create Makefile for ML-POD

cmake/CMakeLists.txt

@@ -630,10 +630,6 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
   endif()
 endforeach()
 
-if(PKG_ELECTRODE)
-  target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
-endif()
-
 if(PKG_ELECTRODE OR PKG_ML-POD)
   target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
 endif()

lib/mlpod/Install.py

@@ -0,0 +1,97 @@
+#!/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
+from argparse import ArgumentParser
+
+sys.path.append('..')
+from install_helpers import get_cpus, fullpath
+
+parser = ArgumentParser(prog='Install.py',
+                        description="LAMMPS library build wrapper script")
+
+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
+
+Examples:
+
+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 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)
+"""
+
+# parse and process arguments
+
+parser.add_argument("-m", "--machine",
+                    help="suffix of a <libname>/Makefile.* file used for compiling this library")
+parser.add_argument("-e", "--extramake",
+                    help="set EXTRAMAKE variable in <libname>/Makefile.<machine> to Makefile.lammps.<extramake>")
+
+args = parser.parse_args()
+
+# print help message and exit, if neither build nor path options are given
+if not args.machine and not args.extramake:
+  parser.print_help()
+  sys.exit(HELP)
+
+machine = args.machine
+extraflag = args.extramake
+if extraflag:
+    suffix = args.extramake
+else:
+    suffix = 'empty'
+
+# set lib from working dir
+
+cwd = fullpath('.')
+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):
+  sys.exit("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 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 optionally with parallel make
+n_cpus = get_cpus()
+
+print("Building lib%s.a ..." % lib)
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
+try:
+  txt = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
+  print(txt.decode('UTF-8'))
+except subprocess.CalledProcessError as e:
+  print("Make failed with:\n %s" % e.output.decode('UTF-8'))
+  sys.exit(1)
+
+if os.path.exists("lib%s.a" % lib):
+  print("Build was successful")
+else:
+  sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib, lib))
+
+if has_extramake and not os.path.exists("Makefile.lammps"):
+  print("WARNING: lib/%s/Makefile.lammps was NOT created" % lib)

lib/mlpod/Makefile.lammps.empty

@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+mlpod_SYSINC =
+mlpod_SYSLIB =
+mlpod_SYSPATH =

lib/mlpod/Makefile.lammps.installed

@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+mlpod_SYSINC =
+mlpod_SYSLIB = -lblas -llapack
+mlpod_SYSPATH =

lib/mlpod/Makefile.lammps.linalg

@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+mlpod_SYSINC =
+mlpod_SYSLIB = -llinalg -lgfortran
+mlpod_SYSPATH = -L../../lib/linalg$(LIBOBJDIR)

lib/mlpod/Makefile.mpi

@@ -0,0 +1,48 @@
+SHELL = /bin/sh
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.linalg
+
+# ------ DEFINITIONS ------
+
+LIB = libmlpod.a
+OBJ =   $(SRC:.cpp=.o)
+
+# ------ SETTINGS ------
+
+# include any MPI settings needed for the ELECTRODE library to build with
+# the same MPI library that LAMMPS is built with
+
+CC =	    mpicxx
+CCFLAGS = -O3 -fPIC -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+
+ARCHIVE =	ar
+ARCHFLAG =	-rc
+DEPFLAGS =  -M
+#LINK =         
+#LINKFLAGS =	
+USRLIB =
+SYSLIB =
+
+# ------ MAKE PROCEDURE ------
+
+lib: 	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
+	@cp $(EXTRAMAKE) Makefile.lammps
+
+# ------ COMPILE RULES ------
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) -c $< -o $@
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
+
+# ------ DEPENDENCIES ------
+
+DEPENDS = $(OBJ:.o=.d)
+
+# ------ CLEAN ------
+
+clean:
+	-rm -f *.d *~ $(OBJ) $(LIB)

lib/mlpod/Makefile.serial

@@ -0,0 +1,48 @@
+SHELL = /bin/sh
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.linalg
+
+# ------ DEFINITIONS ------
+
+LIB = libmlpod.a
+OBJ =   $(SRC:.cpp=.o)
+
+# ------ SETTINGS ------
+
+# include any MPI settings needed for the mlpod library to build with
+# the same MPI library that LAMMPS is built with
+
+CC =	    g++
+CCFLAGS = -O3 -fPIC -I../../src/STUBS
+
+ARCHIVE =	ar
+ARCHFLAG =	-rc
+DEPFLAGS =  -M
+#LINK =         
+#LINKFLAGS =	
+USRLIB =
+SYSLIB =
+
+# ------ MAKE PROCEDURE ------
+
+lib: 	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
+	@cp $(EXTRAMAKE) Makefile.lammps
+
+# ------ COMPILE RULES ------
+
+%.o:%.cpp
+	$(CC) $(CCFLAGS) -c $< -o $@
+%.d:%.cpp
+	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
+
+# ------ DEPENDENCIES ------
+
+DEPENDS = $(OBJ:.o=.d)
+
+# ------ CLEAN ------
+
+clean:
+	-rm -f *.d *~ $(OBJ) $(LIB)