From 9d74984144681be23cc758fab16a25b19ae0092d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 16 Jun 2020 07:20:09 -0400 Subject: [PATCH] Fix whitespace --- doc/github-development-workflow.md | 6 +- doc/include-file-conventions.md | 2 +- doc/src/compute_mesont.rst | 14 ++--- doc/src/compute_orientorder_atom.rst | 2 +- doc/src/compute_property_atom.rst | 2 +- doc/src/pair_mesont_tpm.rst | 6 +- src/GPU/Install.sh | 8 +-- src/KOKKOS/Install.sh | 22 +++---- src/Make.sh | 8 +-- src/OPT/Install.sh | 2 +- src/SPIN/README | 10 ++-- src/USER-ADIOS/Install.sh | 2 +- src/USER-ADIOS/README | 14 ++--- src/USER-BOCS/README | 4 +- src/USER-CGDNA/README.md | 44 +++++++------- src/USER-DIFFRACTION/README | 34 +++++------ src/USER-EFF/README | 16 ++--- src/USER-FEP/README | 2 +- src/USER-INTEL/TEST/run_benchmarks.sh | 2 +- src/USER-LB/README | 6 +- src/USER-MESONT/README | 84 +++++++++++++-------------- src/USER-MGPT/README | 26 ++++----- src/USER-MOFFF/README | 22 +++---- src/USER-PLUMED/README | 46 +++++++-------- src/USER-QUIP/README | 2 +- src/USER-SCAFACOS/Install.sh | 2 +- src/USER-SPH/README | 6 +- src/USER-TALLY/README | 2 +- src/VORONOI/README | 4 +- 29 files changed, 200 insertions(+), 200 deletions(-) diff --git a/doc/github-development-workflow.md b/doc/github-development-workflow.md index a000dbe453..fd38c983a2 100644 --- a/doc/github-development-workflow.md +++ b/doc/github-development-workflow.md @@ -25,10 +25,10 @@ In the interest of consistency, ONLY ONE of the core LAMMPS developers should doing the merging itself. This is currently [@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer). If this assignment needs to be changed, it shall be done right after a -stable release. If the currently assigned developer cannot merge outstanding pull -requests in a timely manner, or in other extenuating circumstances, +stable release. If the currently assigned developer cannot merge outstanding pull +requests in a timely manner, or in other extenuating circumstances, other core LAMMPS developers with merge rights can merge pull requests, -when necessary. +when necessary. ## Pull Requests diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index 1b8e79d71e..51f67afbbb 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -65,7 +65,7 @@ Header files will typically contain the definition of a (single) class. These header files should have as few include statements as possible. This is particularly important for classes that implement a "style" and thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will -all be included in the auto-generated `"some_style.h"` files which +all be included in the auto-generated `"some_style.h"` files which results in a high potential for direct or indirect symbol name clashes. In the ideal case, the header would only include one file defining the diff --git a/doc/src/compute_mesont.rst b/doc/src/compute_mesont.rst index 8352d43726..654b06c4a3 100644 --- a/doc/src/compute_mesont.rst +++ b/doc/src/compute_mesont.rst @@ -26,23 +26,23 @@ Examples Description """"""""""" -These computes define computations for the stretching (estretch), bending -(ebend), and intertube (etube) per-node (atom) and total energies. The -evaluated value is selected by a parameter passed to the compute: estretch, +These computes define computations for the stretching (estretch), bending +(ebend), and intertube (etube) per-node (atom) and total energies. The +evaluated value is selected by a parameter passed to the compute: estretch, ebend, etube. **Output info:** -These computes calculate per-node (per-atom) vectors, which can be accessed by -any command that uses per-atom values from a compute as input, and global -scalars. See the :doc:`Howto output ` doc page for an overview of +These computes calculate per-node (per-atom) vectors, which can be accessed by +any command that uses per-atom values from a compute as input, and global +scalars. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. The computed values are provided in energy :doc:`units `. Restrictions """""""""""" -These computes are part of the USER-MESONT package. They are only enabled if +These computes are part of the USER-MESONT package. They are only enabled if LAMMPS is built with that package. See the :doc:`Build package ` doc page for more info. In addition, :doc:`mesont pair_style ` must be used. diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index 3b432e7df9..828442ceaf 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -26,7 +26,7 @@ Syntax *wl* value = yes or no *wl/hat* value = yes or no *components* value = ldegree - *chunksize* value = number of atoms in each pass + *chunksize* value = number of atoms in each pass Examples """""""" diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index 33bc573c41..021518713d 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -64,7 +64,7 @@ Syntax end12x, end12y, end12z = end points of line segment corner123x, corner123y, corner123z = corner points of triangle nbonds = number of bonds assigned to an atom - buckling = buckling flag used in mesoscopic simulation of nanotubes + buckling = buckling flag used in mesoscopic simulation of nanotubes .. parsed-literal:: diff --git a/doc/src/pair_mesont_tpm.rst b/doc/src/pair_mesont_tpm.rst index 492e8cb97b..f5b5789315 100644 --- a/doc/src/pair_mesont_tpm.rst +++ b/doc/src/pair_mesont_tpm.rst @@ -9,7 +9,7 @@ Syntax .. parsed-literal:: - pair_style mesont/tpm cut table_path BendingMode TPMType + pair_style mesont/tpm cut table_path BendingMode TPMType * cut = the cutoff distance * table_path = the path to the potential table @@ -114,7 +114,7 @@ study the thermal transport properties of carbon nanotube films The methods for modeling of the mechanical energy dissipation into heat (energy exchange between the dynamic degrees of freedom of the mesoscopic model and the energy of atomic -vibrations that are not explicitly represented in the model) +vibrations that are not explicitly represented in the model) :ref:`(Zhigilei10) ` and mesoscopic description of covalent cross-links between nanotubes :ref:`(Banna) ` have also been developed but are not included in this first release of the LAMMPS implementation of the force field. @@ -144,7 +144,7 @@ pair interactions. The cutoff distance should be set to be at least :math:`max\left[2L,\sqrt{L^2/2+(2R+T_{cut})^2}\right]` , where L is the maximum segment length, R is the maximum tube radius, and :math:`T_{cut}` = 10.2 A is the maximum distance between the surfaces of interacting -segments. Because of the use of extended chain concept at CNT ends, the recommended +segments. Because of the use of extended chain concept at CNT ends, the recommended cutoff is 3L. The MESONT-TABTP_10_10.xrs potential file provided with LAMMPS (see the diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index 243c15bef2..b83423eaa7 100755 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -32,7 +32,7 @@ action fix_gpu.cpp action fix_gpu.h action gpu_extra.h action pair_beck_gpu.cpp -action pair_beck_gpu.h +action pair_beck_gpu.h action pair_born_coul_long_gpu.cpp pair_born_coul_long.cpp action pair_born_coul_long_gpu.h pair_born_coul_long.cpp action pair_born_coul_long_cs_gpu.cpp pair_born_coul_long_cs.cpp @@ -71,9 +71,9 @@ action pair_lj_sf_dipole_sf_gpu.cpp pair_lj_sf_dipole_sf.cpp action pair_lj_sf_dipole_sf_gpu.h pair_lj_sf_dipole_sf.cpp action pair_eam_alloy_gpu.cpp pair_eam.cpp action pair_eam_alloy_gpu.h pair_eam.cpp -action pair_eam_fs_gpu.cpp pair_eam.cpp +action pair_eam_fs_gpu.cpp pair_eam.cpp action pair_eam_fs_gpu.h pair_eam.cpp -action pair_eam_gpu.cpp pair_eam.cpp +action pair_eam_gpu.cpp pair_eam.cpp action pair_eam_gpu.h pair_eam.cpp action pair_gauss_gpu.cpp action pair_gauss_gpu.h @@ -112,7 +112,7 @@ action pair_lj_sdk_coul_long_gpu.h pair_lj_sdk_coul_long.cpp action pair_lj_sdk_gpu.cpp pair_lj_sdk.cpp action pair_lj_sdk_gpu.h pair_lj_sdk.cpp action pair_mie_cut_gpu.cpp -action pair_mie_cut_gpu.h +action pair_mie_cut_gpu.h action pair_morse_gpu.cpp action pair_morse_gpu.h action pair_resquared_gpu.cpp pair_resquared.cpp diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index e9a8ff96c8..03508578ae 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -31,7 +31,7 @@ action () { KOKKOS_INSTALLED=0 if (test -e ../Makefile.package) then KOKKOS_INSTALLED=`grep DLMP_KOKKOS ../Makefile.package | wc -l` -fi +fi if (test $mode = 1) then if (test $KOKKOS_INSTALLED = 0) then @@ -45,14 +45,14 @@ fi # list of files with optional dependcies -action angle_charmm_kokkos.cpp angle_charmm.cpp +action angle_charmm_kokkos.cpp angle_charmm.cpp action angle_charmm_kokkos.h angle_charmm.h -action angle_class2_kokkos.cpp angle_class2.cpp +action angle_class2_kokkos.cpp angle_class2.cpp action angle_class2_kokkos.h angle_class2.h -action angle_cosine_kokkos.cpp angle_cosine.cpp +action angle_cosine_kokkos.cpp angle_cosine.cpp action angle_cosine_kokkos.h angle_cosine.h -action angle_harmonic_kokkos.cpp angle_harmonic.cpp -action angle_harmonic_kokkos.h angle_harmonic.h +action angle_harmonic_kokkos.cpp angle_harmonic.cpp +action angle_harmonic_kokkos.h angle_harmonic.h action atom_kokkos.cpp action atom_kokkos.h action atom_vec_angle_kokkos.cpp atom_vec_angle.cpp @@ -75,7 +75,7 @@ action atom_vec_molecular_kokkos.cpp atom_vec_molecular.cpp action atom_vec_molecular_kokkos.h atom_vec_molecular.h action atom_vec_sphere_kokkos.cpp atom_vec_sphere.cpp action atom_vec_sphere_kokkos.h atom_vec_sphere.h -action bond_class2_kokkos.cpp bond_class2.cpp +action bond_class2_kokkos.cpp bond_class2.cpp action bond_class2_kokkos.h bond_class2.h action bond_fene_kokkos.cpp bond_fene.cpp action bond_fene_kokkos.h bond_fene.h @@ -93,9 +93,9 @@ action compute_temp_kokkos.cpp action compute_temp_kokkos.h action dihedral_charmm_kokkos.cpp dihedral_charmm.cpp action dihedral_charmm_kokkos.h dihedral_charmm.h -action dihedral_class2_kokkos.cpp dihedral_class2.cpp +action dihedral_class2_kokkos.cpp dihedral_class2.cpp action dihedral_class2_kokkos.h dihedral_class2.h -action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp +action dihedral_harmonic_kokkos.cpp dihedral_harmonic.cpp action dihedral_harmonic_kokkos.h dihedral_harmonic.h action dihedral_opls_kokkos.cpp dihedral_opls.cpp action dihedral_opls_kokkos.h dihedral_opls.h @@ -109,7 +109,7 @@ action fix_deform_kokkos.h action fix_enforce2d_kokkos.cpp action fix_enforce2d_kokkos.h action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp -action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h +action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h action fix_freeze_kokkos.cpp fix_freeze.cpp action fix_freeze_kokkos.h fix_freeze.h action fix_gravity_kokkos.cpp @@ -156,7 +156,7 @@ action fix_rx_kokkos.cpp fix_rx.cpp action fix_rx_kokkos.h fix_rx.h action gridcomm_kokkos.cpp gridcomm.cpp action gridcomm_kokkos.h gridcomm.h -action improper_class2_kokkos.cpp improper_class2.cpp +action improper_class2_kokkos.cpp improper_class2.cpp action improper_class2_kokkos.h improper_class2.h action improper_harmonic_kokkos.cpp improper_harmonic.cpp action improper_harmonic_kokkos.h improper_harmonic.h diff --git a/src/Make.sh b/src/Make.sh index 49a673d8ee..0fe39f0224 100755 --- a/src/Make.sh +++ b/src/Make.sh @@ -1,4 +1,4 @@ -# Make.sh = update Makefile.lib, Makefile.shlib, Makefile.list +# Make.sh = update Makefile.lib, Makefile.shlib, Makefile.list # or style_*.h files # Syntax: sh Make.sh style # sh Make.sh Makefile.lib @@ -31,7 +31,7 @@ style () { rm -f style_$3.h touch style_$3.h rm -f Obj_*/$4.d - if (test $5) then + if (test $5) then rm -f Obj_*/$5.d fi rm -f Obj_*/lammps.d @@ -39,14 +39,14 @@ style () { elif (test ! -e style_$3.h) then mv style_$3.tmp style_$3.h rm -f Obj_*/$4.d - if (test $5) then + if (test $5) then rm -f Obj_*/$5.d fi rm -f Obj_*/lammps.d elif (test "`diff --brief style_$3.h style_$3.tmp`" != "") then mv style_$3.tmp style_$3.h rm -f Obj_*/$4.d - if (test $5) then + if (test $5) then rm -f Obj_*/$5.d fi rm -f Obj_*/lammps.d diff --git a/src/OPT/Install.sh b/src/OPT/Install.sh index c6ae2b914b..b059dab491 100755 --- a/src/OPT/Install.sh +++ b/src/OPT/Install.sh @@ -41,7 +41,7 @@ action pair_lj_cut_coul_long_opt.h pair_lj_cut_coul_long.cpp action pair_lj_cut_opt.cpp action pair_lj_cut_opt.h action pair_lj_cut_tip4p_long_opt.cpp pair_lj_cut_tip4p_long.cpp -action pair_lj_cut_tip4p_long_opt.h pair_lj_cut_tip4p_long.cpp +action pair_lj_cut_tip4p_long_opt.h pair_lj_cut_tip4p_long.cpp action pair_lj_long_coul_long_opt.cpp pair_lj_long_coul_long.cpp action pair_lj_long_coul_long_opt.h pair_lj_long_coul_long.cpp action pair_morse_opt.cpp diff --git a/src/SPIN/README b/src/SPIN/README index 6dbad91d8d..233cf3a140 100644 --- a/src/SPIN/README +++ b/src/SPIN/README @@ -1,5 +1,5 @@ -The SPIN package enables coupled spin dynamics and molecular -dynamics simulations. +The SPIN package enables coupled spin dynamics and molecular +dynamics simulations. The package provides the following features: @@ -12,11 +12,11 @@ atom in the system * computing and outputting magnetic quantities * minimizing the energy or total torque of a magnetic system -The different options provided by this package are explained in the +The different options provided by this package are explained in the LAMMPS documentation. -Once you have successfully built LAMMPS with this package, you can test -it using one of the input files provided from the examples/SPIN dir. +Once you have successfully built LAMMPS with this package, you can test +it using one of the input files provided from the examples/SPIN dir. For example: ./lmp_serial < lammps/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp diff --git a/src/USER-ADIOS/Install.sh b/src/USER-ADIOS/Install.sh index 434df14f60..b8a2f1f9a9 100644 --- a/src/USER-ADIOS/Install.sh +++ b/src/USER-ADIOS/Install.sh @@ -52,7 +52,7 @@ if (test $1 = 1) then "installation directory or adios2-config should be in PATH" fi - if [ "$CONFIGSCRIPT" != "none" ]; then + if [ "$CONFIGSCRIPT" != "none" ]; then ADIOS2_INC=`$CONFIGSCRIPT --cxx-flags` ADIOS2_LIB=`$CONFIGSCRIPT --cxx-libs` diff --git a/src/USER-ADIOS/README b/src/USER-ADIOS/README index 85e8132956..2b66f27f6b 100644 --- a/src/USER-ADIOS/README +++ b/src/USER-ADIOS/README @@ -1,16 +1,16 @@ This package provides the adios dump and read_dump styles. -See the doc page for the "dump adios" and "read_dump ... format adios" commands. +See the doc page for the "dump adios" and "read_dump ... format adios" commands. These styles require having ADIOS 2.x itself installed on your system. -Configure LAMMPS with CMake - a. set the environment variable - ADIOS2_DIR +Configure LAMMPS with CMake + a. set the environment variable + ADIOS2_DIR to the ADIOS 2.x installation path - b. use the cmake option - -D PKG_USER-ADIOS=yes + b. use the cmake option + -D PKG_USER-ADIOS=yes -The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory); +The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory); If you need help, please submit a ticket at the OLCF ticket user support mentioning his name in the ticket. https://www.olcf.ornl.gov/support/submit-ticket diff --git a/src/USER-BOCS/README b/src/USER-BOCS/README index adeb34c387..45aecc278c 100644 --- a/src/USER-BOCS/README +++ b/src/USER-BOCS/README @@ -1,7 +1,7 @@ -This user package implements the pressure correction to the barostat as +This user package implements the pressure correction to the barostat as outlined in: -N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that +N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids," J. Chem. Phys. 143, 243148 (2015). diff --git a/src/USER-CGDNA/README.md b/src/USER-CGDNA/README.md index 138638525e..015c1db188 100644 --- a/src/USER-CGDNA/README.md +++ b/src/USER-CGDNA/README.md @@ -2,49 +2,49 @@ This package contains a LAMMPS implementation of coarse-grained models of DNA, which can be used to model sequence-specific DNA strands. -Please cite +Please cite [![DOI](https://zenodo.org/badge/132764768.svg)](https://zenodo.org/badge/latestdoi/132764768) -as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles +as well as [1] and the relevant oxDNA, oxDNA2 and oxRNA2 articles in any publication that uses this package. -See the doc pages and [2,3,4,5,6] for the individual bond and pair styles. +See the doc pages and [2,3,4,5,6] for the individual bond and pair styles. The packages contains also a new Langevin-type rigid-body integrator, which has also its own doc page and is explained in [7]. [1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, -"Coarse-grained simulation of DNA using LAMMPS", +"Coarse-grained simulation of DNA using LAMMPS", Eur. Phys. J. E 41, 57 (2018). -[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, +[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model", J. Chem. Phys. 134, 085101 (2011). -[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA +[3] T.E. Ouldridge, "Coarse-grained modelling of DNA and DNA self-assembly", DPhil. University of Oxford (2011). [4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., "Introducing Improved structural properties and salt dependence into a coarse-grained model of DNA", J. Chem. Phys. 142, 234901 (2015). -[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level +[5] P. Sulc, F. Romano, T.E. Ouldridge, et al., "A nucleotide-level coarse-grained model of RNA", J. Chem. Phys. 140, 235102 (2014). -[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent +[6] P. Sulc, F. Romano, T.E. Ouldridge, et al., "Sequence-dependent thermodynamics of a coarse-grained DNA model", -J. Chem. Phys. 137, 135101 (2012). +J. Chem. Phys. 137, 135101 (2012). -[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and -gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, +[7] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and +gradient thermostats for rigid body dynamics", J. Chem. Phys. 142, 144114 (2015). Example input and data files can be found in -/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. -Python setup tools which create single straight or helical DNA or RNA -strands as well as DNA or RNA duplexes or arrays of duplexes can be -found in /examples/USER/cgdna/util/. A technical report with more -general information on the model, its implementation and performance +/examples/USER/cgdna/examples/oxDNA/, /oxDNA2/ and /oxRNA2/. +Python setup tools which create single straight or helical DNA or RNA +strands as well as DNA or RNA duplexes or arrays of duplexes can be +found in /examples/USER/cgdna/util/. A technical report with more +general information on the model, its implementation and performance as well as the structure of the data and input file can be found in /doc/src/PDF/USER-CGDNA.pdf. @@ -65,7 +65,7 @@ oliver d o t henrich a t strath d o t ac d o t uk ** Bond styles provided by this package: -bond_oxdna_fene.cpp: backbone connectivity, +bond_oxdna_fene.cpp: backbone connectivity, a modified FENE potential (see [2,3]) bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [4]) @@ -86,20 +86,20 @@ pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides -pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: +pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp: corresponding pair styles in oxDNA2 (see [4]) -pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp, -pair_oxrna2_xstk.cpp: +pair_oxrna2_excv.cpp, pair_oxrna2_stk.cpp, pair_oxrna2_hbond.cpp, +pair_oxrna2_xstk.cpp: corresponding pair styles in oxDNA2 (see [5]) -pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp: +pair_oxdna2_dh.cpp, pair_oxrna2_dh.cpp: Debye-Hueckel electrostatic interaction between backbone sites ** Fixes provided by this package: fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C" - in above Ref. [7] + in above Ref. [7] fix_nve_dot.cpp: NVE-type rigid body integrator without noise diff --git a/src/USER-DIFFRACTION/README b/src/USER-DIFFRACTION/README index 00203aeae2..2f146c4c94 100644 --- a/src/USER-DIFFRACTION/README +++ b/src/USER-DIFFRACTION/README @@ -1,41 +1,41 @@ This package contains the commands needed to calculate x-ray and -electron diffraction intensities based on kinematic diffraction +electron diffraction intensities based on kinematic diffraction theory. Detailed discription of the computation can be found in the following works: -Coleman, S.P., Spearot, D.E., Capolungo, L. (2013) Virtual -diffraction analysis of Ni [010] symmetric tilt grain boundaries, -Modelling and Simulation in Materials Science and Engineering, 21 +Coleman, S.P., Spearot, D.E., Capolungo, L. (2013) Virtual +diffraction analysis of Ni [010] symmetric tilt grain boundaries, +Modelling and Simulation in Materials Science and Engineering, 21 055020. doi:10.1088/0965-0393/21/5/055020 -Coleman, S.P., Sichani, M.M., Spearot, D.E. (2014) A computational -algorithm to produce virtual x-ray and electron diffraction patterns -from atomistic simulations, JOM, 66 (3), 408-416. -doi:10.1007/s11837-013-0829-3 +Coleman, S.P., Sichani, M.M., Spearot, D.E. (2014) A computational +algorithm to produce virtual x-ray and electron diffraction patterns +from atomistic simulations, JOM, 66 (3), 408-416. +doi:10.1007/s11837-013-0829-3 -Coleman, S.P., Pamidighantam, S. Van Moer, M., Wang, Y., Koesterke, L. -Spearot D.E (2014) Performance improvement and workflow development -of virtual diffraction calculations, XSEDE14, +Coleman, S.P., Pamidighantam, S. Van Moer, M., Wang, Y., Koesterke, L. +Spearot D.E (2014) Performance improvement and workflow development +of virtual diffraction calculations, XSEDE14, doi:10.1145/2616498.2616552 --------------------------------- User-diffraction includes: -1) compute_xrd : calculate x-ray diffraction intensities as a +1) compute_xrd : calculate x-ray diffraction intensities as a scattering angle (2theta) 2) compute_xrd_consts.h : coefficients used for x-ray atomic scattering factors listed by element -3) compute saed : calculate 3D diffraction intensities for the - purpose of creating selected area electron +3) compute saed : calculate 3D diffraction intensities for the + purpose of creating selected area electron diffraction patterns 4) compute_xrd_consts.h : coefficients used for electron atomic scattering factors listed by element -3) fix saed/vtk : writes 3D diffraction intensity data calculated +3) fix saed/vtk : writes 3D diffraction intensity data calculated with "compute saed" in vtk format @@ -48,8 +48,8 @@ examples/USER/diffraction. AUTHOR INFORMATION: -The person who created this package is Shawn P. Coleman -(shawn.p.coleman8.ctr at mail.mil) while at the University of +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. Co-Author: Douglas Spearot (University of Arkansas) diff --git a/src/USER-EFF/README b/src/USER-EFF/README index aaa11c3494..5caa1cd7da 100644 --- a/src/USER-EFF/README +++ b/src/USER-EFF/README @@ -46,7 +46,7 @@ Chemistry and Chemical Engineering, 139-74 Phone: (626) 395-3591 e-mail: ajaramil@wag.caltech.edu -Co-Authors: +Co-Authors: Julius Su (jsu@wag.caltech.edu) William A. Goddard III (wag@wag.caltech.edu) @@ -57,11 +57,11 @@ LAMMPS architecture and for their help in customizing some of the required LAMMPS core modules. Version 01/2010: Special thanks to: -- Hai Xiao (Caltech) for reviewing the fixed-core implementation and +- Hai Xiao (Caltech) for reviewing the fixed-core implementation and providing useful insights to improve it, and for his work on the effective core pseudopotential. -- Vaclav Cvicek (Caltech) for thoroughly revising the units, for finding a bug in the +- Vaclav Cvicek (Caltech) for thoroughly revising the units, for finding a bug in the fix_langevin_eff radial scaling factors, and for suggesting changes to clean-up the code. -- Patrick Theofanis (Caltech) for providing an optimized set of parameters for the Si ECP +- Patrick Theofanis (Caltech) for providing an optimized set of parameters for the Si ECP (default) and for providing basic cases. - Qi An (Caltech) for providing feedback on usage, application cases, and testing. @@ -76,16 +76,16 @@ different eFF energy components (eke, epauli, ecoul and errestrain), fixed radial scaling factors in the eff langevin thermostat. 12/2011: Added support for "zero" option in fix langevin/eff (see doc), and -adjusted fix_langevin_eff.cpp to correctly thermostat between nuclear and electronic dof +adjusted fix_langevin_eff.cpp to correctly thermostat between nuclear and electronic dof (required additional scaling of friction term in the Langevin equations of motion). Radial electron mass now scales as a function of system dimension. Bug fixes: (10-2011): Thanks to Christian Chenard-Lemire (U Montreal) for reporting a bug in the fixed pair_eff_cut.cpp fixedcore-pseudocore interactions (an incorrect index and a missing -elec-core call to account for the 2 electrons from the fixed core.) -(12-2011): Corrected undefined natom variable in fix_langevin_eff (recent changes in -main fix_langevin class caused compilation error in user-eff). +elec-core call to account for the 2 electrons from the fixed core.) +(12-2011): Corrected undefined natom variable in fix_langevin_eff (recent changes in +main fix_langevin class caused compilation error in user-eff). Corrected thermostat in fix langevin/eff as described in version 12/2011. diff --git a/src/USER-FEP/README b/src/USER-FEP/README index 90e58f9e82..83ee6b3543 100644 --- a/src/USER-FEP/README +++ b/src/USER-FEP/README @@ -17,6 +17,6 @@ Applied Physics/Theory of Polymers and Soft Matter, Eindhoven University of Technology (TU/e), The Netherlands Contact him in case of problems with this pair style. -Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at +Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at Technical University of Darmstadt (e.voyiatzis at theo.chemie.tu-darmstadt.de) Contact him in case of problems with these pair styles. diff --git a/src/USER-INTEL/TEST/run_benchmarks.sh b/src/USER-INTEL/TEST/run_benchmarks.sh index e26c633b68..01ddfbebf3 100755 --- a/src/USER-INTEL/TEST/run_benchmarks.sh +++ b/src/USER-INTEL/TEST/run_benchmarks.sh @@ -6,7 +6,7 @@ # --------------------- MPI Launch Command -export MPI="mpirun" +export MPI="mpirun" #export MPI="numactl -p 1 mpirun" # -- Systems w/ MCDRAM in flat mode # ------------- Name and location of the LAMMPS binary diff --git a/src/USER-LB/README b/src/USER-LB/README index 290c2f923d..4f22986d84 100644 --- a/src/USER-LB/README +++ b/src/USER-LB/README @@ -39,15 +39,15 @@ cdennist@uwo.ca Fixes provided by this package: -fix_lb_fluid.cpp: fix used to create the lattice-Boltzmann fluid on a +fix_lb_fluid.cpp: fix used to create the lattice-Boltzmann fluid on a grid covering the LAMMPS simulation domain. -fix_momentum_lb.cpp: fix used to subtract off the total (atom plus fluid) +fix_momentum_lb.cpp: fix used to subtract off the total (atom plus fluid) linear momentum from the system. fix_pc.cpp: integration algorithm for individual atoms. -fix_rigid_pc_sphere.cpp: integration algorithm for rigid spherical +fix_rigid_pc_sphere.cpp: integration algorithm for rigid spherical collections of atoms. fix_viscous_lb.cpp: fix to add the fluid force to the atoms when using a diff --git a/src/USER-MESONT/README b/src/USER-MESONT/README index 8f481d9859..ce08731734 100644 --- a/src/USER-MESONT/README +++ b/src/USER-MESONT/README @@ -1,19 +1,19 @@ -USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon -nanotubes (CNTs). The model is based on a coarse-grained representation -of CNTs as "flexible cylinders" consisting of a variable number of -segments. Internal interactions within a CNT and the van der Waals -interaction between the tubes are described by a mesoscopic force -field designed and parameterized based on the results of atomic-level -molecular dynamics simulations. The description of the force field +USER-MESONT is a LAMMPS package for simulation of nanomechanics of carbon +nanotubes (CNTs). The model is based on a coarse-grained representation +of CNTs as "flexible cylinders" consisting of a variable number of +segments. Internal interactions within a CNT and the van der Waals +interaction between the tubes are described by a mesoscopic force +field designed and parameterized based on the results of atomic-level +molecular dynamics simulations. The description of the force field is provided in the papers listed below. -- -This package was created by Maxim Shugaev (mvs9t@virginia.edu) +This package was created by Maxim Shugaev (mvs9t@virginia.edu) at the University of Virginia. -The Fortran library implementing basic level functions describing stretching, +The Fortran library implementing basic level functions describing stretching, bending, and intertube components of the mesoscopic CNT force field, used -by this package is developed by Alexey N. Volkov (avolkov1@ua.edu) +by this package is developed by Alexey N. Volkov (avolkov1@ua.edu) at the University of Alabama. -- @@ -21,69 +21,69 @@ at the University of Alabama. The following commands are contained in this package: atom_style mesont - This command enables mesont atom_style containing variables used for + This command enables mesont atom_style containing variables used for further commands in USER-MESONT. -pair_style mesont/tpm cut table_path BendingMode TPMType - This command activates a pair_style describing CNT mesoscopic tubular - potential model (TPM) force field. "cut" is cutoff distance that should - be set to be at least max(2.0*L, sqrt(L^2/2 + (2.0*R + Tcut)^2)), - where L is the maximum segment length, R is the maximum tube radius, - and Tcut = 10.2 A is the maximum distance between surfaces of interacting +pair_style mesont/tpm cut table_path BendingMode TPMType + This command activates a pair_style describing CNT mesoscopic tubular + potential model (TPM) force field. "cut" is cutoff distance that should + be set to be at least max(2.0*L, sqrt(L^2/2 + (2.0*R + Tcut)^2)), + where L is the maximum segment length, R is the maximum tube radius, + and Tcut = 10.2 A is the maximum distance between surfaces of interacting segments. However, the recommended cutoff is 3L. compute mesont - This command allows evaluation of per atom and total values of stretching, - bending, and intertube interaction components of energies. Use the following + This command allows evaluation of per atom and total values of stretching, + bending, and intertube interaction components of energies. Use the following flags: 'estretch', 'ebend', 'etube'. -- References: -L. V. Zhigilei, C. Wei, and D. Srivastava, Mesoscopic model for dynamic +L. V. Zhigilei, C. Wei, and D. Srivastava, Mesoscopic model for dynamic simulations of carbon nanotubes, Phys. Rev. B 71, 165417, 2005. -A. N. Volkov and L. V. Zhigilei, Structural stability of carbon nanotube +A. N. Volkov and L. V. Zhigilei, Structural stability of carbon nanotube films: The role of bending buckling, ACS Nano 4, 6187-6195, 2010. -A. N. Volkov, K. R. Simov, and L. V. Zhigilei, Mesoscopic model for simulation -of CNT-based materials, Proceedings of the ASME International Mechanical -Engineering Congress and Exposition (IMECE2008), ASME paper IMECE2008-68021, +A. N. Volkov, K. R. Simov, and L. V. Zhigilei, Mesoscopic model for simulation +of CNT-based materials, Proceedings of the ASME International Mechanical +Engineering Congress and Exposition (IMECE2008), ASME paper IMECE2008-68021, 2008. -A. N. Volkov and L. V. Zhigilei, Mesoscopic interaction potential for carbon -nanotubes of arbitrary length and orientation, J. Phys. Chem. C 114, 5513-5531, +A. N. Volkov and L. V. Zhigilei, Mesoscopic interaction potential for carbon +nanotubes of arbitrary length and orientation, J. Phys. Chem. C 114, 5513-5531, 2010. -B. K. Wittmaack, A. H. Banna, A. N. Volkov, L. V. Zhigilei, Mesoscopic -modeling of structural self-organization of carbon nanotubes into vertically +B. K. Wittmaack, A. H. Banna, A. N. Volkov, L. V. Zhigilei, Mesoscopic +modeling of structural self-organization of carbon nanotubes into vertically aligned networks of nanotube bundles, Carbon 130, 69-86, 2018. -B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Mesoscopic modeling of the -uniaxial compression and recovery of vertically aligned carbon nanotube +B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Mesoscopic modeling of the +uniaxial compression and recovery of vertically aligned carbon nanotube forests, Compos. Sci. Technol. 166, 66-85, 2018. -B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Phase transformation as the -mechanism of mechanical deformation of vertically aligned carbon nanotube +B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Phase transformation as the +mechanism of mechanical deformation of vertically aligned carbon nanotube arrays: Insights from mesoscopic modeling, Carbon 143, 587-597, 2019. -A. N. Volkov and L. V. Zhigilei, Scaling laws and mesoscopic modeling of -thermal conductivity in carbon nanotube materials, Phys. Rev. Lett. 104, +A. N. Volkov and L. V. Zhigilei, Scaling laws and mesoscopic modeling of +thermal conductivity in carbon nanotube materials, Phys. Rev. Lett. 104, 215902, 2010. -A. N. Volkov, T. Shiga, D. Nicholson, J. Shiomi, and L. V. Zhigilei, Effect -of bending buckling of carbon nanotubes on thermal conductivity of carbon +A. N. Volkov, T. Shiga, D. Nicholson, J. Shiomi, and L. V. Zhigilei, Effect +of bending buckling of carbon nanotubes on thermal conductivity of carbon nanotube materials, J. Appl. Phys. 111, 053501, 2012. -A. N. Volkov and L. V. Zhigilei, Heat conduction in carbon nanotube materials: -Strong effect of intrinsic thermal conductivity of carbon nanotubes, Appl. +A. N. Volkov and L. V. Zhigilei, Heat conduction in carbon nanotube materials: +Strong effect of intrinsic thermal conductivity of carbon nanotubes, Appl. Phys. Lett. 101, 043113, 2012. -W. M. Jacobs, D. A. Nicholson, H. Zemer, A. N. Volkov, and L. V. Zhigilei, -Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic +W. M. Jacobs, D. A. Nicholson, H. Zemer, A. N. Volkov, and L. V. Zhigilei, +Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic modeling and mesoscopic description, Phys. Rev. B 86, 165414, 2012. -A. N. Volkov and A. H. Banna, Mesoscopic computational model of covalent -cross-links and mechanisms of load transfer in cross-linked carbon nanotube +A. N. Volkov and A. H. Banna, Mesoscopic computational model of covalent +cross-links and mechanisms of load transfer in cross-linked carbon nanotube films with continuous networks of bundles, Comp. Mater. Sci. 176, 109410, 2020. diff --git a/src/USER-MGPT/README b/src/USER-MGPT/README index dac08c5f0e..151bd02b5d 100644 --- a/src/USER-MGPT/README +++ b/src/USER-MGPT/README @@ -1,17 +1,17 @@ -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 +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 +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 +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. +optimized matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. See the doc page for the pair_style mgpt command for full details on using this package in LAMMPS. In particular, the user should note that @@ -22,10 +22,10 @@ steps to perform constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples before proceeding to more complex simulations. -Specific MGPT potential data for the transition metals tantalum +Specific MGPT potential data for the transition metals tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), and -vanadium (V6.1 potentials) are contained in the LAMMPS "potentials" -directory. It is expected that MGPT potentials for additional +vanadium (V6.1 potentials) are contained in the LAMMPS "potentials" +directory. It is expected that MGPT potentials for additional materials will be added over time. The persons who created the USER-MGPT package are Tomas Oppelstrup diff --git a/src/USER-MOFFF/README b/src/USER-MOFFF/README index 1cc74392dc..237ac9ba53 100644 --- a/src/USER-MOFFF/README +++ b/src/USER-MOFFF/README @@ -1,32 +1,32 @@ -This Package implements pair, angle and improper styles needed to employ -the MOF-FF force field by Schmid and coworkers with LAMMPS. +This Package implements pair, angle and improper styles needed to employ +the MOF-FF force field by Schmid and coworkers with LAMMPS. MOF-FF is a first principles derived force field with the primary aim -to simulate MOFs and related porous framework materials, using spherical +to simulate MOFs and related porous framework materials, using spherical Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B 2013, 250, 1128-1141. -For the usage of MOF-FF see the example in the example directory as +For the usage of MOF-FF see the example in the example directory as well as the "MOF+" website (https://www.mofplus.org/content/show/MOF-FF). -The package provides the following features: +The package provides the following features: -* a dispersion damped Buckhingham potential with spherical Gaussian type +* a dispersion damped Buckhingham potential with spherical Gaussian type charges (dsf and long-range treatment of charges) * a modified angle/class2 including 6th order polynomial -* a modified angle/cosine style which adds a dispersion damped Buckhingham +* a modified angle/cosine style which adds a dispersion damped Buckhingham 1-3 interaction analog to the dihedral/charmm style -* an improper style following the Wilson-Decius definition of the +* an improper style following the Wilson-Decius definition of the out-of-plane angle See the file doc/drude_tutorial.html for getting started. -See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2", +See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2", "angle_style cosine/buck6d", and "improper_style inversion/harmonic" -commands to get started. Also see the above mentioned website and +commands to get started. Also see the above mentioned website and literature for further documentation about the force field. There are example scripts for using this force field in examples/USER/mofff. The creators of this package are Hendrik Heenen (hendrik.heenen at mytum.de) -and Rochus Schmid (rochus.schmid at rub.de). Contact them directly if you +and Rochus Schmid (rochus.schmid at rub.de). Contact them directly if you have questions. diff --git a/src/USER-PLUMED/README b/src/USER-PLUMED/README index 11ca0a7281..f46b2cd9bd 100644 --- a/src/USER-PLUMED/README +++ b/src/USER-PLUMED/README @@ -1,43 +1,43 @@ This package implements the "fix plumed" command, which can be used in a LAMMPS input script. -The fix allows enhanced sampling methods such as umbrella sampling and -metadynamics to be used. Furthermore, PLUMED can be used to perform a +The fix allows enhanced sampling methods such as umbrella sampling and +metadynamics to be used. Furthermore, PLUMED can be used to perform a wide range of analyses on trajectories on the fly as they are generated. The package uses the "PLUMED" library, whose source code is not included -in the LAMMPS source code distribution. The files in the USER-PLUMED package -folder implement an interface between LAMMPS and PLUMED, that are written +in the LAMMPS source code distribution. The files in the USER-PLUMED package +folder implement an interface between LAMMPS and PLUMED, that are written and maintained by Gareth Tribello (gareth.tribello@gmail.com). -PLUMED must instead be downloaded and compiled separately to LAMMPS. This building -and compiling of PLUMED can be done before or after the building of LAMMPS as LAMMPS -can call PLUMED as a dynamic library. There is also the possibility to link PLUEMD -statically. In this case a copy of PLUMED must be downloaded into the lib/plumed -directory. This copy of PLUMED will then always be linked into the code at compile -time. +PLUMED must instead be downloaded and compiled separately to LAMMPS. This building +and compiling of PLUMED can be done before or after the building of LAMMPS as LAMMPS +can call PLUMED as a dynamic library. There is also the possibility to link PLUEMD +statically. In this case a copy of PLUMED must be downloaded into the lib/plumed +directory. This copy of PLUMED will then always be linked into the code at compile +time. However you decide to link PLUMED (statically or dynamically) you must run the command: make yes-user-plumed -before compiling LAMMPS in order to enable the module. In addition, if you have chosen to -link PLUMED dynamically you must ensure that PLUMED is in your -PATH when running a LAMMPS calculation that takes advantage of PLUMED. If -PLUMED is linked as a runtime library and if PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters -the fix plumed command in its input. To be clear, however, a LAMMPS executable that was dynamically linked with PLUMED will run -even if PLUMED is not in the path if as long as the input does not contain a fix +before compiling LAMMPS in order to enable the module. In addition, if you have chosen to +link PLUMED dynamically you must ensure that PLUMED is in your +PATH when running a LAMMPS calculation that takes advantage of PLUMED. If +PLUMED is linked as a runtime library and if PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters +the fix plumed command in its input. To be clear, however, a LAMMPS executable that was dynamically linked with PLUMED will run +even if PLUMED is not in the path if as long as the input does not contain a fix plumed command. -If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS. You can -download a tar ball into that directory or you can clone the plumed2 repository from github there. Once you have created a -directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing -the usual commands. It is worth noting that we have provided a script that will download and build PLUMED for you with +If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS. You can +download a tar ball into that directory or you can clone the plumed2 repository from github there. Once you have created a +directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing +the usual commands. It is worth noting that we have provided a script that will download and build PLUMED for you with a minimal set of options. To run this script you need to issue the following command: make lib-plumed args="-b" -in the src directory. +in the src directory. More info about the PLUMED library can be found at: @@ -55,8 +55,8 @@ M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Don Comp. Phys. Comm. 180, 1961 (2009) https://doi.org/10.1016/j.cpc.2009.05.011 -Instructions explaining how to use PLUMED and LAMMPS in tandem can be found on the PLUMED website, which also gives -numerous example scripts for PLUMED as well as citations to articles that dcoment the various methods that are +Instructions explaining how to use PLUMED and LAMMPS in tandem can be found on the PLUMED website, which also gives +numerous example scripts for PLUMED as well as citations to articles that dcoment the various methods that are implemented within PLUMED. There are also example scripts for using this package in the folder diff --git a/src/USER-QUIP/README b/src/USER-QUIP/README index f7bd811236..5bd9c45181 100644 --- a/src/USER-QUIP/README +++ b/src/USER-QUIP/README @@ -1,6 +1,6 @@ This package provides the pair_style quip command. This pair style provides an interface to the QUIP/libAtoms library, which includes a -variety of interatomic potentials, including Gaussian Approximation +variety of interatomic potentials, including Gaussian Approximation Potential (GAP) models. See lib/quip/README for more information on how to build LAMMPS diff --git a/src/USER-SCAFACOS/Install.sh b/src/USER-SCAFACOS/Install.sh index 964212fc51..f7df569cf2 100755 --- a/src/USER-SCAFACOS/Install.sh +++ b/src/USER-SCAFACOS/Install.sh @@ -46,7 +46,7 @@ if (test $1 = 1) then elif (test $1 = 0) then - if (test -e ../Makefile.package) then + if (test -e ../Makefile.package) then sed -i -e 's/`.*scafacos.*` //' ../Makefile.package sed -i -e 's/[^ \t]*scafacos[^ \t]* //' ../Makefile.package fi diff --git a/src/USER-SPH/README b/src/USER-SPH/README index 1658ff2f7a..97afba8d12 100644 --- a/src/USER-SPH/README +++ b/src/USER-SPH/README @@ -1,13 +1,13 @@ 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 +* 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 +* commands to set internal energy and density of particles from the input script -* output commands to access internal energy and density for dumping and +* output commands to access internal energy and density for dumping and thermo output See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started. diff --git a/src/USER-TALLY/README b/src/USER-TALLY/README index 2167c72eb5..8cb9bcdd6b 100644 --- a/src/USER-TALLY/README +++ b/src/USER-TALLY/README @@ -7,7 +7,7 @@ users have asked for such a facility over time. The currently provided compute styles are mostly meant as a demonstration for how to use this facility and provide an alternative approach to using features like compute group/group -or compute heat/flux. Its application is limited to pairwise +or compute heat/flux. Its application is limited to pairwise additive potentials that use the standard Pair::ev_tally() method to accumulate energy (and virial). diff --git a/src/VORONOI/README b/src/VORONOI/README index ede104a678..d099cf9177 100644 --- a/src/VORONOI/README +++ b/src/VORONOI/README @@ -20,8 +20,8 @@ you can test it using an input file from the examples dir: ./lmp_serial < lammps/examples/voronoi/in.voronoi | grep '^TEST_' -The output should conclude with 'TEST_DONE' and every line should -report an error of 0%. +The output should conclude with 'TEST_DONE' and every line should +report an error of 0%. == Credits and license ==