diff --git a/lib/.gitignore b/lib/.gitignore
index cbeae7705..4f9ebba6a 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 6b9025433..d30cbffcf 100644
--- a/lib/Install.py
+++ b/lib/Install.py
@@ -1,92 +1,101 @@
#!/usr/bin/env python
# install.py tool to do a generic build of a library
# soft linked to by many of the lib/Install.py files
# used to automate the steps described in the corresponding lib/README
from __future__ import print_function
import sys,os,subprocess
# help message
help = """
Syntax from src dir: make lib-libname args="-m machine -e suffix"
Syntax from lib dir: python Install.py -m machine -e suffix
libname = name of lib dir (e.g. atc, h5md, meam, poems, etc)
specify -m and optionally -e, order does not matter
-m = peform a clean followed by "make -f Makefile.machine"
machine = suffix of a lib/Makefile.* file
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
does not alter existing Makefile.machine
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
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
extraflag = 0
iarg = 0
while iarg < nargs:
if args[iarg] == "-m":
if iarg+2 > nargs: error()
machine = args[iarg+1]
iarg += 2
elif args[iarg] == "-e":
if iarg+2 > nargs: error()
extraflag = 1
suffix = args[iarg+1]
iarg += 2
else: error()
# set lib from working dir
cwd = os.getcwd()
lib = os.path.basename(cwd)
# create Makefile.auto as copy of Makefile.machine
# reset EXTRAMAKE if requested
if not os.path.exists("Makefile.%s" % machine):
error("lib/%s/Makefile.%s does not exist" % (lib,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.mpicc b/lib/awpmd/Makefile.mpi
similarity index 83%
copy from lib/awpmd/Makefile.mpicc
copy to lib/awpmd/Makefile.mpi
index 4c289ad88..e4b424e77 100644
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.mpi
@@ -1,69 +1,71 @@
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.installed
+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 = 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
#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 *.d *~ $(OBJ) $(LIB)
+ -rm -f *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mpicc b/lib/awpmd/Makefile.mpicc
index 4c289ad88..5cf6a75bd 100644
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.mpicc
@@ -1,69 +1,71 @@
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.installed
# ------ 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 = 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
#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 *.d *~ $(OBJ) $(LIB)
+ -rm -f *.d *~ $(OBJ) $(LIB)
diff --git a/lib/awpmd/Makefile.mpicc b/lib/awpmd/Makefile.serial
similarity index 85%
copy from lib/awpmd/Makefile.mpicc
copy to lib/awpmd/Makefile.serial
index 4c289ad88..f51714fc9 100644
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.serial
@@ -1,69 +1,71 @@
SHELL = /bin/sh
# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.installed
+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 = mpic++
-CCFLAGS = -O -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
+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 *.d *~ $(OBJ) $(LIB)
+ -rm -f *.d *~ $(OBJ) $(LIB)
diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py
index 2fc207710..01e70543f 100644
--- a/lib/colvars/Install.py
+++ b/lib/colvars/Install.py
@@ -1,142 +1,142 @@
#!/usr/bin/env python
# Install.py tool to do automate build of Colvars
from __future__ import print_function
import sys,os,subprocess
# help message
help = """
Syntax from src dir: make lib-colvars args="-m machine -e suffix"
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
does not alter existing Makefile.machine
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
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
extraflag = False
iarg = 0
while iarg < nargs:
if args[iarg] == "-m":
if iarg+2 > len(args): error()
machine = args[iarg+1]
iarg += 2
elif args[iarg] == "-e":
if iarg+2 > len(args): error()
extraflag = True
suffix = args[iarg+1]
iarg += 2
else: error()
# set lib from working dir
cwd = os.getcwd()
lib = os.path.basename(cwd)
def get_lammps_machine_flags(machine):
"""Parse Makefile.machine from LAMMPS, return dictionary of compiler flags"""
if not os.path.exists("../../src/MAKE/MACHINES/Makefile.%s" % machine):
error("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)
lines = open("../../src/MAKE/MACHINES/Makefile.%s" % machine,
'r').readlines()
machine_flags = {}
for line in lines:
line = line.partition('#')[0]
line = line.rstrip()
words = line.split()
if (len(words) > 2):
if ((words[0] == 'CC') or (words[0] == 'CCFLAGS') or
(words[0] == 'SHFLAGS') or (words[0] == 'ARCHIVE') or
(words[0] == 'ARFLAGS') or (words[0] == 'SHELL')):
machine_flags[words[0]] = ' '.join(words[2:])
return machine_flags
def gen_colvars_makefile_machine(machine, machine_flags):
"""Generate Makefile.machine for Colvars given the compiler flags"""
machine_makefile = open("Makefile.%s" % machine, 'w')
machine_makefile.write('''# -*- makefile -*- to build Colvars module with %s
COLVARS_LIB = libcolvars.a
COLVARS_OBJ_DIR =
CXX = %s
CXXFLAGS = %s %s
AR = %s
ARFLAGS = %s
SHELL = %s
include Makefile.common
.PHONY: default clean
default: $(COLVARS_LIB) Makefile.lammps
clean:
-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
''' % (machine, machine_flags['CC'],
machine_flags['CCFLAGS'], machine_flags['SHFLAGS'] ,
machine_flags['ARCHIVE'], machine_flags['ARFLAGS'],
machine_flags['SHELL']))
if not os.path.exists("Makefile.%s" % machine):
machine_flags = get_lammps_machine_flags(machine)
gen_colvars_makefile_machine(machine, machine_flags)
if not os.path.exists("Makefile.%s" % machine):
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
# create Makefile.auto as copy of Makefile.machine
# reset EXTRAMAKE if requested
lines = open("Makefile.%s" % machine,'r').readlines()
fp = open("Makefile.auto",'w')
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)
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"]
-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))
if not os.path.exists("Makefile.lammps"):
print("lib/%s/Makefile.lammps was NOT created" % lib)
diff --git a/lib/colvars/Makefile.mingw32-cross b/lib/colvars/Makefile.mingw32-cross
deleted file mode 100644
index 29c64b26a..000000000
--- 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 1e35c5b46..000000000
--- 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 2fd1c6fc6..000000000
--- 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 ca6f4a6d4..000000000
--- 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 000000000..6343ed7c0
--- /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 000000000..556e39d07
--- /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 228a9f773..9ad6046a0 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 c6cd1f302..657f1c8fc 100644
--- a/lib/gpu/Install.py
+++ b/lib/gpu/Install.py
@@ -1,155 +1,159 @@
#!/usr/bin/env python
# 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
args = sys.argv[1:]
nargs = len(args)
if nargs == 0: error()
isuffix = "linux"
hflag = aflag = pflag = eflag = 0
makeflag = 0
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
elif args[iarg] == "-h":
if iarg+2 > nargs: error()
hflag = 1
hdir = args[iarg+1]
iarg += 2
elif args[iarg] == "-a":
if iarg+2 > nargs: error()
aflag = 1
arch = args[iarg+1]
iarg += 2
elif args[iarg] == "-p":
if iarg+2 > nargs: error()
pflag = 1
precision = args[iarg+1]
iarg += 2
elif args[iarg] == "-e":
if iarg+2 > nargs: error()
eflag = 1
lmpsuffix = args[iarg+1]
iarg += 2
- elif args[iarg] == "-m":
+ elif args[iarg] == "-b":
makeflag = 1
iarg += 1
elif args[iarg] == "-o":
if iarg+2 > nargs: error()
outflag = 1
osuffix = args[iarg+1]
iarg += 2
else: error()
if pflag:
if precision == "double": precstr = "-D_DOUBLE_DOUBLE"
elif precision == "mixed": precstr = "-D_SINGLE_DOUBLE"
elif precision == "single": precstr = "-D_SINGLE_SINGLE"
else: error("Invalid precision setting")
# create Makefile.auto
# reset EXTRAMAKE, CUDA_HOME, CUDA_ARCH, CUDA_PRECISION if requested
if not os.path.exists("Makefile.%s" % isuffix):
error("lib/gpu/Makefile.%s does not exist" % isuffix)
lines = open("Makefile.%s" % isuffix,'r').readlines()
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] == '=':
line = line.replace(words[2],"-arch=sm_%s" % arch)
if pflag and words[0] == "CUDA_PRECISION" and words[1] == '=':
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"):
error("lib/gpu/Makefile.lammps was NOT created")
# 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 d72c0ba43..dfcc5bf7d 100644
--- a/lib/gpu/Makefile.linux
+++ b/lib/gpu/Makefile.linux
@@ -1,52 +1,52 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.standard
ifeq ($(CUDA_HOME),)
CUDA_HOME = /usr/local/cuda
endif
NVCC = nvcc
# Tesla CUDA
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
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 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
BIN_DIR = ./
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh
CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
include Nvidia.makefile
diff --git a/lib/gpu/Makefile.mingw32-cross b/lib/gpu/Makefile.mingw32-cross
deleted file mode 100644
index 6f7763475..000000000
--- a/lib/gpu/Makefile.mingw32-cross
+++ /dev/null
@@ -1,17 +0,0 @@
-CUDA_HOME = ../../tools/mingw-cross/OpenCL
-
-OCL_CPP = i686-w64-mingw32-g++ -O2 -march=i686 -mtune=generic -mfpmath=387 \
- -mpc64 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS \
- -I$(CUDA_HOME)/include
-OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw32 -Wl,-Bdynamic,-lOpenCL,-Bstatic -L../../src/STUBS -lmpi_mingw32
-OCL_PREC = -D_SINGLE_DOUBLE
-OCL_TUNE = -DFERMI_OCL
-EXTRAMAKE = Makefile.lammps.mingw-cross
-
-BIN_DIR = Obj_mingw32
-OBJ_DIR = Obj_mingw32
-LIB_DIR = Obj_mingw32
-AR = i686-w64-mingw32-ar
-BSH = /bin/sh
-
-include Opencl.makefile
diff --git a/lib/gpu/Makefile.mingw32-cross-mpi b/lib/gpu/Makefile.mingw32-cross-mpi
deleted file mode 100644
index 94099cd90..000000000
--- a/lib/gpu/Makefile.mingw32-cross-mpi
+++ /dev/null
@@ -1,19 +0,0 @@
-CUDA_HOME = ../../tools/mingw-cross/OpenCL
-
-OCL_CPP = i686-w64-mingw32-g++ -O2 -march=i686 -mtune=generic -mfpmath=387 \
- -mpc64 -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include \
- -I../../tools/mingw-cross/mpich2-win32/include/ \
- -DMPICH_IGNORE_CXX_SEEK
-OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw32 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
- -L../../tools/mingw-cross/mpich2-win32/lib -lmpi
-OCL_PREC = -D_SINGLE_DOUBLE
-OCL_TUNE = -DFERMI_OCL
-EXTRAMAKE = Makefile.lammps.mingw-cross
-
-BIN_DIR = Obj_mingw32-mpi
-OBJ_DIR = Obj_mingw32-mpi
-LIB_DIR = Obj_mingw32-mpi
-AR = i686-w64-mingw32-ar
-BSH = /bin/sh
-
-include Opencl.makefile
diff --git a/lib/gpu/Makefile.mingw64-cross b/lib/gpu/Makefile.mingw64-cross
deleted file mode 100644
index 54f6af8c6..000000000
--- a/lib/gpu/Makefile.mingw64-cross
+++ /dev/null
@@ -1,18 +0,0 @@
-CUDA_HOME = ../../tools/mingw-cross/OpenCL
-
-OCL_CPP = x86_64-w64-mingw32-g++ -O3 -march=core2 -mtune=core2 -mpc64 \
- -msse2 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS \
- -I$(CUDA_HOME)/include
-OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw64 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
- -L../../src/STUBS -lmpi_mingw64
-OCL_PREC = -D_SINGLE_DOUBLE
-OCL_TUNE = -DFERMI_OCL
-EXTRAMAKE = Makefile.lammps.mingw-cross
-
-BIN_DIR = Obj_mingw64
-OBJ_DIR = Obj_mingw64
-LIB_DIR = Obj_mingw64
-AR = x86_64-w64-mingw32-ar
-BSH = /bin/sh
-
-include Opencl.makefile
diff --git a/lib/gpu/Makefile.mingw64-cross-mpi b/lib/gpu/Makefile.mingw64-cross-mpi
deleted file mode 100644
index 2ff72d98b..000000000
--- a/lib/gpu/Makefile.mingw64-cross-mpi
+++ /dev/null
@@ -1,20 +0,0 @@
-CUDA_HOME = ../../tools/mingw-cross/OpenCL
-
-OCL_CPP = x86_64-w64-mingw32-g++ -O3 -march=core2 -mtune=core2 -mpc64 \
- -msse2 -DMPI_GERYON -DUCL_NO_EXIT -I$(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 000000000..8bad27d08
--- /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 809e99cc9..9348dc565 100644
--- a/lib/gpu/Makefile.serial
+++ b/lib/gpu/Makefile.serial
@@ -1,35 +1,52 @@
# /* ----------------------------------------------------------------------
-# Generic Makefile for CUDA using MPI STUBS library
+# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
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 = ./
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 bd3e8a978..9feed2d74 100644
--- a/lib/h5md/Makefile.h5cc
+++ b/lib/h5md/Makefile.h5cc
@@ -1,33 +1,38 @@
EXTRAMAKE=Makefile.lammps.empty
CC=h5cc
# -DH5_NO_DEPRECATED_SYMBOLS is required here to ensure we are using
# the v1.8 API when HDF5 is configured to default to using the v1.6 API.
CFLAGS=-D_DEFAULT_SOURCE -O2 -DH5_NO_DEPRECATED_SYMBOLS -Wall -fPIC
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 $@
Makefile.lammps:
cp $(EXTRAMAKE) $@
.PHONY: all lib clean
-$(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)
clean:
rm -f build/*.o $(LIB)
diff --git a/lib/kim/Install.py b/lib/kim/Install.py
index 315bb4e11..06479d2d4 100644
--- a/lib/kim/Install.py
+++ b/lib/kim/Install.py
@@ -1,276 +1,280 @@
#!/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:
https://openkim.org/kim-items/model-drivers/alphabetical
See the list of all KIM models here:
https://openkim.org/kim-items/models/by-model-drivers
See the list of example KIM models included by default here:
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
# 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:]
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
pathflag = False
iarg = 0
while iarg < len(args):
if args[iarg] == "-v":
if iarg+2 > len(args): error()
version = args[iarg+1]
iarg += 2
elif args[iarg] == "-b":
buildflag = True
iarg += 1
elif args[iarg] == "-n":
buildflag = False
iarg += 1
elif args[iarg] == "-p":
if iarg+2 > len(args): error()
kimdir = fullpath(args[iarg+1])
pathflag = True
buildflag = False
iarg += 2
elif args[iarg] == "-a":
addflag = True
if iarg+2 > len(args): error()
addmodelname = args[iarg+1]
if addmodelname == "everything":
buildflag = True
everythingflag = True
addflag = False
iarg += 2
elif args[iarg] == "-vv":
verboseflag = True
iarg += 1
else: error()
thisdir = os.path.abspath(thisdir)
url = "https://s3.openkim.org/kim-api/%s.tgz" % version
# set KIM API directory
if pathflag:
if not os.path.isdir(kimdir):
print("\nkim-api is not installed at %s" % kimdir)
error()
# configure LAMMPS to use existing kim-api installation
with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
mkfile.write(".DUMMY: print_dir\n\n")
mkfile.write("print_dir:\n")
mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir))
else:
kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
# download KIM tarball, unpack, build KIM
if buildflag:
# check to see if an installed kim-api already exists and wipe it out.
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
with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
mkfile.write(".DUMMY: print_dir\n\n")
mkfile.write("print_dir:\n")
mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir))
# download entire kim-api tarball
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
if addflag:
if not os.path.isdir(kimdir):
print("\nkim-api is not installed")
error()
# download single model
print("Downloading tarball for %s..." % addmodelname)
url = "https://openkim.org/download/%s.tgz" % addmodelname
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:
# 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:
print(e.output)
sys.exit()
if verboseflag: print(txt.decode("UTF-8"))
# 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:
print(e.output)
sys.exit()
print(txt.decode("UTF-8"))
sys.exit()
else:
print(firstRunOutput)
print("Error, unable to build and install OpenKIM item: %s" \
% addmodelname)
sys.exit()
# success the first time
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 560afecec..000000000
--- 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 000000000..ffe709d44
--- /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 89b7f2d7a..7e1d97a5b 100644
--- a/lib/linalg/Makefile.gfortran
+++ b/lib/linalg/Makefile.gfortran
@@ -1,54 +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 = 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
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 *.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 02aa3f71a..000000000
--- 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 1e35c5b46..000000000
--- 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 ee6eef819..000000000
--- 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 ca6f4a6d4..000000000
--- 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.gfortran b/lib/linalg/Makefile.mpi
similarity index 69%
copy from lib/linalg/Makefile.gfortran
copy to lib/linalg/Makefile.mpi
index 89b7f2d7a..dd22ff134 100644
--- a/lib/linalg/Makefile.gfortran
+++ b/lib/linalg/Makefile.mpi
@@ -1,54 +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 = 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
+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 *.o *.mod *~ $(LIB)
+ -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 000000000..c52fbcb98
--- /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%
copy from lib/colvars/Makefile.lammps
copy to lib/meam/Makefile.lammps.empty
index 99f57b050..10394b68a 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 d4d2dad09..000000000
--- 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 1e35c5b46..000000000
--- 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 ca6f4a6d4..000000000
--- 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 1a8e97feb..fd3dbde55 100644
--- a/lib/meam/Makefile.mingw64-cross
+++ b/lib/meam/Makefile.mpi
@@ -1,69 +1,61 @@
-# * -*- 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
+EXTRAMAKE = Makefile.lammps.empty
# ------ 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_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 000000000..c52fbcb98
--- /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 000000000..7d45bcb60
--- /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 7b10be189..e4e5ec561 100644
--- a/lib/mscg/Install.py
+++ b/lib/mscg/Install.py
@@ -1,129 +1,151 @@
#!/usr/bin/env python
# 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:]
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 b/lib/mscg/Makefile.lammps.default
similarity index 58%
copy from lib/mscg/Makefile.lammps
copy to lib/mscg/Makefile.lammps.default
index f0d9a9b8a..7f04ff2ea 100644
--- a/lib/mscg/Makefile.lammps
+++ b/lib/mscg/Makefile.lammps.default
@@ -1,5 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
-mscg_SYSINC = -std=c++11
-mscg_SYSLIB = -lm -lgsl -llapack -lgslcblas
+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%
copy from lib/mscg/Makefile.lammps
copy to lib/mscg/Makefile.lammps.g++_simple
diff --git a/lib/mscg/Makefile.lammps b/lib/mscg/Makefile.lammps.mpi
similarity index 58%
copy from lib/mscg/Makefile.lammps
copy to lib/mscg/Makefile.lammps.mpi
index f0d9a9b8a..7f04ff2ea 100644
--- a/lib/mscg/Makefile.lammps
+++ b/lib/mscg/Makefile.lammps.mpi
@@ -1,5 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
-mscg_SYSINC = -std=c++11
-mscg_SYSLIB = -lm -lgsl -llapack -lgslcblas
+mscg_SYSINC =
+mscg_SYSLIB = -lgsl -lgslcblas
mscg_SYSPATH =
diff --git a/lib/mscg/Makefile.lammps b/lib/mscg/Makefile.lammps.serial
similarity index 58%
rename from lib/mscg/Makefile.lammps
rename to lib/mscg/Makefile.lammps.serial
index f0d9a9b8a..7f04ff2ea 100644
--- a/lib/mscg/Makefile.lammps
+++ b/lib/mscg/Makefile.lammps.serial
@@ -1,5 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
-mscg_SYSINC = -std=c++11
-mscg_SYSLIB = -lm -lgsl -llapack -lgslcblas
+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 000000000..d5088176b
--- /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 000000000..4e34706f0
--- /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 b73c8563c..329eebba9 100755
--- a/lib/mscg/README
+++ b/lib/mscg/README
@@ -1,67 +1,69 @@
This directory contains links to the Multi-scale Coarse-graining
(MS-CG) library which is required to use the MSCG package and its fix
command in a LAMMPS input script.
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.
-----------------
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
directory. E.g if you built MS-CG in this dir:
% ln -s src includelink
% ln -s src liblink
These links could instead be set to the include and lib
directories created by a MS-CG install, e.g.
% 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
package installed:
% cd lammps/src
% make yes-USER-MSCG
% make g++ (or whatever target you wish)
Note that if you download and unpack a new LAMMPS tarball, the
"includelink" and "liblink" files will be lost and you will need to
re-create them (step 4). If you built MS-CG in this directory (as
opposed to somewhere else on your system) and did not install it
somewhere else, you will also need to repeat steps 1,2,3.
The Makefile.lammps file in this directory is there for compatibility
with the way other libraries under the lib dir are linked with by
LAMMPS. MS-CG requires the GSL and LAPACK libraries as listed in
Makefile.lammps. If they are not in default locations where your
LD_LIBRARY_PATH environment settings can find them, then you should
add the approrpriate -L paths to the mscg_SYSPATH variable in
Makefile.lammps.
diff --git a/lib/poems/Makefile.g++ b/lib/poems/Makefile.g++
index 54c897a22..afcbc4a01 100644
--- a/lib/poems/Makefile.g++
+++ b/lib/poems/Makefile.g++
@@ -1,101 +1,101 @@
# *
# *_________________________________________________________________________*
# * 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 ------
LIB = libpoems.a
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
LINK = g++
LINKFLAGS = -O
USRLIB =
SYSLIB =
# ------ MAKE PROCEDURE ------
lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
# ------ COMPILE RULES ------
%.o:%.cpp
$(CC) $(CCFLAGS) -c $<
# ------ DEPENDENCIES ------
include .depend
# ------ CLEAN ------
clean:
-rm *.o *.d *~ $(LIB)
tar:
-tar -cvf ../POEMS.tar $(FILES)
diff --git a/lib/poems/Makefile.mingw32-cross b/lib/poems/Makefile.mingw32-cross
deleted file mode 100644
index 17e81b51f..000000000
--- 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 1e35c5b46..000000000
--- 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 ca6f4a6d4..000000000
--- 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 2df43dea9..0f0546419 100644
--- a/lib/poems/Makefile.mingw64-cross
+++ b/lib/poems/Makefile.mpi
@@ -1,110 +1,101 @@
# *
# *_________________________________________________________________________*
# * 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_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 ------
include .depend
# ------ CLEAN ------
clean:
- -rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
+ -rm *.o *.d *~ $(LIB)
tar:
-tar -cvf ../POEMS.tar $(FILES)
diff --git a/lib/poems/Makefile.serial b/lib/poems/Makefile.serial
new file mode 120000
index 000000000..9d7bb000f
--- /dev/null
+++ b/lib/poems/Makefile.serial
@@ -0,0 +1 @@
+Makefile.g++
\ No newline at end of file
diff --git a/lib/qmmm/Makefile.mpi b/lib/qmmm/Makefile.mpi
new file mode 100644
index 000000000..590b1047f
--- /dev/null
+++ b/lib/qmmm/Makefile.mpi
@@ -0,0 +1,66 @@
+# -*- Makefile -*- for coupling LAMMPS to PWscf for QM/MM molecular dynamics
+
+# this file will be copied to Makefile.lammps
+EXTRAMAKE = Makefile.lammps.empty
+
+# top level directory of Quantum ESPRESSO 5.4.1 or later
+QETOPDIR=$(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 $(LAMMPSCFG)
+
+clean :
+ -rm -f *.x *.o *.a *~ *.F90 *.d *.mod *.i *.L
+
+# explicit dependencies
+
+pwqmmm.o: pwqmmm.c libqmmm.h
+libqmmm.o: libqmmm.c libqmmm.h
diff --git a/lib/qmmm/Makefile.serial b/lib/qmmm/Makefile.serial
new file mode 100644
index 000000000..f09148279
--- /dev/null
+++ b/lib/qmmm/Makefile.serial
@@ -0,0 +1,66 @@
+# -*- Makefile -*- for coupling LAMMPS to PWscf for QM/MM molecular dynamics
+
+# this file will be copied to Makefile.lammps
+EXTRAMAKE = Makefile.lammps.empty
+
+# top level directory of Quantum ESPRESSO 5.4.1 or later
+QETOPDIR=$(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 b2b16fcc5..ab4230168 100644
--- a/lib/reax/Makefile.gfortran
+++ b/lib/reax/Makefile.gfortran
@@ -1,51 +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.gfortran
# ------ 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 = gfortran
-F90FLAGS = -O -fPIC -fno-second-underscore
+F90FLAGS = -O3 -fPIC -fno-second-underscore
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/colvars/Makefile.lammps b/lib/reax/Makefile.lammps.empty
similarity index 60%
rename from lib/colvars/Makefile.lammps
rename to lib/reax/Makefile.lammps.empty
index 99f57b050..758755f3c 100644
--- a/lib/colvars/Makefile.lammps
+++ b/lib/reax/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 =
+reax_SYSINC =
+reax_SYSLIB =
+reax_SYSPATH =
diff --git a/lib/reax/Makefile.gfortran b/lib/reax/Makefile.mpi
similarity index 91%
copy from lib/reax/Makefile.gfortran
copy to lib/reax/Makefile.mpi
index b2b16fcc5..142f7e9bc 100644
--- a/lib/reax/Makefile.gfortran
+++ b/lib/reax/Makefile.mpi
@@ -1,51 +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.gfortran
+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 = gfortran
-F90FLAGS = -O -fPIC -fno-second-underscore
+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 000000000..c52fbcb98
--- /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 337f993be..1c270bea5 100644
--- a/lib/smd/Install.py
+++ b/lib/smd/Install.py
@@ -1,117 +1,123 @@
#!/usr/bin/env python
# Install.py tool to download, unpack, and point to the Eigen library
# used to automate the steps described in the README file in this dir
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)
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
version = '3.3.4'
tarball = "eigen.tar.gz"
# print error message or help
def error(str=None):
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:]
nargs = len(args)
+if nargs == 0: error()
homepath = "."
homedir = "eigen3"
-grabflag = True
-buildflag = True
+buildflag = False
pathflag = False
linkflag = True
iarg = 0
while iarg < nargs:
if args[iarg] == "-v":
if iarg+2 > nargs: error()
version = args[iarg+1]
iarg += 2
elif args[iarg] == "-p":
if iarg+2 > nargs: error()
eigenpath = fullpath(args[iarg+1])
pathflag = True
- buildflag = False
iarg += 2
elif args[iarg] == "-b":
buildflag = True
iarg += 1
else: error()
homepath = fullpath(homepath)
if (pathflag):
if not os.path.isdir(eigenpath): error("Eigen path does not exist")
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
if buildflag:
print("Downloading Eigen ...")
url = "http://bitbucket.org/eigen/eigen/get/%s.tar.gz" % version
geturl(url,"%s/%s" % (homepath,tarball))
print("Unpacking Eigen tarball ...")
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)
os.rename(edir[0],"%s/%s" % (homepath,homedir))
os.remove(tarball)
# create link in lib/smd to Eigen src dir
if linkflag:
print("Creating link to Eigen files")
if os.path.isfile("includelink") or os.path.islink("includelink"):
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 7bbf3924e..6951a1394 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 17bba5e8e..5a246bbeb 100644
--- a/lib/voronoi/Install.py
+++ b/lib/voronoi/Install.py
@@ -1,128 +1,134 @@
#!/usr/bin/env python
# Install.py tool to download, unpack, build, and link to the Voro++ library
# used to automate the steps described in the README file in this dir
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
version = "voro++-0.4.6"
url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
# print error message or help
def error(str=None):
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:]
nargs = len(args)
+if nargs == 0: error()
homepath = "."
homedir = version
-grabflag = True
-buildflag = True
+buildflag = False
pathflag = False
linkflag = True
iarg = 0
while iarg < nargs:
if args[iarg] == "-v":
if iarg+2 > nargs: error()
version = args[iarg+1]
iarg += 2
elif args[iarg] == "-p":
if iarg+2 > nargs: error()
voropath = fullpath(args[iarg+1])
pathflag = True
- buildflag = False
iarg += 2
elif args[iarg] == "-b":
buildflag = True
iarg += 1
else: error()
homepath = fullpath(homepath)
homedir = "%s/%s" % (homepath,version)
if (pathflag):
if not os.path.isdir(voropath): error("Voro++ path does not exist")
homedir = voropath
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))
print("Unpacking Voro++ tarball ...")
if os.path.exists("%s/%s" % (homepath,version)):
cmd = 'rm -rf "%s/%s"' % (homepath,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
os.remove("%s/%s.tar.gz" % (homepath,version))
if os.path.basename(homedir) != version:
if os.path.exists(homedir):
cmd = 'rm -rf "%s"' % homedir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
os.rename("%s/%s" % (homepath,version),homedir)
# build Voro++
if buildflag:
print("Building Voro++ ...")
cmd = 'cd "%s"; make' % homedir
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print(txt.decode('UTF-8'))
# create 2 links in lib/voronoi to Voro++ src dir
if linkflag:
print("Creating links to Voro++ 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, '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 b5bfa926a..fba198c81 100644
--- a/src/MSCG/fix_mscg.cpp
+++ b/src/MSCG/fix_mscg.cpp
@@ -1,330 +1,331 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Lauren Abbott (Sandia)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include <stdlib.h>
#include "fix_mscg.h"
+#include "mscg.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "input.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "region.h"
#include "update.h"
#include "variable.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixMSCG::FixMSCG(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal fix mscg command");
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix mscg command");
me = comm->me;
nprocs = comm->nprocs;
if (nprocs > 1) error->all(FLERR,"Fix mscg does not yet support "
"parallel use via MPI");
if (sizeof(tagint) != sizeof(smallint))
error->all(FLERR,"Fix mscg must be used with 32-bit atom IDs");
// initialize
int natoms = atom->natoms;
int ntypes = atom->ntypes;
max_partners_bond = 4;
max_partners_angle = 12;
max_partners_dihedral = 36;
nframes = n_frames = block_size = 0;
range_flag = 0;
name_flag = 0;
f = NULL;
type_names = new char*[natoms];
for (int i = 0; i < natoms; i++) type_names[i] = new char[24];
// parse remaining arguments
int iarg = 4;
while(iarg < narg) {
if (strcmp(arg[iarg],"range") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix mscg command");
if (strcmp(arg[iarg+1],"on") == 0)
range_flag = 1;
else if (strcmp(arg[iarg+1],"off") == 0)
range_flag = 0;
else error->all(FLERR,"Illegal fix mscg command");
iarg += 2;
} else if (strcmp(arg[iarg],"name") == 0) {
if (iarg+ntypes+1 > narg)
error->all(FLERR,"Illegal fix mscg command");
name_flag = 1;
for (int i = 0; i < ntypes; i++) {
iarg += 1;
std::string str = arg[iarg];
type_names[i] = strcat(strdup(str.c_str()),"\0");
}
iarg += 1;
} else if (strcmp(arg[iarg],"max") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix mscg command");
max_partners_bond = atoi(arg[iarg+1]);
max_partners_angle = atoi(arg[iarg+2]);
max_partners_dihedral = atoi(arg[iarg+3]);
iarg += 4;
} else error->all(FLERR,"Illegal fix mscg command");
}
if (name_flag == 0) {
for (int i = 0; i < natoms; i++) {
std::string str = std::to_string(i+1);
type_names[i] = strcat(strdup(str.c_str()),"\0");
}
}
}
/* ---------------------------------------------------------------------- */
FixMSCG::~FixMSCG()
{
memory->destroy(f);
}
/* ---------------------------------------------------------------------- */
int FixMSCG::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixMSCG::post_constructor()
{
if (domain->triclinic == 1)
error->all(FLERR,"Fix mscg does not yet support triclinic geometries");
// topology information
// sort by atom id to send to mscg lib
int natoms = atom->natoms;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
int *type = atom->type;
int *num_bond = atom->num_bond;
int **bond_atom = atom->bond_atom;
int *num_angle = atom->num_angle;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom3 = atom->angle_atom3;
int *num_dihedral = atom->num_dihedral;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom3 = atom->dihedral_atom3;
int **dihedral_atom4 = atom->dihedral_atom4;
double *prd_half = domain->prd_half;
int i,ii,j,jj,jnum,k,l;
n_cg_sites = natoms;
n_cg_types = atom->ntypes;
memory->grow(f,nlocal,3,"fix_mscg:f");
f1d = new double[n_cg_sites*3]();
x1d = new double[n_cg_sites*3]();
cg_site_types = new int[n_cg_sites]();
n_partners_bond = new unsigned[n_cg_sites]();
n_partners_angle = new unsigned[n_cg_sites]();
n_partners_dihedral = new unsigned[n_cg_sites]();
partners_bond = new unsigned*[n_cg_sites];
for (i = 0; i < n_cg_sites; i++)
partners_bond[i] = new unsigned[1*max_partners_bond]();
partners_angle = new unsigned*[n_cg_sites];
for (i = 0; i < n_cg_sites; i++)
partners_angle[i] = new unsigned[2*max_partners_angle]();
partners_dihedral = new unsigned*[n_cg_sites];
for (i = 0; i < n_cg_sites; i++)
partners_dihedral[i] = new unsigned[3*max_partners_dihedral]();
for (i = 0; i < 3; i++)
box_half_lengths[i] = prd_half[i];
for (i = 0; i < nlocal; i++) {
cg_site_types[i] = 0;
n_partners_bond[i] = 0;
n_partners_angle[i] = 0;
n_partners_dihedral[i] = 0;
}
for (ii = 0; ii < nlocal; ii++) {
i = tag[ii];
cg_site_types[i-1] = type[ii];
jnum = num_bond[ii];
for (jj = 0; jj < jnum; jj++) {
j = bond_atom[ii][jj];
if (n_partners_bond[i-1] >= max_partners_bond ||
n_partners_bond[j-1] >= max_partners_bond)
error->all(FLERR,"Bond list overflow, boost fix_mscg max");
partners_bond[i-1][n_partners_bond[i-1]] = j-1;
partners_bond[j-1][n_partners_bond[j-1]] = i-1;
n_partners_bond[i-1]++;
n_partners_bond[j-1]++;
}
jnum = num_angle[ii];
for (jj = 0; jj < jnum; jj++) {
j = angle_atom1[ii][jj];
k = angle_atom3[ii][jj];
if (n_partners_angle[j-1] >= max_partners_angle ||
n_partners_angle[k-1] >= max_partners_angle)
error->all(FLERR,"Angle list overflow, boost fix_mscg max");
partners_angle[j-1][n_partners_angle[j-1]*2] = i-1;
partners_angle[j-1][n_partners_angle[j-1]*2+1] = k-1;
partners_angle[k-1][n_partners_angle[k-1]*2] = i-1;
partners_angle[k-1][n_partners_angle[k-1]*2+1] = j-1;
n_partners_angle[j-1]++;
n_partners_angle[k-1]++;
}
jnum = num_dihedral[ii];
for (jj = 0; jj < jnum; jj++) {
j = dihedral_atom1[ii][jj];
k = dihedral_atom3[ii][jj];
l = dihedral_atom4[ii][jj];
if (n_partners_dihedral[j-1] >= max_partners_dihedral ||
n_partners_dihedral[l-1] >= max_partners_dihedral)
error->all(FLERR,"Dihedral list overflow, boost fix_mscg max");
partners_dihedral[j-1][n_partners_dihedral[j-1]*3] = i-1;
partners_dihedral[j-1][n_partners_dihedral[j-1]*3+1] = k-1;
partners_dihedral[j-1][n_partners_dihedral[j-1]*3+2] = l-1;
partners_dihedral[l-1][n_partners_dihedral[l-1]*3] = k-1;
partners_dihedral[l-1][n_partners_dihedral[l-1]*3+1] = i-1;
partners_dihedral[l-1][n_partners_dihedral[l-1]*3+2] = j-1;
n_partners_dihedral[j-1]++;
n_partners_dihedral[l-1]++;
}
}
// pass topology data to mscg code and run startup
fprintf(screen,"Initializing MSCG with topology data ...\n");
if (range_flag)
mscg_struct = rangefinder_startup_part1(mscg_struct);
else
mscg_struct = mscg_startup_part1(mscg_struct);
n_frames = get_n_frames(mscg_struct);
block_size = get_block_size(mscg_struct);
mscg_struct =
setup_topology_and_frame(mscg_struct,n_cg_sites,n_cg_types,type_names,
cg_site_types,box_half_lengths);
mscg_struct =
set_bond_topology(mscg_struct,partners_bond,n_partners_bond);
mscg_struct =
set_angle_topology(mscg_struct,partners_angle,n_partners_angle);
mscg_struct =
set_dihedral_topology(mscg_struct,partners_dihedral,n_partners_dihedral);
mscg_struct =
generate_exclusion_topology(mscg_struct);
if (range_flag)
mscg_struct = rangefinder_startup_part2(mscg_struct);
else
mscg_struct = mscg_startup_part2(mscg_struct);
}
/* ---------------------------------------------------------------------- */
void FixMSCG::init()
{
int nlocal = atom->nlocal;
double **force = atom->f;
int i;
// forces are reset to 0 before pre_force, saved here
// init called for each frame of dump in rerun command
for (i = 0; i < nlocal; i++) {
f[i][0] = force[i][0];
f[i][1] = force[i][1];
f[i][2] = force[i][2];
}
}
/* ---------------------------------------------------------------------- */
void FixMSCG::end_of_step()
{
if (domain->triclinic == 1)
error->all(FLERR,"Fix mscg does not yet support triclinic geometries");
int natoms = atom->natoms;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
double **x = atom->x;
double *prd_half = domain->prd_half;
int i,ii,j;
// trajectory information
for (ii = 0; ii < nlocal; ii++) {
i = tag[ii];
for (j = 0; j < 3; j++) {
x1d[(i-1)*3+j] = x[ii][j];
f1d[(i-1)*3+j] = f[ii][j];
}
}
// pass x,f to mscg to update matrix
nframes++;
if (range_flag)
mscg_struct = rangefinder_process_frame(mscg_struct,x1d,f1d);
else
mscg_struct = mscg_process_frame(mscg_struct,x1d,f1d);
}
/* ---------------------------------------------------------------------- */
void FixMSCG::post_run()
{
// call mscg to solve matrix and generate output
fprintf(screen,"Finalizing MSCG ...\n");
if (nframes != n_frames)
error->warning(FLERR,"Fix mscg n_frames is inconsistent with control.in");
if (nframes % block_size != 0)
error->warning(FLERR,"Fix mscg n_frames is not divisible by "
"block_size in control.in");
if (range_flag)
rangefinder_solve_and_output(mscg_struct);
else
mscg_solve_and_output(mscg_struct);
}
diff --git a/src/MSCG/fix_mscg.h b/src/MSCG/fix_mscg.h
index f6dcf4f0f..2c235d436 100644
--- a/src/MSCG/fix_mscg.h
+++ b/src/MSCG/fix_mscg.h
@@ -1,91 +1,90 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(mscg,FixMSCG)
#else
#ifndef LMP_FIX_MSCG_H
#define LMP_FIX_MSCG_H
#include "fix.h"
-#include "mscg.h"
namespace LAMMPS_NS {
class FixMSCG : public Fix {
public:
FixMSCG(class LAMMPS *, int, char **);
~FixMSCG();
int setmask();
void post_constructor();
void init();
void end_of_step();
void post_run();
private:
int range_flag,name_flag,me,nprocs;
int nframes,n_frames,block_size,n_cg_sites,n_cg_types,*cg_site_types;
int max_partners_bond,max_partners_angle,max_partners_dihedral;
unsigned *n_partners_bond,*n_partners_angle,*n_partners_dihedral;
unsigned **partners_bond,**partners_angle,**partners_dihedral;
double *x1d,*f1d,**f;
double box_half_lengths[3];
char **type_names;
void *mscg_struct;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Fix mscg does not yet support mpi
Self-explanatory.
E: Fix mscg does not yet support triclinic geometries
Self-explanatory.
E: Bond/Angle/Dihedral list overflow, boost fix_mscg max
A site has more bond/angle/dihedral partners that the maximum and
has overflowed the bond/angle/dihedral partners list. Increase the
corresponding fix_mscg max arg.
W: Fix mscg n_frames is inconsistent with control.in
The control.in file read by the MSCG lib has a parameter n_frames
that should be equal to the number of frames processed by the
fix mscg command. If not equal, the fix will still run, but the
calculated residuals may be normalized incorrectly.
W: Fix mscg n_frames is not divisible by block_size in control.in
The control.in file read by the MSCG lib has a parameter block_size
that should be a divisor of the number of frames processed by the
fix mscg command. If not, the fix will still run, but some frames may
not be included in the MSCG calculations.
*/
diff --git a/src/Makefile b/src/Makefile
index 3d1085e0b..7dfc2c312 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,384 +1,384 @@
# LAMMPS multiple-machine -*- Makefile -*-
SHELL = /bin/bash
PYTHON = python
#.IGNORE:
# Definitions
ROOT = lmp
EXE = lmp_$@
ARLIB = liblammps_$@.a
SHLIB = liblammps_$@.so
ARLINK = liblammps.a
SHLINK = liblammps.so
OBJDIR = Obj_$@
OBJSHDIR = Obj_shared_$@
SRC = $(wildcard *.cpp)
INC = $(wildcard *.h)
OBJ = $(SRC:.cpp=.o)
SRCLIB = $(filter-out main.cpp,$(SRC))
OBJLIB = $(filter-out main.o,$(OBJ))
# Command-line options for mode: exe (default), shexe, lib, shlib
mode = exe
objdir = $(OBJDIR)
ifeq ($(mode),shexe)
objdir = $(OBJSHDIR)
endif
ifeq ($(mode),lib)
objdir = $(OBJDIR)
endif
ifeq ($(mode),shlib)
objdir = $(OBJSHDIR)
endif
# Package variables
# PACKAGE = standard packages
# PACKUSER = user packagse
# PACKLIB = all packages that require an additional lib
# should be PACKSYS + PACKINT + PACKEXT
# PACKSYS = subset that reqiure a common system library
# include MPIIO and LB b/c require full MPI, not just STUBS
# PACKINT = subset that require an internal (provided) library
# PACKEXT = subset that require an external (downloaded) library
PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
granular kim kokkos kspace manybody mc meam misc molecule \
mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap srd voronoi
PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-meamc user-mgpt user-misc user-molfile \
user-netcdf user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-vtk
PACKLIB = compress gpu kim kokkos meam mpiio mscg poems \
python reax voronoi \
user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
user-netcdf user-qmmm user-quip user-smd user-vtk
PACKSYS = compress mpiio python user-lb
PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
PACKEXT = kim mscg voronoi \
user-h5md user-molfile user-netcdf user-qmmm user-quip \
user-smd user-vtk
PACKALL = $(PACKAGE) $(PACKUSER)
PACKAGEUC = $(shell echo $(PACKAGE) | tr a-z A-Z)
PACKUSERUC = $(shell echo $(PACKUSER) | tr a-z A-Z)
YESDIR = $(shell echo $(@:yes-%=%) | tr a-z A-Z)
NODIR = $(shell echo $(@:no-%=%) | tr a-z A-Z)
LIBDIR = $(shell echo $(@:lib-%=%))
LIBUSERDIR = $(shell echo $(@:lib-user-%=%))
# List of all targets
help:
@echo ''
@echo 'make clean-all delete all object files'
@echo 'make clean-machine delete object files for one machine'
@echo 'make mpi-stubs build dummy MPI library in STUBS'
@echo 'make install-python install LAMMPS wrapper in Python'
@echo 'make tar create lmp_src.tar.gz for src dir and packages'
@echo ''
@echo 'make package list available packages and their dependencies'
@echo 'make package-status (ps) status of all packages'
@echo 'make yes-package install a single pgk in src dir'
@echo 'make no-package remove a single pkg from src dir'
@echo 'make yes-all install all pgks in src dir'
@echo 'make no-all remove all pkgs from src dir'
@echo 'make yes-standard (yes-std) install all standard pkgs'
@echo 'make no-standard (no-std) remove all standard pkgs'
@echo 'make yes-user install all user pkgs'
@echo 'make no-user remove all user pkgs'
@echo 'make yes-lib install all pkgs with libs (included or ext)'
@echo 'make no-lib remove all pkgs with libs (included or ext)'
@echo 'make yes-ext install all pkgs with external libs'
@echo 'make no-ext remove all pkgs with external libs'
@echo ''
@echo 'make package-update (pu) replace src files with updated package files'
@echo 'make package-overwrite replace package files with src files'
@echo 'make package-diff (pd) diff src files against package files'
@echo ''
@echo 'make lib-package help for download/build/install a package library'
@echo 'make lib-package args="..." download/build/install a package library'
@echo 'make purge purge obsolete copies of source files'
@echo ''
@echo 'make machine build LAMMPS for machine'
@echo 'make mode=lib machine build LAMMPS as static lib for machine'
@echo 'make mode=shlib machine build LAMMPS as shared lib for machine'
@echo 'make mode=shexe machine build LAMMPS as shared exe for machine'
@echo 'make makelist create Makefile.list used by old makes'
@echo 'make -f Makefile.list machine build LAMMPS for machine (old)'
@echo ''
@echo 'machine is one of these from src/MAKE:'
@echo ''
@files="`ls MAKE/Makefile.*`"; \
for file in $$files; do head -1 $$file; done
@echo ''
@echo '... or one of these from src/MAKE/OPTIONS:'
@echo ''
@files="`ls MAKE/OPTIONS/Makefile.*`"; \
for file in $$files; do head -1 $$file; done
@echo ''
@echo '... or one of these from src/MAKE/MACHINES:'
@echo ''
@files="`ls MAKE/MACHINES/Makefile.*`"; \
for file in $$files; do head -1 $$file; done
@echo ''
@echo '... or one of these from src/MAKE/MINE:'
@echo ''
@files="`ls MAKE/MINE/Makefile.* 2>/dev/null`"; \
for file in $$files; do head -1 $$file; done
@echo ''
# Build LAMMPS in one of 4 modes
# exe = exe with static compile in Obj_machine (default)
# shexe = exe with shared compile in Obj_shared_machine
# lib = static lib in Obj_machine
# shlib = shared lib in Obj_shared_machine
.DEFAULT:
@if [ $@ = "serial" -a ! -f STUBS/libmpi_stubs.a ]; \
then $(MAKE) mpi-stubs; fi
@test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \
-f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@
@if [ ! -d $(objdir) ]; then mkdir $(objdir); fi
@$(SHELL) Make.sh style
@if [ -f MAKE/MACHINES/Makefile.$@ ]; \
then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi
@if [ -f MAKE/OPTIONS/Makefile.$@ ]; \
then cp MAKE/OPTIONS/Makefile.$@ $(objdir)/Makefile; fi
@if [ -f MAKE/Makefile.$@ ]; \
then cp MAKE/Makefile.$@ $(objdir)/Makefile; fi
@if [ -f MAKE/MINE/Makefile.$@ ]; \
then cp MAKE/MINE/Makefile.$@ $(objdir)/Makefile; fi
@if [ ! -e Makefile.package ]; \
then cp Makefile.package.empty Makefile.package; fi
@if [ ! -e Makefile.package.settings ]; \
then cp Makefile.package.settings.empty Makefile.package.settings; fi
@cp Makefile.package Makefile.package.settings $(objdir)
@cd $(objdir); rm -f .depend; \
$(MAKE) $(MFLAGS) "SRC = $(SRC)" "INC = $(INC)" depend || :
ifeq ($(mode),exe)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" "SHFLAGS =" \
"EXE = ../$(EXE)" ../$(EXE)
endif
ifeq ($(mode),shexe)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJ)" "INC = $(INC)" \
"EXE = ../$(EXE)" ../$(EXE)
endif
ifeq ($(mode),lib)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" "SHFLAGS =" \
"EXE = ../$(ARLIB)" lib
@rm -f $(ARLINK)
@ln -s $(ARLIB) $(ARLINK)
endif
ifeq ($(mode),shlib)
@cd $(objdir); \
$(MAKE) $(MFLAGS) "OBJ = $(OBJLIB)" "INC = $(INC)" \
"EXE = ../$(SHLIB)" shlib
@rm -f $(SHLINK)
@ln -s $(SHLIB) $(SHLINK)
endif
# Remove machine-specific object files
clean:
@echo 'make clean-all delete all object files'
@echo 'make clean-machine delete object files for one machine'
clean-all:
rm -rf Obj_*
clean-%:
rm -rf Obj_$(@:clean-%=%) Obj_shared_$(@:clean-%=%)
# Create Makefile.list
makelist:
@$(SHELL) Make.sh style
@$(SHELL) Make.sh Makefile.list
# Make MPI STUBS library
mpi-stubs:
@cd STUBS; $(MAKE) clean; $(MAKE)
# install LAMMPS shared lib and Python wrapper for Python usage
-# include python package settings to
+# include python package settings to
# automatically adapt name of python interpreter
sinclude ../lib/python/Makefile.lammps
install-python:
@$(PYTHON) ../python/install.py
# Create a tarball of src dir and packages
tar:
@cd STUBS; $(MAKE) clean
@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
src/Make* src/Package.sh src/Depend.sh src/Install.sh \
src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \
$(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
--exclude=*/.svn
@cd STUBS; $(MAKE)
@echo "Created $(ROOT)_src.tar.gz"
# Package management
package:
@echo 'Standard packages:' $(PACKAGE)
@echo ''
@echo 'User-contributed packages:' $(PACKUSER)
@echo ''
@echo 'Packages that need system libraries:' $(PACKSYS)
@echo ''
@echo 'Packages that need provided libraries:' $(PACKINT)
@echo ''
@echo 'Packages that need external libraries:' $(PACKEXT)
@echo ''
@echo 'make package list available packages'
@echo 'make package list available packages'
@echo 'make package-status (ps) status of all packages'
@echo 'make yes-package install a single pgk in src dir'
@echo 'make no-package remove a single pkg from src dir'
@echo 'make yes-all install all pgks in src dir'
@echo 'make no-all remove all pkgs from src dir'
@echo 'make yes-standard (yes-std) install all standard pkgs'
@echo 'make no-standard (no-srd) remove all standard pkgs'
@echo 'make yes-user install all user pkgs'
@echo 'make no-user remove all user pkgs'
@echo 'make yes-lib install all pkgs with libs (included or ext)'
@echo 'make no-lib remove all pkgs with libs (included or ext)'
@echo 'make yes-ext install all pkgs with external libs'
@echo 'make no-ext remove all pkgs with external libs'
@echo ''
@echo 'make package-update (pu) replace src files with package files'
@echo 'make package-overwrite replace package files with src files'
@echo 'make package-diff (pd) diff src files against package file'
@echo ''
@echo 'make lib-package build and/or download a package library'
yes-all:
@for p in $(PACKALL); do $(MAKE) yes-$$p; done
no-all:
@for p in $(PACKALL); do $(MAKE) no-$$p; done
yes-standard yes-std:
@for p in $(PACKAGE); do $(MAKE) yes-$$p; done
no-standard no-std:
@for p in $(PACKAGE); do $(MAKE) no-$$p; done
yes-user:
@for p in $(PACKUSER); do $(MAKE) yes-$$p; done
no-user:
@for p in $(PACKUSER); do $(MAKE) no-$$p; done
yes-lib:
@for p in $(PACKLIB); do $(MAKE) yes-$$p; done
no-lib:
@for p in $(PACKLIB); do $(MAKE) no-$$p; done
yes-ext:
@for p in $(PACKEXT); do $(MAKE) yes-$$p; done
no-ext:
@for p in $(PACKEXT); do $(MAKE) no-$$p; done
yes-%:
@if [ ! -e Makefile.package ]; \
then cp Makefile.package.empty Makefile.package; fi
@if [ ! -e Makefile.package.settings ]; \
then cp Makefile.package.settings.empty Makefile.package.settings; fi
@if [ ! -e $(YESDIR) ]; then \
echo "Package $(@:yes-%=%) does not exist"; \
elif [ -e $(YESDIR)/Install.sh ]; then \
echo "Installing package $(@:yes-%=%)"; \
cd $(YESDIR); $(SHELL) Install.sh 1; cd ..; \
$(SHELL) Depend.sh $(YESDIR) 1; \
else \
echo "Installing package $(@:yes-%=%)"; \
cd $(YESDIR); $(SHELL) ../Install.sh 1; cd ..; \
$(SHELL) Depend.sh $(YESDIR) 1; \
fi;
no-%:
@if [ ! -e $(NODIR) ]; then \
echo "Package $(@:no-%=%) does not exist"; \
elif [ -e $(NODIR)/Install.sh ]; then \
echo "Uninstalling package $(@:no-%=%)"; \
cd $(NODIR); $(SHELL) Install.sh 0; cd ..; \
$(SHELL) Depend.sh $(NODIR) 0; \
else \
echo "Uninstalling package $(@:no-%=%)"; \
cd $(NODIR); $(SHELL) ../Install.sh 0; cd ..; \
$(SHELL) Depend.sh $(NODIR) 0; \
fi;
# download/build/install a package library
lib-%:
@if [ -e ../lib/$(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;
# status = list src files that differ from package files
# update = replace src files with newer package files
# overwrite = overwrite package files with newer src files
# diff = show differences between src and package files
# purge = delete obsolete and auto-generated package files
package-status ps:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p status; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p status; done
package-update pu:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p update; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p update; done
package-overwrite:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p overwrite; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p overwrite; done
package-diff pd:
@for p in $(PACKAGEUC); do $(SHELL) Package.sh $$p diff; done
@echo ''
@for p in $(PACKUSERUC); do $(SHELL) Package.sh $$p diff; done
purge: Purge.list
@echo 'Purging obsolete and auto-generated source files'
@for f in `grep -v '#' Purge.list` ; \
do test -f $$f && rm $$f && echo $$f || : ; \
done