arcanis/moldyn
1
0
Fork 0
mirror of https://github.com/arcan1s/moldyn.git synced 2025-06-28 06:41:42 +00:00
Code Issues Projects Releases Wiki Activity
Files
51d31d0a2f750b6bfa3a061686375a820f654d87
moldyn/statgen/main.c
arcan1s 51d31d0a2f + added CMakeLists.txt 
+ added headers
+ added library 'add_main.c'
+ some optimization
2013-07-22 06:06:01 +04:00

468 lines
15 KiB
C
Raw Blame History

#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "add_main.h"
#include "coords.h"
#include "int2char.h"
#include "messages.h"
#include "stat_print.h"
#include "stat_select.h"
#include "stat_sort.h"
#include "summary_stat.h"
int main (int argc, char *argv[])
{
char filename[256], tmp_str[2048];
int error, i, index, j, k, label[2];
float label_fl;
FILE *f_inp, *f_log;
char input[256], logfile[256], output[256];
float cell[3], *coords, *crit;
int *agl, *connect, from, *label_atom, *label_mol, log, max_depth, num_atoms,
num_mol, *num_mol_agl, num_of_inter, *stat, *stat_all, step, to,
*true_label_mol, *type_agl, *type_atoms, type_inter, quiet;
/* input - mask of input files
* logfile - log file name
* output - output file name
*
* cell - cell dimension
* coords - massive of coordinates
* crit - massive of criteria
*
* agl - massive of aglomerates
* connect - connectivity graph for all molecules
* from - start point
* label_atom - types of atom for interaction
* label_mol - massive of numbers of molecule for atoms
* log - status of log-mode
* max_depth - max depth for check cycles in graph analyze
* num_atoms - number of atoms for writing coordinates
* num_mol - number of molecules for writing coordinates
* num_mol_agl - massive of numbers of molecule in aglomerates
* num_of_inter - number of different interactions
* stat - massive of statistics
* stat_all - massive of summary statistics
* step - $(to - from + 1)
* to - finish point
* true_label_mol - massive of true numbers of molecule for atoms
* type_agl - massive of numbers of aglomerate types
* type_atoms - massive of atom types for atoms
* type_inter - type interaction (number of molecules for interaction)
* quiet - status of quiet-mode
*/
set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to,
&type_inter, &quiet);
// reading number of interactions
for (i=1; i<argc; i++)
if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
num_of_inter++;
if (num_of_inter > 0)
{
crit = (float *) malloc ( 16 * num_of_inter * sizeof (float));
for (i=0; i<16*num_of_inter; i++)
crit[i] = 0.0;
num_of_inter = 0;
}
// reading arguments
for (i=1; i<argc; i++)
{
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
{
sprintf (tmp_str, " statgen\n");
sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.0 License : GPL\n", tmp_str);
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
sprintf (tmp_str, "%sUsage:\n", tmp_str);
sprintf (tmp_str, "%sstatgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ] [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
sprintf (tmp_str, "%s -i - mask of input files\n", tmp_str);
sprintf (tmp_str, "%s -s - trajectory steps (integer)\n", tmp_str);
sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
sprintf (tmp_str, "%s -a - atom types (integer). Format: 'ATOM1' or 'ATOM1,ATOM2' or etc\n", tmp_str);
sprintf (tmp_str, "%s -r - criteria (float), A. Format: '0-0:2.4,0-1:3.0' means 0-0-interaction\n", tmp_str);
sprintf (tmp_str, "%s (<2.4 A) and 0-1 (<3.0) are needed. This flag can be used multiple times\n", tmp_str);
sprintf (tmp_str, "%s -o - output file name\n", tmp_str);
sprintf (tmp_str, "%s -g - check graph isomorphism. DEPTH is max depth for check cycles (>= 3)\n", tmp_str);
sprintf (tmp_str, "%s -l - log enable\n", tmp_str);
sprintf (tmp_str, "%s -q - quiet enable\n", tmp_str);
sprintf (tmp_str, "%s -h - show this help and exit\n", tmp_str);
fputs (tmp_str, stdout);
return 0;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
// mask of input files
{
strcpy (input, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
// steps
{
sscanf (argv[i+1], "%i,%i", &from, &to);
if (from > to)
{
to += from;
from = to - from;
to -= from;
}
step = to - from + 1;
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
// cell size
{
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
// atom types
{
type_inter = 1;
for (j=0; j<strlen(argv[i+1]); j++)
if (argv[i+1][j] == ',')
type_inter++;
label_atom = (int *) malloc (type_inter * sizeof (int));
switch (type_inter)
{
case 1:
sscanf (argv[i+1], "%i", &label_atom[0]);
break;
case 2:
sscanf (argv[i+1], "%i,%i", &label_atom[0], &label_atom[1]);
break;
case 3:
sscanf (argv[i+1], "%i,%i,%i", &label_atom[0], &label_atom[1], &label_atom[2]);
break;
case 4:
sscanf (argv[i+1], "%i,%i,%i,%i", &label_atom[0], &label_atom[1], &label_atom[2], &label_atom[3]);
break;
}
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
// criteria
{
index = 0;
sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
crit[16*num_of_inter+4*label[0]+label[1]] = label_fl;
crit[16*num_of_inter+4*label[1]+label[0]] = label_fl;
for (j=index; j<strlen(argv[i+1]); j++)
if (argv[i+1][j] == ',')
{
index = j+1;
sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
crit[16*num_of_inter+4*label[0]+label[1]] = label_fl;
crit[16*num_of_inter+4*label[1]+label[0]] = label_fl;
}
num_of_inter++;
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
// output file
{
strcpy (output, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'g'))
// graph isomorphism scan
{
sscanf (argv[i+1], "%i", &max_depth);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
// log mode
{
log = 1;
strcpy (logfile, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
// quiet mode
{
quiet = 1;
}
}
if (log == 1)
f_log = fopen (logfile, "w");
if (quiet != 1)
{
message (0, 0, argv[0], stdout);
message (0, 1, argv[0], stdout);
}
if (log == 1)
{
message (1, 0, argv[0], f_log);
message (1, 1, argv[0], f_log);
}
// error checking
error = error_checking (cell, from, input, max_depth, num_of_inter, output, to,
type_inter);
if (error != 0)
{
sprintf (tmp_str, "Something wrong (error code: %i)!\nSee 'statgen -h' for more details\n", error);
fputs (tmp_str, stderr);
if (log == 1)
fputs (tmp_str, f_log);
return 1;
}
if (quiet != 1)
message (0, 2, argv[0], stdout);
if (log == 1)
message (1, 2, argv[0], f_log);
// processing
// initial variables
k = strlen (input);
strcpy (filename, input);
filename[k] = '.';
filename[k+1] = conv (from, 3);
filename[k+2] = conv (from, 2);
filename[k+3] = conv (from, 1);
filename[k+4] = '\0';
if (quiet != 1)
message (0, 3, filename, stdout);
if (log == 1)
message (1, 3, filename, f_log);
f_inp = fopen (filename, "r");
if (f_inp == NULL)
{
sprintf (tmp_str, "\nFile '%s' not found\nError", filename);
fputs (tmp_str, stderr);
if (log == 1)
fputs (tmp_str, f_log);
return 1;
}
fscanf (f_inp, "%i", &num_atoms);
fclose (f_inp);
coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
true_label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
type_agl = (int *) malloc ((max_depth + 2) * sizeof (int));
type_atoms = (int *) malloc (8 * num_atoms * sizeof (int));
// temporary declaration of variables
agl = (int *) malloc (2 * 2 * sizeof (int));
connect = (int *) malloc (2 * 2 * sizeof (int));
num_mol_agl = (int *) malloc (2 * sizeof (int));
stat = (int *) malloc (2 * sizeof (int));
stat_all = (int *) malloc (2 * sizeof (int));
// error checking
if ((coords == NULL) ||
(label_mol == NULL) ||
(true_label_mol == NULL) ||
(type_agl == NULL) ||
(type_atoms == NULL) ||
(agl == NULL) ||
(connect == NULL) ||
(num_mol_agl == NULL) ||
(stat == NULL) ||
(stat_all == NULL))
{
sprintf (tmp_str, "\nMemory error (error code: 17)\n");
fputs (tmp_str, stderr);
if (log == 1)
fputs (tmp_str, f_log);
return 17;
}
// set type_agl to zero
for (i=0; i<max_depth+2; i++)
type_agl[i] = 0;
if (quiet != 1)
{
sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n\
%6cMask: %s;\n%6cFirst step: %i;\n%6cLast step: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n\
%6cSelect atoms: %i", ' ', output, ' ', log, ' ', quiet, ' ', input, ' ', from,
' ' , to, ' ', cell[0], cell[1], cell[2], ' ' , label_atom[0]);
for (i=1; i<type_inter; i++)
sprintf (tmp_str, "%s,%i", tmp_str, label_atom[i]);
sprintf (tmp_str, "%s;\n", tmp_str);
for (i=0; i<num_of_inter; i++)
{
sprintf (tmp_str, "%s%6cInteraction: ", tmp_str, ' ');
for (j=0; j<16; j++)
if ((crit[16*i+j] != 0.0) &&
((j != 4) && (j != 8) && (j != 9) && (j != 12) && (j != 13) && (j != 14)))
sprintf (tmp_str, "%s%i-%i:%4.2f,", tmp_str, j/4, j%4, crit[16*i+j]);
sprintf (tmp_str, "%s;\n", tmp_str);
}
sprintf (tmp_str, "%s%6cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
message (0, 5, tmp_str, stdout);
}
if (log == 1)
{
sprintf (tmp_str, "%34cOutput file: '%s';\n%34cLog: %i;\n%34cQuiet: %i;\n\
%34cMask: %s;\n%34cFirst step: %i;\n%34cLast step: %i;\n%34cCell size: %.4f, %.4f, %.4f;\n\
%34cSelect atoms: %i", ' ', output, ' ', log, ' ', quiet, ' ', input, ' ', from,
' ' , to, ' ', cell[0], cell[1], cell[2], ' ' , label_atom[0]);
for (i=1; i<type_inter; i++)
sprintf (tmp_str, "%s,%i", tmp_str, label_atom[i]);
sprintf (tmp_str, "%s;\n", tmp_str);
for (i=0; i<num_of_inter; i++)
{
sprintf (tmp_str, "%s%34cInteraction: ", tmp_str, ' ');
for (j=0; j<16; j++)
if ((crit[16*i+j] != 0.0) &&
((j != 4) && (j != 8) && (j != 9) && (j != 12) && (j != 13) && (j != 14)))
sprintf (tmp_str, "%s%i-%i:%4.2f,", tmp_str, j/4, j%4, crit[16*i+j]);
sprintf (tmp_str, "%s;\n", tmp_str);
}
sprintf (tmp_str, "%s%34cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
message (1, 5, tmp_str, f_log);
}
// head
printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
num_of_inter, crit, max_depth);
// main cycle
if (quiet != 1)
message (0, 6, argv[0], stdout);
if (log == 1)
message (1, 6, argv[0], f_log);
for (i=from; i<to+1; i++)
{
// reading coordinates
filename[k+1] = conv (i, 3);
filename[k+2] = conv (i, 2);
filename[k+3] = conv (i, 1);
filename[k+4] = '\0';
if (quiet != 1)
message (0, 7, filename, stdout);
if (log == 1)
message (1, 7, filename, f_log);
error = reading_coords (filename, type_inter, label_atom, cell, &num_mol,
&num_atoms, true_label_mol, label_mol, type_atoms, coords);
if (error != 1)
{
if (quiet != 1)
{
sprintf (tmp_str, "%6cNumber of molecules: %i\n%6cNumber of atoms: %i\n",
' ', num_mol, ' ', num_atoms);
message (0, 8, tmp_str, stdout);
}
if (log == 1)
{
sprintf (tmp_str, "%6cNumber of molecules: %i\n%34cNumber of atoms: %i\n",
' ', num_mol, ' ', num_atoms);
message (1, 8, tmp_str, f_log);
}
}
// resize dynamic arrays
agl = (int *) realloc (agl, num_mol * num_mol * sizeof (int));
connect = (int *) realloc (connect, num_mol * num_mol * sizeof (int));
num_mol_agl = (int *) realloc (num_mol_agl, num_mol * sizeof (int));
stat = (int *) realloc (stat, num_mol * sizeof (int));
if (i == from)
{
stat_all = (int *) realloc (stat_all, num_mol * sizeof (int));
for (j=0; j<num_mol; j++)
stat_all[j] = 0;
}
// error checking
if ((agl == NULL) ||
(connect == NULL) ||
(num_mol_agl == NULL) ||
(stat == NULL) ||
(stat_all == NULL))
{
sprintf (tmp_str, "\nMemory error (error code: 18)\n");
fputs (tmp_str, stderr);
if (log == 1)
fputs (tmp_str, f_log);
return 18;
}
if (quiet != 1)
message (0, 9, argv[0], stdout);
if (log == 1)
message (1, 9, argv[0], f_log);
// analyze
if (error == 0)
{
error = 1;
error = create_matrix (num_mol, num_atoms, label_mol, type_atoms, coords,
num_of_inter, crit, connect);
if (error == 0)
{
if (quiet != 1)
message (0, 10, argv[0], stdout);
if (log == 1)
message (1, 10, argv[0], f_log);
error = 1;
error = proc_matrix (num_mol, connect, num_mol_agl, agl, stat, stat_all);
if (error == 0)
{
if (quiet != 1)
message (0, 11, argv[0], stdout);
if (log == 1)
message (1, 11, argv[0], f_log);
error = printing_agl (filename, output, connect, num_mol, true_label_mol,
num_mol_agl, agl, stat, max_depth, type_agl);
if (error == 0)
{
if (quiet != 1)
message (0, 12, output, stdout);
if (log == 1)
message (1, 12, output, f_log);
}
}
}
}
}
if (quiet != 1)
{
message (0, 13, argv[0], stdout);
message (0, 14, output, stdout);
}
if (log == 1)
{
message (1, 13, argv[0], f_log);
message (1, 14, output, f_log);
}
// tail
summary_statistic (output, step, num_mol, max_depth, type_agl, stat_all);
if (quiet != 1)
message (0, 15, argv[0], stdout);
if (log == 1)
message (1, 15, argv[0], f_log);
// free memory
free (agl);
free (connect);
free (coords);
free (crit);
free (label_mol);
free (num_mol_agl);
free (stat);
free (stat_all);
free (true_label_mol);
free (type_agl);
free (type_atoms);
if (quiet != 1)
message (0, 16, argv[0], stdout);
if (log == 1)
message (1, 16, argv[0], f_log);
if (log == 1)
fclose (f_log);
return 0;
}
Reference in New Issue View Git Blame Copy Permalink