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Release mathmech 1.0.1

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arcan1s
2013-08-29 04:46:58 +04:00
parent 69fd9fd15e
commit d049cd091c
38 changed files with 623 additions and 516 deletions
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4
mathmech/mm_agl/src/add_main.c
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@ -18,7 +18,7 @@ int error_checking (const char *aglinp, const float *cell, const char *input,
* error_checking (aglinp, cell, input, output);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param cell massive of cell size
* @param input input file name
* @param output output file name
@ -83,7 +83,7 @@ int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output
* set_defaults (aglinp, cell, input, &log, output, &quiet);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param cell massive of cell size
* @param input mask of trajectory files
* @param log status of log-mode

14
mathmech/mm_agl/src/main.c
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@ -9,7 +9,7 @@
*
* <b>About this program</b>:
* <ul>
* <li>Program that creates PDB file with chosen aglomerate
* <li>Program that creates PDB file with chosen agglomerate
* </ul>
*
* <b>Developer</b>:
@ -27,7 +27,7 @@
* mm_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]
*
* Parametrs:
* -a - input file with aglomerates (in format statgen)
* -a - input file with agglomerates (in format statgen)
* -i - input file with coordinates
* -c - cell size (float), A
* -o - output file name
@ -100,7 +100,7 @@ int main(int argc, char *argv[])
int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet,
*true_label_mol;
/* aglinp aglomerate file name
/* aglinp agglomerate file name
* ch_type_atoms massive of char atom types
* input input file name
* logfile log file name
@ -127,14 +127,14 @@ int main(int argc, char *argv[])
if ((argv[i][0] == '-') && (argv[i][1] == 'h') && (argv[i][2] == '\0'))
{
sprintf (tmp_str, " mm_agl\n");
sprintf (tmp_str, "%sProgram for create PDB file with chosen aglomerate\n", tmp_str);
sprintf (tmp_str, "%sProgram for create PDB file with chosen agglomerate\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_agl -a AGL_INP -i INPUT -c X,Y,Z -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n", tmp_str);
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
sprintf (tmp_str, "%s -a - input file with aglomerates (in format statgen)\n", tmp_str);
sprintf (tmp_str, "%s -a - input file with agglomerates (in format statgen)\n", tmp_str);
sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str);
sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
sprintf (tmp_str, "%s -o - output file name\n", tmp_str);
@ -238,13 +238,13 @@ int main(int argc, char *argv[])
print_message (quiet, stdout, log, f_log, 6, argv[0]);
// reading aglomerate
// reading agglomerate
print_message (quiet, stdout, log, f_log, 7, aglinp);
error = reading_agl (aglinp, &num_needed_mol, tmp_str, needed_mol);
if (error == 0)
{
sprintf (tmp_str, "%6cNumber of molecules in aglomerate: %i\n", ' ', num_needed_mol);
sprintf (tmp_str, "%6cNumber of molecules in agglomerate: %i\n", ' ', num_needed_mol);
print_message (quiet, stdout, log, f_log, 8, tmp_str);
// reading coordinates
print_message (quiet, stdout, log, f_log, 7, input);

2
mathmech/mm_agl/src/messages.c
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@ -53,7 +53,7 @@ int message (const int log, const int mode, const char *text, FILE *output)
sprintf (out, "Initialization of variables from file '%s'\n", text);
break;
case 4:
sprintf (out, "%6cAglomerate was selected successfully\n", ' ');
sprintf (out, "%6cAgglomerate was selected successfully\n", ' ');
break;
case 5:
sprintf (out, "Initial parametrs: \n%s", text);

10
mathmech/mm_agl/src/read_agl.c
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@ -1,7 +1,7 @@
/**
* @file
*/
/* Library for reading aglomerate from statgen-file
/* Library for reading agglomerate from statgen-file
*
* Usage:
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol)
@ -15,14 +15,14 @@
*/
int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *needed_mol)
/**
* @brief function that reads aglomerate from statgen-formated file
* @brief function that reads agglomerate from statgen-formated file
* @code
* reading_agl (aglinput, &num_needed_mol, agl_class, needed_mol);
* @endcode
*
* @param aglinp aglomerate file name
* @param aglinp agglomerate file name
* @param num_needed_mol number of needed molecules
* @param agl_class aglomerate class
* @param agl_class agglomerate class
* @param needed_mol massive of numbed of needed molecules
*
* @return 0 - exit without errors
@ -33,7 +33,7 @@ int reading_agl (const char *aglinp, int *num_needed_mol, char *agl_class, int *
FILE *f_agl;
/* connect - connectivity matrix for molecule
* f_agl - aglomerate file
* f_agl - agglomerate file
*/
f_agl = fopen (aglinp, "r");