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fixed agl

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arcan1s
2014-01-28 03:45:36 +04:00
parent d88f3b317f
commit 0714cb6541
3 changed files with 104 additions and 93 deletions
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57
mathmech/agl/src/add_main.c
View File

@ -5,32 +5,16 @@
#include <stdio.h>
#include <mathmech/messages.h>
#include <mathmech/var_types.h>
/**
* @fn error_checking
*/
int error_checking (const char *aglinp, const float *cell, const char *input,
int error_checking (const char *aglinp, const system_info _system_info, const char *input,
const char *output)
/**
* @brief function that checks errors in input variables
* @code
* error_checking (aglinp, cell, input, output);
* @endcode
*
* @param aglinp agglomerate file name
* @param cell massive of cell size
* @param input input file name
* @param output output file name
*
* @return 11 - error in 'cell'
* @return 12 - error in 'input'
* @return 13 - error in 'output'
* @return 14 - error in 'aglinp'
* @return 0 - exit without errors
*/
{
if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
if ((_system_info.cell[0] == 0.0) || (_system_info.cell[1] == 0.0) || (_system_info.cell[2] == 0.0))
return 11;
if (input[0] == '#')
return 12;
@ -48,21 +32,6 @@ int error_checking (const char *aglinp, const float *cell, const char *input,
*/
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
const int mode, const char *str)
/**
* @brief function that prints message in log and stdout
* @code
* print_message (quiet, stdout, log, f_log, 0, str);
* @endcode
*
* @param quiet status of quiet-mode
* @param std_output stdout
* @param log status of log-mode
* @param f_log log file
* @param mode number of message in "messages.c"
* @param str additional text in message
*
* @return 0 - exit without errors
*/
{
if ((quiet != 1) && (std_output != stderr))
message (0, mode, str, std_output);
@ -76,28 +45,14 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
/**
* @fn set_defaults
*/
int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output, int *quiet)
/**
* @brief function that sets default values of variables
* @code
* set_defaults (aglinp, cell, input, &log, output, &quiet);
* @endcode
*
* @param aglinp agglomerate file name
* @param cell massive of cell size
* @param input mask of trajectory files
* @param log status of log-mode
* @param output output file name
* @param quiet status of quiet-mode
*
* @return 0 - exit without errors
*/
int set_defaults (char *aglinp, system_info *_system_info, char *input, int *log,
char *output, int *quiet)
{
int i;
aglinp[0] = '#';
for (i=0; i<3; i++)
cell[i] = 0.0;
(*_system_info).cell[i] = 0.0;
input[0] = '#';
*log = 0;
output[0] = '#';

73
mathmech/agl/src/add_main.h
View File

@ -5,18 +5,83 @@
#ifndef ADD_MAIN_H
#define ADD_MAIN_H
/**
* @file
*/
#include <stdio.h>
#include <mathmech/messages.h>
#include <mathmech/var_types.h>
/**
* @fn error_checking
*/
int error_checking (const char *aglinp, const system_info _system_info,
const char *input, const char *output);
/**
* @brief function that checks errors in input variables
* @code
* error_checking (aglinp, _system_info, input, output);
* @endcode
*
* @param aglinp agglomerate file name
* @param _system_info system information structure
* @param input input file name
* @param output output file name
*
* @return 11 - error in 'cell'
* @return 12 - error in 'input'
* @return 13 - error in 'output'
* @return 14 - error in 'aglinp'
* @return 0 - exit without errors
*/
/**
* @fn print_message
*/
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
const int mode, const char *str);
/**
* @brief function that prints message in log and stdout
* @code
* print_message (quiet, stdout, log, f_log, 0, str);
* @endcode
*
* @param quiet status of quiet-mode
* @param std_output stdout
* @param log status of log-mode
* @param f_log log file
* @param mode number of message in "messages.c"
* @param str additional text in message
*
* @return 0 - exit without errors
*/
/**
* @fn set_defaults
*/
int set_defaults (char *aglinp, system_info *_system_info, char *input, int *log, char *output,
int *quiet);
/**
* @brief function that sets default values of variables
* @code
* set_defaults (aglinp, &_system_info, input, &log, output, &quiet);
* @endcode
*
* @param aglinp agglomerate file name
* @param _system_info system information structure
* @param input mask of trajectory files
* @param log status of log-mode
* @param output output file name
* @param quiet status of quiet-mode
*
* @return 0 - exit without errors
*/
int error_checking (const char *, const float *, const char *, const char *);
int print_message (const int, FILE *, const int, FILE *, const int, const char *);
int set_defaults (char *, float *, char *, int *, char *, int *);
#endif /* ADD_MAIN_H */
#endif /* ADD_MAIN_H */

67
mathmech/agl/src/main.c
View File

@ -15,6 +15,7 @@
#include <mathmech/read_agl.h>
#include <mathmech/select_mol.h>
#include <mathmech/set_center.h>
#include <mathmech/var_types.h>
/**
@ -30,35 +31,33 @@ int main(int argc, char *argv[])
*/
{
char tmp_str[2048];
int error, i, *tmp_int;
int error, i;
FILE *f_inp, *f_log;
char aglinp[256], *ch_type_atoms, input[256], logfile[256], output[256];
float cell[3], *centr_coords, *coords;
int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet,
*true_label_mol;
char aglinp[256], input[256], logfile[256], output[256];
float *centr_coords;
int log, num_needed_mol, *needed_mol, quiet, *true_label_mol;
atom_info *_atom_info;
system_info _system_info;
/* aglinp agglomerate file name
* ch_type_atoms massive of char atom types
* input input file name
* logfile log file name
* output output file name
*
* cell massive of cell size
* centr_coords massive of centered coordinates
* coords massive of coordinates
*
* label_mol massive of numbers of molecule for atoms
* log status of log-mode
* num_atoms number of atoms
* num_mol number of molecules
* num_needed_mol number of needed molecules
* needed_mol massive of number of needed molecules
* quiet status of quiet-mode
* true_label_mol massive of true numbers of molecule for atoms
*
* _atom_info atom information structure
* _system_info system information structure
*/
set_defaults (aglinp, cell, input, &log, output, &quiet);
set_defaults (aglinp, &_system_info, input, &log, output, &quiet);
for (i=1; i<argc; i++)
{
@ -97,7 +96,8 @@ int main(int argc, char *argv[])
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]);
sscanf (argv[i+1], "%f,%f,%f", &_system_info.cell[0], &_system_info.cell[1],
&_system_info.cell[2]);
i++;
}
else if ((argv[i][0] == '-') && (argv[i][1] == 'o') && (argv[i][2] == '\0'))
@ -132,7 +132,7 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 1, argv[0]);
// error check
error = error_checking (aglinp, cell, input, output);
error = error_checking (aglinp, _system_info, input, output);
if (error != 0)
{
print_message (quiet, stderr, log, f_log, 17, argv[0]);
@ -150,20 +150,14 @@ int main(int argc, char *argv[])
print_message (quiet, stderr, log, f_log, 18, input);
return 2;
}
fscanf (f_inp, "%i", &num_atoms);
fscanf (f_inp, "%i", &_system_info.num_atoms);
fclose (f_inp);
ch_type_atoms = (char *) malloc (2 * num_atoms * sizeof (char));
coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
needed_mol = (int *) malloc (num_atoms * sizeof (int));
tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
_atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
needed_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
true_label_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
// error checking
if ((ch_type_atoms == NULL) ||
(coords == NULL) ||
(label_mol == NULL) ||
if ((_atom_info == NULL) ||
(needed_mol == NULL) ||
(tmp_int == NULL) ||
(true_label_mol == NULL))
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
@ -171,7 +165,8 @@ int main(int argc, char *argv[])
}
sprintf (tmp_str, "%6cAglomerate file: '%s';\n%6cInput file: '%s';\n\
%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f\n",
' ', aglinp, ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0], cell[1], cell[2]);
' ', aglinp, ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', _system_info.cell[0],
_system_info.cell[1], _system_info.cell[2]);
print_message (quiet, stdout, log, f_log, 5, tmp_str);
print_message (quiet, stdout, log, f_log, 6, argv[0]);
@ -187,10 +182,9 @@ int main(int argc, char *argv[])
// reading coordinates
print_message (quiet, stdout, log, f_log, 7, input);
error = 1;
error = reading_coords (2, input, num_needed_mol, needed_mol, cell, &num_mol,
&num_atoms, true_label_mol, label_mol, tmp_int, coords,
ch_type_atoms);
centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
error = reading_coords (2, input, num_needed_mol, needed_mol, &_system_info,
true_label_mol, _atom_info);
centr_coords = (float *) malloc (3 * 8 * _system_info.num_mol * sizeof (float));
if (centr_coords == NULL)
{
print_message (quiet, stderr, log, f_log, 19, argv[0]);
@ -202,10 +196,10 @@ int main(int argc, char *argv[])
if (error == 0)
{
sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
' ', num_mol, ' ', num_atoms);
' ', _system_info.num_mol, ' ', _system_info.num_atoms);
print_message (quiet, stdout, log, f_log, 8, tmp_str);
error = 1;
error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
error = set_center (_system_info, _atom_info, centr_coords);
}
if (error == 0)
{
@ -217,8 +211,8 @@ int main(int argc, char *argv[])
{
print_message (quiet, stderr, log, f_log, 4, argv[0]);
error = 1;
error = print_structure (output, num_needed_mol, needed_mol, num_atoms,
label_mol, ch_type_atoms, coords);
error = print_structure (output, num_needed_mol, needed_mol, _system_info,
_atom_info);
}
if (error == 0)
print_message (quiet, stderr, log, f_log, 12, output);
@ -227,12 +221,9 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 15, argv[0]);
// free memory
free (ch_type_atoms);
free (_atom_info);
free (centr_coords);
free (coords);
free (label_mol);
free (needed_mol);
free (tmp_int);
free (true_label_mol);
print_message (quiet, stdout, log, f_log, 16, argv[0]);