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moldyn/mathmech/trj/src/main.c
arcan1s 34a2c5c090 edited documentation
2014-01-29 02:42:45 +04:00

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/*
* ----------------------------------------------------------------------------
* "THE BEER-WARE LICENSE" (Revision 42):
* Evgeniy Alekseev wrote this file. As long as you retain this notice you
* can do whatever you want with this stuff. If we meet some day, and you think
* this stuff is worth it, you can buy me a beer in return
* ----------------------------------------------------------------------------
*/
/**
* @file main.c
* Source code of trj
* @author Evgeniy Alekseev (arcanis)
* @copyright Beerware
* @bug No known bugs
*/
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "add_main.h"
#include <version.h>
#include <mathmech/atom_types.h>
#include <mathmech/messages.h>
#include <mathmech/print_trj.h>
#include <mathmech/read_gmx.h>
#include <mathmech/read_puma.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 tmp_str[2048];
int error, i;
FILE *f_inp, *f_log;
char *ch_atom_types, input[256], input_at[256], logfile[256], output[256];
float *coords;
int *atom_types, log, *num_atoms, *num_mol, num_types, quiet, step, total_types, type;
/* ch_atom_types massive of char atom types
* input input file name
* input_at input file name with atom types
* logfile log file name
* output mask of output files
*
* coords massive of coordinates
*
* atom_types massive of atom types
* log status of log-mode
* num_atoms massive of number of atoms of selected molecule
* num_mol massive of number of molecule of selected type
* num_types number of molecule types
* quiet status of quiet-mode
* step number of trajectory steps
* total_types number of different atom types
* type type of trajectory
*/
set_defaults (input, input_at, &log, output, &step, &total_types, &type, &quiet);
for (i=1; i<argc; i++)
{
if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
{
sprintf (tmp_str, " mm_trj\n");
sprintf (tmp_str, "%sProgram that generates trajectory files\n", tmp_str);
sprintf (tmp_str, "%sVersion : %s License : Beerware\n", tmp_str, PROJ_VERSION);
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_trj -i INPUT_TRJ -t INPUT_TYPE -s NUMBER -a INPUT_ATOMS -o OUTPUT\n", tmp_str);
sprintf (tmp_str, "%s [ -tt TOTAL_TYPES ] [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
sprintf (tmp_str, "%s -i - input file name\n", tmp_str);
sprintf (tmp_str, "%s -t - type of trajectory. Supported formats: gmx, puma\n", tmp_str);
sprintf (tmp_str, "%s -s - number of trajectory steps (integer)\n", tmp_str);
sprintf (tmp_str, "%s -a - input file with atom types. See file format in manual\n", tmp_str);
sprintf (tmp_str, "%s -o - mask of output files\n", tmp_str);
sprintf (tmp_str, "%s -tt - number of different atom types. Default is 1024\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'))
// input file
{
strcpy (input, argv[i+1]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 't') && (argv[i][2] == '\0'))
// type
{
if ((argv[i+1][0] == 'g') && (argv[i+1][1] == 'm') && (argv[i+1][2] == 'x') &&
(argv[i+1][3] == '\0'))
// gromacs text file
type = 0;
else if ((argv[i+1][0] == 'p') && (argv[i+1][1] == 'u') && (argv[i+1][2] == 'm') &&
(argv[i+1][3] == 'a') && (argv[i+1][4] == '\0'))
// puma
type = 1;
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
// steps
{
sscanf (argv[i+1], "%i", &step);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
// atom types
{
strcpy (input_at, argv[i+1]);
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] == 't') && (argv[i][2] == 't') && (argv[i][3] == '\0'))
// number of atom types
{
sscanf (argv[i+1], "%i", &total_types);
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 check
error = error_checking (input, input_at, output, step, type);
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
print_message (quiet, stdout, log, f_log, 3, input);
f_inp = fopen (input, "r");
if (f_inp == NULL)
return 2;
switch (type)
{
case 0:
fgets (tmp_str, 256, f_inp);
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, " natoms=%i%s", &i, tmp_str);
break;
case 1:
fgets (tmp_str, 256, f_inp);
sscanf (tmp_str, "%s%s%i%s", tmp_str, tmp_str, &i, tmp_str);
break;
}
fclose (f_inp);
atom_types = (int *) malloc (total_types * sizeof (int));
ch_atom_types = (char *) malloc (2 * total_types * sizeof (char));
coords = (float *) malloc (3 * i * sizeof (float));
num_atoms = (int *) malloc (total_types * sizeof (int));
num_mol = (int *) malloc (total_types * sizeof (int));
num_types = 0;
if ((atom_types == NULL) ||
(ch_atom_types == NULL) ||
(coords == NULL) ||
(num_atoms == NULL) ||
(num_mol == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
return 3;
}
print_message (quiet, stdout, log, f_log, 6, argv[0]);
// read atom types
error = 1;
error = reading_atoms (input_at, &num_types, num_mol, num_atoms, ch_atom_types,
atom_types, total_types);
if (error == 0)
{
sprintf (tmp_str, "%6cLog: %i;\n%6cQuiet: %i;\n%6cInput file: %s;\n%6cTrajectory type: %i;\n\
%6cNumber of trajectory step: %i;\n%6cInput file with atom types: %s;\n%6cMask of output file: %s;\n\
%6cNumber of different atom types: %i;\n%6cNumber of different molecules: %i;\n%6cNumber of atoms in system: %i\n",
' ', log, ' ', quiet, ' ', input, ' ', type, ' ', step, ' ', input_at, ' ', output,
' ', total_types, ' ', num_types, ' ', i);
print_message (quiet, stdout, log, f_log, 5, tmp_str);
}
else
return 2;
print_message (quiet, stdout, log, f_log, 6, argv[0]);
// main cycle
switch (type)
{
case 0:
rw_gmx (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
atom_types, coords);
break;
case 1:
rw_puma (input, step, output, num_types, num_mol, num_atoms, ch_atom_types,
atom_types, coords);
break;
}
print_message (quiet, stdout, log, f_log, 13, argv[0]);
print_message (quiet, stdout, log, f_log, 15, argv[0]);
// free memory
free (atom_types);
free (ch_atom_types);
free (coords);
free (num_atoms);
free (num_mol);
print_message (quiet, stdout, log, f_log, 16, argv[0]);
if (log == 1)
fclose (f_log);
return 0;
}
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