diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 784deb3186..e83da43116 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -10,7 +10,7 @@ scripts, and pictures/movies (if available) that illustrate use of the package. The majority of packages can be included in a LAMMPS build with a -single setting (-D PGK\_NAME for CMake) or command ("make yes-name" for +single setting (-D PGK_NAME for CMake) or command ("make yes-name" for make). See the :doc:`Build package ` doc page for more info. A few packages may require additional steps; this is indicated in the descriptions below. The :doc:`Build extras ` doc @@ -60,7 +60,6 @@ page gives those details. * :ref:`SRD ` * :ref:`VORONOI ` - .. table_from_list:: :columns: 6 @@ -81,7 +80,7 @@ page gives those details. * :ref:`USER-LB ` * :ref:`USER-MANIFOLD ` * :ref:`USER-MEAMC ` - * :ref:`USER-MESO ` + * :ref:`USER-MESODPD ` * :ref:`USER-MESONT ` * :ref:`USER-MGPT ` * :ref:`USER-MISC ` @@ -107,10 +106,8 @@ page gives those details. * :ref:`USER-VTK ` * :ref:`USER-YAFF ` - ---------- - .. _PKG-ASPHERE: ASPHERE package @@ -127,17 +124,15 @@ particle models including ellipsoids, 2d lines, and 3d triangles. * :doc:`Howto spherical ` * :doc:`pair_style gayberne ` * :doc:`pair_style resquared ` -* `doc/PDF/pair\_gayberne\_extra.pdf `_ -* `doc/PDF/pair\_resquared\_extra.pdf `_ +* `doc/PDF/pair_gayberne_extra.pdf `_ +* `doc/PDF/pair_resquared_extra.pdf `_ * examples/ASPHERE * examples/ellipse -* http://lammps.sandia.gov/movies.html#line -* http://lammps.sandia.gov/movies.html#tri - +* https://lammps.sandia.gov/movies.html#line +* https://lammps.sandia.gov/movies.html#tri ---------- - .. _PKG-BODY: BODY package @@ -153,16 +148,14 @@ overview. **Supporting info:** * src/BODY filenames -> commands -* :doc:`Howto\_body ` +* :doc:`Howto_body ` * :doc:`atom_style body ` * :doc:`fix nve/body ` * :doc:`pair_style body/nparticle ` * examples/body - ---------- - .. _PKG-CLASS2: CLASS2 package @@ -182,10 +175,8 @@ CLASS2 molecular force field. * :doc:`improper_style class2 ` * :doc:`pair_style lj/class2 ` - ---------- - .. _PKG-COLLOID: COLLOID package @@ -214,10 +205,8 @@ Higdon's group at UIUC. * examples/colloid * examples/srd - ---------- - .. _PKG-COMPRESS: COMPRESS package @@ -247,10 +236,8 @@ This package has :ref:`specific installation instructions ` on the :do * :doc:`dump custom/gz ` * :doc:`dump xyz/gz ` - ---------- - .. _PKG-CORESHELL: CORESHELL package @@ -277,10 +264,8 @@ this package. * :doc:`pair_style lj/cut/coul/long/cs ` * examples/coreshell - ---------- - .. _PKG-DIPOLE: DIPOLE package @@ -300,10 +285,8 @@ short-range or long-range interactions. * :doc:`pair_style lj/long/dipole/long ` * examples/dipole - ---------- - .. _PKG-GPU: GPU package @@ -340,12 +323,10 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * :doc:`package gpu ` * :doc:`Commands ` pages (:doc:`pair `, :doc:`kspace `) for styles followed by (g) -* `Benchmarks page `_ of web site - +* `Benchmarks page `_ of web site ---------- - .. _PKG-GRANULAR: GRANULAR package @@ -368,16 +349,14 @@ potentials. * examples/granregion * examples/pour * bench/in.chute -* http://lammps.sandia.gov/pictures.html#jamming -* http://lammps.sandia.gov/movies.html#hopper -* http://lammps.sandia.gov/movies.html#dem -* http://lammps.sandia.gov/movies.html#brazil -* http://lammps.sandia.gov/movies.html#granregion - +* https://lammps.sandia.gov/pictures.html#jamming +* https://lammps.sandia.gov/movies.html#hopper +* https://lammps.sandia.gov/movies.html#dem +* https://lammps.sandia.gov/movies.html#brazil +* https://lammps.sandia.gov/movies.html#granregion ---------- - .. _PKG-KIM: KIM package @@ -389,7 +368,7 @@ This package contains a set of commands that serve as a wrapper on the `Open Knowledgebase of Interatomic Models (OpenKIM) `_ repository of interatomic models (IMs) enabling compatible ones to be used in LAMMPS simulations. -This includes :doc:`kim_init and kim\_interactions ` +This includes :doc:`kim_init and kim_interactions ` commands to select, initialize and instantiate the IM, and a :doc:`kim_query ` command to perform web queries for material property predictions of OpenKIM IMs. @@ -399,7 +378,7 @@ is provided by the :doc:`pair_style kim ` command. .. note:: - The command *pair\_style kim* is called by *kim\_interactions* and + The command *pair_style kim* is called by *kim_interactions* and is not recommended to be directly used in input scripts. To use this package you must have the KIM API library available on your @@ -414,7 +393,7 @@ The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota) and is funded by the `National Science Foundation `_. **Authors:** Ryan Elliott (U Minnesota) is the main developer for the KIM -API and the *pair\_style kim* command. Axel Kohlmeyer (Temple U) and +API and the *pair_style kim* command. Axel Kohlmeyer (Temple U) and Ellad Tadmor (U Minnesota) contributed to the :doc:`kim_commands ` interface in close collaboration with Ryan Elliott. @@ -431,10 +410,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * lib/kim/README * examples/kim - ---------- - .. _PKG-KOKKOS: KOKKOS package @@ -485,12 +462,10 @@ This package has :ref:`specific installation instructions ` on the :doc: * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (k) -* `Benchmarks page `_ of web site - +* `Benchmarks page `_ of web site ---------- - .. _PKG-KSPACE: KSPACE package @@ -524,10 +499,8 @@ different FFT options for your LAMPMS build. * examples/peptide * bench/in.rhodo - ---------- - .. _PKG-LATTE: LATTE package @@ -545,8 +518,6 @@ description is given with the :doc:`fix latte ` command. .. _latte-home: https://github.com/lanl/LATTE - - **Authors:** Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE itself is developed at Los Alamos National Laboratory by Marc Cawkwell, Anders Niklasson, and Christian Negre. @@ -564,10 +535,8 @@ This package has :ref:`specific installation instructions ` on the :doc:` * examples/latte * `LAMMPS-LATTE tutorial `_ - ---------- - .. _PKG-MANYBODY: MANYBODY package @@ -590,10 +559,8 @@ A variety of many-body and bond-order potentials. These include * examples/vashishta * bench/in.eam - ---------- - .. _PKG-MC: MC package @@ -615,12 +582,10 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`fix bond/swap ` * :doc:`fix gcmc ` * :doc:`pair_style dsmc ` -* http://lammps.sandia.gov/movies.html#gcmc - +* https://lammps.sandia.gov/movies.html#gcmc ---------- - .. _PKG-MESSAGE: MESSAGE package @@ -645,10 +610,8 @@ This package has :ref:`specific installation instructions ` on the :doc * :doc:`server mc ` * examples/message - ---------- - .. _PKG-MISC: MISC package @@ -676,13 +639,11 @@ listing, "ls src/MISC", to see the list of commands. * :doc:`fix viscosity ` * examples/KAPPA * examples/VISCOSITY -* http://lammps.sandia.gov/pictures.html#ttm -* http://lammps.sandia.gov/movies.html#evaporation - +* https://lammps.sandia.gov/pictures.html#ttm +* https://lammps.sandia.gov/movies.html#evaporation ---------- - .. _PKG-MOLECULE: MOLECULE package @@ -713,10 +674,8 @@ force fields, and a TIP4P water model. * bench/in.chain * bench/in.rhodo - ---------- - .. _PKG-MPIIO: MPIIO package @@ -737,10 +696,8 @@ written and read in parallel. * :doc:`write_restart ` * :doc:`read_restart ` - ---------- - .. _PKG-mscg: MSCG package @@ -753,8 +710,6 @@ Multi-Scale Coarse-Graining (MSCG) model using the open-source `MS-CG library ` on the :doc:`B * lib/mscg/README * examples/mscg - ---------- - .. _PKG-OPT: OPT package @@ -794,7 +747,7 @@ invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switch have styles optimized for CPU performance. **Authors:** James Fischer (High Performance Technologies), David Richie, -and Vincent Natoli (Stone Ridge Technolgy). +and Vincent Natoli (Stone Ridge Technology). **Install:** @@ -807,12 +760,10 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * :doc:`Speed opt ` * :doc:`Section 2.6 -sf opt ` * Search the :doc:`pair style ` page for styles followed by (t) -* `Benchmarks page `_ of web site - +* `Benchmarks page `_ of web site ---------- - .. _PKG-PERI: PERI package @@ -832,20 +783,18 @@ Foster (UTSA). **Supporting info:** * src/PERI: filenames -> commands -* `doc/PDF/PDLammps\_overview.pdf `_ -* `doc/PDF/PDLammps\_EPS.pdf `_ -* `doc/PDF/PDLammps\_VES.pdf `_ +* `doc/PDF/PDLammps_overview.pdf `_ +* `doc/PDF/PDLammps_EPS.pdf `_ +* `doc/PDF/PDLammps_VES.pdf `_ * :doc:`atom_style peri ` * :doc:`pair_style peri/\* ` * :doc:`compute damage/atom ` * :doc:`compute plasticity/atom ` * examples/peri -* http://lammps.sandia.gov/movies.html#peri - +* https://lammps.sandia.gov/movies.html#peri ---------- - .. _PKG-POEMS: POEMS package @@ -873,10 +822,8 @@ This package has :ref:`specific installation instructions ` on the :doc:` * :doc:`fix poems ` * examples/rigid - ---------- - .. _PKG-PYTHON: PYTHON package @@ -908,10 +855,8 @@ This package has :ref:`specific installation instructions ` on the :doc: * lib/python/README * examples/python - ---------- - .. _PKG-QEQ: QEQ package @@ -930,10 +875,8 @@ part of their formulation. * examples/qeq * examples/streitz - ---------- - .. _PKG-REPLICA: REPLICA package @@ -963,10 +906,8 @@ another set. * examples/prd * examples/tad - ---------- - .. _PKG-RIGID: RIGID package @@ -989,13 +930,11 @@ Also several computes which calculate properties of rigid bodies. * examples/ASPHERE * examples/rigid * bench/in.rhodo -* http://lammps.sandia.gov/movies.html#box -* http://lammps.sandia.gov/movies.html#star - +* https://lammps.sandia.gov/movies.html#box +* https://lammps.sandia.gov/movies.html#star ---------- - .. _PKG-SHOCK: SHOCK package @@ -1016,10 +955,8 @@ a material. * examples/hugoniostat * examples/msst - ---------- - .. _PKG-SNAP: SNAP package @@ -1043,10 +980,8 @@ computes which analyze attributes of the potential. * :doc:`compute snav/atom ` * examples/snap - ---------- - .. _PKG-SPIN: SPIN package @@ -1075,10 +1010,8 @@ the usual manner via MD. Various pair, fix, and compute styles. * :doc:`neb/spin ` * examples/SPIN - ---------- - .. _PKG-SRD: SRD package @@ -1097,14 +1030,12 @@ colloidal particles. * :doc:`fix wall/srd ` * examples/srd * examples/ASPHERE -* http://lammps.sandia.gov/movies.html#tri -* http://lammps.sandia.gov/movies.html#line -* http://lammps.sandia.gov/movies.html#poly - +* https://lammps.sandia.gov/movies.html#tri +* https://lammps.sandia.gov/movies.html#line +* https://lammps.sandia.gov/movies.html#poly ---------- - .. _PKG-VORONOI: VORONOI package @@ -1119,8 +1050,6 @@ neighbors. .. _voro-home: http://math.lbl.gov/voro++ - - To use this package you must have the Voro++ library available on your system. @@ -1140,10 +1069,8 @@ This package has :ref:`specific installation instructions ` on the :doc * :doc:`compute voronoi/atom ` * examples/voronoi - ---------- - .. _PKG-USER-ADIOS: USER-ADIOS package @@ -1172,11 +1099,8 @@ This package has :ref:`specific installation instructions ` on the : * :doc:`dump custom/adios ` * :doc:`read_dump ` - - ---------- - .. _PKG-USER-ATC: USER-ATC package @@ -1200,12 +1124,10 @@ This package has :ref:`specific installation instructions ` on the :do * src/USER-ATC/README * :doc:`fix atc ` * examples/USER/atc -* http://lammps.sandia.gov/pictures.html#atc - +* https://lammps.sandia.gov/pictures.html#atc ---------- - .. _PKG-USER-AWPMD: USER-AWPMD package @@ -1231,10 +1153,8 @@ This package has :ref:`specific installation instructions ` on the : * :doc:`pair_style awpmd/cut ` * examples/USER/awpmd - ---------- - .. _PKG-USER-BOCS: USER-BOCS package @@ -1266,10 +1186,8 @@ J. Phys. Chem. B. 122, 13, 3363-3377 (2018). Example inputs are in the examples/USER/bocs folder. - ---------- - .. _PKG-USER-CGDNA: USER-CGDNA package @@ -1296,10 +1214,8 @@ rigid-body integrators with improved stability. * :doc:`bond_style oxrna2/\* ` * :doc:`fix nve/dotc/langevin ` - ---------- - .. _PKG-USER-CGSDK: USER-CGSDK package @@ -1321,12 +1237,10 @@ acids. * :doc:`pair_style lj/sdk/\* ` * :doc:`angle_style sdk ` * examples/USER/cgsdk -* http://lammps.sandia.gov/pictures.html#cg - +* https://lammps.sandia.gov/pictures.html#cg ---------- - .. _PKG-USER-COLVARS: USER-COLVARS package @@ -1360,10 +1274,8 @@ This package has :ref:`specific installation instructions ` on the * :doc:`fix colvars ` * examples/USER/colvars - ---------- - .. _PKG-USER-PLUMED: USER-PLUMED package @@ -1380,9 +1292,7 @@ script by using the :doc:`fix plumed ` command. Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth Tribello. -.. _PLUMED: http://www.plumed.org - - +.. _PLUMED: https://www.plumed.org **Install:** @@ -1395,10 +1305,8 @@ This package has :ref:`specific installation instructions ` on the * :doc:`fix plumed ` * examples/USER/plumed - ---------- - .. _PKG-USER-DIFFRACTION: USER-DIFFRACTION package @@ -1419,10 +1327,8 @@ intensities based on kinematic diffraction theory. * :doc:`fix saed/vtk ` * examples/USER/diffraction - ---------- - .. _PKG-USER-DPD: USER-DPD package @@ -1462,10 +1368,8 @@ Brennan (ARL). * :doc:`pair_style multi/lucy/rx ` * examples/USER/dpd - ---------- - .. _PKG-USER-DRUDE: USER-DRUDE package @@ -1496,10 +1400,8 @@ Devemy (CNRS), and Agilio Padua (U Blaise Pascal). * examples/USER/drude * tools/drude - ---------- - .. _PKG-USER-EFF: USER-EFF package @@ -1532,12 +1434,10 @@ tools/eff; see its README file. * examples/USER/eff * tools/eff/README * tools/eff -* http://lammps.sandia.gov/movies.html#eff - +* https://lammps.sandia.gov/movies.html#eff ---------- - .. _PKG-USER-FEP: USER-FEP package @@ -1563,10 +1463,8 @@ for using this package in tools/fep; see its README file. * tools/fep/README * tools/fep - ---------- - .. _PKG-USER-H5MD: USER-H5MD package @@ -1582,8 +1480,6 @@ LAMMPS snapshots in this format. .. _HDF5: http://www.hdfgroup.org/HDF5 - - To use this package you must have the HDF5 library available on your system. @@ -1601,10 +1497,8 @@ This package has :ref:`specific installation instructions ` on the :d * lib/h5md/README * :doc:`dump h5md ` - ---------- - .. _PKG-USER-INTEL: USER-INTEL package @@ -1648,12 +1542,10 @@ This package has :ref:`specific installation instructions ` on the : * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) * src/USER-INTEL/TEST -* `Benchmarks page `_ of web site - +* `Benchmarks page `_ of web site ---------- - .. _PKG-USER-LB: USER-LB package @@ -1676,10 +1568,8 @@ Ontario). * :doc:`fix lb/viscous ` * examples/USER/lb - ---------- - .. _PKG-USER-MGPT: USER-MGPT package @@ -1705,10 +1595,8 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. * :doc:`pair_style mgpt ` * examples/USER/mgpt - ---------- - .. _PKG-USER-MISC: USER-MISC package @@ -1730,10 +1618,8 @@ src/USER-MISC/README file. * one doc page per individual command listed in src/USER-MISC/README * examples/USER/misc - ---------- - .. _PKG-USER-MANIFOLD: USER-MANIFOLD package @@ -1761,12 +1647,10 @@ Waltham, MA, USA) * :doc:`fix nve/manifold/rattle ` * :doc:`fix nvt/manifold/rattle ` * examples/USER/manifold -* http://lammps.sandia.gov/movies.html#manifold - +* https://lammps.sandia.gov/movies.html#manifold ---------- - .. _PKG-USER-MEAMC: USER-MEAMC package @@ -1790,14 +1674,12 @@ Sandia. * :doc:`pair_style meam/c ` * examples/meamc - ---------- +.. _PKG-USER-MESODPD: -.. _PKG-USER-MESO: - -USER-MESO package ------------------ +USER-MESODPD package +-------------------- **Contents:** @@ -1813,20 +1695,21 @@ algorithm. **Supporting info:** -* src/USER-MESO: filenames -> commands -* src/USER-MESO/README +* src/USER-MESODPD: filenames -> commands +* src/USER-MESODPD/README * :doc:`atom_style edpd ` -* :doc:`pair_style edpd ` -* :doc:`pair_style mdpd ` -* :doc:`pair_style tdpd ` +* :doc:`pair_style edpd ` +* :doc:`pair_style mdpd ` +* :doc:`pair_style tdpd ` * :doc:`fix mvv/dpd ` +* examples/USER/mesodpd +* https://lammps.sandia.gov/movies.html#mesodpd + * examples/USER/meso * http://lammps.sandia.gov/movies.html#mesodpd - ---------- - .. _PKG-USER-MESONT: USER-MESONT package @@ -1855,10 +1738,8 @@ is provided in the papers listed below. * examples/USER/mesont * tools/mesont - ---------- - .. _PKG-USER-MOFFF: USER-MOFFF package @@ -1877,8 +1758,6 @@ well as the `MOF+ `_ website. .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF - - **Author:** Hendrik Heenen (Technical U of Munich), Rochus Schmid (Ruhr-University Bochum). @@ -1892,10 +1771,8 @@ Rochus Schmid (Ruhr-University Bochum). * :doc:`improper_style inversion/harmonic ` * examples/USER/mofff - ---------- - .. _PKG-USER-MOLFILE: USER-MOLFILE package @@ -1936,10 +1813,8 @@ This package has :ref:`specific installation instructions ` on the * lib/molfile/README * :doc:`dump molfile ` - ---------- - .. _PKG-USER-NETCDF: USER-NETCDF package @@ -1960,20 +1835,11 @@ tools: * `Ovito `_ (Ovito supports the AMBER convention and the extensions mentioned above) * `VMD `_ -* `AtomEye `_ (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) .. _ovito: http://www.ovito.org - - .. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/ - - -.. _atomeye: http://www.libatoms.org - - - **Author:** Lars Pastewka (Karlsruhe Institute of Technology). **Install:** @@ -1987,10 +1853,8 @@ This package has :ref:`specific installation instructions ` on the * lib/netcdf/README * :doc:`dump netcdf ` - ---------- - .. _PKG-USER-OMP: USER-OMP package @@ -2041,12 +1905,10 @@ This package has :ref:`specific installation instructions ` on the :do * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (o) -* `Benchmarks page `_ of web site - +* `Benchmarks page `_ of web site ---------- - .. _PKG-USER-PHONON: USER-PHONON package @@ -2062,7 +1924,7 @@ And a :doc:`dynamical_matrix ` as well as a and third order tensor from finite differences. **Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" -and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order" +and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order" **Supporting info:** @@ -2073,10 +1935,8 @@ and Charlie Sievers (UC Davis) for "dynamical\_matrix" and "third\_order" * :doc:`third_order ` * examples/USER/phonon - ---------- - .. _PKG-USER-PTM: USER-PTM package @@ -2092,15 +1952,13 @@ Matching methodology. **Supporting info:** -* src/USER-PTM: filenames not starting with ptm\\_ -> commands -* src/USER-PTM: filenames starting with ptm\\_ -> supporting code +* src/USER-PTM: filenames not starting with ptm\_ -> commands +* src/USER-PTM: filenames starting with ptm\_ -> supporting code * src/USER-PTM/LICENSE * :doc:`compute ptm/atom ` - ---------- - .. _PKG-USER-QMMM: USER-QMMM package @@ -2130,7 +1988,6 @@ changes to LAMMPS itself. **Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy) - **Install:** This package has :ref:`specific installation instructions ` @@ -2145,10 +2002,8 @@ on the :doc:`Build extras ` doc page. * lib/qmmm/example-ec/README * lib/qmmm/example-mc/README - ---------- - .. _PKG-USER-QTB: USER-QTB package @@ -2175,10 +2030,8 @@ simulation. * :doc:`fix qbmsst ` * examples/USER/qtb - ---------- - .. _PKG-USER-QUIP: USER-QUIP package @@ -2192,8 +2045,6 @@ developed by the Cambridge University group. .. _quip: https://github.com/libAtoms/QUIP - - To use this package you must have the QUIP libAtoms library available on your system. @@ -2210,10 +2061,8 @@ This package has :ref:`specific installation instructions ` on the :d * :doc:`pair_style quip ` * examples/USER/quip - ---------- - .. _PKG-USER-REACTION: USER-REACTION package @@ -2243,10 +2092,8 @@ molecules, and chiral-sensitive reactions. * `2019 LAMMPS Workshop `_ * disarmmd.org - ---------- - .. _PKG-USER-REAXC: USER-REAXC package @@ -2270,10 +2117,8 @@ for monitoring molecules as bonds are created and destroyed. * :doc:`fix reax/c/species ` * examples/reax - ---------- - .. _PKG-USER-SCAFACOS: USER-SCAFACOS package @@ -2307,10 +2152,8 @@ This package has :ref:`specific installation instructions ` on th * :doc:`kspace_modify ` * examples/USER/scafacos - ---------- - .. _PKG-USER-SDPD: USER-SDPD package @@ -2323,7 +2166,7 @@ is an extension of smoothed particle hydrodynamics (SPH) to mesoscale where thermal fluctuations are important (see the :ref:`USER-SPH package `). Also two fixes for moving and rigid body integration of SPH/SDPD particles -(particles of atom\_style meso). +(particles of atom_style meso). **Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic Sciences, Iran). @@ -2337,10 +2180,8 @@ Sciences, Iran). * :doc:`fix rigid/meso ` * examples/USER/sdpd - ---------- - .. _PKG-USER-SMD: USER-SMD package @@ -2373,14 +2214,12 @@ This package has :ref:`specific installation instructions ` on the :do * src/USER-SMD: filenames -> commands * src/USER-SMD/README -* doc/PDF/SMD\_LAMMPS\_userguide.pdf +* doc/PDF/SMD_LAMMPS_userguide.pdf * examples/USER/smd -* http://lammps.sandia.gov/movies.html#smd - +* https://lammps.sandia.gov/movies.html#smd ---------- - .. _PKG-USER-SMTBQ: USER-SMTBQ package @@ -2402,10 +2241,8 @@ Tetot (LAAS-CNRS, France). * :doc:`pair_style smtbq ` * examples/USER/smtbq - ---------- - .. _PKG-USER-SPH: USER-SPH package @@ -2434,14 +2271,12 @@ Dynamics, Ernst Mach Institute, Germany). * src/USER-SPH: filenames -> commands * src/USER-SPH/README -* doc/PDF/SPH\_LAMMPS\_userguide.pdf +* doc/PDF/SPH_LAMMPS_userguide.pdf * examples/USER/sph -* http://lammps.sandia.gov/movies.html#sph - +* https://lammps.sandia.gov/movies.html#sph ---------- - .. _PKG-USER-TALLY: USER-TALLY package @@ -2462,10 +2297,8 @@ stress, etc) about individual interactions. * :doc:`compute \*/tally ` * examples/USER/tally - ---------- - .. _PKG-USER-UEF: USER-UEF package @@ -2490,10 +2323,8 @@ supporting compute styles and an output option. * :doc:`dump cfg/uef ` * examples/uef - ---------- - .. _PKG-USER-VTK: USER-VTK package @@ -2507,12 +2338,8 @@ other visualization packages. .. _vtk: http://www.vtk.org - - .. _paraview: http://www.paraview.org - - To use this package you must have VTK library available on your system. @@ -2529,10 +2356,8 @@ This package has :ref:`specific installation instructions ` on the :do * lib/vtk/README * :doc:`dump vtk ` - ---------- - .. _PKG-USER-YAFF: USER-YAFF package @@ -2548,8 +2373,8 @@ The expressions and their use are discussed in the following papers which discuss the `QuickFF `_ methodology. -.. _vanduyfhuys2015: http://dx.doi.org/10.1002/jcc.23877 -.. _vanduyfhuys2018: http://dx.doi.org/10.1002/jcc.25173 +.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877 +.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173 .. _quickff: http://molmod.github.io/QuickFF .. _yaff: https://github.com/molmod/yaff diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index 8b938563e8..563e0cf211 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -28,93 +28,93 @@ package: * int = internal library: provided with LAMMPS, but you may need to build it * ext = external library: you will need to download and install it on your machine -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| Package | Description | Doc page | Example | Library | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-ADIOS ` | dump output via ADIOS | :doc:`dump adios ` | USER/adios | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-ATC ` | Atom-to-Continuum coupling | :doc:`fix atc ` | USER/atc | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair_style awpmd/cut ` | USER/awpmd | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-DIFFRACTION ` | virtual x-ray and electron diffraction | :doc:`compute xrd ` | USER/diffraction | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-DPD ` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MESO ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/meso | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MESONT ` | mesoscopic tubular potential model for nanotubes | :doc:`pair_style mesont/tpm ` | USER/mesont | int | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MISC ` | single-file contributions | USER-MISC/README | USER/misc | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair_style buck6d/coul/gauss ` | USER/mofff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-MOLFILE ` | `VMD `_ molfile plug-ins | :doc:`dump molfile ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-PLUMED ` | :ref:`PLUMED ` free energy library | :doc:`fix plumed ` | USER/plumed | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-PTM ` | Polyhedral Template Matching | :doc:`compute ptm/atom ` | n/a | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-QMMM ` | QM/MM coupling | :doc:`fix qmmm ` | USER/qmmm | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SMD ` | smoothed Mach dynamics | `SMD User Guide `_ | USER/smd | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair_style smtbq ` | USER/smtbq | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-TALLY ` | pairwise tally computes | :doc:`compute XXX/tally ` | USER/tally | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-UEF ` | extensional flow | :doc:`fix nvt/uef ` | USER/uef | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ -| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | -+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+-----------------------------------------------------+---------+ ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| Package | Description | Doc page | Example | Library | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-ADIOS ` | dump output via ADIOS | :doc:`dump adios ` | USER/adios | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-ATC ` | Atom-to-Continuum coupling | :doc:`fix atc ` | USER/atc | int | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-AWPMD ` | wave packet MD | :doc:`pair_style awpmd/cut ` | USER/awpmd | int | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-BOCS ` | BOCS bottom up coarse graining | :doc:`fix bocs ` | USER/bocs | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-CGDNA ` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-CGSDK ` | SDK coarse-graining model | :doc:`pair_style lj/sdk ` | USER/cgsdk | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-COLVARS ` | collective variables library | :doc:`fix colvars ` | USER/colvars | int | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-DIFFRACTION ` | virtual x-ray and electron diffraction | :doc:`compute xrd ` | USER/diffraction | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-DPD ` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-DRUDE ` | Drude oscillators | :doc:`Howto drude ` | USER/drude | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-EFF ` | electron force field | :doc:`pair_style eff/cut ` | USER/eff | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-FEP ` | free energy perturbation | :doc:`compute fep ` | USER/fep | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-H5MD ` | dump output via HDF5 | :doc:`dump h5md ` | n/a | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-INTEL ` | optimized Intel CPU and KNL styles | :doc:`Speed intel ` | `Benchmarks `_ | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-LB ` | Lattice Boltzmann fluid | :doc:`fix lb/fluid ` | USER/lb | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MANIFOLD ` | motion on 2d surfaces | :doc:`fix manifoldforce ` | USER/manifold | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MEAMC ` | modified EAM potential (C++) | :doc:`pair_style meam/c ` | meamc | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MESODPD ` | mesoscale DPD models | :doc:`pair_style edpd ` | USER/mesodpd | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MESONT ` | mesoscopic tubular potential model for nanotubes | :doc:`pair_style mesont/tpm ` | USER/mesont | int | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MGPT ` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt ` | USER/mgpt | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MISC ` | single-file contributions | USER-MISC/README | USER/misc | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MOFFF ` | styles for `MOF-FF `_ force field | :doc:`pair_style buck6d/coul/gauss ` | USER/mofff | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-MOLFILE ` | `VMD `_ molfile plug-ins | :doc:`dump molfile ` | n/a | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-NETCDF ` | dump output via NetCDF | :doc:`dump netcdf ` | n/a | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PLUMED ` | :ref:`PLUMED ` free energy library | :doc:`fix plumed ` | USER/plumed | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PTM ` | Polyhedral Template Matching | :doc:`compute ptm/atom ` | n/a | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-QMMM ` | QM/MM coupling | :doc:`fix qmmm ` | USER/qmmm | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-QTB ` | quantum nuclear effects | :doc:`fix qtb ` :doc:`fix qbmsst ` | qtb | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-QUIP ` | QUIP/libatoms interface | :doc:`pair_style quip ` | USER/quip | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-REACTION ` | chemical reactions in classical MD | :doc:`fix bond/react ` | USER/reaction | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-REAXC ` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc ` | reax | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SCAFACOS ` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos ` | USER/scafacos | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SDPD ` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal ` | USER/sdpd | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SMD ` | smoothed Mach dynamics | `SMD User Guide `_ | USER/smd | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SMTBQ ` | second moment tight binding QEq potential | :doc:`pair_style smtbq ` | USER/smtbq | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-SPH ` | smoothed particle hydrodynamics | `SPH User Guide `_ | USER/sph | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-TALLY ` | pairwise tally computes | :doc:`compute XXX/tally ` | USER/tally | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-UEF ` | extensional flow | :doc:`fix nvt/uef ` | USER/uef | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-VTK ` | dump output via VTK | :doc:`compute vtk ` | n/a | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-YAFF ` | additional styles implemented in YAFF | :doc:`angle_style cross ` | USER/yaff | no | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ .. _MOFplus: https://www.mofplus.org/content/show/MOF-FF -.. _PLUMED: http://www.plumed.org +.. _PLUMED: https://www.plumed.org diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 7f4ac8414f..fe368326ce 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -6,15 +6,14 @@ atom_style command Syntax """""" - .. code-block:: LAMMPS atom_style style args * style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *mdpd* or *tdpd* or *electron* or *ellipsoid* or *full* or *line* or *meso* or *molecular* or *peri* or *smd* or *sphere* or *spin* 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 @@ -28,11 +27,9 @@ Syntax * accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* - Examples """""""" - .. code-block:: LAMMPS atom_style atomic @@ -124,7 +121,7 @@ quantities. +--------------+-----------------------------------------------------+--------------------------------------+ | *tri* | corner points, angular momentum | rigid bodies | +--------------+-----------------------------------------------------+--------------------------------------+ -| *wavepacket* | charge, spin, eradius, etag, cs\_re, cs\_im | AWPMD | +| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD | +--------------+-----------------------------------------------------+--------------------------------------+ .. note:: @@ -163,7 +160,7 @@ 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 +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 @@ -176,14 +173,14 @@ per-particle mass and volume. The *dpd* style is for dissipative particle dynamics (DPD) particles. Note that it is part of the USER-DPD package, and is not for use with the :doc:`pair_style dpd or dpd/stat ` commands, which can -simply use atom\_style atomic. Atom\_style dpd extends DPD particle +simply use atom_style atomic. Atom_style dpd extends DPD particle properties with internal temperature (dpdTheta), internal conductive energy (uCond), internal mechanical energy (uMech), and internal chemical energy (uChem). The *edpd* style is for energy-conserving dissipative particle -dynamics (eDPD) particles which store a temperature (edpd\_temp), and -heat capacity(edpd\_cv). +dynamics (eDPD) particles which store a temperature (edpd_temp), and +heat capacity(edpd_cv). The *mdpd* style is for many-body dissipative particle dynamics (mDPD) particles which store a density (rho) for considering @@ -191,7 +188,7 @@ density-dependent many-body interactions. The *tdpd* style is for transport dissipative particle dynamics (tDPD) particles which store a set of chemical concentration. An integer -"cc\_species" is required to specify the number of chemical species +"cc_species" is required to specify the number of chemical species involved in a tDPD system. The *meso* style is for smoothed particle hydrodynamics (SPH) @@ -210,7 +207,7 @@ Those spins have a norm (their magnetic moment) and a direction. 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 +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. @@ -222,10 +219,6 @@ 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). -For the *mesont* style, the particles represent nodes of Nanotube -segments, and each stores a per-particle mass, radius, segment -length, tube id, buckling flag, and connections with neighbor nodes. - The *template* style allows molecular topology (bonds,angles,etc) to be defined via a molecule template using the :doc:`molecule ` command. The template stores one or more molecules with a single copy @@ -241,7 +234,7 @@ 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 + 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 @@ -265,13 +258,11 @@ 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 +*bstyle* specification, in the atom_style body command. These arguments are described on the :doc:`Howto 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 @@ -282,7 +273,7 @@ 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 +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. @@ -293,10 +284,8 @@ per-atom basis. LAMMPS can be extended with new atom styles as well as new body styles; see the :doc:`Modify ` doc page. - ---------- - Styles with a *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 on @@ -321,7 +310,6 @@ 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. @@ -344,7 +332,7 @@ The *electron* style is part of the USER-EFF package for :doc:`electronic force The *dpd* style is part of the USER-DPD package for dissipative particle dynamics (DPD). -The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESO package +The *edpd*\ , *mdpd*\ , and *tdpd* styles are part of the USER-MESODPD package for energy-conserving dissipative particle dynamics (eDPD), many-body dissipative particle dynamics (mDPD), and transport dissipative particle dynamics (tDPD), respectively. @@ -367,15 +355,11 @@ Related commands Default """"""" -atom\_style atomic - +atom_style atomic ---------- - .. _Grime: - - **(Grime)** Grime and Voth, to appear in J Chem Theory & Computation (2014). diff --git a/doc/src/compute.rst b/doc/src/compute.rst index aa501f351b..bcf53aecdf 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -6,7 +6,6 @@ compute command Syntax """""" - .. parsed-literal:: compute ID group-ID style args @@ -19,8 +18,7 @@ Syntax Examples """""""" - -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all temp compute newtemp flow temp/partial 1 1 0 @@ -43,10 +41,8 @@ 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 @@ -76,11 +72,11 @@ 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 | entire scalar, vector, or array | +-------------+--------------------------------------------+ -| c\_ID[I] | one element of vector, one column of array | +| c_ID[I] | one element of vector, one column of array | +-------------+--------------------------------------------+ -| c\_ID[I][J] | one element of array | +| c_ID[I][J] | one element of array | +-------------+--------------------------------------------+ In other words, using one bracket reduces the dimension of the @@ -92,14 +88,12 @@ 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 +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: @@ -115,7 +109,6 @@ ways: 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, @@ -123,23 +116,20 @@ 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. +"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 +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:: +.. code-block:: LAMMPS compute thermo_temp all temp compute thermo_press all pressure thermo_temp @@ -166,10 +156,8 @@ Code for new computes can be added to LAMMPS; see the :doc:`Modify ` doc page for details. 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 listed in more compact form on the @@ -237,7 +225,6 @@ The individual style names on the :doc:`Commands compute ` doc * :doc:`ke/atom/eff ` - per-atom translational and radial kinetic energy in the electron force field model * :doc:`ke/eff ` - kinetic energy of a group of nuclei and electrons in the electron force field model * :doc:`ke/rigid ` - translational kinetic energy of rigid bodies -* :doc:`mesont ` - Nanotube bending,stretching, and intertube energies * :doc:`meso/e/atom ` - per-atom internal energy of Smooth-Particle Hydrodynamics atoms * :doc:`meso/rho/atom ` - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms * :doc:`meso/t/atom ` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms @@ -251,6 +238,7 @@ The individual style names on the :doc:`Commands compute ` doc * :doc:`pair/local ` - distance/energy/force of each pairwise interaction * :doc:`pe ` - potential energy * :doc:`pe/atom ` - potential energy for each atom +* :doc:`mesont ` - Nanotube bending,stretching, and intertube energies * :doc:`pe/mol/tally ` - * :doc:`pe/tally ` - * :doc:`plasticity/atom ` - Peridynamic plasticity for each atom @@ -332,4 +320,4 @@ Related commands :doc:`uncompute `, :doc:`compute_modify `, :doc:`fix ave/atom `, :doc:`fix ave/time `, :doc:`fix ave/histo ` -**Default:** none \ No newline at end of file +**Default:** none diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst new file mode 100644 index 0000000000..b6d1af2a79 --- /dev/null +++ b/doc/src/pair_airebo.rst @@ -0,0 +1,272 @@ +.. index:: pair_style airebo + +pair_style airebo command +========================= + +pair_style airebo/intel command +=============================== + +pair_style airebo/omp command +============================= + +pair_style airebo/morse command +=============================== + +pair_style airebo/morse/intel command +===================================== + +pair_style airebo/morse/omp command +=================================== + +pair_style rebo command +======================= + +pair_style rebo/intel command +============================= + +pair_style rebo/omp command +=========================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style style cutoff LJ_flag TORSION_flag cutoff_min + +* style = *airebo* or *airebo/morse* or *rebo* +* cutoff = LJ or Morse cutoff (:math:`\sigma` scale factor) (AIREBO and AIREBO-M only) +* LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional) +* TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional) +* cutoff_min = Start of the transition region of cutoff (:math:`\sigma` scale factor) (AIREBO and AIREBO-M only, optional) + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style airebo 3.0 + pair_style airebo 2.5 1 0 + pair_coeff * * ../potentials/CH.airebo H C + + pair_style airebo/morse 3.0 + pair_coeff * * ../potentials/CH.airebo-m H C + + pair_style rebo + pair_coeff * * ../potentials/CH.rebo H C + +Description +""""""""""" + +The *airebo* pair style computes the Adaptive Intermolecular Reactive +Empirical Bond Order (AIREBO) Potential of :ref:`(Stuart) ` for a +system of carbon and/or hydrogen atoms. Note that this is the initial +formulation of AIREBO from 2000, not the later formulation. + +The *airebo/morse* pair style computes the AIREBO-M potential, which +is equivalent to AIREBO, but replaces the LJ term with a Morse potential. +The Morse potentials are parameterized by high-quality quantum chemistry +(MP2) calculations and do not diverge as quickly as particle density +increases. This allows AIREBO-M to retain accuracy to much higher pressures +than AIREBO (up to 40 GPa for Polyethylene). Details for this potential +and its parameterization are given in :ref:`(O'Conner) `. + +The *rebo* pair style computes the Reactive Empirical Bond Order (REBO) +Potential of :ref:`(Brenner) `. Note that this is the so-called +2nd generation REBO from 2002, not the original REBO from 1990. +As discussed below, 2nd generation REBO is closely related to the +initial AIREBO; it is just a subset of the potential energy terms +with a few slightly different parameters + +The AIREBO potential consists of three terms: + +.. math:: + + E & = \frac{1}{2} \sum_i \sum_{j \neq i} + \left[ E^{\text{REBO}}_{ij} + E^{\text{LJ}}_{ij} + + \sum_{k \neq i,j} \sum_{l \neq i,j,k} E^{\text{TORSION}}_{kijl} \right] \\ + +By default, all three terms are included. For the *airebo* style, if +the first two optional flag arguments to the pair_style command are +included, the LJ and torsional terms can be turned off. Note that +both or neither of the flags must be included. If both of the LJ an +torsional terms are turned off, it becomes the 2nd-generation REBO +potential, with a small caveat on the spline fitting procedure +mentioned below. This can be specified directly as pair_style *rebo* +with no additional arguments. + +The detailed formulas for this potential are given in +:ref:`(Stuart) `; here we provide only a brief description. + +The :math:`E^{\text{REBO}}` term has the same functional form as the hydrocarbon REBO +potential developed in :ref:`(Brenner) `. The coefficients for +:math:`E^{\text{REBO}}` in AIREBO are essentially the same as Brenner's potential, but +a few fitted spline values are slightly different. For most cases the +:math:`E^{\text{REBO}}` term in AIREBO will produce the same energies, forces and +statistical averages as the original REBO potential from which it was +derived. The :math:`E^{\text{REBO}}` term in the AIREBO potential gives the model its +reactive capabilities and only describes short-ranged C-C, C-H and H-H +interactions (:math:`r < 2` Angstroms). These interactions have strong +coordination-dependence through a bond order parameter, which adjusts +the attraction between the I,J atoms based on the position of other +nearby atoms and thus has 3- and 4-body dependence. + +The :math:`E^{\text{LJ}}` term adds longer-ranged interactions (:math:`2 < r < \text{cutoff}`) using a +form similar to the standard :doc:`Lennard Jones potential `. +The :math:`E^{\text{LJ}}` term in AIREBO contains a series of switching functions so +that the short-ranged LJ repulsion (:math:`1/r^{12}`) does not interfere with +the energetics captured by the :math:`E^{\text{REBO}}` term. The extent of the :math:`E^{\text{LJ}}` +interactions is determined by the *cutoff* argument to the pair_style +command which is a scale factor. For each type pair (C-C, C-H, H-H) +the cutoff is obtained by multiplying the scale factor by the sigma +value defined in the potential file for that type pair. In the +standard AIREBO potential, :math:`\sigma_{CC} = 3.4` Angstroms, so with a scale +factor of 3.0 (the argument in pair_style), the resulting :math:`E^{\text{LJ}}` cutoff +would be 10.2 Angstroms. + +By default, the longer-ranged interaction is smoothly switched off +between 2.16 and 3.0 :math:`\sigma`. By specifying *cutoff_min* in addition +to *cutoff*\ , the switching can be configured to take place between +*cutoff_min* and *cutoff*\ . *cutoff_min* can only be specified if all +optional arguments are given. + +The :math:`E^{\text{TORSION}}` term is an explicit 4-body potential that describes +various dihedral angle preferences in hydrocarbon configurations. + +---------- + +Only a single pair_coeff command is used with the *airebo*\ , *airebo* +or *rebo* style which specifies an AIREBO, REBO, or AIREBO-M potential +file with parameters for C and H. Note that as of LAMMPS version +15 May 2019 the *rebo* style in LAMMPS uses its own potential +file (CH.rebo). These are mapped to LAMMPS atom types by specifying +N additional arguments after the filename in the pair_coeff command, +where N is the number of LAMMPS atom types: + +* filename +* :math:`N` element names = mapping of AIREBO elements to atom types + +See the :doc:`pair_coeff ` doc page for alternate ways +to specify the path for the potential file. + +As an example, if your LAMMPS simulation has 4 atom types and you want +the 1st 3 to be C, and the 4th to be H, you would use the following +pair_coeff command: + +.. code-block:: LAMMPS + + pair_coeff * * CH.airebo C C C H + +The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. +The first three C arguments map LAMMPS atom types 1,2,3 to the C +element in the AIREBO file. The final H argument maps LAMMPS atom +type 4 to the H element in the SW file. If a mapping value is +specified as NULL, the mapping is not performed. This can be used +when a *airebo* potential is used as part of the *hybrid* pair style. +The NULL values are placeholders for atom types that will be used with +other potentials. + +The parameters/coefficients for the AIREBO potentials are listed in +the CH.airebo file to agree with the original :ref:`(Stuart) ` +paper. Thus the parameters are specific to this potential and the way +it was fit, so modifying the file should be done cautiously. + +Similarly the parameters/coefficients for the AIREBO-M potentials are +listed in the CH.airebo-m file to agree with the :ref:`(O'Connor) ` +paper. Thus the parameters are specific to this potential and the way +it was fit, so modifying the file should be done cautiously. The +AIREBO-M Morse potentials were parameterized using a cutoff of +3.0 (:math:`\sigma`). Modifying this cutoff may impact simulation accuracy. + +This pair style tallies a breakdown of the total AIREBO potential +energy into sub-categories, which can be accessed via the :doc:`compute pair ` command as a vector of values of length 3. +The 3 values correspond to the following sub-categories: + +1. :math:`E_{\text{REBO}}` = REBO energy +2. :math:`E_{\text{LJ}}` = Lennard-Jones energy +3. :math:`E_{\text{TORSION}}` = Torsion energy + +To print these quantities to the log file (with descriptive column +headings) the following commands could be included in an input script: + +.. code-block:: LAMMPS + + compute 0 all pair airebo + variable REBO equal c_0[1] + variable LJ equal c_0[2] + variable TORSION equal c_0[3] + thermo_style custom step temp epair v_REBO v_LJ v_TORSION + +---------- + +Styles with a *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 on the :doc:`Speed packages ` doc +page. 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 GPU, USER-INTEL, KOKKOS, +USER-OMP and OPT packages, respectively. They are only enabled if +LAMMPS was built with those packages. See the :doc:`Build package ` doc page for more info. + +You can specify the accelerated styles explicitly in your input script +by including their suffix, or you can use the :doc:`-suffix command-line switch ` when you invoke LAMMPS, or you can use the +:doc:`suffix ` command in your input script. + +See the :doc:`Speed packages ` doc page for more +instructions on how to use the accelerated styles effectively. + +---------- + +**Mixing, shift, table, tail correction, restart, rRESPA info**\ : + +These pair styles do not support the :doc:`pair_modify ` +mix, shift, table, and tail options. + +These pair styles do not write their information to :doc:`binary restart files `, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +These pair styles can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. They do not support the +*inner* , *middle*, *outer* keywords. + +Restrictions +"""""""""""" + +These pair styles are part of the MANYBODY package. They are only +enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. + +These pair potentials require the :doc:`newton ` setting to be +"on" for pair interactions. + +The CH.airebo and CH.airebo-m potential files provided with LAMMPS +(see the potentials directory) are parameterized for metal :doc:`units `. +You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units, +but you would need to create your own AIREBO or AIREBO-M potential file +with coefficients listed in the appropriate units, if your simulation +does not use "metal" units. + +Related commands +"""""""""""""""" + +:doc:`pair_coeff ` + +**Default:** none + +---------- + +.. _Stuart: + +**(Stuart)** Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486 +(2000). + +.. _Brenner: + +**(Brenner)** Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J +Physics: Condensed Matter, 14, 783-802 (2002). + +.. _OConnor: + +**(O'Connor)** O'Connor et al., J. Chem. Phys. 142, 024903 (2015). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 4d54532ed6..294ea15b1f 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -243,8 +243,8 @@ accelerated styles exist. * :doc:`meam/spline ` - splined version of MEAM * :doc:`meam/sw/spline ` - splined version of MEAM with a Stillinger-Weber term * :doc:`mesocnt ` - mesoscale model for (carbon) nanotubes -* :doc:`mesont/tpm ` - nanotubes mesoscopic force field * :doc:`mgpt ` - simplified model generalized pseudopotential theory (MGPT) potential +* :doc:`mesont/tpm ` - nanotubes mesoscopic force field * :doc:`mie/cut ` - Mie potential * :doc:`mm3/switch3/coulgauss/long ` - smoothed MM3 vdW potential with Gaussian electrostatics * :doc:`momb ` - Many-Body Metal-Organic (MOMB) force field