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Merge branch 'master' into plugin-loader

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This commit is contained in:
Axel Kohlmeyer
2021-03-16 19:46:21 -04:00
parent 15e30ed44d 42895ac6df
commit 31009b0517
162 changed files with 2715 additions and 2777 deletions
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2
cmake/Modules/Packages/GPU.cmake
View File

@ -35,7 +35,7 @@ if(GPU_API STREQUAL "CUDA")
if(NOT BIN2C)
message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
endif()
option(CUDPP_OPT "Enable CUDPP_OPT" ON)
option(CUDPP_OPT "Enable GPU binning via CUDAPP (should be off for modern GPUs)" OFF)
option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
if(CUDA_MPS_SUPPORT)
if(CUDPP_OPT)

3
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -51,10 +51,12 @@ if(DOWNLOAD_KOKKOS)
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.3.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@ -66,6 +68,7 @@ else()
${LAMMPS_LIB_KOKKOS_BIN_DIR})
target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE kokkos)
target_link_libraries(lmp PRIVATE kokkos)
endif()
target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)

18
cmake/presets/oneapi.cmake Normal file
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@ -0,0 +1,18 @@
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
set(MPI_CXX "icpx" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)

8
doc/src/Build_basics.rst
View File

@ -234,6 +234,8 @@ LAMMPS.
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
# Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
# Building with Intel oneAPI Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
# Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
# Building with PGI/Nvidia Compilers:
@ -243,8 +245,10 @@ LAMMPS.
provided that can be loaded with
`-C ../cmake/presets/clang.cmake`. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the compiler
toolchain to the Intel compilers and `-C ../cmake/presets/pgi.cmake`
should switch the compiler to the PGI compilers.
toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
will switch to the LLVM based oneAPI Intel compilers,
and `-C ../cmake/presets/pgi.cmake`
will switch the compiler to the PGI compilers.
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. By

13
doc/src/Build_extras.rst
View File

@ -128,9 +128,9 @@ CMake build
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
# enables CUDA Performance Primitives Optimizations, must be "no" for CUDA_MPS_SUPPORT=yes
# value = yes (default) or no
-D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs)
# enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
# value = yes or no (default)
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
@ -230,11 +230,12 @@ GPU architectures as supported by the CUDA toolkit in use. This is done
through using the "--gencode " flag, which can be used multiple times and
thus support all GPU architectures supported by your CUDA compiler.
To include CUDA performance primitives set the Makefile variable
``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.
To enable GPU binning via CUDA performance primitives set the Makefile variable
``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``. This should **not** be used with
most modern GPUs.
To support the CUDA multiprocessor server you can set the define
``-DCUDA_PROXY``. Please note that in this case you should **not** use
``-DCUDA_PROXY``. Please note that in this case you must **not** use
the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
to empty.

8
doc/src/Howto_cmake.rst
View File

@ -411,10 +411,10 @@ interface (``ccmake`` or ``cmake-gui``).
.. note::
Using a preset to select a compiler package (``clang.cmake``,
``gcc.cmake``, or ``intel.cmake``) are an exception to the option
of updating the configuration incrementally, as they will trigger
a reset of cached internal CMake settings and thus reset them to
their default values.
``gcc.cmake``, ``intel.cmake``, ``oneapi.cmake``, or ``pgi.cmake``)
are an exception to the mechanism of updating the configuration incrementally,
as they will trigger a reset of cached internal CMake settings and thus
reset settings to their default values.
Compilation and build targets
-----------------------------

34
doc/src/Tools.rst
View File

@ -93,6 +93,7 @@ Miscellaneous tools
* :ref:`i-pi <ipi>`
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`singularity <singularity_tool>`
* :ref:`SWIG interface <swig>`
* :ref:`vim <vim>`
@ -641,6 +642,39 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
----------
.. _magic:
Magic patterns for the "file" command
-------------------------------------
.. versionadded:: 10Mar2021
The file ``magic`` contains patterns that are used by the
`file program <https://en.wikipedia.org/wiki/File_(command)>`_
available on most Unix-like operating systems which enables it
to detect various LAMMPS files and print some useful information
about them. To enable these patterns, append or copy the contents
of the file to either the file ``.magic`` in your home directory
or (as administrator) to ``/etc/magic`` (for a system-wide
installation). Afterwards the ``file`` command should be able to
detect most LAMMPS restarts, dump, data and log files. Examples:
.. code-block:: bash
$ file *.*
dihedral-quadratic.restart: LAMMPS binary restart file (rev 2), Version 10 Mar 2021, Little Endian
mol-pair-wf_cut.restart: LAMMPS binary restart file (rev 2), Version 24 Dec 2020, Little Endian
atom.bin: LAMMPS atom style binary dump (rev 2), Little Endian, First time step: 445570
custom.bin: LAMMPS custom style binary dump (rev 2), Little Endian, First time step: 100
bn1.lammpstrj: LAMMPS text mode dump, First time step: 5000
data.fourmol: LAMMPS data file written by LAMMPS
pnc.data: LAMMPS data file written by msi2lmp
data.spce: LAMMPS data file written by TopoTools
B.data: LAMMPS data file written by OVITO
log.lammps: LAMMPS log file written by version 10 Feb 2021
----------
.. _matlab:
matlab tool

3
doc/utils/sphinx-config/false_positives.txt
View File

@ -160,6 +160,7 @@ atwt
augt
AuO
automagically
Auvergne
Avalos
avalue
aveforce
@ -1740,6 +1741,7 @@ lwsock
lx
ly
Lybrand
lyon
Lyulin
lz
Maaravi
@ -3256,6 +3258,7 @@ Tz
Tzou
ub
Uberuaga
uca
uChem
uCond
uef

22
examples/ELASTIC_T/displace.mod
View File

@ -100,22 +100,12 @@ run ${nrun}
# Obtain new stress tensor
variable tmp equal pe
variable e1 equal ${tmp}
variable tmp equal press
variable p1 equal ${tmp}
variable tmp equal pxx
variable pxx1 equal ${tmp}
variable tmp equal pyy
variable pyy1 equal ${tmp}
variable tmp equal pzz
variable pzz1 equal ${tmp}
variable tmp equal pxy
variable pxy1 equal ${tmp}
variable tmp equal pxz
variable pxz1 equal ${tmp}
variable tmp equal pyz
variable pyz1 equal ${tmp}
variable pxx1 equal f_avp[1]
variable pyy1 equal f_avp[2]
variable pzz1 equal f_avp[3]
variable pxy1 equal f_avp[4]
variable pxz1 equal f_avp[5]
variable pyz1 equal f_avp[6]
# Compute elastic constant from pressure tensor

3
lib/gpu/Makefile.cuda
View File

@ -29,7 +29,8 @@ LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
# GPU binning not recommended for modern GPUs
CUDPP_OPT = # -DUSE_CUDPP -Icudpp_mini
CUDA_MPS =
# device code compiler and settings

3
lib/gpu/Makefile.linux
View File

@ -70,7 +70,8 @@ LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
# GPU binning not recommended with modern GPUs
CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

3
lib/gpu/Makefile.linux_multi
View File

@ -77,7 +77,8 @@ LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
# GPU binning not recommended with modern GPUs
CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile_multi

3
lib/gpu/Makefile.serial
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@ -66,7 +66,8 @@ LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
# GPU binning not recommended for most modern GPUs
CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

1
lib/gpu/Makefile.turing
View File

@ -16,6 +16,7 @@ LIB_DIR = .
AR = ar
BSH = /bin/sh
# GPU binning not recommended with most modern GPUs
CUDPP_OPT = #-DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

4
lib/gpu/geryon/nvd_device.h
View File

@ -24,6 +24,10 @@
#ifndef NVD_DEVICE
#define NVD_DEVICE
// workaround after GPU package Feb2021 update
// todo: make new neighbor code work with CUDA
#define LAL_USE_OLD_NEIGHBOR
#include <string>
#include <vector>
#include <iostream>

28
python/examples/pylammps/README
View File

@ -1,28 +0,0 @@
# Compile LAMMPS as shared library
git clone https://github.com/lammps/lammps.git
cd lammps/src
python Make.py -m mpi -png -s ffmpeg exceptions -a file
make -j 4 mode=shlib auto
cd ../..
# Install Python package
virtualenv testing
source testing/bin/activate
(testing) cd lammps/python
(testing) python install.py
(testing) pip install jupyter matplotlib mpi4py
(testing) cd ../../examples
# Launch jupter and work inside browser
(testing) jupyter notebook
# Use Ctrl+c to stop jupyter
# finally exit the virtualenv
(testing) deactivate

89
python/examples/pylammps/README.md Normal file
View File

@ -0,0 +1,89 @@
# PyLammps and Jupyter Notebooks
This folder contains examples showcasing the usage of the PyLammps Python
interface and Jupyter notebooks. To use this you will need LAMMPS compiled as
a shared library and the LAMMPS Python package installed.
An extensive guide on how to achieve this is documented in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a [PyLammps tutorial](https://lammps.sandia.gov/doc/Howto_pylammps.html).
The following will show one way of creating a Python virtual environment
which has both LAMMPS and its Python package installed:
1. Clone the LAMMPS source code
```shell
$ git clone -b stable https://github.com/lammps/lammps.git
$ cd lammps
```
2. Create a build folder
```shell
$ mkdir build
$ cd build
```
3. Create a virtual environment for Python
```shell
$ python3 -m venv myenv
```
4. Extend `LD_LIBRARY_PATH` (Unix/Linux) or `DYLD_LIBRARY_PATH` (MacOS)
On Unix/Linux:
```shell
$ echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> myenv/bin/activate
```
On MacOS:
```shell
echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> myenv/bin/activate
```
5. Activate the virtual environment
```shell
$ source myenv/bin/activate
(myenv)$
```
6. Configure LAMMPS compilation (CMake)
```shell
(myenv)$ cmake -C ../cmake/presets/minimal.cmake \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on \
-D CMAKE_INSTALL_PREFIX=$VIRTUAL_ENV \
../cmake
```
7. Compile LAMMPS
```shell
(myenv)$ cmake --build .
```
8. Install LAMMPS and Python package into virtual environment
```shell
(myenv)$ cmake --install .
```
9. Install other Python packages into virtual environment
```shell
(myenv)$ pip install jupyter matplotlib mpi4py
```
10. Navigate to pylammps examples folder
```shell
(myenv)$ cd ../python/examples/pylammmps
```
11. Launch Jupyter and work inside browser
```shell
(myenv)$ jupyter notebook
```

18
python/examples/pylammps/dihedrals/dihedral.ipynb
View File

@ -19,9 +19,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"import matplotlib.pyplot as plt"
@ -30,9 +28,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"from lammps import IPyLammps"
@ -194,9 +190,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"K = 80.0\n",
@ -232,9 +226,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": []
}
@ -255,7 +247,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.2"
"version": "3.9.2"
}
},
"nbformat": 4,

142
python/examples/pylammps/interface_usage.ipynb
View File

@ -4,71 +4,29 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using LAMMPS with iPython and Jupyter"
"# Example 2: Using the PyLammps interface"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up."
"## Prerequisites\n",
"\n",
"Before running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a dedicated [PyLammps HowTo](https://lammps.sandia.gov/doc/Howto_pylammps.html)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Installation"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"1. Download the latest version of LAMMPS into a folder (we will calls this `$LAMMPS_DIR` from now on)\n",
"2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
" ```bash\n",
" cd $LAMMPS_DIR/src\n",
" make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
" ```\n",
"\n",
"3. Create a python virtualenv\n",
" ```bash\n",
" virtualenv testing\n",
" source testing/bin/activate\n",
" ```\n",
"\n",
"4. Inside the virtualenv install the lammps package\n",
" ```\n",
" (testing) cd $LAMMPS_DIR/python\n",
" (testing) python install.py\n",
" (testing) cd # move to your working directory\n",
" ```\n",
"\n",
"5. Install jupyter and ipython in the virtualenv\n",
" ```bash\n",
" (testing) pip install ipython jupyter\n",
" ```\n",
"\n",
"6. Run jupyter notebook\n",
" ```bash\n",
" (testing) jupyter notebook\n",
" ```"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example"
"## Setup system"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"from lammps import IPyLammps"
@ -90,7 +48,6 @@
"outputs": [],
"source": [
"# 3d Lennard-Jones melt\n",
"\n",
"L.units(\"lj\")\n",
"L.atom_style(\"atomic\")\n",
"L.atom_modify(\"map array\")\n",
@ -116,6 +73,13 @@
"L.run(10)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Visualize the initial state"
]
},
{
"cell_type": "code",
"execution_count": null,
@ -205,9 +169,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"a index 2\")"
@ -225,9 +187,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"t equal temp\")"
@ -283,9 +243,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"b index a b c\")"
@ -321,9 +279,16 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.lmp.command('variable i loop 10')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"i loop 10\")"
@ -379,7 +344,7 @@
"metadata": {},
"outputs": [],
"source": [
"[x for x in dir(L.atoms[0]) if not x.startswith('__')]"
"dir(L.atoms[0])"
]
},
{
@ -479,6 +444,15 @@
"L.runs[0].thermo"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"dir(L.runs[0].thermo)"
]
},
{
"cell_type": "markdown",
"metadata": {},
@ -486,14 +460,48 @@
"## Saving session to as LAMMPS input file"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"PyLammps can keep track of all LAMMPS commands that are executed. This allows you to prototype a script and then later on save it as a regular input script:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L = IPyLammps()\n",
"\n",
"# enable command history\n",
"L.enable_cmd_history = True\n",
"\n",
"# 3d Lennard-Jones melt\n",
"L.units(\"lj\")\n",
"L.atom_style(\"atomic\")\n",
"L.atom_modify(\"map array\")\n",
"\n",
"L.lattice(\"fcc\", 0.8442)\n",
"L.region(\"box block\", 0, 4, 0, 4, 0, 4)\n",
"L.create_box(1, \"box\")\n",
"L.create_atoms(1, \"box\")\n",
"L.mass(1, 1.0)\n",
"\n",
"L.velocity(\"all create\", 1.44, 87287, \"loop geom\")\n",
"\n",
"L.pair_style(\"lj/cut\", 2.5)\n",
"L.pair_coeff(1, 1, 1.0, 1.0, 2.5)\n",
"\n",
"L.neighbor(0.3, \"bin\")\n",
"L.neigh_modify(\"delay 0 every 20 check no\")\n",
"\n",
"L.fix(\"1 all nve\")\n",
"\n",
"L.run(10)\n",
"\n",
"# write LAMMPS input script with all commands executed so far (including implicit ones)\n",
"L.write_script(\"in.output\")"
]
},
@ -503,7 +511,7 @@
"metadata": {},
"outputs": [],
"source": [
"dir(L.runs[0].thermo)"
"!cat in.output"
]
},
{
@ -530,7 +538,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.2"
"version": "3.9.2"
}
},
"nbformat": 4,

93
python/examples/pylammps/interface_usage_bonds.ipynb
View File

@ -4,72 +4,29 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using LAMMPS with iPython and Jupyter"
"# Example 3: 2D circle of particles inside of box with LJ walls"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up."
"## Prerequisites\n",
"\n",
"Before running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a dedicated [PyLammps HowTo](https://lammps.sandia.gov/doc/Howto_pylammps.html)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Installation"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"1. Download the latest version of LAMMPS into a folder (we will calls this `$LAMMPS_DIR` from now on)\n",
"2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
" ```bash\n",
" cd $LAMMPS_DIR/src\n",
" make yes-molecule\n",
" make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
" ```\n",
"\n",
"3. Create a python virtualenv\n",
" ```bash\n",
" virtualenv testing\n",
" source testing/bin/activate\n",
" ```\n",
"\n",
"4. Inside the virtualenv install the lammps package\n",
" ```\n",
" (testing) cd $LAMMPS_DIR/python\n",
" (testing) python install.py\n",
" (testing) cd # move to your working directory\n",
" ```\n",
"\n",
"5. Install jupyter and ipython in the virtualenv\n",
" ```bash\n",
" (testing) pip install ipython jupyter\n",
" ```\n",
"\n",
"6. Run jupyter notebook\n",
" ```bash\n",
" (testing) jupyter notebook\n",
" ```"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example"
"## Setup system"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"from lammps import IPyLammps"
@ -135,6 +92,13 @@
"L.fix(3, \"all wall/lj93 ylo 0.0 1 1 2.5 yhi\", y, \"1 1 2.5\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Visualize initial state"
]
},
{
"cell_type": "code",
"execution_count": null,
@ -144,6 +108,13 @@
"L.image(zoom=1.8)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Run simulation and visualize new state"
]
},
{
"cell_type": "code",
"execution_count": null,
@ -254,9 +225,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"a index 2\")"
@ -274,9 +243,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"t equal temp\")"
@ -332,9 +299,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"b index a b c\")"
@ -370,9 +335,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"L.variable(\"i loop 10\")"
@ -428,7 +391,7 @@
"metadata": {},
"outputs": [],
"source": [
"[x for x in dir(L.atoms[0]) if not x.startswith('__')]"
"dir(L.atoms[0])"
]
},
{
@ -479,9 +442,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": []
}
@ -502,7 +463,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.2"
"version": "3.9.2"
}
},
"nbformat": 4,

1032
python/examples/pylammps/montecarlo/mc.ipynb
View File

File diff suppressed because one or more lines are too long

274
python/examples/pylammps/simple.ipynb
View File

@ -4,74 +4,32 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Using LAMMPS with iPython and Jupyter"
"# Example 1: Using LAMMPS with PyLammps"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up."
"The LAMMPS Python package provides multiple interfaces. The `PyLammps` interface is a high-level abstration of the low-level `lammps` interface. `IPyLammps` further extends this interface with functions that are useful for Jupyter notebooks to enable embedding generated graphics and videos."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Installation"
"## Prerequisites\n",
"\n",
"Before Running this example, make sure your Python environment can find the LAMMPS shared library (`liblammps.so`) and the LAMMPS Python package is installed. If you followed the [README](README.md) in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the [LAMMPS manual](https://lammps.sandia.gov/doc/Python_install.html). There is also a dedicated [PyLammps HowTo](https://lammps.sandia.gov/doc/Howto_pylammps.html)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"1. Download the latest version of LAMMPS into a folder (we will calls this `$LAMMPS_DIR` from now on)\n",
"2. Compile LAMMPS as a shared library and enable exceptions and PNG support\n",
" ```bash\n",
" cd $LAMMPS_DIR/src\n",
" make mpi mode=shlib LMP_INC=\"-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS\" JPG_LIB=\"-lpng\"\n",
" ```\n",
"## Creating a new simulation\n",
"\n",
"3. Create a python virtualenv\n",
" ```bash\n",
" virtualenv testing\n",
" source testing/bin/activate\n",
" ```\n",
"\n",
"4. Inside the virtualenv install the lammps package\n",
" ```\n",
" (testing) cd $LAMMPS_DIR/python\n",
" (testing) python install.py\n",
" (testing) cd # move to your working directory\n",
" ```\n",
"\n",
"5. Install jupyter and ipython in the virtualenv\n",
" ```bash\n",
" (testing) pip install ipython jupyter\n",
" ```\n",
"\n",
"6. Run jupyter notebook\n",
" ```bash\n",
" (testing) jupyter notebook\n",
" ```"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from lammps import IPyLammps"
"Once the LAMMPS shared library and the LAMMPS Python package are installed, you can create a new LAMMMPS instance in your Python interpreter as follows:"
]
},
{
@ -80,22 +38,53 @@
"metadata": {},
"outputs": [],
"source": [
"from lammps import IPyLammps\n",
"L = IPyLammps()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"With `PyLammps`/`IPyLammps` you can write LAMMPS simulations similar to the input script language. Take the following LAMMPS input script:\n",
"\n",
"```bash\n",
"# 3d Lennard-Jones melt\n",
"\n",
"units lj\n",
"atom_style atomic\n",
"\n",
"lattice fcc 0.8442\n",
"region box block 0 4 0 4 0 4\n",
"create_box 1 box\n",
"create_atoms 1 box\n",
"mass 1 1.0\n",
"\n",
"velocity all create 1.44 87287 loop geom\n",
"\n",
"pair_style lj/cut 2.5\n",
"pair_coeff 1 1 1.0 1.0 2.5\n",
"\n",
"neighbor 0.3 bin\n",
"neigh_modify delay 0 every 20 check no\n",
"\n",
"fix 1 all nve\n",
"\n",
"thermo 50\n",
"```\n",
"The equivalent can be written with `PyLammps`/`IPyLammps`:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import math\n",
"\n",
"# 3d Lennard-Jones melt\n",
"\n",
"L.units(\"lj\")\n",
"L.atom_style(\"atomic\")\n",
"L.atom_modify(\"map array\")\n",
"\n",
"L.lattice(\"fcc\", 0.8442)\n",
"L.region(\"box\", \"block\", 0, 4, 0, 4, 0, 4)\n",
@ -111,13 +100,18 @@
"L.neighbor(0.3, \"bin\")\n",
"L.neigh_modify(\"delay\", 0, \"every\", 20, \"check no\")\n",
"\n",
"L.fix(\"1 all nve\")\n",
"L.fix(\"1\", \"all\", \"nve\")\n",
"\n",
"L.variable(\"fx atom fx\")\n",
"L.thermo(50)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Visualizing the initial state\n",
"\n",
"L.info(\"all\")\n",
"\n",
"L.run(10)"
"`IPyLammps` allows you to visualize the current simulation state with the [image](https://lammps.sandia.gov/doc/Python_module.html#lammps.IPyLammps.image) command. Here we use it to create an image of the initial state of the system."
]
},
{
@ -128,6 +122,170 @@
"source": [
"L.image(zoom=1.0)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Running simulations\n",
"\n",
"Use the `run` command to start the simulation. In Jupyter the return value of the last command will be displayed. The `run` command will return the output of the simulation."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.run(150)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You can suppress it by adding a semicolon `;`."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.run(100);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Visualizing the system will now show us how the atoms have moved."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.image(zoom=1.0)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Post-processing thermo output\n",
"\n",
"Independent of whether or not you suppress or show the output of the `run` command, `PyLammps` will record the output. Each `run` command creates a new entry in the `L.runs` list. So far our PyLammps instance `L` executed two `run` commands:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"len(L.runs)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Each entry contains information about the simulation run, including the thermo output for the printed out time steps.\n",
"\n",
"```bash\n",
"# thermo output of a LAMMPS simulation run\n",
"Step Temp E_pair E_mol TotEng Press\n",
" 0 1.44 -6.7733681 0 -4.6218056 -5.0244179\n",
" 50 0.70303849 -5.6796164 0 -4.629178 0.50453907\n",
" 100 0.72628044 -5.7150774 0 -4.6299123 0.29765862\n",
" 150 0.78441711 -5.805142 0 -4.6331125 -0.086709661\n",
"```\n",
"\n",
"`PyLammps` already parses this information and makes it available as dictionaries and arrays."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.runs[0]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.runs[1]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"For example, the first run was 150 time steps, with printing out a line every 50 steps. You can access the list of time steps using `{entry}.thermo.Step`."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.runs[0].thermo.Step"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The corresponding values of each thermo quantity are also accessed this way:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"L.runs[0].thermo.TotEng"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Together you can use this information to run post-processing on these values or even plot it using `matplotlib`:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%matplotlib inline\n",
"import matplotlib.pyplot as plt\n",
"\n",
"plt.xlabel('time step')\n",
"plt.ylabel('Total Energy')\n",
"plt.plot(L.runs[0].thermo.Step, L.runs[0].thermo.TotEng)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
@ -146,7 +304,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.2"
"version": "3.9.2"
}
},
"nbformat": 4,

6
python/lammps/pylammps.py
View File

@ -132,6 +132,9 @@ class Atom(object):
self._pylmp = pylammps_instance
self.index = index
def __dir__(self):
return [k for k in super().__dir__() if not k.startswith('_')]
@property
def id(self):
"""
@ -298,6 +301,9 @@ class variable_set:
def __str__(self):
return "{}({})".format(self._name, ','.join(["{}={}".format(k, self.__dict__[k]) for k in self.__dict__.keys() if not k.startswith('_')]))
def __dir__(self):
return [k for k in self.__dict__.keys() if not k.startswith('_')]
def __repr__(self):
return self.__str__()

2
src/GPU/pair_beck_gpu.cpp
View File

@ -158,7 +158,7 @@ void PairBeckGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = beck_gpu_init(atom->ntypes+1, cutsq, aa, alpha, beta,

2
src/GPU/pair_born_coul_long_cs_gpu.cpp
View File

@ -194,7 +194,7 @@ void PairBornCoulLongCSGPU::init_style()
g_ewald = force->kspace->g_ewald;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = bornclcs_gpu_init(atom->ntypes+1, cutsq, rhoinv,

2
src/GPU/pair_born_coul_long_gpu.cpp
View File

@ -193,7 +193,7 @@ void PairBornCoulLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = borncl_gpu_init(atom->ntypes+1, cutsq, rhoinv,

2
src/GPU/pair_born_coul_wolf_cs_gpu.cpp
View File

@ -179,7 +179,7 @@ void PairBornCoulWolfCSGPU::init_style()
cut_coul;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = borncwcs_gpu_init(atom->ntypes+1, cutsq, rhoinv,

2
src/GPU/pair_born_coul_wolf_gpu.cpp
View File

@ -177,7 +177,7 @@ void PairBornCoulWolfGPU::init_style()
cut_coul;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = borncw_gpu_init(atom->ntypes+1, cutsq, rhoinv,

2
src/GPU/pair_born_gpu.cpp
View File

@ -161,7 +161,7 @@ void PairBornGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = born_gpu_init(atom->ntypes+1, cutsq, rhoinv,

2
src/GPU/pair_buck_coul_cut_gpu.cpp
View File

@ -165,7 +165,7 @@ void PairBuckCoulCutGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = buckc_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,

2
src/GPU/pair_buck_coul_long_gpu.cpp
View File

@ -189,7 +189,7 @@ void PairBuckCoulLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = buckcl_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,

2
src/GPU/pair_buck_gpu.cpp
View File

@ -159,7 +159,7 @@ void PairBuckGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = buck_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,

2
src/GPU/pair_colloid_gpu.cpp
View File

@ -169,7 +169,7 @@ void PairColloidGPU::init_style()
}
}
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = colloid_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_coul_cut_gpu.cpp
View File

@ -164,7 +164,7 @@ void PairCoulCutGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = coul_gpu_init(atom->ntypes+1, scale, cutsq,

2
src/GPU/pair_coul_debye_gpu.cpp
View File

@ -165,7 +165,7 @@ void PairCoulDebyeGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = cdebye_gpu_init(atom->ntypes+1, scale, cutsq,

2
src/GPU/pair_coul_dsf_gpu.cpp
View File

@ -182,7 +182,7 @@ void PairCoulDSFGPU::init_style()
e_shift = erfcc/cut_coul - f_shift*cut_coul;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = cdsf_gpu_init(atom->ntypes+1, atom->nlocal,

2
src/GPU/pair_coul_long_cs_gpu.cpp
View File

@ -184,7 +184,7 @@ void PairCoulLongCSGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = clcs_gpu_init(atom->ntypes+1, scale,

2
src/GPU/pair_coul_long_gpu.cpp
View File

@ -179,7 +179,7 @@ void PairCoulLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = cl_gpu_init(atom->ntypes+1, scale,

2
src/GPU/pair_dpd_gpu.cpp
View File

@ -306,7 +306,7 @@ void PairDPDGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = dpd_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,

2
src/GPU/pair_dpd_tstat_gpu.cpp
View File

@ -325,7 +325,7 @@ void PairDPDTstatGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = dpd_tstat_gpu_init(atom->ntypes+1, cutsq, a0, gamma, sigma,

2
src/GPU/pair_eam_alloy_gpu.cpp
View File

@ -181,7 +181,7 @@ void PairEAMAlloyGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int fp_size;
int mnf = 5e-2 * neighbor->oneatom;

2
src/GPU/pair_eam_fs_gpu.cpp
View File

@ -180,7 +180,7 @@ void PairEAMFSGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int fp_size;
int mnf = 5e-2 * neighbor->oneatom;

2
src/GPU/pair_eam_gpu.cpp
View File

@ -182,7 +182,7 @@ void PairEAMGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int fp_size;
int mnf = 5e-2 * neighbor->oneatom;

2
src/GPU/pair_gauss_gpu.cpp
View File

@ -157,7 +157,7 @@ void PairGaussGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = gauss_gpu_init(atom->ntypes+1, cutsq, a, b,

2
src/GPU/pair_gayberne_gpu.cpp
View File

@ -205,7 +205,7 @@ void PairGayBerneGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = gb_gpu_init(atom->ntypes+1, gamma, upsilon, mu,

2
src/GPU/pair_lj96_cut_gpu.cpp
View File

@ -158,7 +158,7 @@ void PairLJ96CutGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = lj96_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_charmm_coul_charmm_gpu.cpp
View File

@ -165,7 +165,7 @@ void PairLJCharmmCoulCharmmGPU::init_style()
double cell_size = sqrt(cut_bothsq) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
bool arithmetic = true;

2
src/GPU/pair_lj_charmm_coul_long_gpu.cpp
View File

@ -191,7 +191,7 @@ void PairLJCharmmCoulLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
bool arithmetic = true;

2
src/GPU/pair_lj_class2_coul_long_gpu.cpp
View File

@ -186,7 +186,7 @@ void PairLJClass2CoulLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = c2cl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_class2_gpu.cpp
View File

@ -155,7 +155,7 @@ void PairLJClass2GPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = lj96_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cubic_gpu.cpp
View File

@ -163,7 +163,7 @@ void PairLJCubicGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljcb_gpu_init(atom->ntypes+1, cutsq, cut_inner_sq,

2
src/GPU/pair_lj_cut_coul_cut_gpu.cpp
View File

@ -166,7 +166,7 @@ void PairLJCutCoulCutGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljc_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cut_coul_debye_gpu.cpp
View File

@ -168,7 +168,7 @@ void PairLJCutCoulDebyeGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljcd_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
View File

@ -183,7 +183,7 @@ void PairLJCutCoulDSFGPU::init_style()
e_shift = erfcc/cut_coul - f_shift*cut_coul;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljd_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cut_coul_long_gpu.cpp
View File

@ -191,7 +191,7 @@ void PairLJCutCoulLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljcl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cut_coul_msm_gpu.cpp
View File

@ -177,7 +177,7 @@ void PairLJCutCoulMSMGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljcm_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
View File

@ -171,7 +171,7 @@ void PairLJCutDipoleCutGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = dpl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cut_dipole_long_gpu.cpp
View File

@ -195,7 +195,7 @@ void PairLJCutDipoleLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,nullptr);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = dplj_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cut_gpu.cpp
View File

@ -162,7 +162,7 @@ void PairLJCutGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
View File

@ -210,7 +210,7 @@ void PairLJCutTIP4PLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
// set alpha parameter

2
src/GPU/pair_lj_expand_coul_long_gpu.cpp
View File

@ -191,7 +191,7 @@ void PairLJExpandCoulLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,cut_respa);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ljecl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_expand_gpu.cpp
View File

@ -159,7 +159,7 @@ void PairLJExpandGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = lje_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_lj_gromacs_gpu.cpp
View File

@ -162,7 +162,7 @@ void PairLJGromacsGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;

2
src/GPU/pair_lj_sdk_coul_long_gpu.cpp
View File

@ -195,7 +195,7 @@ void PairLJSDKCoulLongGPU::init_style()
if (ncoultablebits) init_tables(cut_coul,nullptr);
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = sdkl_gpu_init(atom->ntypes+1, cutsq, lj_type, lj1, lj2, lj3,

2
src/GPU/pair_lj_sdk_gpu.cpp
View File

@ -164,7 +164,7 @@ void PairLJSDKGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = sdk_gpu_init(atom->ntypes+1,cutsq,lj_type,lj1,lj2,lj3,lj4,

2
src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
View File

@ -170,7 +170,7 @@ void PairLJSFDipoleSFGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = dplsf_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,

2
src/GPU/pair_mie_cut_gpu.cpp
View File

@ -159,7 +159,7 @@ void PairMIECutGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = mie_gpu_init(atom->ntypes+1, cutsq, mie1, mie2, mie3, mie4,

2
src/GPU/pair_morse_gpu.cpp
View File

@ -155,7 +155,7 @@ void PairMorseGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = mor_gpu_init(atom->ntypes+1, cutsq, morse1, r0, alpha, d0,

2
src/GPU/pair_resquared_gpu.cpp
View File

@ -203,7 +203,7 @@ void PairRESquaredGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = re_gpu_init(atom->ntypes+1, shape1, well, cutsq, sigma,

2
src/GPU/pair_soft_gpu.cpp
View File

@ -160,7 +160,7 @@ void PairSoftGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = soft_gpu_init(atom->ntypes+1, cutsq, prefactor, cut,

2
src/GPU/pair_table_gpu.cpp
View File

@ -229,7 +229,7 @@ void PairTableGPU::init_style()
}
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = table_gpu_init(atom->ntypes+1, cutsq, table_coeffs, table_data,

2
src/GPU/pair_ufm_gpu.cpp
View File

@ -163,7 +163,7 @@ void PairUFMGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ufml_gpu_init(atom->ntypes+1, cutsq, uf1, uf2, uf3,

2
src/GPU/pair_yukawa_colloid_gpu.cpp
View File

@ -168,7 +168,7 @@ void PairYukawaColloidGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = ykcolloid_gpu_init(atom->ntypes+1, cutsq, a,

2
src/GPU/pair_yukawa_gpu.cpp
View File

@ -157,7 +157,7 @@ void PairYukawaGPU::init_style()
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = yukawa_gpu_init(atom->ntypes+1, cutsq, kappa, a,

2
src/GPU/pair_zbl_gpu.cpp
View File

@ -163,7 +163,7 @@ void PairZBLGPU::init_style()
cut_globalsq = cut_global * cut_global;
int maxspecial=0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
maxspecial=atom->maxspecial;
int mnf = 5e-2 * neighbor->oneatom;
int success = zbl_gpu_init(atom->ntypes+1, cutsq, sw1, sw2, sw3, sw4,

2
src/KOKKOS/min_kokkos.cpp
View File

@ -462,7 +462,7 @@ double MinKokkos::energy_force(int resetflag)
timer->stamp(Timer::PAIR);
}
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) {
atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
force->bond->compute(eflag,vflag);

42
src/KOKKOS/npair_kokkos.cpp
View File

@ -189,7 +189,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::build(NeighList *list_)
k_bins.sync<DeviceType>();
k_atom2bin.sync<DeviceType>();
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (exclude)
atomKK->sync(Device,X_MASK|RADIUS_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
else
@ -545,14 +545,14 @@ __device__ __forceinline__ int __syncthreads_count(int predicate) {
#ifdef LMP_KOKKOS_GPU
template<class DeviceType> template<int HalfNeigh,int Newton,int Tri>
__device__ inline
void NeighborKokkosExecute<DeviceType>::build_ItemCuda(typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const
{
#ifdef KOKKOS_ENABLE_HIP
HIP_DYNAMIC_SHARED(X_FLOAT, sharedmem);
#else
extern __shared__ X_FLOAT sharedmem[];
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
__device__
#endif
inline
void NeighborKokkosExecute<DeviceType>::build_ItemGPU(typename Kokkos::TeamPolicy<DeviceType>::member_type dev,
size_t sharedsize) const
{
auto* sharedmem = static_cast<X_FLOAT *>(dev.team_shmem().get_shmem(sharedsize));
/* loop over atoms in i's bin,
*/
const int atoms_per_bin = c_bins.extent(1);
@ -657,7 +657,7 @@ void NeighborKokkosExecute<DeviceType>::build_ItemCuda(typename Kokkos::TeamPoli
}
}
__syncthreads();
dev.team_barrier();
const typename ArrayTypes<DeviceType>::t_int_1d_const_um stencil
= d_stencil;
@ -678,7 +678,7 @@ void NeighborKokkosExecute<DeviceType>::build_ItemCuda(typename Kokkos::TeamPoli
other_id[MY_II] = j;
__syncthreads();
dev.team_barrier();
if (i >= 0 && i < nlocal) {
#pragma unroll 8
@ -735,7 +735,7 @@ void NeighborKokkosExecute<DeviceType>::build_ItemCuda(typename Kokkos::TeamPoli
}
}
__syncthreads();
dev.team_barrier();
}
if (i >= 0 && i < nlocal) {
@ -988,14 +988,14 @@ void NeighborKokkosExecute<DeviceType>::
#ifdef LMP_KOKKOS_GPU
template<class DeviceType> template<int HalfNeigh,int Newton,int Tri>
__device__ inline
void NeighborKokkosExecute<DeviceType>::build_ItemSizeCuda(typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const
{
#ifdef KOKKOS_ENABLE_HIP
HIP_DYNAMIC_SHARED(X_FLOAT, sharedmem);
#else
extern __shared__ X_FLOAT sharedmem[];
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
__device__
#endif
inline
void NeighborKokkosExecute<DeviceType>::build_ItemSizeGPU(typename Kokkos::TeamPolicy<DeviceType>::member_type dev,
size_t sharedsize) const
{
auto* sharedmem = static_cast<X_FLOAT *>(dev.team_shmem().get_shmem(sharedsize));
/* loop over atoms in i's bin,
*/
const int atoms_per_bin = c_bins.extent(1);
@ -1086,7 +1086,7 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeCuda(typename Kokkos::Team
}
}
}
__syncthreads();
dev.team_barrier();
const typename ArrayTypes<DeviceType>::t_int_1d_const_um stencil
= d_stencil;
@ -1108,7 +1108,7 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeCuda(typename Kokkos::Team
other_id[MY_II] = j;
__syncthreads();
dev.team_barrier();
if (i >= 0 && i < nlocal) {
#pragma unroll 8
@ -1147,7 +1147,7 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeCuda(typename Kokkos::Team
}
}
}
__syncthreads();
dev.team_barrier();
}
if (i >= 0 && i < nlocal) {

31
src/KOKKOS/npair_kokkos.h
View File

@ -312,12 +312,20 @@ class NeighborKokkosExecute
#ifdef LMP_KOKKOS_GPU
template<int HalfNeigh, int Newton, int Tri>
__device__ inline
void build_ItemCuda(typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const;
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
__device__
#endif
inline
void build_ItemGPU(typename Kokkos::TeamPolicy<DeviceType>::member_type dev,
size_t sharedsize) const;
template<int HalfNeigh, int Newton, int Tri>
__device__ inline
void build_ItemSizeCuda(typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const;
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
__device__
#endif
inline
void build_ItemSizeGPU(typename Kokkos::TeamPolicy<DeviceType>::member_type dev,
size_t sharedsize) const;
#endif
KOKKOS_INLINE_FUNCTION
@ -388,10 +396,12 @@ struct NPairKokkosBuildFunctor {
c.template build_Item<HALF_NEIGH,GHOST_NEWTON,TRI>(i);
}
#ifdef LMP_KOKKOS_GPU
__device__ inline
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
__device__
#endif
inline
void operator() (typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const {
c.template build_ItemCuda<HALF_NEIGH,GHOST_NEWTON,TRI>(dev);
c.template build_ItemGPU<HALF_NEIGH,GHOST_NEWTON,TRI>(dev, sharedsize);
}
size_t team_shmem_size(const int team_size) const { (void) team_size; return sharedsize; }
#endif
@ -446,9 +456,12 @@ struct NPairKokkosBuildFunctorSize {
}
#ifdef LMP_KOKKOS_GPU
__device__ inline
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
__device__
#endif
inline
void operator() (typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const {
c.template build_ItemSizeCuda<HALF_NEIGH,GHOST_NEWTON,TRI>(dev);
c.template build_ItemSizeGPU<HALF_NEIGH,GHOST_NEWTON,TRI>(dev, sharedsize);
}
size_t team_shmem_size(const int team_size) const { (void) team_size; return sharedsize; }
#endif

2
src/MC/fix_atom_swap.cpp
View File

@ -504,7 +504,7 @@ double FixAtomSwap::energy_full()
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);

2
src/MC/fix_bond_break.cpp
View File

@ -80,7 +80,7 @@ FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
// error check
if (atom->molecular != 1)
if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR,"Cannot use fix bond/break with non-molecular systems");
// initialize Marsaglia RNG with processor-unique seed

2
src/MC/fix_bond_create.cpp
View File

@ -148,7 +148,7 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
// error check
if (atom->molecular != 1)
if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR,"Cannot use fix bond/create with non-molecular systems");
if (iatomtype == jatomtype &&
((imaxbond != jmaxbond) || (inewtype != jnewtype)))

2
src/MC/fix_bond_swap.cpp
View File

@ -80,7 +80,7 @@ FixBondSwap::FixBondSwap(LAMMPS *lmp, int narg, char **arg) :
// error check
if (atom->molecular != 1)
if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR,"Cannot use fix bond/swap with non-molecular systems");
// create a new compute temp style

2
src/MC/fix_gcmc.cpp
View File

@ -2318,7 +2318,7 @@ double FixGCMC::energy_full()
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);

2
src/MC/fix_widom.cpp
View File

@ -1045,7 +1045,7 @@ double FixWidom::energy_full()
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);

6
src/MLIAP/mliap_model_nn.cpp
View File

@ -378,7 +378,7 @@ void MLIAPModelNN::compute_gradients(MLIAPData* data)
egradient is derivative of energy w.r.t. parameters
---------------------------------------------------------------------- */
void MLIAPModelNN::compute_gradgrads(class MLIAPData* data)
void MLIAPModelNN::compute_gradgrads(class MLIAPData * /*data*/)
{
error->all(FLERR,"compute_gradgrads not implemented");
}
@ -388,7 +388,7 @@ void MLIAPModelNN::compute_gradgrads(class MLIAPData* data)
egradient is derivative of energy w.r.t. parameters
---------------------------------------------------------------------- */
void MLIAPModelNN::compute_force_gradients(class MLIAPData* data)
void MLIAPModelNN::compute_force_gradients(class MLIAPData * /*data*/)
{
error->all(FLERR,"compute_force_gradients not implemented");
}
@ -397,7 +397,7 @@ void MLIAPModelNN::compute_force_gradients(class MLIAPData* data)
count the number of non-zero entries in gamma matrix
---------------------------------------------------------------------- */
int MLIAPModelNN::get_gamma_nnz(class MLIAPData* data)
int MLIAPModelNN::get_gamma_nnz(class MLIAPData * /*data*/)
{
// todo: get_gamma_nnz
return 0;

2
src/REPLICA/verlet_split.cpp
View File

@ -367,7 +367,7 @@ void VerletSplit::run(int n)
timer->stamp(Timer::PAIR);
}
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);

2
src/USER-INTEL/npair_full_bin_intel.cpp
View File

@ -74,7 +74,7 @@ fbi(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
_fix->nbor_pack_width());
int need_ic = 0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
neighbor->cutneighmax);

2
src/USER-INTEL/npair_half_bin_newton_intel.cpp
View File

@ -73,7 +73,7 @@ hbni(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
buffers->grow_list(list, atom->nlocal, comm->nthreads, 0, off_end);
int need_ic = 0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
neighbor->cutneighmax);

2
src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
View File

@ -73,7 +73,7 @@ hbnti(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
buffers->grow_list(list, atom->nlocal, comm->nthreads, 0, off_end);
int need_ic = 0;
if (atom->molecular)
if (atom->molecular != Atom::ATOMIC)
dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
neighbor->cutneighmax);

2
src/USER-INTEL/verlet_lrt_intel.cpp
View File

@ -316,7 +316,7 @@ void VerletLRTIntel::run(int n)
timer->stamp(Timer::PAIR);
}
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);

38
src/USER-MEAMC/meam.h
View File

@ -17,7 +17,7 @@
#include "math_const.h" // IWYU pragma: export
#include <cmath>
#include <cstring>
#include <string>
#define maxelt 5
@ -242,29 +242,29 @@ public:
// only use single-element lattices if single=true
// return false on failure
// return true and set lat on success
static bool str_to_lat(const char* str, bool single, lattice_t& lat)
static bool str_to_lat(const std::string & str, bool single, lattice_t& lat)
{
if (strcmp(str,"fcc") == 0) lat = FCC;
else if (strcmp(str,"bcc") == 0) lat = BCC;
else if (strcmp(str,"hcp") == 0) lat = HCP;
else if (strcmp(str,"dim") == 0) lat = DIM;
else if (strcmp(str,"dia") == 0) lat = DIA;
else if (strcmp(str,"dia3") == 0) lat = DIA3;
else if (strcmp(str,"lin") == 0) lat = LIN;
else if (strcmp(str,"zig") == 0) lat = ZIG;
else if (strcmp(str,"tri") == 0) lat = TRI;
if (str == "fcc") lat = FCC;
else if (str == "bcc") lat = BCC;
else if (str == "hcp") lat = HCP;
else if (str == "dim") lat = DIM;
else if (str == "dia") lat = DIA;
else if (str == "dia3") lat = DIA3;
else if (str == "lin") lat = LIN;
else if (str == "zig") lat = ZIG;
else if (str == "tri") lat = TRI;
else {
if (single)
return false;
if (strcmp(str,"b1") == 0) lat = B1;
else if (strcmp(str,"c11") == 0) lat = C11;
else if (strcmp(str,"l12") == 0) lat = L12;
else if (strcmp(str,"b2") == 0) lat = B2;
else if (strcmp(str,"ch4") == 0) lat = CH4;
else if (strcmp(str,"lin") == 0) lat =LIN;
else if (strcmp(str,"zig") == 0) lat = ZIG;
else if (strcmp(str,"tri") == 0) lat = TRI;
if (str == "b1") lat = B1;
else if (str == "c11") lat = C11;
else if (str == "l12") lat = L12;
else if (str == "b2") lat = B2;
else if (str == "ch4") lat = CH4;
else if (str == "lin") lat =LIN;
else if (str == "zig") lat = ZIG;
else if (str == "tri") lat = TRI;
else return false;
}
return true;

373
src/USER-MEAMC/pair_meamc.cpp
View File

@ -17,7 +17,7 @@
#include "pair_meamc.h"
#include <cstring>
#include <memory>
#include "meam.h"
#include "atom.h"
@ -28,6 +28,8 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
using namespace LAMMPS_NS;
@ -54,8 +56,6 @@ PairMEAMC::PairMEAMC(LAMMPS *lmp) : Pair(lmp)
allocated = 0;
nelements = 0;
elements = nullptr;
mass = nullptr;
meam_inst = new MEAM(memory);
scale = nullptr;
@ -74,10 +74,6 @@ PairMEAMC::~PairMEAMC()
{
delete meam_inst;
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete [] mass;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
@ -192,7 +188,7 @@ void PairMEAMC::allocate()
global settings
------------------------------------------------------------------------- */
void PairMEAMC::settings(int narg, char **/*arg*/)
void PairMEAMC::settings(int narg, char ** /*arg*/)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
@ -247,9 +243,8 @@ void PairMEAMC::coeff(int narg, char **arg)
// elements = list of unique element names
if (nelements) {
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
delete [] mass;
elements.clear();
mass.clear();
}
nelements = paridx - 3;
@ -258,13 +253,10 @@ void PairMEAMC::coeff(int narg, char **arg)
error->all(FLERR,fmt::format("Too many elements extracted from MEAM "
"library (current limit: {}). Increase "
"'maxelt' in meam.h and recompile.", maxelt));
elements = new char*[nelements];
mass = new double[nelements];
for (int i = 0; i < nelements; i++) {
n = strlen(arg[i+3]) + 1;
elements[i] = new char[n];
strcpy(elements[i],arg[i+3]);
elements.push_back(arg[i+3]);
mass.push_back(0.0);
}
// read MEAM library and parameter files
@ -281,7 +273,7 @@ void PairMEAMC::coeff(int narg, char **arg)
m = i - (4+nelements) + 1;
int j;
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
if (elements[j] == arg[i]) break;
if (j < nelements) map[m] = j;
else if (strcmp(arg[i],"NULL") == 0) map[m] = -1;
else error->all(FLERR,"Incorrect args for pair coefficients");
@ -358,272 +350,214 @@ double PairMEAMC::init_one(int i, int j)
void PairMEAMC::read_files(const std::string &globalfile,
const std::string &userfile)
{
read_global_meamc_file(globalfile);
read_user_meamc_file(userfile);
}
/* ---------------------------------------------------------------------- */
void PairMEAMC::read_global_meamc_file(const std::string &globalfile)
{
// allocate parameter arrays
std::vector<lattice_t> lat(nelements);
std::vector<int> ielement(nelements);
std::vector<int> ibar(nelements);
std::vector<double> z(nelements);
std::vector<double> atwt(nelements);
std::vector<double> alpha(nelements);
std::vector<double> b0(nelements);
std::vector<double> b1(nelements);
std::vector<double> b2(nelements);
std::vector<double> b3(nelements);
std::vector<double> alat(nelements);
std::vector<double> esub(nelements);
std::vector<double> asub(nelements);
std::vector<double> t0(nelements);
std::vector<double> t1(nelements);
std::vector<double> t2(nelements);
std::vector<double> t3(nelements);
std::vector<double> rozero(nelements);
std::vector<bool> found(nelements, false);
// open global meamf file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = utils::open_potential(globalfile,lmp,nullptr);
if (fp == nullptr)
error->one(FLERR,fmt::format("Cannot open MEAM potential file {}",
globalfile));
}
PotentialFileReader reader(lmp, globalfile, "MEAM", " library");
char * line;
// allocate parameter arrays
int params_per_line = 19;
lattice_t *lat = new lattice_t[nelements];
int *ielement = new int[nelements];
int *ibar = new int[nelements];
double *z = new double[nelements];
double *atwt = new double[nelements];
double *alpha = new double[nelements];
double *b0 = new double[nelements];
double *b1 = new double[nelements];
double *b2 = new double[nelements];
double *b3 = new double[nelements];
double *alat = new double[nelements];
double *esub = new double[nelements];
double *asub = new double[nelements];
double *t0 = new double[nelements];
double *t1 = new double[nelements];
double *t2 = new double[nelements];
double *t3 = new double[nelements];
double *rozero = new double[nelements];
bool *found = new bool[nelements];
for (int i = 0; i < nelements; i++) found[i] = false;
// read each set of params from global MEAM file
// one set of params can span multiple lines
// store params if element name is in element list
// if element name appears multiple times, only store 1st entry
if (comm->me == 0) {
const int params_per_line = 19;
int nset = 0;
char **words = new char*[params_per_line+1];
char line[MAXLINE];
while (1) {
char *ptr;
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
fclose(fp);
break;
while ((line = reader.next_line(params_per_line))) {
try {
ValueTokenizer values(line, "' \t\n\r\f");
// read each set of params from global MEAM file
// one set of params can span multiple lines
// store params if element name is in element list
// if element name appears multiple times, only store 1st entry
std::string element = values.next_string();
// skip if element name isn't in element list
int index;
for (index = 0; index < nelements; index++)
if (elements[index] == element) break;
if (index == nelements) continue;
// skip if element already appeared (technically error in library file, but always ignored)
if (found[index]) continue;
found[index] = true;
// map lat string to an integer
std::string lattice_type = values.next_string();
if (!MEAM::str_to_lat(lattice_type.c_str(), true, lat[index]))
error->one(FLERR,fmt::format("Unrecognized lattice type in MEAM "
"library file: {}", lattice_type));
// store parameters
z[index] = values.next_double();
ielement[index] = values.next_int();
atwt[index] = values.next_double();
alpha[index] = values.next_double();
b0[index] = values.next_double();
b1[index] = values.next_double();
b2[index] = values.next_double();
b3[index] = values.next_double();
alat[index] = values.next_double();
esub[index] = values.next_double();
asub[index] = values.next_double();
t0[index] = values.next_double();
t1[index] = values.next_double();
t2[index] = values.next_double();
t3[index] = values.next_double();
rozero[index] = values.next_double();
ibar[index] = values.next_int();
if (!isone(t0[index]))
error->one(FLERR,"Unsupported parameter in MEAM library file: t0!=1");
// z given is ignored: if this is mismatched, we definitely won't do what the user said -> fatal error
if (z[index] != MEAM::get_Zij(lat[index]))
error->one(FLERR,"Mismatched parameter in MEAM library file: z!=lat");
nset++;
} catch (TokenizerException &e) {
error->one(FLERR, e.what());
}
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
int nwords = utils::count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
while (nwords < params_per_line) {
int n = strlen(line);
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == nullptr) {
fclose(fp);
break;
}
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = utils::count_words(line);
}
if (nwords != params_per_line)
error->one(FLERR,"Incorrect format in MEAM library file");
// words = ptrs to all words in line
// strip single and double quotes from words
nwords = 0;
words[nwords++] = strtok(line,"' \t\n\r\f");
while ((words[nwords++] = strtok(nullptr,"' \t\n\r\f"))) continue;
// skip if element name isn't in element list
int index;
for (index = 0; index < nelements; index++)
if (strcmp(words[0],elements[index]) == 0) break;
if (index == nelements) continue;
// skip if element already appeared (technically error in library file, but always ignored)
if (found[index] == true) continue;
found[index] = true;
// map lat string to an integer
if (!MEAM::str_to_lat(words[1], true, lat[index]))
error->one(FLERR,fmt::format("Unrecognized lattice type in MEAM "
"library file: {}", words[1]));
// store parameters
z[index] = atof(words[2]);
ielement[index] = atoi(words[3]);
atwt[index] = atof(words[4]);
alpha[index] = atof(words[5]);
b0[index] = atof(words[6]);
b1[index] = atof(words[7]);
b2[index] = atof(words[8]);
b3[index] = atof(words[9]);
alat[index] = atof(words[10]);
esub[index] = atof(words[11]);
asub[index] = atof(words[12]);
t0[index] = atof(words[13]);
t1[index] = atof(words[14]);
t2[index] = atof(words[15]);
t3[index] = atof(words[16]);
rozero[index] = atof(words[17]);
ibar[index] = atoi(words[18]);
if (!isone(t0[index]))
error->one(FLERR,"Unsupported parameter in MEAM library file: t0!=1");
// z given is ignored: if this is mismatched, we definitely won't do what the user said -> fatal error
if (z[index] != MEAM::get_Zij(lat[index]))
error->one(FLERR,"Mismatched parameter in MEAM library file: z!=lat");
nset++;
}
// error if didn't find all elements in file
if (nset != nelements) {
char str[128] = "Did not find all elements in MEAM library file, missing:";
std::string msg = "Did not find all elements in MEAM library file, missing:";
for (int i = 0; i < nelements; i++)
if (!found[i]) {
strcat(str," ");
strcat(str,elements[i]);
msg += " ";
msg += elements[i];
}
error->one(FLERR,str);
error->one(FLERR,msg);
}
delete [] words;
}
// distribute complete parameter sets
MPI_Bcast(lat, nelements, MPI_INT, 0, world);
MPI_Bcast(ielement, nelements, MPI_INT, 0, world);
MPI_Bcast(ibar, nelements, MPI_INT, 0, world);
MPI_Bcast(z, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(atwt, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(alpha, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(b0, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(b1, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(b2, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(b3, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(alat, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(esub, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(asub, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(t0, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(t1, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(t2, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(t3, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(rozero, nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(lat.data(), nelements, MPI_INT, 0, world);
MPI_Bcast(ielement.data(), nelements, MPI_INT, 0, world);
MPI_Bcast(ibar.data(), nelements, MPI_INT, 0, world);
MPI_Bcast(z.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(atwt.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(alpha.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(b0.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(b1.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(b2.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(b3.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(alat.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(esub.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(asub.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(t0.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(t1.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(t2.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(t3.data(), nelements, MPI_DOUBLE, 0, world);
MPI_Bcast(rozero.data(), nelements, MPI_DOUBLE, 0, world);
// pass element parameters to MEAM package
meam_inst->meam_setup_global(nelements,lat,ielement,atwt,alpha,b0,b1,b2,b3,
alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
meam_inst->meam_setup_global(nelements, lat.data(), ielement.data(), atwt.data(),
alpha.data(), b0.data(), b1.data(), b2.data(), b3.data(),
alat.data(), esub.data(), asub.data(), t0.data(), t1.data(),
t2.data(), t3.data(), rozero.data(), ibar.data());
// set element masses
for (int i = 0; i < nelements; i++) mass[i] = atwt[i];
}
// clean-up memory
delete [] lat;
delete [] ielement;
delete [] ibar;
delete [] z;
delete [] atwt;
delete [] alpha;
delete [] b0;
delete [] b1;
delete [] b2;
delete [] b3;
delete [] alat;
delete [] esub;
delete [] asub;
delete [] t0;
delete [] t1;
delete [] t2;
delete [] t3;
delete [] rozero;
delete [] found;
/* ---------------------------------------------------------------------- */
void PairMEAMC::read_user_meamc_file(const std::string &userfile)
{
// done if user param file is "NULL"
if (userfile == "NULL") return;
// open user param file on proc 0
std::shared_ptr<PotentialFileReader> reader;
if (comm->me == 0) {
fp = utils::open_potential(userfile,lmp,nullptr);
if (fp == nullptr)
error->one(FLERR,fmt::format("Cannot open MEAM potential file {}",
userfile));
reader = std::make_shared<PotentialFileReader>(lmp, userfile, "MEAM");
}
// read settings
// pass them one at a time to MEAM package
// match strings to list of corresponding ints
char * line = nullptr;
char buffer[MAXLINE];
int maxparams = 6;
char **params = new char*[maxparams];
while (1) {
int which;
int nindex, index[3];
double value;
char line[MAXLINE];
int nline;
char *ptr;
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
fclose(fp);
line = reader->next_line();
if (line == nullptr) {
nline = -1;
} else nline = strlen(line) + 1;
} else {
line = buffer;
}
MPI_Bcast(&nline,1,MPI_INT,0,world);
if (nline<0) break;
MPI_Bcast(line,nline,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
if (utils::count_words(line) == 0) continue;
// params = ptrs to all fields in line
int nparams = 0;
params[nparams++] = strtok(line,"=(), '\t\n\r\f");
while (nparams < maxparams &&
(params[nparams++] = strtok(nullptr,"=(), '\t\n\r\f")))
continue;
nparams--;
ValueTokenizer values(line, "=(), '\t\n\r\f");
int nparams = values.count();
std::string keyword = values.next_string();
for (which = 0; which < nkeywords; which++)
if (strcmp(params[0],keywords[which]) == 0) break;
if (keyword == keywords[which]) break;
if (which == nkeywords)
error->all(FLERR,fmt::format("Keyword {} in MEAM parameter file not "
"recognized", params[0]));
"recognized", keyword));
nindex = nparams - 2;
for (int i = 0; i < nindex; i++) index[i] = atoi(params[i+1]) - 1;
for (int i = 0; i < nindex; i++) index[i] = values.next_int() - 1;
// map lattce_meam value to an integer
if (which == 4) {
std::string lattice_type = values.next_string();
lattice_t latt;
if (!MEAM::str_to_lat(params[nparams-1], false, latt))
if (!MEAM::str_to_lat(lattice_type, false, latt))
error->all(FLERR, fmt::format("Unrecognized lattice type in MEAM "
"parameter file: {}", params[nparams-1]));
"parameter file: {}", lattice_type));
value = latt;
}
else value = atof(params[nparams-1]);
else value = values.next_double();
// pass single setting to MEAM package
@ -634,13 +568,10 @@ void PairMEAMC::read_files(const std::string &globalfile,
"is out of range (please report a bug)",
"expected more indices",
"has out of range element index"};
char str[256];
if ((errorflag < 0) || (errorflag > 3)) errorflag = 0;
snprintf(str,256,"Error in MEAM parameter file: keyword %s %s",params[0],descr[errorflag]);
error->all(FLERR,str);
error->all(FLERR, fmt::format("Error in MEAM parameter file: keyword {} {}", keyword, descr[errorflag]));
}
}
delete [] params;
}
/* ---------------------------------------------------------------------- */

9
src/USER-MEAMC/pair_meamc.h
View File

@ -22,7 +22,8 @@ PairStyle(meam,PairMEAMC)
#define LMP_PAIR_MEAMC_H
#include "pair.h"
#include <vector>
#include <string>
namespace LAMMPS_NS {
@ -48,14 +49,16 @@ class PairMEAMC : public Pair {
class MEAM *meam_inst;
double cutmax; // max cutoff for all elements
int nelements; // # of unique elements
char **elements; // names of unique elements
double *mass; // mass of each element
std::vector<std::string> elements; // names of unique elements
std::vector<double> mass; // mass of each element
int *map; // mapping from atom types (1-indexed) to elements (1-indexed)
double **scale; // scaling factor for adapt
void allocate();
void read_files(const std::string &, const std::string &);
void read_global_meamc_file(const std::string &);
void read_user_meamc_file(const std::string &);
void neigh_strip(int, int *, int *, int **);
};

14
src/USER-OMP/thr_data.cpp
View File

@ -139,20 +139,6 @@ void ThrData::init_adp(int nall, double *rho, double **mu, double **lambda)
/* ---------------------------------------------------------------------- */
void ThrData::init_cdeam(int nall, double *rho, double *rhoB, double *D_values)
{
init_eam(nall, rho);
if (nall >= 0 && rhoB && D_values) {
_rhoB = rhoB + _tid*nall;
_D_values = D_values + _tid*nall;
memset(_rhoB, 0, nall*sizeof(double));
memset(_D_values, 0, nall*sizeof(double));
}
}
/* ---------------------------------------------------------------------- */
void ThrData::init_eim(int nall, double *rho, double *fp)
{
init_eam(nall, rho);

1
src/USER-OMP/thr_data.h
View File

@ -52,7 +52,6 @@ class ThrData {
// setup and erase per atom arrays
void init_adp(int, double *, double **, double **); // ADP (+ EAM)
void init_cdeam(int, double *, double *, double *); // CDEAM (+ EAM)
void init_eam(int, double *); // EAM
void init_eim(int, double *, double *); // EIM (+ EAM)

6
src/arg_info.h
View File

@ -67,14 +67,14 @@ namespace LAMMPS_NS {
/*! get dimension of reference
*
* This will return either 0, 1, 2 depending on whether the
* reference has no, one or two "[<number>]" postfixes.
* reference has no, one or two "[{number}]" postfixes.
*
* \return integer with the dimensionality of the reference */
int get_dim() const { return dim; }
/*! get index of first dimension
*
* This will return the <number> in the first "[<number>]"
* This will return the number in the first "[{number}]"
* postfix or 0 if there is no postfix.
*
* \return integer with index or the postfix or 0 */
@ -82,7 +82,7 @@ namespace LAMMPS_NS {
/*! get index of second dimension
*
* This will return the <number> in the second "[<number>]"
* This will return the number in the second "[{number}]"
* postfix or -1 if there is no second postfix.
*
* \return integer with index of the postfix or -1 */

100
src/atom.cpp
View File

@ -341,11 +341,8 @@ void Atom::settings(Atom *old)
map_style = old->map_style;
sortfreq = old->sortfreq;
userbinsize = old->userbinsize;
if (old->firstgroupname) {
int n = strlen(old->firstgroupname) + 1;
firstgroupname = new char[n];
strcpy(firstgroupname,old->firstgroupname);
}
if (old->firstgroupname)
firstgroupname = utils::strdup(old->firstgroupname);
}
/* ----------------------------------------------------------------------
@ -532,9 +529,7 @@ void Atom::add_peratom(const char *name, void *address,
memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
}
int n = strlen(name) + 1;
peratom[nperatom].name = new char[n];
strcpy(peratom[nperatom].name,name);
peratom[nperatom].name = utils::strdup(name);
peratom[nperatom].address = address;
peratom[nperatom].datatype = datatype;
peratom[nperatom].cols = cols;
@ -582,9 +577,7 @@ void Atom::add_peratom_vary(const char *name, void *address,
memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
}
int n = strlen(name) + 1;
peratom[nperatom].name = new char[n];
strcpy(peratom[nperatom].name,name);
peratom[nperatom].name = utils::strdup(name);
peratom[nperatom].address = address;
peratom[nperatom].datatype = datatype;
peratom[nperatom].cols = -1;
@ -670,7 +663,7 @@ void Atom::create_avec(const std::string &style, int narg, char **arg, int trysu
// map style will be reset to array vs hash to by map_init()
molecular = avec->molecular;
if (molecular && tag_enable == 0)
if ((molecular != Atom::ATOMIC) && (tag_enable == 0))
error->all(FLERR,"Atom IDs must be used for molecular systems");
if (molecular != Atom::ATOMIC) map_style = MAP_YES;
}
@ -815,9 +808,7 @@ void Atom::modify_params(int narg, char **arg)
delete [] firstgroupname;
firstgroupname = nullptr;
} else {
int n = strlen(arg[iarg+1]) + 1;
firstgroupname = new char[n];
strcpy(firstgroupname,arg[iarg+1]);
firstgroupname = utils::strdup(arg[iarg+1]);
sortfreq = 0;
}
iarg += 2;
@ -1114,13 +1105,13 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
if (values[0] == nullptr)
error->all(FLERR,"Incorrect atom format in data file");
for (m = 1; m < nwords; m++) {
values[m] = strtok(nullptr," \t\n\r\f");
if (values[m] == nullptr)
for (m = 0; m < nwords; m++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
if (strlen(buf) == 0)
error->all(FLERR,"Incorrect atom format in data file");
values[m] = buf;
buf += strlen(buf)+1;
}
int imx = 0, imy = 0, imz = 0;
@ -1217,9 +1208,12 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(nullptr," \t\n\r\f");
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
@ -1569,9 +1563,12 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(nullptr," \t\n\r\f");
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
@ -1611,8 +1608,10 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
// else skip values
for (int i = 0; i < n; i++) {
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f")) + id_offset;
else tagdata = ATOTAGINT(strtok(nullptr," \t\n\r\f")) + id_offset;
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
tagdata = utils::tnumeric(FLERR,buf,false,lmp) + id_offset;
buf += strlen(buf)+1;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
@ -1622,8 +1621,15 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
else
error->one(FLERR,"Duplicate atom ID in Bodies section of data file");
ninteger = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
ndouble = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ninteger = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ndouble = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
if ((m = map(tagdata)) >= 0) {
if (ninteger > maxint) {
@ -1637,17 +1643,29 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
dvalues = new double[maxdouble];
}
for (j = 0; j < ninteger; j++)
ivalues[j] = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
for (j = 0; j < ndouble; j++)
dvalues[j] = utils::numeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
for (j = 0; j < ninteger; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ivalues[j] = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
for (j = 0; j < ndouble; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
dvalues[j] = utils::numeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++)
strtok(nullptr," \t\n\r\f");
for (j = 0; j < nvalues; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
buf += strlen(buf)+1;
}
}
}
@ -2400,9 +2418,7 @@ int Atom::add_custom(const char *name, int flag)
nivector++;
iname = (char **) memory->srealloc(iname,nivector*sizeof(char *),
"atom:iname");
int n = strlen(name) + 1;
iname[index] = new char[n];
strcpy(iname[index],name);
iname[index] = utils::strdup(name);
ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
"atom:ivector");
memory->create(ivector[index],nmax,"atom:ivector");
@ -2411,9 +2427,7 @@ int Atom::add_custom(const char *name, int flag)
ndvector++;
dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *),
"atom:dname");
int n = strlen(name) + 1;
dname[index] = new char[n];
strcpy(dname[index],name);
dname[index] = utils::strdup(name);
dvector = (double **) memory->srealloc(dvector,ndvector*sizeof(double *),
"atom:dvector");
memory->create(dvector[index],nmax,"atom:dvector");

7
src/atom_vec.cpp
View File

@ -154,11 +154,8 @@ void AtomVec::store_args(int narg, char **arg)
nargcopy = narg;
if (nargcopy) argcopy = new char*[nargcopy];
else argcopy = nullptr;
for (int i = 0; i < nargcopy; i++) {
int n = strlen(arg[i]) + 1;
argcopy[i] = new char[n];
strcpy(argcopy[i],arg[i]);
}
for (int i = 0; i < nargcopy; i++)
argcopy[i] = utils::strdup(arg[i]);
}
/* ----------------------------------------------------------------------

10
src/atom_vec_hybrid.cpp
View File

@ -109,8 +109,7 @@ void AtomVecHybrid::process_args(int narg, char **arg)
if (strcmp(arg[iarg],keywords[i]) == 0)
error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
styles[nstyles] = atom->new_avec(arg[iarg],1,dummy);
keywords[nstyles] = new char[strlen(arg[iarg])+1];
strcpy(keywords[nstyles],arg[iarg]);
keywords[nstyles] = utils::strdup(arg[iarg]);
jarg = iarg + 1;
while (jarg < narg && !known_style(arg[jarg])) jarg++;
styles[nstyles]->process_args(jarg-iarg-1,&arg[iarg+1]);
@ -601,13 +600,10 @@ void AtomVecHybrid::build_styles()
allstyles = new char*[nallstyles];
int n;
nallstyles = 0;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
n = strlen(#key) + 1; \
allstyles[nallstyles] = new char[n]; \
strcpy(allstyles[nallstyles],#key); \
#define AtomStyle(key,Class) \
allstyles[nallstyles] = utils::strdup(#key); \
nallstyles++;
#include "style_atom.h" // IWYU pragma: keep
#undef AtomStyle

4
src/body.cpp
View File

@ -20,9 +20,7 @@ using namespace LAMMPS_NS;
Body::Body(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
{
int n = strlen(arg[0]) + 1;
style = new char[n];
strcpy(style,arg[0]);
style = utils::strdup(arg[0]);
icp = nullptr;
dcp = nullptr;
}

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