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changed printing suspicious distances to status_file not stderr #32

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changed printing suspicious distances to status_file not stderr #32

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23 changes: 12 additions & 11 deletions tightbind/distance_mat.c
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Original file line number Diff line number Diff line change
Expand Up @@ -263,10 +263,6 @@ void build_distance_matrix(cell,details)

num_atoms = cell->num_atoms;

/* space for the list of symbols */
symbols = (char *)calloc(num_atoms*4,sizeof(char));
if(!symbols) fatal("Can't get space for symbols");

/********
get space for the distance matrix
(we only need half of the matrix, since it's symmetrical)
Expand All @@ -290,7 +286,7 @@ void build_distance_matrix(cell,details)

/* check to see if the distance is too short */
if( dist < TOO_SHORT && cell->atoms[i].at_number > 0 && cell->atoms[j].at_number > 0){
fprintf(stderr,"!!! Warning !!! Distance between atoms %d and %d (%f A) \
fprintf(status_file,"!!! Warning !!! Distance between atoms %d and %d (%f A) \
is suspicious.\n",i+1,j+1,dist);
}
if( dist > max_dist ) max_dist = dist;
Expand All @@ -300,16 +296,22 @@ is suspicious.\n",i+1,j+1,dist);
/* put in the diagonal element */
cell->distance_mat[num_so_far++] = 0.0;

/* copy the symbol into the list of symbols */
symbols[i*4] = cell->atoms[i].symb[0];
symbols[i*4+1] = cell->atoms[i].symb[1];
symbols[i*4+2] = 0;
}

if( details->distance_mat_PRT ){
/* space for the list of symbols */
symbols = (char *)calloc(num_atoms*4,sizeof(char));
if(!symbols) fatal("Can't get space for symbols");
for(i=0;i<num_atoms;i++){
/* copy the symbol into the list of symbols */
symbols[i*4] = cell->atoms[i].symb[0];
symbols[i*4+1] = cell->atoms[i].symb[1];
symbols[i*4+2] = 0;
}

print_sym_mat(cell->distance_mat,num_atoms,num_atoms,output_file,
"\n\n;****** DISTANCE MATRIX *********",symbols,details->line_width);

free(symbols);
/* check close contacts to nearest neighbors */
if( cell->dim > 0 ){
fprintf(output_file,"# Inter-Cell distances less than %6.4lf Angstroms:\n",
Expand All @@ -318,7 +320,6 @@ is suspicious.\n",i+1,j+1,dist);

}
}
free(symbols);

if(details->dump_dist_mat) dump_distance_mats(cell,details);

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