory for the dvSSA arrays + dvSSA = new double*[nall]; + for (ii = 0; ii < nall; ii++) { + dvSSA[ii] = new double[3]; + } + + // Zero the momenta + for (ii = 0; ii < nlocal; ii++) { + dvSSA[ii][0] = double(0.0); + dvSSA[ii][1] = double(0.0); + dvSSA[ii][2] = double(0.0); + if(pairDPDE){ + duCond[ii] = double(0.0); + duMech[ii] = double(0.0); + } + } + + // Communicate the updated momenta and velocities to all nodes + comm->forward_comm_fix(this); + + // Define pointers to access the neighbor list + if(pairDPDE){ + inum = pairDPDE->list->inum; + ilist = pairDPDE->list->ilist; + numneigh = pairDPDE->list->numneigh; + firstneigh = pairDPDE->list->firstneigh; + } else { + inum = pairDPD->list->inum; + ilist = pairDPD->list->ilist; + numneigh = pairDPD->list->numneigh; + firstneigh = pairDPD->list->firstneigh; + } + + //Loop over all 14 directions (8 stages) + for (int idir = 1; idir <=8; idir++){ + + // Loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // Loop over Directional Neighbors only + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + if (neighbor->ssa_airnum[j] != idir) continue; + jtype = type[j]; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if(pairDPDE){ + cut2 = pairDPDE->cutsq[itype][jtype]; + cut = pairDPDE->cut[itype][jtype]; + } else { + cut2 = pairDPD->cutsq[itype][jtype]; + cut = pairDPD->cut[itype][jtype]; + } + + // if (rsq < pairDPD->cutsq[itype][jtype]) { + if (rsq < cut2) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = double(1.0)/r; + + // Store the velocities from previous Shardlow step + vx0i = v[i][0] + dvSSA[i][0]; + vy0i = v[i][1] + dvSSA[i][1]; + vz0i = v[i][2] + dvSSA[i][2]; + + vx0j = v[j][0] + dvSSA[j][0]; + vy0j = v[j][1] + dvSSA[j][1]; + vz0j = v[j][2] + dvSSA[j][2]; + + // Compute the velocity difference between atom i and atom j + delvx = vx0i - vx0j; + delvy = vy0i - vy0j; + delvz = vz0i - vz0j; + + dot = (delx*delvx + dely*delvy + delz*delvz); + // wr = double(1.0) - r/pairDPD->cut[itype][jtype]; + wr = double(1.0) - r/cut; + wd = wr*wr; + + if(pairDPDE){ + // Compute the current temperature + theta_ij = double(0.5)*(double(1.0)/dpdTheta[i] + double(1.0)/dpdTheta[j]); + theta_ij = double(1.0)/theta_ij; + sigma_ij = pairDPDE->sigma[itype][jtype]; + randnum = pairDPDE->random->gaussian(); + } else { + theta_ij = pairDPD->temperature; + sigma_ij = pairDPD->sigma[itype][jtype]; + randnum = pairDPD->random->gaussian(); + } + + gamma_ij = sigma_ij*sigma_ij / (2.0*force->boltz*theta_ij); + randPair = sigma_ij*wr*randnum*dtsqrt; + + factor_dpd = -dt*gamma_ij*wd*dot*rinv; + factor_dpd += randPair; + factor_dpd *= double(0.5); + + // Compute momentum change between t and t+dt + dpx = factor_dpd*delx*rinv; + dpy = factor_dpd*dely*rinv; + dpz = factor_dpd*delz*rinv; + + if (rmass) { + mass_i = rmass[i]; + mass_j = rmass[j]; + } else { + mass_i = mass[itype]; + mass_j = mass[jtype]; + } + massinv_i = double(1.0) / mass_i; + massinv_j = double(1.0) / mass_j; + + // Update the delta velocity on i + dvSSA[i][0] += dpx*force->ftm2v*massinv_i; + dvSSA[i][1] += dpy*force->ftm2v*massinv_i; + dvSSA[i][2] += dpz*force->ftm2v*massinv_i; + + if (newton_pair || j < nlocal) { + // Update the delta velocity on j + dvSSA[j][0] -= dpx*force->ftm2v*massinv_j; + dvSSA[j][1] -= dpy*force->ftm2v*massinv_j; + dvSSA[j][2] -= dpz*force->ftm2v*massinv_j; + } + + //ii. Compute the velocity diff + delvx = v[i][0] + dvSSA[i][0] - v[j][0] - dvSSA[j][0]; + delvy = v[i][1] + dvSSA[i][1] - v[j][1] - dvSSA[j][1]; + delvz = v[i][2] + dvSSA[i][2] - v[j][2] - dvSSA[j][2]; + + dot = delx*delvx + dely*delvy + delz*delvz; + + //iii. Compute dpi again + mu_ij = massinv_i + massinv_j; + denom = double(1.0) + double(0.5)*mu_ij*gamma_ij*wd*dt*force->ftm2v; + factor_dpd = -double(0.5)*dt*gamma_ij*wd*force->ftm2v/denom; + factor_dpd1 = factor_dpd*(mu_ij*randPair); + factor_dpd1 += randPair; + factor_dpd1 *= double(0.5); + + // Compute the momentum change between t and t+dt + dpx = (factor_dpd*dot*rinv/force->ftm2v + factor_dpd1)*delx*rinv; + dpy = (factor_dpd*dot*rinv/force->ftm2v + factor_dpd1)*dely*rinv; + dpz = (factor_dpd*dot*rinv/force->ftm2v + factor_dpd1)*delz*rinv; + + //Update the velocity change on i + dvSSA[i][0] += dpx*force->ftm2v*massinv_i; + dvSSA[i][1] += dpy*force->ftm2v*massinv_i; + dvSSA[i][2] += dpz*force->ftm2v*massinv_i; + + if (newton_pair || j < nlocal) { + //Update the velocity change on j + dvSSA[j][0] -= dpx*force->ftm2v*massinv_j; + dvSSA[j][1] -= dpy*force->ftm2v*massinv_j; + dvSSA[j][2] -= dpz*force->ftm2v*massinv_j; + } + + if(pairDPDE){ + // Compute uCond + randnum = pairDPDE->random->gaussian(); + kappa_ij = pairDPDE->kappa[itype][jtype]; + alpha_ij = sqrt(2.0*force->boltz*kappa_ij); + randPair = alpha_ij*wr*randnum*dtsqrt; + + factor_dpd = kappa_ij*(double(1.0)/dpdTheta[i] - double(1.0)/dpdTheta[j])*wd*dt; + factor_dpd += randPair; + + duCond[i] += factor_dpd; + if (newton_pair || j < nlocal) { + duCond[j] -= factor_dpd; + } + + // Compute uMech + vxi = v[i][0] + dvSSA[i][0]; + vyi = v[i][1] + dvSSA[i][1]; + vzi = v[i][2] + dvSSA[i][2]; + + vxj = v[j][0] + dvSSA[j][0]; + vyj = v[j][1] + dvSSA[j][1]; + vzj = v[j][2] + dvSSA[j][2]; + + dot1 = vxi*vxi + vyi*vyi + vzi*vzi; + dot2 = vxj*vxj + vyj*vyj + vzj*vzj; + dot3 = vx0i*vx0i + vy0i*vy0i + vz0i*vz0i; + dot4 = vx0j*vx0j + vy0j*vy0j + vz0j*vz0j; + + dot1 = dot1*mass_i; + dot2 = dot2*mass_j; + dot3 = dot3*mass_i; + dot4 = dot4*mass_j; + + factor_dpd = double(0.25)*(dot1+dot2-dot3-dot4)/force->ftm2v; + duMech[i] -= factor_dpd; + if (newton_pair || j < nlocal) { + duMech[j] -= factor_dpd; + } + } + } + } + } + + // Communicate the ghost delta velocities to the locally owned atoms + comm->reverse_comm_fix(this); + + // Zero the dv + for (ii = 0; ii < nlocal; ii++) { + // Shardlow update + v[ii][0] += dvSSA[ii][0]; + v[ii][1] += dvSSA[ii][1]; + v[ii][2] += dvSSA[ii][2]; + dvSSA[ii][0] = double(0.0); + dvSSA[ii][1] = double(0.0); + dvSSA[ii][2] = double(0.0); + if(pairDPDE){ + uCond[ii] += duCond[ii]; + uMech[ii] += duMech[ii]; + duCond[ii] = double(0.0); + duMech[ii] = double(0.0); + } + } + + // Communicate the updated momenta and velocities to all nodes + comm->forward_comm_fix(this); + + } //End Loop over all directions For idir = Top, Top-Right, Right, Bottom-Right, Back + + for (ii = 0; ii < nall; ii++) { + delete dvSSA[ii]; + } + delete [] dvSSA; +} + +/* ---------------------------------------------------------------------- + * assign owned and ghost atoms their ssa active interaction region numbers +------------------------------------------------------------------------- */ + +void FixShardlow::setup_pre_neighbor() +{ + neighbor->assign_ssa_airnums(); +} + +void FixShardlow::pre_neighbor() +{ + neighbor->assign_ssa_airnums(); +} + +/* ---------------------------------------------------------------------- */ + +int FixShardlow::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +{ + int ii,jj,m; + double **v = atom->v; + double *duCond = atom->duCond; + double *duMech = atom->duMech; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + + m = 0; + for (ii = 0; ii < n; ii++) { + jj = list[ii]; + buf[m++] = dvSSA[jj][0]; + buf[m++] = dvSSA[jj][1]; + buf[m++] = dvSSA[jj][2]; + buf[m++] = v[jj][0]; + buf[m++] = v[jj][1]; + buf[m++] = v[jj][2]; + if(pairDPDE){ + buf[m++] = duCond[jj]; + buf[m++] = duMech[jj]; + buf[m++] = uCond[jj]; + buf[m++] = uMech[jj]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixShardlow::unpack_forward_comm(int n, int first, double *buf) +{ + int ii,m,last; + double **v = atom->v; + double *duCond = atom->duCond; + double *duMech = atom->duMech; + double *uCond = atom->uCond; + double *uMech = atom->uMech; + + m = 0; + last = first + n ; + for (ii = first; ii < last; ii++) { + dvSSA[ii][0] = buf[m++]; + dvSSA[ii][1] = buf[m++]; + dvSSA[ii][2] = buf[m++]; + v[ii][0] = buf[m++]; + v[ii][1] = buf[m++]; + v[ii][2] = buf[m++]; + if(pairDPDE){ + duCond[ii] = buf[m++]; + duMech[ii] = buf[m++]; + uCond[ii] = buf[m++]; + uMech[ii] = buf[m++]; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int FixShardlow::pack_reverse_comm(int n, int first, double *buf) +{ + int i,m,last; + double *duCond = atom->duCond; + double *duMech = atom->duMech; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = dvSSA[i][0]; + buf[m++] = dvSSA[i][1]; + buf[m++] = dvSSA[i][2]; + if(pairDPDE){ + buf[m++] = duCond[i]; + buf[m++] = duMech[i]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixShardlow::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,m; + double *duCond = atom->duCond; + double *duMech = atom->duMech; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + + dvSSA[j][0] += buf[m++]; + dvSSA[j][1] += buf[m++]; + dvSSA[j][2] += buf[m++]; + if(pairDPDE){ + duCond[j] += buf[m++]; + duMech[j] += buf[m++]; + } + } +} diff --git a/src/USER-DPD/fix_shardlow.h b/src/USER-DPD/fix_shardlow.h new file mode 100644 index 0000000000..6c25fd86e2 --- /dev/null +++ b/src/USER-DPD/fix_shardlow.h @@ -0,0 +1,115 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: + James Larentzos and Timothy I. Mattox (Engility Corporation) + + Martin Lisal (Institute of Chemical Process Fundamentals + of the Czech Academy of Sciences and J. E. Purkinje University) + + John Brennan, Joshua Moore and William Mattson (Army Research Lab) + + Please cite the related publications: + J. P. Larentzos, J. K. Brennan, J. D. Moore, M. Lisal, W. D. Mattson, + "Parallel implementation of isothermal and isoenergetic Dissipative + Particle Dynamics using Shardlow-like splitting algorithms", + Computer Physics Communications, 2014, 185, pp 1987--1998. + + M. Lisal, J. K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics + at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using + Shardlow-like splitting algorithms", Journal of Chemical Physics, 2011, + 135, 204105. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(shardlow,FixShardlow) + +#else + +#ifndef LMP_FIX_SHARDLOW_H +#define LMP_FIX_SHARDLOW_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixShardlow : public Fix { + public: + FixShardlow(class LAMMPS *, int, char **); + virtual ~FixShardlow() {} + int setmask(); + virtual void init_list(int,class NeighList *); + virtual void setup(int); + virtual void setup_pre_force(int); + virtual void initial_integrate(int); + + void setup_pre_neighbor(); + void pre_neighbor(); + + protected: + int pack_reverse_comm(int, int, double *); + void unpack_reverse_comm(int, int *, double *); + int pack_forward_comm(int , int *, double *, int, int *); + void unpack_forward_comm(int , int , double *); + + class PairDPDfdt *pairDPD; + class PairDPDfdtEnergy *pairDPDE; + double **dvSSA; + + private: + class NeighList *list; + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Must use dpd/fdt pair_style with fix shardlow + +Self-explanatory. + +E: Must use pair_style dpd/fdt or dpd/fdt/energy with fix shardlow + +E: A deterministic integrator must be specified after fix shardlow in input +file (e.g. fix nve or fix nph). + +Self-explanatory. + +E: Cannot use constant temperature integration routines with DPD + +Self-explanatory. Must use deterministic integrators such as nve or nph + +E: Fix shardlow does not yet support triclinic geometries + +Self-explanatory. + +E: Shardlow algorithm requires sub-domain length > 2*(rcut+skin). Either +reduce the number of processors requested, or change the cutoff/skin + +The Shardlow splitting algorithm requires the size of the sub-domain lengths +to be are larger than twice the cutoff+skin. Generally, the domain decomposition +is dependant on the number of processors requested. + +*/ diff --git a/src/USER-DPD/pair_dpd_conservative.cpp b/src/USER-DPD/pair_dpd_conservative.cpp new file mode 100644 index 0000000000..8707023110 --- /dev/null +++ b/src/USER-DPD/pair_dpd_conservative.cpp @@ -0,0 +1,320 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_dpd_conservative.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "update.h" +#include "fix.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "memory.h" +#include "modify.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDconservative::PairDPDconservative(LAMMPS *lmp) : Pair(lmp) +{ +} + +/* ---------------------------------------------------------------------- */ + +PairDPDconservative::~PairDPDconservative() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(a0); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDconservative::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r,rinv,wd,wr,factor_dpd; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + wr = 1.0 - r/cut[itype][jtype]; + wd = wr*wr; + + // conservative force = a0 * wr + fpair = a0[itype][jtype]*wr; + fpair *= factor_dpd*rinv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd; + evdwl *= factor_dpd; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairDPDconservative::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(a0,n+1,n+1,"pair:a0"); + +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDconservative::settings(int narg, char **arg) +{ + // process keywords + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + cut_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDconservative::coeff(int narg, char **arg) +{ + if (narg < 3 || narg > 4) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double a0_one = force->numeric(FLERR,arg[2]); + double cut_one = cut_global; + + if (narg == 4) cut_one = force->numeric(FLERR,arg[3]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairDPDconservative::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + cut[j][i] = cut[i][j]; + a0[j][i] = a0[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDconservative::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a0[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDconservative::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&a0[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDconservative::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDconservative::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_global,sizeof(double),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDconservative::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_dpd, double &fforce) +{ + double r,rinv,wr,wd,phi; + + r = sqrt(rsq); + if (r < EPSILON) { + fforce = 0.0; + return 0.0; + } + + rinv = 1.0/r; + wr = 1.0 - r/cut[itype][jtype]; + wd = wr*wr; + fforce = a0[itype][jtype]*wr * factor_dpd*rinv; + + phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd; + return factor_dpd*phi; +} + diff --git a/src/USER-DPD/pair_dpd_conservative.h b/src/USER-DPD/pair_dpd_conservative.h new file mode 100644 index 0000000000..15402be6d8 --- /dev/null +++ b/src/USER-DPD/pair_dpd_conservative.h @@ -0,0 +1,77 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(dpd/conservative,PairDPDconservative) + +#else + +#ifndef LMP_PAIR_DPD_CONSERVATIVE_H +#define LMP_PAIR_DPD_CONSERVATIVE_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairDPDconservative : public Pair { + public: + PairDPDconservative(class LAMMPS *); + virtual ~PairDPDconservative(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + double single(int, int, int, int, double, double, double, double &); + + double **cut; + double **a0; + + protected: + double cut_global; + + void allocate(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp new file mode 100644 index 0000000000..e03d913f9f --- /dev/null +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -0,0 +1,376 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "update.h" +#include "fix.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "random_mars.h" +#include "memory.h" +#include "modify.h" +#include "pair_dpd_fdt.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDfdt::PairDPDfdt(LAMMPS *lmp) : Pair(lmp) +{ + random = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDfdt::~PairDPDfdt() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(a0); + memory->destroy(sigma); + } + + + if (random) delete random; +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDfdt::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r,rinv,wd,wr,factor_dpd; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + wr = 1.0 - r/cut[itype][jtype]; + wd = wr*wr; + + // conservative force = a0 * wr + fpair = a0[itype][jtype]*wr; + fpair *= factor_dpd*rinv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd; + evdwl *= factor_dpd; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairDPDfdt::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(a0,n+1,n+1,"pair:a0"); + memory->create(sigma,n+1,n+1,"pair:sigma"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDfdt::settings(int narg, char **arg) +{ + // process keywords + if (narg != 3) error->all(FLERR,"Illegal pair_style command"); + + temperature = force->numeric(FLERR,arg[0]); + cut_global = force->numeric(FLERR,arg[1]); + seed = force->inumeric(FLERR,arg[2]); + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0) error->all(FLERR,"Illegal pair_style command"); + delete random; + random = new RanMars(lmp,seed + comm->me); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDfdt::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double a0_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double cut_one = cut_global; + double kappa_one; + + if (narg == 5) cut_one = force->numeric(FLERR,arg[4]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + sigma[i][j] = sigma_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairDPDfdt::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair dpd/fdt requires ghost atoms store velocity"); + + // if newton off, forces between atoms ij will be double computed + // using different random numbers + + if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, + "Pair dpd/fdt requires newton pair on"); + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->ssa = 0; + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"shardlow") == 0) + neighbor->requests[irequest]->ssa = 1; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairDPDfdt::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + cut[j][i] = cut[i][j]; + a0[j][i] = a0[i][j]; + sigma[j][i] = sigma[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDfdt::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a0[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDfdt::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&a0[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDfdt::write_restart_settings(FILE *fp) +{ + fwrite(&temperature,sizeof(double),1,fp); + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDfdt::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&temperature,sizeof(double),1,fp); + fread(&cut_global,sizeof(double),1,fp); + fread(&seed,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDfdt::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_dpd, double &fforce) +{ + double r,rinv,wr,wd,phi; + + r = sqrt(rsq); + if (r < EPSILON) { + fforce = 0.0; + return 0.0; + } + + rinv = 1.0/r; + wr = 1.0 - r/cut[itype][jtype]; + wd = wr*wr; + fforce = a0[itype][jtype]*wr * factor_dpd*rinv; + + phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd; + return factor_dpd*phi; +} + diff --git a/src/USER-DPD/pair_dpd_fdt.h b/src/USER-DPD/pair_dpd_fdt.h new file mode 100644 index 0000000000..8384e3b682 --- /dev/null +++ b/src/USER-DPD/pair_dpd_fdt.h @@ -0,0 +1,91 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(dpd/fdt,PairDPDfdt) + +#else + +#ifndef LMP_PAIR_DPD_FDT_H +#define LMP_PAIR_DPD_FDT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairDPDfdt : public Pair { + public: + PairDPDfdt(class LAMMPS *); + virtual ~PairDPDfdt(); + void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + void init_style(); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + double single(int, int, int, int, double, double, double, double &); + + double **cut; + double **a0; + double **sigma; + double temperature; + + class RanMars *random; + + protected: + double cut_global; + int seed; + + void allocate(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair dpd/fdt requires ghost atoms store velocity + +Use the communicate vel yes command to enable this. + +E: Pair dpd/fdt requires newton pair on + +Self-explanatory. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp new file mode 100644 index 0000000000..8d71479f0b --- /dev/null +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -0,0 +1,382 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "update.h" +#include "fix.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "random_mars.h" +#include "memory.h" +#include "modify.h" +#include "pair_dpd_fdt_energy.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-10 + +/* ---------------------------------------------------------------------- */ + +PairDPDfdtEnergy::PairDPDfdtEnergy(LAMMPS *lmp) : Pair(lmp) +{ + random = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairDPDfdtEnergy::~PairDPDfdtEnergy() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(a0); + memory->destroy(sigma); + memory->destroy(kappa); + } + + + if (random) delete random; +} + +/* ---------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r,rinv,wd,wr,factor_dpd; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_dpd = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r = sqrt(rsq); + if (r < EPSILON) continue; // r can be 0.0 in DPD systems + rinv = 1.0/r; + wr = 1.0 - r/cut[itype][jtype]; + wd = wr*wr; + + // conservative force = a0 * wr + fpair = a0[itype][jtype]*wr; + fpair *= factor_dpd*rinv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + // unshifted eng of conservative term: + // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]); + // eng shifted to 0.0 at cutoff + evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd; + evdwl *= factor_dpd; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(a0,n+1,n+1,"pair:a0"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(kappa,n+1,n+1,"pair:kappa"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::settings(int narg, char **arg) +{ + // process keywords + if (narg != 2) error->all(FLERR,"Illegal pair_style command"); + + cut_global = force->numeric(FLERR,arg[0]); + seed = force->inumeric(FLERR,arg[1]); + if (atom->dpd_flag != 1) + error->all(FLERR,"pair_style dpd/fdt/energy requires atom_style with internal temperature and energies (e.g. dpd)"); + + // initialize Marsaglia RNG with processor-unique seed + + if (seed <= 0) error->all(FLERR,"Illegal pair_style command"); + delete random; + random = new RanMars(lmp,seed + comm->me); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double a0_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double cut_one = cut_global; + double kappa_one; + + kappa_one = force->numeric(FLERR,arg[4]); + if (narg == 6) cut_one = force->numeric(FLERR,arg[5]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + a0[i][j] = a0_one; + sigma[i][j] = sigma_one; + kappa[i][j] = kappa_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::init_style() +{ + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair dpd/fdt/energy requires ghost atoms store velocity"); + + // if newton off, forces between atoms ij will be double computed + // using different random numbers + + if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR, + "Pair dpd/fdt/energy requires newton pair on"); + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->ssa = 0; + for (int i = 0; i < modify->nfix; i++) + if (strcmp(modify->fix[i]->style,"shardlow") == 0) + neighbor->requests[irequest]->ssa = 1; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairDPDfdtEnergy::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + cut[j][i] = cut[i][j]; + a0[j][i] = a0[i][j]; + sigma[j][i] = sigma[i][j]; + kappa[j][i] = kappa[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&a0[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&kappa[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&a0[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&kappa[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&kappa[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::write_restart_settings(FILE *fp) +{ + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&seed,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairDPDfdtEnergy::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_global,sizeof(double),1,fp); + fread(&seed,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&seed,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + + // initialize Marsaglia RNG with processor-unique seed + // same seed that pair_style command initially specified + + if (random) delete random; + random = new RanMars(lmp,seed + comm->me); +} + +/* ---------------------------------------------------------------------- */ + +double PairDPDfdtEnergy::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_dpd, double &fforce) +{ + double r,rinv,wr,wd,phi; + + r = sqrt(rsq); + if (r < EPSILON) { + fforce = 0.0; + return 0.0; + } + + rinv = 1.0/r; + wr = 1.0 - r/cut[itype][jtype]; + wd = wr*wr; + fforce = a0[itype][jtype]*wr * factor_dpd*rinv; + + phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd; + return factor_dpd*phi; +} + diff --git a/src/USER-DPD/pair_dpd_fdt_energy.h b/src/USER-DPD/pair_dpd_fdt_energy.h new file mode 100644 index 0000000000..4a68383398 --- /dev/null +++ b/src/USER-DPD/pair_dpd_fdt_energy.h @@ -0,0 +1,90 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: James Larentzos (Engility Corporation) +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(dpd/fdt/energy,PairDPDfdtEnergy) + +#else + +#ifndef LMP_PAIR_DPD_FDT_ENERGY_H +#define LMP_PAIR_DPD_FDT_ENERGY_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairDPDfdtEnergy : public Pair { + public: + PairDPDfdtEnergy(class LAMMPS *); + virtual ~PairDPDfdtEnergy(); + virtual void compute(int, int); + virtual void settings(int, char **); + virtual void coeff(int, char **); + void init_style(); + double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + double single(int, int, int, int, double, double, double, double &); + + double **cut; + double **a0; + double **sigma,**kappa; + + class RanMars *random; + + protected: + double cut_global; + int seed; + + void allocate(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair dpd/fdt/energy requires ghost atoms store velocity + +Use the communicate vel yes command to enable this. + +E: Pair dpd/fdt/energy requires newton pair on + +Self-explanatory. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ diff --git a/src/neigh_shardlow.cpp b/src/neigh_shardlow.cpp new file mode 100644 index 0000000000..0163e6eb4d --- /dev/null +++ b/src/neigh_shardlow.cpp @@ -0,0 +1,471 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: + James Larentzos and Timothy I. Mattox (Engility Corporation) +------------------------------------------------------------------------- */ + +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "domain.h" +#include "group.h" +#include "memory.h" +#include "error.h" +#include "update.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- + convert atom coords into the ssa active interaction region number +------------------------------------------------------------------------- */ + +int Neighbor::coord2ssa_airnum(double *x) +{ + int ix, iy, iz; + + ix = iy = iz = 0; + if (x[2] < domain->sublo[2]) iz = -1; + if (x[2] > domain->subhi[2]) iz = 1; + if (x[1] < domain->sublo[1]) iy = -1; + if (x[1] > domain->subhi[1]) iy = 1; + if (x[0] < domain->sublo[0]) ix = -1; + if (x[0] > domain->subhi[0]) ix = 1; + + if(iz < 0) return 0; + + if(iz == 0){ + if( iy<0 ) return 0; // bottom left/middle/right + if( (iy==0) && (ix<0) ) return 0; // left atoms + if( (iy==0) && (ix==0) ) return 1; // Locally owned atoms + if( (iy==0) && (ix>0) ) return 3; // Right atoms + if( (iy>0) && (ix==0) ) return 2; // Top-middle atoms + if( (iy>0) && (ix!=0) ) return 4; // Top-right and top-left atoms + } else if(iz > 0) { + if((ix==0) && (iy==0)) return 5; // Back atoms + if((ix==0) && (iy!=0)) return 6; // Top-back and bottom-back atoms + if((ix!=0) && (iy==0)) return 7; // Left-back and right-back atoms + if((ix!=0) && (iy!=0)) return 8; // Back corner atoms + } + + return 0; +} + +/* ---------------------------------------------------------------------- + * assign owned and ghost atoms their ssa active interaction region numbers + * Called in the pre_neighbor and setup_pre_neighbor fix stages +------------------------------------------------------------------------- */ + +void Neighbor::assign_ssa_airnums() +{ + int i,ibin; + double **x = atom->x; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + if (nall > len_ssa_airnum) { + len_ssa_airnum = nall; + memory->destroy(ssa_airnum); + memory->create(ssa_airnum,len_ssa_airnum,"ssa_airnum"); + } + + // bin in reverse order so linked list will be in forward order + + if (includegroup) { + int bitmask = group->bitmask[includegroup]; + for (i = nall-1; i >= nlocal; i--) { + if (mask[i] & bitmask) { + ibin = coord2ssa_airnum(x[i]); + } else { + ibin = 0; + } + ssa_airnum[i] = ibin; + } + // All the local excluded atoms are in the zero airnum + ibin = 0; + for (i = atom->nlocal-1; i >= atom->nfirst; i--) { + ssa_airnum[i] = ibin; + } + } else { + for (i = nall-1; i >= nlocal; i--) { + ibin = coord2ssa_airnum(x[i]); + ssa_airnum[i] = ibin; + } + } + + // All the local included atoms are in the same airnum (#1) + if (i >= 0) { + ibin = coord2ssa_airnum(x[i]); + do { + ssa_airnum[i] = ibin; + } while (--i >= 0); + } +} + +/* ---------------------------------------------------------------------- + routines to create a stencil = list of bin offsets + stencil = bins whose closest corner to central bin is within cutoff + sx,sy,sz = bin bounds = furthest the stencil could possibly extend + 3d creates xyz stencil, 2d creates xy stencil + for half list with newton on: + stencil is bins to the "upper right" of central bin + stencil does not include self +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- */ + +void Neighbor::stencil_half_bin_2d_ssa(NeighList *list, + int sx, int sy, int sz) +{ + int i,j; + int *stencil = list->stencil; + int nstencil = 0; + + for (j = 0; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (j > 0 || (j == 0 && i > 0)) + if (bin_distance(i,j,0) < cutneighmaxsq) + stencil[nstencil++] = j*mbinx + i; + + list->nstencil = nstencil; + + // Now include additional bins for AIR ghosts only + for (j = -sy; j <= 0; j++) + for (i = -sx; i <= sx; i++) { + if (j == 0 && i > 0) continue; + if (bin_distance(i,j,0) < cutneighmaxsq) + stencil[nstencil++] = j*mbinx + i; + } + + while (nstencil < list->maxstencil) { + stencil[nstencil++] = INT_MAX; + } +} + +/* ---------------------------------------------------------------------- */ + +void Neighbor::stencil_half_bin_3d_ssa(NeighList *list, + int sx, int sy, int sz) +{ + int i,j,k; + int *stencil = list->stencil; + int nstencil = 0; + + for (k = 0; k <= sz; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (k > 0 || j > 0 || (j == 0 && i > 0)) + if (bin_distance(i,j,k) < cutneighmaxsq) + stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; + + list->nstencil = nstencil; + + // Now include additional bins for AIR ghosts only + for (k = -sz; k < 0; k++) + for (j = -sy; j <= sy; j++) + for (i = -sx; i <= sx; i++) + if (bin_distance(i,j,k) < cutneighmaxsq) + stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; + k = 0; // skip already included bins at k == 0 + for (j = -sy; j <= 0; j++) + for (i = -sx; i <= sx; i++) { + if (j == 0 && i > 0) continue; + if (bin_distance(i,j,k) < cutneighmaxsq) + stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i; + } + + while (nstencil < list->maxstencil) { + stencil[nstencil++] = INT_MAX; + } +} + +/* ---------------------------------------------------------------------- + build half list from full list for use by Shardlow Spliting Algorithm + pair stored once if i,j are both owned and i < j + if j is ghost, only store if j coords are "above and to the right" of i + works if full list is a skip list +------------------------------------------------------------------------- */ + +void Neighbor::half_from_full_newton_ssa(NeighList *list) +{ + int i,j,ii,jj,n,jnum,joriginal; + int *neighptr,*jlist; + + int nlocal = atom->nlocal; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + MyPage *ipage = list->ipage; + + int *ilist_full = list->listfull->ilist; + int *numneigh_full = list->listfull->numneigh; + int **firstneigh_full = list->listfull->firstneigh; + int inum_full = list->listfull->inum; + + int inum = 0; + ipage->reset(); + + // loop over parent full list + + for (ii = 0; ii < inum_full; ii++) { + n = 0; + neighptr = ipage->vget(); + + i = ilist_full[ii]; + + // loop over full neighbor list + + jlist = firstneigh_full[i]; + jnum = numneigh_full[i]; + + for (jj = 0; jj < jnum; jj++) { + joriginal = jlist[jj]; + j = joriginal & NEIGHMASK; + if (j < nlocal) { + if (i > j) continue; + } else { + if (ssa_airnum[j] <= 0) continue; + } + neighptr[n++] = joriginal; + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} + +/* ---------------------------------------------------------------------- + for Shardlow Spliting Algorithm: + binned neighbor list construction with full Newton's 3rd law + each owned atom i checks its own bin and other bins in Newton stencil + every pair stored exactly once by some processor +------------------------------------------------------------------------- */ + +void Neighbor::half_bin_newton_ssa(NeighList *list) +{ + int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate; + tagint tagprev; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *neighptr; + + double **x = atom->x; + int *type = atom->type; + int *mask = atom->mask; + tagint *tag = atom->tag; + tagint *molecule = atom->molecule; + tagint **special = atom->special; + int **nspecial = atom->nspecial; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + int *molindex = atom->molindex; + int *molatom = atom->molatom; + Molecule **onemols = atom->avec->onemols; + int molecular = atom->molecular; + if (molecular == 2) moltemplate = 1; + else moltemplate = 0; + + int *ilist = list->ilist; + int *numneigh = list->numneigh; + int **firstneigh = list->firstneigh; + int nstencil = list->nstencil; + int maxstencil = list->maxstencil; + int *stencil = list->stencil; + MyPage *ipage = list->ipage; + + int inum = 0; + +/* ---------------------------------------------------------------------- + bin owned and ghost atoms for use by Shardlow Splitting Algorithm + exclude ghost atoms that are not in the Active Interaction Regions (AIR) +------------------------------------------------------------------------- */ + + if (mbins > maxhead_ssa) { + maxhead_ssa = mbins; + memory->destroy(gbinhead_ssa); + memory->destroy(binhead_ssa); + memory->create(binhead_ssa,maxhead_ssa,"binhead_ssa"); + memory->create(gbinhead_ssa,maxhead_ssa,"gbinhead_ssa"); + } + for (i = 0; i < mbins; i++) { + gbinhead_ssa[i] = -1; + binhead_ssa[i] = -1; + } + + if (maxbin > maxbin_ssa) { + maxbin_ssa = maxbin; + memory->destroy(bins_ssa); + memory->create(bins_ssa,maxbin_ssa,"bins_ssa"); + } + + // bin in reverse order so linked list will be in forward order + + if (includegroup) { + int bitmask = group->bitmask[includegroup]; + for (i = nall-1; i >= nlocal; i--) { + if (ssa_airnum[i] <= 0) continue; // skip ghost atoms not in AIR + if (mask[i] & bitmask) { + ibin = coord2bin(x[i]); + bins_ssa[i] = gbinhead_ssa[ibin]; + gbinhead_ssa[ibin] = i; + } + } + nlocal = atom->nfirst; // This is important for the code that follows! + } else { + for (i = nall-1; i >= nlocal; i--) { + if (ssa_airnum[i] <= 0) continue; // skip ghost atoms not in AIR + ibin = coord2bin(x[i]); + bins_ssa[i] = gbinhead_ssa[ibin]; + gbinhead_ssa[ibin] = i; + } + } + for (i = nlocal-1; i >= 0; i--) { + ibin = coord2bin(x[i]); + bins_ssa[i] = binhead_ssa[ibin]; + binhead_ssa[ibin] = i; + } + + ipage->reset(); + + // loop over owned atoms, storing half of the neighbors + + for (i = 0; i < nlocal; i++) { + n = 0; + neighptr = ipage->vget(); + + itype = type[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + if (moltemplate) { + imol = molindex[i]; + iatom = molatom[i]; + tagprev = tag[i] - iatom - 1; + } + + // loop over rest of local atoms in i's bin + // just store them, since j is beyond i in linked list + + for (j = bins_ssa[i]; j >= 0; j = bins_ssa[j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + + ibin = coord2bin(x[i]); + + // loop over all local atoms in other bins in "half" stencil + for (k = 0; k < nstencil; k++) { + for (j = binhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + // loop over AIR ghost atoms in all bins in "full" stencil + // Note: the non-AIR ghost atoms have already been filtered out + for (k = 0; k < maxstencil; k++) { + if (stencil[k] > mbins) break; /* Check if ghost stencil bins are exhausted */ + for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) { + + jtype = type[j]; + if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= cutneighsq[itype][jtype]) { + if (molecular) { + if (!moltemplate) + which = find_special(special[i],nspecial[i],tag[j]); + else if (imol >= 0) + which = find_special(onemols[imol]->special[iatom], + onemols[imol]->nspecial[iatom], + tag[j]-tagprev); + else which = 0; + if (which == 0) neighptr[n++] = j; + else if (domain->minimum_image_check(delx,dely,delz)) + neighptr[n++] = j; + else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); + } else neighptr[n++] = j; + } + } + } + + ilist[inum++] = i; + firstneigh[i] = neighptr; + numneigh[i] = n; + ipage->vgot(n); + if (ipage->status()) + error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); + } + + list->inum = inum; +} diff --git a/src/neighbor.cpp b/src/neighbor.cpp index db28f6d309..e9ee23e37f 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -162,7 +162,6 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp) improperlist = NULL; copymode = 0; - last_binning_timestep = -1; } /* ---------------------------------------------------------------------- */ @@ -2015,11 +2014,6 @@ void Neighbor::bin_atoms() { int i,ibin; - // NOTE: added for USER-DPD, why do we need this? - - //if (last_binning_timestep == update->ntimestep) return; - //last_binning_timestep = update->ntimestep; - for (i = 0; i < mbins; i++) binhead[i] = -1; // bin in reverse order so linked list will be in forward order diff --git a/src/neighbor.h b/src/neighbor.h index 8059e699bf..bb944b7a3b 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -71,7 +71,7 @@ class Neighbor : protected Pointers { int cluster_check; // 1 if check bond/angle/etc satisfies minimg - // USER-DPD package - better to make this private? + // USER-DPD package int *ssa_airnum; // AIR number of each atom for SSA in USER-DPD @@ -94,6 +94,10 @@ class Neighbor : protected Pointers { bigint memory_usage(); int exclude_setting(); + // USER-DPD package + + void assign_ssa_airnums(); // set ssa_airnum values + protected: int me,nprocs; @@ -121,7 +125,6 @@ class Neighbor : protected Pointers { int binatomflag; // bin atoms or not when build neigh list // turned off by build_one() - bigint last_binning_timestep; // last step neighbor binning was done int nbinx,nbiny,nbinz; // # of global bins int *bins; // ptr to next atom in each bin @@ -180,7 +183,12 @@ class Neighbor : protected Pointers { // USER-DPD package - int len_ssa_airnum; // length of ssa_airnum array + int len_ssa_airnum; // length of ssa_airnum array + int *bins_ssa; // ptr to next atom in each bin used by SSA + int maxbin_ssa; // size of bins array used by SSA + int *binhead_ssa; // ptr to 1st atom in each bin used by SSA + int *gbinhead_ssa; // ptr to 1st ghost atom in each bin used by SSA + int maxhead_ssa; // size of binhead array used by SSA // methods @@ -320,13 +328,12 @@ class Neighbor : protected Pointers { // SSA neighboring for USER-DPD - //int coord2ssa_airnum(double *); // map atom coord to an AIR number - //void assign_ssa_airnums(); // set ssa_airnum values + int coord2ssa_airnum(double *); // map atom coord to an AIR number - void half_bin_newton_ssa(NeighList *) {} - void half_from_full_newton_ssa(class NeighList *) {} - void stencil_half_bin_2d_ssa(class NeighList *, int, int, int) {} - void stencil_half_bin_3d_ssa(class NeighList *, int, int, int) {} + void half_bin_newton_ssa(NeighList *); + void half_from_full_newton_ssa(class NeighList *); + void stencil_half_bin_2d_ssa(class NeighList *, int, int, int); + void stencil_half_bin_3d_ssa(class NeighList *, int, int, int); // find_special: determine if atom j is in special list of atom i // if it is not, return 0 diff --git a/src/version.h b/src/version.h index 5e5f646117..09770e4b0a 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "29 Jan 2016" +#define LAMMPS_VERSION "3 Feb 2016"