From a085b0203209a319158d2a85dcb673428a9d8174 Mon Sep 17 00:00:00 2001
From: KAO <ohearnk@seawolf.cis.gvsu.edu>
Date: Fri, 25 Nov 2016 17:50:29 -0500
Subject: [PATCH] PuReMD-GPU: begin build system refactor.
---
PuReMD-GPU/Makefile.am | 26 +-
PuReMD-GPU/src/allocate.c | 277 ++++++++++++
PuReMD-GPU/src/allocate.h | 8 -
PuReMD-GPU/src/bond_orders.cu | 20 +-
PuReMD-GPU/src/{box.cu => box.c} | 0
PuReMD-GPU/src/box.h | 3 +-
.../src/{allocate.cu => cuda_allocate.cu} | 377 ++++------------
PuReMD-GPU/src/cuda_allocate.h | 31 ++
PuReMD-GPU/src/cuda_helpers.h | 22 +-
.../{system_props.cu => cuda_system_props.cu} | 402 ++----------------
PuReMD-GPU/src/cuda_system_props.h | 32 ++
PuReMD-GPU/src/forces.cu | 13 +-
PuReMD-GPU/src/four_body_interactions.cu | 18 +-
PuReMD-GPU/src/init_md.cu | 11 +-
PuReMD-GPU/src/integrate.cu | 3 +
PuReMD-GPU/src/mytypes.h | 5 +
PuReMD-GPU/src/neighbors.cu | 2 +-
PuReMD-GPU/src/random.h | 6 +-
PuReMD-GPU/src/single_body_interactions.cu | 32 +-
PuReMD-GPU/src/system_props.c | 348 +++++++++++++++
PuReMD-GPU/src/system_props.h | 7 -
PuReMD-GPU/src/{testmd.cu => testmd.c} | 1 +
PuReMD-GPU/src/three_body_interactions.cu | 30 +-
PuReMD-GPU/src/{traj.cu => traj.c} | 9 +-
PuReMD-GPU/src/traj.h | 8 +-
PuReMD-GPU/src/two_body_interactions.cu | 6 +-
PuReMD-GPU/src/{vector.cu => vector.c} | 0
PuReMD-GPU/src/vector.h | 48 +--
28 files changed, 937 insertions(+), 808 deletions(-)
create mode 100644 PuReMD-GPU/src/allocate.c
rename PuReMD-GPU/src/{box.cu => box.c} (100%)
rename PuReMD-GPU/src/{allocate.cu => cuda_allocate.cu} (66%)
create mode 100644 PuReMD-GPU/src/cuda_allocate.h
rename PuReMD-GPU/src/{system_props.cu => cuda_system_props.cu} (56%)
create mode 100644 PuReMD-GPU/src/cuda_system_props.h
create mode 100644 PuReMD-GPU/src/system_props.c
rename PuReMD-GPU/src/{testmd.cu => testmd.c} (99%)
rename PuReMD-GPU/src/{traj.cu => traj.c} (99%)
rename PuReMD-GPU/src/{vector.cu => vector.c} (100%)
diff --git a/PuReMD-GPU/Makefile.am b/PuReMD-GPU/Makefile.am
index 1a914816..f4da052f 100644
--- a/PuReMD-GPU/Makefile.am
+++ b/PuReMD-GPU/Makefile.am
@@ -18,29 +18,33 @@ NVCCFLAGS += --compiler-options "$(DEFS) -D__SM_35__ -O3 -funroll-loops -fstrict
#NVCCFLAGS += --ptxas-options -v
bin_PROGRAMS = bin/puremd-gpu
-bin_puremd_gpu_SOURCES = src/analyze.c src/print_utils.c src/restart.c src/param.c src/pdb_tools.c \
- src/GMRES.cu src/QEq.cu src/allocate.cu src/bond_orders.cu \
- src/box.cu src/forces.cu src/four_body_interactions.cu \
+bin_puremd_gpu_SOURCES = src/analyze.c src/print_utils.c \
+ src/restart.c src/param.c src/pdb_tools.c src/box.c \
+ src/GMRES.cu src/QEq.cu src/allocate.c src/bond_orders.cu \
+ src/forces.cu src/four_body_interactions.cu \
src/grid.cu src/init_md.cu src/integrate.cu src/list.cu \
src/lookup.cu src/neighbors.cu \
src/reset_utils.cu src/single_body_interactions.cu \
- src/system_props.cu src/three_body_interactions.cu \
- src/traj.cu src/two_body_interactions.cu src/vector.cu \
- src/testmd.cu \
+ src/system_props.c src/three_body_interactions.cu \
+ src/traj.c src/two_body_interactions.cu src/vector.c \
src/cuda_utils.cu src/cuda_copy.cu src/cuda_init.cu src/reduction.cu \
- src/center_mass.cu src/helpers.cu src/validation.cu src/matvec.cu
-
+ src/center_mass.cu src/helpers.cu src/validation.cu src/matvec.cu \
+ src/cuda_allocate.cu \
+ src/cuda_system_props.cu \
+ src/testmd.c
include_HEADERS = src/mytypes.h src/analyze.h src/print_utils.h \
- src/restart.h src/param.h src/pdb_tools.h \
+ src/restart.h src/param.h src/pdb_tools.h src/box.h \
src/GMRES.h src/QEq.h src/allocate.h src/bond_orders.h \
- src/box.h src/forces.h src/four_body_interactions.h \
+ src/forces.h src/four_body_interactions.h \
src/grid.h src/init_md.h src/integrate.h src/list.h \
src/lookup.h src/neighbors.h \
src/reset_utils.h src/single_body_interactions.h \
src/system_props.h src/three_body_interactions.h \
src/traj.h src/two_body_interactions.h src/vector.h \
src/cuda_utils.h src/cuda_copy.h src/cuda_init.h src/reduction.h \
- src/center_mass.h src/helpers.h src/validation.h src/matvec.h
+ src/center_mass.h src/helpers.h src/validation.h src/matvec.h \
+ src/cuda_allocate.h \
+ src/cuda_system_props.h
# dummy source to cause C linking
nodist_EXTRA_bin_puremd_gpu_SOURCES = src/dummy.c
diff --git a/PuReMD-GPU/src/allocate.c b/PuReMD-GPU/src/allocate.c
new file mode 100644
index 00000000..b776a6a7
--- /dev/null
+++ b/PuReMD-GPU/src/allocate.c
@@ -0,0 +1,277 @@
+/*----------------------------------------------------------------------
+ PuReMD-GPU - Reax Force Field Simulator
+
+ Copyright (2014) Purdue University
+ Sudhir Kylasa, skylasa@purdue.edu
+ Hasan Metin Aktulga, haktulga@cs.purdue.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 "allocate.h"
+
+#include "list.h"
+
+
+void Reallocate_Neighbor_List( list *far_nbrs, int n, int num_intrs )
+{
+ Delete_List( far_nbrs, TYP_HOST );
+ if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs, TYP_HOST )){
+ fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
+ exit( INIT_ERR );
+ }
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "num_far = %d, far_nbrs = %d -> reallocating!\n",
+ num_intrs, far_nbrs->num_intrs );
+ fprintf( stderr, "memory allocated: far_nbrs = %ldMB\n",
+ num_intrs * sizeof(far_neighbor_data) / (1024*1024) );
+#endif
+}
+
+
+int Allocate_Matrix( sparse_matrix *H, int n, int m )
+{
+ H->n = n;
+ H->m = m;
+ if( (H->start = (int*) malloc(sizeof(int) * n+1)) == NULL )
+ return 0;
+
+ if( (H->end = (int*) malloc(sizeof(int) * n+1)) == NULL )
+ return 0;
+
+ if( (H->entries =
+ (sparse_matrix_entry*) malloc(sizeof(sparse_matrix_entry)*m)) == NULL )
+ return 0;
+
+ return 1;
+}
+
+
+void Deallocate_Matrix( sparse_matrix *H )
+{
+ free(H->start);
+ free(H->entries);
+ free(H->end);
+}
+
+
+int Reallocate_Matrix( sparse_matrix *H, int n, int m, char *name )
+{
+ Deallocate_Matrix( H );
+ if( !Allocate_Matrix( H, n, m ) ) {
+ fprintf(stderr, "not enough space for %s matrix. terminating!\n", name);
+ exit( 1 );
+ }
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "reallocating %s matrix, n = %d, m = %d\n",
+ name, n, m );
+ fprintf( stderr, "memory allocated: %s = %ldMB\n",
+ name, m * sizeof(sparse_matrix_entry) / (1024*1024) );
+#endif
+ return 1;
+}
+
+
+int Allocate_HBond_List( int n, int num_h, int *h_index, int *hb_top,
+ list *hbonds )
+{
+ int i, num_hbonds;
+
+ num_hbonds = 0;
+ /* find starting indexes for each H and the total number of hbonds */
+ for( i = 1; i < n; ++i )
+ hb_top[i] += hb_top[i-1];
+ num_hbonds = hb_top[n-1];
+
+ if( !Make_List(num_h, num_hbonds, TYP_HBOND, hbonds, TYP_HOST ) ) {
+ fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
+ exit( INIT_ERR );
+ }
+
+ for( i = 0; i < n; ++i )
+ if( h_index[i] == 0 ){
+ Set_Start_Index( 0, 0, hbonds );
+ Set_End_Index( 0, 0, hbonds );
+ }
+ else if( h_index[i] > 0 ){
+ Set_Start_Index( h_index[i], hb_top[i-1], hbonds );
+ Set_End_Index( h_index[i], hb_top[i-1], hbonds );
+ }
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "allocating hbonds - num_hbonds: %d\n", num_hbonds );
+ fprintf( stderr, "memory allocated: hbonds = %ldMB\n",
+ num_hbonds * sizeof(hbond_data) / (1024*1024) );
+#endif
+ return 1;
+}
+
+
+int Reallocate_HBonds_List( int n, int num_h, int *h_index, list *hbonds )
+{
+ int i;
+ int *hb_top;
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "reallocating hbonds\n" );
+#endif
+ hb_top = (int *)calloc( n, sizeof(int) );
+ for( i = 0; i < n; ++i )
+ if( h_index[i] >= 0 )
+ hb_top[i] = MAX(Num_Entries(h_index[i],hbonds)*SAFE_HBONDS, MIN_HBONDS);
+
+ Delete_List( hbonds, TYP_HOST );
+
+ Allocate_HBond_List( n, num_h, h_index, hb_top, hbonds );
+
+ free( hb_top );
+
+ return 1;
+}
+
+
+int Allocate_Bond_List( int n, int *bond_top, list *bonds )
+{
+ int i, num_bonds;
+
+ num_bonds = 0;
+ /* find starting indexes for each atom and the total number of bonds */
+ for( i = 1; i < n; ++i )
+ bond_top[i] += bond_top[i-1];
+ num_bonds = bond_top[n-1];
+
+ if( !Make_List(n, num_bonds, TYP_BOND, bonds, TYP_HOST ) ) {
+ fprintf( stderr, "not enough space for bonds list. terminating!\n" );
+ exit( INIT_ERR );
+ }
+
+ Set_Start_Index( 0, 0, bonds );
+ Set_End_Index( 0, 0, bonds );
+ for( i = 1; i < n; ++i ) {
+ Set_Start_Index( i, bond_top[i-1], bonds );
+ Set_End_Index( i, bond_top[i-1], bonds );
+ }
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "allocating bonds - num_bonds: %d\n", num_bonds );
+ fprintf( stderr, "memory allocated: bonds = %ldMB\n",
+ num_bonds * sizeof(bond_data) / (1024*1024) );
+#endif
+ return 1;
+}
+
+
+int Reallocate_Bonds_List( int n, list *bonds, int *num_bonds, int *est_3body )
+{
+ int i;
+ int *bond_top;
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "reallocating bonds\n" );
+#endif
+ bond_top = (int *)calloc( n, sizeof(int) );
+ *est_3body = 0;
+ for( i = 0; i < n; ++i ){
+ *est_3body += SQR( Num_Entries( i, bonds ) );
+ bond_top[i] = MAX( Num_Entries( i, bonds ) * 2, MIN_BONDS );
+ }
+
+ Delete_List( bonds, TYP_HOST );
+
+ Allocate_Bond_List( n, bond_top, bonds );
+ *num_bonds = bond_top[n-1];
+
+ free( bond_top );
+
+ return 1;
+}
+
+
+void Reallocate( reax_system *system, static_storage *workspace, list **lists,
+ int nbr_flag )
+{
+ int num_bonds, est_3body;
+ reallocate_data *realloc;
+ grid *g;
+
+ realloc = &(workspace->realloc);
+ g = &(system->g);
+
+ if( realloc->num_far > 0 && nbr_flag ) {
+ fprintf (stderr, " Reallocating neighbors \n");
+ Reallocate_Neighbor_List( (*lists)+FAR_NBRS,
+ system->N, realloc->num_far * SAFE_ZONE );
+ realloc->num_far = -1;
+ }
+
+ if( realloc->Htop > 0 ){
+ fprintf (stderr, " Reallocating Matrix \n");
+ Reallocate_Matrix(&(workspace->H), system->N, realloc->Htop*SAFE_ZONE,"H");
+ realloc->Htop = -1;
+
+ Deallocate_Matrix( &workspace->L );
+ Deallocate_Matrix( &workspace->U );
+ }
+
+ if( realloc->hbonds > 0 ){
+ fprintf (stderr, " Reallocating hbonds \n");
+ Reallocate_HBonds_List(system->N, workspace->num_H, workspace->hbond_index,
+ (*lists)+HBONDS );
+ realloc->hbonds = -1;
+ }
+
+ num_bonds = est_3body = -1;
+ if( realloc->bonds > 0 ){
+ fprintf (stderr, " Reallocating bonds \n");
+ Reallocate_Bonds_List( system->N, (*lists)+BONDS, &num_bonds, &est_3body );
+ realloc->bonds = -1;
+ realloc->num_3body = MAX( realloc->num_3body, est_3body );
+ }
+
+ if( realloc->num_3body > 0 ) {
+ fprintf (stderr, " Reallocating 3Body \n");
+ Delete_List( (*lists)+THREE_BODIES, TYP_HOST );
+
+ if( num_bonds == -1 )
+ num_bonds = ((*lists)+BONDS)->num_intrs;
+ realloc->num_3body *= SAFE_ZONE;
+
+ if( !Make_List( num_bonds, realloc->num_3body,
+ TYP_THREE_BODY, (*lists)+THREE_BODIES, TYP_HOST ) ) {
+ fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
+ exit( INIT_ERR );
+ }
+ realloc->num_3body = -1;
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "reallocating 3 bodies\n" );
+ fprintf( stderr, "reallocated - num_bonds: %d\n", num_bonds );
+ fprintf( stderr, "reallocated - num_3body: %d\n", realloc->num_3body );
+ fprintf( stderr, "reallocated 3body memory: %ldMB\n",
+ realloc->num_3body*sizeof(three_body_interaction_data)/
+ (1024*1024) );
+#endif
+ }
+
+ if( realloc->gcell_atoms > -1 ){
+#if defined(DEBUG_FOCUS)
+ fprintf(stderr, "reallocating gcell: g->max_atoms: %d\n", g->max_atoms);
+#endif
+
+ free (g->atoms);
+ g->atoms = (int *) calloc ( g->ncell[0]*g->ncell[1]*g->ncell[2],
+ sizeof (int) * workspace->realloc.gcell_atoms);
+ realloc->gcell_atoms = -1;
+ }
+}
diff --git a/PuReMD-GPU/src/allocate.h b/PuReMD-GPU/src/allocate.h
index 7ab146bb..4ec4b541 100644
--- a/PuReMD-GPU/src/allocate.h
+++ b/PuReMD-GPU/src/allocate.h
@@ -32,13 +32,5 @@ int Allocate_HBond_List( int, int, int*, int*, list* );
int Allocate_Bond_List( int, int*, list* );
-//Cuda Functions
-int Cuda_Allocate_Matrix( sparse_matrix*, int, int );
-int Cuda_Allocate_HBond_List( int, int, int*, int*, list* );
-int Cuda_Allocate_Bond_List( int, int*, list* );
-void Cuda_Reallocate( reax_system*, static_storage*, list*, int, int );
-
-GLOBAL void Init_HBond_Indexes ( int *, int *, list , int );
-GLOBAL void Init_Bond_Indexes ( int *, list , int );
#endif
diff --git a/PuReMD-GPU/src/bond_orders.cu b/PuReMD-GPU/src/bond_orders.cu
index d39f1b41..bb72417b 100644
--- a/PuReMD-GPU/src/bond_orders.cu
+++ b/PuReMD-GPU/src/bond_orders.cu
@@ -36,6 +36,7 @@ inline real Cf45( real p1, real p2 )
( SQR( EXP(-p1 / 2) + EXP(p1 / 2) ) * (EXP(-p2 / 2) + EXP(p2 / 2)) );
}
+
#ifdef TEST_FORCES
void Get_dBO( reax_system *system, list **lists,
int i, int pj, real C, rvec *v )
@@ -66,7 +67,8 @@ void Get_dBOpinpi2( reax_system *system, list **lists,
start_pj = Start_Index(pj, dBOs);
end_pj = End_Index(pj, dBOs);
- for( k = start_pj; k < end_pj; ++k ) {
+ for( k = start_pj; k < end_pj; ++k )
+ {
dbo_k = &(dBOs->select.dbo_list[k]);
rvec_Scale( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
rvec_Scale( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
@@ -179,7 +181,6 @@ void Add_dDelta_to_Forces( reax_system *system, list **lists, int i, real C )
}
-
HOST_DEVICE void Calculate_dBO( int i, int pj, static_storage p_workspace,
list p_bonds, list p_dBOs, int *top )
{
@@ -367,7 +368,6 @@ HOST_DEVICE void Calculate_dBO( int i, int pj, static_storage p_workspace,
#endif
-
void Add_dBond_to_Forces_NPT( int i, int pj, reax_system *system,
simulation_data *data, static_storage *workspace,
list **lists )
@@ -521,10 +521,10 @@ void Add_dBond_to_Forces_NPT( int i, int pj, reax_system *system,
temp[0], temp[1], temp[2] ); */
}
+
/////////////////////////////////////////////////////////////
//Cuda Functions
/////////////////////////////////////////////////////////////
-
HOST_DEVICE void Cuda_Add_dBond_to_Forces_NPT( int i, int pj, reax_atom *atoms,
simulation_data *data, static_storage *workspace,
list *bonds )
@@ -646,6 +646,7 @@ HOST_DEVICE void Cuda_Add_dBond_to_Forces_NPT( int i, int pj, reax_atom *atoms,
rvec_Add( data->ext_press, ext_press );
}
+
/////////////////////////////////////////////////////////////
//Cuda Functions
/////////////////////////////////////////////////////////////
@@ -761,6 +762,7 @@ void Add_dBond_to_Forces( int i, int pj, reax_system *system,
/*3rd, dBOpi2*/
}
+
HOST_DEVICE void Cuda_Add_dBond_to_Forces ( int i, int pj, reax_atom *atoms,
static_storage *workspace, list *bonds )
{
@@ -890,6 +892,7 @@ HOST_DEVICE void Cuda_Add_dBond_to_Forces ( int i, int pj, reax_atom *atoms,
}
}
+
HOST_DEVICE void Cuda_dbond_to_Forces_postprocess (int i, reax_atom *atoms, list *bonds)
{
int pk;
@@ -910,6 +913,7 @@ HOST_DEVICE void Cuda_dbond_to_Forces_postprocess (int i, reax_atom *atoms, list
}
}
+
/* Locate j on i's list.
This function assumes that j is there for sure!
And this is the case given our method of neighbor generation*/
@@ -1377,7 +1381,6 @@ GLOBAL void Cuda_Calculate_Bond_Orders_Init ( reax_atom *atoms, global_paramete
/* A very important and crucial assumption here is that each segment
belonging to a different atom in nbrhoods->nbr_list is sorted in its own.
This can either be done in the general coordinator function or here */
-
GLOBAL void Cuda_Calculate_Bond_Orders ( reax_atom *atoms, global_parameters g_params, single_body_parameters *sbp,
two_body_parameters *tbp, static_storage workspace, list bonds,
list dDeltas, list dBOs, int num_atom_types, int N )
@@ -1398,7 +1401,6 @@ GLOBAL void Cuda_Calculate_Bond_Orders ( reax_atom *atoms, global_parameters g_
bond_order_data *bo_ij, *bo_ji;
single_body_parameters *sbp_i, *sbp_j;
-
#if defined(TEST_FORCES)
int k, pk, start_j, end_j;
int top_dbo=0, top_dDelta=0;
@@ -1433,7 +1435,6 @@ GLOBAL void Cuda_Calculate_Bond_Orders ( reax_atom *atoms, global_parameters g_
// fprintf( stderr, "done with uncorrected bond orders\n" );
-
/* Corrected Bond Order calculations */
//for( i = 0; i < system->N; ++i ) {
type_i = atoms[i].type;
@@ -1778,6 +1779,7 @@ workspace.dDelta_lp_temp[j] = workspace.Clp[j];
#endif
}
+
GLOBAL void Cuda_Update_Uncorrected_BO ( static_storage workspace, list bonds, int N )
{
int i, j, pj;
@@ -1812,6 +1814,7 @@ GLOBAL void Cuda_Update_Uncorrected_BO ( static_storage workspace, list bonds,
}
}
+
GLOBAL void Cuda_Update_Workspace_After_Bond_Orders( reax_atom *atoms, global_parameters g_params, single_body_parameters *sbp,
static_storage workspace, int N )
{
@@ -1867,8 +1870,8 @@ GLOBAL void Cuda_Update_Workspace_After_Bond_Orders( reax_atom *atoms, global_p
}
-//Import from the forces file.
+//Import from the forces file.
GLOBAL void Cuda_Compute_Total_Force (reax_atom *atoms, simulation_data *data,
static_storage workspace, list p_bonds, int ensemble, int N)
{
@@ -1889,6 +1892,7 @@ GLOBAL void Cuda_Compute_Total_Force (reax_atom *atoms, simulation_data *data,
}
}
+
GLOBAL void Cuda_Compute_Total_Force_PostProcess (reax_atom *atoms, simulation_data *data,
static_storage workspace, list p_bonds, int ensemble, int N)
{
diff --git a/PuReMD-GPU/src/box.cu b/PuReMD-GPU/src/box.c
similarity index 100%
rename from PuReMD-GPU/src/box.cu
rename to PuReMD-GPU/src/box.c
diff --git a/PuReMD-GPU/src/box.h b/PuReMD-GPU/src/box.h
index ed8cc9f4..4d97e424 100644
--- a/PuReMD-GPU/src/box.h
+++ b/PuReMD-GPU/src/box.h
@@ -21,8 +21,10 @@
#ifndef __BOX_H__
#define __BOX_H__
+
#include "mytypes.h"
+
/* Initializes box from CRYST1 line of PDB */
void Init_Box_From_CRYST(real, real, real, real, real, real,
simulation_box*/*, int*/);
@@ -98,7 +100,6 @@ void Print_Box_Information( simulation_box*, FILE* );
//CUDA Device Functions
//HOST_DEVICE inline void Inc_on_T3( rvec, rvec, simulation_box* );
-
HOST_DEVICE inline void Inc_on_T3( rvec x, rvec dx, simulation_box *box )
{
int i;
diff --git a/PuReMD-GPU/src/allocate.cu b/PuReMD-GPU/src/cuda_allocate.cu
similarity index 66%
rename from PuReMD-GPU/src/allocate.cu
rename to PuReMD-GPU/src/cuda_allocate.cu
index bae0dde8..5f2b322b 100644
--- a/PuReMD-GPU/src/allocate.cu
+++ b/PuReMD-GPU/src/cuda_allocate.cu
@@ -18,27 +18,17 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "allocate.h"
+#include "cuda_allocate.h"
+
#include "list.h"
#include "cuda_utils.h"
#include "reduction.h"
-void Reallocate_Neighbor_List( list *far_nbrs, int n, int num_intrs )
-{
- Delete_List( far_nbrs, TYP_HOST );
- if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs, TYP_HOST )){
- fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
- exit( INIT_ERR );
- }
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "num_far = %d, far_nbrs = %d -> reallocating!\n",
- num_intrs, far_nbrs->num_intrs );
- fprintf( stderr, "memory allocated: far_nbrs = %ldMB\n",
- num_intrs * sizeof(far_neighbor_data) / (1024*1024) );
-#endif
-}
+GLOBAL void Init_HBond_Indexes ( int *, int *, list , int );
+GLOBAL void Init_Bond_Indexes ( int *, list , int );
+
void Cuda_Reallocate_Neighbor_List( list *far_nbrs, int n, int num_intrs )
{
@@ -57,23 +47,6 @@ void Cuda_Reallocate_Neighbor_List( list *far_nbrs, int n, int num_intrs )
}
-int Allocate_Matrix( sparse_matrix *H, int n, int m )
-{
- H->n = n;
- H->m = m;
- if( (H->start = (int*) malloc(sizeof(int) * n+1)) == NULL )
- return 0;
-
- if( (H->end = (int*) malloc(sizeof(int) * n+1)) == NULL )
- return 0;
-
- if( (H->entries =
- (sparse_matrix_entry*) malloc(sizeof(sparse_matrix_entry)*m)) == NULL )
- return 0;
-
- return 1;
-}
-
int Cuda_Allocate_Matrix( sparse_matrix *H, int n, int m )
{
H->n = n;
@@ -87,13 +60,6 @@ int Cuda_Allocate_Matrix( sparse_matrix *H, int n, int m )
}
-void Deallocate_Matrix( sparse_matrix *H )
-{
- free(H->start);
- free(H->entries);
- free(H->end);
-}
-
void Cuda_Deallocate_Matrix( sparse_matrix *H )
{
cuda_free(H->start, RES_SPARSE_MATRIX_INDEX);
@@ -106,23 +72,6 @@ void Cuda_Deallocate_Matrix( sparse_matrix *H )
}
-int Reallocate_Matrix( sparse_matrix *H, int n, int m, char *name )
-{
- Deallocate_Matrix( H );
- if( !Allocate_Matrix( H, n, m ) ) {
- fprintf(stderr, "not enough space for %s matrix. terminating!\n", name);
- exit( 1 );
- }
-
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reallocating %s matrix, n = %d, m = %d\n",
- name, n, m );
- fprintf( stderr, "memory allocated: %s = %ldMB\n",
- name, m * sizeof(sparse_matrix_entry) / (1024*1024) );
-#endif
- return 1;
-}
-
int Cuda_Reallocate_Matrix( sparse_matrix *H, int n, int m, char *name )
{
Cuda_Deallocate_Matrix( H );
@@ -142,56 +91,6 @@ int Cuda_Reallocate_Matrix( sparse_matrix *H, int n, int m, char *name )
}
-int Allocate_HBond_List( int n, int num_h, int *h_index, int *hb_top,
- list *hbonds )
-{
- int i, num_hbonds;
-
- num_hbonds = 0;
- /* find starting indexes for each H and the total number of hbonds */
- for( i = 1; i < n; ++i )
- hb_top[i] += hb_top[i-1];
- num_hbonds = hb_top[n-1];
-
- if( !Make_List(num_h, num_hbonds, TYP_HBOND, hbonds, TYP_HOST ) ) {
- fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
- exit( INIT_ERR );
- }
-
- for( i = 0; i < n; ++i )
- if( h_index[i] == 0 ){
- Set_Start_Index( 0, 0, hbonds );
- Set_End_Index( 0, 0, hbonds );
- }
- else if( h_index[i] > 0 ){
- Set_Start_Index( h_index[i], hb_top[i-1], hbonds );
- Set_End_Index( h_index[i], hb_top[i-1], hbonds );
- }
-
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "allocating hbonds - num_hbonds: %d\n", num_hbonds );
- fprintf( stderr, "memory allocated: hbonds = %ldMB\n",
- num_hbonds * sizeof(hbond_data) / (1024*1024) );
-#endif
- return 1;
-}
-
-GLOBAL void Init_HBond_Indexes ( int *h_index, int *hb_top, list hbonds, int N )
-{
- int index = blockIdx.x * blockDim.x + threadIdx.x;
-
- if (index >= N) return;
-
- if( h_index[index] == 0 ){
- Set_Start_Index( 0, 0, &hbonds );
- Set_End_Index( 0, 0, &hbonds );
- }
- else if( h_index[index] > 0 ){
- Set_Start_Index( h_index[index], hb_top[index-1], &hbonds );
- Set_End_Index( h_index[index], hb_top[index-1], &hbonds );
- }
-}
-
int Cuda_Allocate_HBond_List( int n, int num_h, int *h_index, int *hb_top, list *hbonds )
{
int i, num_hbonds;
@@ -225,27 +124,6 @@ int Cuda_Allocate_HBond_List( int n, int num_h, int *h_index, int *hb_top, list
return 1;
}
-int Reallocate_HBonds_List( int n, int num_h, int *h_index, list *hbonds )
-{
- int i;
- int *hb_top;
-
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reallocating hbonds\n" );
-#endif
- hb_top = (int *)calloc( n, sizeof(int) );
- for( i = 0; i < n; ++i )
- if( h_index[i] >= 0 )
- hb_top[i] = MAX(Num_Entries(h_index[i],hbonds)*SAFE_HBONDS, MIN_HBONDS);
-
- Delete_List( hbonds, TYP_HOST );
-
- Allocate_HBond_List( n, num_h, h_index, hb_top, hbonds );
-
- free( hb_top );
-
- return 1;
-}
int Cuda_Reallocate_HBonds_List( int n, int num_h, int *h_index, list *hbonds )
{
@@ -281,21 +159,6 @@ int Cuda_Reallocate_HBonds_List( int n, int num_h, int *h_index, list *hbonds )
return 1;
}
-GLOBAL void Init_Bond_Indexes ( int *b_top, list bonds, int N )
-{
- int index = blockIdx.x * blockDim.x + threadIdx.x;
-
- if (index >= N) return;
-
- if( index == 0 ){
- Set_Start_Index( 0, 0, &bonds );
- Set_End_Index( 0, 0, &bonds );
- }
- else if( index > 0 ){
- Set_Start_Index( index, b_top[index-1], &bonds );
- Set_End_Index( index, b_top[index-1], &bonds );
- }
-}
int Cuda_Allocate_Bond_List( int num_b, int *b_top, list *bonds )
{
@@ -326,93 +189,6 @@ int Cuda_Allocate_Bond_List( int num_b, int *b_top, list *bonds )
}
-int Allocate_Bond_List( int n, int *bond_top, list *bonds )
-{
- int i, num_bonds;
-
- num_bonds = 0;
- /* find starting indexes for each atom and the total number of bonds */
- for( i = 1; i < n; ++i )
- bond_top[i] += bond_top[i-1];
- num_bonds = bond_top[n-1];
-
- if( !Make_List(n, num_bonds, TYP_BOND, bonds, TYP_HOST ) ) {
- fprintf( stderr, "not enough space for bonds list. terminating!\n" );
- exit( INIT_ERR );
- }
-
- Set_Start_Index( 0, 0, bonds );
- Set_End_Index( 0, 0, bonds );
- for( i = 1; i < n; ++i ) {
- Set_Start_Index( i, bond_top[i-1], bonds );
- Set_End_Index( i, bond_top[i-1], bonds );
- }
-
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "allocating bonds - num_bonds: %d\n", num_bonds );
- fprintf( stderr, "memory allocated: bonds = %ldMB\n",
- num_bonds * sizeof(bond_data) / (1024*1024) );
-#endif
- return 1;
-}
-
-
-int Reallocate_Bonds_List( int n, list *bonds, int *num_bonds, int *est_3body )
-{
- int i;
- int *bond_top;
-
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reallocating bonds\n" );
-#endif
- bond_top = (int *)calloc( n, sizeof(int) );
- *est_3body = 0;
- for( i = 0; i < n; ++i ){
- *est_3body += SQR( Num_Entries( i, bonds ) );
- bond_top[i] = MAX( Num_Entries( i, bonds ) * 2, MIN_BONDS );
- }
-
- Delete_List( bonds, TYP_HOST );
-
- Allocate_Bond_List( n, bond_top, bonds );
- *num_bonds = bond_top[n-1];
-
- free( bond_top );
-
- return 1;
-}
-
-void GLOBAL Calculate_Bond_Indexes (int *bond_top, list bonds, int *per_block_results, int n)
-{
- extern __shared__ int sh_input[];
- unsigned int i = blockIdx.x * blockDim.x + threadIdx.x;
- real x = 0;
-
- if(i < n)
- {
- x = SQR (Num_Entries( i, &bonds ) );
- bond_top[i] = MAX( Num_Entries( i, &bonds ) * 2, MIN_BONDS );
- }
- sh_input[threadIdx.x] = x;
- __syncthreads();
-
- for(int offset = blockDim.x / 2; offset > 0; offset >>= 1)
- {
- if(threadIdx.x < offset)
- {
- sh_input[threadIdx.x] += sh_input[threadIdx.x + offset];
- }
-
- __syncthreads();
- }
-
- if(threadIdx.x == 0)
- {
- per_block_results[blockIdx.x] = sh_input[0];
- }
-}
-
-
int Cuda_Reallocate_Bonds_List( int n, list *bonds, int *num_3body )
{
int i;
@@ -450,6 +226,7 @@ int Cuda_Reallocate_Bonds_List( int n, list *bonds, int *num_3body )
return i;
}
+
int Cuda_Reallocate_ThreeBody_List ( list *thblist, int count )
{
int i;
@@ -542,83 +319,6 @@ cuda_memset (d_bond_top, 0, (n+BLOCKS_POW_2+1) * INT_SIZE, RES_SCRATCH );
*/
-void Reallocate( reax_system *system, static_storage *workspace, list **lists,
- int nbr_flag )
-{
- int num_bonds, est_3body;
- reallocate_data *realloc;
- grid *g;
-
- realloc = &(workspace->realloc);
- g = &(system->g);
-
- if( realloc->num_far > 0 && nbr_flag ) {
- fprintf (stderr, " Reallocating neighbors \n");
- Reallocate_Neighbor_List( (*lists)+FAR_NBRS,
- system->N, realloc->num_far * SAFE_ZONE );
- realloc->num_far = -1;
- }
-
- if( realloc->Htop > 0 ){
- fprintf (stderr, " Reallocating Matrix \n");
- Reallocate_Matrix(&(workspace->H), system->N, realloc->Htop*SAFE_ZONE,"H");
- realloc->Htop = -1;
-
- Deallocate_Matrix( &workspace->L );
- Deallocate_Matrix( &workspace->U );
- }
-
- if( realloc->hbonds > 0 ){
- fprintf (stderr, " Reallocating hbonds \n");
- Reallocate_HBonds_List(system->N, workspace->num_H, workspace->hbond_index,
- (*lists)+HBONDS );
- realloc->hbonds = -1;
- }
-
- num_bonds = est_3body = -1;
- if( realloc->bonds > 0 ){
- fprintf (stderr, " Reallocating bonds \n");
- Reallocate_Bonds_List( system->N, (*lists)+BONDS, &num_bonds, &est_3body );
- realloc->bonds = -1;
- realloc->num_3body = MAX( realloc->num_3body, est_3body );
- }
-
- if( realloc->num_3body > 0 ) {
- fprintf (stderr, " Reallocating 3Body \n");
- Delete_List( (*lists)+THREE_BODIES, TYP_HOST );
-
- if( num_bonds == -1 )
- num_bonds = ((*lists)+BONDS)->num_intrs;
- realloc->num_3body *= SAFE_ZONE;
-
- if( !Make_List( num_bonds, realloc->num_3body,
- TYP_THREE_BODY, (*lists)+THREE_BODIES, TYP_HOST ) ) {
- fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
- exit( INIT_ERR );
- }
- realloc->num_3body = -1;
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reallocating 3 bodies\n" );
- fprintf( stderr, "reallocated - num_bonds: %d\n", num_bonds );
- fprintf( stderr, "reallocated - num_3body: %d\n", realloc->num_3body );
- fprintf( stderr, "reallocated 3body memory: %ldMB\n",
- realloc->num_3body*sizeof(three_body_interaction_data)/
- (1024*1024) );
-#endif
- }
-
- if( realloc->gcell_atoms > -1 ){
-#if defined(DEBUG_FOCUS)
- fprintf(stderr, "reallocating gcell: g->max_atoms: %d\n", g->max_atoms);
-#endif
-
- free (g->atoms);
- g->atoms = (int *) calloc ( g->ncell[0]*g->ncell[1]*g->ncell[2],
- sizeof (int) * workspace->realloc.gcell_atoms);
- realloc->gcell_atoms = -1;
- }
-}
-
void Cuda_Reallocate( reax_system *system, static_storage *workspace, list *lists,
int nbr_flag, int step )
{
@@ -724,3 +424,68 @@ void Cuda_Reallocate( reax_system *system, static_storage *workspace, list *list
realloc->gcell_atoms = -1;
}
}
+
+
+GLOBAL void Init_HBond_Indexes ( int *h_index, int *hb_top, list hbonds, int N )
+{
+ int index = blockIdx.x * blockDim.x + threadIdx.x;
+
+ if (index >= N) return;
+
+ if( h_index[index] == 0 ){
+ Set_Start_Index( 0, 0, &hbonds );
+ Set_End_Index( 0, 0, &hbonds );
+ }
+ else if( h_index[index] > 0 ){
+ Set_Start_Index( h_index[index], hb_top[index-1], &hbonds );
+ Set_End_Index( h_index[index], hb_top[index-1], &hbonds );
+ }
+}
+
+
+GLOBAL void Init_Bond_Indexes ( int *b_top, list bonds, int N )
+{
+ int index = blockIdx.x * blockDim.x + threadIdx.x;
+
+ if (index >= N) return;
+
+ if( index == 0 ){
+ Set_Start_Index( 0, 0, &bonds );
+ Set_End_Index( 0, 0, &bonds );
+ }
+ else if( index > 0 ){
+ Set_Start_Index( index, b_top[index-1], &bonds );
+ Set_End_Index( index, b_top[index-1], &bonds );
+ }
+}
+
+
+void GLOBAL Calculate_Bond_Indexes (int *bond_top, list bonds, int *per_block_results, int n)
+{
+ extern __shared__ int sh_input[];
+ unsigned int i = blockIdx.x * blockDim.x + threadIdx.x;
+ real x = 0;
+
+ if(i < n)
+ {
+ x = SQR (Num_Entries( i, &bonds ) );
+ bond_top[i] = MAX( Num_Entries( i, &bonds ) * 2, MIN_BONDS );
+ }
+ sh_input[threadIdx.x] = x;
+ __syncthreads();
+
+ for(int offset = blockDim.x / 2; offset > 0; offset >>= 1)
+ {
+ if(threadIdx.x < offset)
+ {
+ sh_input[threadIdx.x] += sh_input[threadIdx.x + offset];
+ }
+
+ __syncthreads();
+ }
+
+ if(threadIdx.x == 0)
+ {
+ per_block_results[blockIdx.x] = sh_input[0];
+ }
+}
diff --git a/PuReMD-GPU/src/cuda_allocate.h b/PuReMD-GPU/src/cuda_allocate.h
new file mode 100644
index 00000000..1de435a0
--- /dev/null
+++ b/PuReMD-GPU/src/cuda_allocate.h
@@ -0,0 +1,31 @@
+/*----------------------------------------------------------------------
+ PuReMD-GPU - Reax Force Field Simulator
+
+ Copyright (2014) Purdue University
+ Sudhir Kylasa, skylasa@purdue.edu
+ Hasan Metin Aktulga, haktulga@cs.purdue.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 __CUDA_ALLOCATE_H_
+#define __CUDA_ALLOCATE_H_
+
+#include "mytypes.h"
+
+int Cuda_Allocate_Matrix( sparse_matrix*, int, int );
+int Cuda_Allocate_HBond_List( int, int, int*, int*, list* );
+int Cuda_Allocate_Bond_List( int, int*, list* );
+void Cuda_Reallocate( reax_system*, static_storage*, list*, int, int );
+
+#endif
diff --git a/PuReMD-GPU/src/cuda_helpers.h b/PuReMD-GPU/src/cuda_helpers.h
index adbf73ce..292d5613 100644
--- a/PuReMD-GPU/src/cuda_helpers.h
+++ b/PuReMD-GPU/src/cuda_helpers.h
@@ -25,7 +25,7 @@
#include "mytypes.h"
-DEVICE static inline int cuda_strcmp(char *a, char *b, int len)
+DEVICE inline int cuda_strcmp(char *a, char *b, int len)
{
char *src, *dst;
@@ -52,8 +52,7 @@ DEVICE static inline int cuda_strcmp(char *a, char *b, int len)
}
-#if __CUDA_ARCH__ < 600
-DEVICE static inline real atomicAdd(double* address, double val)
+DEVICE inline real myAtomicAdd(double* address, double val)
{
unsigned long long int* address_as_ull =
(unsigned long long int*)address;
@@ -67,22 +66,21 @@ DEVICE static inline real atomicAdd(double* address, double val)
while (assumed != old);
return __longlong_as_double(old);
}
-#endif
-DEVICE static inline void atomic_rvecAdd( rvec ret, rvec v )
+DEVICE inline void atomic_rvecAdd( rvec ret, rvec v )
{
- atomicAdd( (double*)&ret[0], (double)v[0] );
- atomicAdd( (double*)&ret[1], (double)v[1] );
- atomicAdd( (double*)&ret[2], (double)v[2] );
+ MYATOMICADD( (double*)&ret[0], (double)v[0] );
+ MYATOMICADD( (double*)&ret[1], (double)v[1] );
+ MYATOMICADD( (double*)&ret[2], (double)v[2] );
}
-DEVICE static inline void atomic_rvecScaledAdd( rvec ret, real c, rvec v )
+DEVICE inline void atomic_rvecScaledAdd( rvec ret, real c, rvec v )
{
- atomicAdd( (double*)&ret[0], (double)(c * v[0]) );
- atomicAdd( (double*)&ret[1], (double)(c * v[1]) );
- atomicAdd( (double*)&ret[2], (double)(c * v[2]) );
+ MYATOMICADD( (double*)&ret[0], (double)(c * v[0]) );
+ MYATOMICADD( (double*)&ret[1], (double)(c * v[1]) );
+ MYATOMICADD( (double*)&ret[2], (double)(c * v[2]) );
}
diff --git a/PuReMD-GPU/src/system_props.cu b/PuReMD-GPU/src/cuda_system_props.cu
similarity index 56%
rename from PuReMD-GPU/src/system_props.cu
rename to PuReMD-GPU/src/cuda_system_props.cu
index e0bb2626..dfbc5892 100644
--- a/PuReMD-GPU/src/system_props.cu
+++ b/PuReMD-GPU/src/cuda_system_props.cu
@@ -18,57 +18,21 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "system_props.h"
+#include "cuda_system_props.h"
+
#include "box.h"
#include "vector.h"
-#include "cuda_utils.h"
+#include "center_mass.h"
#include "cuda_copy.h"
+#include "cuda_utils.h"
#include "reduction.h"
-#include "center_mass.h"
-#include "validation.h"
-
-
-real Get_Time( )
-{
- struct timeval tim;
-
- gettimeofday(&tim, NULL );
- return( tim.tv_sec + (tim.tv_usec / 1000000.0) );
-}
-
-
-real Get_Timing_Info( real t_start )
-{
- struct timeval tim;
- real t_end;
-
- gettimeofday(&tim, NULL );
- t_end = tim.tv_sec + (tim.tv_usec / 1000000.0);
- return (t_end - t_start);
-}
-void Temperature_Control( control_params *control, simulation_data *data,
- output_controls *out_control )
-{
- real tmp;
-
- if( control->T_mode == 1 ) { // step-wise temperature control
- if( (data->step - data->prev_steps) %
- ((int)(control->T_freq / control->dt)) == 0 ) {
- if( fabs( control->T - control->T_final ) >= fabs( control->T_rate ) )
- control->T += control->T_rate;
- else control->T = control->T_final;
- }
- }
- else if( control->T_mode == 2 ) { // constant slope control
- tmp = control->T_rate * control->dt / control->T_freq;
+GLOBAL void k_Compute_Total_Mass(single_body_parameters *, reax_atom *, real *, size_t );
+GLOBAL void k_Compute_Kinetic_Energy(single_body_parameters *, reax_atom *, unsigned int , real *);
+GLOBAL void k_Kinetic_Energy_Reduction(simulation_data *, real *, int);
- if( fabs( control->T - control->T_final ) >= fabs( tmp ) )
- control->T += tmp;
- }
-}
void prep_dev_system (reax_system *system)
{
@@ -77,21 +41,6 @@ void prep_dev_system (reax_system *system)
}
-void Compute_Total_Mass( reax_system *system, simulation_data *data )
-{
- int i;
- int blocks;
- int block_size;
- real *partial_sums = 0;
-
- data->M = 0;
-
- for( i = 0; i < system->N; i++ )
- data->M += system->reaxprm.sbp[ system->atoms[i].type ].mass;
-
- data->inv_M = 1. / data->M;
-}
-
void Cuda_Compute_Total_Mass( reax_system *system, simulation_data *data )
{
real *partial_sums = (real *) scratch;
@@ -133,158 +82,6 @@ void Cuda_Compute_Total_Mass( reax_system *system, simulation_data *data )
}
-GLOBAL void k_Compute_Total_Mass (single_body_parameters *sbp, reax_atom *atoms, real *per_block_results, size_t n)
-{
- extern __shared__ real sdata[];
- unsigned int i = blockIdx.x * blockDim.x + threadIdx.x;
- real x = 0;
-
- if(i < n)
- x = sbp [ atoms[ i ].type ].mass;
-
- sdata[threadIdx.x] = x;
- __syncthreads();
-
- for(int offset = blockDim.x / 2; offset > 0; offset >>= 1)
- {
- if(threadIdx.x < offset)
- {
- sdata[threadIdx.x] += sdata[threadIdx.x + offset];
- }
- __syncthreads();
- }
-
- if(threadIdx.x == 0)
- {
- per_block_results[blockIdx.x] = sdata[0];
- }
-}
-
-
-void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
- FILE *fout )
-{
- int i;
- real m, xx, xy, xz, yy, yz, zz, det;
- rvec tvec, diff;
- rtensor mat, inv;
-
- int blocks;
- int block_size;
- rvec *l_xcm, *l_vcm, *l_amcm;
- real t_start, t_end;
-
- rvec_MakeZero( data->xcm ); // position of CoM
- rvec_MakeZero( data->vcm ); // velocity of CoM
- rvec_MakeZero( data->amcm ); // angular momentum of CoM
- rvec_MakeZero( data->avcm ); // angular velocity of CoM
-
- /* Compute the position, velocity and angular momentum about the CoM */
- for( i = 0; i < system->N; ++i ) {
- m = system->reaxprm.sbp[ system->atoms[i].type ].mass;
-
- rvec_ScaledAdd( data->xcm, m, system->atoms[i].x );
- rvec_ScaledAdd( data->vcm, m, system->atoms[i].v );
-
- rvec_Cross( tvec, system->atoms[i].x, system->atoms[i].v );
- rvec_ScaledAdd( data->amcm, m, tvec );
-
- /*fprintf( fout,"%3d %g %g %g\n",
- i+1,
- system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2] );
- fprintf( fout, "vcm: %g %g %g\n",
- data->vcm[0], data->vcm[1], data->vcm[2] );
- */
- }
-
- rvec_Scale( data->xcm, data->inv_M, data->xcm );
- rvec_Scale( data->vcm, data->inv_M, data->vcm );
-
- rvec_Cross( tvec, data->xcm, data->vcm );
- rvec_ScaledAdd( data->amcm, -data->M, tvec );
-
- data->etran_cm = 0.5 * data->M * rvec_Norm_Sqr( data->vcm );
-
- /* Calculate and then invert the inertial tensor */
- xx = xy = xz = yy = yz = zz = 0;
-
- for( i = 0; i < system->N; ++i ) {
- m = system->reaxprm.sbp[ system->atoms[i].type ].mass;
-
- rvec_ScaledSum( diff, 1., system->atoms[i].x, -1., data->xcm );
- xx += diff[0] * diff[0] * m;
- xy += diff[0] * diff[1] * m;
- xz += diff[0] * diff[2] * m;
- yy += diff[1] * diff[1] * m;
- yz += diff[1] * diff[2] * m;
- zz += diff[2] * diff[2] * m;
- }
-
-#ifdef __DEBUG_CUDA__
- fprintf (stderr, " xx: %f \n", xx);
- fprintf (stderr, " xy: %f \n", xy);
- fprintf (stderr, " xz: %f \n", xz);
- fprintf (stderr, " yy: %f \n", yy);
- fprintf (stderr, " yz: %f \n", yz);
- fprintf (stderr, " zz: %f \n", zz);
-#endif
-
- mat[0][0] = yy + zz;
- mat[0][1] = mat[1][0] = -xy;
- mat[0][2] = mat[2][0] = -xz;
- mat[1][1] = xx + zz;
- mat[2][1] = mat[1][2] = -yz;
- mat[2][2] = xx + yy;
-
- /* invert the inertial tensor */
- det = ( mat[0][0] * mat[1][1] * mat[2][2] +
- mat[0][1] * mat[1][2] * mat[2][0] +
- mat[0][2] * mat[1][0] * mat[2][1] ) -
- ( mat[0][0] * mat[1][2] * mat[2][1] +
- mat[0][1] * mat[1][0] * mat[2][2] +
- mat[0][2] * mat[1][1] * mat[2][0] );
-
- inv[0][0] = mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1];
- inv[0][1] = mat[0][2] * mat[2][1] - mat[0][1] * mat[2][2];
- inv[0][2] = mat[0][1] * mat[1][2] - mat[0][2] * mat[1][1];
- inv[1][0] = mat[1][2] * mat[2][0] - mat[1][0] * mat[2][2];
- inv[1][1] = mat[0][0] * mat[2][2] - mat[0][2] * mat[2][0];
- inv[1][2] = mat[0][2] * mat[1][0] - mat[0][0] * mat[1][2];
- inv[2][0] = mat[1][0] * mat[2][1] - mat[2][0] * mat[1][1];
- inv[2][1] = mat[2][0] * mat[0][1] - mat[0][0] * mat[2][1];
- inv[2][2] = mat[0][0] * mat[1][1] - mat[1][0] * mat[0][1];
-
- if( fabs(det) > ALMOST_ZERO )
- rtensor_Scale( inv, 1./det, inv );
- else
- rtensor_MakeZero( inv );
-
- /* Compute the angular velocity about the centre of mass */
- rtensor_MatVec( data->avcm, inv, data->amcm );
- data->erot_cm = 0.5 * E_CONV * rvec_Dot( data->avcm, data->amcm );
-
-#if defined(DEBUG)
- fprintf( stderr, "xcm: %24.15e %24.15e %24.15e\n",
- data->xcm[0], data->xcm[1], data->xcm[2] );
- fprintf( stderr, "vcm: %24.15e %24.15e %24.15e\n",
- data->vcm[0], data->vcm[1], data->vcm[2] );
- fprintf( stderr, "amcm: %24.15e %24.15e %24.15e\n",
- data->amcm[0], data->amcm[1], data->amcm[2] );
- /* fprintf( fout, "mat: %f %f %f\n %f %f %f\n %f %f %f\n",
- mat[0][0], mat[0][1], mat[0][2],
- mat[1][0], mat[1][1], mat[1][2],
- mat[2][0], mat[2][1], mat[2][2] );
- fprintf( fout, "inv: %g %g %g\n %g %g %g\n %g %g %g\n",
- inv[0][0], inv[0][1], inv[0][2],
- inv[1][0], inv[1][1], inv[1][2],
- inv[2][0], inv[2][1], inv[2][2] );
- fflush( fout ); */
- fprintf( stderr, "avcm: %24.15e %24.15e %24.15e\n",
- data->avcm[0], data->avcm[1], data->avcm[2] );
-#endif
-}
-
-
void Cuda_Compute_Center_of_Mass( reax_system *system, simulation_data *data,
FILE *fout )
{
@@ -489,34 +286,51 @@ void Cuda_Compute_Center_of_Mass( reax_system *system, simulation_data *data,
}
-
-void Compute_Kinetic_Energy( reax_system* system, simulation_data* data )
+void Cuda_Compute_Kinetic_Energy (reax_system *system, simulation_data *data)
{
- int i;
- rvec p;
- real m;
+ real *results = (real *) scratch;
+ cuda_memset (results, 0, REAL_SIZE * BLOCKS_POW_2, RES_SCRATCH);
+ k_Compute_Kinetic_Energy <<<BLOCKS_POW_2, BLOCK_SIZE, REAL_SIZE * BLOCK_SIZE>>>
+ (system->reaxprm.d_sbp, system->d_atoms, system->N, (real *) results);
+ cudaThreadSynchronize ();
+ cudaCheckError ();
- data->E_Kin = 0.0;
+ k_Kinetic_Energy_Reduction <<< 1, BLOCKS_POW_2, REAL_SIZE * BLOCKS_POW_2 >>>
+ ((simulation_data *)data->d_simulation_data, results, BLOCKS_POW_2);
+ cudaThreadSynchronize ();
+ cudaCheckError ();
+}
- for (i=0; i < system->N; i++) {
- m = system->reaxprm.sbp[system->atoms[i].type].mass;
- rvec_Scale( p, m, system->atoms[i].v );
- data->E_Kin += 0.5 * rvec_Dot( p, system->atoms[i].v );
+GLOBAL void k_Compute_Total_Mass (single_body_parameters *sbp, reax_atom *atoms, real *per_block_results, size_t n)
+{
+ extern __shared__ real sdata[];
+ unsigned int i = blockIdx.x * blockDim.x + threadIdx.x;
+ real x = 0;
- /* fprintf(stderr,"%d, %lf, %lf, %lf %lf\n",
- i,system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2],
- system->reaxprm.sbp[system->atoms[i].type].mass); */
- }
+ if(i < n)
+ x = sbp [ atoms[ i ].type ].mass;
- data->therm.T = (2. * data->E_Kin) / (data->N_f * K_B);
+ sdata[threadIdx.x] = x;
+ __syncthreads();
- if ( fabs(data->therm.T) < ALMOST_ZERO ) /* avoid T being an absolute zero! */
- data->therm.T = ALMOST_ZERO;
+ for(int offset = blockDim.x / 2; offset > 0; offset >>= 1)
+ {
+ if(threadIdx.x < offset)
+ {
+ sdata[threadIdx.x] += sdata[threadIdx.x + offset];
+ }
+ __syncthreads();
+ }
+
+ if(threadIdx.x == 0)
+ {
+ per_block_results[blockIdx.x] = sdata[0];
+ }
}
-GLOBAL void Compute_Kinetic_Energy( single_body_parameters* sbp, reax_atom* atoms,
+GLOBAL void k_Compute_Kinetic_Energy( single_body_parameters* sbp, reax_atom* atoms,
unsigned int N, real *output)
{
extern __shared__ real sh_ekin[];
@@ -547,8 +361,8 @@ GLOBAL void Compute_Kinetic_Energy( single_body_parameters* sbp, reax_atom* atom
}
}
-GLOBAL void Kinetic_Energy_Reduction (simulation_data *data,
- real *input, int n)
+
+GLOBAL void k_Kinetic_Energy_Reduction (simulation_data *data, real *input, int n)
{
extern __shared__ real sdata[];
unsigned int i = blockIdx.x * blockDim.x + threadIdx.x;
@@ -582,20 +396,6 @@ GLOBAL void Kinetic_Energy_Reduction (simulation_data *data,
}
}
-void Cuda_Compute_Kinetic_Energy (reax_system *system, simulation_data *data)
-{
- real *results = (real *) scratch;
- cuda_memset (results, 0, REAL_SIZE * BLOCKS_POW_2, RES_SCRATCH);
- Compute_Kinetic_Energy <<<BLOCKS_POW_2, BLOCK_SIZE, REAL_SIZE * BLOCK_SIZE>>>
- (system->reaxprm.d_sbp, system->d_atoms, system->N, (real *) results);
- cudaThreadSynchronize ();
- cudaCheckError ();
-
- Kinetic_Energy_Reduction <<< 1, BLOCKS_POW_2, REAL_SIZE * BLOCKS_POW_2 >>>
- ((simulation_data *)data->d_simulation_data, results, BLOCKS_POW_2);
- cudaThreadSynchronize ();
- cudaCheckError ();
-}
/*
GLOBAL void Compute_Kinetic_Energy( single_body_parameters* sbp, reax_atom* atoms,
@@ -660,117 +460,3 @@ data->therm.T = ALMOST_ZERO;
*/
-/* IMPORTANT: This function assumes that current kinetic energy and
- * the center of mass of the system is already computed before.
- *
- * IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
- * to be added when there are long-range interactions or long-range
- * corrections to short-range interactions present.
- * We may want to add that for more accuracy.
- */
-void Compute_Pressure_Isotropic( reax_system* system, control_params *control,
- simulation_data* data,
- output_controls *out_control )
-{
- int i;
- reax_atom *p_atom;
- rvec tx;
- rvec tmp;
- simulation_box *box = &(system->box);
-
- /* Calculate internal pressure */
- rvec_MakeZero( data->int_press );
-
- // 0: both int and ext, 1: ext only, 2: int only
- if( control->press_mode == 0 || control->press_mode == 2 ) {
- for( i = 0; i < system->N; ++i ) {
- p_atom = &( system->atoms[i] );
-
- /* transform x into unitbox coordinates */
- Transform_to_UnitBox( p_atom->x, box, 1, tx );
-
- /* this atom's contribution to internal pressure */
- rvec_Multiply( tmp, p_atom->f, tx );
- rvec_Add( data->int_press, tmp );
-
- if( out_control->debug_level > 0 ) {
- fprintf( out_control->prs, "%-8d%8.2f%8.2f%8.2f",
- i+1, p_atom->x[0], p_atom->x[1], p_atom->x[2] );
- fprintf( out_control->prs, "%8.2f%8.2f%8.2f",
- p_atom->f[0], p_atom->f[1], p_atom->f[2] );
- fprintf( out_control->prs, "%8.2f%8.2f%8.2f\n",
- data->int_press[0],data->int_press[1],data->int_press[2]);
- }
- }
- }
-
- /* kinetic contribution */
- data->kin_press = 2. * (E_CONV * data->E_Kin) / ( 3. * box->volume * P_CONV );
-
- /* Calculate total pressure in each direction */
- data->tot_press[0] = data->kin_press -
- ((data->int_press[0] + data->ext_press[0]) /
- (box->box_norms[1] * box->box_norms[2] * P_CONV));
-
- data->tot_press[1] = data->kin_press -
- ((data->int_press[1] + data->ext_press[1])/
- (box->box_norms[0] * box->box_norms[2] * P_CONV));
-
- data->tot_press[2] = data->kin_press -
- ((data->int_press[2] + data->ext_press[2])/
- (box->box_norms[0] * box->box_norms[1] * P_CONV));
-
- /* Average pressure for the whole box */
- data->iso_bar.P=(data->tot_press[0]+data->tot_press[1]+data->tot_press[2])/3;
-}
-
-
-void Compute_Pressure_Isotropic_Klein( reax_system* system,
- simulation_data* data )
-{
- int i;
- reax_atom *p_atom;
- rvec dx;
-
- // IMPORTANT: This function assumes that current kinetic energy and
- // the center of mass of the system is already computed before.
- data->iso_bar.P = 2.0 * data->E_Kin;
-
- for( i = 0; i < system->N; ++i )
- {
- p_atom = &( system->atoms[i] );
- rvec_ScaledSum(dx,1.0,p_atom->x,-1.0,data->xcm);
- data->iso_bar.P += ( -F_CONV * rvec_Dot(p_atom->f, dx) );
- }
-
- data->iso_bar.P /= (3.0 * system->box.volume);
-
- // IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
- // to be added when there are long-range interactions or long-range
- // corrections to short-range interactions present.
- // We may want to add that for more accuracy.
-}
-
-
-void Compute_Pressure( reax_system* system, simulation_data* data,
- static_storage *workspace )
-{
- int i;
- reax_atom *p_atom;
- rtensor temp;
-
- rtensor_MakeZero( data->flex_bar.P );
-
- for( i = 0; i < system->N; ++i ) {
- p_atom = &( system->atoms[i] );
- // Distance_on_T3_Gen( data->rcm, p_atom->x, &(system->box), &dx );
- rvec_OuterProduct( temp, p_atom->v, p_atom->v );
- rtensor_ScaledAdd( data->flex_bar.P,
- system->reaxprm.sbp[ p_atom->type ].mass, temp );
- // rvec_OuterProduct(temp, workspace->virial_forces[i], p_atom->x );
- rtensor_ScaledAdd( data->flex_bar.P, -F_CONV, temp );
- }
-
- rtensor_Scale( data->flex_bar.P, 1.0 / system->box.volume, data->flex_bar.P );
- data->iso_bar.P = rtensor_Trace( data->flex_bar.P ) / 3.0;
-}
diff --git a/PuReMD-GPU/src/cuda_system_props.h b/PuReMD-GPU/src/cuda_system_props.h
new file mode 100644
index 00000000..28aea013
--- /dev/null
+++ b/PuReMD-GPU/src/cuda_system_props.h
@@ -0,0 +1,32 @@
+/*----------------------------------------------------------------------
+ PuReMD-GPU - Reax Force Field Simulator
+
+ Copyright (2014) Purdue University
+ Sudhir Kylasa, skylasa@purdue.edu
+ Hasan Metin Aktulga, haktulga@cs.purdue.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 __CUDA_SYSTEM_PROP_H_
+#define __CUDA_SYSTEM_PROP_H_
+
+#include "mytypes.h"
+
+void prep_dev_system (reax_system *system);
+
+void Cuda_Compute_Total_Mass( reax_system*, simulation_data* );
+void Cuda_Compute_Center_of_Mass( reax_system*, simulation_data*, FILE* );
+void Cuda_Compute_Kinetic_Energy( reax_system*, simulation_data* );
+
+#endif
diff --git a/PuReMD-GPU/src/forces.cu b/PuReMD-GPU/src/forces.cu
index e8e1e291..a2ad8ea7 100644
--- a/PuReMD-GPU/src/forces.cu
+++ b/PuReMD-GPU/src/forces.cu
@@ -36,7 +36,6 @@
#include "cuda_init.h"
#include "reduction.h"
//#include "matrix.h"
-
#include "validation.h"
#include "cudaProfiler.h"
@@ -2634,7 +2633,7 @@ GLOBAL void Estimate_Storage_Sizes (reax_atom *atoms,
if( nbr_pj->d <= control->r_cut ) {
//++(*Htop);
- atomicAdd (Htop, 1);
+ atomicAdd(Htop, 1);
/* hydrogen bond lists */
//TODO - CHANGE ORIGINAL
@@ -2643,11 +2642,11 @@ GLOBAL void Estimate_Storage_Sizes (reax_atom *atoms,
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 )
//++hb_top[i];
- atomicAdd (&hb_top[i], 1);
+ atomicAdd(&hb_top[i], 1);
else if( ihb == 2 && jhb == 1 )
//++hb_top[j];
- //atomicAdd (&hb_top[j], 1);
- atomicAdd (&hb_top[i], 1);
+ //atomicAdd(&hb_top[j], 1);
+ atomicAdd(&hb_top[i], 1);
}
//TODO -- CHANGE ORIGINAL
@@ -2685,8 +2684,8 @@ GLOBAL void Estimate_Storage_Sizes (reax_atom *atoms,
if( BO >= control->bo_cut ) {
//++bond_top[i];
//++bond_top[j];
- atomicAdd (&bond_top[i], 1);
- atomicAdd (&bond_top[j], 1);
+ atomicAdd(&bond_top[i], 1);
+ atomicAdd(&bond_top[j], 1);
}
}
}
diff --git a/PuReMD-GPU/src/four_body_interactions.cu b/PuReMD-GPU/src/four_body_interactions.cu
index af134bab..35a907f8 100644
--- a/PuReMD-GPU/src/four_body_interactions.cu
+++ b/PuReMD-GPU/src/four_body_interactions.cu
@@ -889,7 +889,7 @@ GLOBAL void Four_Body_Interactions ( reax_atom *atoms,
//PERFORMANCE IMPACT
e_tor = fn10 * sin_ijk * sin_jkl * CV;
- //atomicAdd (&data->E_Tor ,e_tor );
+ //MYATOMICADD(&data->E_Tor ,e_tor );
E_Tor [j] += e_tor;
//sh_tor [threadIdx.x] += e_tor;
@@ -933,7 +933,7 @@ GLOBAL void Four_Body_Interactions ( reax_atom *atoms,
fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
//PERFORMANCE IMPACT
e_con = fbp->p_cot1 * fn12 * (1. + (SQR(cos_omega)-1.) * sin_ijk*sin_jkl);
- //atomicAdd (&data->E_Con ,e_con );
+ //MYATOMICADD(&data->E_Con ,e_con );
E_Con [j] += e_con ;
//sh_con [threadIdx.x] += e_con;
@@ -971,12 +971,12 @@ GLOBAL void Four_Body_Interactions ( reax_atom *atoms,
/* forces */
//PERFORMANCE IMPACT
/*
- atomicAdd ( &bo_jk->Cdbopi, CEtors2 );
- atomicAdd ( &workspace->CdDelta[j], CEtors3 );
- atomicAdd ( &workspace->CdDelta[k], CEtors3 );
- atomicAdd ( &bo_ij->Cdbo, (CEtors4 + CEconj1) );
- atomicAdd ( &bo_jk->Cdbo, (CEtors5 + CEconj2) );
- atomicAdd ( &bo_kl->Cdbo, (CEtors6 + CEconj3) );
+ MYATOMICADD( &bo_jk->Cdbopi, CEtors2 );
+ MYATOMICADD( &workspace->CdDelta[j], CEtors3 );
+ MYATOMICADD( &workspace->CdDelta[k], CEtors3 );
+ MYATOMICADD( &bo_ij->Cdbo, (CEtors4 + CEconj1) );
+ MYATOMICADD( &bo_jk->Cdbo, (CEtors5 + CEconj2) );
+ MYATOMICADD( &bo_kl->Cdbo, (CEtors6 + CEconj3) );
*/
//PERFORMANCE IMPACT
@@ -987,7 +987,7 @@ GLOBAL void Four_Body_Interactions ( reax_atom *atoms,
bo_jk->Cdbo += CEtors5 + CEconj2;
//TODO REMOVE THIS ATOMIC OPERATION IF POSSIBLE
- atomicAdd (&pbond_kl->Cdbo_kl, CEtors6 + CEconj3 );
+ MYATOMICADD(&pbond_kl->Cdbo_kl, CEtors6 + CEconj3 );
//TODO REMOVE THIS ATOMIC OPERATION IF POSSIBLE
if( control->ensemble == NVE || control->ensemble == NVT ||control->ensemble == bNVT) {
diff --git a/PuReMD-GPU/src/init_md.cu b/PuReMD-GPU/src/init_md.cu
index 87b84a76..92691bbb 100644
--- a/PuReMD-GPU/src/init_md.cu
+++ b/PuReMD-GPU/src/init_md.cu
@@ -34,17 +34,20 @@
#include "traj.h"
#include "vector.h"
-
#include "cuda_init.h"
#include "cuda_copy.h"
#include "cuda_utils.h"
#include "helpers.h"
#include "reduction.h"
-#include "index_utils.h"
+#include "cuda_allocate.h"
+#include "cuda_system_props.h"
+
+#include "index_utils.h"
#include "validation.h"
+
void Generate_Initial_Velocities(reax_system *system, real T )
{
int i;
@@ -967,7 +970,7 @@ void compare_far_neighbors (int *test, int *start, int *end, far_neighbor_data *
fprintf (stderr, "Serial NumNeighbors ---> %d \n", num_nbrs);
#endif
- if( !Make_List(system->N, num_nbrs, TYP_FAR_NEIGHBOR, (*lists)+FAR_NBRS), TYP_HOST ) {
+ if( !Make_List(system->N, num_nbrs, TYP_FAR_NEIGHBOR, (*lists)+FAR_NBRS, TYP_HOST ) ) {
fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
exit( INIT_ERR );
}
@@ -1036,7 +1039,7 @@ void compare_far_neighbors (int *test, int *start, int *end, far_neighbor_data *
#endif
/* 3bodies list */
- if(!Make_List(num_bonds, num_3body, TYP_THREE_BODY, (*lists)+THREE_BODIES), TYP_HOST) {
+ if(!Make_List(num_bonds, num_3body, TYP_THREE_BODY, (*lists)+THREE_BODIES, TYP_HOST )) {
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
exit( INIT_ERR );
}
diff --git a/PuReMD-GPU/src/integrate.cu b/PuReMD-GPU/src/integrate.cu
index d0790286..c54603b5 100644
--- a/PuReMD-GPU/src/integrate.cu
+++ b/PuReMD-GPU/src/integrate.cu
@@ -36,6 +36,9 @@
#include "reduction.h"
#include "validation.h"
+#include "cuda_allocate.h"
+#include "cuda_system_props.h"
+
void Velocity_Verlet_NVE(reax_system* system, control_params* control,
simulation_data *data, static_storage *workspace,
diff --git a/PuReMD-GPU/src/mytypes.h b/PuReMD-GPU/src/mytypes.h
index 91b9438d..eacde6b9 100644
--- a/PuReMD-GPU/src/mytypes.h
+++ b/PuReMD-GPU/src/mytypes.h
@@ -31,6 +31,11 @@
#include <cuda.h>
#include <cublas_v2.h>
#include <cusparse_v2.h>
+ #if __CUDA_ARCH__ < 600
+ #define MYATOMICADD myAtomicAdd
+ #else
+ #define MYATOMICADD atomicAdd
+ #endif
#endif
#else
#ifndef __MYTYPES_H_
diff --git a/PuReMD-GPU/src/neighbors.cu b/PuReMD-GPU/src/neighbors.cu
index 90779538..0f902de6 100644
--- a/PuReMD-GPU/src/neighbors.cu
+++ b/PuReMD-GPU/src/neighbors.cu
@@ -782,7 +782,7 @@ int Estimate_NumNeighbors( reax_system *system, control_params *control,
}
//__syncthreads ();
- //atomicAdd ( &warp_sync [threadIdx.x / __THREADS_PER_ATOM__ ], 1);
+ //MYATOMICADD( &warp_sync [threadIdx.x / __THREADS_PER_ATOM__ ], 1);
//while ( warp_sync [threadIdx.x / __THREADS_PER_ATOM__ ] < __THREADS_PER_ATOM__ ) ;
if (nbrgen)
diff --git a/PuReMD-GPU/src/random.h b/PuReMD-GPU/src/random.h
index f7edb397..f5685b8b 100644
--- a/PuReMD-GPU/src/random.h
+++ b/PuReMD-GPU/src/random.h
@@ -23,10 +23,6 @@
#include "mytypes.h"
-HOST_DEVICE inline double Random(double);
-HOST_DEVICE inline void Randomize();
-HOST_DEVICE inline double GRandom(double , double );
-
/* System random number generator used linear congruance method with
large periodicity for generation of pseudo random number. function
@@ -37,6 +33,7 @@ HOST_DEVICE inline double Random(double range)
return (random() * range) / 2147483647L;
}
+
/* This function seeds the system pseudo random number generator with
current time. Use this function once in the begining to initialize
the system */
@@ -45,6 +42,7 @@ HOST_DEVICE inline void Randomize()
srandom(time(NULL));
}
+
/* GRandom return random number with gaussian distribution with mean
and standard deviation "sigma" */
HOST_DEVICE inline double GRandom(double mean, double sigma)
diff --git a/PuReMD-GPU/src/single_body_interactions.cu b/PuReMD-GPU/src/single_body_interactions.cu
index 3c6c0882..9b8438a6 100644
--- a/PuReMD-GPU/src/single_body_interactions.cu
+++ b/PuReMD-GPU/src/single_body_interactions.cu
@@ -374,7 +374,7 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
e_lp = p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
//PERFORMANCE IMPACT
- atomicAdd (&data->E_Lp, e_lp);
+ MYATOMICADD(&data->E_Lp, e_lp);
dElp = p_lp2 * inv_expvd2 +
75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
@@ -382,7 +382,7 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
//PERFORMANCE IMPACT
//workspace->CdDelta[i] += CElp; // lp - 1st term
- atomicAdd (&workspace->CdDelta[i], CElp);
+ MYATOMICADD(&workspace->CdDelta[i], CElp);
#ifdef TEST_ENERGY
@@ -416,7 +416,7 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
//PERFORMANCE IMPACT
e_lph = p_lp3 * SQR(vov3-3.0);
- atomicAdd (&data->E_Lp, e_lph );
+ MYATOMICADD(&data->E_Lp, e_lph );
//estrain(i) += e_lph;
deahu2dbo = 2.*p_lp3*(vov3 - 3.);
@@ -426,7 +426,7 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
//PERFORMANCE IMPACT
- atomicAdd (&workspace->CdDelta[i], deahu2dsbo);
+ MYATOMICADD(&workspace->CdDelta[i], deahu2dsbo);
#ifdef TEST_ENERGY
//TODO
//fprintf(out_control->elp,"C2cor%6d%6d%23.15e%23.15e%23.15e\n",
@@ -500,7 +500,7 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
//PERFORMANCE IMPACT
//data->E_Ov += e_ov = sum_ovun1 * CEover1;
e_ov = sum_ovun1 * CEover1;
- atomicAdd (&data->E_Ov, e_ov );
+ MYATOMICADD(&data->E_Ov, e_ov );
CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 *
( 1.0 - Delta_lpcorr*( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 ) );
@@ -523,7 +523,7 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
//PERFORMANCE IMPACT
e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
- atomicAdd (&data->E_Un, e_un );
+ MYATOMICADD(&data->E_Un, e_un );
CEunder1 = inv_exp_ovun2n * ( p_ovun5*p_ovun6*exp_ovun6*inv_exp_ovun8 +
p_ovun2 * e_un * exp_ovun2n);
@@ -537,8 +537,8 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
// forces
//PERFORMANCE IMPACT
- atomicAdd (&workspace->CdDelta[i] , CEover3); // OvCoor - 2nd term
- atomicAdd (&workspace->CdDelta[i], CEunder3); // UnCoor - 1st term
+ MYATOMICADD(&workspace->CdDelta[i] , CEover3); // OvCoor - 2nd term
+ MYATOMICADD(&workspace->CdDelta[i], CEunder3); // UnCoor - 1st term
#ifdef TEST_FORCES
//TODO
@@ -559,7 +559,7 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s; // OvCoor - 1st
//PERFORMANCE IMPACT
- atomicAdd (&workspace->CdDelta[j], CEover4*(1.0 - dfvl*workspace->dDelta_lp[j])* (bo_ij->BO_pi + bo_ij->BO_pi2)); // OvCoor - 3a
+ MYATOMICADD(&workspace->CdDelta[j], CEover4*(1.0 - dfvl*workspace->dDelta_lp[j])* (bo_ij->BO_pi + bo_ij->BO_pi2)); // OvCoor - 3a
bo_ij->Cdbopi += CEover4 *
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);//OvCoor-3b
@@ -568,7 +568,7 @@ GLOBAL void Cuda_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
//PERFORMANCE IMPACT
- atomicAdd (&workspace->CdDelta[j], CEunder4*(1.0-dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2) ); // UnCoor - 2a
+ MYATOMICADD(&workspace->CdDelta[j], CEunder4*(1.0-dfvl*workspace->dDelta_lp[j]) * (bo_ij->BO_pi + bo_ij->BO_pi2) ); // UnCoor - 2a
bo_ij->Cdbopi += CEunder4 *
(workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);//UnCoor-2b
@@ -705,7 +705,7 @@ GLOBAL void test_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
// calculate the energy
e_lp = p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
- //atomicAdd (&data->E_Lp, e_lp );
+ //MYATOMICADD(&data->E_Lp, e_lp );
E_Lp [ i ] = e_lp;
dElp = p_lp2 * inv_expvd2 +
@@ -732,7 +732,7 @@ GLOBAL void test_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
e_lph = p_lp3 * SQR(vov3-3.0);
E_Lp [i] += e_lph;
- //atomicAdd (&data->E_Lp, e_lph );
+ //MYATOMICADD(&data->E_Lp, e_lph );
//estrain(i) += e_lph;
deahu2dbo = 2.*p_lp3*(vov3 - 3.);
@@ -790,7 +790,7 @@ GLOBAL void test_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
e_ov = sum_ovun1 * CEover1;
E_Ov [ i ] = e_ov;
- //atomicAdd ( &data->E_Ov, e_ov );
+ //MYATOMICADD( &data->E_Ov, e_ov );
CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 *
( 1.0 - Delta_lpcorr*( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 ) );
@@ -813,7 +813,7 @@ GLOBAL void test_LonePair_OverUnder_Coordination_Energy ( reax_atom *atoms, glob
e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
E_Un [i] = e_un;
- //atomicAdd ( &data->E_Un, e_un );
+ //MYATOMICADD( &data->E_Un, e_un );
CEunder1 = inv_exp_ovun2n * ( p_ovun5*p_ovun6*exp_ovun6*inv_exp_ovun8 +
p_ovun2 * e_un * exp_ovun2n);
@@ -903,7 +903,7 @@ GLOBAL void test_LonePair_OverUnder_Coordination_Energy_LP ( reax_atom *atoms, g
// calculate the energy
e_lp = p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
- //atomicAdd (&data->E_Lp, e_lp );
+ //MYATOMICADD(&data->E_Lp, e_lp );
E_Lp [ i ] = e_lp;
dElp = p_lp2 * inv_expvd2 +
@@ -930,7 +930,7 @@ GLOBAL void test_LonePair_OverUnder_Coordination_Energy_LP ( reax_atom *atoms, g
e_lph = p_lp3 * SQR(vov3-3.0);
E_Lp [i] += e_lph;
- //atomicAdd (&data->E_Lp, e_lph );
+ //MYATOMICADD(&data->E_Lp, e_lph );
//estrain(i) += e_lph;
deahu2dbo = 2.*p_lp3*(vov3 - 3.);
diff --git a/PuReMD-GPU/src/system_props.c b/PuReMD-GPU/src/system_props.c
new file mode 100644
index 00000000..491b0d93
--- /dev/null
+++ b/PuReMD-GPU/src/system_props.c
@@ -0,0 +1,348 @@
+/*----------------------------------------------------------------------
+ PuReMD-GPU - Reax Force Field Simulator
+
+ Copyright (2014) Purdue University
+ Sudhir Kylasa, skylasa@purdue.edu
+ Hasan Metin Aktulga, haktulga@cs.purdue.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 "system_props.h"
+
+#include "box.h"
+#include "vector.h"
+
+
+real Get_Time( )
+{
+ struct timeval tim;
+
+ gettimeofday(&tim, NULL );
+ return( tim.tv_sec + (tim.tv_usec / 1000000.0) );
+}
+
+
+real Get_Timing_Info( real t_start )
+{
+ struct timeval tim;
+ real t_end;
+
+ gettimeofday(&tim, NULL );
+ t_end = tim.tv_sec + (tim.tv_usec / 1000000.0);
+ return (t_end - t_start);
+}
+
+
+void Temperature_Control( control_params *control, simulation_data *data,
+ output_controls *out_control )
+{
+ real tmp;
+
+ if( control->T_mode == 1 ) { // step-wise temperature control
+ if( (data->step - data->prev_steps) %
+ ((int)(control->T_freq / control->dt)) == 0 ) {
+ if( fabs( control->T - control->T_final ) >= fabs( control->T_rate ) )
+ control->T += control->T_rate;
+ else control->T = control->T_final;
+ }
+ }
+ else if( control->T_mode == 2 ) { // constant slope control
+ tmp = control->T_rate * control->dt / control->T_freq;
+
+ if( fabs( control->T - control->T_final ) >= fabs( tmp ) )
+ control->T += tmp;
+ }
+}
+
+
+void Compute_Total_Mass( reax_system *system, simulation_data *data )
+{
+ int i;
+ int blocks;
+ int block_size;
+ real *partial_sums = 0;
+
+ data->M = 0;
+
+ for( i = 0; i < system->N; i++ )
+ data->M += system->reaxprm.sbp[ system->atoms[i].type ].mass;
+
+ data->inv_M = 1. / data->M;
+}
+
+
+void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
+ FILE *fout )
+{
+ int i;
+ real m, xx, xy, xz, yy, yz, zz, det;
+ rvec tvec, diff;
+ rtensor mat, inv;
+
+ int blocks;
+ int block_size;
+ rvec *l_xcm, *l_vcm, *l_amcm;
+ real t_start, t_end;
+
+ rvec_MakeZero( data->xcm ); // position of CoM
+ rvec_MakeZero( data->vcm ); // velocity of CoM
+ rvec_MakeZero( data->amcm ); // angular momentum of CoM
+ rvec_MakeZero( data->avcm ); // angular velocity of CoM
+
+ /* Compute the position, velocity and angular momentum about the CoM */
+ for( i = 0; i < system->N; ++i ) {
+ m = system->reaxprm.sbp[ system->atoms[i].type ].mass;
+
+ rvec_ScaledAdd( data->xcm, m, system->atoms[i].x );
+ rvec_ScaledAdd( data->vcm, m, system->atoms[i].v );
+
+ rvec_Cross( tvec, system->atoms[i].x, system->atoms[i].v );
+ rvec_ScaledAdd( data->amcm, m, tvec );
+
+ /*fprintf( fout,"%3d %g %g %g\n",
+ i+1,
+ system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2] );
+ fprintf( fout, "vcm: %g %g %g\n",
+ data->vcm[0], data->vcm[1], data->vcm[2] );
+ */
+ }
+
+ rvec_Scale( data->xcm, data->inv_M, data->xcm );
+ rvec_Scale( data->vcm, data->inv_M, data->vcm );
+
+ rvec_Cross( tvec, data->xcm, data->vcm );
+ rvec_ScaledAdd( data->amcm, -data->M, tvec );
+
+ data->etran_cm = 0.5 * data->M * rvec_Norm_Sqr( data->vcm );
+
+ /* Calculate and then invert the inertial tensor */
+ xx = xy = xz = yy = yz = zz = 0;
+
+ for( i = 0; i < system->N; ++i ) {
+ m = system->reaxprm.sbp[ system->atoms[i].type ].mass;
+
+ rvec_ScaledSum( diff, 1., system->atoms[i].x, -1., data->xcm );
+ xx += diff[0] * diff[0] * m;
+ xy += diff[0] * diff[1] * m;
+ xz += diff[0] * diff[2] * m;
+ yy += diff[1] * diff[1] * m;
+ yz += diff[1] * diff[2] * m;
+ zz += diff[2] * diff[2] * m;
+ }
+
+#ifdef __DEBUG_CUDA__
+ fprintf (stderr, " xx: %f \n", xx);
+ fprintf (stderr, " xy: %f \n", xy);
+ fprintf (stderr, " xz: %f \n", xz);
+ fprintf (stderr, " yy: %f \n", yy);
+ fprintf (stderr, " yz: %f \n", yz);
+ fprintf (stderr, " zz: %f \n", zz);
+#endif
+
+ mat[0][0] = yy + zz;
+ mat[0][1] = mat[1][0] = -xy;
+ mat[0][2] = mat[2][0] = -xz;
+ mat[1][1] = xx + zz;
+ mat[2][1] = mat[1][2] = -yz;
+ mat[2][2] = xx + yy;
+
+ /* invert the inertial tensor */
+ det = ( mat[0][0] * mat[1][1] * mat[2][2] +
+ mat[0][1] * mat[1][2] * mat[2][0] +
+ mat[0][2] * mat[1][0] * mat[2][1] ) -
+ ( mat[0][0] * mat[1][2] * mat[2][1] +
+ mat[0][1] * mat[1][0] * mat[2][2] +
+ mat[0][2] * mat[1][1] * mat[2][0] );
+
+ inv[0][0] = mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1];
+ inv[0][1] = mat[0][2] * mat[2][1] - mat[0][1] * mat[2][2];
+ inv[0][2] = mat[0][1] * mat[1][2] - mat[0][2] * mat[1][1];
+ inv[1][0] = mat[1][2] * mat[2][0] - mat[1][0] * mat[2][2];
+ inv[1][1] = mat[0][0] * mat[2][2] - mat[0][2] * mat[2][0];
+ inv[1][2] = mat[0][2] * mat[1][0] - mat[0][0] * mat[1][2];
+ inv[2][0] = mat[1][0] * mat[2][1] - mat[2][0] * mat[1][1];
+ inv[2][1] = mat[2][0] * mat[0][1] - mat[0][0] * mat[2][1];
+ inv[2][2] = mat[0][0] * mat[1][1] - mat[1][0] * mat[0][1];
+
+ if( fabs(det) > ALMOST_ZERO )
+ rtensor_Scale( inv, 1./det, inv );
+ else
+ rtensor_MakeZero( inv );
+
+ /* Compute the angular velocity about the centre of mass */
+ rtensor_MatVec( data->avcm, inv, data->amcm );
+ data->erot_cm = 0.5 * E_CONV * rvec_Dot( data->avcm, data->amcm );
+
+#if defined(DEBUG)
+ fprintf( stderr, "xcm: %24.15e %24.15e %24.15e\n",
+ data->xcm[0], data->xcm[1], data->xcm[2] );
+ fprintf( stderr, "vcm: %24.15e %24.15e %24.15e\n",
+ data->vcm[0], data->vcm[1], data->vcm[2] );
+ fprintf( stderr, "amcm: %24.15e %24.15e %24.15e\n",
+ data->amcm[0], data->amcm[1], data->amcm[2] );
+ /* fprintf( fout, "mat: %f %f %f\n %f %f %f\n %f %f %f\n",
+ mat[0][0], mat[0][1], mat[0][2],
+ mat[1][0], mat[1][1], mat[1][2],
+ mat[2][0], mat[2][1], mat[2][2] );
+ fprintf( fout, "inv: %g %g %g\n %g %g %g\n %g %g %g\n",
+ inv[0][0], inv[0][1], inv[0][2],
+ inv[1][0], inv[1][1], inv[1][2],
+ inv[2][0], inv[2][1], inv[2][2] );
+ fflush( fout ); */
+ fprintf( stderr, "avcm: %24.15e %24.15e %24.15e\n",
+ data->avcm[0], data->avcm[1], data->avcm[2] );
+#endif
+}
+
+
+void Compute_Kinetic_Energy( reax_system* system, simulation_data* data )
+{
+ int i;
+ rvec p;
+ real m;
+
+ data->E_Kin = 0.0;
+
+ for (i=0; i < system->N; i++) {
+ m = system->reaxprm.sbp[system->atoms[i].type].mass;
+
+ rvec_Scale( p, m, system->atoms[i].v );
+ data->E_Kin += 0.5 * rvec_Dot( p, system->atoms[i].v );
+
+ /* fprintf(stderr,"%d, %lf, %lf, %lf %lf\n",
+ i,system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2],
+ system->reaxprm.sbp[system->atoms[i].type].mass); */
+ }
+
+ data->therm.T = (2. * data->E_Kin) / (data->N_f * K_B);
+
+ if ( fabs(data->therm.T) < ALMOST_ZERO ) /* avoid T being an absolute zero! */
+ data->therm.T = ALMOST_ZERO;
+}
+
+
+/* IMPORTANT: This function assumes that current kinetic energy and
+ * the center of mass of the system is already computed before.
+ *
+ * IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
+ * to be added when there are long-range interactions or long-range
+ * corrections to short-range interactions present.
+ * We may want to add that for more accuracy.
+ */
+void Compute_Pressure_Isotropic( reax_system* system, control_params *control,
+ simulation_data* data,
+ output_controls *out_control )
+{
+ int i;
+ reax_atom *p_atom;
+ rvec tx;
+ rvec tmp;
+ simulation_box *box = &(system->box);
+
+ /* Calculate internal pressure */
+ rvec_MakeZero( data->int_press );
+
+ // 0: both int and ext, 1: ext only, 2: int only
+ if( control->press_mode == 0 || control->press_mode == 2 ) {
+ for( i = 0; i < system->N; ++i ) {
+ p_atom = &( system->atoms[i] );
+
+ /* transform x into unitbox coordinates */
+ Transform_to_UnitBox( p_atom->x, box, 1, tx );
+
+ /* this atom's contribution to internal pressure */
+ rvec_Multiply( tmp, p_atom->f, tx );
+ rvec_Add( data->int_press, tmp );
+
+ if( out_control->debug_level > 0 ) {
+ fprintf( out_control->prs, "%-8d%8.2f%8.2f%8.2f",
+ i+1, p_atom->x[0], p_atom->x[1], p_atom->x[2] );
+ fprintf( out_control->prs, "%8.2f%8.2f%8.2f",
+ p_atom->f[0], p_atom->f[1], p_atom->f[2] );
+ fprintf( out_control->prs, "%8.2f%8.2f%8.2f\n",
+ data->int_press[0],data->int_press[1],data->int_press[2]);
+ }
+ }
+ }
+
+ /* kinetic contribution */
+ data->kin_press = 2. * (E_CONV * data->E_Kin) / ( 3. * box->volume * P_CONV );
+
+ /* Calculate total pressure in each direction */
+ data->tot_press[0] = data->kin_press -
+ ((data->int_press[0] + data->ext_press[0]) /
+ (box->box_norms[1] * box->box_norms[2] * P_CONV));
+
+ data->tot_press[1] = data->kin_press -
+ ((data->int_press[1] + data->ext_press[1])/
+ (box->box_norms[0] * box->box_norms[2] * P_CONV));
+
+ data->tot_press[2] = data->kin_press -
+ ((data->int_press[2] + data->ext_press[2])/
+ (box->box_norms[0] * box->box_norms[1] * P_CONV));
+
+ /* Average pressure for the whole box */
+ data->iso_bar.P=(data->tot_press[0]+data->tot_press[1]+data->tot_press[2])/3;
+}
+
+
+void Compute_Pressure_Isotropic_Klein( reax_system* system,
+ simulation_data* data )
+{
+ int i;
+ reax_atom *p_atom;
+ rvec dx;
+
+ // IMPORTANT: This function assumes that current kinetic energy and
+ // the center of mass of the system is already computed before.
+ data->iso_bar.P = 2.0 * data->E_Kin;
+
+ for( i = 0; i < system->N; ++i )
+ {
+ p_atom = &( system->atoms[i] );
+ rvec_ScaledSum(dx,1.0,p_atom->x,-1.0,data->xcm);
+ data->iso_bar.P += ( -F_CONV * rvec_Dot(p_atom->f, dx) );
+ }
+
+ data->iso_bar.P /= (3.0 * system->box.volume);
+
+ // IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
+ // to be added when there are long-range interactions or long-range
+ // corrections to short-range interactions present.
+ // We may want to add that for more accuracy.
+}
+
+
+void Compute_Pressure( reax_system* system, simulation_data* data,
+ static_storage *workspace )
+{
+ int i;
+ reax_atom *p_atom;
+ rtensor temp;
+
+ rtensor_MakeZero( data->flex_bar.P );
+
+ for( i = 0; i < system->N; ++i ) {
+ p_atom = &( system->atoms[i] );
+ // Distance_on_T3_Gen( data->rcm, p_atom->x, &(system->box), &dx );
+ rvec_OuterProduct( temp, p_atom->v, p_atom->v );
+ rtensor_ScaledAdd( data->flex_bar.P,
+ system->reaxprm.sbp[ p_atom->type ].mass, temp );
+ // rvec_OuterProduct(temp, workspace->virial_forces[i], p_atom->x );
+ rtensor_ScaledAdd( data->flex_bar.P, -F_CONV, temp );
+ }
+
+ rtensor_Scale( data->flex_bar.P, 1.0 / system->box.volume, data->flex_bar.P );
+ data->iso_bar.P = rtensor_Trace( data->flex_bar.P ) / 3.0;
+}
diff --git a/PuReMD-GPU/src/system_props.h b/PuReMD-GPU/src/system_props.h
index d152c254..90f43d76 100644
--- a/PuReMD-GPU/src/system_props.h
+++ b/PuReMD-GPU/src/system_props.h
@@ -30,21 +30,14 @@ real Get_Timing_Info( real );
void Temperature_Control( control_params*, simulation_data*, output_controls* );
void Compute_Total_Mass( reax_system*, simulation_data* );
-void Cuda_Compute_Total_Mass( reax_system*, simulation_data* );
void Compute_Center_of_Mass( reax_system*, simulation_data*, FILE* );
-void Cuda_Compute_Center_of_Mass( reax_system*, simulation_data*, FILE* );
void Compute_Kinetic_Energy( reax_system*, simulation_data* );
-void Cuda_Compute_Kinetic_Energy( reax_system*, simulation_data* );
void Compute_Pressure( reax_system*, simulation_data*, static_storage* );
void Compute_Pressure_Isotropic( reax_system*, control_params*, simulation_data*, output_controls* );
-void prep_dev_system (reax_system *system);
-GLOBAL void k_Compute_Total_Mass (single_body_parameters *, reax_atom *, real *, size_t );
-//GLOBAL void Compute_Kinetic_Energy (single_body_parameters *, reax_atom *, unsigned int , simulation_data *, real *);
-
#endif
diff --git a/PuReMD-GPU/src/testmd.cu b/PuReMD-GPU/src/testmd.c
similarity index 99%
rename from PuReMD-GPU/src/testmd.cu
rename to PuReMD-GPU/src/testmd.c
index 93f286cc..f2f27d19 100644
--- a/PuReMD-GPU/src/testmd.cu
+++ b/PuReMD-GPU/src/testmd.c
@@ -39,6 +39,7 @@
#include "cuda_copy.h"
#include "validation.h"
+#include "cuda_system_props.h"
interaction_function Interaction_Functions[NO_OF_INTERACTIONS];
diff --git a/PuReMD-GPU/src/three_body_interactions.cu b/PuReMD-GPU/src/three_body_interactions.cu
index c2eed63b..1edd41ae 100644
--- a/PuReMD-GPU/src/three_body_interactions.cu
+++ b/PuReMD-GPU/src/three_body_interactions.cu
@@ -871,7 +871,7 @@ where i < k */
e_ang = f7_ij * f7_jk * f8_Dj * expval12theta;
//PERFORMANCE IMPACT
- //atomicAdd (&data->E_Ang, e_ang);
+ //MYATOMICADD(&data->E_Ang, e_ang);
E_Ang [j] += e_ang;
/* END ANGLE ENERGY*/
@@ -895,7 +895,7 @@ where i < k */
e_pen = p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
//PERFORMANCE IMPACT
- //atomicAdd (&data->E_Pen, e_pen);
+ //MYATOMICADD(&data->E_Pen, e_pen);
E_Pen [j] += e_pen;
@@ -921,7 +921,7 @@ where i < k */
EXP( -p_coa4 * SQR(BOA_jk - 1.5) );
//PERFORMANCE IMPACT
- //atomicAdd (&data->E_Coa, e_coa);
+ //MYATOMICADD(&data->E_Coa, e_coa);
E_Coa [j] += e_coa;
CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa;
@@ -933,19 +933,19 @@ where i < k */
/* FORCES */
/*
- atomicAdd (&bo_ij->Cdbo, (CEval1 + CEpen2 + (CEcoa1-CEcoa4)) );
- atomicAdd (&bo_jk->Cdbo, (CEval2 + CEpen3 + (CEcoa2-CEcoa5)) );
- atomicAdd (&workspace->CdDelta[j], ((CEval3 + CEval7) + CEpen1 + CEcoa3) );
- atomicAdd (&workspace->CdDelta[i], CEcoa4 );
- atomicAdd (&workspace->CdDelta[k], CEcoa5 );
+ MYATOMICADD(&bo_ij->Cdbo, (CEval1 + CEpen2 + (CEcoa1-CEcoa4)) );
+ MYATOMICADD(&bo_jk->Cdbo, (CEval2 + CEpen3 + (CEcoa2-CEcoa5)) );
+ MYATOMICADD(&workspace->CdDelta[j], ((CEval3 + CEval7) + CEpen1 + CEcoa3) );
+ MYATOMICADD(&workspace->CdDelta[i], CEcoa4 );
+ MYATOMICADD(&workspace->CdDelta[k], CEcoa5 );
*/
bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1-CEcoa4)) ;
bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2-CEcoa5)) ;
workspace->CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3) ;
- //atomicAdd (&workspace->CdDelta[i], CEcoa4 );
+ //MYATOMICADD(&workspace->CdDelta[i], CEcoa4 );
pbond_ij->CdDelta_ij += CEcoa4 ;
- //atomicAdd (&workspace->CdDelta[k], CEcoa5 );
+ //MYATOMICADD(&workspace->CdDelta[k], CEcoa5 );
pbond_jk->CdDelta_ij += CEcoa5;
for( t = start_j; t < end_j; ++t ) {
@@ -960,9 +960,9 @@ where i < k */
// (CEval6 * pBOjt7) );
/*
- atomicAdd (&bo_jt->Cdbo, (CEval6 * pBOjt7) );
- atomicAdd (&bo_jt->Cdbopi, CEval5 );
- atomicAdd (&bo_jt->Cdbopi2, CEval5 );
+ MYATOMICADD(&bo_jt->Cdbo, (CEval6 * pBOjt7) );
+ MYATOMICADD(&bo_jt->Cdbopi, CEval5 );
+ MYATOMICADD(&bo_jt->Cdbopi2, CEval5 );
*/
bo_jt->Cdbo += (CEval6 * pBOjt7) ;
bo_jt->Cdbopi += CEval5 ;
@@ -1670,7 +1670,7 @@ GLOBAL void Hydrogen_Bonds ( reax_atom *atoms,
//PERFORMANCE IMPACT
e_hb = hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
- //atomicAdd ( &data->E_HB, e_hb );
+ //MYATOMICADD( &data->E_HB, e_hb );
//E_HB [j] += e_hb;
sh_hb [threadIdx.x] += e_hb;
@@ -2050,7 +2050,7 @@ GLOBAL void Hydrogen_Bonds ( reax_atom *atoms,
//PERFORMANCE IMPACT
e_hb = hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
- //atomicAdd ( &data->E_HB, e_hb );
+ //MYATOMICADD( &data->E_HB, e_hb );
//E_HB [j] += e_hb;
sh_hb [threadIdx.x] += e_hb;
diff --git a/PuReMD-GPU/src/traj.cu b/PuReMD-GPU/src/traj.c
similarity index 99%
rename from PuReMD-GPU/src/traj.cu
rename to PuReMD-GPU/src/traj.c
index 97496e7f..afe3b1d2 100644
--- a/PuReMD-GPU/src/traj.cu
+++ b/PuReMD-GPU/src/traj.c
@@ -20,7 +20,10 @@
#include "traj.h"
#include "list.h"
-#include "cuda_copy.h"
+
+#ifdef __PRINT_CPU_RESULTS__
+ #include "cuda_copy.h"
+#endif
/************************************************/
/* CUSTOM FORMAT ROUTINES */
@@ -207,7 +210,7 @@ int Append_Custom_Frame( reax_system *system, control_params *control,
if( write_bonds )
{
-#ifndef __PRINT_CPU_RESULTS__
+#ifdef __PRINT_CPU_RESULTS__
//fprintf (stderr, "Synching bonds from device for printing ....\n");
Sync_Host_Device (bonds, (dev_lists + BONDS), TYP_BOND );
#endif
@@ -239,7 +242,7 @@ int Append_Custom_Frame( reax_system *system, control_params *control,
num_thb_intrs = 0;
if( write_angles ) {
-#ifndef __PRINT_CPU_RESULTS__
+#ifdef __PRINT_CPU_RESULTS__
//fprintf (stderr, "Synching three bodies from deivce for printing ... \n");
Sync_Host_Device (thb_intrs, dev_lists + THREE_BODIES, TYP_THREE_BODY );
if ( !write_bonds) {
diff --git a/PuReMD-GPU/src/traj.h b/PuReMD-GPU/src/traj.h
index d8c1792d..35d92602 100644
--- a/PuReMD-GPU/src/traj.h
+++ b/PuReMD-GPU/src/traj.h
@@ -22,8 +22,8 @@
#define __TRAJ_H__
#include "mytypes.h"
-#include "zlib.h"
+#include <zlib.h>
#define BLOCK_MARK "REAX_BLOCK_MARK "
#define BLOCK_MARK_LEN 16
@@ -73,12 +73,14 @@
#define SIZE_INFO_LINE3 "%-10d %-10d %-10d\n"
#define SIZE_INFO_LEN3 33
+
enum ATOM_LINE_OPTS {OPT_NOATOM = 0, OPT_ATOM_BASIC = 4, OPT_ATOM_wF = 5,
OPT_ATOM_wV = 6, OPT_ATOM_FULL = 7
};
enum BOND_LINE_OPTS {OPT_NOBOND, OPT_BOND_BASIC, OPT_BOND_FULL};
enum ANGLE_LINE_OPTS {OPT_NOANGLE, OPT_ANGLE_BASIC};
+
struct
{
int no_of_sub_blocks;
@@ -89,11 +91,11 @@ struct
typedef struct __block block;
+
int Write_Block( gzFile, block* );
int Read_Next_Block( gzFile, block*, int* );
int Skip_Next_Block( gzFile, int*);
-
/*
Format for trajectory file
@@ -141,8 +143,6 @@ int Skip_Next_Block( gzFile, int*);
No. of torsion entries (int)
Torsion info lines as per torsion format.
*/
-
-
int Write_Custom_Header( reax_system*, control_params*,
static_storage*, output_controls* );
int Write_xyz_Header ( reax_system*, control_params*,
diff --git a/PuReMD-GPU/src/two_body_interactions.cu b/PuReMD-GPU/src/two_body_interactions.cu
index f53b0cfb..60cfbd0b 100644
--- a/PuReMD-GPU/src/two_body_interactions.cu
+++ b/PuReMD-GPU/src/two_body_interactions.cu
@@ -221,7 +221,7 @@ GLOBAL void Cuda_Bond_Energy ( reax_atom *atoms, global_parameters g_params,
-twbp->De_pp * bo_ij->BO_pi2;
//PERFORMANCE IMAPCT
- //atomicAdd (&data->E_BE, ebond);
+ //MYATOMICADD(&data->E_BE, ebond);
//TODO
//E_BE [ i ] += ebond/2.0;
E_BE [ i ] += ebond;
@@ -274,7 +274,7 @@ GLOBAL void Cuda_Bond_Energy ( reax_atom *atoms, global_parameters g_params,
//estrain(j2) = estrain(j2) + 0.50*estriph;
//PERFORMANCE IMPACT
- //atomicAdd (&data->E_BE, estriph);
+ //MYATOMICADD(&data->E_BE, estriph);
E_BE [ i] += estriph;
//data->E_BE += estriph;
@@ -289,7 +289,7 @@ GLOBAL void Cuda_Bond_Energy ( reax_atom *atoms, global_parameters g_params,
//PERFORMANCE IMAPCT
workspace->CdDelta[i] += decobdboua;
- //atomicAdd (&workspace->CdDelta[j], decobdboub);
+ //MYATOMICADD(&workspace->CdDelta[j], decobdboub);
//CdDelta [ i * N + i ] += decobdboua;
//CdDelta [ i * N + j ] += decobdboua;
//workspace->CdDelta [i] += decobdboua;
diff --git a/PuReMD-GPU/src/vector.cu b/PuReMD-GPU/src/vector.c
similarity index 100%
rename from PuReMD-GPU/src/vector.cu
rename to PuReMD-GPU/src/vector.c
diff --git a/PuReMD-GPU/src/vector.h b/PuReMD-GPU/src/vector.h
index 33653478..ee1375ee 100644
--- a/PuReMD-GPU/src/vector.h
+++ b/PuReMD-GPU/src/vector.h
@@ -22,8 +22,10 @@
#define __VECTOR_H_
#include "mytypes.h"
+
#include "random.h"
+
int Vector_isZero( real*, int );
void Vector_MakeZero( real*, int );
void Vector_Copy( real*, real*, int );
@@ -33,8 +35,6 @@ void Vector_Copy( real*, real*, int );
void Vector_Print( FILE*, char*, real*, int );
real Norm( real*, int );
-HOST_DEVICE inline real Dot( real*, real*, int );
-
void rvec_Sum( rvec, rvec, rvec );
real rvec_ScaledDot( real, rvec, real, rvec );
void rvec_Multiply( rvec, rvec, rvec );
@@ -44,19 +44,6 @@ void rvec_Invert( rvec, rvec );
void rvec_OuterProduct( rtensor, rvec, rvec );
int rvec_isZero( rvec );
-HOST_DEVICE inline real rvec_Dot( rvec, rvec );
-HOST_DEVICE inline void rvec_Scale( rvec, real, rvec );
-HOST_DEVICE inline real rvec_Norm_Sqr( rvec );
-HOST_DEVICE inline void rvec_Random( rvec );
-HOST_DEVICE inline void rvec_MakeZero( rvec );
-HOST_DEVICE inline void rvec_Add( rvec, rvec );
-HOST_DEVICE inline void rvec_Copy( rvec, rvec );
-HOST_DEVICE inline void rvec_Cross( rvec, rvec, rvec );
-HOST_DEVICE inline void rvec_ScaledAdd( rvec, real, rvec );
-HOST_DEVICE inline void rvec_ScaledSum( rvec, real, rvec, real, rvec );
-HOST_DEVICE inline void rvec_iMultiply( rvec, ivec, rvec );
-HOST_DEVICE inline real rvec_Norm( rvec );
-
void rtensor_MakeZero( rtensor );
void rtensor_Multiply( rtensor, rtensor, rtensor );
void rtensor_MatVec( rvec, rtensor, rvec );
@@ -80,15 +67,6 @@ void ivec_MakeZero( ivec );
void ivec_rScale( ivec, real, rvec );
-HOST_DEVICE inline void ivec_Copy( ivec, ivec );
-HOST_DEVICE inline void ivec_Scale( ivec, real, ivec );
-HOST_DEVICE inline void ivec_Sum( ivec, ivec, ivec );
-
-/*
- * Code which is common to multiple HOST and DEVICE
- *
- */
-
HOST_DEVICE inline real Dot( real* v1, real* v2, int k )
{
real ret = 0;
@@ -100,17 +78,15 @@ HOST_DEVICE inline real Dot( real* v1, real* v2, int k )
}
-
-
/////////////////////////////
//rvec functions
/////////////////////////////
-
HOST_DEVICE inline void rvec_MakeZero( rvec v )
{
v[0] = v[1] = v[2] = ZERO;
}
+
HOST_DEVICE inline void rvec_Add( rvec ret, rvec v )
{
ret[0] += v[0];
@@ -118,11 +94,13 @@ HOST_DEVICE inline void rvec_Add( rvec ret, rvec v )
ret[2] += v[2];
}
+
HOST_DEVICE inline void rvec_Copy( rvec dest, rvec src )
{
dest[0] = src[0], dest[1] = src[1], dest[2] = src[2];
}
+
HOST_DEVICE inline void rvec_Cross( rvec ret, rvec v1, rvec v2 )
{
ret[0] = v1[1] * v2[2] - v1[2] * v2[1];
@@ -130,11 +108,13 @@ HOST_DEVICE inline void rvec_Cross( rvec ret, rvec v1, rvec v2 )
ret[2] = v1[0] * v2[1] - v1[1] * v2[0];
}
+
HOST_DEVICE inline void rvec_ScaledAdd( rvec ret, real c, rvec v )
{
ret[0] += c * v[0], ret[1] += c * v[1], ret[2] += c * v[2];
}
+
HOST_DEVICE inline void rvec_ScaledSum( rvec ret, real c1, rvec v1 , real c2, rvec v2 )
{
ret[0] = c1 * v1[0] + c2 * v2[0];
@@ -142,6 +122,7 @@ HOST_DEVICE inline void rvec_ScaledSum( rvec ret, real c1, rvec v1 , real c2, rv
ret[2] = c1 * v1[2] + c2 * v2[2];
}
+
HOST_DEVICE inline void rvec_Random( rvec v )
{
v[0] = Random(2.0) - 1.0;
@@ -149,21 +130,25 @@ HOST_DEVICE inline void rvec_Random( rvec v )
v[2] = Random(2.0) - 1.0;
}
+
HOST_DEVICE inline real rvec_Norm_Sqr( rvec v )
{
return SQR(v[0]) + SQR(v[1]) + SQR(v[2]);
}
+
HOST_DEVICE inline void rvec_Scale( rvec ret, real c, rvec v )
{
ret[0] = c * v[0], ret[1] = c * v[1], ret[2] = c * v[2];
}
+
HOST_DEVICE inline real rvec_Dot( rvec v1, rvec v2 )
{
return v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2];
}
+
HOST_DEVICE inline void rvec_iMultiply( rvec r, ivec v1, rvec v2 )
{
r[0] = v1[0] * v2[0];
@@ -171,23 +156,22 @@ HOST_DEVICE inline void rvec_iMultiply( rvec r, ivec v1, rvec v2 )
r[2] = v1[2] * v2[2];
}
+
HOST_DEVICE inline real rvec_Norm( rvec v )
{
return SQRT( SQR(v[0]) + SQR(v[1]) + SQR(v[2]) );
}
-
/////////////////
//ivec functions
/////////////////
-
-
HOST_DEVICE inline void ivec_Copy( ivec dest , ivec src )
{
dest[0] = src[0], dest[1] = src[1], dest[2] = src[2];
}
+
HOST_DEVICE inline void ivec_Scale( ivec dest, real C, ivec src )
{
dest[0] = C * src[0];
@@ -195,6 +179,7 @@ HOST_DEVICE inline void ivec_Scale( ivec dest, real C, ivec src )
dest[2] = C * src[2];
}
+
HOST_DEVICE inline void ivec_Sum( ivec dest, ivec v1, ivec v2 )
{
dest[0] = v1[0] + v2[0];
@@ -203,7 +188,6 @@ HOST_DEVICE inline void ivec_Sum( ivec dest, ivec v1, ivec v2 )
}
-
/////////////////
//vector functions
/////////////////
@@ -213,12 +197,14 @@ HOST_DEVICE inline void Vector_Sum( real* dest, real c, real* v, real d, real* y
dest[k] = c * v[k] + d * y[k];
}
+
HOST_DEVICE inline void Vector_Scale( real* dest, real c, real* v, int k )
{
for (k--; k >= 0; k--)
dest[k] = c * v[k];
}
+
HOST_DEVICE inline void Vector_Add( real* dest, real c, real* v, int k )
{
for (k--; k >= 0; k--)
--
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