PG-PuReMD: port sPuReMD logic for seperating into library and driver.

PG-PuReMD/Makefile.am

@@ -16,15 +16,15 @@ NVCCFLAGS += --compiler-options "$(DEFS) $(NVCC_OPT_CODE_DEFS) -O3 -funroll-loop
 endif
 
 
-bin_PROGRAMS = bin/pg-puremd
-bin_pg_puremd_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c src/list.c \
+lib_LTLIBRARIES = lib/libpuremd.la
+lib_libpuremd_la_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c src/list.c \
 	src/lookup.c src/io_tools.c src/reset_tools.c src/restart.c src/random.c \
 	src/tool_box.c src/traj.c src/analyze.c src/box.c src/system_props.c \
 	src/control.c src/comm_tools.c src/geo_tools.c src/lin_alg.c src/neighbors.c \
 	src/charges.c src/bond_orders.c src/multi_body.c src/bonds.c src/valence_angles.c \
 	src/hydrogen_bonds.c src/torsion_angles.c src/nonbonded.c src/forces.c \
-	src/integrate.c src/init_md.c src/parallelreax.c
-include_HEADERS = src/reax_types.h src/index_utils.h \
+	src/integrate.c src/init_md.c src/puremd.c
+lib_libpuremd_la_SOURCES += src/reax_types.h src/index_utils.h \
         src/allocate.h src/basic_comm.h src/ffield.h src/grid.h src/list.h \
 	src/lookup.h src/io_tools.h src/reset_tools.h src/restart.h src/random.h src/vector.h \
 	src/tool_box.h src/traj.h src/analyze.h src/box.h src/system_props.h \
@@ -32,9 +32,10 @@ include_HEADERS = src/reax_types.h src/index_utils.h \
 	src/charges.h src/bond_orders.h src/multi_body.h src/bonds.h src/valence_angles.h \
 	src/hydrogen_bonds.h src/torsion_angles.h src/nonbonded.h src/forces.h \
 	src/integrate.h src/init_md.h
+include_HEADERS = src/puremd.h
 
 if USE_CUDA
-bin_pg_puremd_SOURCES += src/cuda/cuda_utils.cu src/cuda/cuda_allocate.cu src/cuda/cuda_environment.cu \
+lib_libpuremd_la_SOURCES += src/cuda/cuda_utils.cu src/cuda/cuda_allocate.cu src/cuda/cuda_environment.cu \
       src/cuda/cuda_system_props.cu src/cuda/cuda_reduction.cu src/cuda/cuda_box.cu src/cuda/cuda_list.cu \
       src/cuda/cuda_copy.cu src/cuda/cuda_reset_tools.cu src/cuda/cuda_random.cu \
       src/cuda/cuda_neighbors.cu src/cuda/cuda_bond_orders.cu src/cuda/cuda_bonds.cu \
@@ -43,7 +44,7 @@ bin_pg_puremd_SOURCES += src/cuda/cuda_utils.cu src/cuda/cuda_allocate.cu src/cu
       src/cuda/cuda_charges.cu src/cuda/cuda_lin_alg.cu \
       src/cuda/cuda_nonbonded.cu src/cuda/cuda_integrate.cu src/cuda/cuda_post_evolve.cu \
       src/cuda/cuda_init_md.cu src/cuda/cuda_lookup.cu
-include_HEADERS += src/cuda/cuda_helpers.h src/cuda/cuda_shuffle.h \
+lib_libpuremd_la_SOURCES += src/cuda/cuda_helpers.h src/cuda/cuda_shuffle.h \
       src/cuda/cuda_utils.h src/cuda/cuda_allocate.h src/cuda/cuda_environment.h \
       src/cuda/cuda_system_props.h src/cuda/cuda_reduction.h src/cuda/cuda_box.h src/cuda/cuda_list.h \
       src/cuda/cuda_copy.h src/cuda/cuda_reset_tools.h src/cuda/cuda_random.h src/cuda/cuda_vector.h \
@@ -55,20 +56,28 @@ include_HEADERS += src/cuda/cuda_helpers.h src/cuda/cuda_shuffle.h \
       src/cuda/cuda_init_md.h src/cuda/cuda_lookup.h
 
 if DEBUG
-bin_pg_puremd_SOURCES += src/cuda/cuda_validation.cu
-include_HEADERS += src/cuda/cuda_validation.h
+lib_libpuremd_la_SOURCES += src/cuda/cuda_validation.cu
+lib_libpuremd_la_SOURCES += src/cuda/cuda_validation.h
 endif
 
 # dummy source to cause C linking
-nodist_EXTRA_bin_pg_puremd_SOURCES = src/dummy.c
-
+nodist_EXTRA_lib_libpuremd_la_SOURCES = src/dummy.c
 endif
 
+lib_libpuremd_la_CFLAGS = $(AM_CFLAGS) $(MPI_CFLAGS) $(CFLAGS)
+lib_libpuremd_la_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS)
+lib_libpuremd_la_LIBADD = $(AM_LDADD) $(MPI_LIBS) $(LDADD) -lstdc++
+lib_libpuremd_la_LDFLAGS = -version-info 1:0:0
+if USE_CUDA
+lib_libpuremd_la_CFLAGS += $(CUDA_CFLAGS)
+lib_libpuremd_la_LIBADD += $(CUDA_LIBS)
+endif
 
+bin_PROGRAMS = bin/pg-puremd
+bin_pg_puremd_SOURCES = src/driver.c
 bin_pg_puremd_CFLAGS = $(AM_CFLAGS) $(MPI_CFLAGS) $(CFLAGS)
-bin_pg_puremd_CPPFLAGS = $(AM_CPPFLAGS) $(CPPFLAGS)
-bin_pg_puremd_LDADD = $(AM_LDADD) $(MPI_LIBS) $(LDADD) -lstdc++
-
+bin_pg_puremd_CPPFLAGS = -I src $(AM_CPPFLAGS) $(CPPFLAGS)
+bin_pg_puremd_LDADD = lib/libpuremd.la $(AM_LDADD) $(MPI_LIBS) $(LDADD) -lstdc++
 if USE_CUDA
 bin_pg_puremd_CFLAGS += $(CUDA_CFLAGS)
 bin_pg_puremd_LDADD += $(CUDA_LIBS)

PG-PuReMD/aclocal.m4

@@ -56,6 +56,66 @@ m4_ifndef([AC_AUTOCONF_VERSION],
   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
 _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
 
+# Copyright (C) 2011-2017 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_PROG_AR([ACT-IF-FAIL])
+# -------------------------
+# Try to determine the archiver interface, and trigger the ar-lib wrapper
+# if it is needed.  If the detection of archiver interface fails, run
+# ACT-IF-FAIL (default is to abort configure with a proper error message).
+AC_DEFUN([AM_PROG_AR],
+[AC_BEFORE([$0], [LT_INIT])dnl
+AC_BEFORE([$0], [AC_PROG_LIBTOOL])dnl
+AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([ar-lib])dnl
+AC_CHECK_TOOLS([AR], [ar lib "link -lib"], [false])
+: ${AR=ar}
+
+AC_CACHE_CHECK([the archiver ($AR) interface], [am_cv_ar_interface],
+  [AC_LANG_PUSH([C])
+   am_cv_ar_interface=ar
+   AC_COMPILE_IFELSE([AC_LANG_SOURCE([[int some_variable = 0;]])],
+     [am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
+      AC_TRY_EVAL([am_ar_try])
+      if test "$ac_status" -eq 0; then
+        am_cv_ar_interface=ar
+      else
+        am_ar_try='$AR -NOLOGO -OUT:conftest.lib conftest.$ac_objext >&AS_MESSAGE_LOG_FD'
+        AC_TRY_EVAL([am_ar_try])
+        if test "$ac_status" -eq 0; then
+          am_cv_ar_interface=lib
+        else
+          am_cv_ar_interface=unknown
+        fi
+      fi
+      rm -f conftest.lib libconftest.a
+     ])
+   AC_LANG_POP([C])])
+
+case $am_cv_ar_interface in
+ar)
+  ;;
+lib)
+  # Microsoft lib, so override with the ar-lib wrapper script.
+  # FIXME: It is wrong to rewrite AR.
+  # But if we don't then we get into trouble of one sort or another.
+  # A longer-term fix would be to have automake use am__AR in this case,
+  # and then we could set am__AR="$am_aux_dir/ar-lib \$(AR)" or something
+  # similar.
+  AR="$am_aux_dir/ar-lib $AR"
+  ;;
+unknown)
+  m4_default([$1],
+             [AC_MSG_ERROR([could not determine $AR interface])])
+  ;;
+esac
+AC_SUBST([AR])dnl
+])
+
 # AM_AUX_DIR_EXPAND                                         -*- Autoconf -*-
 
 # Copyright (C) 2001-2017 Free Software Foundation, Inc.
@@ -1153,3 +1213,8 @@ AC_SUBST([am__untar])
 m4_include([../m4/acx_mpi.m4])
 m4_include([../m4/ax_compiler_vendor.m4])
 m4_include([../m4/ax_cuda.m4])
+m4_include([../m4/libtool.m4])
+m4_include([../m4/ltoptions.m4])
+m4_include([../m4/ltsugar.m4])
+m4_include([../m4/ltversion.m4])
+m4_include([../m4/lt~obsolete.m4])

PG-PuReMD/configure.ac

@@ -10,8 +10,9 @@ sav_CFLAGS="$CFLAGS"
 AM_INIT_AUTOMAKE([1.15 subdir-objects -Wall -Werror foreign])
 # Enable silent build rules by default.
 m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])], [AC_SUBST([AM_DEFAULT_VERBOSITY],[1])])
-#LT_PREREQ([2.2])
-#LT_INIT([dlopen])
+AM_PROG_AR
+LT_PREREQ([2.2])
+LT_INIT([dlopen])
 
 AC_CONFIG_MACRO_DIR([../m4])
 

PG-PuReMD/src/driver.c

+
+/*----------------------------------------------------------------------
+  SerialReax - Reax Force Field Simulator
+
+  Copyright (2010) Purdue University
+  Hasan Metin Aktulga, haktulga@cs.purdue.edu
+  Joseph Fogarty, jcfogart@mail.usf.edu
+  Sagar Pandit, pandit@usf.edu
+  Ananth Y Grama, ayg@cs.purdue.edu
+
+  This program is free software; you can redistribute it and/or
+  modify it under the terms of the GNU General Public License as
+  published by the Free Software Foundation; either version 2 of
+  the License, or (at your option) any later version.
+
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+  See the GNU General Public License for more details:
+  <http://www.gnu.org/licenses/>.
+  ----------------------------------------------------------------------*/
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "puremd.h"
+
+#define INVALID_INPUT (-1)
+
+
+static void usage( char * argv[] )
+{
+    fprintf( stderr, "usage: ./%s geometry_file force_field_params_file control_file\n", argv[0] );
+}
+
+
+int main( int argc, char* argv[] )
+{
+    void *handle;
+    int ret;
+
+    MPI_Init( &argc, &argv );
+
+    if ( argc != 4 )
+    {
+        usage( argv );
+        MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
+    }
+
+    handle = setup( argv[1], argv[2], argv[3] );
+    ret = PUREMD_FAILURE;
+
+    if ( handle != NULL )
+    {
+        ret = simulate( handle );
+    }
+
+    MPI_Finalized( &ret );
+    if ( !ret )
+    { 
+        MPI_Finalize( );
+    }
+
+    if ( ret == PUREMD_SUCCESS )
+    {
+        ret = cleanup( handle );
+    }
+
+    return (ret == PUREMD_SUCCESS) ? 0 : (-1);
+}

PG-PuReMD/src/ffield.c

@@ -30,7 +30,7 @@
 #endif
 
 
-void Read_Force_Field( char *ffield_file, reax_interaction *reax,
+void Read_Force_Field_File( char *ffield_file, reax_interaction *reax,
         reax_system *system, control_params *control )
 {
     FILE *fp;

PG-PuReMD/src/ffield.h

@@ -29,7 +29,7 @@
 extern "C" {
 #endif
 
-void Read_Force_Field( char*, reax_interaction*, reax_system *, control_params* );
+void Read_Force_Field_File( char*, reax_interaction*, reax_system *, control_params* );
 
 #ifdef __cplusplus
 }

PG-PuReMD/src/geo_tools.c

@@ -67,7 +67,7 @@ void Count_Geo_Atoms( FILE *geo, reax_system *system )
 }
 
 
-void Read_Geo( char* geo_file, reax_system* system, control_params *control,
+void Read_Geo_File( char* geo_file, reax_system* system, control_params *control,
         simulation_data *data, storage *workspace, mpi_datatypes *mpi_data )
 {
     int i, j, serial, top;
@@ -79,7 +79,7 @@ void Read_Geo( char* geo_file, reax_system* system, control_params *control,
     reax_atom *atom;
 
     /* open the geometry file */
-    geo = sfopen( geo_file, "r", "Read_Geo::geo" );
+    geo = sfopen( geo_file, "r", "Read_Geo_File::geo" );
 
     /* read box information */
     fscanf( geo, CUSTOM_BOXGEO_FORMAT,
@@ -136,7 +136,7 @@ void Read_Geo( char* geo_file, reax_system* system, control_params *control,
         }
     }
 
-    sfclose( geo, "Read_Geo::geo" );
+    sfclose( geo, "Read_Geo_File::geo" );
 
 #if defined(DEBUG_FOCUS)
     fprintf( stderr, "p%d: finished reading the geo file\n", system->my_rank );
@@ -247,7 +247,7 @@ void Count_PDB_Atoms( FILE *geo, reax_system *system )
 }
 
 
-void Read_PDB( char* pdb_file, reax_system* system, control_params *control,
+void Read_PDB_File( char* pdb_file, reax_system* system, control_params *control,
         simulation_data *data, storage *workspace, mpi_datatypes *mpi_data )
 {
     FILE *pdb;
@@ -264,7 +264,7 @@ void Read_PDB( char* pdb_file, reax_system* system, control_params *control,
     rvec x;
     reax_atom *atom;
 
-    pdb = sfopen( pdb_file, "r", "Read_PDB::pdb" );
+    pdb = sfopen( pdb_file, "r", "Read_PDB_File::pdb" );
 
     /* allocate memory for tokenizing pdb lines */
     Allocate_Tokenizer_Space( &s, &s1, &tmp );
@@ -451,14 +451,14 @@ void Read_PDB( char* pdb_file, reax_system* system, control_params *control,
         }
     }
 
-    sfclose( pdb, "Read_PDB::pdb" );
+    sfclose( pdb, "Read_PDB_File::pdb" );
 }
 
 
 /* PDB serials are written without regard to the order, we'll see if this
  * cause trouble, if so we'll have to rethink this approach
  * Also, we do not write connect lines yet.  */
-void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
+void Write_PDB_File( reax_system* system, reax_list* bonds, simulation_data *data,
         control_params *control, mpi_datatypes *mpi_data, output_controls *out_control )
 {
     int i, cnt, me, np, buffer_req, buffer_len;
@@ -477,7 +477,7 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
     np = control->nprocs;
 
     /* Allocation*/
-    line = smalloc( sizeof(char) * PDB_ATOM_FORMAT_O_LENGTH, "Write_PDB::line" );
+    line = smalloc( sizeof(char) * PDB_ATOM_FORMAT_O_LENGTH, "Write_PDB_File::line" );
     if ( me == MASTER_NODE )
     {
         buffer_req = system->bigN * PDB_ATOM_FORMAT_O_LENGTH;
@@ -487,7 +487,7 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
         buffer_req = system->n * PDB_ATOM_FORMAT_O_LENGTH;
     }
 
-    buffer = smalloc( sizeof(char) * buffer_req, "Write_PDB::buffer" );
+    buffer = smalloc( sizeof(char) * buffer_req, "Write_PDB_File::buffer" );
 
     pdb = NULL;
     line[0] = 0;
@@ -512,7 +512,7 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
 
 
         sprintf( fname, "%s-%d.pdb", control->sim_name, data->step );
-        pdb = sfopen( fname, "w", "Write_PDB::pdb" );
+        pdb = sfopen( fname, "w", "Write_PDB_File::pdb" );
         fprintf( pdb, PDB_CRYST1_FORMAT_O,
                  "CRYST1",
                  system->big_box.box_norms[0], system->big_box.box_norms[1],
@@ -563,7 +563,7 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
     if ( me == MASTER_NODE)
     {
         fprintf( pdb, "%s", buffer );
-        sfclose( pdb, "Write_PDB::pdb" );
+        sfclose( pdb, "Write_PDB_File::pdb" );
     }
 
     /* Writing connect information */
@@ -585,6 +585,6 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
     }
     */
 
-    sfree( buffer, "Write_PDB::buffer" );
-    sfree( line, "Write_PDB::line" );
+    sfree( buffer, "Write_PDB_File::buffer" );
+    sfree( line, "Write_PDB_File::line" );
 }

PG-PuReMD/src/geo_tools.h

@@ -115,13 +115,13 @@ COLUMNS       DATA TYPE       FIELD         DEFINITION
 extern "C" {
 #endif
 
-void Read_Geo( char*, reax_system*, control_params*,
+void Read_Geo_File( char*, reax_system*, control_params*,
         simulation_data*, storage*, mpi_datatypes* );
 
-void Read_PDB( char*, reax_system*, control_params*,
+void Read_PDB_File( char*, reax_system*, control_params*,
         simulation_data*, storage*, mpi_datatypes* );
 
-void Write_PDB( reax_system*, reax_list*, simulation_data*,
+void Write_PDB_File( reax_system*, reax_list*, simulation_data*,
         control_params*, mpi_datatypes*, output_controls* );
 
 #ifdef __cplusplus

PG-PuReMD/src/puremd.h

+/*----------------------------------------------------------------------
+  SerialReax - Reax Force Field Simulator
+
+  Copyright (2010) Purdue University
+  Hasan Metin Aktulga, haktulga@cs.purdue.edu
+  Joseph Fogarty, jcfogart@mail.usf.edu
+  Sagar Pandit, pandit@usf.edu
+  Ananth Y Grama, ayg@cs.purdue.edu
+
+  This program is free software; you can redistribute it and/or
+  modify it under the terms of the GNU General Public License as
+  published by the Free Software Foundation; either version 2 of
+  the License, or (at your option) any later version.
+
+  This program is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+  See the GNU General Public License for more details:
+  <http://www.gnu.org/licenses/>.
+  ----------------------------------------------------------------------*/
+
+#ifndef __PUREMD_H_
+#define __PUREMD_H_
+
+#include "reax_types.h"
+
+
+#define PUREMD_SUCCESS (0)
+#define PUREMD_FAILURE (-1)
+
+
+#ifdef __cplusplus
+extern "C"  {
+#endif
+
+void* setup( const char * const, const char * const,
+        const char * const );
+
+int setup_callback( const void * const, const callback_function );
+
+int simulate( const void * const );
+
+int cleanup( const void * const );
+
+reax_atom* get_atoms( const void * const );
+
+int set_output_enabled( const void * const, const int );
+
+#ifdef __cplusplus
+}
+#endif
+
+
+#endif

PG-PuReMD/src/reax_types.h

@@ -548,6 +548,7 @@ typedef struct molecule molecule;
 typedef struct LR_data LR_data;
 typedef struct cubic_spline_coef cubic_spline_coef;
 typedef struct LR_lookup_table LR_lookup_table;
+typedef struct puremd_handle puremd_handle;
 
 
 /* function pointer definitions */
@@ -563,6 +564,8 @@ typedef real (*lookup_function)( real );
 typedef void (*message_sorter)( reax_system*, int, int, int, mpi_out_data* );
 /**/
 typedef void (*unpacker)( reax_system*, int, void*, int, neighbor_proc*, int );
+/**/
+typedef void (*callback_function)(reax_atom*, simulation_data*, reax_list*);
 
 
 /* struct definitions */
@@ -2458,6 +2461,30 @@ struct LR_lookup_table
 };
 
 
+/* Handle for working with an instance of the PuReMD library */
+struct puremd_handle
+{
+    /* System info. struct pointer */
+    reax_system *system;
+    /* System struct pointer */
+    control_params *control;
+    /* Control parameters struct pointer */
+    simulation_data *data;
+    /* Internal workspace struct pointer */
+    storage *workspace;
+    /* Reax interaction list struct pointer */
+    reax_list **lists;
+    /* Output controls struct pointer */
+    output_controls *out_control;
+    /* MPI datatypes struct pointer */
+    mpi_datatypes *mpi_data;
+    /* TRUE if file I/O for simulation output enabled, FALSE otherwise */
+    int output_enabled;
+    /* Callback for getting simulation state at the end of each time step */
+    callback_function callback;
+};
+
+
 /* CUDA-specific globals */
 extern reax_list **dev_lists;
 extern storage *dev_workspace;

PG-PuReMD/src/restart.c

@@ -29,7 +29,7 @@
 #include "vector.h"
 
 
-void Write_Binary_Restart( reax_system *system, control_params *control,
+void Write_Binary_Restart_File( reax_system *system, control_params *control,
         simulation_data *data, output_controls *out_control,
         mpi_datatypes *mpi_data )
 {
@@ -49,7 +49,7 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
     {
         /* master handles the restart file */
         sprintf( fname, "%s.res%d", control->sim_name, data->step );
-        fres = sfopen( fname, "wb", "Write_Binary_Restart::fres" );
+        fres = sfopen( fname, "wb", "Write_Binary_Restart_File::fres" );
 
         /* master can write the header by itself */
         res_header.step = data->step;
@@ -64,12 +64,12 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
 
         /* master needs to allocate space for all atoms */
         buffer = scalloc( system->bigN, sizeof(restart_atom),
-                "Write_Binary_Restart::buffer" );
+                "Write_Binary_Restart_File::buffer" );
     }
     else
     {
         buffer = scalloc( system->n, sizeof(restart_atom),
-                "Write_Binary_Restart::buffer" );
+                "Write_Binary_Restart_File::buffer" );
     }
 
     /* fill in the buffers */
@@ -108,14 +108,14 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
     if ( me == MASTER_NODE )
     {
         fwrite( buffer, system->bigN, sizeof(restart_atom), fres );
-        sfclose( fres, "Write_Binary_Restart::fres" );
+        sfclose( fres, "Write_Binary_Restart_File::fres" );
     }
 
-    sfree( buffer, "Write_Binary_Restart::buffer" );
+    sfree( buffer, "Write_Binary_Restart_File::buffer" );
 }
 
 
-void Write_Restart( reax_system *system, control_params *control,
+void Write_Restart_File( reax_system *system, control_params *control,
         simulation_data *data, output_controls *out_control,
         mpi_datatypes *mpi_data )
 {
@@ -135,7 +135,7 @@ void Write_Restart( reax_system *system, control_params *control,
     if ( me == MASTER_NODE )
     {
         sprintf( fname, "%s.res%d", control->sim_name, data->step );
-        fres = sfopen( fname, "w", "Write_Restart::fres" );
+        fres = sfopen( fname, "w", "Write_Restart_File::fres" );
 
         /* write the header - only master writes it */
         fprintf( fres, RESTART_HEADER,
@@ -156,7 +156,7 @@ void Write_Restart( reax_system *system, control_params *control,
         buffer_req = system->n * RESTART_LINE_LEN + 1;
     }
 
-    buffer = smalloc( sizeof(char) * buffer_req, "Write_Restart::buffer" );
+    buffer = smalloc( sizeof(char) * buffer_req, "Write_Restart_File::buffer" );
     line[0] = 0;
     buffer[0] = 0;
 
@@ -200,10 +200,10 @@ void Write_Restart( reax_system *system, control_params *control,
     if ( me == MASTER_NODE )
     {
         fprintf( fres, "%s", buffer );
-        sfclose( fres, "Write_Restart::fres" );
+        sfclose( fres, "Write_Restart_File::fres" );
     }
-    sfree( buffer, "Write_Restart::buffer" );
-    sfree( line, "Write_Restart::line" );
+    sfree( buffer, "Write_Restart_File::buffer" );
+    sfree( line, "Write_Restart_File::line" );
 }
 
 
@@ -235,7 +235,7 @@ void Count_Binary_Restart_Atoms( FILE *fres, reax_system *system )
 }
 
 
-void Read_Binary_Restart( char *res_file, reax_system *system,
+void Read_Binary_Restart_File( char *res_file, reax_system *system,
         control_params *control, simulation_data *data,
         storage *workspace, mpi_datatypes *mpi_data )
 {
@@ -245,7 +245,7 @@ void Read_Binary_Restart( char *res_file, reax_system *system,
     restart_atom res_atom;
     reax_atom *p_atom;
 
-    fres = sfopen( res_file, "rb", "Read_Binary_Restart::fres" );
+    fres = sfopen( res_file, "rb", "Read_Binary_Restart_File::fres" );
 
     /* first read the header lines */
     fread( &res_header, sizeof(restart_header), 1, fres );
@@ -305,7 +305,7 @@ void Read_Binary_Restart( char *res_file, reax_system *system,
         }
     }
 
-    sfclose( fres, "Read_Binary_Restart::fres" );
+    sfclose( fres, "Read_Binary_Restart_File::fres" );
 
     data->step = data->prev_steps;
     // nsteps is updated based on the number of steps in the previous run
@@ -350,7 +350,7 @@ void Count_Restart_Atoms( FILE *fres, reax_system *system )
 }
 
 
-void Read_Restart( char *res_file, reax_system *system,
+void Read_Restart_File( char *res_file, reax_system *system,
         control_params *control, simulation_data *data,
         storage *workspace, mpi_datatypes *mpi_data )
 {
@@ -362,13 +362,13 @@ void Read_Restart( char *res_file, reax_system *system,
     rvec x_temp, v_temp;
     rtensor box;
 
-    fres = sfopen( res_file, "r", "Read_Restart::fres" );
+    fres = sfopen( res_file, "r", "Read_Restart_File::fres" );
 
-    s = smalloc( sizeof(char) * MAX_LINE, "Read_Restart::s" );
-    tmp = smalloc( sizeof(char*) * MAX_TOKENS, "Read_Restart::tmp" );
+    s = smalloc( sizeof(char) * MAX_LINE, "Read_Restart_File::s" );
+    tmp = smalloc( sizeof(char*) * MAX_TOKENS, "Read_Restart_File::tmp" );
     for (i = 0; i < MAX_TOKENS; i++)
     {
-        tmp[i] = smalloc( sizeof(char) * MAX_LINE, "Read_Restart::tmp[i]" );
+        tmp[i] = smalloc( sizeof(char) * MAX_LINE, "Read_Restart_File::tmp[i]" );
     }
 
     //read first header lines
@@ -486,15 +486,15 @@ void Read_Restart( char *res_file, reax_system *system,
             top++;
         }
     }
-    sfclose( fres, "Read_Restart::fres" );
+    sfclose( fres, "Read_Restart_File::fres" );
 
     /* free memory allocations at the top */
     for ( i = 0; i < MAX_TOKENS; i++ )
     {
-        sfree( tmp[i], "Read_Restart::tmp[i]" );
+        sfree( tmp[i], "Read_Restart_File::tmp[i]" );
     }
-    sfree( tmp, "Read_Restart::tmp" );
-    sfree( s, "Read_Restart::s" );
+    sfree( tmp, "Read_Restart_File::tmp" );
+    sfree( s, "Read_Restart_File::s" );
 
     data->step = data->prev_steps;
     // nsteps is updated based on the number of steps in the previous run

PG-PuReMD/src/restart.h

@@ -45,16 +45,16 @@
 extern "C"  {
 #endif
 
-void Write_Binary_Restart( reax_system*, control_params*,
+void Write_Binary_Restart_File( reax_system*, control_params*,
         simulation_data*, output_controls*, mpi_datatypes* );
 
-void Write_Restart( reax_system*, control_params*,
+void Write_Restart_File( reax_system*, control_params*,
         simulation_data*, output_controls*, mpi_datatypes* );
 
-void Read_Binary_Restart( char*, reax_system*, control_params*,
+void Read_Binary_Restart_File( char*, reax_system*, control_params*,
         simulation_data*, storage*, mpi_datatypes* );
 
-void Read_Restart( char*, reax_system*, control_params*,
+void Read_Restart_File( char*, reax_system*, control_params*,
         simulation_data*, storage*, mpi_datatypes* );
 
 #ifdef __cplusplus