Merge branch 'master' into lammps-icms

doc/Section_python.html

@@ -58,12 +58,13 @@ operations within LAMMPS, such as running a simulation for a
 reasonable number of timesteps, then the overhead cost of invoking
 LAMMPS thru Python will be negligible.
 </P>
-<P>Before using LAMMPS from a Python script, you have to do two things.
+<P>Before using LAMMPS from a Python script, you need to do two things.
-You need to set two environment variables.  And you need to build
+You need to build LAMMPS as a dynamic shared library, so it can be
-LAMMPS as a dynamic shared library, so it can be loaded by Python.
+loaded by Python.  And you need to tell Python how to find the library
-Both these steps are discussed below.  If you wish to run LAMMPS in
+and the Python wrapper file python/lammps.py.  Both these steps are
-parallel from Python, you also need to extend your Python with MPI.
+discussed below.  If you wish to run LAMMPS in parallel from Python,
-This is also discussed below.
+you also need to extend your Python with MPI.  This is also discussed
+below.
 </P>
 <P>The Python wrapper for LAMMPS uses the amazing and magical (to me)
 "ctypes" package in Python, which auto-generates the interface code
@@ -131,7 +132,7 @@ python/lammps.py file.
 </P>
 <P>You can invoke install.py from the python directory as
 </P>
-<PRE>% python install.py <B>libdir</B> <B>pydir</B> 
+<PRE>% python install.py [libdir] [pydir] 
 </PRE>
 <P>The optional libdir is where to copy the LAMMPS shared library to; the
 default is /usr/local/lib.  The optional pydir is where to copy the
@@ -146,12 +147,12 @@ non-standard locations, such as within your own user space, you will
 need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
 accordingly, as above.
 </P>
-<P>If the instally.py script does not allow you to copy files into system
+<P>If the install.py script does not allow you to copy files into system
 directories, prefix the python command with "sudo".  If you do this,
 make sure that the Python that root runs is the same as the Python you
 run.  E.g. you may need to do something like
 </P>
-<PRE>% sudo /usr/local/bin/python install.py <B>libdir</B> <B>pydir</B> 
+<PRE>% sudo /usr/local/bin/python install.py [libdir] [pydir] 
 </PRE>
 <P>You can also invoke install.py from the make command in the src
 directory as
@@ -269,20 +270,27 @@ and type:
 <PRE>>>> from lammps import lammps
 >>> lmp = lammps() 
 </PRE>
-<P>If you get no errors, you're ready to use LAMMPS from Python.
+<P>If you get no errors, you're ready to use LAMMPS from Python.  If the
-If the load fails, the most common error to see is
+2nd command fails, the most common error to see is
 </P>
 <PRE>OSError: Could not load LAMMPS dynamic library 
 </PRE>
 <P>which means Python was unable to load the LAMMPS shared library.  This
-typically occurs if the system can't find the LAMMMPS shared library
+typically occurs if the system can't find the LAMMPS shared library or
-or one of the auxiliary shared libraries it depends on.
+one of the auxiliary shared libraries it depends on, or if something
+about the library is incompatible with your Python.  The error message
+should give you an indication of what went wrong.
 </P>
-<P>Python (actually the operating system) isn't verbose about telling you
+<P>You can also test the load directly in Python as follows, without
-why the load failed, so carefully go through the steps above regarding
+first importing from the lammps.py file:
-environment variables, and the instructions in <A HREF = "Section_start.html#start_5">Section_start
+</P>
-5</A> about building a shared library and
+<PRE>>>> from ctypes import CDLL
-about setting the LD_LIBRARY_PATH envirornment variable.
+>>> CDLL("liblammps.so") 
+</PRE>
+<P>If an error occurs, carefully go thru the steps in <A HREF = "Section_start.html#start_5">Section_start
+5</A> and above about building a shared
+library and about insuring Python can find the necessary two files
+it needs.
 </P>
 <H5><B>Test LAMMPS and Python in serial:</B> 
 </H5>

doc/Section_python.txt

@@ -55,12 +55,13 @@ operations within LAMMPS, such as running a simulation for a
 reasonable number of timesteps, then the overhead cost of invoking
 LAMMPS thru Python will be negligible.
 
-Before using LAMMPS from a Python script, you have to do two things.
+Before using LAMMPS from a Python script, you need to do two things.
-You need to set two environment variables.  And you need to build
+You need to build LAMMPS as a dynamic shared library, so it can be
-LAMMPS as a dynamic shared library, so it can be loaded by Python.
+loaded by Python.  And you need to tell Python how to find the library
-Both these steps are discussed below.  If you wish to run LAMMPS in
+and the Python wrapper file python/lammps.py.  Both these steps are
-parallel from Python, you also need to extend your Python with MPI.
+discussed below.  If you wish to run LAMMPS in parallel from Python,
-This is also discussed below.
+you also need to extend your Python with MPI.  This is also discussed
+below.
 
 The Python wrapper for LAMMPS uses the amazing and magical (to me)
 "ctypes" package in Python, which auto-generates the interface code
@@ -127,7 +128,7 @@ python/lammps.py file.
 
 You can invoke install.py from the python directory as
 
-% python install.py [libdir] [pydir] :pre
+% python install.py \[libdir\] \[pydir\] :pre
 
 The optional libdir is where to copy the LAMMPS shared library to; the
 default is /usr/local/lib.  The optional pydir is where to copy the
@@ -142,12 +143,12 @@ non-standard locations, such as within your own user space, you will
 need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
 accordingly, as above.
 
-If the instally.py script does not allow you to copy files into system
+If the install.py script does not allow you to copy files into system
 directories, prefix the python command with "sudo".  If you do this,
 make sure that the Python that root runs is the same as the Python you
 run.  E.g. you may need to do something like
 
-% sudo /usr/local/bin/python install.py [libdir] [pydir] :pre
+% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
 
 You can also invoke install.py from the make command in the src
 directory as
@@ -265,20 +266,27 @@ and type:
 >>> from lammps import lammps
 >>> lmp = lammps() :pre
 
-If you get no errors, you're ready to use LAMMPS from Python.
+If you get no errors, you're ready to use LAMMPS from Python.  If the
-If the load fails, the most common error to see is
+2nd command fails, the most common error to see is
 
 OSError: Could not load LAMMPS dynamic library :pre
 
 which means Python was unable to load the LAMMPS shared library.  This
-typically occurs if the system can't find the LAMMMPS shared library
+typically occurs if the system can't find the LAMMPS shared library or
-or one of the auxiliary shared libraries it depends on.
+one of the auxiliary shared libraries it depends on, or if something
+about the library is incompatible with your Python.  The error message
+should give you an indication of what went wrong.
 
-Python (actually the operating system) isn't verbose about telling you
+You can also test the load directly in Python as follows, without
-why the load failed, so carefully go through the steps above regarding
+first importing from the lammps.py file:
-environment variables, and the instructions in "Section_start
+
-5"_Section_start.html#start_5 about building a shared library and
+>>> from ctypes import CDLL
-about setting the LD_LIBRARY_PATH envirornment variable.
+>>> CDLL("liblammps.so") :pre
+
+If an error occurs, carefully go thru the steps in "Section_start
+5"_Section_start.html#start_5 and above about building a shared
+library and about insuring Python can find the necessary two files
+it needs.
 
 [Test LAMMPS and Python in serial:] :h5
 

doc/Section_start.html

@@ -850,7 +850,7 @@ should be the file /usr/local/lib/libmpich.so.
 the environment variable LD_LIBRARY_PATH.  So you may wish to copy the
 file src/liblammps.so or src/liblammps_g++.so (for example) to a place
 the system can find it by default, such as /usr/local/lib, or you may
-wish to add the lammps src directory to LD_LIBRARY_PATH, so that the
+wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
 current version of the shared library is always available to programs
 that use it.
 </P>

doc/Section_start.txt

@@ -844,7 +844,7 @@ The operating system finds shared libraries to load at run-time using
 the environment variable LD_LIBRARY_PATH.  So you may wish to copy the
 file src/liblammps.so or src/liblammps_g++.so (for example) to a place
 the system can find it by default, such as /usr/local/lib, or you may
-wish to add the lammps src directory to LD_LIBRARY_PATH, so that the
+wish to add the LAMMPS src directory to LD_LIBRARY_PATH, so that the
 current version of the shared library is always available to programs
 that use it.
 

examples/COUPLE/fortran2/LAMMPS-wrapper.cpp

@@ -30,6 +30,7 @@
 #include <compute.h>
 #include <modify.h>
 #include <error.h>
+#include <cstdlib>
 
 using namespace LAMMPS_NS;
 

examples/COUPLE/fortran2/LAMMPS-wrapper.h

@@ -21,12 +21,6 @@
    library.h.  All prototypes herein COULD be added to library.h instead of
    including this as a separate file. See the README for instructions. */
 
-/* These prototypes probably belong in mpi.h in the src/STUBS directory. */
-#ifndef OPEN_MPI
-#define MPI_Comm_f2c(a) a
-#define MPI_Fint int
-#endif
-
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -38,7 +32,7 @@ int lammps_extract_compute_vectorsize (void*, char*, int);
 void lammps_extract_compute_arraysize (void*, char*, int, int*, int*);
 int lammps_extract_fix_vectorsize (void*, char*, int);
 void lammps_extract_fix_arraysize (void*, char*, int, int*, int*);
-void lammps_error_all (void *ptr, const char*, int, const char*);
+void lammps_error_all (void*, const char*, int, const char*);
 
 #ifdef __cplusplus
 }

examples/COUPLE/fortran2/README

@@ -12,7 +12,7 @@ questions:
 Karl D. Hammond
 University of Tennessee, Knoxville
 karlh at ugcs.caltech.edu
-karlh atutk.edu
+karlh at utk.edu
 
 -------------------------------------
 
@@ -27,7 +27,7 @@ compile.
 The following steps will work to compile this module (replace ${LAMMPS_SRC}
 with the path to your LAMMPS source directory):
  (1) Compile LAMMPS as a static library.  Call the resulting file ${LAMMPS_LIB},
-     which will have an actual name lake liblammps_openmpi.a.  If compiling
+     which will have an actual name lake liblmp_openmpi.a.  If compiling
      using the MPI stubs in ${LAMMPS_SRC}/STUBS, you will need to know where
      libmpi.a is as well (I'll call it ${MPI_STUBS} hereafter)
  (2) Copy said library to your Fortran program's source directory or include
@@ -61,7 +61,7 @@ with the path to your LAMMPS source directory):
      need to have the .mod file from part (3).
 
      It is also possible to add LAMMPS.o and LAMMPS-wrapper.o into the
-     LAMMPS library (e.g., liblammps_openmpi.a) instead of creating a separate
+     LAMMPS library (e.g., liblmp_openmpi.a) instead of creating a separate
      library, like so:
         ar rs ${LAMMPS_LIB} LAMMPS.o LAMMPS-wrapper.o
      In this case, you can now use the Fortran wrapper functions as if they

examples/COUPLE/fortran2/makefile

@@ -1,7 +1,7 @@
 SHELL = /bin/sh
 
 # Path to LAMMPS extraction directory
-LAMMPS_ROOT = ../svn-dist
+LAMMPS_ROOT = ../../..
 LAMMPS_SRC = $(LAMMPS_ROOT)/src
 
 # Remove the line below if using mpicxx/mpic++ as your C++ compiler

python/install.py

@@ -1,35 +1,67 @@
 #!/usr/local/bin/python
 
-# copy LAMMPS shared library src/liblammps.so and lammps.py to system dirs
+# copy LAMMPS src/liblammps.so and lammps.py to system dirs
-# Syntax: python install.py [libdir] [pydir]
-#         libdir = target dir for src/liblammps.so, default = /usr/local/lib
-#         pydir = target dir for lammps.py, default = Python site-packages dir
 
-import sys,commands
+instructions = """
+Syntax: python install.py [-h] [libdir] [pydir]
+        libdir = target dir for src/liblammps.so, default = /usr/local/lib
+        pydir = target dir for lammps.py, default = Python site-packages dir
+"""
 
-if len(sys.argv) > 3:
+import sys,os,commands
-  print "Syntax: python install.py [libdir] [pydir]"
+
+if (len(sys.argv) > 1 and sys.argv[1] == "-h") or len(sys.argv) > 3:
+  print instructions
   sys.exit()
 
 if len(sys.argv) >= 2: libdir = sys.argv[1]
 else: libdir = "/usr/local/lib"
 
 if len(sys.argv) == 3: pydir = sys.argv[2]
+else: pydir = ""
+
+# copy C lib to libdir if it exists
+# warn if not in LD_LIBRARY_PATH or LD_LIBRARY_PATH is undefined
+
+if not os.path.isdir(libdir):
+  print "ERROR: libdir %s does not exist" % libdir
+  sys.exit()
+  
+if "LD_LIBRARY_PATH" not in os.environ:
+  print "WARNING: LD_LIBRARY_PATH undefined, cannot check libdir %s" % libdir
 else:
-  paths = sys.path
+  libpaths = os.environ['LD_LIBRARY_PATH'].split(':')
-  for i,path in enumerate(paths):
+  if libdir not in libpaths:
-    index = path.rfind("site-packages")
+    print "WARNING: libdir %s not in LD_LIBRARY_PATH" % libdir
-    if index < 0: continue
-    if index == len(path) - len("site-packages"): break
-  pydir = paths[i]
 
 str = "cp ../src/liblammps.so %s" % libdir
 print str
 outstr = commands.getoutput(str)
 if len(outstr.strip()): print outstr
 
-str = "cp ../python/lammps.py %s" % pydir
+# copy lammps.py to pydir if it exists
-print str
+# if pydir not specified, install in site-packages via distutils setup()
-outstr = commands.getoutput(str)
-if len(outstr.strip()): print outstr
 
+if pydir:
+  if not os.path.isdir(pydir):
+    print "ERROR: pydir %s does not exist" % pydir
+    sys.exit()
+  str = "cp ../python/lammps.py %s" % pydir
+  print str
+  outstr = commands.getoutput(str)
+  if len(outstr.strip()): print outstr
+  sys.exit()
+  
+print "installing lammps.py in Python site-packages dir"
+
+os.chdir('../python')                # in case invoked via make in src dir
+
+from distutils.core import setup
+sys.argv = ["setup.py","install"]    # as if had run "python setup.py install"
+setup(name = "lammps",
+      version = "15Aug12",
+      author = "Steve Plimpton",
+      author_email = "sjplimp@sandia.gov",
+      url = "http://lammps.sandia.gov",
+      description = "LAMMPS molecular dynamics library",
+      py_modules = ["lammps"])

python/lammps.py

@@ -13,7 +13,7 @@
 
 # Python wrapper on LAMMPS library via ctypes
 
-import types
+import sys,traceback,types
 from ctypes import *
 import os.path
 
@@ -27,6 +27,8 @@ class lammps:
       if not name: self.lib = CDLL("liblammps.so")
       else: self.lib = CDLL("liblammps_%s.so" % name)
     except:
+      type,value,tb = sys.exc_info()
+      traceback.print_exception(type,value,tb)
       raise OSError,"Could not load LAMMPS dynamic library"
 
     # create an instance of LAMMPS

src/KSPACE/fft3d_wrap.h

@@ -39,6 +39,8 @@ class FFT3d : protected Pointers {
 
 E: Could not create 3d FFT plan
 
-The FFT setup in pppm failed.
+The FFT setup for the PPPM solver failed, typically due
+to lack of memory.  This is an unusual error.  Check the
+size of the FFT grid you are requesting.
 
 */

src/KSPACE/pppm.cpp

@@ -100,7 +100,6 @@ PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
   // see JCP 109, pg 7698 for derivation of coefficients
   // higher order coefficients may be computed if needed
 
-  memory->destroy(acons);
   memory->create(acons,8,7,"pppm:acons");
   acons[1][0] = 2.0 / 3.0;
   acons[2][0] = 1.0 / 50.0;

src/MAKE/Makefile.g++

@@ -85,9 +85,6 @@ $(EXE):	$(OBJ)
 lib:	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
 
-#shlib:	$(OBJ)
-#	$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
-
 shlib:	$(OBJ)
 	$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
         $(OBJ) $(EXTRA_LIB) $(LIB)

src/Make.sh

@@ -1,6 +1,8 @@
-# Make.sh = update Makefile.lib or Makefile.list or style_*.h files
+# Make.sh = update Makefile.lib, Makefile.shlib, Makefile.list 
+#           or style_*.h files
 # Syntax: sh Make.sh style
 #         sh Make.sh Makefile.lib
+#         sh Make.sh Makefile.shlib
 #         sh Make.sh Makefile.list
 
 # function to create one style_*.h file

src/Makefile

@@ -130,7 +130,7 @@ makelist:
 	@$(SHELL) Make.sh style
 	@$(SHELL) Make.sh Makefile.list
 
-# install LAMMPS shared lib and Python wrapper in Python
+# install LAMMPS shared lib and Python wrapper for Python usage
 
 install-python:
 	@python ../python/install.py

src/Makefile.lib

@@ -21,9 +21,6 @@ help:
 	@files="`ls MAKE/Makefile.*`"; \
 	for file in $$files; do head -1 $$file; done
 
-clean:
-	rm -rf Obj_*
-
 .DEFAULT:
 	@test -f MAKE/Makefile.$@
 	@if [ ! -d Obj_$@ ]; then mkdir Obj_$@; fi

src/Makefile.list

@@ -21,9 +21,6 @@ help:
 	@files="`ls MAKE/Makefile.*`"; \
 	for file in $$files; do head -1 $$file; done
 
-clean:
-	rm -rf Obj_*
-
 .DEFAULT:
 	@test -f MAKE/Makefile.$@
 	@if [ ! -d Obj_$@ ]; then mkdir Obj_$@; fi

src/USER-CUDA/cuda.cpp

@@ -410,6 +410,8 @@ void Cuda::setDomainParams()
       cu_domain->boxlo_lamda[i] = domain->boxlo_lamda[i];
       cu_domain->boxhi_lamda[i] = domain->boxhi_lamda[i];
       cu_domain->prd_lamda[i] = domain->prd_lamda[i];
+      cu_domain->sublo[i] = domain->sublo_lamda[i];
+      cu_domain->subhi[i] = domain->subhi_lamda[i];
     }
 
     cu_domain->xy = domain->xy;

src/USER-OMP/pair_lj_expand_omp.h

@@ -17,7 +17,7 @@
 
 #ifdef PAIR_CLASS
 
-PairStyle(lj/cut/omp,PairLJExpandOMP)
+PairStyle(lj/expand/omp,PairLJExpandOMP)
 
 #else
 

src/library.cpp

@@ -30,7 +30,9 @@
 #include "modify.h"
 #include "compute.h"
 #include "fix.h"
+#include "comm.h"
 #include "memory.h"
+#include "error.h"
 
 using namespace LAMMPS_NS;
 
@@ -383,8 +385,13 @@ void lammps_gather_atoms(void *ptr, char *name,
 
   // error if tags are not defined or not consecutive
 
-  if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) return;
+  int flag = 0;
-  if (lmp->atom->natoms > MAXSMALLINT) return;
+  if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
+  if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
+  if (flag && lmp->comm->me == 0) {
+    lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
+    return;
+  }
 
   int natoms = static_cast<int> (lmp->atom->natoms);
 
@@ -464,10 +471,16 @@ void lammps_scatter_atoms(void *ptr, char *name,
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
 
-  // error if tags are not defined or not consecutive
+  // error if tags are not defined or not consecutive or no atom map
 
-  if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) return;
+  int flag = 0;
-  if (lmp->atom->natoms > MAXSMALLINT) return;
+  if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
+  if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
+  if (lmp->atom->map_style == 0) flag = 1;
+  if (flag && lmp->comm->me == 0) {
+    lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms");
+    return;
+  }
 
   int natoms = static_cast<int> (lmp->atom->natoms);