fixed statgen

mathmech/mm/include/mathmech/stat_print.h

@@ -18,9 +18,8 @@ int printing_agl (const char *input, const char *output, const int *connect,
 /**
  * @brief function that prints agglomerates to output file
  * @code
- * printing_agl (input_file, output_file, number_of_molecules, true_label_molecules, 
+ * printing_agl (input, output, connect, _system_info, true_label_mol, num_mol_agl, 
- *               num_of_molecules_in_agglomerates, agglomerates, statistic, max_depth, 
+ *               agl, stat, max_depth, type_agl);
- *               type_of_agglomerate);
  * @endcode
  * 
  * @param input           input file name

mathmech/mm/include/mathmech/stat_select.h

@@ -16,7 +16,7 @@ int create_matrix (const system_info _system_info, const atom_info *_atom_info,
 /**
  * @brief function that creates connectivity matrix
  * @code
- * int create_matrix (_system_info, _atom_info, num_of_inter, crit, connect);
+ * create_matrix (_system_info, _atom_info, num_of_inter, crit, connect);
  * @endcode
  * 
  * @param _system_info    system information structure

mathmech/mm/include/mathmech/summary_stat.h

@@ -5,11 +5,29 @@
 #ifndef SUMMARY_STAT_H
 #define SUMMARY_STAT_H
 
+#include <mathmech/var_types.h>
+
+
 /**
  * @fn summary_statistic
  */
+int summary_statistic (const char *filename, const system_info _system_info, 
+                       const int max_depth, const int *type_agl, const int *stat_all);
+/**
+ * @brief function that prints summary statistic
+ * @code
+ * summary_statistic (filename, _system_info, max_depth, type_agl, stat_all);
+ * @endcode
+ * 
+ * @param filename        output file name
+ * @param _system_info    system information structure
+ * @param num_mol         number of molecules
+ * @param max_depth       maximum depth for check cycles in graph analyze
+ * @param type_agl        massive of number of agglomerate types
+ * @param stat_all        massive of summary statistic
+ * 
+ * @return 0              - exit without errors
+ */
 
-int summary_statistic (const char *, const int, const int, const int, const int *, 
-                       const int *);
 
-#endif /* SUMMARY_STAT_H */
+#endif /* SUMMARY_STAT_H */

mathmech/mm/src/summary_stat.c

@@ -4,28 +4,15 @@
 
 #include <stdio.h>
 
+#include <mathmech/summary_stat.h>
+#include <mathmech/var_types.h>
+
 
 /**
  * @fn summary_statistic
  */
-int summary_statistic (const char *filename, const int step, const int num_mol, 
+int summary_statistic (const char *filename, const system_info _system_info, 
                        const int max_depth, const int *type_agl, const int *stat_all)
-/**
- * @brief function that prints summary statistic
- * @code
- * summary_statistic (filename, number_of_step, number_of_molecules, max_depth, 
- *                    type_of_agglomerate, summary_statistic);
- * @endcode
- * 
- * @param filename        output file name
- * @param step            number of steps
- * @param num_mol         number of molecules
- * @param max_depth       maximum depth for check cycles in graph analyze
- * @param type_agl        massive of number of agglomerate types
- * @param stat_all        massive of summary statistic
- * 
- * @return 0              - exit without errors
- */
 {
   float conc, p, pn, type[2], x, y;
   int i, index;
@@ -38,7 +25,7 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
  */
   
   index = 0;
-  for (i=0; i<num_mol; i++)
+  for (i=0; i<_system_info.num_mol; i++)
     if (stat_all[i] != 0)
       index = i;
   
@@ -51,12 +38,12 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
   {
 // calculating concentrates
     x = stat_all[i];
-    y = step;
+    y = _system_info.to - _system_info.from + 1;
     conc = x / y;
     
 // calculating probabilityes
     x = (i + 1) * stat_all[i];
-    y = step * num_mol;
+    y = (_system_info.to - _system_info.from + 1) * _system_info.num_mol;
     p = x / y;
     pn = (i + 1) * p;
     
@@ -90,4 +77,4 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
   fclose (f_out);
   
   return 0;
-}
+}

mathmech/statgen/src/add_main.c

@@ -4,47 +4,23 @@
 
 #include <stdio.h>
 
+#include "add_main.h"
 #include <version.h>
 #include <mathmech/messages.h>
+#include <mathmech/var_types.h>
 
 
 /**
  * @fn error_checking
  */
-int error_checking (const float *cell, const int from, const char *input, 
+int error_checking (const system_info _system_info, const char *input, const int max_depth, 
-                    const int max_depth, const int num_of_inter, const char *output, 
+                    const int num_of_inter, const char *output, const int type_inter)
-                    const int to, const int type_inter)
-/**
- * @brief function that checks errors in input variables
- * @code
- * error_checking (cell, from, input, max_depth, num_of_inter, output, to, 
- *                 type_inter);
- * @endcode
- * 
- * @param cell            massive of cell size
- * @param from            first trajectory step
- * @param input           mask of trajectory files
- * @param max_depth       max depth for check cycles in graph analyze
- * @param num_of_inter    number of different interactions
- * @param output          output file name
- * @param to              last trajectory step
- * @param type_inter      number of atoms for interactions
- * 
- * @return 11             - error in 'type_inter'
- * @return 12             - error in 'cell'
- * @return 13             - error in 'to' or 'from'
- * @return 14             - error in 'num_of_inter'
- * @return 15             - error in 'input'
- * @return 16             - error in 'output'
- * @return 19             - error in 'max_depth'
- * @return 0              - exit without errors
- */
 {
   if ((type_inter == 0) || (type_inter > 4))
     return 11;
-  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 12;
-  if ((to == -1) || (from == -1))
+  if ((_system_info.to == -1) || (_system_info.from == -1))
     return 13;
   if (num_of_inter == 0)
     return 14;
@@ -63,31 +39,9 @@ int error_checking (const float *cell, const int from, const char *input,
  * @fn printing_head
  */
 int printing_head (const char *output, const int log, const int quiet, 
-                   const char *input, const int from, const int to, const float *cell, 
+                   const char *input, const system_info _system_info,
                    const int type_inter, const int *label_atom, 
                    const int num_of_inter, const float *crit, const int max_depth)
-/**
- * @brief function that prints header in output file
- * @code
- * printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom, 
- *                num_of_inter, crit, max_depth);
- * @endcode
- * 
- * @param output          output file nams
- * @param log             status of log-mode
- * @param quiet           status of quiet-mode
- * @param input           mask of trajectory files
- * @param from            first trajectory step
- * @param to              last trajectory step
- * @param cell            massive of cell size
- * @param type_inter      number of atoms for interactions
- * @param label_atom      massive of atom types for interactions
- * @param num_of_inter    number of different interactions
- * @param crit            massive of criteria
- * @param max_depth       maximum depth for check cycles in graph analyze
- * 
- * @return 0              - exit without errors
- */
 {
   int i, j;
   FILE *f_out;
@@ -97,8 +51,9 @@ int printing_head (const char *output, const int log, const int quiet,
   fprintf (f_out, "CONFIGURATION\n");
   
   fprintf (f_out, "LOG=%i\nQUIET=%i\n", log, quiet);
-  fprintf (f_out, "MASK=%s\nFIRST=%i\nLAST=%i\n", input, from, to);
+  fprintf (f_out, "MASK=%s\nFIRST=%i\nLAST=%i\n", input, _system_info.from, _system_info.to);
-  fprintf (f_out, "CELL=%.4f,%.4f,%.4f\n", cell[0], cell[1], cell[2]);
+  fprintf (f_out, "CELL=%.4f,%.4f,%.4f\n", _system_info.cell[0], _system_info.cell[1], 
+           _system_info.cell[2]);
   fprintf (f_out, "ATOMS=%i", label_atom[0]);
   for (i=1; i<type_inter; i++)
     fprintf (f_out, ",%i", label_atom[i]);
@@ -126,21 +81,6 @@ int printing_head (const char *output, const int log, const int quiet,
  */
 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);
@@ -154,40 +94,20 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
 /**
  * @fn set_defaults
  */
-int set_defaults (float *cell, int *from, char *input, int *log, int *max_depth, 
+int set_defaults (system_info *_system_info, char *input, int *log, int *max_depth, 
-                  int *num_of_inter, char *output, int *to, int *type_inter, int *quiet)
+                  int *num_of_inter, char *output, int *type_inter, int *quiet)
-/**
- * @brief function that sets default values of variables
- * @code
- * set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to, 
- *               &type_inter, &quiet);
- * @endcode
- * 
- * @param cell            massive of cell size
- * @param from            first trajectory step
- * @param input           mask of trajectory files
- * @param log             status of log-mode
- * @param max_depth       maximum depth for check cycles in graph analyze
- * @param num_of_inter    number of different interactions
- * @param output          output file name
- * @param to              last trajectory step
- * @param type_inter      number of atoms for interactions
- * @param quiet           status of quiet-mode
- * 
- * @return 0              - exit without errors
- */
 {
   int i;
   
   for (i=0; i<3; i++)
-    cell[i] = 0.0;
+    (*_system_info).cell[i] = 0.0;
-  *from = -1;
+  (*_system_info).from = -1;
   input[0] = '#';
   *log = 0;
   *max_depth = 0;
   *num_of_inter = 0;
   output[0] = '#';
-  *to = -1;
+  (*_system_info).to = -1;
   *type_inter = 0;
   *quiet = 0;
   

mathmech/statgen/src/add_main.h

@@ -5,26 +5,112 @@
 #ifndef ADD_MAIN_H
 #define ADD_MAIN_H
 
+#include <mathmech/var_types.h>
+
+
 /**
  * @fn error_checking
  */
+int error_checking (const system_info _system_info, const char *input, const int max_depth, 
+                    const int num_of_inter, const char *output, const int type_inter);
+/**
+ * @brief function that checks errors in input variables
+ * @code
+ * error_checking (_system_info, input, max_depth, num_of_inter, output, type_inter);
+ * @endcode
+ * 
+ * @param _system_info    system information structure
+ * @param input           mask of trajectory files
+ * @param max_depth       max depth for check cycles in graph analyze
+ * @param num_of_inter    number of different interactions
+ * @param output          output file name
+ * @param type_inter      number of atoms for interactions
+ * 
+ * @return 11             - error in 'type_inter'
+ * @return 12             - error in 'cell'
+ * @return 13             - error in 'to' or 'from'
+ * @return 14             - error in 'num_of_inter'
+ * @return 15             - error in 'input'
+ * @return 16             - error in 'output'
+ * @return 19             - error in 'max_depth'
+ * @return 0              - exit without errors
+ */
+
+
 /**
  * @fn printing_head
  */
+int printing_head (const char *output, const int log, const int quiet, 
+                   const char *input, const system_info _system_info,
+                   const int type_inter, const int *label_atom, 
+                   const int num_of_inter, const float *crit, const int max_depth);
+/**
+ * @brief function that prints header in output file
+ * @code
+ * printing_head (output, log, quiet, input, _system_info, type_inter, label_atom, 
+ *                num_of_inter, crit, max_depth);
+ * @endcode
+ * 
+ * @param output          output file nams
+ * @param log             status of log-mode
+ * @param quiet           status of quiet-mode
+ * @param input           mask of trajectory files
+ * @param _system_info    system information structure
+ * @param type_inter      number of atoms for interactions
+ * @param label_atom      massive of atom types for interactions
+ * @param num_of_inter    number of different interactions
+ * @param crit            massive of criteria
+ * @param max_depth       maximum depth for check cycles in graph analyze
+ * 
+ * @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 (system_info *_system_info, char *input, int *log, int *max_depth, 
+                  int *num_of_inter, char *output, int *type_inter, int *quiet);
+/**
+ * @brief function that sets default values of variables
+ * @code
+ * set_defaults (&_system_info, input, &log, &max_depth, &num_of_inter, output, 
+ *               &type_inter, &quiet);
+ * @endcode
+ * 
+ * @param _system_info    system information structure
+ * @param input           mask of trajectory files
+ * @param log             status of log-mode
+ * @param max_depth       maximum depth for check cycles in graph analyze
+ * @param num_of_inter    number of different interactions
+ * @param output          output file name
+ * @param type_inter      number of atoms for interactions
+ * @param quiet           status of quiet-mode
+ * 
+ * @return 0              - exit without errors
+ */
 
-int error_checking (const float *, const int, const char *, const int, const int, 
-                    const char *, const int, const int);
-int printing_head (const char *, const int, const int, const char *, const int, 
-                   const int, const float *, const int, const int *, const int, 
-                   const float *, const int);
-int print_message (const int, FILE *, const int, FILE *, const int, const char *);
-int set_defaults (float *, int *, char *, int *, int *, int *, char *, int *, 
-                  int *, int *);
 
-#endif /* ADD_MAIN_H */
+#endif /* ADD_MAIN_H */

mathmech/statgen/src/main.c

@@ -16,6 +16,7 @@
 #include <mathmech/stat_select.h>
 #include <mathmech/stat_sort.h>
 #include <mathmech/summary_stat.h>
+#include <mathmech/var_types.h>
 
 
 /**
@@ -36,42 +37,37 @@ int main (int argc, char *argv[])
   FILE *f_inp, *f_log;
   
   char input[256], logfile[256], output[256];
-  float cell[3], *coords, *crit;
+  float *crit;
-  int *agl, *connect, from, *label_atom, *label_mol, log, max_depth, num_atoms, 
+  int *agl, *connect, *label_atom, log, max_depth, *num_mol_agl, num_of_inter, *stat, 
-      num_mol, *num_mol_agl, num_of_inter, *stat, *stat_all, step, to, 
+      *stat_all, *true_label_mol, *type_agl, type_inter, quiet;
-      *true_label_mol, *type_agl, *type_atoms, type_inter, quiet;
+  atom_info *_atom_info;
+  system_info _system_info;
   
 /* 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 agglomerates
  * 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 agglomerates
  * 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 agglomerate types
- * type_atoms             massive of atom types
  * type_inter             number of atoms for interactions
  * quiet                  status of quiet-mode
+ * 
+ * _atom_info             atom information structure
+ * _system_info           system information structure
  */
   
-  set_defaults (cell, &from, input, &log, &max_depth, &num_of_inter, output, &to, 
+  set_defaults (&_system_info, input, &log, &max_depth, &num_of_inter, output, 
                 &type_inter, &quiet);
   
 // reading number of interactions
@@ -125,20 +121,19 @@ int main (int argc, char *argv[])
     else if ((argv[i][0] == '-') && (argv[i][1] == 's') && (argv[i][2] == '\0'))
 // steps
     {
-      sscanf (argv[i+1], "%i,%i", &from, &to);
+      sscanf (argv[i+1], "%i,%i", &_system_info.from, &_system_info.to);
-      if (from > to)
+      if (_system_info.from > _system_info.to)
       {
-        to += from;
+        _system_info.to += _system_info.from;
-        from = to - from;
+        _system_info.from = _system_info.to - _system_info.from;
-        to -= from;
+        _system_info.to -= _system_info.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]);
+      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] == 'a') && (argv[i][2] == '\0'))
@@ -227,7 +222,7 @@ int main (int argc, char *argv[])
   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, 
+  error = error_checking (_system_info, input, max_depth, num_of_inter, output, 
                           type_inter);
   if (error != 0)
   {
@@ -239,7 +234,7 @@ int main (int argc, char *argv[])
   
 // processing
 // initial variables
-  sprintf (filename, "%s.%03i", input, from);
+  sprintf (filename, "%s.%03i", input, _system_info.from);
   print_message (quiet, stdout, log, f_log, 3, filename);
   f_inp = fopen (filename, "r");
   if (f_inp == NULL)
@@ -247,13 +242,11 @@ int main (int argc, char *argv[])
     print_message (quiet, stderr, log, f_log, 18, filename);
     return 2;
   }
-  fscanf (f_inp, "%i", &num_atoms);
+  fscanf (f_inp, "%i", &_system_info.num_atoms);
   fclose (f_inp);
-  coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
+  _atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
-  label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
+  true_label_mol = (int *) malloc (_system_info.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));
@@ -261,11 +254,9 @@ int main (int argc, char *argv[])
   stat = (int *) malloc (2 * sizeof (int));
   stat_all = (int *) malloc (2 * sizeof (int));
 // error checking
-  if ((coords == NULL) || 
+  if ((_atom_info == NULL) || 
-     (label_mol == NULL) || 
      (true_label_mol == NULL) || 
      (type_agl == NULL) || 
-     (type_atoms == NULL) || 
      (agl == NULL) || 
      (connect == NULL) || 
      (num_mol_agl == NULL) || 
@@ -280,8 +271,9 @@ int main (int argc, char *argv[])
     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, 
+%6cSelect atoms: %i", ' ', output, ' ', log, ' ', quiet, ' ', input, ' ', _system_info.from, 
-' ' , to, ' ', cell[0], cell[1], cell[2], ' ' , label_atom[0]);
+' ' , _system_info.to, ' ', _system_info.cell[0], _system_info.cell[1], _system_info.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);
@@ -298,35 +290,34 @@ int main (int argc, char *argv[])
   print_message (quiet, stdout, log, f_log, 5, tmp_str);
   
 // head
-  printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom, 
+  printing_head (output, log, quiet, input, _system_info, 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++)
+  for (i=_system_info.from; i<_system_info.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, 
+    error = reading_coords (0, filename, type_inter, label_atom, &_system_info, 
-                            &num_atoms, true_label_mol, label_mol, type_atoms, 
+                            true_label_mol, _atom_info);
-                            coords, tmp_str);
     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);
     }
     
 // resize dynamic arrays
-    agl = (int *) realloc (agl, num_mol * num_mol * sizeof (int));
+    agl = (int *) realloc (agl, _system_info.num_mol * _system_info.num_mol * sizeof (int));
-    connect = (int *) realloc (connect, num_mol * num_mol * sizeof (int));
+    connect = (int *) realloc (connect, _system_info.num_mol * _system_info.num_mol * sizeof (int));
-    num_mol_agl = (int *) realloc (num_mol_agl, num_mol * sizeof (int));
+    num_mol_agl = (int *) realloc (num_mol_agl, _system_info.num_mol * sizeof (int));
-    stat = (int *) realloc (stat, num_mol * sizeof (int));
+    stat = (int *) realloc (stat, _system_info.num_mol * sizeof (int));
-    if (i == from)
+    if (i == _system_info.from)
     {
-      stat_all = (int *) realloc (stat_all, num_mol * sizeof (int));
+      stat_all = (int *) realloc (stat_all, _system_info.num_mol * sizeof (int));
-      for (j=0; j<num_mol; j++)
+      for (j=0; j<_system_info.num_mol; j++)
         stat_all[j] = 0;
     }
 // error checking
@@ -345,19 +336,18 @@ int main (int argc, char *argv[])
     if (error == 0)
     {
       error = 1;
-      error = create_matrix (num_mol, num_atoms, label_mol, type_atoms, coords, 
+      error = create_matrix (_system_info, _atom_info, num_of_inter, crit, connect);
-                             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);
+      error = proc_matrix (_system_info, 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, 
+      error = printing_agl (filename, output, connect, _system_info, true_label_mol, 
                             num_mol_agl, agl, stat, max_depth, type_agl);
     }
     if (error == 0)
@@ -367,21 +357,19 @@ int main (int argc, char *argv[])
   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);
+  summary_statistic (output, _system_info, max_depth, type_agl, stat_all);
   
   print_message (quiet, stdout, log, f_log, 15, argv[0]);
 // free memory
+  free (_atom_info);
   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]);