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lammps/src/USER-REAXC/reaxc_tool_box.cpp
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reaxc_tool_box.cpp
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/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "reaxc_types.h"
#if defined(PURE_REAX)
#include "tool_box.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_tool_box.h"
#endif
#if defined(PURE_REAX)
/************** taken from comm_tools.c **************/
int SumScan( int n, int me, int root, MPI_Comm comm )
{
int i, my_order, wsize;;
int *nbuf = NULL;
if( me == root ) {
MPI_Comm_size( comm, &wsize );
nbuf = (int *) calloc( wsize, sizeof(int) );
MPI_Gather( &n, 1, MPI_INT, nbuf, 1, MPI_INT, root, comm );
for( i = 0; i < wsize-1; ++i ) {
nbuf[i+1] += nbuf[i];
}
MPI_Scatter( nbuf, 1, MPI_INT, &my_order, 1, MPI_INT, root, comm );
free( nbuf );
}
else {
MPI_Gather( &n, 1, MPI_INT, nbuf, 1, MPI_INT, root, comm );
MPI_Scatter( nbuf, 1, MPI_INT, &my_order, 1, MPI_INT, root, comm );
}
return my_order;
}
void SumScanB( int n, int me, int wsize, int root, MPI_Comm comm, int *nbuf )
{
int i;
MPI_Gather( &n, 1, MPI_INT, nbuf, 1, MPI_INT, root, comm );
if( me == root ) {
for( i = 0; i < wsize-1; ++i )
nbuf[i+1] += nbuf[i];
}
MPI_Bcast( nbuf, wsize, MPI_INT, root, comm );
}
#endif
/************** taken from box.c **************/
void Transform( rvec x1, simulation_box *box, char flag, rvec x2 )
{
int i, j;
real tmp;
// printf(">x1: (%lf, %lf, %lf)\n",x1[0],x1[1],x1[2]);
if (flag > 0) {
for (i=0; i < 3; i++) {
tmp = 0.0;
for (j=0; j < 3; j++)
tmp += box->trans[i][j]*x1[j];
x2[i] = tmp;
}
}
else {
for (i=0; i < 3; i++) {
tmp = 0.0;
for (j=0; j < 3; j++)
tmp += box->trans_inv[i][j]*x1[j];
x2[i] = tmp;
}
}
// printf(">x2: (%lf, %lf, %lf)\n", x2[0], x2[1], x2[2]);
}
void Transform_to_UnitBox( rvec x1, simulation_box *box, char flag, rvec x2 )
{
Transform( x1, box, flag, x2 );
x2[0] /= box->box_norms[0];
x2[1] /= box->box_norms[1];
x2[2] /= box->box_norms[2];
}
/* determine whether point p is inside the box */
void Fit_to_Periodic_Box( simulation_box *box, rvec *p )
{
int i;
for( i = 0; i < 3; ++i ) {
if( (*p)[i] < box->min[i] ) {
/* handle lower coords */
while( (*p)[i] < box->min[i] )
(*p)[i] += box->box_norms[i];
}
else if( (*p)[i] >= box->max[i] ) {
/* handle higher coords */
while( (*p)[i] >= box->max[i] )
(*p)[i] -= box->box_norms[i];
}
}
}
#if defined(PURE_REAX)
/* determine the touch point, tp, of a box to
its neighbor denoted by the relative coordinate rl */
inline void Box_Touch_Point( simulation_box *box, ivec rl, rvec tp )
{
int d;
for( d = 0; d < 3; ++d )
if( rl[d] == -1 )
tp[d] = box->min[d];
else if( rl[d] == 0 )
tp[d] = NEG_INF - 1.;
else
tp[d] = box->max[d];
}
/* determine whether point p is inside the box */
/* assumes orthogonal box */
inline int is_Inside_Box( simulation_box *box, rvec p )
{
if( p[0] < box->min[0] || p[0] >= box->max[0] ||
p[1] < box->min[1] || p[1] >= box->max[1] ||
p[2] < box->min[2] || p[2] >= box->max[2] )
return 0;
return 1;
}
inline int iown_midpoint( simulation_box *box, rvec p1, rvec p2 )
{
rvec midp;
midp[0] = (p1[0] + p2[0]) / 2;
midp[1] = (p1[1] + p2[1]) / 2;
midp[2] = (p1[2] + p2[2]) / 2;
if( midp[0] < box->min[0] || midp[0] >= box->max[0] ||
midp[1] < box->min[1] || midp[1] >= box->max[1] ||
midp[2] < box->min[2] || midp[2] >= box->max[2] )
return 0;
return 1;
}
/**************** from grid.c ****************/
/* finds the closest point of grid cell cj to ci.
no need to consider periodic boundary conditions as in the serial case
because the box of a process is not periodic in itself */
inline void GridCell_Closest_Point( grid_cell *gci, grid_cell *gcj,
ivec ci, ivec cj, rvec cp )
{
int d;
for( d = 0; d < 3; d++ )
if( cj[d] > ci[d] )
cp[d] = gcj->min[d];
else if ( cj[d] == ci[d] )
cp[d] = NEG_INF - 1.;
else
cp[d] = gcj->max[d];
}
inline void GridCell_to_Box_Points( grid_cell *gc, ivec rl, rvec cp, rvec fp )
{
int d;
for( d = 0; d < 3; ++d )
if( rl[d] == -1 ) {
cp[d] = gc->min[d];
fp[d] = gc->max[d];
}
else if( rl[d] == 0 ) {
cp[d] = fp[d] = NEG_INF - 1.;
}
else{
cp[d] = gc->max[d];
fp[d] = gc->min[d];
}
}
inline real DistSqr_between_Special_Points( rvec sp1, rvec sp2 )
{
int i;
real d_sqr = 0;
for( i = 0; i < 3; ++i )
if( sp1[i] > NEG_INF && sp2[i] > NEG_INF )
d_sqr += SQR( sp1[i] - sp2[i] );
return d_sqr;
}
inline real DistSqr_to_Special_Point( rvec cp, rvec x )
{
int i;
real d_sqr = 0;
for( i = 0; i < 3; ++i )
if( cp[i] > NEG_INF )
d_sqr += SQR( cp[i] - x[i] );
return d_sqr;
}
inline int Relative_Coord_Encoding( ivec c )
{
return 9 * (c[0] + 1) + 3 * (c[1] + 1) + (c[2] + 1);
}
#endif
/************** from geo_tools.c *****************/
void Make_Point( real x, real y, real z, rvec* p )
{
(*p)[0] = x;
(*p)[1] = y;
(*p)[2] = z;
}
int is_Valid_Serial( storage *workspace, int serial )
{
// if( workspace->map_serials[ serial ] < 0 )
// {
// fprintf( stderr, "CONECT line includes invalid pdb serial number %d.\n",
// serial );
// fprintf( stderr, "Please correct the input file.Terminating...\n" );
// MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
// }
return SUCCESS;
}
int Check_Input_Range( int val, int lo, int hi, char *message, MPI_Comm comm )
{
if( val < lo || val > hi ) {
fprintf( stderr, "%s\nInput %d - Out of range %d-%d. Terminating...\n",
message, val, lo, hi );
MPI_Abort( comm, INVALID_INPUT );
}
return 1;
}
void Trim_Spaces( char *element )
{
int i, j;
for( i = 0; element[i] == ' '; ++i ); // skip initial space chars
for( j = i; j < (int)(strlen(element)) && element[j] != ' '; ++j )
element[j-i] = toupper( element[j] ); // make uppercase, offset to 0
element[j-i] = 0; // finalize the string
}
/************ from system_props.c *************/
struct timeval tim;
real t_end;
real Get_Time( )
{
gettimeofday(&tim, NULL );
return( tim.tv_sec + (tim.tv_usec / 1000000.0) );
}
real Get_Timing_Info( real t_start )
{
gettimeofday(&tim, NULL );
t_end = tim.tv_sec + (tim.tv_usec / 1000000.0);
return (t_end - t_start);
}
void Update_Timing_Info( real *t_start, real *timing )
{
gettimeofday(&tim, NULL );
t_end = tim.tv_sec + (tim.tv_usec / 1000000.0);
*timing += (t_end - *t_start);
*t_start = t_end;
}
/*********** from io_tools.c **************/
int Get_Atom_Type( reax_interaction *reax_param, char *s, MPI_Comm comm )
{
int i;
for( i = 0; i < reax_param->num_atom_types; ++i )
if( !strcmp( reax_param->sbp[i].name, s ) )
return i;
fprintf( stderr, "Unknown atom type %s. Terminating...\n", s );
MPI_Abort( comm, UNKNOWN_ATOM_TYPE );
return -1;
}
char *Get_Element( reax_system *system, int i )
{
return &( system->reax_param.sbp[system->my_atoms[i].type].name[0] );
}
char *Get_Atom_Name( reax_system *system, int i )
{
return &(system->my_atoms[i].name[0]);
}
int Allocate_Tokenizer_Space( char **line, char **backup, char ***tokens )
{
int i;
if( (*line = (char*) malloc( sizeof(char) * MAX_LINE )) == NULL )
return FAILURE;
if( (*backup = (char*) malloc( sizeof(char) * MAX_LINE )) == NULL )
return FAILURE;
if( (*tokens = (char**) malloc( sizeof(char*) * MAX_TOKENS )) == NULL )
return FAILURE;
for( i = 0; i < MAX_TOKENS; i++ )
if( ((*tokens)[i] = (char*) malloc(sizeof(char) * MAX_TOKEN_LEN)) == NULL )
return FAILURE;
return SUCCESS;
}
int Tokenize( char* s, char*** tok )
{
char test[MAX_LINE];
char *sep = "\t \n!=";
char *word;
int count=0;
strncpy( test, s, MAX_LINE );
for( word = strtok(test, sep); word; word = strtok(NULL, sep) ) {
strncpy( (*tok)[count], word, MAX_LINE );
count++;
}
return count;
}
/***************** taken from lammps ************************/
/* safe malloc */
void *smalloc( long n, char *name, MPI_Comm comm )
{
void *ptr;
if( n <= 0 ) {
fprintf( stderr, "WARNING: trying to allocate %ld bytes for array %s. ",
n, name );
fprintf( stderr, "returning NULL.\n" );
return NULL;
}
ptr = malloc( n );
if( ptr == NULL ) {
fprintf( stderr, "ERROR: failed to allocate %ld bytes for array %s",
n, name );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
return ptr;
}
/* safe calloc */
void *scalloc( int n, int size, char *name, MPI_Comm comm )
{
void *ptr;
if( n <= 0 ) {
fprintf( stderr, "WARNING: trying to allocate %d elements for array %s. ",
n, name );
fprintf( stderr, "returning NULL.\n" );
return NULL;
}
if( size <= 0 ) {
fprintf( stderr, "WARNING: elements size for array %s is %d. ",
name, size );
fprintf( stderr, "returning NULL.\n" );
return NULL;
}
ptr = calloc( n, size );
if( ptr == NULL ) {
fprintf( stderr, "ERROR: failed to allocate %d bytes for array %s",
n*size, name );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
return ptr;
}
/* safe free */
void destroy( void *ptr, char *name )
{
if( ptr == NULL ) {
fprintf( stderr, "WARNING: trying to free the already NULL pointer %s!\n",
name );
return;
}
free( ptr );
ptr = NULL;
}
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