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Merge pull request #2654 from akohlmey/collected-small-changes

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Collected small changes
This commit is contained in:
Axel Kohlmeyer
2021-03-16 19:34:54 -04:00
committed by GitHub
parent 1b5a7e2e1e 3b9d5916c9
commit 42895ac6df
113 changed files with 361 additions and 203 deletions
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2
cmake/Modules/Packages/GPU.cmake
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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

3
lib/gpu/Makefile.cuda
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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>

2
src/GPU/pair_beck_gpu.cpp
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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
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@ -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);

2
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

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);

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 */

2
src/atom.cpp
View File

@ -663,7 +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;
}

2
src/compute_fragment_atom.cpp
View File

@ -82,7 +82,7 @@ void ComputeFragmentAtom::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use compute fragment/atom unless atoms have IDs");
if (!atom->molecular)
if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR,"Compute fragment/atom requires a molecular system");
int count = 0;

2
src/compute_pe.cpp
View File

@ -83,7 +83,7 @@ double ComputePE::compute_scalar()
if (pairflag && force->pair)
one += force->pair->eng_vdwl + force->pair->eng_coul;
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (bondflag && force->bond) one += force->bond->energy;
if (angleflag && force->angle) one += force->angle->energy;
if (dihedralflag && force->dihedral) one += force->dihedral->energy;

2
src/create_bonds.cpp
View File

@ -48,7 +48,7 @@ void CreateBonds::command(int narg, char **arg)
error->all(FLERR,"Create_bonds command before simulation box is defined");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use create_bonds unless atoms have IDs");
if (atom->molecular != 1)
if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR,"Cannot use create_bonds with non-molecular system");
if (narg < 4) error->all(FLERR,"Illegal create_bonds command");

2
src/create_box.cpp
View File

@ -83,7 +83,7 @@ void CreateBox::command(int narg, char **arg)
// if molecular, zero out topology info
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
atom->bond_per_atom = 0;
atom->angle_per_atom = 0;
atom->dihedral_per_atom = 0;

2
src/delete_bonds.cpp
View File

@ -40,7 +40,7 @@ void DeleteBonds::command(int narg, char **arg)
error->all(FLERR,"Delete_bonds command before simulation box is defined");
if (atom->natoms == 0)
error->all(FLERR,"Delete_bonds command with no atoms existing");
if (atom->molecular != 1)
if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR,"Cannot use delete_bonds with non-molecular system");
if (narg < 2) error->all(FLERR,"Illegal delete_bonds command");

12
src/deprecated.cpp
View File

@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void Deprecated::command(int /* narg */, char ** /* arg */)
void Deprecated::command(int narg, char **arg)
{
const std::string cmd = input->command;
@ -38,7 +38,15 @@ void Deprecated::command(int /* narg */, char ** /* arg */)
utils::logmesg(lmp,"\n'reset_ids' has been renamed to 'reset_atom_ids'\n\n");
} else if (utils::strmatch(cmd,"^kim_")) {
if (lmp->comm->me == 0)
utils::logmesg(lmp,"\n'kim_<command>' has been renamed to 'kim <command>'\n\n");
utils::logmesg(lmp,"\nWARNING: 'kim_<command>' has been renamed to "
"'kim <command>'. Please update your input.\n\n");
std::string newcmd("kim");
newcmd += " " + cmd.substr(4);
for (int i=0; i < narg; ++i) {
newcmd.append(1,' ');
newcmd.append(arg[i]);
}
input->one(newcmd);
}
error->all(FLERR,"This command is no longer available");
}

2
src/fix_numdiff.cpp
View File

@ -292,7 +292,7 @@ double FixNumDiff::update_energy()
if (pair_compute_flag) force->pair->compute(eflag,0);
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (force->bond) force->bond->compute(eflag,0);
if (force->angle) force->angle->compute(eflag,0);
if (force->dihedral) force->dihedral->compute(eflag,0);

4
src/fmt/os.h
View File

@ -375,11 +375,7 @@ struct ostream_params {
};
} // namespace detail
#if defined(__PGI)
static detail::buffer_size buffer_size;
#else
static constexpr detail::buffer_size buffer_size;
#endif
// A fast output stream which is not thread-safe.
class ostream final : private detail::buffer<char> {

11
src/info.cpp
View File

@ -432,7 +432,7 @@ void Info::command(int narg, char **arg)
fmt::print(out,"Units = {}\n", update->unit_style);
fmt::print(out,"Atom style = {}\n", atom->atom_style);
fmt::print(out,"Atom map = {}\n", mapstyles[atom->map_style]);
if (atom->molecular > 0) {
if (atom->molecular != Atom::ATOMIC) {
const char *msg;
msg = (atom->molecular == Atom::TEMPLATE) ? "template" : "standard";
fmt::print(out,"Molecule type = {}\n",msg);
@ -447,7 +447,7 @@ void Info::command(int narg, char **arg)
fmt::print(out," {}", hybrid->keywords[i]);
fputc('\n',out);
}
if (atom->molecular > 0) {
if (atom->molecular != Atom::ATOMIC) {
const char *msg;
msg = force->bond_style ? force->bond_style : "none";
fmt::print(out,"Bonds = {:12}, types = {:8}, style = {}\n",
@ -1316,13 +1316,16 @@ std::string Info::get_os_info()
std::string Info::get_compiler_info()
{
std::string buf;
#if __clang__
#if __INTEL_LLVM_COMPILER
double version = static_cast<double>(__INTEL_LLVM_COMPILER)*0.01;
buf = fmt::format("Intel LLVM C++ {:.1f} / {}", version, __VERSION__);
#elif __clang__
buf = fmt::format("Clang C++ {}", __VERSION__);
#elif __PGI
buf = fmt::format("PGI C++ {}.{}",__PGIC__,__PGIC_MINOR__);
#elif __INTEL_COMPILER
double version = static_cast<double>(__INTEL_COMPILER)*0.01;
buf = fmt::format("Intel C++ {:.2f}.{} / {}", version,
buf = fmt::format("Intel Classic C++ {:.2f}.{} / {}", version,
__INTEL_COMPILER_UPDATE, __VERSION__);
#elif __GNUC__
buf = fmt::format("GNU C++ {}", __VERSION__);

17
src/library.cpp
View File

@ -483,11 +483,15 @@ void lammps_commands_string(void *handle, const char *str)
{
LAMMPS *lmp = (LAMMPS *) handle;
// make copy of str so can strtok() it
// copy str and convert from CR-LF (DOS-style) to LF (Unix style) line
int n = strlen(str);
char *ptr, *copy = new char[n+1];
int n = strlen(str) + 1;
char *copy = new char[n];
strcpy(copy,str);
for (ptr = copy; *str != '\0'; ++str) {
if ((str[0] == '\r') && (str[1] == '\n')) continue;
*ptr++ = *str;
}
*ptr = '\0';
BEGIN_CAPTURE
{
@ -495,8 +499,9 @@ void lammps_commands_string(void *handle, const char *str)
lmp->error->all(FLERR,"Library error: issuing LAMMPS command during run");
}
char *ptr = copy;
for (int i=0; i < n-1; ++i) {
n = strlen(copy);
ptr = copy;
for (int i=0; i < n; ++i) {
// handle continuation character as last character in line or string
if ((copy[i] == '&') && (copy[i+1] == '\n'))

4
src/lmptype.h
View File

@ -242,7 +242,7 @@ The typecasts prevent compiler warnings about possible truncation issues.
// define stack variable alignment
#if defined(__INTEL_COMPILER)
#if defined(__INTEL_LLVM_COMPILER) || defined(__INTEL_COMPILER)
#define _alignvar(expr,val) __declspec(align(val)) expr
#elif defined(__GNUC__)
#define _alignvar(expr,val) expr __attribute((aligned(val)))
@ -252,7 +252,7 @@ The typecasts prevent compiler warnings about possible truncation issues.
// declaration to lift aliasing restrictions
#if defined(__INTEL_COMPILER)
#if defined(__INTEL_LLVM_COMPILER) || defined(__INTEL_COMPILER)
#define _noalias restrict
#elif defined(__GNUC__)
#define _noalias __restrict

6
src/min.cpp
View File

@ -304,7 +304,7 @@ void Min::setup(int flag)
if (pair_compute_flag) force->pair->compute(eflag,vflag);
else if (force->pair) force->pair->compute_dummy(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);
@ -386,7 +386,7 @@ void Min::setup_minimal(int flag)
if (pair_compute_flag) force->pair->compute(eflag,vflag);
else if (force->pair) force->pair->compute_dummy(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);
@ -558,7 +558,7 @@ double Min::energy_force(int resetflag)
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);

4
src/omp_compat.h
View File

@ -29,7 +29,9 @@
// autodetect OpenMP compatibility if not explicitly set
#ifndef LAMMPS_OMP_COMPAT
# if defined(__INTEL_COMPILER)
# if defined(__INTEL_LLVM_COMPILER)
# define LAMMPS_OMP_COMPAT 4
# elif defined(__INTEL_COMPILER)
# if __INTEL_COMPILER > 18
# define LAMMPS_OMP_COMPAT 4
# endif

2
src/pair.cpp
View File

@ -221,7 +221,7 @@ void Pair::init()
// for manybody potentials
// check if bonded exclusions could invalidate the neighbor list
if (manybody_flag && atom->molecular) {
if (manybody_flag && (atom->molecular != Atom::ATOMIC)) {
int flag = 0;
if (atom->nbonds > 0 && force->special_lj[1] == 0.0 &&
force->special_coul[1] == 0.0) flag = 1;

10
src/read_data.cpp
View File

@ -221,7 +221,7 @@ void ReadData::command(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"extra/bond/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (! atom->molecular)
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR,"No bonds allowed with this atom style");
atom->extra_bond_per_atom = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (atom->extra_bond_per_atom < 0)
@ -229,7 +229,7 @@ void ReadData::command(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"extra/angle/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (! atom->molecular)
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR,"No angles allowed with this atom style");
atom->extra_angle_per_atom = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (atom->extra_angle_per_atom < 0)
@ -237,7 +237,7 @@ void ReadData::command(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"extra/dihedral/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (! atom->molecular)
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR,"No dihedrals allowed with this atom style");
atom->extra_dihedral_per_atom = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (atom->extra_dihedral_per_atom < 0)
@ -245,7 +245,7 @@ void ReadData::command(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"extra/improper/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (! atom->molecular)
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR,"No impropers allowed with this atom style");
atom->extra_improper_per_atom = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (atom->extra_improper_per_atom < 0)
@ -253,7 +253,7 @@ void ReadData::command(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"extra/special/per/atom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal read_data command");
if (! atom->molecular)
if (atom->molecular == Atom::ATOMIC)
error->all(FLERR,"No bonded interactions allowed with this atom style");
force->special_extra = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (force->special_extra < 0)

4
src/replicate.cpp
View File

@ -602,7 +602,7 @@ void Replicate::command(int narg, char **arg)
atom->tag[i] += atom_offset;
atom->image[i] = image;
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (atom->molecule[i] > 0)
atom->molecule[i] += mol_offset;
if (atom->molecular == Atom::MOLECULAR) {
@ -704,7 +704,7 @@ void Replicate::command(int narg, char **arg)
atom->tag[i] += atom_offset;
atom->image[i] = image;
if (atom->molecular) {
if (atom->molecular != Atom::ATOMIC) {
if (atom->molecule[i] > 0)
atom->molecule[i] += mol_offset;
if (atom->molecular == Atom::MOLECULAR) {

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