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6
doc/src/Section_example.txt
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@ -105,8 +105,8 @@ web site.
If you uncomment the "dump image"_dump_image.html line(s) in the input If you uncomment the "dump image"_dump_image.html line(s) in the input
script a series of JPG images will be produced by the run (assuming script a series of JPG images will be produced by the run (assuming
you built LAMMPS with JPG support; see "Section start you built LAMMPS with JPG support; see "Section
2.2"_Section_start.html for details). These can be viewed 2.2"_Section_start.html#start_2 for details). These can be viewed
individually or turned into a movie or animated by tools like individually or turned into a movie or animated by tools like
ImageMagick or QuickTime or various Windows-based tools. See the ImageMagick or QuickTime or various Windows-based tools. See the
"dump image"_dump_image.html doc page for more details. E.g. this "dump image"_dump_image.html doc page for more details. E.g. this
@ -136,5 +136,5 @@ The USER directory has a large number of sub-directories which
correspond by name to a USER package. They contain scripts that correspond by name to a USER package. They contain scripts that
illustrate how to use the command(s) provided in that package. Many illustrate how to use the command(s) provided in that package. Many
of the sub-directories have their own README files which give further of the sub-directories have their own README files which give further
instructions. See the "Section packages"_Section_packages.html doc instructions. See the "Section 4"_Section_packages.html doc
page for more info on specific USER packages. page for more info on specific USER packages.

109
doc/src/Section_packages.txt
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@ -71,16 +71,16 @@ Package, Description, Author(s), Doc page, Example, Library
"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, - "COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, - "CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
"DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, - "DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu "GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section 5.3.1"_accelerate_gpu.html, gpu, lib/gpu
"GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, - "GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM "KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5"_accelerate_kokkos.html, kokkos, lib/kokkos "KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5.3.3"_accelerate_kokkos.html, kokkos, lib/kokkos
"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, - "KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, - "MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam "MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, - "MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, - "MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, - "OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section 5.3.5"_accelerate_opt.html, -, -
"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, - "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
@ -127,7 +127,6 @@ of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution. it is a third-party library not included in the LAMMPS distribution.
See details on all of this below for individual packages. See details on all of this below for individual packages.
p.s.: are we ever going to get commit messages from you? ;-)
:line :line
@ -150,7 +149,7 @@ make machine :pre
Make.py -p ^asphere -a machine :pre Make.py -p ^asphere -a machine :pre
Supporting info: "Section howto 6.14"_Section_howto.html#howto_14, Supporting info: "Section 6.14"_Section_howto.html#howto_14,
"pair_style gayberne"_pair_gayberne.html, "pair_style "pair_style gayberne"_pair_gayberne.html, "pair_style
resquared"_pair_resquared.html, resquared"_pair_resquared.html,
"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf, "doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,
@ -279,9 +278,8 @@ Contents: Compute and pair styles that implement the adiabatic
core/shell model for polarizability. The compute temp/cs command core/shell model for polarizability. The compute temp/cs command
measures the temperature of a system with core/shell particles. The measures the temperature of a system with core/shell particles. The
pair styles augment Born, Buckingham, and Lennard-Jones styles with pair styles augment Born, Buckingham, and Lennard-Jones styles with
core/shell capabilities. See "Section howto core/shell capabilities. See "Section 6.26"_Section_howto.html#howto_26
6.26"_Section_howto.html#howto_26 for an overview of how to use the for an overview of how to use the package.
package.
To install via make or Make.py: To install via make or Make.py:
@ -297,8 +295,8 @@ make machine :pre
Make.py -p ^coreshell -a machine :pre Make.py -p ^coreshell -a machine :pre
Supporting info: "Section howto Supporting info: "Section 6.26"_Section_howto.html#howto_26,
6.26"_Section_howto.html#howto_26, "compute temp/cs"_compute_temp_cs.html, "compute temp/cs"_compute_temp_cs.html,
"pair_style born/coul/long/cs"_pair_cs.html, "pair_style "pair_style born/coul/long/cs"_pair_cs.html, "pair_style
buck/coul/long/cs"_pair_cs.html, pair_style buck/coul/long/cs"_pair_cs.html, pair_style
lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell
@ -335,7 +333,7 @@ GPU package :link(GPU),h5
Contents: Dozens of pair styles and a version of the PPPM long-range Contents: Dozens of pair styles and a version of the PPPM long-range
Coulombic solver for NVIDIA GPUs. All of them have a "gpu" in their Coulombic solver for NVIDIA GPUs. All of them have a "gpu" in their
style name. "Section accelerate gpu"_accelerate_gpu.html gives style name. "Section 5.3.1"_accelerate_gpu.html gives
details of what hardware and Cuda software is required on your system, details of what hardware and Cuda software is required on your system,
and how to build and use this package. See the KOKKOS package, which and how to build and use this package. See the KOKKOS package, which
also has GPU-enabled styles. also has GPU-enabled styles.
@ -380,10 +378,11 @@ make machine :pre
Make.py -p ^gpu -a machine :pre Make.py -p ^gpu -a machine :pre
Supporting info: src/GPU/README, lib/gpu/README, "Section Supporting info: src/GPU/README, lib/gpu/README,
acclerate"_Section_accelerate.html, "Section accelerate "Section 5.3"_Section_accelerate.html#acc_3,
gpu"_accelerate_gpu.html, Pair Styles section of "Section commands "Section 5.3.1"_accelerate_gpu.html,
3.5"_Section_commands.html#cmd_5 for any pair style listed with a (g), Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
for any pair style listed with a (g),
"kspace_style"_kspace_style.html, "package gpu"_package.html, "kspace_style"_kspace_style.html, "package gpu"_package.html,
examples/accelerate, bench/FERMI, bench/KEPLER examples/accelerate, bench/FERMI, bench/KEPLER
@ -409,7 +408,7 @@ make machine :pre
Make.py -p ^granular -a machine :pre Make.py -p ^granular -a machine :pre
Supporting info: "Section howto 6.6"_Section_howto.html#howto_6, "fix Supporting info: "Section 6.6"_Section_howto.html#howto_6, "fix
pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style
gran/hooke"_pair_gran.html, "pair_style gran/hooke"_pair_gran.html, "pair_style
gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
@ -453,7 +452,7 @@ Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
which run with the Kokkos library to provide optimization for which run with the Kokkos library to provide optimization for
multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
native mode). All of them have a "kk" in their style name. "Section native mode). All of them have a "kk" in their style name. "Section
accelerate kokkos"_accelerate_kokkos.html gives details of what 5.3.3"_accelerate_kokkos.html gives details of what
hardware and software is required on your system, and how to build and hardware and software is required on your system, and how to build and
use this package. See the GPU, OPT, USER-INTEL, USER-OMP packages, use this package. See the GPU, OPT, USER-INTEL, USER-OMP packages,
which also provide optimizations for the same range of hardware. which also provide optimizations for the same range of hardware.
@ -473,9 +472,8 @@ the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
below, you can use the Make.py script with its "-kokkos" option to below, you can use the Make.py script with its "-kokkos" option to
choose which hardware to build for. Type "python src/Make.py -h choose which hardware to build for. Type "python src/Make.py -h
-kokkos" to see the details. If these methods do not work on your -kokkos" to see the details. If these methods do not work on your
system, you will need to read the "Section accelerate system, you will need to read the "Section 5.3.3"_accelerate_kokkos.html
kokkos"_accelerate_kokkos.html doc page for details of what doc page for details of what Makefile.machine settings are needed.
Makefile.machine settings are needed.
To install via make or Make.py for each of 3 hardware options: To install via make or Make.py for each of 3 hardware options:
@ -495,11 +493,11 @@ make machine :pre
Make.py -p ^kokkos -a machine :pre Make.py -p ^kokkos -a machine :pre
Supporting info: src/KOKKOS/README, lib/kokkos/README, "Section Supporting info: src/KOKKOS/README, lib/kokkos/README,
acclerate"_Section_accelerate.html, "Section accelerate "Section 5.3"_Section_accelerate.html#acc_3,
kokkos"_accelerate_kokkos.html, Pair Styles section of "Section "Section 5.3.3"_accelerate_kokkos.html,
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
with a (k), "package kokkos"_package.html, for any pair style listed with a (k), "package kokkos"_package.html,
examples/accelerate, bench/FERMI, bench/KEPLER examples/accelerate, bench/FERMI, bench/KEPLER
:line :line
@ -514,7 +512,7 @@ particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
Building with the KSPACE package requires a 1d FFT library be present Building with the KSPACE package requires a 1d FFT library be present
on your system for use by the PPPM solvers. This can be the KISS FFT on your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, or 3rd party libraries like FFTW or a library provided with LAMMPS, or 3rd party libraries like FFTW or a
vendor-supplied FFT library. See step 6 of "Section start vendor-supplied FFT library. See step 6 of "Section
2.2.2"_Section_start.html#start_2_2 of the manual for details of how 2.2.2"_Section_start.html#start_2_2 of the manual for details of how
to select different FFT options in your machine Makefile. The Make.py to select different FFT options in your machine Makefile. The Make.py
tool has an "-fft" option which can insert these settings into your tool has an "-fft" option which can insert these settings into your
@ -536,12 +534,13 @@ make machine :pre
Make.py -p ^kspace -a machine :pre Make.py -p ^kspace -a machine :pre
Supporting info: "kspace_style"_kspace_style.html, Supporting info: "kspace_style"_kspace_style.html,
"doc/PDF/kspace.pdf"_PDF/kspace.pdf, "Section howto "doc/PDF/kspace.pdf"_PDF/kspace.pdf,
6.7"_Section_howto.html#howto_7, "Section howto "Section 6.7"_Section_howto.html#howto_7,
6.8"_Section_howto.html#howto_8, "Section howto "Section 6.8"_Section_howto.html#howto_8,
6.9"_Section_howto.html#howto_9, "pair_style coul"_pair_coul.html, "Section 6.9"_Section_howto.html#howto_9,
other pair style command doc pages which have "long" or "msm" in their "pair_style coul"_pair_coul.html, other pair style command doc pages
style name, examples/peptide, bench/in.rhodo which have "long" or "msm" in their style name,
examples/peptide, bench/in.rhodo
:line :line
@ -568,7 +567,7 @@ Make.py -p ^manybody -a machine :pre
Supporting info: Supporting info:
Examples: Pair Styles section of "Section commands Examples: Pair Styles section of "Section
3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim, 3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
examples/nb3d, examples/vashishta examples/nb3d, examples/vashishta
@ -700,9 +699,9 @@ Supporting info:"atom_style"_atom_style.html,
"dihedral_style"_dihedral_style.html, "dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html, "pair_style "improper_style"_improper_style.html, "pair_style
hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style
lj/charmm/coul/charmm"_pair_charmm.html, "Section howto lj/charmm/coul/charmm"_pair_charmm.html,
6.3"_Section_howto.html#howto_3, examples/micelle, examples/peptide, "Section 6.3"_Section_howto.html#howto_3,
bench/in.chain, bench/in.rhodo examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo
:line :line
@ -738,7 +737,7 @@ OPT package :link(OPT),h5
Contents: A handful of pair styles with an "opt" in their style name Contents: A handful of pair styles with an "opt" in their style name
which are optimized for improved CPU performance on single or multiple which are optimized for improved CPU performance on single or multiple
cores. These include EAM, LJ, CHARMM, and Morse potentials. "Section cores. These include EAM, LJ, CHARMM, and Morse potentials. "Section
accelerate opt"_accelerate_opt.html gives details of how to build and 5.3.5"_accelerate_opt.html gives details of how to build and
use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages, use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages,
which also have styles optimized for CPU performance. which also have styles optimized for CPU performance.
@ -763,10 +762,10 @@ make machine :pre
Make.py -p ^opt -a machine :pre Make.py -p ^opt -a machine :pre
Supporting info: "Section acclerate"_Section_accelerate.html, "Section Supporting info: "Section 5.3"_Section_accelerate.html#acc_3,
accelerate opt"_accelerate_opt.html, Pair Styles section of "Section "Section 5.3.5"_accelerate_opt.html, Pair Styles section of
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed "Section 3.5"_Section_commands.html#cmd_5 for any pair style
with an (o), examples/accelerate, bench/KEPLER listed with an (t), examples/accelerate, bench/KEPLER
:line :line
@ -845,14 +844,14 @@ PYTHON package :link(PYTHON),h5
Contents: A "python"_python.html command which allow you to execute Contents: A "python"_python.html command which allow you to execute
Python code from a LAMMPS input script. The code can be in a separate Python code from a LAMMPS input script. The code can be in a separate
file or embedded in the input script itself. See "Section python file or embedded in the input script itself. See "Section
11.2"_Section_python.html" for an overview of using Python from 11.2"_Section_python.html#py-2 for an overview of using Python from
LAMMPS and for other ways to use LAMMPS and Python together. LAMMPS and for other ways to use LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python shared Building with the PYTHON package assumes you have a Python shared
library available on your system, which needs to be a Python 2 library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not supported. The build uses the version, 2.6 or later. Python 3 is not yet supported. The build uses
contents of the lib/python/Makefile.lammps file to find all the Python the contents of the lib/python/Makefile.lammps file to find all the Python
files required in the build/link process. See the lib/python/README files required in the build/link process. See the lib/python/README
file if the settings in that file do not work on your system. Note file if the settings in that file do not work on your system. Note
that the Make.py script has a "-python" option to allow an alternate that the Make.py script has a "-python" option to allow an alternate
@ -950,7 +949,7 @@ REPLICA package :link(REPLICA),h5
Contents: A collection of multi-replica methods that are used by Contents: A collection of multi-replica methods that are used by
invoking multiple instances (replicas) of LAMMPS invoking multiple instances (replicas) of LAMMPS
simulations. Communication between individual replicas is performed in simulations. Communication between individual replicas is performed in
different ways by the different methods. See "Section howto different ways by the different methods. See "Section
6.5"_Section_howto.html#howto_5 for an overview of how to run 6.5"_Section_howto.html#howto_5 for an overview of how to run
multi-replica simulations in LAMMPS. Multi-replica methods included multi-replica simulations in LAMMPS. Multi-replica methods included
in the package are nudged elastic band (NEB), parallel replica in the package are nudged elastic band (NEB), parallel replica
@ -973,7 +972,7 @@ make machine :pre
Make.py -p ^replica -a machine :pre Make.py -p ^replica -a machine :pre
Supporting info: "Section howto 6.5"_Section_howto.html#howto_5, Supporting info: "Section 6.5"_Section_howto.html#howto_5,
"neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html, "neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html,
"run_style verlet/split"_run_style.html, examples/neb, examples/prd, "run_style verlet/split"_run_style.html, examples/neb, examples/prd,
examples/tad examples/tad
@ -1148,13 +1147,13 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
"USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, - "USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
"USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, - "USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
"USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md "USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, - "USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section 5.3.2"_accelerate_intel.html, examples/intel, -, -
"USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, - "USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, - "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, - "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, - "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, - "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, - "USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -
@ -1353,12 +1352,12 @@ USER-DRUDE package :link(USER-DRUDE),h5
Contents: This package contains methods for simulating polarizable Contents: This package contains methods for simulating polarizable
systems using thermalized Drude oscillators. It has computes, fixes, systems using thermalized Drude oscillators. It has computes, fixes,
and pair styles for this purpose. See "Section howto and pair styles for this purpose. See "Section
6.27"_Section_howto.html#howto_27 for an overview of how to use the 6.27"_Section_howto.html#howto_27 for an overview of how to use the
package. See src/USER-DRUDE/README for additional details. There are package. See src/USER-DRUDE/README for additional details. There are
auxiliary tools for using this package in tools/drude. auxiliary tools for using this package in tools/drude.
Supporting info: "Section howto 6.27"_Section_howto.html#howto_27, Supporting info: "Section 6.27"_Section_howto.html#howto_27,
src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix
drude/transform/*"_fix_drude_transform.html, "compute drude/transform/*"_fix_drude_transform.html, "compute
temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html, temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,
@ -1432,7 +1431,7 @@ USER-INTEL package :link(USER-INTEL),h5
Contents: Dozens of pair, bond, angle, dihedral, and improper styles Contents: Dozens of pair, bond, angle, dihedral, and improper styles
that are optimized for Intel CPUs and the Intel Xeon Phi (in offload that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
mode). All of them have an "intel" in their style name. "Section mode). All of them have an "intel" in their style name. "Section
accelerate intel"_accelerate_intel.html gives details of what hardware 5.3.2"_accelerate_intel.html gives details of what hardware
and compilers are required on your system, and how to build and use and compilers are required on your system, and how to build and use
this package. Also see src/USER-INTEL/README for more details. See this package. Also see src/USER-INTEL/README for more details. See
the KOKKOS, OPT, and USER-OMP packages, which also have CPU and the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
@ -1440,7 +1439,7 @@ Phi-enabled styles.
Supporting info: examples/accelerate, src/USER-INTEL/TEST Supporting info: examples/accelerate, src/USER-INTEL/TEST
"Section 5"_Section_accelerate.html#acc_3 "Section 5.3"_Section_accelerate.html#acc_3
Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
him directly if you have questions. him directly if you have questions.
@ -1532,7 +1531,7 @@ More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows: input script commands is as follows:
"Section 3"_Section_commands.html#cmd_5 "Section 3.5"_Section_commands.html#cmd_5
User-contributed features are listed at the bottom of the fix, User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections. compute, pair, etc sections.
@ -1609,7 +1608,7 @@ styles, and fix styles.
See this section of the manual to get started: See this section of the manual to get started:
"Section 5"_Section_accelerate.html#acc_3 "Section 5.3"_Section_accelerate.html#acc_3
The person who created this package is Axel Kohlmeyer at Temple U The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions. (akohlmey at gmail.com). Contact him directly if you have questions.

2
doc/src/Section_perf.txt
View File

@ -51,7 +51,7 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI
and bench/KEPLER dirs have input files and scripts and instructions and bench/KEPLER dirs have input files and scripts and instructions
for running the same (or similar) problems using OpenMP or GPU or Xeon for running the same (or similar) problems using OpenMP or GPU or Xeon
Phi acceleration options. See the README files in those dirs and the Phi acceleration options. See the README files in those dirs and the
"Section accelerate"_Section_accelerate.html doc pages for "Section 5.3"_Section_accelerate.html#acc_3 doc pages for
instructions on how to build LAMMPS and run on that kind of hardware. instructions on how to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the The bench/POTENTIALS directory has input files which correspond to the

56
doc/src/Section_start.txt
View File

@ -21,7 +21,6 @@ experienced users.
2.8 "Screen output"_#start_8 2.8 "Screen output"_#start_8
2.9 "Tips for users of previous versions"_#start_9 :all(b) 2.9 "Tips for users of previous versions"_#start_9 :all(b)
:line
:line :line
2.1 What's in the LAMMPS distribution :h4,link(start_1) 2.1 What's in the LAMMPS distribution :h4,link(start_1)
@ -70,12 +69,12 @@ launch a LAMMPS Windows executable on a Windows box.
This section has the following sub-sections: This section has the following sub-sections:
"Read this first"_#start_2_1 2.2.1 "Read this first"_#start_2_1
"Steps to build a LAMMPS executable"_#start_2_2 2.2.1 "Steps to build a LAMMPS executable"_#start_2_2
"Common errors that can occur when making LAMMPS"_#start_2_3 2.2.3 "Common errors that can occur when making LAMMPS"_#start_2_3
"Additional build tips"_#start_2_4 2.2.4 "Additional build tips"_#start_2_4
"Building for a Mac"_#start_2_5 2.2.5 "Building for a Mac"_#start_2_5
"Building for Windows"_#start_2_6 :ul 2.2.6 "Building for Windows"_#start_2_6 :all(b)
:line :line
@ -559,8 +558,7 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
files created when LAMMPS is built, for either all builds or for a files created when LAMMPS is built, for either all builds or for a
particular machine. particular machine.
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
As explained above, any of these 3 settings can be specified on the As explained above, any of these 3 settings can be specified on the
LMP_INC line in your low-level src/MAKE/Makefile.foo. LMP_INC line in your low-level src/MAKE/Makefile.foo.
@ -612,7 +610,7 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
Building for a Mac :h5,link(start_2_5) Building for a Mac :h5,link(start_2_5)
OS X is BSD Unix, so it should just work. See the OS X is a derivative of BSD Unix, so it should just work. See the
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files. src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
:line :line
@ -637,9 +635,9 @@ happy to distribute contributed instructions and modifications, but
we cannot provide support for those. we cannot provide support for those.
With the so-called "Anniversary Update" to Windows 10, there is a With the so-called "Anniversary Update" to Windows 10, there is a
Ubuntu subsystem available for Windows, that can be installed and Ubuntu Linux subsystem available for Windows, that can be installed
then it can be used to compile/install LAMMPS as if you are running and then used to compile/install LAMMPS as if you are running on a
on a Ubuntu Linux system. Ubuntu Linux system instead of Windows.
As an alternative, you can download "daily builds" (and some older As an alternative, you can download "daily builds" (and some older
versions) of the installer packages from versions) of the installer packages from
@ -654,10 +652,10 @@ many examples, but no source code.
This section has the following sub-sections: This section has the following sub-sections:
"Package basics"_#start_3_1 2.3.1 "Package basics"_#start_3_1
"Including/excluding packages"_#start_3_2 2.3.2 "Including/excluding packages"_#start_3_2
"Packages that require extra libraries"_#start_3_3 2.3.3 "Packages that require extra libraries"_#start_3_3
"Packages that require Makefile.machine settings"_#start_3_4 :ul 2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
Note that the following "Section 2.4"_#start_4 describes the Make.py Note that the following "Section 2.4"_#start_4 describes the Make.py
tool which can be used to install/un-install packages and build the tool which can be used to install/un-install packages and build the
@ -673,7 +671,7 @@ are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages. fields for molecular systems or granular systems are in packages.
"Section packages"_Section_packages.html in the manual has details "Section 4"_Section_packages.html in the manual has details
about all the packages, including specific instructions for building about all the packages, including specific instructions for building
LAMMPS with each package, which are covered in a more general manner LAMMPS with each package, which are covered in a more general manner
below. below.
@ -727,15 +725,15 @@ before building LAMMPS. From the src directory, this is typically as
simple as: simple as:
make yes-colloid make yes-colloid
make g++ :pre make mpi :pre
or or
make no-manybody make no-manybody
make g++ :pre make mpi :pre
NOTE: You should NOT include/exclude packages and build LAMMPS in a NOTE: You should NOT include/exclude packages and build LAMMPS in a
single make command using multiple targets, e.g. make yes-colloid g++. single make command using multiple targets, e.g. make yes-colloid mpi.
This is because the make procedure creates a list of source files that This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes will be out-of-date for the build if the package configuration changes
within the same command. within the same command.
@ -826,7 +824,7 @@ where to find them.
For libraries with provided code, the sub-directory README file For libraries with provided code, the sub-directory README file
(e.g. lib/atc/README) has instructions on how to build that library. (e.g. lib/atc/README) has instructions on how to build that library.
This information is also summarized in "Section This information is also summarized in "Section
packages"_Section_packages.html. Typically this is done by typing 4"_Section_packages.html. Typically this is done by typing
something like: something like:
make -f Makefile.g++ :pre make -f Makefile.g++ :pre
@ -885,17 +883,17 @@ A few packages require specific settings in Makefile.machine, to
either build or use the package effectively. These are the either build or use the package effectively. These are the
USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
code performance on CPUs or other hardware, as discussed in "Section code performance on CPUs or other hardware, as discussed in "Section
acclerate"_Section_accelerate.html. 5.3"_Section_accelerate.html#acc_3.
A summary of what Makefile.machine changes are needed for each of A summary of what Makefile.machine changes are needed for each of
these packages is given in "Section packages"_Section_packages.html. these packages is given in "Section 4"_Section_packages.html.
The details are given on the doc pages that describe each of these The details are given on the doc pages that describe each of these
accelerator packages in detail: accelerator packages in detail:
"USER-INTEL package"_accelerate_intel.html 5.3.1 "USER-INTEL package"_accelerate_intel.html
"KOKKOS package"_accelerate_kokkos.html 5.3.3 "KOKKOS package"_accelerate_kokkos.html
"USER-OMP package"_accelerate_omp.html 5.3.4 "USER-OMP package"_accelerate_omp.html
"OPT package"_accelerate_opt.html :ul 5.3.5 "OPT package"_accelerate_opt.html :all(b)
You can also look at the following machine Makefiles in You can also look at the following machine Makefiles in
src/MAKE/OPTIONS, which include the changes. Note that the USER-INTEL src/MAKE/OPTIONS, which include the changes. Note that the USER-INTEL
@ -1367,7 +1365,7 @@ Note that the keywords do not use a leading minus sign. I.e. the
keyword is "t", not "-t". Also note that each of the keywords has a keyword is "t", not "-t". Also note that each of the keywords has a
default setting. Example of when to use these options and what default setting. Example of when to use these options and what
settings to use on different platforms is given in "Section settings to use on different platforms is given in "Section
5.8"_Section_accelerate.html#acc_3. 5.3"_Section_accelerate.html#acc_3.
d or device d or device
g or gpus g or gpus

38
doc/src/accelerate_kokkos.txt
View File

@ -156,19 +156,25 @@ CPU-only (run all-MPI or with OpenMP threading):
cd lammps/src cd lammps/src
make yes-kokkos make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP :pre make kokkos_omp :pre
Intel Xeon Phi: CPU-only (only MPI, no threading):
cd lammps/src cd lammps/src
make yes-kokkos make yes-kokkos
make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC :pre make kokkos_mpi :pre
CPUs and GPUs: Intel Xeon Phi (Intel Compiler, Intel MPI):
cd lammps/src cd lammps/src
make yes-kokkos make yes-kokkos
make cuda KOKKOS_DEVICES=Cuda :pre make kokkos_phi :pre
CPUs and GPUs (with MPICH):
cd lammps/src
make yes-kokkos
make kokkos_cuda_mpich :pre
These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try make command line which requires a GNU-compatible make command. Try
@ -180,26 +186,6 @@ first two examples above, then you *must* perform a "make clean-all"
or "make clean-machine" before each build. This is to force all the or "make clean-machine" before each build. This is to force all the
KOKKOS-dependent files to be re-compiled with the new options. KOKKOS-dependent files to be re-compiled with the new options.
You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
with a line like:
KOKKOS_ARCH = KNC :pre
Note that if you build LAMMPS multiple times in this manner, using
different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a "clean" in between. This is
because the targets will be different.
NOTE: The 3rd example above for a GPU, uses a different machine
makefile, in this case src/MAKE/Makefile.cuda, which is included in
the LAMMPS distribution. To build the KOKKOS package for a GPU, this
makefile must use the NVIDA "nvcc" compiler. And it must have a
KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and
installed software. Typical values for KOKKOS_ARCH are given below,
as well as other settings that must be included in the machine
makefile, if you create your own.
NOTE: Currently, there are no precision options with the KOKKOS NOTE: Currently, there are no precision options with the KOKKOS
package. All compilation and computation is performed in double package. All compilation and computation is performed in double
precision. precision.
@ -246,7 +232,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is threads to hardware cores. More info on binding threads to cores is
given in "this section"_Section_accelerate.html#acc_3. given in "Section 5.3"_Section_accelerate.html#acc_3.
KOKKOS_ARCH=KNC enables compiler switches needed when compling for an KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor. Intel Phi processor.

6
doc/src/accelerate_omp.txt
View File

@ -7,7 +7,7 @@
:line :line
"Return to Section accelerate overview"_Section_accelerate.html "Return to Section 5 overview"_Section_accelerate.html
5.3.4 USER-OMP package :h5 5.3.4 USER-OMP package :h5
@ -103,8 +103,8 @@ USER-OMP style (in serial or parallel) with a single thread per MPI
task, versus running standard LAMMPS with its standard un-accelerated task, versus running standard LAMMPS with its standard un-accelerated
styles (in serial or all-MPI parallelization with 1 task/core). This styles (in serial or all-MPI parallelization with 1 task/core). This
is because many of the USER-OMP styles contain similar optimizations is because many of the USER-OMP styles contain similar optimizations
to those used in the OPT package, described in "Section accelerate to those used in the OPT package, described in "Section
5.3.6"_accelerate_opt.html. 5.3.5"_accelerate_opt.html.
With multiple threads/task, the optimal choice of number of MPI With multiple threads/task, the optimal choice of number of MPI
tasks/node and OpenMP threads/task can vary a lot and should always be tasks/node and OpenMP threads/task can vary a lot and should always be

9
doc/src/compute_tally.txt
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@ -35,7 +35,12 @@ group/group"_compute_group_group.html only that the data is
accumulated directly during the non-bonded force computation. The accumulated directly during the non-bonded force computation. The
computes {force/tally}, {pe/tally}, {stress/tally}, and computes {force/tally}, {pe/tally}, {stress/tally}, and
{heat/flux/tally} are primarily provided as example how to program {heat/flux/tally} are primarily provided as example how to program
additional, more sophisticated computes using the tally mechanism. additional, more sophisticated computes using the tally callback
mechanism. Compute {pe/mol/tally} is one such style, that can
- through using this mechanism - separately tally intermolecular
and intramolecular energies. Something that would otherwise be
impossible without integrating this as a core functionality into
the based classes of LAMMPS.
:line :line
@ -56,7 +61,7 @@ atom scalar (the contributions of the single atom to the global
scalar). Compute {pe/mol/tally} calculates a global 4-element vector scalar). Compute {pe/mol/tally} calculates a global 4-element vector
containing (in this order): {evdwl} and {ecoul} for intramolecular pairs containing (in this order): {evdwl} and {ecoul} for intramolecular pairs
and {evdwl} and {ecoul} for intermolecular pairs. Since molecules are and {evdwl} and {ecoul} for intermolecular pairs. Since molecules are
identified my their molecule IDs, the partitioning does not have to be identified by their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or slots depending on whether the molecule IDs of a pair are the same or
different. Compute {force/tally} calculates a global scalar (the force different. Compute {force/tally} calculates a global scalar (the force

8
doc/src/dump.txt
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@ -328,8 +328,8 @@ bonds and colors.
Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
popular molecular viewing program. See "Section popular molecular viewing program. See
tools"_Section_tools.html#vmd of the manual and the "Section 9"_Section_tools.html#vmd of the manual and the
tools/lmp2vmd/README.txt file for more information about support in tools/lmp2vmd/README.txt file for more information about support in
VMD for reading and visualizing LAMMPS dump files. VMD for reading and visualizing LAMMPS dump files.
@ -390,7 +390,7 @@ Using MPI-IO requires two steps. First, build LAMMPS with its MPIIO
package installed, e.g. package installed, e.g.
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre make mpi # build LAMMPS for your platform :pre
Second, use a dump filename which contains ".mpiio". Note that it Second, use a dump filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters. does not have to end in ".mpiio", just contain those characters.
@ -531,7 +531,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. (tilted), then all atom coords will still be between 0.0 and 1.0.
I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
the non-orthogonal vectors of the simulation box edges, as discussed the non-orthogonal vectors of the simulation box edges, as discussed
in "Section howto 6.12"_Section_howto.html#howto_12. in "Section 6.12"_Section_howto.html#howto_12.
Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
image flags for each atom. Unwrapped means that if the atom has image flags for each atom. Unwrapped means that if the atom has

2
doc/src/dump_molfile.txt
View File

@ -34,7 +34,7 @@ to one or more files every N timesteps in one of several formats.
Only information for atoms in the specified group is dumped. This Only information for atoms in the specified group is dumped. This
specific dump style uses molfile plugins that are bundled with the specific dump style uses molfile plugins that are bundled with the
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
analysis program. See "Section tools"_Section_tools.html#vmd of the analysis program. See "Section 9"_Section_tools.html#vmd of the
manual and the tools/lmp2vmd/README.txt file for more information manual and the tools/lmp2vmd/README.txt file for more information
about support in VMD for reading and visualizing native LAMMPS dump about support in VMD for reading and visualizing native LAMMPS dump
files. files.

4
doc/src/fix_ti_spring.txt
View File

@ -99,8 +99,8 @@ center-of-mass fixed during the thermodynamic integration. A nonzero
total velocity will result in divergences during the integration due total velocity will result in divergences during the integration due
to the fact that the atoms are 'attached' to their equilibrium to the fact that the atoms are 'attached' to their equilibrium
positions by the Einstein crystal. Check the option {zero} of "fix positions by the Einstein crystal. Check the option {zero} of "fix
langevin"_fix_langevin_html and "velocity"_velocity.html. The use of langevin"_fix_langevin.html and "velocity"_velocity.html. The use of
the Nose-Hoover thermostat ("fix nvt"_fix_nvt.html) is {NOT} the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT}
recommended due to its well documented issues with the canonical recommended due to its well documented issues with the canonical
sampling of harmonic degrees of freedom (notice that the {chain} sampling of harmonic degrees of freedom (notice that the {chain}
option will {NOT} solve this problem). The Langevin thermostat ("fix option will {NOT} solve this problem). The Langevin thermostat ("fix

1
doc/src/fixes.txt
View File

@ -138,7 +138,6 @@ Fixes :h1
fix_temp_rescale_eff fix_temp_rescale_eff
fix_tfmc fix_tfmc
fix_thermal_conductivity fix_thermal_conductivity
fix_ti_rs
fix_ti_spring fix_ti_spring
fix_tmd fix_tmd
fix_ttm fix_ttm

2
doc/src/package.txt
View File

@ -142,7 +142,7 @@ the style options are set, either to default values or to specified
settings. I.e. settings from previous invocations do not persist settings. I.e. settings from previous invocations do not persist
across multiple invocations. across multiple invocations.
See the "Section Accelerate"_Section_accelerate.html section of the See the "Section 5.3"_Section_accelerate.html#acc_3 section of the
manual for more details about using the various accelerator packages manual for more details about using the various accelerator packages
for speeding up LAMMPS simulations. for speeding up LAMMPS simulations.

8
doc/src/pair_gauss.txt
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@ -63,7 +63,7 @@ solvent simulations of salt ions "(Lenart)"_#Lenart and of surfactants
"(Jusufi)"_#Jusufi. In these instances the Gaussian potential mimics "(Jusufi)"_#Jusufi. In these instances the Gaussian potential mimics
the hydration barrier between a pair of particles. The hydration the hydration barrier between a pair of particles. The hydration
barrier is located at r_mh and has a width of sigma_h. The prefactor barrier is located at r_mh and has a width of sigma_h. The prefactor
determines the hight of the potential barrier. determines the height of the potential barrier.
The following coefficients must be defined for each pair of atom types The following coefficients must be defined for each pair of atom types
via the "pair_coeff"_pair_coeff.html command as in the example above, via the "pair_coeff"_pair_coeff.html command as in the example above,
@ -73,9 +73,11 @@ commands:
H (energy * distance units) H (energy * distance units)
r_mh (distance units) r_mh (distance units)
sigma_h (distance units) :ul sigma_h (distance units)
cutoff (distance units) :ul
The global cutoff (r_c) specified in the pair_style command is used. The last coefficient is optional. If not specified, the global cutoff
is used.
:line :line

2
doc/src/python.txt
View File

@ -97,7 +97,7 @@ be passed to various commands as arguments, so that the variable is
evaluated during a simulation run. evaluated during a simulation run.
A broader overview of how Python can be used with LAMMPS is A broader overview of how Python can be used with LAMMPS is
given in "Section python"_Section_python.html. There is an given in "Section 11"_Section_python.html. There is an
examples/python directory which illustrates use of the python examples/python directory which illustrates use of the python
command. command.

2
doc/src/read_restart.txt
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@ -124,7 +124,7 @@ MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g. installed, e.g.
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre make mpi # build LAMMPS for your platform :pre
Second, use a restart filename which contains ".mpiio". Note that it Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters. does not have to end in ".mpiio", just contain those characters.

6
doc/src/region.txt
View File

@ -186,7 +186,7 @@ functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent radius. time. Thus it is easy to specify a time-dependent radius.
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS, for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used and how to transform these parameters to and from other commonly used
triclinic representations. triclinic representations.
@ -361,7 +361,7 @@ sub-regions can be defined with the {open} keyword.
Styles with a {kk} suffix are functionally the same as the Styles with a {kk} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in run faster, depending on your available hardware, as discussed in
"Section_accelerate"_Section_accelerate.html of the manual. The "Section 5"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues. results, except for round-off and precision issues.
@ -378,7 +378,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script. use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively. more instructions on how to use the accelerated styles effectively.
:line :line

2
doc/src/restart.txt
View File

@ -82,7 +82,7 @@ versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g. build LAMMPS with its MPIIO package installed, e.g.
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre make mpi # build LAMMPS for your platform :pre
Second, use a restart filename which contains ".mpiio". Note that it Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters. does not have to end in ".mpiio", just contain those characters.

2
doc/src/variable.txt
View File

@ -1121,7 +1121,7 @@ with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_"
(e.g. v_x or v_abc). The former can be used in any input script (e.g. v_x or v_abc). The former can be used in any input script
command, including a variable command. The input script parser command, including a variable command. The input script parser
evaluates the reference variable immediately and substitutes its value evaluates the reference variable immediately and substitutes its value
into the command. As explained in "Section commands into the command. As explained in "Section
3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use 3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use
un-named "immediate" variables for this purpose. For example, a un-named "immediate" variables for this purpose. For example, a
string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script

6
doc/src/velocity.txt
View File

@ -139,7 +139,7 @@ if rot = yes, the angular momentum is zeroed.
If specified, the {temp} keyword is used by {create} and {scale} to If specified, the {temp} keyword is used by {create} and {scale} to
specify a "compute"_compute.html that calculates temperature in a specify a "compute"_compute.html that calculates temperature in a
desired way, e.g. by first subtracting out a velocity bias, as desired way, e.g. by first subtracting out a velocity bias, as
discussed in "Section howto 16"_Section_howto.html#howto_15 of the doc discussed in "Section 6.16"_Section_howto.html#howto_16 of the doc
pages. If this keyword is not specified, {create} and {scale} pages. If this keyword is not specified, {create} and {scale}
calculate temperature using a compute that is defined internally as calculate temperature using a compute that is defined internally as
follows: follows:
@ -161,8 +161,8 @@ The {bias} keyword with a {yes} setting is used by {create} and
If the temperature compute also calculates a velocity bias, the the If the temperature compute also calculates a velocity bias, the the
bias is subtracted from atom velocities before the {create} and bias is subtracted from atom velocities before the {create} and
{scale} operations are performed. After the operations, the bias is {scale} operations are performed. After the operations, the bias is
added back to the atom velocities. See "Section howto added back to the atom velocities. See "Section
16"_Section_howto.html#howto_15 of the doc pages for more discussion 6.16"_Section_howto.html#howto_16 of the doc pages for more discussion
of temperature computes with biases. Note that the velocity bias is of temperature computes with biases. Note that the velocity bias is
only applied to atoms in the temperature compute specified with the only applied to atoms in the temperature compute specified with the
{temp} keyword. {temp} keyword.

2
doc/src/write_restart.txt
View File

@ -55,7 +55,7 @@ versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g. build LAMMPS with its MPIIO package installed, e.g.
make yes-mpiio # installs the MPIIO package make yes-mpiio # installs the MPIIO package
make g++ # build LAMMPS for your platform :pre make mpi # build LAMMPS for your platform :pre
Second, use a restart filename which contains ".mpiio". Note that it Second, use a restart filename which contains ".mpiio". Note that it
does not have to end in ".mpiio", just contain those characters. does not have to end in ".mpiio", just contain those characters.

28
python/lammps.py
View File

@ -28,6 +28,15 @@ import os
import select import select
import re import re
class MPIAbortException(Exception):
def __init__(self, message):
self.message = message
def __str__(self):
return repr(self.message)
class lammps(object): class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator # detect if Python is using version of mpi4py that can pass a communicator
@ -43,6 +52,7 @@ class lammps(object):
# create instance of LAMMPS # create instance of LAMMPS
def __init__(self,name="",cmdargs=None,ptr=None,comm=None): def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
self.comm = comm
# determine module location # determine module location
@ -150,10 +160,14 @@ class lammps(object):
if cmd: cmd = cmd.encode() if cmd: cmd = cmd.encode()
self.lib.lammps_command(self.lmp,cmd) self.lib.lammps_command(self.lmp,cmd)
if self.lib.lammps_has_error(self.lmp): if self.uses_exceptions and self.lib.lammps_has_error(self.lmp):
sb = create_string_buffer(100) sb = create_string_buffer(100)
self.lib.lammps_get_last_error_message(self.lmp, sb, 100) error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
raise Exception(sb.value.decode().strip()) error_msg = sb.value.decode().strip()
if error_type == 2:
raise MPIAbortException(error_msg)
raise Exception(error_msg)
def extract_global(self,name,type): def extract_global(self,name,type):
if name: name = name.encode() if name: name = name.encode()
@ -286,6 +300,14 @@ class lammps(object):
if name: name = name.encode() if name: name = name.encode()
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data) self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
@property
def uses_exceptions(self):
try:
if self.lib.lammps_has_error:
return True
except(AttributeError):
return False
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------
# ------------------------------------------------------------------------- # -------------------------------------------------------------------------

1
src/GPU/pair_eam_alloy_gpu.h
View File

@ -33,6 +33,7 @@ public:
void init_style(); void init_style();
double single(int, int, int, int, double, double, double, double &); double single(int, int, int, int, double, double, double, double &);
double memory_usage(); double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *); int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *); void unpack_forward_comm(int, int, double *);

1
src/GPU/pair_eam_fs_gpu.h
View File

@ -33,6 +33,7 @@ public:
void init_style(); void init_style();
double single(int, int, int, int, double, double, double, double &); double single(int, int, int, int, double, double, double, double &);
double memory_usage(); double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *); int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *); void unpack_forward_comm(int, int, double *);

1
src/GPU/pair_eam_gpu.h
View File

@ -34,6 +34,7 @@ class PairEAMGPU : public PairEAM {
void init_style(); void init_style();
double single(int, int, int, int, double, double, double, double &); double single(int, int, int, int, double, double, double, double &);
double memory_usage(); double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *); int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *); void unpack_forward_comm(int, int, double *);

1
src/KOKKOS/pair_eam_alloy_kokkos.h
View File

@ -61,6 +61,7 @@ class PairEAMAlloyKokkos : public PairEAM {
virtual ~PairEAMAlloyKokkos(); virtual ~PairEAMAlloyKokkos();
virtual void compute(int, int); virtual void compute(int, int);
void init_style(); void init_style();
void *extract(const char *, int &) { return NULL; }
void coeff(int, char **); void coeff(int, char **);
KOKKOS_INLINE_FUNCTION KOKKOS_INLINE_FUNCTION

1
src/KOKKOS/pair_eam_fs_kokkos.h
View File

@ -61,6 +61,7 @@ class PairEAMFSKokkos : public PairEAM {
virtual ~PairEAMFSKokkos(); virtual ~PairEAMFSKokkos();
virtual void compute(int, int); virtual void compute(int, int);
void init_style(); void init_style();
void *extract(const char *, int &) { return NULL; }
void coeff(int, char **); void coeff(int, char **);
KOKKOS_INLINE_FUNCTION KOKKOS_INLINE_FUNCTION

1
src/KOKKOS/pair_eam_kokkos.h
View File

@ -59,6 +59,7 @@ class PairEAMKokkos : public PairEAM {
virtual ~PairEAMKokkos(); virtual ~PairEAMKokkos();
virtual void compute(int, int); virtual void compute(int, int);
void init_style(); void init_style();
void *extract(const char *, int &) { return NULL; }
KOKKOS_INLINE_FUNCTION KOKKOS_INLINE_FUNCTION
void operator()(TagPairEAMPackForwardComm, const int&) const; void operator()(TagPairEAMPackForwardComm, const int&) const;

4
src/MANYBODY/pair_eam.cpp
View File

@ -54,6 +54,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
frho = NULL; frho = NULL;
rhor = NULL; rhor = NULL;
z2r = NULL; z2r = NULL;
scale = NULL;
frho_spline = NULL; frho_spline = NULL;
rhor_spline = NULL; rhor_spline = NULL;
@ -232,6 +233,7 @@ void PairEAM::compute(int eflag, int vflag)
if (eflag) { if (eflag) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi; if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi; if (eflag_atom) eatom[i] += phi;
} }
@ -306,7 +308,7 @@ void PairEAM::compute(int eflag, int vflag)
f[j][2] -= delz*fpair; f[j][2] -= delz*fpair;
} }
if (eflag) evdwl = phi; if (eflag) evdwl = scale[itype][jtype]*phi;
if (evflag) ev_tally(i,j,nlocal,newton_pair, if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz); evdwl,0.0,fpair,delx,dely,delz);
} }

2
src/MANYBODY/pair_eam.h
View File

@ -54,7 +54,7 @@ class PairEAM : public Pair {
void init_style(); void init_style();
double init_one(int, int); double init_one(int, int);
double single(int, int, int, int, double, double, double, double &); double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &); virtual void *extract(const char *, int &);
virtual int pack_forward_comm(int, int *, double *, int, int *); virtual int pack_forward_comm(int, int *, double *, int, int *);
virtual void unpack_forward_comm(int, int, double *); virtual void unpack_forward_comm(int, int, double *);

7
src/OPT/pair_eam_opt.cpp
View File

@ -247,6 +247,7 @@ void PairEAMOpt::eval()
if (EFLAG) { if (EFLAG) {
double phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; double phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi; if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi; if (eflag_atom) eatom[i] += phi;
} }
@ -273,6 +274,7 @@ void PairEAMOpt::eval()
double tmpfz = 0.0; double tmpfz = 0.0;
fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr]; fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr];
double* _noalias scale_i = scale[itype1+1]+1;
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
j = jlist[jj]; j = jlist[jj];
@ -316,12 +318,13 @@ void PairEAMOpt::eval()
// psip needs both fp[i] and fp[j] terms since r_ij appears in two // psip needs both fp[i] and fp[j] terms since r_ij appears in two
// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji) // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
// scale factor can be applied by thermodynamic integration
double recip = 1.0/r; double recip = 1.0/r;
double phi = z2*recip; double phi = z2*recip;
double phip = z2p*recip - phi*recip; double phip = z2p*recip - phi*recip;
double psip = fp[i]*rhojp + fp[j]*rhoip + phip; double psip = fp[i]*rhojp + fp[j]*rhoip + phip;
double fpair = -psip*recip; double fpair = -scale_i[jtype]*psip*recip;
tmpfx += delx*fpair; tmpfx += delx*fpair;
tmpfy += dely*fpair; tmpfy += dely*fpair;
@ -332,7 +335,7 @@ void PairEAMOpt::eval()
ff[j].z -= delz*fpair; ff[j].z -= delz*fpair;
} }
if (EFLAG) evdwl = phi; if (EFLAG) evdwl = scale_i[jtype]*phi;
if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR, if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz); evdwl,0.0,fpair,delx,dely,delz);

2
src/USER-MISC/pair_cdeam.h
View File

@ -49,6 +49,8 @@ public:
/// Reports the memory usage of this pair style to LAMMPS. /// Reports the memory usage of this pair style to LAMMPS.
double memory_usage(); double memory_usage();
void *extract(const char *, int &) { return NULL; }
/// Parses the coefficients of the h polynomial from the end of the EAM file. /// Parses the coefficients of the h polynomial from the end of the EAM file.
void read_h_coeff(char* filename); void read_h_coeff(char* filename);

7
src/USER-OMP/pair_eam_omp.cpp
View File

@ -203,7 +203,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
if (EFLAG) { if (EFLAG) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6]; phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax); if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, phi, 0.0, thr); e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, scale[type[i]][type[i]]*phi, 0.0, thr);
} }
} }
@ -230,6 +230,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
ztmp = x[i].z; ztmp = x[i].z;
itype = type[i]; itype = type[i];
fxtmp = fytmp = fztmp = 0.0; fxtmp = fytmp = fztmp = 0.0;
const double * _noalias const scale_i = scale[itype];
jlist = firstneigh[i]; jlist = firstneigh[i];
jnum = numneigh[i]; jnum = numneigh[i];
@ -274,7 +275,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
phi = z2*recip; phi = z2*recip;
phip = z2p*recip - phi*recip; phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip; psip = fp[i]*rhojp + fp[j]*rhoip + phip;
fpair = -psip*recip; fpair = -scale_i[jtype]*psip*recip;
fxtmp += delx*fpair; fxtmp += delx*fpair;
fytmp += dely*fpair; fytmp += dely*fpair;
@ -285,7 +286,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
f[j].z -= delz*fpair; f[j].z -= delz*fpair;
} }
if (EFLAG) evdwl = phi; if (EFLAG) evdwl = scale_i[jtype]*phi;
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR, if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
evdwl,0.0,fpair,delx,dely,delz,thr); evdwl,0.0,fpair,delx,dely,delz,thr);
} }

27
src/error.cpp
View File

@ -22,7 +22,12 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
Error::Error(LAMMPS *lmp) : Pointers(lmp), last_error_message(NULL) {} Error::Error(LAMMPS *lmp) : Pointers(lmp) {
#ifdef LAMMPS_EXCEPTIONS
last_error_message = NULL;
last_error_type = ERROR_NONE;
#endif
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
called by all procs in universe called by all procs in universe
@ -198,6 +203,7 @@ void Error::done(int status)
exit(status); exit(status);
} }
#ifdef LAMMPS_EXCEPTIONS
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
return the last error message reported by LAMMPS (only used if return the last error message reported by LAMMPS (only used if
compiled with -DLAMMPS_EXCEPTIONS) compiled with -DLAMMPS_EXCEPTIONS)
@ -208,13 +214,22 @@ char * Error::get_last_error() const
return last_error_message; return last_error_message;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
set the last error message (only used if compiled with return the type of the last error reported by LAMMPS (only used if
-DLAMMPS_EXCEPTIONS) compiled with -DLAMMPS_EXCEPTIONS)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Error::set_last_error(const char * msg) ErrorType Error::get_last_error_type() const
{
return last_error_type;
}
/* ----------------------------------------------------------------------
set the last error message and error type
(only used if compiled with -DLAMMPS_EXCEPTIONS)
------------------------------------------------------------------------- */
void Error::set_last_error(const char * msg, ErrorType type)
{ {
delete [] last_error_message; delete [] last_error_message;
@ -224,4 +239,6 @@ void Error::set_last_error(const char * msg)
} else { } else {
last_error_message = NULL; last_error_message = NULL;
} }
last_error_type = type;
} }
#endif

46
src/error.h
View File

@ -15,41 +15,14 @@
#define LMP_ERROR_H #define LMP_ERROR_H
#include "pointers.h" #include "pointers.h"
#include <string>
#include <exception> #ifdef LAMMPS_EXCEPTIONS
#include "exceptions.h"
#endif
namespace LAMMPS_NS { namespace LAMMPS_NS {
class LAMMPSException : public std::exception
{
public:
std::string message;
LAMMPSException(std::string msg) : message(msg) {
}
~LAMMPSException() throw() {
}
virtual const char * what() const throw() {
return message.c_str();
}
};
class LAMMPSAbortException : public LAMMPSException {
public:
MPI_Comm universe;
LAMMPSAbortException(std::string msg, MPI_Comm universe) :
LAMMPSException(msg),
universe(universe)
{
}
};
class Error : protected Pointers { class Error : protected Pointers {
char * last_error_message;
public: public:
Error(class LAMMPS *); Error(class LAMMPS *);
@ -63,8 +36,15 @@ class Error : protected Pointers {
void message(const char *, int, const char *, int = 1); void message(const char *, int, const char *, int = 1);
void done(int = 0); // 1 would be fully backwards compatible void done(int = 0); // 1 would be fully backwards compatible
char * get_last_error() const; #ifdef LAMMPS_EXCEPTIONS
void set_last_error(const char * msg); char * get_last_error() const;
ErrorType get_last_error_type() const;
void set_last_error(const char * msg, ErrorType type = ERROR_NORMAL);
private:
char * last_error_message;
ErrorType last_error_type;
#endif
}; };
} }

58
src/exceptions.h Normal file
View File

@ -0,0 +1,58 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_EXCEPTIONS_H
#define LMP_EXCEPTIONS_H
#include <mpi.h>
#include <string>
#include <exception>
namespace LAMMPS_NS {
class LAMMPSException : public std::exception
{
public:
std::string message;
LAMMPSException(std::string msg) : message(msg) {
}
~LAMMPSException() throw() {
}
virtual const char * what() const throw() {
return message.c_str();
}
};
class LAMMPSAbortException : public LAMMPSException {
public:
MPI_Comm universe;
LAMMPSAbortException(std::string msg, MPI_Comm universe) :
LAMMPSException(msg),
universe(universe)
{
}
};
enum ErrorType {
ERROR_NONE = 0,
ERROR_NORMAL = 1,
ERROR_ABORT = 2
};
}
#endif

2
src/fix.cpp
View File

@ -139,7 +139,7 @@ void Fix::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"respa") == 0) { } else if (strcmp(arg[iarg],"respa") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command"); if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
if (!respa_level_support) error->all(FLERR,"Illegal fix_modify command"); if (!respa_level_support) error->all(FLERR,"Illegal fix_modify command");
int lvl = force->inumeric(FLERR,arg[1]); int lvl = force->inumeric(FLERR,arg[iarg+1]);
if (lvl < 0) error->all(FLERR,"Illegal fix_modify command"); if (lvl < 0) error->all(FLERR,"Illegal fix_modify command");
respa_level = lvl-1; respa_level = lvl-1;
iarg += 2; iarg += 2;

2
src/fix_adapt.cpp
View File

@ -321,7 +321,7 @@ void FixAdapt::init()
delete[] psuffix; delete[] psuffix;
} }
if (ad->pair == NULL) ad->pair = force->pair_match(pstyle,1,nsub); if (ad->pair == NULL) ad->pair = force->pair_match(pstyle,1,nsub);
if (ad->pair == NULL) if (ad->pair == NULL)
error->all(FLERR,"Fix adapt pair style does not exist"); error->all(FLERR,"Fix adapt pair style does not exist");
void *ptr = ad->pair->extract(ad->pparam,ad->pdim); void *ptr = ad->pair->extract(ad->pparam,ad->pdim);

557
src/library.cpp
View File

@ -38,6 +38,45 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
Utility macros for optional code path which captures all exceptions
and stores the last error message. These assume there is a variable lmp
which is a pointer to the current LAMMPS instance.
Usage:
BEGIN_CAPTURE
{
// code paths which might throw exception
...
}
END_CAPTURE
------------------------------------------------------------------------- */
#ifdef LAMMPS_EXCEPTIONS
#define BEGIN_CAPTURE \
Error * error = lmp->error; \
try
#define END_CAPTURE \
catch(LAMMPSAbortException & ae) { \
int nprocs = 0; \
MPI_Comm_size(ae.universe, &nprocs ); \
\
if (nprocs > 1) { \
error->set_last_error(ae.message.c_str(), ERROR_ABORT); \
} else { \
error->set_last_error(ae.message.c_str(), ERROR_NORMAL); \
} \
} catch(LAMMPSException & e) { \
error->set_last_error(e.message.c_str(), ERROR_NORMAL); \
}
#else
#define BEGIN_CAPTURE
#define END_CAPTURE
#endif
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
create an instance of LAMMPS and return pointer to it create an instance of LAMMPS and return pointer to it
pass in command-line args and MPI communicator to run on pass in command-line args and MPI communicator to run on
@ -45,8 +84,20 @@ using namespace LAMMPS_NS;
void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr) void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
{ {
#ifdef LAMMPS_EXCEPTIONS
try
{
LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp;
}
catch(LAMMPSException & e) {
fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
*ptr = (void*) NULL;
}
#else
LAMMPS *lmp = new LAMMPS(argc,argv,communicator); LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp; *ptr = (void *) lmp;
#endif
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -68,8 +119,20 @@ void lammps_open_no_mpi(int argc, char **argv, void **ptr)
MPI_Comm communicator = MPI_COMM_WORLD; MPI_Comm communicator = MPI_COMM_WORLD;
#ifdef LAMMPS_EXCEPTIONS
try
{
LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp;
}
catch(LAMMPSException & e) {
fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
*ptr = (void*) NULL;
}
#else
LAMMPS *lmp = new LAMMPS(argc,argv,communicator); LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
*ptr = (void *) lmp; *ptr = (void *) lmp;
#endif
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -99,7 +162,12 @@ int lammps_version(void *ptr)
void lammps_file(void *ptr, char *str) void lammps_file(void *ptr, char *str)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
lmp->input->file(str);
BEGIN_CAPTURE
{
lmp->input->file(str);
}
END_CAPTURE
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -108,15 +176,16 @@ void lammps_file(void *ptr, char *str)
char *lammps_command(void *ptr, char *str) char *lammps_command(void *ptr, char *str)
{ {
LAMMPS * lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
Error * error = lmp->error; char * result = NULL;
try { BEGIN_CAPTURE
return lmp->input->one(str); {
} catch(LAMMPSException & e) { result = lmp->input->one(str);
error->set_last_error(e.message.c_str());
return NULL;
} }
END_CAPTURE
return result;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -215,58 +284,62 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
int icompute = lmp->modify->find_compute(id); BEGIN_CAPTURE
if (icompute < 0) return NULL; {
Compute *compute = lmp->modify->compute[icompute]; int icompute = lmp->modify->find_compute(id);
if (icompute < 0) return NULL;
Compute *compute = lmp->modify->compute[icompute];
if (style == 0) { if (style == 0) {
if (type == 0) { if (type == 0) {
if (!compute->scalar_flag) return NULL; if (!compute->scalar_flag) return NULL;
if (compute->invoked_scalar != lmp->update->ntimestep) if (compute->invoked_scalar != lmp->update->ntimestep)
compute->compute_scalar(); compute->compute_scalar();
return (void *) &compute->scalar; return (void *) &compute->scalar;
}
if (type == 1) {
if (!compute->vector_flag) return NULL;
if (compute->invoked_vector != lmp->update->ntimestep)
compute->compute_vector();
return (void *) compute->vector;
}
if (type == 2) {
if (!compute->array_flag) return NULL;
if (compute->invoked_array != lmp->update->ntimestep)
compute->compute_array();
return (void *) compute->array;
}
} }
if (type == 1) {
if (!compute->vector_flag) return NULL; if (style == 1) {
if (compute->invoked_vector != lmp->update->ntimestep) if (!compute->peratom_flag) return NULL;
compute->compute_vector(); if (type == 1) {
return (void *) compute->vector; if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
} }
if (type == 2) {
if (!compute->array_flag) return NULL; if (style == 2) {
if (compute->invoked_array != lmp->update->ntimestep) if (!compute->local_flag) return NULL;
compute->compute_array(); if (type == 1) {
return (void *) compute->array; if (compute->invoked_local != lmp->update->ntimestep)
} compute->compute_local();
} return (void *) compute->vector_local;
}
if (style == 1) { if (type == 2) {
if (!compute->peratom_flag) return NULL; if (compute->invoked_local != lmp->update->ntimestep)
if (type == 1) { compute->compute_local();
if (compute->invoked_peratom != lmp->update->ntimestep) return (void *) compute->array_local;
compute->compute_peratom(); }
return (void *) compute->vector_atom;
}
if (type == 2) {
if (compute->invoked_peratom != lmp->update->ntimestep)
compute->compute_peratom();
return (void *) compute->array_atom;
}
}
if (style == 2) {
if (!compute->local_flag) return NULL;
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->vector_local;
}
if (type == 2) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
return (void *) compute->array_local;
} }
} }
END_CAPTURE
return NULL; return NULL;
} }
@ -300,40 +373,44 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
int ifix = lmp->modify->find_fix(id); BEGIN_CAPTURE
if (ifix < 0) return NULL; {
Fix *fix = lmp->modify->fix[ifix]; int ifix = lmp->modify->find_fix(id);
if (ifix < 0) return NULL;
Fix *fix = lmp->modify->fix[ifix];
if (style == 0) { if (style == 0) {
double *dptr = (double *) malloc(sizeof(double)); double *dptr = (double *) malloc(sizeof(double));
if (type == 0) { if (type == 0) {
if (!fix->scalar_flag) return NULL; if (!fix->scalar_flag) return NULL;
*dptr = fix->compute_scalar(); *dptr = fix->compute_scalar();
return (void *) dptr; return (void *) dptr;
}
if (type == 1) {
if (!fix->vector_flag) return NULL;
*dptr = fix->compute_vector(i);
return (void *) dptr;
}
if (type == 2) {
if (!fix->array_flag) return NULL;
*dptr = fix->compute_array(i,j);
return (void *) dptr;
}
} }
if (type == 1) {
if (!fix->vector_flag) return NULL; if (style == 1) {
*dptr = fix->compute_vector(i); if (!fix->peratom_flag) return NULL;
return (void *) dptr; if (type == 1) return (void *) fix->vector_atom;
if (type == 2) return (void *) fix->array_atom;
} }
if (type == 2) {
if (!fix->array_flag) return NULL; if (style == 2) {
*dptr = fix->compute_array(i,j); if (!fix->local_flag) return NULL;
return (void *) dptr; if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
} }
} }
END_CAPTURE
if (style == 1) {
if (!fix->peratom_flag) return NULL;
if (type == 1) return (void *) fix->vector_atom;
if (type == 2) return (void *) fix->array_atom;
}
if (style == 2) {
if (!fix->local_flag) return NULL;
if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
}
return NULL; return NULL;
} }
@ -369,23 +446,27 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
int ivar = lmp->input->variable->find(name); BEGIN_CAPTURE
if (ivar < 0) return NULL; {
int ivar = lmp->input->variable->find(name);
if (ivar < 0) return NULL;
if (lmp->input->variable->equalstyle(ivar)) { if (lmp->input->variable->equalstyle(ivar)) {
double *dptr = (double *) malloc(sizeof(double)); double *dptr = (double *) malloc(sizeof(double));
*dptr = lmp->input->variable->compute_equal(ivar); *dptr = lmp->input->variable->compute_equal(ivar);
return (void *) dptr; return (void *) dptr;
} }
if (lmp->input->variable->atomstyle(ivar)) { if (lmp->input->variable->atomstyle(ivar)) {
int igroup = lmp->group->find(group); int igroup = lmp->group->find(group);
if (igroup < 0) return NULL; if (igroup < 0) return NULL;
int nlocal = lmp->atom->nlocal; int nlocal = lmp->atom->nlocal;
double *vector = (double *) malloc(nlocal*sizeof(double)); double *vector = (double *) malloc(nlocal*sizeof(double));
lmp->input->variable->compute_atom(ivar,igroup,vector,1,0); lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
return (void *) vector; return (void *) vector;
}
} }
END_CAPTURE
return NULL; return NULL;
} }
@ -399,7 +480,14 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
int lammps_set_variable(void *ptr, char *name, char *str) int lammps_set_variable(void *ptr, char *name, char *str)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
int err = lmp->input->variable->set_string(name,str); int err = -1;
BEGIN_CAPTURE
{
err = lmp->input->variable->set_string(name,str);
}
END_CAPTURE
return err; return err;
} }
@ -414,9 +502,14 @@ int lammps_set_variable(void *ptr, char *name, char *str)
double lammps_get_thermo(void *ptr, char *name) double lammps_get_thermo(void *ptr, char *name)
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
double dval; double dval = 0.0;
BEGIN_CAPTURE
{
lmp->output->thermo->evaluate_keyword(name,&dval);
}
END_CAPTURE
lmp->output->thermo->evaluate_keyword(name,&dval);
return dval; return dval;
} }
@ -449,79 +542,83 @@ void lammps_gather_atoms(void *ptr, char *name,
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
// error if tags are not defined or not consecutive BEGIN_CAPTURE
{
// error if tags are not defined or not consecutive
int flag = 0; int flag = 0;
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1; if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_gather_atoms"); lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
return; return;
}
int natoms = static_cast<int> (lmp->atom->natoms);
int i,j,offset;
void *vptr = lmp->atom->extract(name);
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1)
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
else
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][0];
}
MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
} else {
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][j];
}
} }
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world); int natoms = static_cast<int> (lmp->atom->natoms);
lmp->memory->destroy(copy);
int i,j,offset;
void *vptr = lmp->atom->extract(name);
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1)
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
else
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][0];
}
MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *copy;
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
for (i = 0; i < nlocal; i++)
copy[tag[i]-1] = vector[i];
} else {
for (i = 0; i < nlocal; i++) {
offset = count*(tag[i]-1);
for (j = 0; j < count; j++)
copy[offset++] = array[i][j];
}
}
MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
lmp->memory->destroy(copy);
}
} }
END_CAPTURE
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -538,69 +635,74 @@ void lammps_scatter_atoms(void *ptr, char *name,
{ {
LAMMPS *lmp = (LAMMPS *) ptr; LAMMPS *lmp = (LAMMPS *) ptr;
// error if tags are not defined or not consecutive or no atom map BEGIN_CAPTURE
{
// error if tags are not defined or not consecutive or no atom map
int flag = 0; int flag = 0;
if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1; if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
if (lmp->atom->natoms > MAXSMALLINT) flag = 1; if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
if (lmp->atom->map_style == 0) flag = 1; if (lmp->atom->map_style == 0) flag = 1;
if (flag) { if (flag) {
if (lmp->comm->me == 0) if (lmp->comm->me == 0)
lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms"); lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms");
return; return;
}
int natoms = static_cast<int> (lmp->atom->natoms);
int i,j,m,offset;
void *vptr = lmp->atom->extract(name);
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *dptr = (int *) data;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
} }
} else {
double *vector = NULL;
double **array = NULL;
if (count == 1) vector = (double *) vptr;
else array = (double **) vptr;
double *dptr = (double *) data;
if (count == 1) { int natoms = static_cast<int> (lmp->atom->natoms);
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0) int i,j,m,offset;
vector[m] = dptr[i]; void *vptr = lmp->atom->extract(name);
// copy = Natom length vector of per-atom values
// use atom ID to insert each atom's values into copy
// MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
if (type == 0) {
int *vector = NULL;
int **array = NULL;
if (count == 1) vector = (int *) vptr;
else array = (int **) vptr;
int *dptr = (int *) data;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
}
} else { } else {
for (i = 0; i < natoms; i++) { double *vector = NULL;
if ((m = lmp->atom->map(i+1)) >= 0) { double **array = NULL;
offset = count*i; if (count == 1) vector = (double *) vptr;
for (j = 0; j < count; j++) else array = (double **) vptr;
array[m][j] = dptr[offset++]; double *dptr = (double *) data;
if (count == 1) {
for (i = 0; i < natoms; i++)
if ((m = lmp->atom->map(i+1)) >= 0)
vector[m] = dptr[i];
} else {
for (i = 0; i < natoms; i++) {
if ((m = lmp->atom->map(i+1)) >= 0) {
offset = count*i;
for (j = 0; j < count; j++)
array[m][j] = dptr[offset++];
}
} }
} }
} }
} }
END_CAPTURE
} }
#ifdef LAMMPS_EXCEPTIONS
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Check if a new error message Check if a new error message
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -613,6 +715,9 @@ int lammps_has_error(void *ptr) {
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Copy the last error message of LAMMPS into a character buffer Copy the last error message of LAMMPS into a character buffer
The return value encodes which type of error it is.
1 = normal error (recoverable)
2 = abort error (non-recoverable)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) { int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
@ -620,9 +725,11 @@ int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
Error * error = lmp->error; Error * error = lmp->error;
if(error->get_last_error()) { if(error->get_last_error()) {
int error_type = error->get_last_error_type();
strncpy(buffer, error->get_last_error(), buffer_size-1); strncpy(buffer, error->get_last_error(), buffer_size-1);
error->set_last_error(NULL); error->set_last_error(NULL, ERROR_NONE);
return 1; return error_type;
} }
return 0; return 0;
} }
#endif

2
src/library.h
View File

@ -45,8 +45,10 @@ int lammps_get_natoms(void *);
void lammps_gather_atoms(void *, char *, int, int, void *); void lammps_gather_atoms(void *, char *, int, int, void *);
void lammps_scatter_atoms(void *, char *, int, int, void *); void lammps_scatter_atoms(void *, char *, int, int, void *);
#ifdef LAMMPS_EXCEPTIONS
int lammps_has_error(void *); int lammps_has_error(void *);
int lammps_get_last_error_message(void *, char *, int); int lammps_get_last_error_message(void *, char *, int);
#endif
#ifdef __cplusplus #ifdef __cplusplus
} }