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Merge branch 'develop' into modify-fix-compute-accessors

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# Conflicts:
#	src/PLUGIN/plugin.cpp
This commit is contained in:
Axel Kohlmeyer
2021-10-27 21:14:05 -04:00
parent 8bf016eaef 4a048e3f57
commit c8512249b7
171 changed files with 1101 additions and 900 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
cmake/CMakeLists.txt
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@ -81,7 +81,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")

2
cmake/Modules/Packages/MACHDYN.cmake
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@ -8,7 +8,7 @@ option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed on
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
set(EIGEN3_URL "https://download.lammps.org/thirdparty/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_URL "${LAMMPS_THIRDPARTY_URL}/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
set(EIGEN3_MD5 "4c527a9171d71a72a9d4186e65bea559" CACHE STRING "MD5 checksum of Eigen3 tarball")
mark_as_advanced(EIGEN3_URL)
mark_as_advanced(EIGEN3_MD5)

21
cmake/Modules/Packages/ML-PACE.cmake
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@ -1,11 +1,11 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "a2ac3315c41a1a4a5c912bcb1bc9c5cc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
# download library sources to build folder
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
# uncompress downloaded sources
execute_process(
@ -14,12 +14,19 @@ execute_process(
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE pace)
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
target_link_libraries(pace PRIVATE yaml-cpp-pace)
target_link_libraries(lammps PRIVATE pace)

2
doc/lammps.1
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@ -1,4 +1,4 @@
.TH LAMMPS "1" "29 September 2021" "2021-09-29"
.TH LAMMPS "1" "27 October 2021" "2021-10-27"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.

12
doc/src/Build_settings.rst
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@ -321,9 +321,7 @@ following settings:
.. code-block:: make
LMP_INC = -DLAMMPS_JPEG
LMP_INC = -DLAMMPS_PNG
LMP_INC = -DLAMMPS_FFMPEG
LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings>
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
@ -372,7 +370,7 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
.. code-block:: make
LMP_INC = -DLAMMPS_GZIP
LMP_INC = -DLAMMPS_GZIP <other LMP_INC settings>
This option requires that your operating system fully supports the
"popen()" function in the standard runtime library and that a ``gzip``
@ -454,7 +452,7 @@ those systems:
.. code-block:: make
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
LMP_INC = -DLAMMPS_LONGLONG_TO_LONG <other LMP_INC settings>
----------
@ -481,7 +479,7 @@ e.g. to Python. Of course, the calling code has to be set up to
.. code-block:: make
LMP_INC = -DLAMMPS_EXCEPTIONS
LMP_INC = -DLAMMPS_EXCEPTIONS <other LMP_INC settings>
.. note::
@ -522,7 +520,7 @@ executable, not the library.
.. code-block:: make
LMP_INC = -DLAMMPS_TRAP_FPE
LMP_INC = -DLAMMPS_TRAP_FPE <other LMP_INC settings>
After compilation with this flag set, the LAMMPS executable will stop
and produce a core dump when a division by zero, overflow, illegal math

3
doc/src/Developer_platform.rst
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@ -42,6 +42,9 @@ Platform information functions
.. doxygenfunction:: mpi_info
:project: progguide
.. doxygenfunction:: compress_info
:project: progguide
File and path functions and global constants
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

2
examples/plugins/CMakeLists.txt
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@ -41,7 +41,7 @@ set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Need -restrict with Intel compilers
if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()

2
lib/gpu/lal_atom.cu
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@ -18,7 +18,7 @@
#endif
__kernel void kernel_cast_x(__global numtyp4 *restrict x_type,
const __global double *restrict x,
const __global numtyp *restrict x,
const __global int *restrict type,
const int nall) {
int ii=GLOBAL_ID_X;

2
lib/gpu/lal_atom.h
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@ -475,7 +475,7 @@ class Atom {
UCL_Vector<numtyp,numtyp> v;
#ifdef GPU_CAST
UCL_Vector<double,double> x_cast;
UCL_Vector<numtyp,numtyp> x_cast;
UCL_Vector<int,int> type_cast;
#endif

12
lib/gpu/lal_zbl.cu
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@ -82,9 +82,9 @@ __kernel void k_zbl(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict coeff1,
const __global numtyp4 *restrict coeff2,
const __global numtyp4 *restrict coeff3,
const double cut_globalsq,
const double cut_innersq,
const double cut_inner,
const numtyp cut_globalsq,
const numtyp cut_innersq,
const numtyp cut_inner,
const int lj_types,
const __global int *dev_nbor,
const __global int *dev_packed,
@ -174,9 +174,9 @@ __kernel void k_zbl_fast(const __global numtyp4 *restrict x_,
const __global numtyp4 *restrict coeff1_in,
const __global numtyp4 *restrict coeff2_in,
const __global numtyp4 *restrict coeff3_in,
const double cut_globalsq,
const double cut_innersq,
const double cut_inner,
const numtyp cut_globalsq,
const numtyp cut_innersq,
const numtyp cut_inner,
const __global int *dev_nbor,
const __global int *dev_packed,
__global acctyp4 *restrict ans,

6
lib/gpu/lal_zbl.h
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@ -67,9 +67,9 @@ class ZBL : public BaseAtomic<numtyp, acctyp> {
/// If atom type constants fit in shared memory, use fast kernels
bool shared_types;
double _cut_globalsq;
double _cut_innersq;
double _cut_inner;
numtyp _cut_globalsq;
numtyp _cut_innersq;
numtyp _cut_inner;
/// Number of atom types
int _lj_types;

4
lib/pace/Install.py
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@ -15,12 +15,14 @@ from install_helpers import fullpath, geturl, checkmd5sum
# settings
thisdir = fullpath('.')
version = 'v.2021.4.9'
version = 'v.2021.10.25'
# known checksums for different PACE versions. used to validate the download.
checksums = { \
'v.2021.2.3.upd2' : '8fd1162724d349b930e474927197f20d',
'v.2021.4.9' : '4db54962fbd6adcf8c18d46e1798ceb5',
'v.2021.9.28' : 'f98363bb98adc7295ea63974738c2a1b',
'v.2021.10.25' : 'a2ac3315c41a1a4a5c912bcb1bc9c5cc'
}

18
lib/pace/Makefile
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@ -2,8 +2,11 @@ SHELL = /bin/sh
# ------ FILES ------
SRC_FILES = $(wildcard src/USER-PACE/*.cpp)
SRC = $(filter-out src/USER-PACE/pair_pace.cpp, $(SRC_FILES))
YAML_CPP_PATH = src/yaml-cpp
YAML_CPP_INC = $(YAML_CPP_PATH)/include
SRC_FILES = $(wildcard src/ML-PACE/*.cpp)
SRC = $(filter-out src/ML-PACE/pair_pace.cpp, $(SRC_FILES))
# ------ DEFINITIONS ------
@ -12,7 +15,7 @@ OBJ = $(SRC:.cpp=.o)
# ------ SETTINGS ------
CXXFLAGS = -O3 -fPIC -Isrc/USER-PACE
CXXFLAGS = -O3 -fPIC -Isrc/ML-PACE -I$(YAML_CPP_INC)
ARCHIVE = ar
ARCHFLAG = -rc
@ -21,9 +24,13 @@ SYSLIB =
# ------ MAKE PROCEDURE ------
lib: $(OBJ)
lib: $(OBJ) lib-yaml-cpp
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
lib-yaml-cpp:
cd $(YAML_CPP_PATH) && $(MAKE) lib
# ------ COMPILE RULES ------
%.o: %.cpp
@ -32,6 +39,9 @@ lib: $(OBJ)
# ------ CLEAN ------
clean-all:
-rm -f *~ $(OBJ) $(LIB)
cd $(YAML_CPP_PATH) && $(MAKE) clean-all
clean-build:
-rm -f *~ $(OBJ)
cd $(YAML_CPP_PATH) && $(MAKE) clean-build

4
lib/pace/Makefile.lammps
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@ -1,3 +1,3 @@
pace_SYSINC =-I../../lib/pace/src/USER-PACE
pace_SYSLIB = -L../../lib/pace/ -lpace
pace_SYSINC =-I../../lib/pace/src/ML-PACE -I../../lib/pace/src/yaml-cpp/include
pace_SYSLIB = -L../../lib/pace/ -lpace -L../../lib/pace/src/yaml-cpp/ -lyaml-cpp
pace_SYSPATH =

1
python/examples/matplotlib_plot.py
View File

@ -62,7 +62,6 @@ if me == 0:
plt.show(block=False)
# run nfreq steps at a time w/out pre/post, query compute, refresh plot
import time
while ntimestep < nsteps:
lmp.command("run %d pre no post no" % nfreq)

1
python/examples/simple.py
View File

@ -13,7 +13,6 @@
from __future__ import print_function
import sys
import numpy as np
import ctypes
# parse command line

18
python/lammps/core.py
View File

@ -99,7 +99,7 @@ class lammps(object):
# load a shared object.
try:
if ptr: self.lib = CDLL("",RTLD_GLOBAL)
if ptr is not None: self.lib = CDLL("",RTLD_GLOBAL)
except OSError:
self.lib = None
@ -329,7 +329,7 @@ class lammps(object):
# ptr is the desired instance of LAMMPS
# just convert it to ctypes ptr and store in self.lmp
if not ptr:
if ptr is None:
# with mpi4py v2+, we can pass MPI communicators to LAMMPS
# need to adjust for type of MPI communicator object
@ -338,7 +338,7 @@ class lammps(object):
from mpi4py import MPI
self.MPI = MPI
if comm:
if comm is not None:
if not self.has_mpi_support:
raise Exception('LAMMPS not compiled with real MPI library')
if not self.has_mpi4py:
@ -354,7 +354,7 @@ class lammps(object):
narg = 0
cargs = None
if cmdargs:
if cmdargs is not None:
cmdargs.insert(0,"lammps")
narg = len(cmdargs)
for i in range(narg):
@ -376,7 +376,7 @@ class lammps(object):
if self.has_mpi4py and self.has_mpi_support:
self.comm = self.MPI.COMM_WORLD
self.opened = 1
if cmdargs:
if cmdargs is not None:
cmdargs.insert(0,"lammps")
narg = len(cmdargs)
for i in range(narg):
@ -1361,7 +1361,7 @@ class lammps(object):
This function is a wrapper around the :cpp:func:`lammps_create_atoms`
function of the C-library interface, and the behavior is similar except
that the *v*, *image*, and *shrinkexceed* arguments are optional and
default to *None*, *None*, and *False*, respectively. With none being
default to *None*, *None*, and *False*, respectively. With *None* being
equivalent to a ``NULL`` pointer in C.
The lists of coordinates, types, atom IDs, velocities, image flags can
@ -1389,7 +1389,7 @@ class lammps(object):
:return: number of atoms created. 0 if insufficient or invalid data
:rtype: int
"""
if id:
if id is not None:
id_lmp = (self.c_tagint*n)()
try:
id_lmp[:] = id[0:n]
@ -1411,7 +1411,7 @@ class lammps(object):
except ValueError:
return 0
if v:
if v is not None:
v_lmp = (c_double*(three_n))()
try:
v_lmp[:] = v[0:three_n]
@ -1420,7 +1420,7 @@ class lammps(object):
else:
v_lmp = None
if image:
if image is not None:
img_lmp = (self.c_imageint*n)()
try:
img_lmp[:] = image[0:n]

10
python/lammps/pylammps.py
View File

@ -854,30 +854,30 @@ class IPyLammps(PyLammps):
"""
cmd_args = [group, "image", filename, color, diameter]
if size:
if size is not None:
width = size[0]
height = size[1]
cmd_args += ["size", width, height]
if view:
if view is not None:
theta = view[0]
phi = view[1]
cmd_args += ["view", theta, phi]
if center:
if center is not None:
flag = center[0]
Cx = center[1]
Cy = center[2]
Cz = center[3]
cmd_args += ["center", flag, Cx, Cy, Cz]
if up:
if up is not None:
Ux = up[0]
Uy = up[1]
Uz = up[2]
cmd_args += ["up", Ux, Uy, Uz]
if zoom:
if zoom is not None:
cmd_args += ["zoom", zoom]
cmd_args.append("modify backcolor " + background_color)

4
src/AWPMD/pair_awpmd_cut.cpp
View File

@ -246,8 +246,8 @@ void PairAWPMDCut::compute(int eflag, int vflag)
fi= new Vector_3[wpmd->ni];
// adding electrons
for (std::map<int,std::vector<int> >::iterator it=etmap.begin(); it!= etmap.end(); ++it) {
std::vector<int> &el=it->second;
for (auto & it : etmap) {
std::vector<int> &el=it.second;
if (!el.size()) // should not happen
continue;
int s=spin[el[0]] >0 ? 0 : 1;

2
src/DPD-REACT/fix_eos_table.cpp
View File

@ -207,7 +207,7 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
// loop until section found with matching keyword
while (1) {
while (true) {
if (fgets(line,MAXLINE,fp) == nullptr)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line

4
src/DPD-REACT/fix_eos_table_rx.cpp
View File

@ -321,7 +321,7 @@ void FixEOStableRX::read_file(char *file)
char line[MAXLINE],*ptr;
int eof = 0;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
@ -427,7 +427,7 @@ void FixEOStableRX::read_table(Table *tb, Table *tb2, char *file, char *keyword)
// loop until section found with matching keyword
while (1) {
while (true) {
if (fgets(line,MAXLINE,fp) == nullptr)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line

12
src/DPD-REACT/fix_rx.cpp
View File

@ -255,7 +255,7 @@ void FixRX::post_constructor()
int eof = 0;
char * word;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
@ -804,7 +804,7 @@ void FixRX::read_file(char *file)
char line[MAXLINE],*ptr;
int eof = 0;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
@ -858,7 +858,7 @@ void FixRX::read_file(char *file)
nreactions=0;
sign = -1.0;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
@ -1155,7 +1155,7 @@ int FixRX::rkf45_h0 (const int neq, const double t, const double /*t_stop*/,
// compute ydot at t=t0
rhs (t, y, ydot, v_params);
while (1)
while (true)
{
// Estimate y'' with finite-difference ...
@ -1254,7 +1254,7 @@ void FixRX::odeDiagnostics()
double max_per_proc[numCounters];
double min_per_proc[numCounters];
if (1)
if (true)
{
static bool firstStep = true;
@ -1285,7 +1285,7 @@ void FixRX::odeDiagnostics()
printf("me= %d nst= %g nfc= %g time= %g nlocal= %g lmpnst= %g weight_idx= %d 1st= %d aveNeigh= %g\n", comm->me, this->diagnosticCounter[0], this->diagnosticCounter[1], this->diagnosticCounter[2], this->diagnosticCounter[3], this->diagnosticCounter[4], rx_weight_index, firstStep, averageNumNeighbors);
if (rx_weight_index != -1 && !firstStep && 0)
if (rx_weight_index != -1 && !firstStep && false)
{
double *rx_weight = atom->dvector[rx_weight_index];

4
src/DPD-REACT/pair_exp6_rx.cpp
View File

@ -731,7 +731,7 @@ void PairExp6rx::read_file(char *file)
char line[MAXLINE],*ptr;
int eof = 0;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {
@ -838,7 +838,7 @@ void PairExp6rx::read_file2(char *file)
char line[MAXLINE],*ptr;
int eof = 0;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == nullptr) {

2
src/DPD-REACT/pair_multi_lucy.cpp
View File

@ -356,7 +356,7 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword)
// loop until section found with matching keyword
while (1) {
while (true) {
if (fgets(line,MAXLINE,fp) == nullptr)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line

2
src/DPD-REACT/pair_multi_lucy_rx.cpp
View File

@ -496,7 +496,7 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword)
// loop until section found with matching keyword
while (1) {
while (true) {
if (fgets(line,MAXLINE,fp) == nullptr)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line

4
src/EXTRA-FIX/fix_gle.cpp
View File

@ -234,7 +234,7 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) :
char line[MAXLINE],*ptr;
int n,nwords,ndone=0,eof=0;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fgle);
if (ptr == nullptr) {
@ -300,7 +300,7 @@ FixGLE::FixGLE(LAMMPS *lmp, int narg, char **arg) :
ndone = eof = 0;
const double cfac = force->boltz / force->mvv2e;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fgle);
if (ptr == nullptr) {

5
src/EXTRA-FIX/fix_ttm.cpp
View File

@ -28,7 +28,6 @@
#include "random_mars.h"
#include "respa.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
#include "update.h"
#include <cmath>
@ -491,10 +490,10 @@ void FixTTM::read_electron_temperatures(const std::string &filename)
// check correctness of input data
if ((ix < 0) || (ix >= nxgrid) || (iy < 0) || (iy >= nygrid) || (iz < 0) || (iz >= nzgrid))
throw parser_error("Fix ttm invalid grid index in fix ttm grid file");
throw TokenizerException("Fix ttm invalid grid index in fix ttm grid file","");
if (T_tmp < 0.0)
throw parser_error("Fix ttm electron temperatures must be > 0.0");
throw TokenizerException("Fix ttm electron temperatures must be > 0.0","");
T_electron[iz][iy][ix] = T_tmp;
T_initial_set[iz][iy][ix] = 1;

8
src/EXTRA-FIX/fix_ttm.h
View File

@ -77,14 +77,6 @@ class FixTTM : public Fix {
virtual void deallocate_grid();
virtual void read_electron_temperatures(const std::string &);
virtual void write_electron_temperatures(const std::string &);
class parser_error : public std::exception {
std::string message;
public:
parser_error(const std::string &mesg) { message = mesg; }
const char *what() const noexcept { return message.c_str(); }
};
};
} // namespace LAMMPS_NS

4
src/EXTRA-FIX/fix_ttm_grid.cpp
View File

@ -306,7 +306,7 @@ void FixTTMGrid::read_electron_temperatures(const std::string &filename)
int iz = values.next_int();
if (ix < 0 || ix >= nxgrid || iy < 0 || iy >= nygrid || iz < 0 || iz >= nzgrid)
throw parser_error("Fix ttm/grid invalid grid index in input");
throw TokenizerException("Fix ttm/grid invalid grid index in input","");
if (ix >= nxlo_in && ix <= nxhi_in && iy >= nylo_in && iy <= nyhi_in
&& iz >= nzlo_in && iz <= nzhi_in) {
@ -314,7 +314,7 @@ void FixTTMGrid::read_electron_temperatures(const std::string &filename)
T_initial_set[iz][iy][ix] = 1;
}
} else {
throw parser_error("Incorrect format in fix ttm electron grid file");
throw TokenizerException("Incorrect format in fix ttm electron grid file","");
}
} catch (std::exception &e) {
error->one(FLERR,e.what());

4
src/EXTRA-FIX/fix_ttm_mod.cpp
View File

@ -584,10 +584,10 @@ void FixTTMMod::read_electron_temperatures(const std::string &filename)
// check correctness of input data
if ((ix < 0) || (ix >= nxgrid) || (iy < 0) || (iy >= nygrid) || (iz < 0) || (iz >= nzgrid))
throw parser_error("Fix ttm invalid grid index in fix ttm/mod grid file");
throw TokenizerException("Fix ttm invalid grid index in fix ttm/mod grid file","");
if (T_tmp < 0.0)
throw parser_error("Fix ttm electron temperatures must be > 0.0");
throw TokenizerException("Fix ttm electron temperatures must be > 0.0","");
T_electron[iz][iy][ix] = T_tmp;
T_initial_set[iz][iy][ix] = 1;

8
src/EXTRA-FIX/fix_ttm_mod.h
View File

@ -87,14 +87,6 @@ class FixTTMMod : public Fix {
void read_parameters(const std::string &);
void read_electron_temperatures(const std::string &);
void write_electron_temperatures(const std::string &);
class parser_error : public std::exception {
std::string message;
public:
parser_error(const std::string &mesg) { message = mesg; }
const char *what() const noexcept { return message.c_str(); }
};
};
} // namespace LAMMPS_NS

6
src/EXTRA-FIX/fix_wall_ees.cpp
View File

@ -121,8 +121,10 @@ void FixWallEES::wall_particle(int m, int which, double coord)
double* shape = bonus[ellipsoid[i]].shape;;
MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
MathExtra::transpose_matvec(A,nhat,tempvec);
for (int k = 0; k<3; k++) tempvec[k] *= shape[k];
for (int k = 0; k<3 ; k++) sigman2 += tempvec[k]*tempvec[k];
for (int k = 0; k<3; k++) {
tempvec[k] *= shape[k];
sigman2 += tempvec[k]*tempvec[k];
}
sigman = sqrt(sigman2);
if (delta <= sigman) {

14
src/EXTRA-FIX/fix_wall_region_ees.cpp
View File

@ -194,8 +194,10 @@ void FixWallRegionEES::post_force(int /*vflag*/)
nhat[(which+2)%3] = 0 ;
sn2 = 0 ;
MathExtra::transpose_matvec(A,nhat,tempvec);
for (int k = 0; k<3; k++) tempvec[k] *= shape[k];
for (int k = 0; k<3 ; k++) sn2 += tempvec[k]*tempvec[k];
for (int k = 0; k<3; k++) {
tempvec[k] *= shape[k];
sn2 += tempvec[k]*tempvec[k];
}
sn = sqrt(sn2);
tooclose[which] = sn;
}
@ -321,9 +323,11 @@ void FixWallRegionEES::ees(int m, int i)
sigman2 = 0.0;
MathExtra::transpose_matvec(A,nhat,tempvec);
for (int k = 0; k<3; k++) tempvec[k] *= shape[k];
for (int k = 0; k<3; k++) sigman2 += tempvec[k]*tempvec[k];
for (int k = 0; k<3; k++) SAn[k] = tempvec[k];
for (int k = 0; k<3; k++) {
tempvec[k] *= shape[k];
sigman2 += tempvec[k]*tempvec[k];
SAn[k] = tempvec[k];
}
sigman = sqrt(sigman2);
delta = fabs(region->contact[m].r);

2
src/GRANULAR/fix_pour.cpp
View File

@ -842,7 +842,7 @@ void FixPour::xyz_random(double h, double *coord)
coord[2] = h;
} else {
double r1,r2;
while (1) {
while (true) {
r1 = random->uniform() - 0.5;
r2 = random->uniform() - 0.5;
if (r1*r1 + r2*r2 < 0.25) break;

10
src/KIM/kim_init.cpp
View File

@ -251,17 +251,15 @@ void KimInit::determine_model_type_and_units(char *model_name, char *user_units,
return;
} else if (unit_conversion_mode) {
KIM_Model_Destroy(&pkim);
int const num_systems = 5;
char const *const systems[num_systems] = {"metal", "real", "si", "cgs", "electron"};
for (int i = 0; i < num_systems; ++i) {
get_kim_unit_names(systems[i], lengthUnit, energyUnit, chargeUnit, temperatureUnit,
timeUnit, error);
const char * unit_systems[] = {"metal", "real", "si", "cgs", "electron"};
for (auto units : unit_systems) {
get_kim_unit_names(units, lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit, error);
kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased, lengthUnit, energyUnit, chargeUnit,
temperatureUnit, timeUnit, model_name, &units_accepted, &pkim);
if (units_accepted) {
logID = fmt::format("{}_Model", comm->me);
KIM_Model_SetLogID(pkim, logID.c_str());
*model_units = utils::strdup(systems[i]);
*model_units = utils::strdup(units);
return;
}
KIM_Model_Destroy(&pkim);

2
src/KIM/kim_interactions.cpp
View File

@ -293,7 +293,7 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) con
char line[MAXLINE], *ptr;
int n, eof = 0;
while (1) {
while (true) {
if (comm->me == 0) {
ptr = fgets(line, MAXLINE,fp);
if (ptr == nullptr) {

2
src/KOKKOS/fix_acks2_reaxff_kokkos.cpp
View File

@ -1966,7 +1966,7 @@ void FixACKS2ReaxFFKokkos<DeviceType>::get_chi_field()
namespace LAMMPS_NS {
template class FixACKS2ReaxFFKokkos<LMPDeviceType>;
#ifdef KOKKOS_ENABLE_CUDA
#ifdef LMP_KOKKOS_GPU
template class FixACKS2ReaxFFKokkos<LMPHostType>;
#endif
}

4
src/KOKKOS/fix_acks2_reaxff_kokkos.h
View File

@ -299,7 +299,7 @@ struct FixACKS2ReaxFFKokkosComputeHFunctor {
c.template compute_h_team<NEIGHFLAG>(team, atoms_per_team, vector_length);
}
size_t team_shmem_size(int team_size) const {
size_t team_shmem_size(int /*team_size*/) const {
size_t shmem_size =
Kokkos::View<int *, scratch_space, Kokkos::MemoryUnmanaged>::shmem_size(
atoms_per_team) + // s_ilist
@ -347,7 +347,7 @@ struct FixACKS2ReaxFFKokkosComputeXFunctor {
c.template compute_x_team<NEIGHFLAG>(team, atoms_per_team, vector_length);
}
size_t team_shmem_size(int team_size) const {
size_t team_shmem_size(int /*team_size*/) const {
size_t shmem_size =
Kokkos::View<int *, scratch_space, Kokkos::MemoryUnmanaged>::shmem_size(
atoms_per_team) + // s_ilist

3
src/KOKKOS/fix_qeq_reaxff_kokkos.h
View File

@ -30,7 +30,6 @@ FixStyle(qeq/reax/kk/host,FixQEqReaxFFKokkos<LMPHostType>);
#include "kokkos_type.h"
#include "neigh_list.h"
#include "neigh_list_kokkos.h"
#include "kokkos_base.h"
namespace LAMMPS_NS {
@ -42,7 +41,7 @@ struct TagFixQEqReaxFFPackForwardComm {};
struct TagFixQEqReaxFFUnpackForwardComm {};
template<class DeviceType>
class FixQEqReaxFFKokkos : public FixQEqReaxFF, public KokkosBase {
class FixQEqReaxFFKokkos : public FixQEqReaxFF {
public:
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;

10
src/KOKKOS/kokkos.cpp
View File

@ -44,7 +44,7 @@
#define GPU_AWARE_UNKNOWN static int have_gpu_aware = -1;
// TODO HIP: implement HIP-aware MPI support (UCX) detection
#if defined(KOKKOS_ENABLE_HIP) || defined(KOKKOS_ENABLE_SYCL)
#if defined(KOKKOS_ENABLE_HIP) || defined(KOKKOS_ENABLE_SYCL) || defined(KOKKOS_ENABLE_OPENMPTARGET)
GPU_AWARE_UNKNOWN
#elif defined(KOKKOS_ENABLE_CUDA)
@ -121,7 +121,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
} else if (strcmp(arg[iarg],"g") == 0 ||
strcmp(arg[iarg],"gpus") == 0) {
#ifndef LMP_KOKKOS_GPU
error->all(FLERR,"GPUs are requested but Kokkos has not been compiled for CUDA, HIP, or SYCL");
error->all(FLERR,"GPUs are requested but Kokkos has not been compiled using a GPU-enabled backend");
#endif
if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args");
ngpus = atoi(arg[iarg+1]);
@ -162,7 +162,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
if (ngpus > 1 && !set_flag)
error->all(FLERR,"Could not determine local MPI rank for multiple "
"GPUs with Kokkos CUDA, HIP, or SYCL because MPI library not recognized");
"GPUs with Kokkos because MPI library not recognized");
} else if (strcmp(arg[iarg],"t") == 0 ||
strcmp(arg[iarg],"threads") == 0) {
@ -204,7 +204,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
#ifdef LMP_KOKKOS_GPU
if (ngpus <= 0)
error->all(FLERR,"Kokkos has been compiled for CUDA, HIP, or SYCL but no GPUs are requested");
error->all(FLERR,"Kokkos has been compiled with GPU-enabled backend but no GPUs are requested");
#endif
#ifndef KOKKOS_ENABLE_SERIAL
@ -311,7 +311,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
error->warning(FLERR,"Detected MPICH. Disabling GPU-aware MPI");
#else
if (me == 0)
error->warning(FLERR,"Kokkos with CUDA, HIP, or SYCL assumes CUDA-aware MPI is available,"
error->warning(FLERR,"Kokkos with GPU-enabled backend assumes GPU-aware MPI is available,"
" but cannot determine if this is the case\n try"
" '-pk kokkos gpu/aware off' if getting segmentation faults");

10
src/KOKKOS/kokkos.h
View File

@ -87,7 +87,7 @@ E: Invalid Kokkos command-line args
Self-explanatory. See Section 2.7 of the manual for details.
E: Could not determine local MPI rank for multiple GPUs with Kokkos CUDA
E: Could not determine local MPI rank for multiple GPUs with Kokkos
because MPI library not recognized
The local MPI rank was not found in one of four supported environment variables.
@ -96,13 +96,13 @@ E: Invalid number of threads requested for Kokkos: must be 1 or greater
Self-explanatory.
E: GPUs are requested but Kokkos has not been compiled for CUDA
E: GPUs are requested but Kokkos has not been compiled using GPU-enabled backend
Recompile Kokkos with CUDA support to use GPUs.
Recompile Kokkos with GPU-enabled backend to use GPUs.
E: Kokkos has been compiled for CUDA, HIP, or SYCL but no GPUs are requested
E: Kokkos has been compiled with GPU-enabled backend but no GPUs are requested
One or more GPUs must be used when Kokkos is compiled for CUDA/HIP/SYCL.
One or more GPUs must be used when Kokkos is compiled for CUDA/HIP/SYCL/OpenMPTarget.
W: Kokkos package already initalized, cannot reinitialize with different parameters

18
src/KOKKOS/kokkos_type.h
View File

@ -20,7 +20,7 @@
#include <Kokkos_Core.hpp>
#include <Kokkos_DualView.hpp>
#include <impl/Kokkos_Timer.hpp>
#include <Kokkos_Timer.hpp>
#include <Kokkos_Vectorization.hpp>
#include <Kokkos_ScatterView.hpp>
#include <Kokkos_UnorderedMap.hpp>
@ -34,7 +34,7 @@ constexpr int HALF = 4;
#define ISFINITE(x) std::isfinite(x)
#endif
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) || defined(KOKKOS_ENABLE_SYCL)
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP) || defined(KOKKOS_ENABLE_SYCL) || defined(KOKKOS_ENABLE_OPENMPTARGET)
#define LMP_KOKKOS_GPU
#endif
@ -223,6 +223,11 @@ template<>
struct ExecutionSpaceFromDevice<Kokkos::Experimental::SYCL> {
static const LAMMPS_NS::ExecutionSpace space = LAMMPS_NS::Device;
};
#elif defined(KOKKOS_ENABLE_OPENMPTARGET)
template<>
struct ExecutionSpaceFromDevice<Kokkos::Experimental::OpenMPTarget> {
static const LAMMPS_NS::ExecutionSpace space = LAMMPS_NS::Device;
};
#endif
// set host pinned space
@ -232,6 +237,8 @@ typedef Kokkos::CudaHostPinnedSpace LMPPinnedHostType;
typedef Kokkos::Experimental::HIPHostPinnedSpace LMPPinnedHostType;
#elif defined(KOKKOS_ENABLE_SYCL)
typedef Kokkos::Experimental::SYCLSharedUSMSpace LMPPinnedHostType;
#elif defined(KOKKOS_ENABLE_OPENMPTARGET)
typedef Kokkos::Serial LMPPinnedHostType;
#endif
// create simple LMPDeviceSpace typedef for non CUDA-, HIP-, or SYCL-specific
@ -242,6 +249,8 @@ typedef Kokkos::Cuda LMPDeviceSpace;
typedef Kokkos::Experimental::HIP LMPDeviceSpace;
#elif defined(KOKKOS_ENABLE_SYCL)
typedef Kokkos::Experimental::SYCL LMPDeviceSpace;
#elif defined(KOKKOS_ENABLE_OPENMPTARGET)
typedef Kokkos::Experimental::OpenMPTarget LMPDeviceSpace;
#endif
@ -280,6 +289,11 @@ template<>
struct AtomicDup<HALFTHREAD,Kokkos::Experimental::SYCL> {
using value = Kokkos::Experimental::ScatterAtomic;
};
#elif defined(KOKKOS_ENABLE_OPENMPTARGET)
template<>
struct AtomicDup<HALFTHREAD,Kokkos::Experimental::OpenMPTarget> {
using value = Kokkos::Experimental::ScatterAtomic;
};
#endif
#ifdef LMP_KOKKOS_USE_ATOMICS

17
src/KOKKOS/npair_kokkos.cpp
View File

@ -226,7 +226,8 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::build(NeighList *list_)
data.h_resize() = 0;
Kokkos::deep_copy(d_scalars, h_scalars);
#ifdef LMP_KOKKOS_GPU
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
#define BINS_PER_BLOCK 2
const int factor = atoms_per_bin<64?2:1;
#else
@ -605,14 +606,15 @@ void NeighborKokkosExecute<DeviceType>::build_ItemGPU(typename Kokkos::TeamPolic
other_x[MY_II + 3 * atoms_per_bin] = itype;
}
other_id[MY_II] = i;
#ifndef KOKKOS_ENABLE_SYCL
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
int test = (__syncthreads_count(i >= 0 && i <= nlocal) == 0);
if (test) return;
#else
#elif defined(KOKKOS_ENABLE_SYCL)
int not_done = (i >= 0 && i <= nlocal);
dev.team_reduce(Kokkos::Max<int>(not_done));
if(not_done == 0) return;
#elif defined(KOKKOS_ENABLE_OPENMPTARGET)
dev.team_barrier();
#endif
if (i >= 0 && i < nlocal) {
@ -1055,14 +1057,15 @@ void NeighborKokkosExecute<DeviceType>::build_ItemSizeGPU(typename Kokkos::TeamP
other_x[MY_II + 4 * atoms_per_bin] = radi;
}
other_id[MY_II] = i;
#ifndef KOKKOS_ENABLE_SYCL
#if defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_HIP)
int test = (__syncthreads_count(i >= 0 && i <= nlocal) == 0);
if (test) return;
#else
#elif defined(KOKKOS_ENABLE_SYCL)
int not_done = (i >= 0 && i <= nlocal);
dev.team_reduce(Kokkos::Max<int>(not_done));
if(not_done == 0) return;
#elif defined(KOKKOS_ENABLE_OPENMPTARGET)
dev.team_barrier();
#endif
if (i >= 0 && i < nlocal) {

4
src/KOKKOS/verlet_kokkos.cpp
View File

@ -283,7 +283,7 @@ void VerletKokkos::run(int n)
atomKK->sync(Device,ALL_MASK);
//static double time = 0.0;
//Kokkos::Impl::Timer ktimer;
//Kokkos::Timer ktimer;
timer->init_timeout();
for (int i = 0; i < n; i++) {
@ -445,7 +445,7 @@ void VerletKokkos::run(int n)
if (pair_compute_flag) {
atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
atomKK->sync(force->pair->execution_space,~(~force->pair->datamask_read|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));
Kokkos::Impl::Timer ktimer;
Kokkos::Timer ktimer;
force->pair->compute(eflag,vflag);
atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
atomKK->modified(force->pair->execution_space,~(~force->pair->datamask_modify|(F_MASK | ENERGY_MASK | VIRIAL_MASK)));

2
src/KSPACE/pppm.cpp
View File

@ -983,7 +983,7 @@ void PPPM::set_grid_global()
h = h_x = h_y = h_z = 4.0/g_ewald;
int count = 0;
while (1) {
while (true) {
// set grid dimensions

2
src/KSPACE/pppm_dipole.cpp
View File

@ -783,7 +783,7 @@ void PPPMDipole::set_grid_global()
h = h_x = h_y = h_z = 4.0/g_ewald;
int count = 0;
while (1) {
while (true) {
// set grid dimension

6
src/KSPACE/pppm_disp.cpp
View File

@ -1471,7 +1471,7 @@ int PPPMDisp::qr_alg(double **A, double **Q, int n)
// start loop for the matrix factorization
int count = 0;
int countmax = 100000;
while (1) {
while (true) {
// make a Wilkinson shift
an1 = A[n-2][n-2];
an = A[n-1][n-1];
@ -2645,7 +2645,7 @@ void PPPMDisp::set_grid()
if (!gridflag) {
h = h_x = h_y = h_z = 4.0/g_ewald;
int count = 0;
while (1) {
while (true) {
// set grid dimension
@ -3663,7 +3663,7 @@ void PPPMDisp::set_n_pppm_6()
// decrease grid spacing until required precision is obtained
int count = 0;
while (1) {
while (true) {
// set grid dimension
nx_pppm_6 = static_cast<int> (xprd/h_x);

7
src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.astra_arm
View File

@ -64,6 +64,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -73,7 +78,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

2
src/MAKE/MACHINES/Makefile.bgq
View File

@ -15,7 +15,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.cori2
View File

@ -75,6 +75,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB = #-ljpeg
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -84,7 +89,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

5
src/MAKE/MACHINES/Makefile.cygwin
View File

@ -65,9 +65,10 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, but should be empty on Windows)
# library for loading shared objects (defaults to -ldl but must be empty on Windows)
override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -77,7 +78,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.mac
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.mac_mpi
View File

@ -66,6 +66,11 @@ JPG_INC = -I/opt/local/include
JPG_PATH = -L/opt/local/lib
JPG_LIB = -ljpeg
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.power
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.summit_kokkos
View File

@ -72,6 +72,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -81,7 +86,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.theta
View File

@ -70,6 +70,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -79,7 +84,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.ubuntu
View File

@ -69,6 +69,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB = -ljpeg -lpng
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -78,7 +83,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.ubuntu_simple
View File

@ -68,6 +68,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -77,7 +82,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.white
View File

@ -69,6 +69,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -78,7 +83,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/MACHINES/Makefile.xe6
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

4
src/MAKE/Makefile.mpi
View File

@ -65,7 +65,7 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl)
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
@ -79,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.big
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.fftw
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.g++_mpich
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.g++_mpich_link
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.g++_openmpi
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.g++_openmpi_link
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.g++_serial
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.gpu
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.hip
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -80,7 +85,7 @@ endif
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.icc_mpich
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.icc_mpich_link
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.icc_openmpi
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.icc_openmpi_link
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.icc_serial
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.intel_coprocessor
View File

@ -70,6 +70,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -79,7 +84,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
View File

@ -69,6 +69,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -78,7 +83,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.intel_cpu_mpich
View File

@ -69,6 +69,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -78,7 +83,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi
View File

@ -70,6 +70,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -79,7 +84,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.jpeg
View File

@ -65,6 +65,11 @@ JPG_INC = -I/usr/include
JPG_PATH = -L/usr/lib
JPG_LIB = -ljpeg
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.knl
View File

@ -68,6 +68,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB = -ljpeg
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -77,7 +82,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
View File

@ -70,6 +70,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -79,7 +84,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.kokkos_mpi_only
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.kokkos_omp
View File

@ -66,6 +66,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -75,7 +80,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.kokkos_phi
View File

@ -67,6 +67,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -76,7 +81,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.mgptfast
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.omp
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.oneapi
View File

@ -68,6 +68,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -77,7 +82,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.opt
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.pgi_mpich_link
View File

@ -65,6 +65,11 @@ JPG_INC =
JPG_PATH =
JPG_LIB =
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

7
src/MAKE/OPTIONS/Makefile.png
View File

@ -65,6 +65,11 @@ JPG_INC = -I/usr/include
JPG_PATH = -L/usr/lib
JPG_LIB = -lpng
# library for loading shared objects (defaults to -ldl, should be empty on Windows)
# uncomment to change the default
# override DYN_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
@ -74,7 +79,7 @@ include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) $(DYN_LIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

14
src/MANIFOLD/fix_nve_manifold_rattle.cpp
View File

@ -140,10 +140,8 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg,
if (strcmp(arg[argi], "every") == 0) {
nevery = utils::inumeric(FLERR,arg[argi+1],false,lmp);
next_output = update->ntimestep + nevery;
if (comm->me == 0) {
fprintf(screen,"Outputting every %d steps, next is %d\n",
nevery, next_output);
}
if (comm->me == 0)
utils::logmesg(lmp,"Outputting every {} steps, next is {}\n",nevery, next_output);
argi += 2;
} else if (error_on_unknown_keyword) {
error->all(FLERR,"Error parsing arg \"{}\".\n",arg[argi]);
@ -211,11 +209,9 @@ void FixNVEManifoldRattle::print_stats( const char *header )
double inv_tdiff = 1.0/( static_cast<double>(ntimestep) - stats.last_out );
stats.last_out = ntimestep;
fprintf(screen, "%s stats for time step " BIGINT_FORMAT " on %d atoms:\n",
header, ntimestep, stats.natoms);
fprintf(screen, " iters/atom: x = %f, v = %f, dofs removed %d",
utils::logmesg(lmp, "{} stats for time step {} on {} atoms:\n", header, ntimestep, stats.natoms);
utils::logmesg(lmp, " iters/atom: x = {}, v = {}, dofs removed = {}\n",
x_iters * inv_tdiff, v_iters * inv_tdiff, stats.dofs_removed);
fprintf(screen,"\n");
}
stats.x_iters_per_atom = 0;
@ -498,7 +494,7 @@ void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v,
const double c_inv = 1.0 / c;
while (1) {
while (true) {
v[0] = vt[0] - l*no_dt[0];
v[1] = vt[1] - l*no_dt[1];
v[2] = vt[2] - l*no_dt[2];

28
src/MANIFOLD/fix_nvt_manifold_rattle.cpp
View File

@ -32,21 +32,21 @@
------------------------------------------------------------------------- */
#include "fix_nvt_manifold_rattle.h"
#include <cstring>
#include <cmath>
#include "atom.h"
#include "force.h"
#include "update.h"
#include "error.h"
#include "group.h"
#include "citeme.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "update.h"
#include "manifold.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
@ -115,9 +115,7 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg,
mtchain = utils::inumeric(FLERR, arg[argi+1],false,lmp);
argi += 2;
} else if (error_on_unknown_keyword) {
char msg[2048];
sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]);
error->all(FLERR, msg);
error->all(FLERR, "Error parsing arg \"{}\".\n", arg[argi]);
} else {
argi += 1;
}
@ -271,12 +269,8 @@ void FixNVTManifoldRattle::nhc_temp_integrate()
factor_eta = exp(-dthalf*eta_dot[0]);
if (factor_eta == 0) {
char msg[2048];
sprintf(msg, "WTF, factor_eta is 0! dthalf = %f, eta_dot[0] = %f",
dthalf, eta_dot[0]);
error->all(FLERR,msg);
}
if (factor_eta == 0)
error->all(FLERR, "factor_eta is 0! dthalf = {}, eta_dot[0] = {}", dthalf, eta_dot[0]);
nh_v_temp();

34
src/MANIFOLD/manifold_gaussian_bump.cpp
View File

@ -67,9 +67,7 @@ public:
double get_t_from_x( double xx ) const
{
if (xx < x0 || xx > x1) {
char msg[2048];
sprintf(msg, "x ( %g ) out of bounds [%g, %g]", xx, x0, x1 );
err->one(FLERR, msg);
err->one(FLERR,"x ( {} ) out of bounds [{}, {}]", xx, x0, x1 );
}
// Newton iterate to get right t.
@ -271,8 +269,6 @@ void manifold_gaussian_bump::post_param_init()
make_lut();
// test_lut();
}
@ -360,31 +356,3 @@ void manifold_gaussian_bump::lut_get_z_and_zp( double rr, double &zz,
zz = zleft * fmin + zright * frac;
zzp = zpleft * fmin + zpright * frac;
}
void manifold_gaussian_bump::test_lut()
{
double x[3], nn[3];
if (comm->me != 0) return;
FILE *fp = fopen( "test_lut_gaussian.dat", "w" );
double dx = 0.1;
for (double xx = 0; xx < 20; xx += dx) {
x[0] = xx;
x[1] = 0.0;
x[2] = 0.0;
double gg = g( x );
n( x, nn );
double taper_z;
if (xx <= rc1) {
taper_z = gaussian_bump(xx);
} else if (xx < rc2) {
taper_z = lut_get_z( xx );
} else {
taper_z = 0.0;
}
fprintf( fp, "%g %g %g %g %g %g %g\n", xx, gaussian_bump(xx), taper_z,
gg, nn[0], nn[1], nn[2] );
}
fclose(fp);
}

2
src/MANIFOLD/manifold_gaussian_bump.h
View File

@ -86,8 +86,6 @@ namespace user_manifold {
double lut_get_zp(double rr) const;
void lut_get_z_and_zp(double rr, double &zz, double &zzp) const;
void test_lut();
double taper(double);
double taper_der(double);
};

86
src/MANIFOLD/manifold_thylakoid.cpp
View File

@ -34,17 +34,13 @@ manifold_thylakoid::manifold_thylakoid( LAMMPS *lmp, int /*narg*/, char ** /*arg
// fix should call post_param_init();
}
manifold_thylakoid::~manifold_thylakoid()
{
for (std::size_t i = 0; i < parts.size(); ++i) {
delete parts[i];
for (auto & part : parts) {
delete part;
}
}
void manifold_thylakoid::post_param_init()
{
// Set coefficients:
@ -59,52 +55,21 @@ void manifold_thylakoid::post_param_init()
LB = params[1];
lB = params[2];
if (comm->me == 0) {
fprintf(screen,"My params are now: lT = %f, LT = %f, pad = %f, "
"wB = %f, LB = %f, lB = %f\n", lT, LT, pad, wB, LB, lB );
fprintf(screen,"Calling init_domains() from post_param_init().\n");
}
init_domains();
checkup();
}
void manifold_thylakoid::checkup()
{
if (comm->me == 0) {
fprintf(screen,"This is checkup of thylakoid %p\n", this);
fprintf(screen,"I have %ld parts. They are:\n", parts.size());
for (int i = 0; i < (int)parts.size(); ++i) {
fprintf(screen, "[%f, %f] x [%f, %f] x [%f, %f]\n",
parts[i]->xlo, parts[i]->xhi,
parts[i]->ylo, parts[i]->yhi,
parts[i]->zlo, parts[i]->zhi );
}
fprintf(screen,"My params are:\n");
for (int i = 0; i < NPARAMS; ++i) {
fprintf(screen,"%f\n", params[i]);
}
}
}
double manifold_thylakoid::g( const double *x )
{
int err = 0;
std::size_t idx;
thyla_part *p = get_thyla_part(x,&err,&idx);
if (err) {
char msg[2048];
sprintf(msg,"Error getting thyla_part for x = (%f, %f, %f)",x[0],x[1],x[2]);
error->one(FLERR,msg);
}
if (err) error->one(FLERR,"Error getting thyla_part for x = ({}, {}, {})",x[0],x[1],x[2]);
double con_val = p->g(x);
if (std::isfinite(con_val)) {
return con_val;
} else {
char msg[2048];
sprintf(msg,"Error, thyla_part of type %d returned %f as constraint val!",
p->type, con_val);
error->one(FLERR,msg);
error->one(FLERR,"Error, thyla_part of type {} returned {} as constraint val!", p->type, con_val);
return 0;
}
}
@ -114,20 +79,14 @@ void manifold_thylakoid::n( const double *x, double *n )
int err = 0;
std::size_t idx;
thyla_part *p = get_thyla_part(x,&err,&idx);
if (err) {
char msg[2048];
sprintf(msg,"Error getting thyla_part for x = (%f, %f, %f)",x[0],x[1],x[2]);
error->one(FLERR,msg);
}
if (err)
error->one(FLERR,"Error getting thyla_part for x = ({}, {}, {})",x[0],x[1],x[2]);
p->n(x,n);
if (std::isfinite(n[0]) && std::isfinite(n[1]) && std::isfinite(n[2])) {
return;
} else {
char msg[2048];
sprintf(msg,"Error, thyla_part of type %d returned (%f,%f,%f) as gradient!",
} else
error->one(FLERR,"thyla_part of type {} returned ({},{},{}) as gradient!",
p->type, n[0], n[1], n[2]);
error->one(FLERR,msg);
}
}
thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int * /*err_flag*/, std::size_t *idx )
@ -140,9 +99,7 @@ thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int * /*err_fla
return p;
}
}
char msg[2048];
sprintf(msg,"Could not find thyla_part for x = (%f,%f,%f)", x[0],x[1],x[2]);
error->one(FLERR,msg);
error->one(FLERR,"Could not find thyla_part for x = ({},{},{})", x[0],x[1],x[2]);
return nullptr;
}
@ -153,12 +110,9 @@ thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int * /*err_fla
void manifold_thylakoid::init_domains()
{
if (wB + 2*lB > LT) {
char msg[2048];
sprintf(msg,"LT = %f not large enough to accommodate bridge with "
"wB = %f and lB = %f! %f > %f\n", LT, wB, lB, wB + 2*lB, LT);
error->one(FLERR,msg);
}
if (wB + 2*lB > LT)
error->one(FLERR,"LT = {} not large enough to accommodate bridge with "
"wB = {} and lB = {}! {} > {}\n", LT, wB, lB, wB + 2*lB, LT);
// Determine some constant coordinates:
x0 = -( 0.5*LB + lB + lT + LT + lT + pad);
@ -375,12 +329,9 @@ void manifold_thylakoid::init_domains()
parts.push_back(p);
// Check if this plane lines up with bl:
if (fabs(plr.pt[0] - bl.pt[0] + lB) > 1e-8) {
char msg[2048];
sprintf(msg,"Origins of plane left right and bridge left misaligned! %f != %f!\n",
if (fabs(plr.pt[0] - bl.pt[0] + lB) > 1e-8)
error->one(FLERR,"Origins of plane left right and bridge left misaligned! {} != {}!\n",
plr.pt[0], bl.pt[0] - lB );
error->one(FLERR,msg);
}
// Now, for the right stack, you can mirror the other...
// To mirror them you need to invert lo[0] and hi[0] and flip their sign.
@ -428,12 +379,9 @@ void manifold_thylakoid::init_domains()
set_domain(p, prr.lo, prr.hi);
parts.push_back(p);
if (fabs(prr.pt[0] - br.pt[0] - lB) > 1e-8) {
char msg[2048];
sprintf(msg,"Origins of plane left right and bridge left misaligned! %f != %f!\n",
if (fabs(prr.pt[0] - br.pt[0] - lB) > 1e-8)
error->one(FLERR,"Origins of plane left right and bridge left misaligned! {} != {}!\n",
prr.pt[0], br.pt[0] + lB);
error->one(FLERR,msg);
}
}

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