From c64018078904bc649b061e23a79ba08445e45e7c Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Wed, 7 Feb 2018 14:47:47 -0500
Subject: [PATCH] sPuReMD: update library interface and driver. Add prototype
driver in Python.
---
sPuReMD/src/driver.c | 27 ++++--
sPuReMD/src/geo_tools.c | 6 +-
sPuReMD/src/geo_tools.h | 6 +-
sPuReMD/src/mytypes.h | 20 ++++
sPuReMD/src/restart.c | 4 +-
sPuReMD/src/restart.h | 4 +-
sPuReMD/src/spuremd.c | 204 ++++++++++++++++++++++++++--------------
sPuReMD/src/spuremd.h | 13 ++-
sPuReMD/src/tool_box.c | 2 -
tools/driver.py | 142 ++++++++++++++++++++++++++++
10 files changed, 328 insertions(+), 100 deletions(-)
create mode 100644 tools/driver.py
diff --git a/sPuReMD/src/driver.c b/sPuReMD/src/driver.c
index 6d2ff6ad..8e48dc1b 100644
--- a/sPuReMD/src/driver.c
+++ b/sPuReMD/src/driver.c
@@ -20,22 +20,24 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "mytypes.h"
+#include <stdio.h>
+#include <stdlib.h>
#include "spuremd.h"
+#define INVALID_INPUT (-1)
+
static void usage( char * argv[] )
{
- fprintf( stderr, "usage: ./%s geometry ffield control\n", argv[0] );
+ fprintf( stderr, "usage: ./%s geometry_file force_field_file control_file\n", argv[0] );
}
int main( int argc, char* argv[] )
{
- reax_system system;
- control_params control;
- simulation_data data;
+ void *handle;
+ int ret;
if ( argc != 4 )
{
@@ -43,11 +45,18 @@ int main( int argc, char* argv[] )
exit( INVALID_INPUT );
}
- Setup( argv + 1, &system, &control, &data );
+ handle = setup( argv[1], argv[2], argv[3] );
+ ret = SPUREMD_FAILURE;
- Run( &system, &control, &data, TRUE );
+ if ( handle != NULL )
+ {
+ ret = simulate( handle );
+ }
- Cleanup( &system, &control, &data, TRUE );
+ if ( ret == SPUREMD_SUCCESS )
+ {
+ ret = cleanup( handle );
+ }
- return 0;
+ return (ret == SPUREMD_SUCCESS) ? 0 : (-1);
}
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index 69675645..740a9648 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -55,7 +55,7 @@ void Count_Geo_Atoms( FILE *geo, reax_system *system )
}
-char Read_Geo( char* geo_file, reax_system* system, control_params *control,
+char Read_Geo( const char * const geo_file, reax_system* system, control_params *control,
simulation_data *data, static_storage *workspace )
{
@@ -221,7 +221,7 @@ void Count_PDB_Atoms( FILE *geo, reax_system *system )
}
-char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
+char Read_PDB( const char * const pdb_file, reax_system* system, control_params *control,
simulation_data *data, static_storage *workspace )
{
@@ -538,7 +538,7 @@ char Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
}
-char Read_BGF( char* bgf_file, reax_system* system, control_params *control,
+char Read_BGF( const char * const bgf_file, reax_system* system, control_params *control,
simulation_data *data, static_storage *workspace )
{
FILE *bgf;
diff --git a/sPuReMD/src/geo_tools.h b/sPuReMD/src/geo_tools.h
index 0339a166..5e70721d 100644
--- a/sPuReMD/src/geo_tools.h
+++ b/sPuReMD/src/geo_tools.h
@@ -29,7 +29,7 @@
// CUSTOM ATOM: serial element name x y z
#define CUSTOM_ATOM_FORMAT " %d %s %s %lf %lf %lf"
-char Read_Geo( char*, reax_system*, control_params*,
+char Read_Geo( const char * const, reax_system*, control_params*,
simulation_data*, static_storage* );
/* PDB format :
@@ -117,10 +117,10 @@ COLUMNS DATA TYPE FIELD DEFINITION
#define BGF_CRYSTX_FORMAT "%8s%11s%11s%11s%11s%11s%11s"
-char Read_PDB( char*, reax_system*, control_params*,
+char Read_PDB( const char * const, reax_system*, control_params*,
simulation_data*, static_storage* );
-char Read_BGF( char*, reax_system*, control_params*,
+char Read_BGF( const char * const, reax_system*, control_params*,
simulation_data*, static_storage* );
char Write_PDB( reax_system*, reax_list*, simulation_data*,
diff --git a/sPuReMD/src/mytypes.h b/sPuReMD/src/mytypes.h
index 023542b9..38d1e35c 100644
--- a/sPuReMD/src/mytypes.h
+++ b/sPuReMD/src/mytypes.h
@@ -1122,6 +1122,26 @@ typedef struct
} LR_lookup_table;
+/* Handle for working with an instance of the sPuReMD library */
+typedef struct
+{
+ /* System info. struct pointer */
+ reax_system *system;
+ /* System struct pointer */
+ control_params *control;
+ /* Control parameters struct pointer */
+ simulation_data *data;
+ /* Internal workspace struct pointer */
+ static_storage *workspace;
+ /* Reax interaction list struct pointer */
+ reax_list *lists;
+ /* Output controls struct pointer */
+ output_controls *out_control;
+ /* TRUE if file I/O for simulation output enabled, FALSE otherwise */
+ int output_enabled;
+} spuremd_handle;
+
+
/* Function pointer definitions */
typedef void (*interaction_function)(reax_system*, control_params*,
simulation_data*, static_storage*, reax_list**, output_controls*);
diff --git a/sPuReMD/src/restart.c b/sPuReMD/src/restart.c
index 82474a8b..23b00726 100644
--- a/sPuReMD/src/restart.c
+++ b/sPuReMD/src/restart.c
@@ -68,7 +68,7 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
}
-void Read_Binary_Restart( char *fname, reax_system *system,
+void Read_Binary_Restart( const char * const fname, reax_system *system,
control_params *control, simulation_data *data,
static_storage *workspace )
{
@@ -185,7 +185,7 @@ void Write_ASCII_Restart( reax_system *system, control_params *control,
}
-void Read_ASCII_Restart( char *fname, reax_system *system,
+void Read_ASCII_Restart( const char * const fname, reax_system *system,
control_params *control, simulation_data *data,
static_storage *workspace )
{
diff --git a/sPuReMD/src/restart.h b/sPuReMD/src/restart.h
index d0ea4ca8..363bb581 100644
--- a/sPuReMD/src/restart.h
+++ b/sPuReMD/src/restart.h
@@ -56,9 +56,9 @@ typedef struct
void Write_Restart( reax_system*, control_params*,
simulation_data*, static_storage*, output_controls* );
-void Read_Binary_Restart( char*, reax_system*, control_params*,
+void Read_Binary_Restart( const char * const, reax_system*, control_params*,
simulation_data*, static_storage* );
-void Read_ASCII_Restart( char*, reax_system*, control_params*,
+void Read_ASCII_Restart( const char * const, reax_system*, control_params*,
simulation_data*, static_storage* );
#endif
diff --git a/sPuReMD/src/spuremd.c b/sPuReMD/src/spuremd.c
index 82958abe..5eca7537 100644
--- a/sPuReMD/src/spuremd.c
+++ b/sPuReMD/src/spuremd.c
@@ -19,6 +19,8 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
+#include "spuremd.h"
+
#include "mytypes.h"
#include "analyze.h"
@@ -36,11 +38,6 @@
#include "vector.h"
-static static_storage workspace;
-static reax_list *lists;
-static output_controls out_control;
-
-
static void Post_Evolve( reax_system * const system, control_params * const control,
simulation_data * const data, static_storage * const workspace,
reax_list ** const lists, output_controls * const out_control )
@@ -82,9 +79,9 @@ static void Post_Evolve( reax_system * const system, control_params * const cont
}
-void static Read_System( char * const geo_file,
- char * const ffield_file,
- char * const control_file,
+static void Read_System( const char * const geo_file,
+ const char * const ffield_file,
+ const char * const control_file,
reax_system * const system,
control_params * const control,
simulation_data * const data,
@@ -151,94 +148,157 @@ void static Read_System( char * const geo_file,
}
-int Setup( char ** args, reax_system * const system, control_params * const control,
- simulation_data * const data )
+void* setup( const char * const geo_file, const char * const ffield_file,
+ const char * const control_file )
{
- lists = (reax_list*) smalloc( sizeof(reax_list) * LIST_N,
- "Setup::lists" );
-
- Read_System( args[0], args[1], args[2], system, control,
- data, &workspace, &out_control );
-
- return SUCCESS;
+ spuremd_handle *spmd_handle;
+
+ /* top-level allocation */
+ spmd_handle = (spuremd_handle*) smalloc( sizeof(spuremd_handle),
+ "setup::spmd_handle" );
+
+ /* second-level allocations */
+ spmd_handle->system = (reax_system*) smalloc( sizeof(reax_system),
+ "Setup::spmd_handle->system" );
+ spmd_handle->control = (control_params*) smalloc( sizeof(control_params),
+ "Setup::spmd_handle->control" );
+ spmd_handle->data = (simulation_data*) smalloc( sizeof(simulation_data),
+ "Setup::spmd_handle->data" );
+ spmd_handle->workspace = (static_storage*) smalloc( sizeof(static_storage),
+ "Setup::spmd_handle->workspace" );
+ spmd_handle->lists = (reax_list*) smalloc( sizeof(reax_list) * LIST_N,
+ "Setup::spmd_handle->lists" );
+ spmd_handle->out_control = (output_controls*) smalloc( sizeof(output_controls),
+ "Setup::spmd_handle->out_control" );
+
+ spmd_handle->output_enabled = TRUE;
+
+ /* parse geometry file */
+ Read_System( geo_file, ffield_file, control_file,
+ spmd_handle->system, spmd_handle->control,
+ spmd_handle->data, spmd_handle->workspace,
+ spmd_handle->out_control );
+
+ //TODO: if errors detected, set handle to NULL to indicate failure
+
+ return (void*) spmd_handle;
}
-int Run( reax_system * const system, control_params * const control, simulation_data * const data,
- const int output_enabled )
+int simulate( const void * const handle )
{
- int steps;
+ int steps, ret;
evolve_function Evolve;
+ spuremd_handle *spmd_handle;
- Initialize( system, control, data, &workspace, &lists,
- &out_control, &Evolve, output_enabled );
-
- /* compute f_0 */
- //if( control.restart == 0 ) {
- Reset( system, control, data, &workspace, &lists );
- Generate_Neighbor_Lists( system, control, data, &workspace,
- &lists, &out_control );
+ ret = SPUREMD_FAILURE;
- //fprintf( stderr, "total: %.2f secs\n", data.timing.nbrs);
- Compute_Forces( system, control, data, &workspace, &lists, &out_control );
- Compute_Kinetic_Energy( system, data );
- if ( output_enabled == TRUE )
- {
- Output_Results( system, control, data, &workspace, &lists, &out_control );
- }
- ++data->step;
- //}
- //
-
- for ( ; data->step <= control->nsteps; data->step++ )
+ if ( handle != NULL )
{
- if ( control->T_mode )
+ spmd_handle = (spuremd_handle*) handle;
+
+ Initialize( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists,
+ spmd_handle->out_control, &Evolve,
+ spmd_handle->output_enabled );
+
+ /* compute f_0 */
+ //if( control.restart == 0 ) {
+ Reset( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists );
+ Generate_Neighbor_Lists( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists, spmd_handle->out_control );
+
+ //fprintf( stderr, "total: %.2f secs\n", data.timing.nbrs);
+ Compute_Forces( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists, spmd_handle->out_control );
+ Compute_Kinetic_Energy( spmd_handle->system, spmd_handle->data );
+ if ( spmd_handle->output_enabled == TRUE )
{
- Temperature_Control( control, data, &out_control );
+ Output_Results( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists, spmd_handle->out_control );
}
-
- Evolve( system, control, data, &workspace, &lists, &out_control );
- Post_Evolve( system, control, data, &workspace, &lists, &out_control );
-
- if ( output_enabled == TRUE )
+ ++spmd_handle->data->step;
+ //}
+
+ for ( ; spmd_handle->data->step <= spmd_handle->control->nsteps; spmd_handle->data->step++ )
{
- Output_Results( system, control, data, &workspace, &lists, &out_control );
- Analysis( system, control, data, &workspace, &lists, &out_control );
+ if ( spmd_handle->control->T_mode )
+ {
+ Temperature_Control( spmd_handle->control, spmd_handle->data,
+ spmd_handle->out_control );
+ }
+
+ Evolve( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists, spmd_handle->out_control );
+ Post_Evolve( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists, spmd_handle->out_control );
+
+ if ( spmd_handle->output_enabled == TRUE )
+ {
+ Output_Results( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists, spmd_handle->out_control );
+ Analysis( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists, spmd_handle->out_control );
+ }
+
+ steps = spmd_handle->data->step - spmd_handle->data->prev_steps;
+ if ( steps && spmd_handle->out_control->restart_freq &&
+ steps % spmd_handle->out_control->restart_freq == 0 &&
+ spmd_handle->output_enabled == TRUE )
+ {
+ Write_Restart( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, spmd_handle->out_control );
+ }
}
- steps = data->step - data->prev_steps;
- if ( steps && out_control.restart_freq &&
- steps % out_control.restart_freq == 0 &&
- output_enabled == TRUE )
+ if ( spmd_handle->out_control->write_steps > 0 && spmd_handle->output_enabled == TRUE )
{
- Write_Restart( system, control, data, &workspace, &out_control );
+ fclose( spmd_handle->out_control->trj );
+ Write_PDB( spmd_handle->system, &(spmd_handle->lists[BONDS]), spmd_handle->data,
+ spmd_handle->control, spmd_handle->workspace, spmd_handle->out_control );
}
- }
- if ( out_control.write_steps > 0 && output_enabled == TRUE )
- {
- fclose( out_control.trj );
- Write_PDB( system, &(lists[BONDS]), data, control, &workspace, &out_control );
- }
+ spmd_handle->data->timing.end = Get_Time( );
+ spmd_handle->data->timing.elapsed = Get_Timing_Info( spmd_handle->data->timing.start );
+ if ( spmd_handle->output_enabled == TRUE )
+ {
+ fprintf( spmd_handle->out_control->log, "total: %.2f secs\n", spmd_handle->data->timing.elapsed );
+ }
- data->timing.end = Get_Time( );
- data->timing.elapsed = Get_Timing_Info( data->timing.start );
- if ( output_enabled == TRUE )
- {
- fprintf( out_control.log, "total: %.2f secs\n", data->timing.elapsed );
+ ret = SPUREMD_SUCCESS;
}
- return SUCCESS;
+ return ret;
}
-int Cleanup( reax_system * const system, control_params * const control,
- simulation_data * const data, const int output_enabled )
+int cleanup( const void * const handle )
{
- Finalize( system, control, data, &workspace, &lists, &out_control,
- output_enabled );
+ int ret;
+ spuremd_handle *spmd_handle;
+
+ ret = SPUREMD_FAILURE;
- sfree( lists, "main::lists" );
+ if ( handle != NULL )
+ {
+ spmd_handle = (spuremd_handle*) handle;
+
+ Finalize( spmd_handle->system, spmd_handle->control, spmd_handle->data,
+ spmd_handle->workspace, &spmd_handle->lists, spmd_handle->out_control,
+ spmd_handle->output_enabled );
+
+ sfree( spmd_handle->out_control, "cleanup::spmd_handle->out_control" );
+ sfree( spmd_handle->lists, "cleanup::spmd_handle->lists" );
+ sfree( spmd_handle->workspace, "cleanup::spmd_handle->workspace" );
+ sfree( spmd_handle->data, "cleanup::spmd_handle->data" );
+ sfree( spmd_handle->control, "cleanup::spmd_handle->control" );
+ sfree( spmd_handle->system, "cleanup::spmd_handle->system" );
+
+ sfree( spmd_handle, "cleanup::spmd_handle" );
+
+ ret = SPUREMD_SUCCESS;
+ }
- return SUCCESS;
+ return ret;
}
diff --git a/sPuReMD/src/spuremd.h b/sPuReMD/src/spuremd.h
index 7cad1a69..7ed56288 100644
--- a/sPuReMD/src/spuremd.h
+++ b/sPuReMD/src/spuremd.h
@@ -22,17 +22,16 @@
#ifndef __SPUREMD_H_
#define __SPUREMD_H_
-#include "mytypes.h"
+#define SPUREMD_SUCCESS (0)
+#define SPUREMD_FAILURE (-1)
-int Setup( char **, reax_system * const, control_params * const,
- simulation_data * const );
+void* setup( const char * const, const char * const,
+ const char * const );
-int Run( reax_system * const, control_params * const,
- simulation_data * const, const int );
+int simulate( const void * const );
-int Cleanup( reax_system * const, control_params * const,
- simulation_data * const, const int );
+int cleanup( const void * const );
#endif
diff --git a/sPuReMD/src/tool_box.c b/sPuReMD/src/tool_box.c
index 6b59d194..3853c270 100644
--- a/sPuReMD/src/tool_box.c
+++ b/sPuReMD/src/tool_box.c
@@ -561,6 +561,4 @@ void sfree( void *ptr, const char *name )
#endif
free( ptr );
-
- ptr = NULL;
}
diff --git a/tools/driver.py b/tools/driver.py
new file mode 100644
index 00000000..0144e62c
--- /dev/null
+++ b/tools/driver.py
@@ -0,0 +1,142 @@
+#!/bin/python3
+
+from ctypes import *
+
+
+class Thermostat(Structure):
+ _fields_ = [
+ ("T", c_double),
+ ("xi", c_double),
+ ("v_xi", c_double),
+ ("v_xi_old", c_double),
+ ("G_xi", c_double),
+ ]
+
+
+class IsotropicBarostat(Structure):
+ _fields_ = [
+ ("P", c_double),
+ ("eps", c_double),
+ ("v_eps", c_double),
+ ("v_eps_old", c_double),
+ ("a_eps", c_double),
+ ]
+
+
+class FlexibleBarostat(Structure):
+ _fields_ = [
+ ("P", c_double * 9),
+ ("P_scalar", c_double),
+ ("eps", c_double),
+ ("v_eps", c_double),
+ ("v_eps_old", c_double),
+ ("a_eps", c_double),
+ ("h0", c_double * 9),
+ ("v_g0", c_double * 9),
+ ("v_g0_old", c_double * 9),
+ ("a_g0", c_double * 9),
+ ]
+
+
+class ReaxTiming(Structure):
+ _fields_ = [
+ ("start", c_double),
+ ("end", c_double),
+ ("elapsed", c_double),
+ ("total", c_double),
+ ("nbrs", c_double),
+ ("init_forces", c_double),
+ ("bonded", c_double),
+ ("nonb", c_double),
+ ("cm", c_double),
+ ("cm_sort_mat_rows", c_double),
+ ("cm_solver_pre_comp", c_double),
+ ("cm_solver_pre_app", c_double),
+ ("cm_solver_iters", c_int),
+ ("cm_solver_spmv", c_double),
+ ("cm_solver_vector_ops", c_double),
+ ("cm_solver_orthog", c_double),
+ ("cm_solver_tri_solve", c_double),
+ ]
+
+
+class SimulationData(Structure):
+ _fields_ = [
+ ("step", c_int),
+ ("prev_step", c_int),
+ ("time", c_double),
+ ("M", c_double),
+ ("inv_M", c_double),
+ ("xcm", c_double * 3),
+ ("vcm", c_double * 3),
+ ("fcm", c_double * 3),
+ ("amcm", c_double * 3),
+ ("avcm", c_double * 3),
+ ("etran_cm", c_double),
+ ("erot_cm", c_double),
+ ("kinetic", c_double * 9),
+ ("virial", c_double * 9),
+ ("E_Tot", c_double),
+ ("E_Kin", c_double),
+ ("E_Pot", c_double),
+ ("E_BE", c_double),
+ ("E_Ov", c_double),
+ ("E_Un", c_double),
+ ("E_Lp", c_double),
+ ("E_Ang", c_double),
+ ("E_Pen", c_double),
+ ("E_Coa", c_double),
+ ("E_HB", c_double),
+ ("E_Tor", c_double),
+ ("E_Con", c_double),
+ ("E_vdW", c_double),
+ ("E_Ele", c_double),
+ ("E_Pol", c_double),
+ ("N_f", c_double),
+ ("t_scale", c_double * 3),
+ ("p_scale", c_double * 9),
+ ("therm", Thermostat),
+ ("iso_bar", IsotropicBarostat),
+ ("flex_bar", FlexibleBarostat),
+ ("inv_W", c_double),
+ ("int_press", c_double * 3),
+ ("ext_press", c_double * 3),
+ ("kin_press", c_double),
+ ("tot_press", c_double * 3),
+ ("tot_press", c_double * 3),
+ ("timing", ReaxTiming),
+ ]
+
+
+class ReaxAtom(Structure):
+ _fields_ = [
+ ("name", c_char * 8),
+ ("x", c_double * 3),
+ ("v", c_double * 3),
+ ("f", c_double * 3),
+ ("q", c_double),
+ ]
+
+
+if __name__ == '__main__':
+ lib = cdll.LoadLibrary("libspuremd.so.1")
+
+ setup = lib.setup
+ setup.argtypes = [c_char_p, c_char_p, c_char_p]
+ setup.restype = c_void_p
+
+ simulate = lib.simulate
+ simulate.argtypes = [c_void_p]
+ simulate.restype = c_int
+
+ cleanup = lib.cleanup
+ cleanup.argtypes = [c_void_p]
+ cleanup.restype = c_int
+
+ handle = setup(b"data/benchmarks/water/water_6540.pdb",
+ b"data/benchmarks/water/ffield.water",
+ b"environ/param.gpu.water")
+
+ simulate(handle)
+
+ cleanup(handle)
--
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