diff --git a/lib/.gitignore b/lib/.gitignore
index cbeae7705e8c95436cc956bd01e60ca0cd1caff7..4f9ebba6a5bcb570e8c9c9ad5ac23e93820b8fa9 100644
--- a/lib/.gitignore
+++ b/lib/.gitignore
@@ -1,2 +1,3 @@
Makefile.lammps
.depend
+Makefile.auto
diff --git a/lib/Install.py b/lib/Install.py
index 6b90254336b6b54adee6453a2ed249e576329640..d30cbffcf140ef3f8b0edfdfe902a78b819d39b3 100644
--- a/lib/Install.py
+++ b/lib/Install.py
@@ -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)
diff --git a/lib/awpmd/Makefile.mpi b/lib/awpmd/Makefile.mpi
new file mode 100644
index 0000000000000000000000000000000000000000..e4b424e77638cdccb681710e09854b3f4fc8f6b6
--- /dev/null
+++ b/lib/awpmd/Makefile.mpi
@@ -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)
diff --git a/lib/awpmd/Makefile.mpicc b/lib/awpmd/Makefile.mpicc
index 4c289ad88ac303ad4cbc6b5f2a67c0d2a446c255..5cf6a75bd760e70666c1a5ea978bb0198d820c20 100644
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.mpicc
@@ -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)
diff --git a/lib/awpmd/Makefile.serial b/lib/awpmd/Makefile.serial
new file mode 100644
index 0000000000000000000000000000000000000000..f51714fc9ac9ffb514754bf23e22b5ad67561005
--- /dev/null
+++ b/lib/awpmd/Makefile.serial
@@ -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)
diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py
index 2fc207710c54e4303dc1ffc9c589be977219b3e9..01e70543f22dd9575821fbaf289521838ecd54ba 100644
--- a/lib/colvars/Install.py
+++ b/lib/colvars/Install.py
@@ -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))
diff --git a/lib/colvars/Makefile.mingw32-cross b/lib/colvars/Makefile.mingw32-cross
deleted file mode 100644
index 29c64b26a29b23924934127fc25939ac6dbda878..0000000000000000000000000000000000000000
--- a/lib/colvars/Makefile.mingw32-cross
+++ /dev/null
@@ -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
diff --git a/lib/colvars/Makefile.mingw32-cross-mpi b/lib/colvars/Makefile.mingw32-cross-mpi
deleted file mode 100644
index 1e35c5b46151a9c380a87c3a501bb6a758d2d4eb..0000000000000000000000000000000000000000
--- a/lib/colvars/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -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
-
diff --git a/lib/colvars/Makefile.mingw64-cross b/lib/colvars/Makefile.mingw64-cross
deleted file mode 100644
index 2fd1c6fc67f26a50b067965a0502a31f7d142ee2..0000000000000000000000000000000000000000
--- a/lib/colvars/Makefile.mingw64-cross
+++ /dev/null
@@ -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
diff --git a/lib/colvars/Makefile.mingw64-cross-mpi b/lib/colvars/Makefile.mingw64-cross-mpi
deleted file mode 100644
index ca6f4a6d43226f15bcf0e0a431b20528cfc7ff4b..0000000000000000000000000000000000000000
--- a/lib/colvars/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -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
-
diff --git a/lib/colvars/Makefile.mpi b/lib/colvars/Makefile.mpi
new file mode 100644
index 0000000000000000000000000000000000000000..6343ed7c06b9c88e4da35e26bb74002cf63d09b3
--- /dev/null
+++ b/lib/colvars/Makefile.mpi
@@ -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
+
diff --git a/lib/colvars/Makefile.serial b/lib/colvars/Makefile.serial
new file mode 100644
index 0000000000000000000000000000000000000000..556e39d070d78b0de98e5775a4e0179d7fdb9db2
--- /dev/null
+++ b/lib/colvars/Makefile.serial
@@ -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
+
diff --git a/lib/gpu/.gitignore b/lib/gpu/.gitignore
index 228a9f7731efcf3ad4344a09126311b7fc2bb538..9ad6046a09c08a3b59f0ba01ad4ad8a5d2fb69c8 100644
--- a/lib/gpu/.gitignore
+++ b/lib/gpu/.gitignore
@@ -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
diff --git a/lib/gpu/Install.py b/lib/gpu/Install.py
index c6cd1f3021b117ec7bf0986e685f840cd59e998c..657f1c8fcc7b0be48db185f318a67f65e1d12635 100644
--- a/lib/gpu/Install.py
+++ b/lib/gpu/Install.py
@@ -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)
diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux
index d72c0ba437fb3e58ff8193fdc44adcc63ec3d500..dfcc5bf7d3339c2e668c551627c783c6c6733970 100644
--- a/lib/gpu/Makefile.linux
+++ b/lib/gpu/Makefile.linux
@@ -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 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./
diff --git a/lib/gpu/Makefile.mingw32-cross b/lib/gpu/Makefile.mingw32-cross
deleted file mode 100644
index 6f77634755c58a9dffa4522085d7c65cb86cf3b8..0000000000000000000000000000000000000000
--- a/lib/gpu/Makefile.mingw32-cross
+++ /dev/null
@@ -1,17 +0,0 @@
-CUDA_HOME = ../../tools/mingw-cross/OpenCL
-
-OCL_CPP = i686-w64-mingw32-g++ -O2 -march=i686 -mtune=generic -mfpmath=387 \
- -mpc64 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS \
- -I$(CUDA_HOME)/include
-OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw32 -Wl,-Bdynamic,-lOpenCL,-Bstatic -L../../src/STUBS -lmpi_mingw32
-OCL_PREC = -D_SINGLE_DOUBLE
-OCL_TUNE = -DFERMI_OCL
-EXTRAMAKE = Makefile.lammps.mingw-cross
-
-BIN_DIR = Obj_mingw32
-OBJ_DIR = Obj_mingw32
-LIB_DIR = Obj_mingw32
-AR = i686-w64-mingw32-ar
-BSH = /bin/sh
-
-include Opencl.makefile
diff --git a/lib/gpu/Makefile.mingw32-cross-mpi b/lib/gpu/Makefile.mingw32-cross-mpi
deleted file mode 100644
index 94099cd90b5a8f43424d75830c504ebcc08c61b9..0000000000000000000000000000000000000000
--- a/lib/gpu/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -1,19 +0,0 @@
-CUDA_HOME = ../../tools/mingw-cross/OpenCL
-
-OCL_CPP = i686-w64-mingw32-g++ -O2 -march=i686 -mtune=generic -mfpmath=387 \
- -mpc64 -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include \
- -I../../tools/mingw-cross/mpich2-win32/include/ \
- -DMPICH_IGNORE_CXX_SEEK
-OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw32 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
- -L../../tools/mingw-cross/mpich2-win32/lib -lmpi
-OCL_PREC = -D_SINGLE_DOUBLE
-OCL_TUNE = -DFERMI_OCL
-EXTRAMAKE = Makefile.lammps.mingw-cross
-
-BIN_DIR = Obj_mingw32-mpi
-OBJ_DIR = Obj_mingw32-mpi
-LIB_DIR = Obj_mingw32-mpi
-AR = i686-w64-mingw32-ar
-BSH = /bin/sh
-
-include Opencl.makefile
diff --git a/lib/gpu/Makefile.mingw64-cross b/lib/gpu/Makefile.mingw64-cross
deleted file mode 100644
index 54f6af8c6579c7a0f07172adf40b25153367fb2a..0000000000000000000000000000000000000000
--- a/lib/gpu/Makefile.mingw64-cross
+++ /dev/null
@@ -1,18 +0,0 @@
-CUDA_HOME = ../../tools/mingw-cross/OpenCL
-
-OCL_CPP = x86_64-w64-mingw32-g++ -O3 -march=core2 -mtune=core2 -mpc64 \
- -msse2 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS \
- -I$(CUDA_HOME)/include
-OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw64 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
- -L../../src/STUBS -lmpi_mingw64
-OCL_PREC = -D_SINGLE_DOUBLE
-OCL_TUNE = -DFERMI_OCL
-EXTRAMAKE = Makefile.lammps.mingw-cross
-
-BIN_DIR = Obj_mingw64
-OBJ_DIR = Obj_mingw64
-LIB_DIR = Obj_mingw64
-AR = x86_64-w64-mingw32-ar
-BSH = /bin/sh
-
-include Opencl.makefile
diff --git a/lib/gpu/Makefile.mingw64-cross-mpi b/lib/gpu/Makefile.mingw64-cross-mpi
deleted file mode 100644
index 2ff72d98b188c2de36862f63217a5a10bd2b785b..0000000000000000000000000000000000000000
--- a/lib/gpu/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -1,20 +0,0 @@
-CUDA_HOME = ../../tools/mingw-cross/OpenCL
-
-OCL_CPP = x86_64-w64-mingw32-g++ -O3 -march=core2 -mtune=core2 -mpc64 \
- -msse2 -DMPI_GERYON -DUCL_NO_EXIT -I$(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
diff --git a/lib/gpu/Makefile.mpi b/lib/gpu/Makefile.mpi
new file mode 120000
index 0000000000000000000000000000000000000000..8bad27d0818849aa7a0e1b83150f80d1eb47cf09
--- /dev/null
+++ b/lib/gpu/Makefile.mpi
@@ -0,0 +1 @@
+Makefile.linux
\ No newline at end of file
diff --git a/lib/gpu/Makefile.serial b/lib/gpu/Makefile.serial
index 809e99cc94d40e1eb4653aa337caef43bd57c466..9348dc565ac7e156774541d315d8eafc986d1966 100644
--- a/lib/gpu/Makefile.serial
+++ b/lib/gpu/Makefile.serial
@@ -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
+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 -I../../src/STUBS
-CUDR_OPTS = -O2
+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
diff --git a/lib/h5md/Makefile.h5cc b/lib/h5md/Makefile.h5cc
index bd3e8a978432448a446d415ccfc7a062e0390f22..9feed2d74e3d93a283bf2c52a89604a2276f37fe 100644
--- a/lib/h5md/Makefile.h5cc
+++ b/lib/h5md/Makefile.h5cc
@@ -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)
diff --git a/lib/kim/Install.py b/lib/kim/Install.py
index 315bb4e11c47cd41ec28935255fa9e76c9bedbc2..06479d2d4dd9480f0de8685f6b1535e61d240e0e 100644
--- a/lib/kim/Install.py
+++ b/lib/kim/Install.py
@@ -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)
diff --git a/lib/linalg/Install.py b/lib/linalg/Install.py
deleted file mode 100644
index 560afecec42a844184b6723f1f87c55177cfd768..0000000000000000000000000000000000000000
--- a/lib/linalg/Install.py
+++ /dev/null
@@ -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))
diff --git a/lib/linalg/Install.py b/lib/linalg/Install.py
new file mode 120000
index 0000000000000000000000000000000000000000..ffe709d44c22d2060ad41538d1f8fc0df2b09b30
--- /dev/null
+++ b/lib/linalg/Install.py
@@ -0,0 +1 @@
+../Install.py
\ No newline at end of file
diff --git a/lib/linalg/Makefile.gfortran b/lib/linalg/Makefile.gfortran
index 89b7f2d7a038831a58a4310a072241bab04d8491..7e1d97a5bce8bc2982fba617541d9f48bee4e0dd 100644
--- a/lib/linalg/Makefile.gfortran
+++ b/lib/linalg/Makefile.gfortran
@@ -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)
diff --git a/lib/linalg/Makefile.mingw32-cross b/lib/linalg/Makefile.mingw32-cross
deleted file mode 100644
index 02aa3f71a34e102130d2e0da9543888c07ca9f2d..0000000000000000000000000000000000000000
--- a/lib/linalg/Makefile.mingw32-cross
+++ /dev/null
@@ -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)
-
diff --git a/lib/linalg/Makefile.mingw32-cross-mpi b/lib/linalg/Makefile.mingw32-cross-mpi
deleted file mode 100644
index 1e35c5b46151a9c380a87c3a501bb6a758d2d4eb..0000000000000000000000000000000000000000
--- a/lib/linalg/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -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
-
diff --git a/lib/linalg/Makefile.mingw64-cross b/lib/linalg/Makefile.mingw64-cross
deleted file mode 100644
index ee6eef819b7dbf58b5dcaa6cfb5cfef0460eaf0a..0000000000000000000000000000000000000000
--- a/lib/linalg/Makefile.mingw64-cross
+++ /dev/null
@@ -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)
-
diff --git a/lib/linalg/Makefile.mingw64-cross-mpi b/lib/linalg/Makefile.mingw64-cross-mpi
deleted file mode 100644
index ca6f4a6d43226f15bcf0e0a431b20528cfc7ff4b..0000000000000000000000000000000000000000
--- a/lib/linalg/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -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
-
diff --git a/lib/linalg/Makefile.mpi b/lib/linalg/Makefile.mpi
new file mode 100644
index 0000000000000000000000000000000000000000..dd22ff134caf02e6350304125af4a0420da1cf25
--- /dev/null
+++ b/lib/linalg/Makefile.mpi
@@ -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)
+
diff --git a/lib/linalg/Makefile.serial b/lib/linalg/Makefile.serial
new file mode 120000
index 0000000000000000000000000000000000000000..c52fbcb986822e3dfdc79a978a876fb39a762f71
--- /dev/null
+++ b/lib/linalg/Makefile.serial
@@ -0,0 +1 @@
+Makefile.gfortran
\ No newline at end of file
diff --git a/lib/colvars/Makefile.lammps b/lib/meam/Makefile.lammps.empty
similarity index 60%
rename from lib/colvars/Makefile.lammps
rename to lib/meam/Makefile.lammps.empty
index 99f57b050bff35859eed023961d703cfdcb2c8c0..10394b68ad3ae35dda3fde8463195ba72b4cb69f 100644
--- a/lib/colvars/Makefile.lammps
+++ b/lib/meam/Makefile.lammps.empty
@@ -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 =
diff --git a/lib/meam/Makefile.mingw32-cross b/lib/meam/Makefile.mingw32-cross
deleted file mode 100644
index d4d2dad09339cfa682e9d908c6402db9449a1670..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.mingw32-cross
+++ /dev/null
@@ -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)
diff --git a/lib/meam/Makefile.mingw32-cross-mpi b/lib/meam/Makefile.mingw32-cross-mpi
deleted file mode 100644
index 1e35c5b46151a9c380a87c3a501bb6a758d2d4eb..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -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
-
diff --git a/lib/meam/Makefile.mingw64-cross-mpi b/lib/meam/Makefile.mingw64-cross-mpi
deleted file mode 100644
index ca6f4a6d43226f15bcf0e0a431b20528cfc7ff4b..0000000000000000000000000000000000000000
--- a/lib/meam/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -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
-
diff --git a/lib/meam/Makefile.mingw64-cross b/lib/meam/Makefile.mpi
similarity index 63%
rename from lib/meam/Makefile.mingw64-cross
rename to lib/meam/Makefile.mpi
index 1a8e97febe2dc3630e889e803ab39e12d730bc7b..fd3dbde5558b6866dd3b870ebd622bb0fa757705 100644
--- a/lib/meam/Makefile.mingw64-cross
+++ b/lib/meam/Makefile.mpi
@@ -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)
diff --git a/lib/meam/Makefile.serial b/lib/meam/Makefile.serial
new file mode 120000
index 0000000000000000000000000000000000000000..c52fbcb986822e3dfdc79a978a876fb39a762f71
--- /dev/null
+++ b/lib/meam/Makefile.serial
@@ -0,0 +1 @@
+Makefile.gfortran
\ No newline at end of file
diff --git a/lib/mscg/.gitignore b/lib/mscg/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..7d45bcb60a974bad8d29a88e15e04c41de049451
--- /dev/null
+++ b/lib/mscg/.gitignore
@@ -0,0 +1,4 @@
+# files to ignore
+/liblink
+/includelink
+/MSCG-release-master
diff --git a/lib/mscg/Install.py b/lib/mscg/Install.py
index 7b10be189fee9b5c60fb84d318dcf388fb510926..e4e5ec5613c2b2f0c290df097b24dea8d257c11c 100644
--- a/lib/mscg/Install.py
+++ b/lib/mscg/Install.py
@@ -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 (buildflag and pathflag):
+ error("Cannot use -b and -p flag at the same time")
-if grabflag:
- print "Downloading MS-CG ..."
- cmd = "curl -L %s > %s/%s" % (url,homepath,zipfile)
- print cmd
- print commands.getoutput(cmd)
+if (not buildflag and not pathflag):
+ error("Have to use either -b or -p flag")
- 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)
+# 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)
diff --git a/lib/mscg/Makefile.lammps.default b/lib/mscg/Makefile.lammps.default
new file mode 100644
index 0000000000000000000000000000000000000000..7f04ff2eac9f96259547736ab12ebfb0734da4cd
--- /dev/null
+++ b/lib/mscg/Makefile.lammps.default
@@ -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 =
diff --git a/lib/mscg/Makefile.lammps b/lib/mscg/Makefile.lammps.g++_simple
similarity index 100%
rename from lib/mscg/Makefile.lammps
rename to lib/mscg/Makefile.lammps.g++_simple
diff --git a/lib/mscg/Makefile.lammps.mpi b/lib/mscg/Makefile.lammps.mpi
new file mode 100644
index 0000000000000000000000000000000000000000..7f04ff2eac9f96259547736ab12ebfb0734da4cd
--- /dev/null
+++ b/lib/mscg/Makefile.lammps.mpi
@@ -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 =
diff --git a/lib/mscg/Makefile.lammps.serial b/lib/mscg/Makefile.lammps.serial
new file mode 100644
index 0000000000000000000000000000000000000000..7f04ff2eac9f96259547736ab12ebfb0734da4cd
--- /dev/null
+++ b/lib/mscg/Makefile.lammps.serial
@@ -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 =
diff --git a/lib/mscg/Makefile.mpi b/lib/mscg/Makefile.mpi
new file mode 100644
index 0000000000000000000000000000000000000000..d5088176b4ba36afc69154b9982ae44b156d6534
--- /dev/null
+++ b/lib/mscg/Makefile.mpi
@@ -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
diff --git a/lib/mscg/Makefile.serial b/lib/mscg/Makefile.serial
new file mode 100644
index 0000000000000000000000000000000000000000..4e34706f01b80d0e4cc9117d7d8500d69fbc73e5
--- /dev/null
+++ b/lib/mscg/Makefile.serial
@@ -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
diff --git a/lib/mscg/README b/lib/mscg/README
index b73c8563cd1bc4d76051fcff05acb6c9d4fbaee2..329eebba969629ce734734dbf4bdaa92e1a097de 100755
--- a/lib/mscg/README
+++ b/lib/mscg/README
@@ -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
diff --git a/lib/poems/Makefile.g++ b/lib/poems/Makefile.g++
index 54c897a22ccf976adcfd24220e6648fe26e86dc0..afcbc4a01df37268840643042ba6cb7921151c40 100644
--- a/lib/poems/Makefile.g++
+++ b/lib/poems/Makefile.g++
@@ -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
diff --git a/lib/poems/Makefile.mingw32-cross b/lib/poems/Makefile.mingw32-cross
deleted file mode 100644
index 17e81b51f0f1836c4b4a910fca09a8381b4a459d..0000000000000000000000000000000000000000
--- a/lib/poems/Makefile.mingw32-cross
+++ /dev/null
@@ -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)
diff --git a/lib/poems/Makefile.mingw32-cross-mpi b/lib/poems/Makefile.mingw32-cross-mpi
deleted file mode 100644
index 1e35c5b46151a9c380a87c3a501bb6a758d2d4eb..0000000000000000000000000000000000000000
--- a/lib/poems/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -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
-
diff --git a/lib/poems/Makefile.mingw64-cross-mpi b/lib/poems/Makefile.mingw64-cross-mpi
deleted file mode 100644
index ca6f4a6d43226f15bcf0e0a431b20528cfc7ff4b..0000000000000000000000000000000000000000
--- a/lib/poems/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -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
-
diff --git a/lib/poems/Makefile.mingw64-cross b/lib/poems/Makefile.mpi
similarity index 86%
rename from lib/poems/Makefile.mingw64-cross
rename to lib/poems/Makefile.mpi
index 2df43dea947724307d9bac6652c81f2c7823ffba..0f0546419c7215f1c0f060874945317e266d0561 100644
--- a/lib/poems/Makefile.mingw64-cross
+++ b/lib/poems/Makefile.mpi
@@ -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 $(FILES)
diff --git a/lib/poems/Makefile.serial b/lib/poems/Makefile.serial
new file mode 120000
index 0000000000000000000000000000000000000000..9d7bb000f9d5074bfe1234ef4c2ade3eea216c31
--- /dev/null
+++ b/lib/poems/Makefile.serial
@@ -0,0 +1 @@
+Makefile.g++
\ No newline at end of file
diff --git a/lib/qmmm/Makefile.mpi b/lib/qmmm/Makefile.mpi
new file mode 100644
index 0000000000000000000000000000000000000000..590b1047f89ac96515061651d1796d372daa7644
--- /dev/null
+++ b/lib/qmmm/Makefile.mpi
@@ -0,0 +1,66 @@
+# -*- Makefile -*- for coupling LAMMPS to PWscf for QM/MM molecular dynamics
+
+# this file will be copied to Makefile.lammps
+EXTRAMAKE = Makefile.lammps.empty
+
+# top level directory of Quantum ESPRESSO 5.4.1 or later
+QETOPDIR=$(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 $(LAMMPSCFG)
+
+clean :
+ -rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
+
+# explicit dependencies
+
+pwqmmm.o: pwqmmm.c libqmmm.h
+libqmmm.o: libqmmm.c libqmmm.h
diff --git a/lib/qmmm/Makefile.serial b/lib/qmmm/Makefile.serial
new file mode 100644
index 0000000000000000000000000000000000000000..f09148279263fc5907be3a55e9df9fae8078c569
--- /dev/null
+++ b/lib/qmmm/Makefile.serial
@@ -0,0 +1,66 @@
+# -*- Makefile -*- for coupling LAMMPS to PWscf for QM/MM molecular dynamics
+
+# this file will be copied to Makefile.lammps
+EXTRAMAKE = Makefile.lammps.empty
+
+# top level directory of Quantum ESPRESSO 5.4.1 or later
+QETOPDIR=$(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
diff --git a/lib/reax/Makefile.gfortran b/lib/reax/Makefile.gfortran
index b2b16fcc57cf5faacc2ca5058dfff014ac91dd76..ab423016887a444548529d84c6a32d03fdb5c880 100644
--- a/lib/reax/Makefile.gfortran
+++ b/lib/reax/Makefile.gfortran
@@ -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 =
diff --git a/lib/reax/Makefile.lammps.empty b/lib/reax/Makefile.lammps.empty
new file mode 100644
index 0000000000000000000000000000000000000000..758755f3c8064d8b40d3d1af1310bd093a366004
--- /dev/null
+++ b/lib/reax/Makefile.lammps.empty
@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+reax_SYSINC =
+reax_SYSLIB =
+reax_SYSPATH =
diff --git a/lib/reax/Makefile.mpi b/lib/reax/Makefile.mpi
new file mode 100644
index 0000000000000000000000000000000000000000..142f7e9bc6ffc01a1e18fe12548af8e1b4638564
--- /dev/null
+++ b/lib/reax/Makefile.mpi
@@ -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)
diff --git a/lib/reax/Makefile.serial b/lib/reax/Makefile.serial
new file mode 120000
index 0000000000000000000000000000000000000000..c52fbcb986822e3dfdc79a978a876fb39a762f71
--- /dev/null
+++ b/lib/reax/Makefile.serial
@@ -0,0 +1 @@
+Makefile.gfortran
\ No newline at end of file
diff --git a/lib/smd/Install.py b/lib/smd/Install.py
index 337f993be5d192623996aa2f1cf361f0ff54eba2..1c270bea5e8e824f3671044dfcef64666c38ebb1 100644
--- a/lib/smd/Install.py
+++ b/lib/smd/Install.py
@@ -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)
diff --git a/lib/smd/Makefile.lammps b/lib/smd/Makefile.lammps
index 7bbf3924ef933076644c6c30c65871fcf2875cb0..6951a1394cfe928a4aa0fc6ac96281fd6d20d3db 100644
--- a/lib/smd/Makefile.lammps
+++ b/lib/smd/Makefile.lammps
@@ -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 =
diff --git a/lib/voronoi/Install.py b/lib/voronoi/Install.py
index 17bba5e8eb5cdfe0e0cd013c74433c894c4f4038..5a246bbeb18a9b340d187b6b87495511bf8169a2 100644
--- a/lib/voronoi/Install.py
+++ b/lib/voronoi/Install.py
@@ -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)
diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp
index b5bfa926a107310f414d28a39b74ab63fba8f481..fba198c814c77b2cf5585fd7e73f8311a271b4ae 100644
--- a/src/MSCG/fix_mscg.cpp
+++ b/src/MSCG/fix_mscg.cpp
@@ -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"
diff --git a/src/MSCG/fix_mscg.h b/src/MSCG/fix_mscg.h
index f6dcf4f0f6f6a4b3ac69ef5f30594a3279e67abb..2c235d436a46300e6ac86f73c69a87ad3442d7c7 100644
--- a/src/MSCG/fix_mscg.h
+++ b/src/MSCG/fix_mscg.h
@@ -21,7 +21,6 @@ FixStyle(mscg,FixMSCG)
#define LMP_FIX_MSCG_H
#include "fix.h"
-#include "mscg.h"
namespace LAMMPS_NS {
diff --git a/src/Makefile b/src/Makefile
index 3d1085e0be5c0a5bda16580dc60a0a6ce5474f8c..7dfc2c312aafe24337c7645e9e399eed2d05f0c9 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -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;