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Merge pull request #607 from akohlmey/final-changes-for-stable 

Final build system changes for stable release
This commit is contained in:
Steve Plimpton 2017-08-08 17:26:22 -06:00 committed by GitHub
parent 0a54c34e34 95ece8a6c0
commit 691d1b730d
64 changed files with 985 additions and 870 deletions
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1
lib/.gitignore vendored
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@ -1,2 +1,3 @@
Makefile.lammps
.depend
Makefile.auto

29
lib/Install.py
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@ -23,8 +23,9 @@ specify -m and optionally -e, order does not matter
Examples:
make lib-poems args="-m g++" # build COLVARS lib with GNU g++ compiler
make lib-meam args="-m ifort" # build MEAM lib with Intel ifort compiler
make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src
make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src
make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran)
"""
# print error message or help
@ -70,23 +71,31 @@ if not os.path.exists("Makefile.%s" % machine):
lines = open("Makefile.%s" % machine,'r').readlines()
fp = open("Makefile.auto",'w')
has_extramake = False
for line in lines:
words = line.split()
if len(words) == 3 and extraflag and \
words[0] == "EXTRAMAKE" and words[1] == '=':
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
print >>fp,line,
if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=':
has_extramake = True
if extraflag:
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
fp.write(line)
fp.close()
# make the library via Makefile.auto
# make the library via Makefile.auto optionally with parallel make
try:
import multiprocessing
n_cpus = multiprocessing.cpu_count()
except:
n_cpus = 1
print("Building lib%s.a ..." % lib)
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
print(txt)
print(txt.decode('UTF-8'))
if os.path.exists("lib%s.a" % lib): print("Build was successful")
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
if not os.path.exists("Makefile.lammps"):
if has_extramake and not os.path.exists("Makefile.lammps"):
print("lib/%s/Makefile.lammps was NOT created" % lib)

71
lib/awpmd/Makefile.mpi Normal file
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@ -0,0 +1,71 @@
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.linalg
# ------ FILES ------
SRC = \
ivutils/src/logexc.cpp \
systems/interact/TCP/wpmd.cpp \
systems/interact/TCP/wpmd_split.cpp
INC = \
cerf.h \
cerf2.h \
cerf_octave.h \
cvector_3.h \
lapack_inter.h \
logexc.h \
pairhash.h \
refobj.h \
tcpdefs.h \
vector_3.h \
wavepacket.h \
wpmd.h \
wpmd_split.h
# ------ DEFINITIONS ------
LIB = libawpmd.a
OBJ = $(SRC:.cpp=.o)
# ------ SETTINGS ------
# include any MPI settings needed for the ATC library to build with
# the same MPI library that LAMMPS is built with
CC = mpicxx
CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
-DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
ARCHIVE = ar
ARCHFLAG = -rc
DEPFLAGS = -M
#LINK =
#LINKFLAGS =
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
# ------ COMPILE RULES ------
%.o:%.cpp
$(CC) $(CCFLAGS) -c $< -o $@
%.d:%.cpp
$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
# ------ DEPENDENCIES ------
DEPENDS = $(OBJ:.o=.d)
# ------ CLEAN ------
clean:
-rm -f *.d *~ $(OBJ) $(LIB)

8
lib/awpmd/Makefile.mpicc
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@ -36,8 +36,10 @@ OBJ = $(SRC:.cpp=.o)
# include any MPI settings needed for the ATC library to build with
# the same MPI library that LAMMPS is built with
CC = mpic++
CCFLAGS = -O -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
CC = mpicxx
CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
-DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
ARCHIVE = ar
ARCHFLAG = -rc
DEPFLAGS = -M
@ -66,4 +68,4 @@ DEPENDS = $(OBJ:.o=.d)
# ------ CLEAN ------
clean:
-rm *.d *~ $(OBJ) $(LIB)
-rm -f *.d *~ $(OBJ) $(LIB)

71
lib/awpmd/Makefile.serial Normal file
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@ -0,0 +1,71 @@
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.linalg
# ------ FILES ------
SRC = \
ivutils/src/logexc.cpp \
systems/interact/TCP/wpmd.cpp \
systems/interact/TCP/wpmd_split.cpp
INC = \
cerf.h \
cerf2.h \
cerf_octave.h \
cvector_3.h \
lapack_inter.h \
logexc.h \
pairhash.h \
refobj.h \
tcpdefs.h \
vector_3.h \
wavepacket.h \
wpmd.h \
wpmd_split.h
# ------ DEFINITIONS ------
LIB = libawpmd.a
OBJ = $(SRC:.cpp=.o)
# ------ SETTINGS ------
# include any MPI settings needed for the ATC library to build with
# the same MPI library that LAMMPS is built with
CC = g++
CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
-I../../src/STUBS
ARCHIVE = ar
ARCHFLAG = -rc
DEPFLAGS = -M
#LINK =
#LINKFLAGS =
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
# ------ COMPILE RULES ------
%.o:%.cpp
$(CC) $(CCFLAGS) -c $< -o $@
%.d:%.cpp
$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
# ------ DEPENDENCIES ------
DEPENDS = $(OBJ:.o=.d)
# ------ CLEAN ------
clean:
-rm -f *.d *~ $(OBJ) $(LIB)

10
lib/colvars/Install.py
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@ -13,7 +13,7 @@ Syntax from lib/colvars dir: python Install.py -m machine -e suffix
specify -m and optionally -e, order does not matter
-m = peform a clean followed by "make -f Makefile.machine"
-m = delete all existing objects, followed by "make -f Makefile.machine"
machine = suffix of a lib/colvars/Makefile.* or of a
src/MAKE/MACHINES/Makefile.* file
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
@ -21,7 +21,7 @@ specify -m and optionally -e, order does not matter
Examples:
make lib-colvars args="-m g++" # build COLVARS lib with GNU g++ compiler
make lib-colvars args="-m mpi" # build COLVARS lib with default mpi compiler wrapper
"""
# print error message or help
@ -122,7 +122,7 @@ for line in lines:
fp.write(line)
fp.close()
# make the library via Makefile.auto
# make the library via Makefile.auto optionally with parallel make
try:
import multiprocessing
@ -132,9 +132,9 @@ except:
print("Building lib%s.a ..." % lib)
cmd = ["make -f Makefile.auto clean"]
print(subprocess.check_output(cmd, shell=True).decode())
print(subprocess.check_output(cmd, shell=True).decode('UTF-8'))
cmd = ["make -f Makefile.auto -j%d" % n_cpus]
print(subprocess.check_output(cmd, shell=True).decode())
print(subprocess.check_output(cmd, shell=True).decode('UTF-8'))
if os.path.exists("lib%s.a" % lib): print("Build was successful")
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))

31
lib/colvars/Makefile.mingw32-cross
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@ -1,31 +0,0 @@
# -*- makefile -*- to build Colvars module with MinGW 32-bit
EXTRAMAKE = Makefile.lammps.empty
COLVARS_LIB = libcolvars.a
COLVARS_OBJ_DIR = Obj_mingw64/
CXX = i686-w64-mingw32-g++
CXXFLAGS = -O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
-fno-rtti -fno-exceptions -finline-functions \
-ffast-math -funroll-loops -fstrict-aliasing \
-Wall -W -Wno-uninitialized
AR = i686-w64-mingw32-ar
ARFLAGS = -rscv
SHELL = /bin/sh
.PHONY: default clean
default: $(COLVARS_OBJ_DIR) $(COLVARS_LIB) Makefile.lammps
include Makefile.common
$(COLVARS_OBJ_DIR):
mkdir $(COLVARS_OBJ_DIR)
clean:
-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
-rmdir $(COLVARS_OBJ_DIR)
Makefile.lammps:
-cp $(EXTRAMAKE) Makefile.lammps

13
lib/colvars/Makefile.mingw32-cross-mpi
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@ -1,13 +0,0 @@
# -*- makefile -*- wrapper for non-MPI libraries
SHELL=/bin/sh
all:
$(MAKE) $(MFLAGS) mingw32-cross
-rm -f Obj_mingw32-mpi
ln -s Obj_mingw32 Obj_mingw32-mpi
clean:
$(MAKE) $(MFLAGS) clean-mingw32-cross
-rm -f Obj_mingw32-mpi

31
lib/colvars/Makefile.mingw64-cross
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@ -1,31 +0,0 @@
# -*- makefile -*- to build Colvars module with MinGW 32-bit
EXTRAMAKE = Makefile.lammps.empty
COLVARS_LIB = libcolvars.a
COLVARS_OBJ_DIR = Obj_mingw32/
CXX = x86_64-w64-mingw32-g++
CXXFLAGS = -O2 -march=core2 -mtune=core2 -mpc64 -msse2 \
-fno-rtti -fno-exceptions -finline-functions \
-ffast-math -funroll-loops -fstrict-aliasing \
-Wall -W -Wno-uninitialized
AR = x86_64-w64-mingw32-ar
ARFLAGS = -rscv
SHELL = /bin/sh
.PHONY: default clean
default: $(COLVARS_OBJ_DIR) $(COLVARS_LIB) Makefile.lammps
include Makefile.common
$(COLVARS_OBJ_DIR):
mkdir $(COLVARS_OBJ_DIR)
clean:
-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
-rmdir $(COLVARS_OBJ_DIR)
Makefile.lammps:
-cp $(EXTRAMAKE) Makefile.lammps

13
lib/colvars/Makefile.mingw64-cross-mpi
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@ -1,13 +0,0 @@
# -*- makefile -*- wrapper for non-MPI libraries
SHELL=/bin/sh
all:
$(MAKE) $(MFLAGS) mingw64-cross
-rm -f Obj_mingw64-mpi
ln -s Obj_mingw64 Obj_mingw64-mpi
clean:
$(MAKE) $(MFLAGS) clean-mingw64-cross
-rm -f Obj_mingw64-mpi

25
lib/colvars/Makefile.mpi Normal file
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@ -0,0 +1,25 @@
# -*- makefile -*- to build Colvars module with default MPI compiler wrapper
EXTRAMAKE = Makefile.lammps.empty
COLVARS_LIB = libcolvars.a
COLVARS_OBJ_DIR =
CXX = mpicxx
CXXFLAGS = -O2 -g -Wall -fPIC -funroll-loops
AR = ar
ARFLAGS = -rscv
SHELL = /bin/sh
.PHONY: default clean
default: $(COLVARS_LIB) Makefile.lammps
include Makefile.common
clean:
-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
Makefile.lammps:
-cp $(EXTRAMAKE) Makefile.lammps

25
lib/colvars/Makefile.serial Normal file
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@ -0,0 +1,25 @@
# -*- makefile -*- to build Colvars module with GNU compiler
EXTRAMAKE = Makefile.lammps.empty
COLVARS_LIB = libcolvars.a
COLVARS_OBJ_DIR =
CXX = g++
CXXFLAGS = -O2 -g -Wall -fPIC -funroll-loops
AR = ar
ARFLAGS = -rscv
SHELL = /bin/sh
.PHONY: default clean
default: $(COLVARS_LIB) Makefile.lammps
include Makefile.common
clean:
-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
Makefile.lammps:
-cp $(EXTRAMAKE) Makefile.lammps

10
lib/gpu/.gitignore vendored
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@ -1,4 +1,6 @@
obj
obj_ocl
ocl_get_devices
nvc_get_devices
/obj
/obj_ocl
/ocl_get_devices
/nvc_get_devices
/*.cubin
/*_cubin.h

58
lib/gpu/Install.py
View File

@ -3,53 +3,57 @@
# Install.py tool to build the GPU library
# used to automate the steps described in the README file in this dir
import sys,os,re,commands
from __future__ import print_function
import sys,os,subprocess
# help message
help = """
Syntax from src dir: make lib-gpu args="-i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix"
Syntax from lib dir: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix
Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix"
Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix
specify one or more options, order does not matter
copies an existing Makefile.isuffix in lib/gpu to Makefile.auto
copies an existing Makefile.machine in lib/gpu to Makefile.auto
optionally edits these variables in Makefile.auto:
CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
optionally uses Makefile.auto to build the GPU library -> libgpu.a
and to copy a Makefile.lammps.esuffix -> Makefile.lammps
optionally copies Makefile.auto to a new Makefile.osuffix
-i = use Makefile.isuffix as starting point, copy to Makefile.auto
default isuffix = linux
-m = use Makefile.machine as starting point, copy to Makefile.auto
default machine = linux
-h = set CUDA_HOME variable in Makefile.auto to hdir
hdir = path to NVIDIA Cuda software, e.g. /usr/local/cuda
-a = set CUDA_ARCH variable in Makefile.auto to arch
use arch = ?? for K40 (Tesla)
use arch = 37 for dual K80 (Tesla)
use arch = 60 for P100 (Pascal)
use arch = 20 for Tesla C2050/C2070 (Fermi) (deprecated as of CUDA 8.0)
or GeForce GTX 580 or similar
use arch = 30 for Tesla K10 (Kepler)
use arch = 35 for Tesla K40 (Kepler) or GeForce GTX Titan or similar
use arch = 37 for Tesla dual K80 (Kepler)
use arch = 60 for Tesla P100 (Pascal)
-p = set CUDA_PRECISION variable in Makefile.auto to precision
use precision = double or mixed or single
-e = set EXTRAMAKE variable in Makefile.auto to Makefile.lammps.esuffix
-m = make the GPU library using Makefile.auto
-b = make the GPU library using Makefile.auto
first performs a "make clean"
produces libgpu.a if successful
then produces libgpu.a if successful
also copies EXTRAMAKE file -> Makefile.lammps
-e can set which Makefile.lammps.esuffix file is copied
-o = copy final Makefile.auto to Makefile.osuffix
Examples:
make lib-gpu args="-m" # build GPU lib with default Makefile.linux
make lib-gpu args="-i xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-i xk7 -p single -o xk7.single -m" # ditto, also build GPU lib
make lib-gpu args="-b" # build GPU lib with default Makefile.linux
make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-m mpi -a 35 -p single -o mpi.mixed -b" # create new Makefile.mpi.mixed, also build GPU lib with these settings
"""
# print error message or help
def error(str=None):
if not str: print help
else: print "ERROR",str
if not str: print(help)
else: print("ERROR",str)
sys.exit()
# parse args
@ -65,7 +69,7 @@ outflag = 0
iarg = 0
while iarg < nargs:
if args[iarg] == "-i":
if args[iarg] == "-m":
if iarg+2 > nargs: error()
isuffix = args[iarg+1]
iarg += 2
@ -89,7 +93,7 @@ while iarg < nargs:
eflag = 1
lmpsuffix = args[iarg+1]
iarg += 2
elif args[iarg] == "-m":
elif args[iarg] == "-b":
makeflag = 1
iarg += 1
elif args[iarg] == "-o":
@ -117,9 +121,9 @@ fp = open("Makefile.auto",'w')
for line in lines:
words = line.split()
if len(words) != 3:
print >>fp,line,
fp.write(line)
continue
if hflag and words[0] == "CUDA_HOME" and words[1] == '=':
line = line.replace(words[2],hdir)
if aflag and words[0] == "CUDA_ARCH" and words[1] == '=':
@ -128,20 +132,20 @@ for line in lines:
line = line.replace(words[2],precstr)
if eflag and words[0] == "EXTRAMAKE" and words[1] == '=':
line = line.replace(words[2],"Makefile.lammps.%s" % lmpsuffix)
print >>fp,line,
fp.write(line)
fp.close()
# perform make
# make operations copies EXTRAMAKE file to Makefile.lammps
if makeflag:
print "Building libgpu.a ..."
print("Building libgpu.a ...")
cmd = "rm -f libgpu.a"
commands.getoutput(cmd)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
commands.getoutput(cmd)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print(txt.decode('UTF-8'))
if not os.path.exists("libgpu.a"):
error("Build of lib/gpu/libgpu.a was NOT successful")
if not os.path.exists("Makefile.lammps"):
@ -150,6 +154,6 @@ if makeflag:
# copy new Makefile.auto to Makefile.osuffix
if outflag:
print "Creating new Makefile.%s" % osuffix
print("Creating new Makefile.%s" % osuffix)
cmd = "cp Makefile.auto Makefile.%s" % osuffix
commands.getoutput(cmd)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

2
lib/gpu/Makefile.linux
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@ -37,7 +37,7 @@ CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC)
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./

17
lib/gpu/Makefile.mingw32-cross
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@ -1,17 +0,0 @@
CUDA_HOME = ../../tools/mingw-cross/OpenCL
OCL_CPP = i686-w64-mingw32-g++ -O2 -march=i686 -mtune=generic -mfpmath=387 \
-mpc64 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS \
-I$(CUDA_HOME)/include
OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw32 -Wl,-Bdynamic,-lOpenCL,-Bstatic -L../../src/STUBS -lmpi_mingw32
OCL_PREC = -D_SINGLE_DOUBLE
OCL_TUNE = -DFERMI_OCL
EXTRAMAKE = Makefile.lammps.mingw-cross
BIN_DIR = Obj_mingw32
OBJ_DIR = Obj_mingw32
LIB_DIR = Obj_mingw32
AR = i686-w64-mingw32-ar
BSH = /bin/sh
include Opencl.makefile

19
lib/gpu/Makefile.mingw32-cross-mpi
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@ -1,19 +0,0 @@
CUDA_HOME = ../../tools/mingw-cross/OpenCL
OCL_CPP = i686-w64-mingw32-g++ -O2 -march=i686 -mtune=generic -mfpmath=387 \
-mpc64 -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include \
-I../../tools/mingw-cross/mpich2-win32/include/ \
-DMPICH_IGNORE_CXX_SEEK
OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw32 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
-L../../tools/mingw-cross/mpich2-win32/lib -lmpi
OCL_PREC = -D_SINGLE_DOUBLE
OCL_TUNE = -DFERMI_OCL
EXTRAMAKE = Makefile.lammps.mingw-cross
BIN_DIR = Obj_mingw32-mpi
OBJ_DIR = Obj_mingw32-mpi
LIB_DIR = Obj_mingw32-mpi
AR = i686-w64-mingw32-ar
BSH = /bin/sh
include Opencl.makefile

18
lib/gpu/Makefile.mingw64-cross
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@ -1,18 +0,0 @@
CUDA_HOME = ../../tools/mingw-cross/OpenCL
OCL_CPP = x86_64-w64-mingw32-g++ -O3 -march=core2 -mtune=core2 -mpc64 \
-msse2 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS \
-I$(CUDA_HOME)/include
OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw64 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
-L../../src/STUBS -lmpi_mingw64
OCL_PREC = -D_SINGLE_DOUBLE
OCL_TUNE = -DFERMI_OCL
EXTRAMAKE = Makefile.lammps.mingw-cross
BIN_DIR = Obj_mingw64
OBJ_DIR = Obj_mingw64
LIB_DIR = Obj_mingw64
AR = x86_64-w64-mingw32-ar
BSH = /bin/sh
include Opencl.makefile

20
lib/gpu/Makefile.mingw64-cross-mpi
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@ -1,20 +0,0 @@
CUDA_HOME = ../../tools/mingw-cross/OpenCL
OCL_CPP = x86_64-w64-mingw32-g++ -O3 -march=core2 -mtune=core2 -mpc64 \
-msse2 -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include \
-I../../tools/mingw-cross/mpich2-win64/include/ \
-DMPICH_IGNORE_CXX_SEEK
OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw64 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
-L../../tools/mingw-cross/mpich2-win64/lib -lmpi
OCL_PREC = -D_SINGLE_DOUBLE
OCL_TUNE = -DFERMI_OCL
EXTRAMAKE = Makefile.lammps.mingw-cross
BIN_DIR = Obj_mingw64-mpi
OBJ_DIR = Obj_mingw64-mpi
LIB_DIR = Obj_mingw64-mpi
AR = x86_64-w64-mingw32-ar
BSH = /bin/sh
include Opencl.makefile

1
lib/gpu/Makefile.mpi Symbolic link
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@ -0,0 +1 @@
Makefile.linux

33
lib/gpu/Makefile.serial
View File

@ -1,5 +1,5 @@
# /* ----------------------------------------------------------------------
# Generic Makefile for CUDA using MPI STUBS library
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
@ -7,23 +7,38 @@
EXTRAMAKE = Makefile.lammps.standard
CUDA_HOME = $(HOME)/cuda
ifeq ($(CUDA_HOME),)
CUDA_HOME = /usr/local/cuda
endif
NVCC = nvcc
# Tesla CUDA
CUDA_ARCH = -arch=sm_20
CUDA_ARCH = -arch=sm_21
# newer CUDA
#CUDA_ARCH = -arch=sm_13
# older CUDA
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
CUDA_ARCH = -arch=sm_35
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG
# precision for GPU calculations
# -D_SINGLE_SINGLE # Single precision for all calculations
# -D_DOUBLE_DOUBLE # Double precision for all calculations
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
CUDA_PRECISION = -D_SINGLE_DOUBLE
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L../../src/STUBS -lmpi
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS
CUDR_OPTS = -O2
CUDA_INCLUDE = -I$(CUDA_HOME)/include
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L../../src/STUBS -lmpi_stubs
CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC)
CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -fPIC -I../../src/STUBS
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./
OBJ_DIR = ./
@ -31,5 +46,7 @@ LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile

11
lib/h5md/Makefile.h5cc
View File

@ -9,12 +9,14 @@ HDF5_PATH=/usr
INC=-I include
AR=ar
ARFLAGS=rc
LIB=libch5md.a
# need to build two libraries to not break compatibility and to support Install.py
LIB=libh5md.a libch5md.a
all: lib Makefile.lammps
build:
mkdir -p build
build/ch5md.o: src/ch5md.c | build
$(CC) $(INC) $(CFLAGS) -c $< -o $@
@ -23,8 +25,11 @@ Makefile.lammps:
.PHONY: all lib clean
$(LIB): build/ch5md.o
$(AR) $(ARFLAGS) $(LIB) build/ch5md.o
libch5md.a : build/ch5md.o
$(AR) $(ARFLAGS) $@ build/ch5md.o
libh5md.a : build/ch5md.o
$(AR) $(ARFLAGS) $@ build/ch5md.o
lib: $(LIB)

80
lib/kim/Install.py
View File

@ -1,44 +1,41 @@
#!/usr/bin/env python
# install.py tool to setup the kim-api library
# install.py tool to download, compile, and setup the kim-api library
# used to automate the steps described in the README file in this dir
from __future__ import print_function
import sys,os,re,subprocess
# transparently use either urllib or an external tool
try:
import ssl
try: from urllib.request import urlretrieve as geturl
except: from urllib import urlretrieve as geturl
except:
def geturl(url,fname):
cmd = "curl -o %s %s" % (fname,url)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
return txt
help = """
Syntax from src dir: make lib-kim args="-v version -a kim-name"
Syntax from lib dir: python Install.py -v version -a kim-name
Syntax from src dir: make lib-kim args="-b -v version -a kim-name"
or: make lib-kim args="-b -a everything"
or: make lib-kim args="-n -a kim-name"
or: make lib-kim args="-p /usr/local/open-kim -a kim-name"
Syntax from lib dir: python Install.py -b -v version -a kim-name
or: python Install.py -b -a everything
or: python Install.py -n -a kim-name
or: python Install.py -p /usr/local/open-kim -a kim-name
specify one or more options, order does not matter
-v = version of KIM API library to use
default = kim-api-v1.8.2 (current as of June 2017)
-b = download and build base KIM API library with example Models (default)
-b = download and build base KIM API library with example Models
this will delete any previous installation in the current folder
-n = do NOT download and build base KIM API library. Use an existing installation
-n = do NOT download and build base KIM API library.
Use an existing installation
-p = specify location of KIM API installation (implies -n)
-a = add single KIM model or model driver with kim-name
to existing KIM API lib (see example below).
If kim-name = everything, then rebuild KIM API library with
all available OpenKIM Models (this implies -b).
*all* available OpenKIM Models (make take a long time).
-vv = be more verbose about what is happening while the script runs
Examples:
make lib-kim # install KIM API lib with only example models
make lib-kim args="-b" # install KIM API lib with only example models
make lib-kim args="-a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # Ditto plus one model
make lib-kim args="-a everything" # install KIM API lib with all models
make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # only add one model or model driver
See the list of KIM model drivers here:
@ -52,8 +49,9 @@ https://openkim.org/kim-api
in the "What is in the KIM API source package?" section
"""
def error():
print(help)
def error(str=None):
if not str: print(help)
else: print("ERROR",str)
sys.exit()
# expand to full path name
@ -62,15 +60,21 @@ def error():
def fullpath(path):
return os.path.abspath(os.path.expanduser(path))
def geturl(url,fname):
cmd = 'curl -L -o "%s" %s' % (fname,url)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
return txt
# parse args
args = sys.argv[1:]
nargs = len(args)
if nargs == 0: error()
thisdir = os.environ['PWD']
version = "kim-api-v1.8.2"
buildflag = True
buildflag = False
everythingflag = False
addflag = False
verboseflag = False
@ -139,7 +143,7 @@ if buildflag:
if os.path.isdir(kimdir):
print("kim-api is already installed at %s.\nRemoving it for re-install" % kimdir)
cmd = "rm -rf %s" % kimdir
cmd = 'rm -rf "%s"' % kimdir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# configure LAMMPS to use kim-api to be installed
@ -160,48 +164,48 @@ if buildflag:
print("Downloading kim-api tarball ...")
geturl(url,"%s/%s.tgz" % (thisdir,version))
print("Unpacking kim-api tarball ...")
cmd = "cd %s; rm -rf %s; tar zxvf %s.tgz" % (thisdir,version,version)
cmd = 'cd "%s"; rm -rf "%s"; tar -xzvf %s.tgz' % (thisdir,version,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# configure kim-api
print("Configuring kim-api ...")
cmd = "cd %s/%s; ./configure --prefix='%s'" % (thisdir,version,kimdir)
cmd = 'cd "%s/%s"; ./configure --prefix="%s"' % (thisdir,version,kimdir)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# build kim-api
print("Configuring example Models")
cmd = "cd %s/%s; make add-examples" % (thisdir,version)
cmd = 'cd "%s/%s"; make add-examples' % (thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print (txt.decode("UTF-8"))
if everythingflag:
print("Configuring all OpenKIM models, this will take a while ...")
cmd = "cd %s/%s; make add-OpenKIM" % (thisdir,version)
cmd = 'cd "%s/%s"; make add-OpenKIM' % (thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))
print("Building kim-api ...")
cmd = "cd %s/%s; make" % (thisdir,version)
cmd = 'cd "%s/%s"; make' % (thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))
# install kim-api
print("Installing kim-api ...")
cmd = "cd %s/%s; make install" % (thisdir,version)
cmd = 'cd "%s/%s"; make install' % (thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))
cmd = "cd %s/%s; make install-set-default-to-v1" %(thisdir,version)
cmd = 'cd "%s/%s"; make install-set-default-to-v1' %(thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))
# remove source files
print("Removing kim-api source and build files ...")
cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" % (thisdir,version,version)
cmd = 'cd "%s"; rm -rf %s; rm -rf %s.tgz' % (thisdir,version,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# add a single model (and possibly its driver) to existing KIM installation
@ -219,11 +223,11 @@ if addflag:
geturl(url,"%s/%s.tgz" % (thisdir,addmodelname))
print("Unpacking item tarball ...")
cmd = "cd %s; tar zxvf %s.tgz" % (thisdir,addmodelname)
cmd = 'cd "%s"; tar -xzvf %s.tgz' % (thisdir,addmodelname)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print("Building item ...")
cmd = "cd %s/%s; make; make install" %(thisdir,addmodelname)
cmd = 'cd "%s/%s"; make; make install' %(thisdir,addmodelname)
try:
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
except subprocess.CalledProcessError as e:
@ -231,18 +235,18 @@ if addflag:
# Error: but first, check to see if it needs a driver
firstRunOutput = e.output.decode("UTF-8")
cmd = "cd %s/%s; make kim-item-type" % (thisdir,addmodelname)
cmd = 'cd "%s/%s"; make kim-item-type' % (thisdir,addmodelname)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
txt = txt.decode("UTF-8")
if txt == "ParameterizedModel":
# Get and install driver
cmd = "cd %s/%s; make model-driver-name" % (thisdir,addmodelname)
cmd = 'cd "%s/%s"; make model-driver-name' % (thisdir,addmodelname)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
adddrivername = txt.decode("UTF-8").strip()
print("First installing model driver: %s..." % adddrivername)
cmd = "cd %s; python Install.py -n -a %s" % (thisdir,adddrivername)
cmd = 'cd "%s"; python Install.py -n -a %s' % (thisdir,adddrivername)
try:
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
except subprocess.CalledProcessError as e:
@ -254,7 +258,7 @@ if addflag:
# now install the model that needed the driver
print("Now installing model : %s" % addmodelname)
cmd = "cd %s; python Install.py -n -a %s" % (thisdir,addmodelname)
cmd = 'cd "%s"; python Install.py -n -a %s' % (thisdir,addmodelname)
try:
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
except subprocess.CalledProcessError as e:
@ -272,5 +276,5 @@ if addflag:
if verboseflag: print(txt.decode("UTF-8"))
print("Removing kim item source and build files ...")
cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" %(thisdir,addmodelname,addmodelname)
cmd = 'cd "%s"; rm -rf %s; rm -rf %s.tgz' %(thisdir,addmodelname,addmodelname)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

58
lib/linalg/Install.py
View File

@ -1,58 +0,0 @@
#!/usr/bin/env python
# install.py tool to do build of the linear algebra library
# used to automate the steps described in the README file in this dir
import sys,commands,os
# help message
help = """
Syntax from src dir: make lib-linalg args="-m machine"
Syntax from lib dir: python Install.py -m machine
-m = peform a clean followed by "make -f Makefile.machine"
machine = suffix of a lib/Makefile.* file
Example:
make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
"""
# print error message or help
def error(str=None):
if not str: print help
else: print "ERROR",str
sys.exit()
# parse args
args = sys.argv[1:]
nargs = len(args)
if nargs == 0: error()
machine = None
iarg = 0
while iarg < nargs:
if args[iarg] == "-m":
if iarg+2 > nargs: error()
machine = args[iarg+1]
iarg += 2
else: error()
# set lib from working dir
cwd = os.getcwd()
lib = os.path.basename(cwd)
# make the library
print "Building lib%s.a ..." % lib
cmd = "make -f Makefile.%s clean; make -f Makefile.%s" % (machine,machine)
txt = commands.getoutput(cmd)
print txt
if os.path.exists("lib%s.a" % lib): print "Build was successful"
else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))

1
lib/linalg/Install.py Symbolic link
View File

@ -0,0 +1 @@
../Install.py

8
lib/linalg/Makefile.gfortran
View File

@ -18,10 +18,8 @@ OBJ = $(SRC:.f=.o)
# ------ SETTINGS ------
FC = gfortran
FFLAGS = -O3 -fPIC -march=native -mpc64 \
-ffast-math -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -fno-second-underscore
FFLAGS0 = -O0 -fPIC -march=native -mpc64 \
-Wall -W -Wno-uninitialized -fno-second-underscore
FFLAGS = -O3 -fPIC -ffast-math -fstrict-aliasing -fno-second-underscore
FFLAGS0 = -O0 -fPIC -fno-second-underscore
ARCHIVE = ar
AR = ar
ARCHFLAG = -rcs
@ -47,7 +45,7 @@ dlamch.o: dlamch.f
# ------ CLEAN ------
clean:
-rm *.o *.mod *~ $(LIB)
-rm -f *.o *.mod *~ $(LIB)
tar:
-tar -czvf ../linalg.tar.gz $(FILES)

67
lib/linalg/Makefile.mingw32-cross
View File

@ -1,67 +0,0 @@
# -*- makefile -*-
# *_________________________________________________________________________*
# * Minimal BLAS/LAPACK Library for use by other LAMMPS packages
SHELL = /bin/sh
# ------ FILES ------
SRC = $(wildcard *.f)
FILES = $(SRC) Makefile.* README
# ------ DEFINITIONS ------
DIR = Obj_mingw32/
LIB = $(DIR)liblinalg.a
OBJ = $(SRC:%.f=$(DIR)%.o)
# ------ SETTINGS ------
FC = i686-w64-mingw32-gfortran
FFLAGS = -O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
-ffast-math -funroll-loops -fstrict-aliasing -Wall -W \
-Wno-uninitialized -fno-second-underscore
FFLAGS0 = -O0 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
-Wall -W -Wno-uninitialized -fno-second-underscore
ARCHIVE = i686-w64-mingw32-ar
AR = i686-w64-mingw32-ar
ARCHFLAG = -rcs
USRLIB =
SYSLIB =
.PHONY: default clean tar
.SUFFIXES:
.SUFFIXES: .F .f .o
# ------ MAKE PROCEDURE ------
default: $(DIR) $(LIB)
$(LIB): $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
$(DIR):
mkdir $(DIR)
# ------ COMPILE RULES ------
$(DIR)%.o:%.F
$(F90) $(F90FLAGS) -c $< -o $@
$(DIR)%.o:%.f
$(FC) $(FFLAGS) -c $< -o $@
$(DIR)dlamch.o: dlamch.f
$(FC) $(FFLAGS0) -c $< -o $@
# ------ CLEAN ------
clean:
-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
-rmdir $(DIR)
tar:
-tar -czvf ../linalg.tar.gz $(FILES)

13
lib/linalg/Makefile.mingw32-cross-mpi
View File

@ -1,13 +0,0 @@
# -*- makefile -*- wrapper for non-MPI libraries
SHELL=/bin/sh
all:
$(MAKE) $(MFLAGS) mingw32-cross
-rm -f Obj_mingw32-mpi
ln -s Obj_mingw32 Obj_mingw32-mpi
clean:
$(MAKE) $(MFLAGS) clean-mingw32-cross
-rm -f Obj_mingw32-mpi

67
lib/linalg/Makefile.mingw64-cross
View File

@ -1,67 +0,0 @@
# -*- makefile -*-
# *_________________________________________________________________________*
# * Minimal BLAS/LAPACK Library for use by other LAMMPS packages
SHELL = /bin/sh
# ------ FILES ------
SRC = $(wildcard *.f)
FILES = $(SRC) Makefile.* README
# ------ DEFINITIONS ------
DIR = Obj_mingw64/
LIB = $(DIR)liblinalg.a
OBJ = $(SRC:%.f=$(DIR)%.o)
# ------ SETTINGS ------
FC = x86_64-w64-mingw32-gfortran
FFLAGS = -O3 -march=core2 -mtune=generic -msse2 -mpc64 \
-ffast-math -funroll-loops -fstrict-aliasing -Wall -W \
-Wno-uninitialized -fno-second-underscore
FFLAGS0 = -O0 -march=core2 -mtune=generic -msse2 -mpc64 \
-Wall -W -Wno-uninitialized -fno-second-underscore
ARCHIVE = x86_64-w64-mingw32-ar
AR = x86_64-w64-mingw32-ar
ARCHFLAG = -rcs
USRLIB =
SYSLIB =
.PHONY: default clean tar
.SUFFIXES:
.SUFFIXES: .F .f .o
# ------ MAKE PROCEDURE ------
default: $(DIR) $(LIB)
$(LIB): $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
$(DIR):
mkdir $(DIR)
# ------ COMPILE RULES ------
$(DIR)%.o:%.F
$(F90) $(F90FLAGS) -c $< -o $@
$(DIR)%.o:%.f
$(FC) $(FFLAGS) -c $< -o $@
$(DIR)dlamch.o: dlamch.f
$(FC) $(FFLAGS0) -c $< -o $@
# ------ CLEAN ------
clean:
-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
-rmdir $(DIR)
tar:
-tar -czvf ../linalg.tar.gz $(FILES)

13
lib/linalg/Makefile.mingw64-cross-mpi
View File

@ -1,13 +0,0 @@
# -*- makefile -*- wrapper for non-MPI libraries
SHELL=/bin/sh
all:
$(MAKE) $(MFLAGS) mingw64-cross
-rm -f Obj_mingw64-mpi
ln -s Obj_mingw64 Obj_mingw64-mpi
clean:
$(MAKE) $(MFLAGS) clean-mingw64-cross
-rm -f Obj_mingw64-mpi

52
lib/linalg/Makefile.mpi Normal file
View File

@ -0,0 +1,52 @@
# -*- makefile -*-
# *_________________________________________________________________________*
# * Minimal BLAS/LAPACK Library for use by other LAMMPS packages
SHELL = /bin/sh
# ------ FILES ------
SRC = $(wildcard *.f)
FILES = $(SRC) Makefile.* README
# ------ DEFINITIONS ------
LIB = liblinalg.a
OBJ = $(SRC:.f=.o)
# ------ SETTINGS ------
FC = mpifort
FFLAGS = -O3 -fPIC
FFLAGS0 = -O0 -fPIC
ARCHIVE = ar
AR = ar
ARCHFLAG = -rcs
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
# ------ COMPILE RULES ------
%.o:%.F
$(F90) $(F90FLAGS) -c $<
%.o:%.f
$(FC) $(FFLAGS) -c $<
dlamch.o: dlamch.f
$(FC) $(FFLAGS0) -c $<
# ------ CLEAN ------
clean:
-rm -f *.o *.mod *~ $(LIB)
tar:
-tar -czvf ../linalg.tar.gz $(FILES)

1
lib/linalg/Makefile.serial Symbolic link
View File

@ -0,0 +1 @@
Makefile.gfortran

6
lib/colvars/Makefile.lammps → lib/meam/Makefile.lammps.empty
View File

@ -1,5 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
colvars_SYSINC =
colvars_SYSLIB =
colvars_SYSPATH =
meam_SYSINC =
meam_SYSLIB =
meam_SYSPATH =

69
lib/meam/Makefile.mingw32-cross
View File

@ -1,69 +0,0 @@
# * -*- makefile -*-
# *_________________________________________________________________________*
# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
# * DESCRIPTION: SEE READ-ME *
# * FILE NAME: Makefile *
# * AUTHORS: Greg Wagner, Sandia National Laboratories *
# * CONTACT: gjwagne@sandia.gov *
# *_________________________________________________________________________*/
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.gfortran
# ------ FILES ------
SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
FILES = $(SRC) Makefile
# ------ DEFINITIONS ------
DIR = Obj_mingw32/
LIB = $(DIR)libmeam.a
OBJ = $(SRC:%.F=$(DIR)%.o) $(DIR)fm_exp.o
# ------ SETTINGS ------
F90 = i686-w64-mingw32-gfortran
F90FLAGS = -O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
-ffast-math -funroll-loops -fstrict-aliasing -J$(DIR) \
-Wall -W -Wno-uninitialized -fno-second-underscore
#F90FLAGS = -O
ARCHIVE = i686-w64-mingw32-ar
ARCHFLAG = -rcs
LINK = i686-w64-mingw32-g++
LINKFLAGS = -O
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
default: $(DIR) $(LIB)
$(DIR):
-mkdir $(DIR)
$(LIB): $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
# ------ COMPILE RULES ------
$(DIR)%.o:%.F
$(F90) $(F90FLAGS) -c $< -o $@
$(DIR)%.o:%.c
$(F90) $(F90FLAGS) -c $< -o $@
include .depend
# ------ CLEAN ------
clean:
-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
-rmdir $(DIR)
tar:
-tar -cvf ../MEAM.tar $(FILES)

13
lib/meam/Makefile.mingw32-cross-mpi
View File

@ -1,13 +0,0 @@
# -*- makefile -*- wrapper for non-MPI libraries
SHELL=/bin/sh
all:
$(MAKE) $(MFLAGS) mingw32-cross
-rm -f Obj_mingw32-mpi
ln -s Obj_mingw32 Obj_mingw32-mpi
clean:
$(MAKE) $(MFLAGS) clean-mingw32-cross
-rm -f Obj_mingw32-mpi

13
lib/meam/Makefile.mingw64-cross-mpi
View File

@ -1,13 +0,0 @@
# -*- makefile -*- wrapper for non-MPI libraries
SHELL=/bin/sh
all:
$(MAKE) $(MFLAGS) mingw64-cross
-rm -f Obj_mingw64-mpi
ln -s Obj_mingw64 Obj_mingw64-mpi
clean:
$(MAKE) $(MFLAGS) clean-mingw64-cross
-rm -f Obj_mingw64-mpi

40
lib/meam/Makefile.mingw64-cross → lib/meam/Makefile.mpi
View File

@ -1,4 +1,4 @@
# * -*- makefile -*-
# *
# *_________________________________________________________________________*
# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
# * DESCRIPTION: SEE READ-ME *
@ -11,7 +11,7 @@ SHELL = /bin/sh
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.gfortran
EXTRAMAKE = Makefile.lammps.empty
# ------ FILES ------
@ -21,49 +21,41 @@ FILES = $(SRC) Makefile
# ------ DEFINITIONS ------
DIR = Obj_mingw64/
LIB = $(DIR)libmeam.a
OBJ = $(SRC:%.F=$(DIR)%.o) $(DIR)fm_exp.o
LIB = libmeam.a
OBJ = $(SRC:.F=.o) fm_exp.o
# ------ SETTINGS ------
F90 = x86_64-w64-mingw32-gfortran
F90FLAGS = -O3 -march=core2 -mtune=core2 -msse2 -mpc64 \
-ffast-math -funroll-loops -fstrict-aliasing -J$(DIR) \
-Wall -W -Wno-uninitialized -fno-second-underscore
F90 = mpifort
CC = mpicc
F90FLAGS = -O3 -fPIC
#F90FLAGS = -O
ARCHIVE = x86_64-w64-mingw32-ar
ARCHFLAG = -rcs
LINK = x86_64-w64-mingw32-g++
ARCHIVE = ar
ARCHFLAG = -rc
LINK = mpicxx
LINKFLAGS = -O
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
default: $(DIR) $(LIB)
$(DIR):
-mkdir $(DIR)
$(LIB): $(OBJ)
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
# ------ COMPILE RULES ------
$(DIR)%.o:%.F
$(F90) $(F90FLAGS) -c $< -o $@
%.o:%.F
$(F90) $(F90FLAGS) -c $<
$(DIR)%.o:%.c
$(F90) $(F90FLAGS) -c $< -o $@
%.o:%.c
$(CC) $(F90FLAGS) -c $<
include .depend
# ------ CLEAN ------
clean:
-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
-rmdir $(DIR)
-rm *.o *.mod *~ $(LIB)
tar:
-tar -cvf ../MEAM.tar $(FILES)

1
lib/meam/Makefile.serial Symbolic link
View File

@ -0,0 +1 @@
Makefile.gfortran

4
lib/mscg/.gitignore vendored Normal file
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@ -0,0 +1,4 @@
# files to ignore
/liblink
/includelink
/MSCG-release-master

154
lib/mscg/Install.py
View File

@ -3,53 +3,55 @@
# Install.py tool to download, unpack, build, and link to the MS-CG library
# used to automate the steps described in the README file in this dir
import sys,os,re,commands
from __future__ import print_function
import sys,os,re,subprocess
# help message
help = """
Syntax from src dir: make lib-mscg args="-h hpath hdir -g -b [suffix] -l"
Syntax from lib dir: python Install.py -h hpath hdir -g -b [suffix] -l
Syntax from src dir: make lib-mscg args="-p [path] -m [suffix]"
or: make lib-mscg args="-b -m [suffix]"
Syntax from lib dir: python Install.py -p [path] -m [suffix]
Syntax from lib dir: python Install.py -b -m [suffix]
specify one or more options, order does not matter
-h = set home dir of MS-CG to be hpath/hdir
hpath can be full path, contain '~' or '.' chars
default hpath = . = lib/mscg
default hdir = MSCG-release-master = what GitHub zipfile unpacks to
-g = grab (download) zipfile from MS-CG GitHub website
unpack it to hpath/hdir
hpath must already exist
if hdir already exists, it will be deleted before unpack
-b = build MS-CG library in its src dir
optional suffix specifies which src/Make/Makefile.suffix to use
-b = download and build MS-CG library
-p = specify folder of existing MS-CG installation
-m = machine suffix specifies which src/Make/Makefile.suffix to use
default suffix = g++_simple
-l = create 2 softlinks (includelink,liblink) in lib/mscg to MS-CG src dir
Example:
make lib-mscg args="-g -b -l" # download/build in lib/mscg/MSCG-release-master
make lib-mscg args="-b -m serial " # download/build in lib/mscg/MSCG-release-master with settings compatible with "make serial"
make lib-mscg args="-b -m mpi " # download/build in lib/mscg/MSCG-release-master with settings compatible with "make mpi"
make lib-mscg args="-p /usr/local/mscg-release " # use existing MS-CG installation in /usr/local/mscg-release
"""
# settings
url = "https://github.com/uchicago-voth/MSCG-release/archive/master.zip"
zipfile = "MS-CG-master.zip"
zipdir = "MSCG-release-master"
url = "http://github.com/uchicago-voth/MSCG-release/archive/master.tar.gz"
tarfile = "MS-CG-master.tar.gz"
tardir = "MSCG-release-master"
# print error message or help
def error(str=None):
if not str: print help
else: print "ERROR",str
if not str: print(help)
else: print("ERROR",str)
sys.exit()
# expand to full path name
# process leading '~' or relative path
def fullpath(path):
return os.path.abspath(os.path.expanduser(path))
def geturl(url,fname):
cmd = 'curl -L -o "%s" %s' % (fname,url)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
return txt
# parse args
args = sys.argv[1:]
@ -57,73 +59,93 @@ nargs = len(args)
if nargs == 0: error()
homepath = "."
homedir = zipdir
homedir = tardir
grabflag = 0
buildflag = 0
buildflag = False
pathflag = False
linkflag = True
msuffix = "g++_simple"
linkflag = 0
iarg = 0
while iarg < nargs:
if args[iarg] == "-h":
if iarg+3 > nargs: error()
homepath = args[iarg+1]
homedir = args[iarg+2]
iarg += 3
elif args[iarg] == "-g":
grabflag = 1
iarg += 1
if args[iarg] == "-p":
if iarg+2 > nargs: error()
mscgpath = fullpath(args[iarg+1])
pathflag = True
iarg += 2
elif args[iarg] == "-m":
if iarg+2 > nargs: error()
msuffix = args[iarg+1]
iarg += 2
elif args[iarg] == "-b":
buildflag = 1
if iarg+1 < nargs and args[iarg+1][0] != '-':
msuffix = args[iarg+1]
iarg += 1
iarg += 1
elif args[iarg] == "-l":
linkflag = 1
buildflag = True
iarg += 1
else: error()
homepath = fullpath(homepath)
if not os.path.isdir(homepath): error("MS-CG path does not exist")
homedir = "%s/%s" % (homepath,homedir)
# download and unpack MS-CG zipfile
if (pathflag):
if not os.path.isdir(mscgpath): error("MS-CG path does not exist")
homedir = mscgpath
if grabflag:
print "Downloading MS-CG ..."
cmd = "curl -L %s > %s/%s" % (url,homepath,zipfile)
print cmd
print commands.getoutput(cmd)
if (buildflag and pathflag):
error("Cannot use -b and -p flag at the same time")
print "Unpacking MS-CG zipfile ..."
if os.path.exists("%s/%s" % (homepath,zipdir)):
commands.getoutput("rm -rf %s/%s" % (homepath,zipdir))
cmd = "cd %s; unzip %s" % (homepath,zipfile)
commands.getoutput(cmd)
if os.path.basename(homedir) != zipdir:
if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
os.rename("%s/%s" % (homepath,zipdir),homedir)
if (not buildflag and not pathflag):
error("Have to use either -b or -p flag")
# download and unpack MS-CG tarfile
if buildflag:
print("Downloading MS-CG ...")
geturl(url,"%s/%s" % (homepath,tarfile))
print("Unpacking MS-CG tarfile ...")
if os.path.exists("%s/%s" % (homepath,tardir)):
cmd = 'rm -rf "%s/%s"' % (homepath,tardir)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = 'cd "%s"; tar -xzvf %s' % (homepath,tarfile)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
os.remove("%s/%s" % (homepath,tarfile))
if os.path.basename(homedir) != tardir:
if os.path.exists(homedir):
cmd = 'rm -rf "%s"' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
os.rename("%s/%s" % (homepath,tardir),homedir)
# build MS-CG
if buildflag:
print "Building MS-CG ..."
cmd = "cd %s/src; cp Make/Makefile.%s .; make -f Makefile.%s" % \
(homedir,msuffix,msuffix)
txt = commands.getoutput(cmd)
print txt
print("Building MS-CG ...")
if os.path.exists("%s/src/Make/Makefile.%s" % (homedir,msuffix)):
cmd = 'cd "%s/src"; cp Make/Makefile.%s .; make -f Makefile.%s' % \
(homedir,msuffix,msuffix)
elif os.path.exists("Makefile.%s" % msuffix):
cmd = 'cd "%s/src"; cp ../../Makefile.%s .; make -f Makefile.%s' % \
(homedir,msuffix,msuffix)
else:
error("Cannot find Makefile.%s" % msuffix)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print(txt.decode('UTF-8'))
if not os.path.exists("Makefile.lammps"):
print("Creating Makefile.lammps")
if os.path.exists("Makefile.lammps.%s" % msuffix):
cmd = 'cp Makefile.lammps.%s Makefile.lammps' % msuffix
else:
cmd = 'cp Makefile.lammps.default Makefile.lammps'
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
else: print("Makefile.lammps exists. Please check its settings")
# create 2 links in lib/mscg to MS-CG src dir
if linkflag:
print "Creating links to MS-CG include and lib files"
print("Creating links to MS-CG include and lib files")
if os.path.isfile("includelink") or os.path.islink("includelink"):
os.remove("includelink")
if os.path.isfile("liblink") or os.path.islink("liblink"):
os.remove("liblink")
cmd = "ln -s %s/src includelink" % homedir
commands.getoutput(cmd)
cmd = "ln -s %s/src liblink" % homedir
commands.getoutput(cmd)
cmd = 'ln -s "%s/src" includelink' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = 'ln -s "%s/src" liblink' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

5
lib/mscg/Makefile.lammps.default Normal file
View File

@ -0,0 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
mscg_SYSINC =
mscg_SYSLIB = -lgsl -lgslcblas
mscg_SYSPATH =

0
lib/mscg/Makefile.lammps → lib/mscg/Makefile.lammps.g++_simple
View File

5
lib/mscg/Makefile.lammps.mpi Normal file
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@ -0,0 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
mscg_SYSINC =
mscg_SYSLIB = -lgsl -lgslcblas
mscg_SYSPATH =

5
lib/mscg/Makefile.lammps.serial Normal file
View File

@ -0,0 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
mscg_SYSINC =
mscg_SYSLIB = -lgsl -lgslcblas
mscg_SYSPATH =

104
lib/mscg/Makefile.mpi Normal file
View File

@ -0,0 +1,104 @@
# This Makefile is meant for use after
# module load gsl/2.2.1+gcc-6.1
# module load gcc/6.1
# It also requires LAPACK
# Module names refer to those on any of RCC's clusters at UChicago.
# This makefile does NOT include GROMACS reading or MKL (sparse matrix)
# It uses the gcc/g++ compiler (v4.9+) for C++11 support
# 1) Try this first (as it is the easiest)
NO_GRO_LIBS = -lgsl -lgslcblas
# 2) If it does not find your libraries automatically, you can specify them manually
# # A) Set the GSL_LIB to the location of your GSL library's lib directory (must be V2+)
GSL_LIB = /software/gsl-2.2.1-el6-x86_64+gcc-6.1/lib
# # B) Set the LAPACK_DIR to the location of your LAPACK library base directory
LAPACK_LIB = $(HOME)/local/lapack-3.7.0
# # C) Uncomment this next line and then run again (after cleaning up any object files)
#NO_GRO_LIBS = -L$(GSL_LIB) -L$(LAPACK_LIB) -lgsl -lgslcblas -llapack -lm
OPT = -O2
NO_GRO_LDFLAGS = $(OPT)
NO_GRO_CFLAGS = $(OPT)
DIMENSION = 3
CC = mpicc
COMMON_SOURCE = control_input.h fm_output.h force_computation.h geometry.h interaction_hashing.h interaction_model.h matrix.h splines.h topology.h trajectory_input.h misc.h mscg.h
NO_GRO_COMMON_OBJECTS = control_input.o fm_output.o force_computation.o geometry.o interaction_hashing.o interaction_model.o matrix.o splines.o topology.o trajectory_input_no_gro.o misc.o
# Target executables
# The library for LAMMPS is lib_mscg.a
libmscg.a: mscg.o $(NO_GRO_COMMON_OBJECTS)
ar rvs libmscg.a *.o
newfm_no_gro.x: newfm.o $(NO_GRO_COMMON_OBJECTS)
$(CC) $(NO_GRO_LDFLAGS) -o $@ newfm.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
combinefm_no_gro.x: combinefm.o batch_fm_combination.o $(NO_GRO_COMMON_OBJECTS)
$(CC) $(NO_GRO_LDFLAGS) -o $@ combinefm.o batch_fm_combination.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
rangefinder_no_gro.x: rangefinder.o range_finding.o $(NO_GRO_COMMON_OBJECTS)
$(CC) $(NO_GRO_LDFLAGS) -o $@ rangefinder.o range_finding.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
# Target objects
mscg.o: mscg.cpp $(COMMON_SOURCE) range_finding.o
$(CC) $(NO_GRO_CFLAGS) -c mscg.cpp -o mscg.o $(NO_GRO_LIBS)
newfm.o: newfm.cpp $(COMMON_SOURCE)
$(CC) $(NO_GRO_CFLAGS) -c newfm.cpp
combinefm.o: combinefm.cpp batch_fm_combination.h $(COMMON_SOURCE)
$(CC) $(NO_GRO_CFLAGS) -c combinefm.cpp
rangefinder.o: rangefinder.cpp range_finding.h $(COMMON_SOURCE)
$(CC) $(NO_GRO_CFLAGS) -c rangefinder.cpp
scalarfm.o: scalarfm.cpp $(COMMON_SOURCE)
$(CC) $(NO_GRO_CFLAGS) -c scalarfm.cpp
batch_fm_combination.o: batch_fm_combination.cpp batch_fm_combination.h external_matrix_routines.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c batch_fm_combination.cpp
control_input.o: control_input.cpp control_input.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c control_input.cpp
geometry.o: geometry.cpp geometry.h
$(CC) $(NO_GRO_CFLAGS) -c geometry.cpp -DDIMENSION=$(DIMENSION)
fm_output.o: fm_output.cpp fm_output.h force_computation.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c fm_output.cpp
force_computation.o: force_computation.cpp force_computation.h interaction_model.h matrix.h trajectory_input.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c force_computation.cpp -DDIMENSION=$(DIMENSION)
interaction_hashing.o: interaction_hashing.cpp interaction_hashing.h
$(CC) $(NO_GRO_CFLAGS) -c interaction_hashing.cpp
interaction_model.o: interaction_model.cpp interaction_model.h control_input.h interaction_hashing.h topology.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c interaction_model.cpp -DDIMENSION=$(DIMENSION)
matrix.o: matrix.cpp matrix.h control_input.h external_matrix_routines.h interaction_model.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c matrix.cpp -DDIMENSION=$(DIMENSION)
misc.o: misc.cpp misc.h
$(CC) $(NO_GRO_CFLAGS) -c misc.cpp
range_finding.o: range_finding.cpp range_finding.h force_computation.h interaction_model.h matrix.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c range_finding.cpp -DDIMENSION=$(DIMENSION)
splines.o: splines.cpp splines.h interaction_model.h
$(CC) $(NO_GRO_CFLAGS) -c splines.cpp -DDIMENSION=$(DIMENSION)
topology.o: topology.cpp topology.h interaction_model.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c topology.cpp -DDIMENSION=$(DIMENSION)
trajectory_input_no_gro.o: trajectory_input.cpp trajectory_input.h control_input.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c trajectory_input.cpp -D"_exclude_gromacs=1" -o trajectory_input_no_gro.o
# Other convenient commands
clean:
rm *.[o]
all: libmscg.a newfm_no_gro.x rangefinder_no_gro.x combinefm_no_gro.x

104
lib/mscg/Makefile.serial Normal file
View File

@ -0,0 +1,104 @@
# This Makefile is meant for use after
# module load gsl/2.2.1+gcc-6.1
# module load gcc/6.1
# It also requires LAPACK
# Module names refer to those on any of RCC's clusters at UChicago.
# This makefile does NOT include GROMACS reading or MKL (sparse matrix)
# It uses the gcc/g++ compiler (v4.9+) for C++11 support
# 1) Try this first (as it is the easiest)
NO_GRO_LIBS = -lgsl -lgslcblas
# 2) If it does not find your libraries automatically, you can specify them manually
# # A) Set the GSL_LIB to the location of your GSL library's lib directory (must be V2+)
GSL_LIB = /software/gsl-2.2.1-el6-x86_64+gcc-6.1/lib
# # B) Set the LAPACK_DIR to the location of your LAPACK library base directory
LAPACK_LIB = $(HOME)/local/lapack-3.7.0
# # C) Uncomment this next line and then run again (after cleaning up any object files)
#NO_GRO_LIBS = -L$(GSL_LIB) -L$(LAPACK_LIB) -lgsl -lgslcblas -llapack -lm
OPT = -O2
NO_GRO_LDFLAGS = $(OPT)
NO_GRO_CFLAGS = $(OPT)
DIMENSION = 3
CC = g++
COMMON_SOURCE = control_input.h fm_output.h force_computation.h geometry.h interaction_hashing.h interaction_model.h matrix.h splines.h topology.h trajectory_input.h misc.h mscg.h
NO_GRO_COMMON_OBJECTS = control_input.o fm_output.o force_computation.o geometry.o interaction_hashing.o interaction_model.o matrix.o splines.o topology.o trajectory_input_no_gro.o misc.o
# Target executables
# The library for LAMMPS is lib_mscg.a
libmscg.a: mscg.o $(NO_GRO_COMMON_OBJECTS)
ar rvs libmscg.a *.o
newfm_no_gro.x: newfm.o $(NO_GRO_COMMON_OBJECTS)
$(CC) $(NO_GRO_LDFLAGS) -o $@ newfm.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
combinefm_no_gro.x: combinefm.o batch_fm_combination.o $(NO_GRO_COMMON_OBJECTS)
$(CC) $(NO_GRO_LDFLAGS) -o $@ combinefm.o batch_fm_combination.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
rangefinder_no_gro.x: rangefinder.o range_finding.o $(NO_GRO_COMMON_OBJECTS)
$(CC) $(NO_GRO_LDFLAGS) -o $@ rangefinder.o range_finding.o $(NO_GRO_COMMON_OBJECTS) -D"_exclude_gromacs=1" $(NO_GRO_LIBS)
# Target objects
mscg.o: mscg.cpp $(COMMON_SOURCE) range_finding.o
$(CC) $(NO_GRO_CFLAGS) -c mscg.cpp -o mscg.o $(NO_GRO_LIBS)
newfm.o: newfm.cpp $(COMMON_SOURCE)
$(CC) $(NO_GRO_CFLAGS) -c newfm.cpp
combinefm.o: combinefm.cpp batch_fm_combination.h $(COMMON_SOURCE)
$(CC) $(NO_GRO_CFLAGS) -c combinefm.cpp
rangefinder.o: rangefinder.cpp range_finding.h $(COMMON_SOURCE)
$(CC) $(NO_GRO_CFLAGS) -c rangefinder.cpp
scalarfm.o: scalarfm.cpp $(COMMON_SOURCE)
$(CC) $(NO_GRO_CFLAGS) -c scalarfm.cpp
batch_fm_combination.o: batch_fm_combination.cpp batch_fm_combination.h external_matrix_routines.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c batch_fm_combination.cpp
control_input.o: control_input.cpp control_input.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c control_input.cpp
geometry.o: geometry.cpp geometry.h
$(CC) $(NO_GRO_CFLAGS) -c geometry.cpp -DDIMENSION=$(DIMENSION)
fm_output.o: fm_output.cpp fm_output.h force_computation.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c fm_output.cpp
force_computation.o: force_computation.cpp force_computation.h interaction_model.h matrix.h trajectory_input.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c force_computation.cpp -DDIMENSION=$(DIMENSION)
interaction_hashing.o: interaction_hashing.cpp interaction_hashing.h
$(CC) $(NO_GRO_CFLAGS) -c interaction_hashing.cpp
interaction_model.o: interaction_model.cpp interaction_model.h control_input.h interaction_hashing.h topology.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c interaction_model.cpp -DDIMENSION=$(DIMENSION)
matrix.o: matrix.cpp matrix.h control_input.h external_matrix_routines.h interaction_model.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c matrix.cpp -DDIMENSION=$(DIMENSION)
misc.o: misc.cpp misc.h
$(CC) $(NO_GRO_CFLAGS) -c misc.cpp
range_finding.o: range_finding.cpp range_finding.h force_computation.h interaction_model.h matrix.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c range_finding.cpp -DDIMENSION=$(DIMENSION)
splines.o: splines.cpp splines.h interaction_model.h
$(CC) $(NO_GRO_CFLAGS) -c splines.cpp -DDIMENSION=$(DIMENSION)
topology.o: topology.cpp topology.h interaction_model.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c topology.cpp -DDIMENSION=$(DIMENSION)
trajectory_input_no_gro.o: trajectory_input.cpp trajectory_input.h control_input.h misc.h
$(CC) $(NO_GRO_CFLAGS) -c trajectory_input.cpp -D"_exclude_gromacs=1" -o trajectory_input_no_gro.o
# Other convenient commands
clean:
rm *.[o]
all: libmscg.a newfm_no_gro.x rangefinder_no_gro.x combinefm_no_gro.x

24
lib/mscg/README
View File

@ -6,12 +6,11 @@ The MS-CG library is available at
https://github.com/uchicago-voth/MSCG-release and was developed by
Jacob Wagner in Greg Voth's group at the University of Chicago.
This library requires a compiler with C++11 support (e.g., g++ v4.9+),
LAPACK, and the GNU scientific library (GSL v 2.1+).
This library requires a the GNU scientific library (GSL v 2.1+).
You can type "make lib-mscg" from the src directory to see help on how
to download and build this library via make commands, or you can do
the same thing by typing "python Install.py" from within this
the same thing by typing "python Install.py -m <machine>" from within this
directory, or you can do it manually by following the instructions
below.
@ -21,17 +20,17 @@ You must perform the following steps yourself.
1. Download MS-CG at https://github.com/uchicago-voth/MSCG-release
either as a tarball or via SVN, and unpack the tarball either in
this /lib/mscg directory or somewhere else on your system.
this lib/mscg directory or somewhere else on your system.
2. Ensure that you have GSL installed and a compiler with support for C++11.
2. Ensure that you have LAPACK and GSL (or Intel MKL) as well as a compiler
with support for C++11.
3. Compile MS-CG from within its home directory using your makefile of choice:
% make -f Makefile."name" libmscg.a
It is recommended that you start with Makefile.g++_simple
for most machines
% make -f Makefile.<machine> libmscg.a
It is recommended that you start with Makefile.g++_simple for
most machines. There are also two Makefile with settings matching
the "mpi" and "serial" makefiles in the main LAMMPS folder.
4. There is no need to install MS-CG if you only wish
4. There is no need to install MS-CG system-wide if you only wish
to use it from LAMMPS.
5. Create two soft links in this dir (lib/mscg) to the MS-CG src
@ -43,6 +42,9 @@ You must perform the following steps yourself.
% ln -s /usr/local/include includelink
% ln -s /usr/local/lib liblink
6. Copy a suitable Makefile.lammps.<machine> to Makefile.lammps or
copy Makefile.lammps.default to Makefile.lammps and edit as needed.
-----------------
When these steps are complete you can build LAMMPS with the MS-CG

2
lib/poems/Makefile.g++
View File

@ -68,7 +68,7 @@ OBJ = $(SRC:.cpp=.o)
# ------ SETTINGS ------
CC = g++
CCFLAGS = -O -g -fPIC -Wall #-Wno-deprecated
CCFLAGS = -O3 -g -fPIC -Wall #-Wno-deprecated
ARCHIVE = ar
ARCHFLAG = -rc
DEPFLAGS = -M

110
lib/poems/Makefile.mingw32-cross
View File

@ -1,110 +0,0 @@
# *
# *_________________________________________________________________________*
# * POEMS: PARALLELIZABLE OPEN SOURCE EFFICIENT MULTIBODY SOFTWARE *
# * DESCRIPTION: SEE READ-ME *
# * FILE NAME: Makefile *
# * AUTHORS: See Author List *
# * GRANTS: See Grants List *
# * COPYRIGHT: (C) 2005 by Authors as listed in Author's List *
# * LICENSE: Please see License Agreement *
# * DOWNLOAD: Free at www.rpi.edu/~anderk5 *
# * ADMINISTRATOR: Prof. Kurt Anderson *
# * Computational Dynamics Lab *
# * Rensselaer Polytechnic Institute *
# * 110 8th St. Troy NY 12180 *
# * CONTACT: anderk5@rpi.edu *
# *_________________________________________________________________________*/
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.empty
# ------ FILES ------
SRC_MAIN = workspace.cpp system.cpp poemsobject.cpp
INC_MAIN = workspace.h system.h poemsobject.h
SRC_BODY = body.cpp rigidbody.cpp particle.cpp inertialframe.cpp
INC_BODY = bodies.h body.h rigidbody.h particle.h inertialframe.h
SRC_JOINT = joint.cpp revolutejoint.cpp prismaticjoint.cpp sphericaljoint.cpp \
freebodyjoint.cpp body23joint.cpp mixedjoint.cpp
INC_JOINT = joints.h joint.h revolutejoint.h prismaticjoint.h sphericaljoint.h \
freebodyjoint.h body23joint.h mixedjoint.h
SRC_POINT = point.cpp fixedpoint.cpp
INC_POINT = points.h point.h fixedpoint.h
SRC_SOLVE = solver.cpp
INC_SOLVE = solver.h
SRC_ORDERN = onsolver.cpp onfunctions.cpp onbody.cpp
INC_ORDERN = onsolver.h onfunctions.h onbody.h
SRC_MAT = virtualmatrix.cpp matrix.cpp matrixfun.cpp mat3x3.cpp virtualcolmatrix.cpp \
colmatrix.cpp vect3.cpp virtualrowmatrix.cpp rowmatrix.cpp mat6x6.cpp vect6.cpp \
fastmatrixops.cpp colmatmap.cpp eulerparameters.cpp vect4.cpp norm.cpp mat4x4.cpp \
INC_MAT = matrices.h virtualmatrix.h matrix.h matrixfun.h mat3x3.h virtualcolmatrix.h \
colmatrix.h vect3.h virtualrowmatrix.h rowmatrix.h mat6x6.h vect6.h \
fastmatrixops.h colmatmap.h eulerparameters.h vect4.h norm.h mat4x4.h
SRC_MISC = poemstreenode.cpp
INC_MISC = poemslist.h poemstreenode.h poemstree.h poemsnodelib.h SystemProcessor.h defines.h POEMSChain.h
SRC = $(SRC_MAIN) $(SRC_BODY) $(SRC_JOINT) $(SRC_POINT) $(SRC_SOLVE) $(SRC_ORDERN) $(SRC_MAT) $(SRC_MISC)
INC = $(INC_MAIN) $(INC_BODY) $(INC_JOINT) $(INC_POINT) $(INC_SOLVE) $(INC_ORDERN) $(INC_MAT) $(INC_MISC)
FILES = $(SRC) $(INC) Makefile Authors_List.txt Grants_List.txt POEMS_License.txt README Copyright_Notice
# ------ DEFINITIONS ------
DIR = Obj_mingw32/
LIB = $(DIR)libpoems.a
OBJ = $(SRC:%.cpp=$(DIR)%.o)
# ------ SETTINGS ------
CC = i686-w64-mingw32-g++
CCFLAGS = -O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
-ffast-math -funroll-loops -finline-functions -fno-rtti \
-fno-exceptions -fstrict-aliasing \
-Wall -W -Wno-uninitialized
ARCHIVE = i686-w64-mingw32-ar
ARCHFLAG = -rcs
DEPFLAGS = -M
LINK = i686-w64-mingw32-g++
LINKFLAGS = -O
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
default: $(DIR) $(LIB)
$(DIR):
-mkdir $(DIR)
$(LIB): $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
# ------ COMPILE RULES ------
$(DIR)%.o:%.cpp
$(CC) $(CCFLAGS) -c $< -o $@
# ------ DEPENDENCIES ------
include .depend
# ------ CLEAN ------
clean:
-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
tar:
-tar -cvf ../POEMS.tar $(FILES)

13
lib/poems/Makefile.mingw32-cross-mpi
View File

@ -1,13 +0,0 @@
# -*- makefile -*- wrapper for non-MPI libraries
SHELL=/bin/sh
all:
$(MAKE) $(MFLAGS) mingw32-cross
-rm -f Obj_mingw32-mpi
ln -s Obj_mingw32 Obj_mingw32-mpi
clean:
$(MAKE) $(MFLAGS) clean-mingw32-cross
-rm -f Obj_mingw32-mpi

13
lib/poems/Makefile.mingw64-cross-mpi
View File

@ -1,13 +0,0 @@
# -*- makefile -*- wrapper for non-MPI libraries
SHELL=/bin/sh
all:
$(MAKE) $(MFLAGS) mingw64-cross
-rm -f Obj_mingw64-mpi
ln -s Obj_mingw64 Obj_mingw64-mpi
clean:
$(MAKE) $(MFLAGS) clean-mingw64-cross
-rm -f Obj_mingw64-mpi

31
lib/poems/Makefile.mingw64-cross → lib/poems/Makefile.mpi
View File

@ -62,40 +62,31 @@ FILES = $(SRC) $(INC) Makefile Authors_List.txt Grants_List.txt POEMS_License.tx
# ------ DEFINITIONS ------
DIR = Obj_mingw64/
LIB = $(DIR)libpoems.a
OBJ = $(SRC:%.cpp=$(DIR)%.o)
LIB = libpoems.a
OBJ = $(SRC:.cpp=.o)
# ------ SETTINGS ------
CC = x86_64-w64-mingw32-g++
CCFLAGS = -O2 -march=core2 -mtune=core2 -msse2 -mpc64 \
-ffast-math -funroll-loops -finline-functions -fno-rtti \
-fno-exceptions -fstrict-aliasing \
-Wall -W -Wno-uninitialized
ARCHIVE = x86_64-w64-mingw32-ar
ARCHFLAG = -rcs
CC = mpicxx
CCFLAGS = -O3 -g -fPIC -Wall #-Wno-deprecated
ARCHIVE = ar
ARCHFLAG = -rc
DEPFLAGS = -M
LINK = x86_64-w64-mingw32-g++
LINK = mpicxx
LINKFLAGS = -O
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
default: $(DIR) $(LIB)
$(DIR):
-mkdir $(DIR)
$(LIB): $(OBJ)
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
# ------ COMPILE RULES ------
$(DIR)%.o:%.cpp
$(CC) $(CCFLAGS) -c $< -o $@
%.o:%.cpp
$(CC) $(CCFLAGS) -c $<
# ------ DEPENDENCIES ------
@ -104,7 +95,7 @@ include .depend
# ------ CLEAN ------
clean:
-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-rm *.o *.d *~ $(LIB)
tar:
-tar -cvf ../POEMS.tar $(FILES)

1
lib/poems/Makefile.serial Symbolic link
View File

@ -0,0 +1 @@
Makefile.g++

66
lib/qmmm/Makefile.mpi Normal file
View File

@ -0,0 +1,66 @@
# -*- Makefile -*- for coupling LAMMPS to PWscf for QM/MM molecular dynamics
# this file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.empty
# top level directory of Quantum ESPRESSO 5.4.1 or later
QETOPDIR=$(HOME)/compile/espresso
# import compiler settings from Quantum ESPRESSO
sinclude $(QETOPDIR)/make.sys
# FLAGS for c++ OpenMPI 1.8.8 or later when QE was compiled with GNU Fortran 4.x
MPICXX=mpicxx
MPICXXFLAGS= -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -O2 -g -fPIC\
-I../../src -I$(QETOPDIR)/COUPLE/include
MPILIBS=-fopenmp -lgfortran -ldl -ljpeg -lpng -lz -lmpi_mpifh -lmpi
# location of required libraries
# part 1: hi-level libraries for building pw.x
PWOBJS = \
$(QETOPDIR)/COUPLE/src/libqecouple.a \
$(QETOPDIR)/PW/src/libpw.a \
$(QETOPDIR)/Modules/libqemod.a
# part 2: lo-level libraries for all of Q-E
LIBOBJS = \
$(QETOPDIR)/FFTXlib/libqefft.a \
$(QETOPDIR)/LAXlib/libqela.a \
$(QETOPDIR)/clib/clib.a \
$(QETOPDIR)/iotk/src/libiotk.a
# part 3: add-on libraries and main library for LAMMPS
sinclude ../../src/Makefile.package
LAMMPSCFG = mpi
LAMMPSLIB = ../../src/liblammps_$(LAMMPSCFG).a
# part 4: local QM/MM library and progams
SRC=pwqmmm.c libqmmm.c
OBJ=$(SRC:%.c=%.o)
default: libqmmm.a
all : tldeps libqmmm.a pwqmmm.x
pwqmmm.x : pwqmmm.o $(OBJ) $(PWOBJS) $(LIBOBJS) $(LAMMPSLIB)
$(MPICXX) $(LDFLAGS) -o $@ $^ $(PKG_PATH) $(PKG_LIB) $(MPILIBS) $(LIBS)
libqmmm.a: libqmmm.o
$(AR) $(ARFLAGS) $@ $^
@cp $(EXTRAMAKE) Makefile.lammps
%.o: %.c
$(MPICXX) -c $(LAMMPSFLAGS) $(MPICXXFLAGS) $< -o $@
tldeps:
( cd $(QETOPDIR) ; $(MAKE) $(MFLAGS) couple || exit 1)
$(MAKE) -C ../../src $(MFLAGS) $(LAMMPSCFG)
$(MAKE) -C ../../src $(MFLAGS) mode=lib $(LAMMPSCFG)
clean :
-rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
# explicit dependencies
pwqmmm.o: pwqmmm.c libqmmm.h
libqmmm.o: libqmmm.c libqmmm.h

66
lib/qmmm/Makefile.serial Normal file
View File

@ -0,0 +1,66 @@
# -*- Makefile -*- for coupling LAMMPS to PWscf for QM/MM molecular dynamics
# this file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.empty
# top level directory of Quantum ESPRESSO 5.4.1 or later
QETOPDIR=$(HOME)/compile/espresso
# import compiler settings from Quantum ESPRESSO
sinclude $(QETOPDIR)/make.sys
# FLAGS for GNU c++ with STUBS. non-functional for real coupling
MPICXX=g++
MPICXXFLAGS= -I../../src/STUBS -O2 -g -fPIC\
-I../../src -I$(QETOPDIR)/COUPLE/include
MPILIBS=-fopenmp -lgfortran -ldl -ljpeg -lpng -lz -lmpi_mpifh -lmpi
# location of required libraries
# part 1: hi-level libraries for building pw.x
PWOBJS = \
$(QETOPDIR)/COUPLE/src/libqecouple.a \
$(QETOPDIR)/PW/src/libpw.a \
$(QETOPDIR)/Modules/libqemod.a
# part 2: lo-level libraries for all of Q-E
LIBOBJS = \
$(QETOPDIR)/FFTXlib/libqefft.a \
$(QETOPDIR)/LAXlib/libqela.a \
$(QETOPDIR)/clib/clib.a \
$(QETOPDIR)/iotk/src/libiotk.a
# part 3: add-on libraries and main library for LAMMPS
sinclude ../../src/Makefile.package
LAMMPSCFG = mpi
LAMMPSLIB = ../../src/liblammps_$(LAMMPSCFG).a
# part 4: local QM/MM library and progams
SRC=pwqmmm.c libqmmm.c
OBJ=$(SRC:%.c=%.o)
default: libqmmm.a
all : tldeps libqmmm.a pwqmmm.x
pwqmmm.x : pwqmmm.o $(OBJ) $(PWOBJS) $(LIBOBJS) $(LAMMPSLIB)
$(MPICXX) $(LDFLAGS) -o $@ $^ $(PKG_PATH) $(PKG_LIB) $(MPILIBS) $(LIBS)
libqmmm.a: libqmmm.o
$(AR) $(ARFLAGS) $@ $^
@cp $(EXTRAMAKE) Makefile.lammps
%.o: %.c
$(MPICXX) -c $(LAMMPSFLAGS) $(MPICXXFLAGS) $< -o $@
tldeps:
( cd $(QETOPDIR) ; $(MAKE) $(MFLAGS) couple || exit 1)
$(MAKE) -C ../../src $(MFLAGS) $(LAMMPSCFG)
$(MAKE) -C ../../src $(MFLAGS) mode=lib $(LAMMPSCFG)
clean :
-rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
# explicit dependencies
pwqmmm.o: pwqmmm.c libqmmm.h
libqmmm.o: libqmmm.c libqmmm.h

2
lib/reax/Makefile.gfortran
View File

@ -28,7 +28,7 @@ OBJ = $(SRC:.F=.o)
# ------ SETTINGS ------
F90 = gfortran
F90FLAGS = -O -fPIC -fno-second-underscore
F90FLAGS = -O3 -fPIC -fno-second-underscore
ARCHIVE = ar
ARCHFLAG = -rc
USRLIB =

5
lib/reax/Makefile.lammps.empty Normal file
View File

@ -0,0 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
reax_SYSINC =
reax_SYSLIB =
reax_SYSPATH =

51
lib/reax/Makefile.mpi Normal file
View File

@ -0,0 +1,51 @@
# *
# *_________________________________________________________________________*
# * Fortran Library for Reactive Force Field *
# * DESCRIPTION: SEE READ-ME *
# * FILE NAME: Makefile *
# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
# * and Greg Wagner(SNL) *
# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
# *_________________________________________________________________________*/
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.empty
# ------ FILES ------
SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
HEADERFILES = reax_defs.h *.blk
# ------ DEFINITIONS ------
LIB = libreax.a
OBJ = $(SRC:.F=.o)
# ------ SETTINGS ------
F90 = mpifort
F90FLAGS = -O3 -fPIC
ARCHIVE = ar
ARCHFLAG = -rc
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
# ------ COMPILE RULES ------
%.o:%.F $(HEADERFILES)
$(F90) $(F90FLAGS) -c $<
# ------ CLEAN ------
clean:
-rm *.o $(LIB)

1
lib/reax/Makefile.serial Symbolic link
View File

@ -0,0 +1 @@
Makefile.gfortran

26
lib/smd/Install.py
View File

@ -5,22 +5,20 @@
from __future__ import print_function
import sys,os,re,glob,subprocess
try: from urllib.request import urlretrieve as geturl
except: from urllib import urlretrieve as geturl
# help message
help = """
Syntax from src dir: make lib-smd
Syntax from src dir: make lib-smd args="-b"
or: make lib-smd args="-p /usr/include/eigen3"
Syntax from lib dir: python Install.py
Syntax from lib dir: python Install.py -b
or: python Install.py -p /usr/include/eigen3"
or: python Install.py -v 3.3.4 -b
specify one or more options, order does not matter
-b = download and unpack/configure the Eigen library (default)
-b = download and unpack/configure the Eigen library
-p = specify folder holding an existing installation of Eigen
-v = set version of Eigen library to download and set up (default = 3.3.4)
@ -28,6 +26,7 @@ specify one or more options, order does not matter
Example:
make lib-smd args="-b" # download/build in default lib/smd/eigen-eigen-*
make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
"""
# settings
@ -48,16 +47,21 @@ def error(str=None):
def fullpath(path):
return os.path.abspath(os.path.expanduser(path))
def geturl(url,fname):
cmd = 'curl -L -o "%s" %s' % (fname,url)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
return txt
# parse args
args = sys.argv[1:]
nargs = len(args)
if nargs == 0: error()
homepath = "."
homedir = "eigen3"
grabflag = True
buildflag = True
buildflag = False
pathflag = False
linkflag = True
@ -71,7 +75,6 @@ while iarg < nargs:
if iarg+2 > nargs: error()
eigenpath = fullpath(args[iarg+1])
pathflag = True
buildflag = False
iarg += 2
elif args[iarg] == "-b":
buildflag = True
@ -86,6 +89,9 @@ if (pathflag):
if (buildflag and pathflag):
error("Cannot use -b and -p flag at the same time")
if (not buildflag and not pathflag):
error("Have to use either -b or -p flag")
# download and unpack Eigen tarball
# use glob to find name of dir it unpacks to
@ -98,7 +104,7 @@ if buildflag:
edir = glob.glob("%s/eigen-eigen-*" % homepath)
for one in edir:
if os.path.isdir(one):
subprocess.check_output("rm -rf %s" % one,stderr=subprocess.STDOUT,shell=True)
subprocess.check_output('rm -rf "%s"' % one,stderr=subprocess.STDOUT,shell=True)
cmd = 'cd "%s"; tar -xzvf %s' % (homepath,tarball)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
edir = glob.glob("%s/eigen-eigen-*" % homepath)
@ -113,5 +119,5 @@ if linkflag:
os.remove("includelink")
if pathflag: linkdir = eigenpath
else: linkdir = "%s/%s" % (homepath,homedir)
cmd = "ln -s %s includelink" % linkdir
cmd = 'ln -s "%s" includelink' % linkdir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

2
lib/smd/Makefile.lammps
View File

@ -1,5 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
user-smd_SYSINC =
user-smd_SYSINC = -I../../lib/includelink/eigen3
user-smd_SYSLIB =
user-smd_SYSPATH =

34
lib/voronoi/Install.py
View File

@ -5,28 +5,27 @@
from __future__ import print_function
import sys,os,re,subprocess
try: from urllib.request import urlretrieve as geturl
except: from urllib import urlretrieve as geturl
# help message
help = """
Syntax from src dir: make lib-voronoi
Syntax from src dir: make lib-voronoi args="-b"
or: make lib-voronoi args="-p /usr/local/voro++-0.4.6"
or: make lib-voronoi args="-v voro++-0.4.6 -b"
Syntax from lib dir: python Install.py -v voro++-0.4.6 -b
or: python Install.py
or: make lib-voronoi args="-b -v voro++-0.4.6"
Syntax from lib dir: python Install.py -b -v voro++-0.4.6
or: python Install.py -b
or: python Install.py -p /usr/local/voro++-0.4.6
specify one or more options, order does not matter
-b = download and build the Voro++ library (default)
-p = specify folder of existing Voro++ installation
-b = download and build the Voro++ library
-p = specify folder of existing Voro++ installation
-v = set version of Voro++ to download and build (default voro++-0.4.6)
Example:
make lib-voronoi args="-b" # download/build in lib/voronoi/voro++-0.4.6
make lib-voronoi args="-p $HOME/voro++-0.4.6" # use existing Voro++ installation in $HOME/voro++-0.4.6
"""
# settings
@ -47,16 +46,21 @@ def error(str=None):
def fullpath(path):
return os.path.abspath(os.path.expanduser(path))
def geturl(url,fname):
cmd = 'curl -L -o "%s" %s' % (fname,url)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
return txt
# parse args
args = sys.argv[1:]
nargs = len(args)
if nargs == 0: error()
homepath = "."
homedir = version
grabflag = True
buildflag = True
buildflag = False
pathflag = False
linkflag = True
@ -70,7 +74,6 @@ while iarg < nargs:
if iarg+2 > nargs: error()
voropath = fullpath(args[iarg+1])
pathflag = True
buildflag = False
iarg += 2
elif args[iarg] == "-b":
buildflag = True
@ -87,9 +90,12 @@ if (pathflag):
if (buildflag and pathflag):
error("Cannot use -b and -p flag at the same time")
if (not buildflag and not pathflag):
error("Have to use either -b or -p flag")
# download and unpack Voro++ tarball
if grabflag:
if buildflag:
print("Downloading Voro++ ...")
geturl(url,"%s/%s.tar.gz" % (homepath,version))
@ -122,7 +128,7 @@ if linkflag:
os.remove("includelink")
if os.path.isfile("liblink") or os.path.islink("liblink"):
os.remove("liblink")
cmd = ['ln -s "%s/src" includelink' % homedir, 'includelink']
cmd = 'ln -s "%s/src" includelink' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = ['ln -s "%s/src" liblink' % homedir]
cmd = 'ln -s "%s/src" liblink' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

1
src/MSCG/fix_mscg.cpp
View File

@ -19,6 +19,7 @@
#include <string.h>
#include <stdlib.h>
#include "fix_mscg.h"
#include "mscg.h"
#include "atom.h"
#include "domain.h"
#include "error.h"

1
src/MSCG/fix_mscg.h
View File

@ -21,7 +21,6 @@ FixStyle(mscg,FixMSCG)
#define LMP_FIX_MSCG_H
#include "fix.h"
#include "mscg.h"
namespace LAMMPS_NS {

6
src/Makefile
View File

@ -224,7 +224,7 @@ mpi-stubs:
@cd STUBS; $(MAKE) clean; $(MAKE)
# install LAMMPS shared lib and Python wrapper for Python usage
# include python package settings to
# include python package settings to
# automatically adapt name of python interpreter
sinclude ../lib/python/Makefile.lammps
@ -343,10 +343,10 @@ no-%:
lib-%:
@if [ -e ../lib/$(LIBDIR)/Install.py ]; then \
echo "Installing lib $(@:lib-%=%)"; \
cd ../lib/$(LIBDIR); python Install.py $(args); \
cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args); \
elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \
echo "Installing lib $(@:lib-user-%=%)"; \
cd ../lib/$(LIBUSERDIR); python Install.py $(args); \
cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args); \
else \
echo "Install script for lib $(@:lib-%=%) does not exist"; \
fi;