fixed trj2pdb and trj

mathmech/trj/src/add_main.c

@@ -4,6 +4,7 @@
 
 #include <stdio.h>
 
+#include "add_main.h"
 #include <mathmech/messages.h>
 
 
@@ -12,25 +13,6 @@
  */
 int error_checking (const char *input, const char *input_at, const char *output, 
                     const int step, const int type)
-/**
- * @brief function that checks errors in input variables
- * @code
- * error_checking (cell, from, input, num_needed_at, needed_at, output, to);
- * @endcode
- * 
- * @param input           input file name
- * @param input_at        input file name with atom types
- * @param output          output file name
- * @param step            number of trajectory steps
- * @param type            type of trajectory
- * 
- * @return 11             - error in 'input_at'
- * @return 12             - error in 'input'
- * @return 13             - error in 'output'
- * @return 14             - error in 'step'
- * @return 15             - error in 'type'
- * @return 0              - exit without errors
- */
 {
   if (input_at[0] == '#')
     return 11;
@@ -52,21 +34,6 @@ int error_checking (const char *input, const char *input_at, const char *output,
  */
 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);
@@ -82,23 +49,6 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
  */
 int set_defaults (char *input, char *input_at, int *log, char *output, int *step, 
                   int *total_types, int *type, int *quiet)
-/**
- * @brief function that sets default values of variables
- * @code
- * set_defaults (input, input_at, &log, output, &step, &type, &quiet);
- * @endcode
- * 
- * @param input           input file name
- * @param input_at        input file name with atom types
- * @param log             status of log-mode
- * @param output          output file name
- * @param step            number of trajectory steps
- * @param total_types     number of different atom types
- * @param type            type of trajectory
- * @param quiet           status of quiet-mode
- * 
- * @return 0              - exit without errors
- */
 {
   input[0] = '#';
   input_at[0] = '#';

mathmech/trj/src/add_main.h

@@ -5,18 +5,77 @@
 #ifndef ADD_MAIN_H
 #define ADD_MAIN_H
 
+
 /**
  * @fn error_checking
  */
+int error_checking (const char *input, const char *input_at, const char *output, 
+                    const int step, const int type);
+/**
+ * @brief function that checks errors in input variables
+ * @code
+ * error_checking (input, input_at, output, step, type);
+ * @endcode
+ * 
+ * @param input           input file name
+ * @param input_at        input file name with atom types
+ * @param output          output file name
+ * @param step            number of trajectory steps
+ * @param type            type of trajectory
+ * 
+ * @return 11             - error in 'input_at'
+ * @return 12             - error in 'input'
+ * @return 13             - error in 'output'
+ * @return 14             - error in 'step'
+ * @return 15             - error in 'type'
+ * @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 *input, char *input_at, int *log, char *output, int *step, 
+                  int *total_types, int *type, int *quiet);
+/**
+ * @brief function that sets default values of variables
+ * @code
+ * set_defaults (input, input_at, &log, output, &step, &total_types, &type, &quiet);
+ * @endcode
+ * 
+ * @param input           input file name
+ * @param input_at        input file name with atom types
+ * @param log             status of log-mode
+ * @param output          output file name
+ * @param step            number of trajectory steps
+ * @param total_types     number of different atom types
+ * @param type            type of trajectory
+ * @param quiet           status of quiet-mode
+ * 
+ * @return 0              - exit without errors
+ */
 
-int error_checking (const char *, const char *, const char *, const int, const int);
-int print_message (const int, FILE *, const int, FILE *, const int, const char *);
-int set_defaults (char *, char *, int *, char *, int *, int *, int *, int *);
 
-#endif /* ADD_MAIN_H */
+#endif /* ADD_MAIN_H */

mathmech/trj2pdb/src/add_main.c

@@ -4,6 +4,7 @@
 
 #include <stdio.h>
 
+#include "add_main.h"
 #include <mathmech/messages.h>
 
 
@@ -11,21 +12,6 @@
  * @fn error_checking
  */
 int error_checking (const const char *input, const char *output)
-/**
- * @brief function that checks errors in input variables
- * @code
- * error_checking (input, output);
- * @endcode
- * 
- * @param aglinp          aglomerate file name
- * @param cell            massive of cell size
- * @param input           input file name
- * @param output          output file name
- * 
- * @return 11             - error in 'input'
- * @return 12             - error in 'output'
- * @return 0              - exit without errors
- */
 {
   if (input[0] == '#')
     return 11;
@@ -41,21 +27,6 @@ int error_checking (const const char *input, const char *output)
  */
 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);
@@ -70,19 +41,6 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
  * @fn set_defaults
  */
 int set_defaults (char *input, int *log, char *output, int *quiet)
-/**
- * @brief function that sets default values of variables
- * @code
- * set_defaults (input, &log, output, &quiet);
- * @endcode
- * 
- * @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
- */
 {
   input[0] = '#';
   *log = 0;

mathmech/trj2pdb/src/add_main.h

@@ -5,18 +5,67 @@
 #ifndef ADD_MAIN_H
 #define ADD_MAIN_H
 
+
 /**
  * @fn error_checking
  */
+int error_checking (const const char *input, const char *output);
+/**
+ * @brief function that checks errors in input variables
+ * @code
+ * error_checking (input, output);
+ * @endcode
+ * 
+ * @param aglinp          aglomerate file name
+ * @param cell            massive of cell size
+ * @param input           input file name
+ * @param output          output file name
+ * 
+ * @return 11             - error in 'input'
+ * @return 12             - error in 'output'
+ * @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 *input, int *log, char *output, int *quiet);
+/**
+ * @brief function that sets default values of variables
+ * @code
+ * set_defaults (input, &log, output, &quiet);
+ * @endcode
+ * 
+ * @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 char *);
-int print_message (const int, FILE *, const int, FILE *, const int, const char *);
-int set_defaults (char *, int *, char *, int *);
 
-#endif /* ADD_MAIN_H */
+#endif /* ADD_MAIN_H */

mathmech/trj2pdb/src/main.c

@@ -9,9 +9,9 @@
 
 #include "add_main.h"
 #include <version.h>
-#include <mathmech/coords.h>
 #include <mathmech/messages.h>
 #include <mathmech/print_struct.h>
+#include <mathmech/var_types.h>
 
 
 /**
@@ -31,22 +31,21 @@ int main(int argc, char *argv[])
   FILE *f_inp, *f_log;
   
   char input[256], logfile[256], output[256];
-  float cell[3];
+  int log, *needed_mol, quiet, *true_label_mol;
-  int log, *needed_mol, num_atoms, num_mol, quiet, *true_label_mol;
   atom_info *_atom_info;
+  system_info _system_info;
   
 /* input                  input file name
  * logfile                log file name
  * output                 output file name
  * 
- * cell                   sell size
- * 
  * log                    status of log-mode
  * needed_mol             massive of numbers of needed molecule
  * num_atoms              number of atoms
  * num_mol                number of molecules
  * quiet                  status of quiet-mode
  * true_label_mol         massive of true numbers of molecule for atoms
+ * 
  * _atom_info             atom information structure
  */
   
@@ -128,11 +127,11 @@ 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);
-  _atom_info = (atom_info *) malloc (8 * num_atoms * sizeof (atom_info));
+  _atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
-  needed_mol = (int *) malloc (num_atoms * sizeof (int));
+  needed_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
-  true_label_mol = (int *) malloc (num_atoms * sizeof (int));
+  true_label_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
 // error checking
   if ((_atom_info == NULL) ||
      (needed_mol == NULL) || 
@@ -142,7 +141,7 @@ int main(int argc, char *argv[])
     return 3;
   }
   for (i=0; i<3; i++)
-    cell[i] = 0.0;
+    _system_info.cell[i] = 0.0;
   sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n", 
 ' ', input, ' ', output, ' ', log, ' ', quiet);
   print_message (quiet, stdout, log, f_log, 5, tmp_str);
@@ -152,18 +151,18 @@ int main(int argc, char *argv[])
 // reading coordinates
   print_message (quiet, stdout, log, f_log, 7, input);
   error = 1;
-  error = reading_coords (1, input, tmp_int, &tmp_int, cell, &num_mol, &num_atoms, 
+  error = reading_coords (1, input, tmp_int, &tmp_int, &_system_info, true_label_mol, 
-                          true_label_mol, _atom_info);
+                          _atom_info);
   
 // print coordinates
   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);
-    for (i=0; i<num_mol; i++)
+    for (i=0; i<_system_info.num_mol; i++)
       needed_mol[i] = 8 * i;
     error = 1;
-    error = print_structure (output, num_mol, needed_mol, num_atoms, _atom_info);
+    error = print_structure (output, _system_info.num_mol, needed_mol, _system_info, _atom_info);
   }
   if (error == 0)
     print_message (quiet, stderr, log, f_log, 12, output);