Skip to content

changed printing suspicious distances to status_file not stderr #32

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
richardjgowers wants to merge 1 commit into
base: master
Choose a base branch
from
Open

changed printing suspicious distances to status_file not stderr #32

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 12 additions & 11 deletions tightbind/distance_mat.c
View file
Open in desktop
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);

Expand Down