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moldyn/mathmech/mm_statgen/src/main.c
arcan1s d50eaeada6 Reorganization
2013-08-24 23:33:26 +04:00

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/**
* @file
*/
/**
* @mainpage mm_statgen
* @image latex ./logo.png
*
* @section intro_sec Introduction
*
* <b>About this program</b>:
* <ul>
* <li>Program that analyzes molecular dynamic trajectories using topological analysis
* </ul>
*
* <b>Developer</b>:
* <ul>
* <li>Evgeniy Alekseev aka arcanis <pre><esalexeev (at) gmail (dot) com></pre>
*</ul>
* <b>License</b>:
* <ul>
* <li>GPL
* </ul>
*
* @section How-To-Use How to use
* Usage:
* <pre>
* mm_statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]
* [ -l LOGFILE ] [ -q ] [ -h ]
*
* Parametrs:
* -i - mask of input files
* -s - trajectory steps (integer)
* -c - cell size (float), A
* -a - atom types (integer). Format: 'ATOM1' or 'ATOM1,ATOM2' or etc
* -r - criteria (float), A. Format: '0-0:2.4,0-1:3.0' means 0-0-interaction
* (<2.4 A) and 0-1 (<3.0) are needed. This flag can be used multiple times
* -o - output file name
* -g - check graph isomorphism. DEPTH is max depth for check cycles (>= 3)
* -l - log enable
* -q - quiet enable
* -h - show this help and exit
* </pre>
*
* @page Install
*
* @section Requirements Requirements
* The application mm_statgen requires the following external stuff:
* - cmake >= 2.8
* - gcc >= 4.8
*
* @section How-To How to install
*
* @subsection Linux Linux
* @code
* mkdir build && cd build
* cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Release ../
* make
* make install
* @endcode
*
* @subsection Windows Windows
* @code
* create project file using 'cmake'
* compile project
* @endcode
* You may also download compiled executable file for Win_x86.
*
* @page Changelog
* V.1.0.1 (2013-07-27)
* * initial release
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "add_main.h"
#include "coords.h"
#include "messages.h"
#include "stat_print.h"
#include "stat_select.h"
#include "stat_sort.h"
#include "summary_stat.h"
/**
* @fn main
*/
int main (int argc, char *argv[])
/**
* @return 1 - error in error_checking
* @return 2 - input file does not exist
* @return 3 - memory error
* @return 4 - unknown flag
* @return 0 - exit without errors
*/
{
char filename[256], tmp_str[2048];
int error, i, index, j, 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 trajectory files
* logfile log file name
* output output file name
*
* cell massive of cell size
* coords massive of coordinates
* crit massive of criteria
*
* agl massive of aglomerates
* connect connectivity graph for all molecules
* from first trajectory step
* label_atom massive of atom types for interactions
* label_mol massive of numbers of molecule for atoms
* log status of log-mode
* max_depth maximum depth for check cycles in graph analyze
* num_atoms number of atoms
* num_mol number of molecules
* num_mol_agl massive of number of molecules in aglomerates
* num_of_inter number of different interactions
* stat massive of statistic
* stat_all massive of summary statistic
* step $(to - from + 1)
* to last trajectory step
* true_label_mol massive of true numbers of molecule for atoms
* type_agl massive of number of aglomerate types
* type_atoms massive of atom types
* type_inter number of atoms for interactions
* 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') && (argv[i][2] == '\0'))
num_of_inter++;
if (num_of_inter > 0)
{
crit = (float *) malloc ( 16 * num_of_inter * sizeof (float));
if (crit == NULL)
return 3;
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') && (argv[i][2] == '\0'))
{
sprintf (tmp_str, " mm_statgen\n");
sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
sprintf (tmp_str, "%sVersion : 1.0.1 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, "%smm_statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -g DEPTH ]\n", tmp_str);
sprintf (tmp_str, "%s [ -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') && (argv[i][2] == '\0'))
// mask of input files
{
strcpy (input, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
// 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') && (argv[i][2] == '\0'))
// 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') && (argv[i][2] == '\0'))
// 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));
if (label_atom == NULL)
return 1;
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') && (argv[i][2] == '\0'))
// 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') && (argv[i][2] == '\0'))
// output file
{
strcpy (output, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'g') && (argv[i][2] == '\0'))
// graph isomorphism scan
{
sscanf (argv[i+1], "%i", &max_depth);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'l') && (argv[i][2] == '\0'))
// log mode
{
log = 1;
strcpy (logfile, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'q') && (argv[i][2] == '\0'))
// quiet mode
{
quiet = 1;
}
else
// unknown flag
{
return 4;
}
}
if (log == 1)
f_log = fopen (logfile, "w");
print_message (quiet, stdout, log, f_log, 0, argv[0]);
print_message (quiet, stdout, log, f_log, 1, argv[0]);
// error checking
error = error_checking (cell, from, input, max_depth, num_of_inter, output, to,
type_inter);
if (error != 0)
{
print_message (quiet, stderr, log, f_log, 17, argv[0]);
return 1;
}
print_message (quiet, stdout, log, f_log, 2, argv[0]);
// processing
// initial variables
sprintf (filename, "%s.%03i", input, from);
print_message (quiet, stdout, log, f_log, 3, filename);
f_inp = fopen (filename, "r");
if (f_inp == NULL)
{
print_message (quiet, stderr, log, f_log, 18, filename);
return 2;
}
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 (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))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 3;
}
// set type_agl to zero
for (i=0; i<max_depth+2; i++)
type_agl[i] = 0;
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);
print_message (quiet, stdout, log, f_log, 5, tmp_str);
// head
printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom,
num_of_inter, crit, max_depth);
// main cycle
print_message (quiet, stdout, log, f_log, 6, argv[0]);
for (i=from; i<to+1; i++)
{
// reading coordinates
sprintf (filename, "%s.%03i", input, i);
print_message (quiet, stdout, log, f_log, 7, filename);
error = reading_coords (0, filename, type_inter, label_atom, cell, &num_mol,
&num_atoms, true_label_mol, label_mol, type_atoms,
coords, tmp_str);
if (error == 0)
{
sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
' ', num_mol, ' ', num_atoms);
print_message (quiet, stdout, log, f_log, 8, tmp_str);
}
// 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))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 3;
}
print_message (quiet, stdout, log, f_log, 9, argv[0]);
// 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)
{
print_message (quiet, stdout, log, f_log, 10, argv[0]);
error = 1;
error = proc_matrix (num_mol, connect, num_mol_agl, agl, stat, stat_all);
}
if (error == 0)
{
print_message (quiet, stdout, log, f_log, 11, argv[0]);
error = printing_agl (filename, output, connect, num_mol, true_label_mol,
num_mol_agl, agl, stat, max_depth, type_agl);
}
if (error == 0)
print_message (quiet, stdout, log, f_log, 12, output);
}
print_message (quiet, stdout, log, f_log, 13, argv[0]);
print_message (quiet, stdout, log, f_log, 14, output);
// tail
summary_statistic (output, step, num_mol, max_depth, type_agl, stat_all);
print_message (quiet, stdout, log, f_log, 15, argv[0]);
// 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);
print_message (quiet, stdout, log, f_log, 16, argv[0]);
if (log == 1)
fclose (f_log);
return 0;
}
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