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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
script a series of JPG images will be produced by the run (assuming
you built LAMMPS with JPG support; see "Section start
2.2"_Section_start.html for details). These can be viewed
you built LAMMPS with JPG support; see "Section
2.2"_Section_start.html#start_2 for details). These can be viewed
individually or turned into a movie or animated by tools like
ImageMagick or QuickTime or various Windows-based tools. See the
"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
illustrate how to use the command(s) provided in that package. Many
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.

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, -, -
"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, -
"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, -
"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, -
"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
"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, -
"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, -
"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
@ -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
it is a third-party library not included in the LAMMPS distribution.
See details on all of this below for individual packages.
p.s.: are we ever going to get commit messages from you? ;-)
:line
@ -150,7 +149,7 @@ make 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
resquared"_pair_resquared.html,
"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
measures the temperature of a system with core/shell particles. The
pair styles augment Born, Buckingham, and Lennard-Jones styles with
core/shell capabilities. See "Section howto
6.26"_Section_howto.html#howto_26 for an overview of how to use the
package.
core/shell capabilities. See "Section 6.26"_Section_howto.html#howto_26
for an overview of how to use the package.
To install via make or Make.py:
@ -297,8 +295,8 @@ make machine :pre
Make.py -p ^coreshell -a machine :pre
Supporting info: "Section howto
6.26"_Section_howto.html#howto_26, "compute temp/cs"_compute_temp_cs.html,
Supporting info: "Section 6.26"_Section_howto.html#howto_26,
"compute temp/cs"_compute_temp_cs.html,
"pair_style born/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
@ -335,7 +333,7 @@ GPU package :link(GPU),h5
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
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,
and how to build and use this package. See the KOKKOS package, which
also has GPU-enabled styles.
@ -380,10 +378,11 @@ make machine :pre
Make.py -p ^gpu -a machine :pre
Supporting info: src/GPU/README, lib/gpu/README, "Section
acclerate"_Section_accelerate.html, "Section accelerate
gpu"_accelerate_gpu.html, Pair Styles section of "Section commands
3.5"_Section_commands.html#cmd_5 for any pair style listed with a (g),
Supporting info: src/GPU/README, lib/gpu/README,
"Section 5.3"_Section_accelerate.html#acc_3,
"Section 5.3.1"_accelerate_gpu.html,
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,
examples/accelerate, bench/FERMI, bench/KEPLER
@ -409,7 +408,7 @@ make 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
gran/hooke"_pair_gran.html, "pair_style
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
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
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
use this package. See the GPU, OPT, USER-INTEL, USER-OMP packages,
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
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
system, you will need to read the "Section accelerate
kokkos"_accelerate_kokkos.html doc page for details of what
Makefile.machine settings are needed.
system, you will need to read the "Section 5.3.3"_accelerate_kokkos.html
doc page for details of what Makefile.machine settings are needed.
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
Supporting info: src/KOKKOS/README, lib/kokkos/README, "Section
acclerate"_Section_accelerate.html, "Section accelerate
kokkos"_accelerate_kokkos.html, Pair Styles section of "Section
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
with a (k), "package kokkos"_package.html,
Supporting info: src/KOKKOS/README, lib/kokkos/README,
"Section 5.3"_Section_accelerate.html#acc_3,
"Section 5.3.3"_accelerate_kokkos.html,
Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
for any pair style listed with a (k), "package kokkos"_package.html,
examples/accelerate, bench/FERMI, bench/KEPLER
: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
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
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
to select different FFT options in your machine Makefile. The Make.py
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
Supporting info: "kspace_style"_kspace_style.html,
"doc/PDF/kspace.pdf"_PDF/kspace.pdf, "Section howto
6.7"_Section_howto.html#howto_7, "Section howto
6.8"_Section_howto.html#howto_8, "Section howto
6.9"_Section_howto.html#howto_9, "pair_style coul"_pair_coul.html,
other pair style command doc pages which have "long" or "msm" in their
style name, examples/peptide, bench/in.rhodo
"doc/PDF/kspace.pdf"_PDF/kspace.pdf,
"Section 6.7"_Section_howto.html#howto_7,
"Section 6.8"_Section_howto.html#howto_8,
"Section 6.9"_Section_howto.html#howto_9,
"pair_style coul"_pair_coul.html, other pair style command doc pages
which have "long" or "msm" in their style name,
examples/peptide, bench/in.rhodo
:line
@ -568,7 +567,7 @@ Make.py -p ^manybody -a machine :pre
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,
examples/nb3d, examples/vashishta
@ -700,9 +699,9 @@ Supporting info:"atom_style"_atom_style.html,
"dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html, "pair_style
hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style
lj/charmm/coul/charmm"_pair_charmm.html, "Section howto
6.3"_Section_howto.html#howto_3, examples/micelle, examples/peptide,
bench/in.chain, bench/in.rhodo
lj/charmm/coul/charmm"_pair_charmm.html,
"Section 6.3"_Section_howto.html#howto_3,
examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo
:line
@ -738,7 +737,7 @@ OPT package :link(OPT),h5
Contents: A handful of pair styles with an "opt" in their style name
which are optimized for improved CPU performance on single or multiple
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,
which also have styles optimized for CPU performance.
@ -763,10 +762,10 @@ make machine :pre
Make.py -p ^opt -a machine :pre
Supporting info: "Section acclerate"_Section_accelerate.html, "Section
accelerate opt"_accelerate_opt.html, Pair Styles section of "Section
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
with an (o), examples/accelerate, bench/KEPLER
Supporting info: "Section 5.3"_Section_accelerate.html#acc_3,
"Section 5.3.5"_accelerate_opt.html, Pair Styles section of
"Section 3.5"_Section_commands.html#cmd_5 for any pair style
listed with an (t), examples/accelerate, bench/KEPLER
:line
@ -845,14 +844,14 @@ PYTHON package :link(PYTHON),h5
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
file or embedded in the input script itself. See "Section python
11.2"_Section_python.html" for an overview of using Python from
file or embedded in the input script itself. See "Section
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.
Building with the PYTHON package assumes you have a Python shared
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
contents of the lib/python/Makefile.lammps file to find all the Python
version, 2.6 or later. Python 3 is not yet supported. The build uses
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
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
@ -950,7 +949,7 @@ REPLICA package :link(REPLICA),h5
Contents: A collection of multi-replica methods that are used by
invoking multiple instances (replicas) of LAMMPS
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
multi-replica simulations in LAMMPS. Multi-replica methods included
in the package are nudged elastic band (NEB), parallel replica
@ -973,7 +972,7 @@ make 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,
"run_style verlet/split"_run_style.html, examples/neb, examples/prd,
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-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-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-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-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-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-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, -, -
@ -1353,12 +1352,12 @@ USER-DRUDE package :link(USER-DRUDE),h5
Contents: This package contains methods for simulating polarizable
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
package. See src/USER-DRUDE/README for additional details. There are
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
drude/transform/*"_fix_drude_transform.html, "compute
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
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
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
this package. Also see src/USER-INTEL/README for more details. See
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
"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
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
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,
compute, pair, etc sections.
@ -1609,7 +1608,7 @@ styles, and fix styles.
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
(akohlmey at gmail.com). Contact him directly if you have questions.

2
doc/src/Section_perf.txt
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@ -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
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
"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.
The bench/POTENTIALS directory has input files which correspond to the

56
doc/src/Section_start.txt
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@ -21,7 +21,6 @@ experienced users.
2.8 "Screen output"_#start_8
2.9 "Tips for users of previous versions"_#start_9 :all(b)
:line
:line
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:
"Read this first"_#start_2_1
"Steps to build a LAMMPS executable"_#start_2_2
"Common errors that can occur when making LAMMPS"_#start_2_3
"Additional build tips"_#start_2_4
"Building for a Mac"_#start_2_5
"Building for Windows"_#start_2_6 :ul
2.2.1 "Read this first"_#start_2_1
2.2.1 "Steps to build a LAMMPS executable"_#start_2_2
2.2.3 "Common errors that can occur when making LAMMPS"_#start_2_3
2.2.4 "Additional build tips"_#start_2_4
2.2.5 "Building for a Mac"_#start_2_5
2.2.6 "Building for Windows"_#start_2_6 :all(b)
: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
particular machine.
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
As explained above, any of these 3 settings can be specified on the
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)
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.
:line
@ -637,9 +635,9 @@ happy to distribute contributed instructions and modifications, but
we cannot provide support for those.
With the so-called "Anniversary Update" to Windows 10, there is a
Ubuntu subsystem available for Windows, that can be installed and
then it can be used to compile/install LAMMPS as if you are running
on a Ubuntu Linux system.
Ubuntu Linux subsystem available for Windows, that can be installed
and then used to compile/install LAMMPS as if you are running on a
Ubuntu Linux system instead of Windows.
As an alternative, you can download "daily builds" (and some older
versions) of the installer packages from
@ -654,10 +652,10 @@ many examples, but no source code.
This section has the following sub-sections:
"Package basics"_#start_3_1
"Including/excluding packages"_#start_3_2
"Packages that require extra libraries"_#start_3_3
"Packages that require Makefile.machine settings"_#start_3_4 :ul
2.3.1 "Package basics"_#start_3_1
2.3.2 "Including/excluding packages"_#start_3_2
2.3.3 "Packages that require extra libraries"_#start_3_3
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
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
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
LAMMPS with each package, which are covered in a more general manner
below.
@ -727,15 +725,15 @@ before building LAMMPS. From the src directory, this is typically as
simple as:
make yes-colloid
make g++ :pre
make mpi :pre
or
make no-manybody
make g++ :pre
make mpi :pre
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
will be out-of-date for the build if the package configuration changes
within the same command.
@ -826,7 +824,7 @@ where to find them.
For libraries with provided code, the sub-directory README file
(e.g. lib/atc/README) has instructions on how to build that library.
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:
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
USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
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
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
accelerator packages in detail:
"USER-INTEL package"_accelerate_intel.html
"KOKKOS package"_accelerate_kokkos.html
"USER-OMP package"_accelerate_omp.html
"OPT package"_accelerate_opt.html :ul
5.3.1 "USER-INTEL package"_accelerate_intel.html
5.3.3 "KOKKOS package"_accelerate_kokkos.html
5.3.4 "USER-OMP package"_accelerate_omp.html
5.3.5 "OPT package"_accelerate_opt.html :all(b)
You can also look at the following machine Makefiles in
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
default setting. Example of when to use these options and what
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
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
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
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
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
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
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
package. All compilation and computation is performed in double
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
provides alternative methods via environment variables for binding
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
Intel Phi processor.

6
doc/src/accelerate_omp.txt
View File

@ -7,7 +7,7 @@
:line
"Return to Section accelerate overview"_Section_accelerate.html
"Return to Section 5 overview"_Section_accelerate.html
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
styles (in serial or all-MPI parallelization with 1 task/core). This
is because many of the USER-OMP styles contain similar optimizations
to those used in the OPT package, described in "Section accelerate
5.3.6"_accelerate_opt.html.
to those used in the OPT package, described in "Section
5.3.5"_accelerate_opt.html.
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

9
doc/src/compute_tally.txt
View File

@ -35,7 +35,12 @@ group/group"_compute_group_group.html only that the data is
accumulated directly during the non-bonded force computation. The
computes {force/tally}, {pe/tally}, {stress/tally}, and
{heat/flux/tally} are primarily provided as example how to program
additional, more sophisticated computes using the tally mechanism.
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
@ -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
containing (in this order): {evdwl} and {ecoul} for intramolecular pairs
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
slots depending on whether the molecule IDs of a pair are the same or
different. Compute {force/tally} calculates a global scalar (the force

8
doc/src/dump.txt
View File

@ -328,8 +328,8 @@ bonds and colors.
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
popular molecular viewing program. See "Section
tools"_Section_tools.html#vmd of the manual and the
popular molecular viewing program. See
"Section 9"_Section_tools.html#vmd of the manual and the
tools/lmp2vmd/README.txt file for more information about support in
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.
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
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.
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
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
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
specific dump style uses molfile plugins that are bundled with the
"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
about support in VMD for reading and visualizing native LAMMPS dump
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
to the fact that the atoms are 'attached' to their equilibrium
positions by the Einstein crystal. Check the option {zero} of "fix
langevin"_fix_langevin_html and "velocity"_velocity.html. The use of
the Nose-Hoover thermostat ("fix nvt"_fix_nvt.html) is {NOT}
langevin"_fix_langevin.html and "velocity"_velocity.html. The use of
the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT}
recommended due to its well documented issues with the canonical
sampling of harmonic degrees of freedom (notice that the {chain}
option will {NOT} solve this problem). The Langevin thermostat ("fix

1
doc/src/fixes.txt
View File

@ -138,7 +138,6 @@ Fixes :h1
fix_temp_rescale_eff
fix_tfmc
fix_thermal_conductivity
fix_ti_rs
fix_ti_spring
fix_tmd
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
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
for speeding up LAMMPS simulations.

8
doc/src/pair_gauss.txt
View File

@ -63,7 +63,7 @@ solvent simulations of salt ions "(Lenart)"_#Lenart and of surfactants
"(Jusufi)"_#Jusufi. In these instances the Gaussian potential mimics
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
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
via the "pair_coeff"_pair_coeff.html command as in the example above,
@ -73,9 +73,11 @@ commands:
H (energy * 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

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.
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
command.

2
doc/src/read_restart.txt
View File

@ -124,7 +124,7 @@ MPI-IO requires two steps. First, build LAMMPS with its MPIIO package
installed, e.g.
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
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
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,
and how to transform these parameters to and from other commonly used
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
corresponding style without the suffix. They have been optimized to
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
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
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.
: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.
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
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
command, including a variable command. The input script parser
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
un-named "immediate" variables for this purpose. For example, a
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
specify a "compute"_compute.html that calculates temperature in a
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}
calculate temperature using a compute that is defined internally as
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
bias is subtracted from atom velocities before the {create} and
{scale} operations are performed. After the operations, the bias is
added back to the atom velocities. See "Section howto
16"_Section_howto.html#howto_15 of the doc pages for more discussion
added back to the atom velocities. See "Section
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
only applied to atoms in the temperature compute specified with the
{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.
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
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 re
class MPIAbortException(Exception):
def __init__(self, message):
self.message = message
def __str__(self):
return repr(self.message)
class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator
@ -43,6 +52,7 @@ class lammps(object):
# create instance of LAMMPS
def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
self.comm = comm
# determine module location
@ -150,10 +160,14 @@ class lammps(object):
if cmd: cmd = cmd.encode()
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)
self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
raise Exception(sb.value.decode().strip())
error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
error_msg = sb.value.decode().strip()
if error_type == 2:
raise MPIAbortException(error_msg)
raise Exception(error_msg)
def extract_global(self,name,type):
if name: name = name.encode()
@ -286,6 +300,14 @@ class lammps(object):
if name: name = name.encode()
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();
double single(int, int, int, int, double, double, double, double &);
double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *);
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();
double single(int, int, int, int, double, double, double, double &);
double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *);
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();
double single(int, int, int, int, double, double, double, double &);
double memory_usage();
void *extract(const char *, int &) { return NULL; }
int pack_forward_comm(int, int *, double *, int, int *);
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 void compute(int, int);
void init_style();
void *extract(const char *, int &) { return NULL; }
void coeff(int, char **);
KOKKOS_INLINE_FUNCTION

1
src/KOKKOS/pair_eam_fs_kokkos.h
View File

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

1
src/KOKKOS/pair_eam_kokkos.h
View File

@ -59,6 +59,7 @@ class PairEAMKokkos : public PairEAM {
virtual ~PairEAMKokkos();
virtual void compute(int, int);
void init_style();
void *extract(const char *, int &) { return NULL; }
KOKKOS_INLINE_FUNCTION
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;
rhor = NULL;
z2r = NULL;
scale = NULL;
frho_spline = NULL;
rhor_spline = NULL;
@ -232,6 +233,7 @@ void PairEAM::compute(int eflag, int vflag)
if (eflag) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi;
}
@ -306,7 +308,7 @@ void PairEAM::compute(int eflag, int vflag)
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,
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();
double init_one(int, int);
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 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) {
double phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
phi *= scale[type[i]][type[i]];
if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi;
}
@ -273,6 +274,7 @@ void PairEAMOpt::eval()
double tmpfz = 0.0;
fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr];
double* _noalias scale_i = scale[itype1+1]+1;
for (jj = 0; jj < jnum; 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
// 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
// scale factor can be applied by thermodynamic integration
double recip = 1.0/r;
double phi = z2*recip;
double phip = z2p*recip - phi*recip;
double psip = fp[i]*rhojp + fp[j]*rhoip + phip;
double fpair = -psip*recip;
double fpair = -scale_i[jtype]*psip*recip;
tmpfx += delx*fpair;
tmpfy += dely*fpair;
@ -332,7 +335,7 @@ void PairEAMOpt::eval()
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,
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.
double memory_usage();
void *extract(const char *, int &) { return NULL; }
/// Parses the coefficients of the h polynomial from the end of the EAM file.
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) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
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;
itype = type[i];
fxtmp = fytmp = fztmp = 0.0;
const double * _noalias const scale_i = scale[itype];
jlist = firstneigh[i];
jnum = numneigh[i];
@ -274,7 +275,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
phi = z2*recip;
phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
fpair = -psip*recip;
fpair = -scale_i[jtype]*psip*recip;
fxtmp += delx*fpair;
fytmp += dely*fpair;
@ -285,7 +286,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
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,
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
@ -198,6 +203,7 @@ void Error::done(int status)
exit(status);
}
#ifdef LAMMPS_EXCEPTIONS
/* ----------------------------------------------------------------------
return the last error message reported by LAMMPS (only used if
compiled with -DLAMMPS_EXCEPTIONS)
@ -208,13 +214,22 @@ char * Error::get_last_error() const
return last_error_message;
}
/* ----------------------------------------------------------------------
set the last error message (only used if compiled with
-DLAMMPS_EXCEPTIONS)
return the type of the last error reported by LAMMPS (only used if
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;
@ -224,4 +239,6 @@ void Error::set_last_error(const char * msg)
} else {
last_error_message = NULL;
}
last_error_type = type;
}
#endif

44
src/error.h
View File

@ -15,41 +15,14 @@
#define LMP_ERROR_H
#include "pointers.h"
#include <string>
#include <exception>
#ifdef LAMMPS_EXCEPTIONS
#include "exceptions.h"
#endif
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 {
char * last_error_message;
public:
Error(class LAMMPS *);
@ -63,8 +36,15 @@ class Error : protected Pointers {
void message(const char *, int, const char *, int = 1);
void done(int = 0); // 1 would be fully backwards compatible
#ifdef LAMMPS_EXCEPTIONS
char * get_last_error() const;
void set_last_error(const char * msg);
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) {
if (iarg+2 > narg) 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");
respa_level = lvl-1;
iarg += 2;

127
src/library.cpp
View File

@ -38,16 +38,67 @@
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
pass in command-line args and MPI communicator to run on
------------------------------------------------------------------------- */
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);
*ptr = (void *) lmp;
#endif
}
/* ----------------------------------------------------------------------
create an instance of LAMMPS and return pointer to it
@ -68,9 +119,21 @@ void lammps_open_no_mpi(int argc, char **argv, void **ptr)
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);
*ptr = (void *) lmp;
#endif
}
/* ----------------------------------------------------------------------
destruct an instance of LAMMPS
@ -99,8 +162,13 @@ int lammps_version(void *ptr)
void lammps_file(void *ptr, char *str)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
lmp->input->file(str);
}
END_CAPTURE
}
/* ----------------------------------------------------------------------
process a single input command in str
@ -109,14 +177,15 @@ void lammps_file(void *ptr, char *str)
char *lammps_command(void *ptr, char *str)
{
LAMMPS *lmp = (LAMMPS *) ptr;
Error * error = lmp->error;
char * result = NULL;
try {
return lmp->input->one(str);
} catch(LAMMPSException & e) {
error->set_last_error(e.message.c_str());
return NULL;
BEGIN_CAPTURE
{
result = lmp->input->one(str);
}
END_CAPTURE
return result;
}
/* ----------------------------------------------------------------------
@ -215,6 +284,8 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
int icompute = lmp->modify->find_compute(id);
if (icompute < 0) return NULL;
Compute *compute = lmp->modify->compute[icompute];
@ -267,6 +338,8 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
return (void *) compute->array_local;
}
}
}
END_CAPTURE
return NULL;
}
@ -300,6 +373,8 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
int ifix = lmp->modify->find_fix(id);
if (ifix < 0) return NULL;
Fix *fix = lmp->modify->fix[ifix];
@ -334,6 +409,8 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
if (type == 1) return (void *) fix->vector_local;
if (type == 2) return (void *) fix->array_local;
}
}
END_CAPTURE
return NULL;
}
@ -369,6 +446,8 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
int ivar = lmp->input->variable->find(name);
if (ivar < 0) return NULL;
@ -386,6 +465,8 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
return (void *) vector;
}
}
END_CAPTURE
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)
{
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;
}
@ -414,9 +502,14 @@ int lammps_set_variable(void *ptr, char *name, char *str)
double lammps_get_thermo(void *ptr, char *name)
{
LAMMPS *lmp = (LAMMPS *) ptr;
double dval;
double dval = 0.0;
BEGIN_CAPTURE
{
lmp->output->thermo->evaluate_keyword(name,&dval);
}
END_CAPTURE
return dval;
}
@ -449,6 +542,8 @@ void lammps_gather_atoms(void *ptr, char *name,
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
// error if tags are not defined or not consecutive
int flag = 0;
@ -523,6 +618,8 @@ void lammps_gather_atoms(void *ptr, char *name,
lmp->memory->destroy(copy);
}
}
END_CAPTURE
}
/* ----------------------------------------------------------------------
scatter the named atom-based entity across all processors
@ -538,6 +635,8 @@ void lammps_scatter_atoms(void *ptr, char *name,
{
LAMMPS *lmp = (LAMMPS *) ptr;
BEGIN_CAPTURE
{
// error if tags are not defined or not consecutive or no atom map
int flag = 0;
@ -600,7 +699,10 @@ void lammps_scatter_atoms(void *ptr, char *name,
}
}
}
END_CAPTURE
}
#ifdef LAMMPS_EXCEPTIONS
/* ----------------------------------------------------------------------
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
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) {
@ -620,9 +725,11 @@ int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
Error * error = lmp->error;
if(error->get_last_error()) {
int error_type = error->get_last_error_type();
strncpy(buffer, error->get_last_error(), buffer_size-1);
error->set_last_error(NULL);
return 1;
error->set_last_error(NULL, ERROR_NONE);
return error_type;
}
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_scatter_atoms(void *, char *, int, int, void *);
#ifdef LAMMPS_EXCEPTIONS
int lammps_has_error(void *);
int lammps_get_last_error_message(void *, char *, int);
#endif
#ifdef __cplusplus
}