reaxc_tool_box.cpp

/*----------------------------------------------------------------------
  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 sfree( 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;
}