From 30630ca54106321b6eec2810e7b50538b0dc8c24 Mon Sep 17 00:00:00 2001
From: arcan1s <esalexeev@gmail.com>
Date: Tue, 28 Jan 2014 04:44:30 +0400
Subject: [PATCH] fixed envir and radf

---
 mathmech/agl/src/add_main.c              |   1 +
 mathmech/envir/src/add_main.c            |  60 ++--------
 mathmech/envir/src/add_main.h            |  65 ++++++++++-
 mathmech/envir/src/main.c                |  68 +++++------
 mathmech/mm/include/mathmech/var_types.h |   8 +-
 mathmech/mm/src/radf_proc.c              |   6 +-
 mathmech/radf/src/add_main.c             | 142 +++++------------------
 mathmech/radf/src/add_main.h             |  98 ++++++++++++++--
 mathmech/radf/src/main.c                 | 132 +++++++++------------
 9 files changed, 280 insertions(+), 300 deletions(-)

diff --git a/mathmech/agl/src/add_main.c b/mathmech/agl/src/add_main.c
index 253f4b3..277668e 100644
--- a/mathmech/agl/src/add_main.c
+++ b/mathmech/agl/src/add_main.c
@@ -4,6 +4,7 @@
 
 #include <stdio.h>
 
+#include "add_main.h"
 #include <mathmech/messages.h>
 #include <mathmech/var_types.h>
 
diff --git a/mathmech/envir/src/add_main.c b/mathmech/envir/src/add_main.c
index 2034b81..d375788 100644
--- a/mathmech/envir/src/add_main.c
+++ b/mathmech/envir/src/add_main.c
@@ -4,30 +4,18 @@
 
 #include <stdio.h>
 
+#include "add_main.h"
 #include <mathmech/messages.h>
+#include <mathmech/var_types.h>
 
 
 /**
  * @fn error_checking
  */
-int error_checking (const float *cell, const char *input, const char *output)
-/**
- * @brief function that checks errors in input variables
- * @code
- * error_checking (cell, input, output);
- * @endcode
- * 
- * @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 0              - exit without errors
- */
+int error_checking (const system_info _system_info, const char *input, 
+                    const char *output)
 {
-  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;
@@ -43,21 +31,6 @@ int error_checking (const float *cell, 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);
@@ -71,30 +44,13 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
 /**
  * @fn set_defaults
  */
-int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *output, 
-                  int *quiet, float *rad)
-/**
- * @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 input           mask of trajectory files
- * @param log             status of log-mode
- * @param num_of_mol      number of molecule
- * @param output          output file name
- * @param quiet           status of quiet-mode
- * @param rad             radius of environment sphere
- * 
- * @return 0              - exit without errors
- */
+int set_defaults (system_info *_system_info, char *input, int *log, int *num_of_mol, 
+                  char *output, int *quiet, float *rad)
 {
   int i;
   
   for (i=0; i<3; i++)
-    cell[i] = 0.0;
+    (*_system_info).cell[i] = 0.0;
   input[0] = '#';
   *log = 0;
   *num_of_mol = 1;
diff --git a/mathmech/envir/src/add_main.h b/mathmech/envir/src/add_main.h
index 785a7b3..ca94408 100644
--- a/mathmech/envir/src/add_main.h
+++ b/mathmech/envir/src/add_main.h
@@ -5,18 +5,75 @@
 #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 char *output);
+/**
+ * @brief function that checks errors in input variables
+ * @code
+ * error_checking (_system_info, input, output);
+ * @endcode
+ * 
+ * @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 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 *num_of_mol, 
+                  char *output, int *quiet, float *rad);
+/**
+ * @brief function that sets default values of variables
+ * @code
+ * set_defaults (&_system_info, &from, input, &log, &max_depth, &num_of_inter, output, &to, 
+ *               &type_inter, &quiet);
+ * @endcode
+ * 
+ * @param _system_info    system information structure
+ * @param input           mask of trajectory files
+ * @param log             status of log-mode
+ * @param num_of_mol      number of molecule
+ * @param output          output file name
+ * @param quiet           status of quiet-mode
+ * @param rad             radius of environment sphere
+ * 
+ * @return 0              - exit without errors
+ */
 
-int error_checking (const float *, const char *, const char *);
-int print_message (const int, FILE *, const int, FILE *, const int, const char *);
-int set_defaults (float *, char *, int *, int *, char *, int *, float *);
 
-#endif /* ADD_MAIN_H */
\ No newline at end of file
+#endif /* ADD_MAIN_H */
diff --git a/mathmech/envir/src/main.c b/mathmech/envir/src/main.c
index abca909..4ad4095 100644
--- a/mathmech/envir/src/main.c
+++ b/mathmech/envir/src/main.c
@@ -14,6 +14,7 @@
 #include <mathmech/messages.h>
 #include <mathmech/print_struct.h>
 #include <mathmech/set_center.h>
+#include <mathmech/var_types.h>
 
 
 /**
@@ -32,33 +33,31 @@ int main(int argc, char *argv[])
   int error, i, *tmp_int;
   FILE *f_inp, *f_log;
   
-  char *ch_type_atoms, input[256], logfile[256], output[256];
-  float cell[3], *centr_coords, *coords, rad;
-  int *label_mol, log, num_atoms, num_mol, num_needed_mol, num_of_mol, 
-      *needed_mol, quiet, *true_label_mol;
+  char input[256], logfile[256], output[256];
+  float *centr_coords, rad;
+  int log, num_needed_mol, num_of_mol, *needed_mol, quiet, *true_label_mol;
+  atom_info *_atom_info;
+  system_info _system_info;
   
-/* ch_type_atoms          massive of char atom types
- * input                  input file name
+/* 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
  * rad                    radius of environment sphere
  * 
- * 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
  * num_of_mol             number of molecule
  * 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 file
+ * _system_info           system information file
  */
   
-  set_defaults (cell, input, &log, &num_of_mol, output, &quiet, &rad);
+  set_defaults (&_system_info, input, &log, &num_of_mol, output, &quiet, &rad);
   
   for (i=1; i<argc; i++)
   {
@@ -93,7 +92,7 @@ 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'))
@@ -140,7 +139,7 @@ int main(int argc, char *argv[])
   print_message (quiet, stdout, log, f_log, 1, argv[0]);
   
 // error check
-  error = error_checking (cell, input, output);
+  error = error_checking (_system_info, input, output);
   if (error != 0)
   {
     print_message (quiet, stderr, log, f_log, 17, argv[0]);
@@ -158,17 +157,13 @@ 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));
-  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));
+  tmp_int = (int *) malloc (8 * _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) || 
      (tmp_int == NULL) || 
      (true_label_mol == NULL))
   {
@@ -177,8 +172,9 @@ int main(int argc, char *argv[])
   }
   sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n\
 %6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cSelect molecule: %i;\n\
-%6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0], 
-           cell[1], cell[2], ' ' , num_of_mol, ' ', rad);
+%6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', 
+_system_info.cell[0], _system_info.cell[1], _system_info.cell[2], ' ' , num_of_mol, 
+' ', rad);
   print_message (quiet, stdout, log, f_log, 5, tmp_str);
   
   print_message (quiet, stdout, log, f_log, 6, argv[0]);
@@ -186,14 +182,14 @@ 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[0], tmp_int, 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));
-  needed_mol = (int *) malloc (num_mol * sizeof (int));
+  error = reading_coords (0, input, tmp_int[0], tmp_int, &_system_info, true_label_mol, 
+                          _atom_info);
+  centr_coords = (float *) malloc (3 * 8 * _system_info.num_mol * sizeof (float));
+  needed_mol = (int *) malloc (_system_info.num_mol * sizeof (int));
   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 checking
@@ -208,21 +204,21 @@ int main(int argc, char *argv[])
   if (error == 0)
   {
     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)
   {
     print_message (quiet, stderr, log, f_log, 20, argv[0]);
     error = 1;
-    error = search_envir (num_of_mol, num_mol, centr_coords, rad, needed_mol, 
+    error = search_envir (num_of_mol, _system_info, centr_coords, rad, needed_mol, 
                           &num_needed_mol);
   }
   if (error == 0)
   {
     print_message (quiet, stderr, log, f_log, 21, 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);
@@ -231,10 +227,8 @@ 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);
diff --git a/mathmech/mm/include/mathmech/var_types.h b/mathmech/mm/include/mathmech/var_types.h
index c211ea2..3c9dacf 100644
--- a/mathmech/mm/include/mathmech/var_types.h
+++ b/mathmech/mm/include/mathmech/var_types.h
@@ -53,16 +53,16 @@ typedef struct
  */
 typedef struct
 {
-  int first;
-  int last;
+  int from;
+  int to;
   float cell[3];
   int num_atoms;
   int num_mol;
 } system_info;
 /**
  * @brief system information structure
- * @var first             last trajectory step
- * @var last              first trajectory step
+ * @var from              last trajectory step
+ * @var to                first trajectory step
  * @var cell              cell size
  * @var num_atoms         number of atoms
  * @var num_mol           number of molecules
diff --git a/mathmech/mm/src/radf_proc.c b/mathmech/mm/src/radf_proc.c
index 23a7509..7f5d381 100644
--- a/mathmech/mm/src/radf_proc.c
+++ b/mathmech/mm/src/radf_proc.c
@@ -49,7 +49,7 @@ int print_result (const char *output, const int matrix, const int mode,
         r = _radf_info.r_min + (0.5 + i) * _radf_info.r_step;
         dv = 4 * M_PI * pow (r, 2) * _radf_info.r_step;
         ro = _system_info.num_atoms  / (2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
-        norm = radf[i] / (dv * ro * _system_info.num_atoms * (_system_info.last - _system_info.first + 1));
+        norm = radf[i] / (dv * ro * _system_info.num_atoms * (_system_info.to - _system_info.from + 1));
         if (matrix == 0)
           fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
         else
@@ -66,7 +66,7 @@ int print_result (const char *output, const int matrix, const int mode,
         r = _radf_info.r_min + (0.5 + i) * _radf_info.r_step;
         dv = 4 * M_PI * pow (r, 2) * _radf_info.r_step;
         ro = _system_info.num_atoms  / (3 * 2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
-        norm = radf[i] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.last - _system_info.first + 1));
+        norm = radf[i] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.to - _system_info.from + 1));
         if (matrix == 0)
           fprintf (f_out, " %9.4f %10.4e %9i %9.6f \n", r, dv, radf[i] / 2, norm);
         else
@@ -96,7 +96,7 @@ int print_result (const char *output, const int matrix, const int mode,
           ang = _radf_info.ang_min + (0.5 + j) * _radf_info.ang_step;
           dv = 4 * M_PI * pow (r, 2) * sin (M_PI * ang / 180) * _radf_info.r_step * (M_PI * _radf_info.ang_step / 180);
           ro = _system_info.num_atoms  / (3 * 2 * _system_info.cell[0] * _system_info.cell[1] * _system_info.cell[2]);
-          norm = radf[n*i+j] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.last - _system_info.first + 1));
+          norm = radf[n*i+j] / (dv * ro * _system_info.num_atoms / 3 * (_system_info.to - _system_info.from + 1));
           if (matrix == 0)
             fprintf (f_out, " %9.4f %9.2f %10.4e %9i %9.6f \n", r, ang, dv, radf[n*i+j] / 2, norm);
           else
diff --git a/mathmech/radf/src/add_main.c b/mathmech/radf/src/add_main.c
index 4b04d44..0ae024d 100644
--- a/mathmech/radf/src/add_main.c
+++ b/mathmech/radf/src/add_main.c
@@ -4,46 +4,25 @@
 
 #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, 
-                    const int num_needed_at, const int *needed_at, 
-                    const char *output, const int to)
-/**
- * @brief function that checks errors in input variables
- * @code
- * error_checking (cell, from, input, num_needed_at, needed_at, output, to);
- * @endcode
- * 
- * @param cell            massive of cell size
- * @param from            first trajectory step
- * @param input           input file name
- * @param num_needed_at   number of needed atom types
- * @param needed_at       massive of number of needed atom types
- * @param output          output file name
- * @param to              last trajectory step
- * 
- * @return 11             - error in 'cell'
- * @return 12             - error in 'input'
- * @return 13             - error in 'output'
- * @return 14             - error in 'from' or 'to'
- * @return 15             - error in 'num_needed_at'
- * @return 16             - error in 'needed_at'
- * @return 0              - exit without errors
- */
+int error_checking (const char *input, const int num_needed_at, const int *needed_at, 
+                    const char *output, const system_info _system_info)
 {
-  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;
   if (output[0] == '#')
     return 13;
-  if ((from == -1) || (to == -1))
+  if ((_system_info.from == -1) || (_system_info.to == -1))
     return 14;
   if ((num_needed_at != 2) && (num_needed_at != 6))
     return 15;
@@ -65,21 +44,6 @@ int error_checking (const float *cell, const int from, 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);
@@ -94,36 +58,8 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
  * @fn printing_head
  */
 int printing_head (const char *output, const int log, const int quiet, const int matrix, 
-                   const char *input, const int from, const int to, const float *cell, 
-                   const int mode, const double r_min, const double r_max, 
-                   const double r_step, const double ang_min, const double ang_max, 
-                   const double ang_step, const int *needed_at)
-/**
- * @brief function that prints header in output file
- * @code
- * printing_head (output, log, quiet, matrix, input, from, to, cell, mode, r_min, 
- *                r_max, r_step, ang_min, ang_max, ang_step, needed_at);
- * @endcode
- * 
- * @param output          output file nams
- * @param log             status of log-mode
- * @param quiet           status of quiet-mode
- * @param matrix          status of matrix-mode
- * @param input           mask of trajectory files
- * @param from            first trajectory step
- * @param to              last trajectory step
- * @param cell            massive of cell size
- * @param mode            0 - if RDF, 1 - if RDF for center mass, 2 - if RADF
- * @param r_max           maximal radius
- * @param r_min           minimal radius
- * @param r_step          radius step
- * @param ang_max         maximal angle for RADF
- * @param ang_min         minimal angle for RADF
- * @param ang_step        anlge step for RADF
- * @param needed_at       massive of number of needed atom types
- * 
- * @return 0              - exit without errors
- */
+                   const char *input, const system_info _system_info, const int mode, 
+                   const radf_info _radf_info, const int *needed_at)
 {
   FILE *f_out;
   
@@ -132,10 +68,13 @@ int printing_head (const char *output, const int log, const int quiet, const int
   fprintf (f_out, "CONFIGURATION\n");
   
   fprintf (f_out, "LOG=%i\nQUIET=%i\nMATRIX=%i\n", log, quiet, matrix);
-  fprintf (f_out, "MASK=%s\nFIRST=%i\nLAST=%i\n", input, from, to);
-  fprintf (f_out, "CELL=%.4f,%.4f,%.4f\n", cell[0], cell[1], cell[2]);
+  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", _system_info.cell[0], _system_info.cell[1], 
+           _system_info.cell[2]);
   fprintf (f_out, "MODE=%i\n", mode);
-  fprintf (f_out, "R_MIN=%.3f\nR_MAX=%.3f\nR_STEP=%.3f\n", r_min, r_max, r_step);
+  fprintf (f_out, "R_MIN=%.3f\nR_MAX=%.3f\nR_STEP=%.3f\n", _radf_info.r_min, 
+           _radf_info.r_max, _radf_info.r_step);
   switch (mode)
   {
     case 0:
@@ -143,12 +82,12 @@ int printing_head (const char *output, const int log, const int quiet, const int
       break;
     case 1:
       fprintf (f_out, "ATOM=%i,%i,%i-%i,%i,%i\n", needed_at[0], needed_at[1], 
-needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
+               needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
       break;
     case 2:
       fprintf (f_out, "ANG_MIN=%.2f\nANG_MAX=%.2f\nANG_STEP=%.2f\n\
-ATOM=%i,%i,%i-%i,%i,%i\n",ang_min, ang_max, ang_step, needed_at[0], needed_at[1], 
-needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
+ATOM=%i,%i,%i-%i,%i,%i\n", _radf_info.ang_min, _radf_info.ang_max, _radf_info.ang_step, 
+needed_at[0], needed_at[1], needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
       break;
   }
   
@@ -162,50 +101,25 @@ needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
 /**
  * @fn set_defaults
  */
-int set_defaults (float *ang_max, float *ang_min, float *ang_step, float *cell, 
-                  int *from, char *input, int *log, int *matrix, float *r_max, 
-                  float *r_min, float *r_step, char *output, int *to, int *quiet)
-/**
- * @brief function that sets default values of variables
- * @code
- * set_defaults (&ang_max, &ang_min, &ang_step, cell, &from, input, &log, &r_max, 
- *               &r_min, &r_step, output, &to, &quiet);
- * @endcode
- * 
- * @param ang_max         maximal angle for RADF
- * @param ang_min         minimal angle for RADF
- * @param ang_step        angle step
- * @param cell            massive of cell size
- * @param from            first trajectory step
- * @param input           mask of trajectory files
- * @param log             status of log-mode
- * @param matrix          status of matrix-mode
- * @param r_max           maximal radius
- * @param r_min           minimal radius
- * @param r_step          radius step
- * @param output          output file name
- * @param to              last trajectory step
- * @param quiet           status of quiet-mode
- * 
- * @return 0              - exit without errors
- */
+int set_defaults (system_info *_system_info, radf_info *_radf_info, char *input, 
+                  int *log, int *matrix, char *output, int *quiet)
 {
   int i;
   
-  *ang_max = 90.0;
-  *ang_min = 0.0;
-  *ang_step = 0.0;
+  (*_radf_info).ang_max = 90.0;
+  (*_radf_info).ang_min = 0.0;
+  (*_radf_info).ang_step = 0.0;
   for (i=0; i<3; i++)
-    cell[i] = 0.0;
-  *from = -1;
+    (*_system_info).cell[i] = 0.0;
+  (*_system_info).from = -1;
   input[0] = '#';
   *log = 0;
   *matrix = 0;
-  *r_max = 15.0;
-  *r_min = 2.0;
-  *r_step = 0.2;
+  (*_radf_info).r_max = 15.0;
+  (*_radf_info).r_min = 2.0;
+  (*_radf_info).r_step = 0.2;
   output[0] = '#';
-  *to = -1;
+  (*_system_info).to = -1;
   *quiet = 0;
   
   return 0;
diff --git a/mathmech/radf/src/add_main.h b/mathmech/radf/src/add_main.h
index d604cda..3077d1b 100644
--- a/mathmech/radf/src/add_main.h
+++ b/mathmech/radf/src/add_main.h
@@ -5,27 +5,105 @@
 #ifndef ADD_MAIN_H
 #define ADD_MAIN_H
 
+#include <mathmech/var_types.h>
+
+
 /**
  * @fn error_checking
  */
+int error_checking (const char *input, const int num_needed_at, const int *needed_at, 
+                    const char *output, const system_info _system_info);
+/**
+ * @brief function that checks errors in input variables
+ * @code
+ * error_checking (input, num_needed_at, needed_at, output, _system_info);
+ * @endcode
+ * 
+ * @param input           input file name
+ * @param num_needed_at   number of needed atom types
+ * @param needed_at       massive of number of needed atom types
+ * @param output          output file name
+ * @param _system_info    system information structure
+ * 
+ * @return 11             - error in 'cell'
+ * @return 12             - error in 'input'
+ * @return 13             - error in 'output'
+ * @return 14             - error in 'from' or 'to'
+ * @return 15             - error in 'num_needed_at'
+ * @return 16             - error in 'needed_at'
+ * @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 printing_head
  */
+int printing_head (const char *output, const int log, const int quiet, const int matrix, 
+                   const char *input, const system_info _system_info, const int mode, 
+                   const radf_info _radf_info, const int *needed_at);
+/**
+ * @brief function that prints header in output file
+ * @code
+ * printing_head (output, log, quiet, matrix, input, _system_info, mode, _radf_info, 
+ *                needed_at);
+ * @endcode
+ * 
+ * @param output          output file nams
+ * @param log             status of log-mode
+ * @param quiet           status of quiet-mode
+ * @param matrix          status of matrix-mode
+ * @param input           mask of trajectory files
+ * @param _system_info    system information structure
+ * @param mode            0 - if RDF, 1 - if RDF for center mass, 2 - if RADF
+ * @param _radf_info      radf information structure
+ * @param needed_at       massive of number of needed atom types
+ * 
+ * @return 0              - exit without errors
+ */
+
+
 /**
  * @fn set_defaults
  */
+int set_defaults (system_info *_system_info, radf_info *_radf_info, char *input, 
+                  int *log, int *matrix, char *output, int *quiet);
+/**
+ * @brief function that sets default values of variables
+ * @code
+ * set_defaults (&_system_info, &_radf_info, input, &log, &matrix, output, &quiet);
+ * @endcode
+ * 
+ * @param _system_info    system information structure
+ * @param _radf_info      radf 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 float *, const int, const char *, const int, const int *, 
-                    const char *, const int);
-int print_message (const int, FILE *, const int, FILE *, const int, const char *);
-int printing_head (const char *, const int, const int, const int, const char *, 
-                   const int, const int, const float *, const int, const double, 
-                   const double, const double, const double, const double, const double, 
-                   const int *);
-int set_defaults (float *, float *, float *, float *, int *, char *, int *, int *,
-                  float *, float *, float *, char *, int *, int *);
 
-#endif /* ADD_MAIN_H */
\ No newline at end of file
+#endif /* ADD_MAIN_H */
diff --git a/mathmech/radf/src/main.c b/mathmech/radf/src/main.c
index 313a350..1cf96f3 100644
--- a/mathmech/radf/src/main.c
+++ b/mathmech/radf/src/main.c
@@ -13,6 +13,7 @@
 #include <mathmech/messages.h>
 #include <mathmech/radf.h>
 #include <mathmech/radf_proc.h>
+#include <mathmech/var_types.h>
 
 
 /**
@@ -32,42 +33,30 @@ int main(int argc, char *argv[])
   FILE *f_inp, *f_log;
   
   char input[256], logfile[256], output[256];
-  float ang_max, ang_min, ang_step, cell[3], *coords, r_max, r_min, r_step;
-  int from, *label_mol, log, matrix, mode, num_atoms, num_mol, num_needed_at, 
-      needed_at[6], quiet, *radf, step, to, *true_label_mol, *type_atoms;
+  int log, matrix, mode, num_needed_at, needed_at[6], quiet, *radf, *true_label_mol;
+  atom_info *_atom_info;
+  radf_info _radf_info;
+  system_info _system_info;
   
 /* input                  input file name
  * logfile                log file name
  * output                 output file name
  * 
- * ang_max                maximal angle for RADF
- * ang_min                minimal angle for RADF
- * ang_step               anlge step for RADF
- * cell                   massive of cell size
- * coords                 massive of coordinates
- * r_max                  maximal radius
- * r_min                  minimal radius
- * r_step                 radius step
- * 
- * from                   first trajectory step
- * label_mol              massive of numbers of molecule for atoms
  * log                    status of log-mode
  * matrix                 status of matrix-mode
  * mode                   0 - if RDF, 1 - if RDF for center mass, 2 - if RADF
- * num_atoms              number of atoms
- * num_mol                number of molecules
  * num_needed_at          number of needed atom types
  * needed_at              massive of number of needed atom types
  * quiet                  status of quiet-mode
  * radf                   not normed RADF
- * step                   $(to - from + 1)
- * to                     last trajectory step
  * true_label_mol         massive of true numbers of molecule for atoms
- * type_atoms             massive of atom types
+ * 
+ * _atom_info             atom information structure
+ * _radf_info             radf information structure
+ * _system_info           system information structure
  */
   
-  set_defaults (&ang_max, &ang_min, &ang_step, cell, &from, input, &log, &matrix, 
-                &r_max, &r_min, &r_step, output, &to, &quiet);
+  set_defaults (&_system_info, &_radf_info, input, &log, &matrix, output, &quiet);
   
   for (i=1; i<argc; i++)
   {
@@ -110,20 +99,19 @@ 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);
-      if (from > to)
+      sscanf (argv[i+1], "%i,%i", &_system_info.from, &_system_info.to);
+      if (_system_info.from > _system_info.to)
       {
-        to += from;
-        from = to - from;
-        to -= from;
+        _system_info.to += _system_info.from;
+        _system_info.from = _system_info.to - _system_info.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] == 't') && (argv[i][3] == '\0'))
@@ -149,37 +137,37 @@ int main(int argc, char *argv[])
     else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == '\0'))
 // radii
     {
-      sscanf (argv[i+1], "%f,%f", &r_min, &r_max);
-      if (r_min > r_max)
+      sscanf (argv[i+1], "%f,%f", &_radf_info.r_min, &_radf_info.r_max);
+      if (_radf_info.r_min > _radf_info.r_max)
       {
-        r_min += r_max;
-        r_max = r_min - r_max;
-        r_min -= r_max;
+        _radf_info.r_min += _radf_info.r_max;
+        _radf_info.r_max = _radf_info.r_min - _radf_info.r_max;
+        _radf_info.r_min -= _radf_info.r_max;
       }
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'r') && (argv[i][2] == 's') && (argv[i][3] == '\0'))
 // radius step
     {
-      sscanf (argv[i+1], "%f", &r_step);
+      sscanf (argv[i+1], "%f", &_radf_info.r_step);
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == '\0'))
 // angles
     {
-      sscanf (argv[i+1], "%f,%f", &ang_min, &ang_max);
-      if (ang_min > ang_max)
+      sscanf (argv[i+1], "%f,%f", &_radf_info.ang_min, &_radf_info.ang_max);
+      if (_radf_info.ang_min > _radf_info.ang_max)
       {
-        ang_min += ang_max;
-        ang_max = ang_min - ang_max;
-        ang_min -= ang_max;
+        _radf_info.ang_min += _radf_info.ang_max;
+        _radf_info.ang_max = _radf_info.ang_min - _radf_info.ang_max;
+        _radf_info.ang_min -= _radf_info.ang_max;
       }
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'a') && (argv[i][2] == 's') && (argv[i][3] == '\0'))
 // angle step
     {
-      sscanf (argv[i+1], "%f", &ang_step);
+      sscanf (argv[i+1], "%f", &_radf_info.ang_step);
       i++;
     }
     else if ((argv[i][0] == '-') && (argv[i][1] == 'm') && (argv[i][2] == '\0'))
@@ -213,7 +201,7 @@ int main(int argc, char *argv[])
   print_message (quiet, stdout, log, f_log, 1, argv[0]);
   
 // error check
-  error = error_checking (cell, from, input, num_needed_at, needed_at, output, to);
+  error = error_checking (input, num_needed_at, needed_at, output, _system_info);
   if (error != 0)
   {
     print_message (quiet, stderr, log, f_log, 17, argv[0]);
@@ -225,14 +213,14 @@ int main(int argc, char *argv[])
 // processing
 // initial variables
 // set mode
-  if ((num_needed_at == 6) && (ang_step != 0.0))
+  if ((num_needed_at == 6) && (_radf_info.ang_step != 0.0))
     mode = 2;
   else if (num_needed_at == 6)
     mode = 1;
   else if (num_needed_at == 2)
     mode = 0;
   
-  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)
@@ -240,29 +228,25 @@ 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 (2 * 3 * 8 * num_atoms * sizeof (float));
-  label_mol = (int *) malloc (2 * 8 * num_atoms * sizeof (int));
+  _atom_info = (atom_info *) malloc (8 * _system_info.num_atoms * sizeof (atom_info));
   if (mode == 2)
   {
-    i = (r_max - r_min) / r_step;
-    j = (ang_max - ang_min) / ang_step;
+    i = (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
+    j = (_radf_info.ang_max - _radf_info.ang_min) / _radf_info.ang_step;
     i *= j;
   }
   else
-    i = (r_max - r_min) / r_step;
+    i = (_radf_info.r_max - _radf_info.r_min) / _radf_info.r_step;
   radf = (int *) malloc (i * sizeof (int));
   for (j=0; j<i; j++)
     radf[j] = 0;
-  true_label_mol = (int *) malloc (num_atoms * sizeof (int));
-  type_atoms = (int *) malloc (2 * 8 * num_atoms * sizeof (int));
+  true_label_mol = (int *) malloc (_system_info.num_atoms * sizeof (int));
 // error checking
-  if ((coords == NULL) || 
-     (label_mol == NULL) || 
+  if ((_atom_info == NULL) || 
      (radf == NULL) || 
-     (true_label_mol == NULL) || 
-     (type_atoms == NULL))
+     (true_label_mol == NULL))
   {
     print_message (quiet, stderr, log, f_log, 19, argv[0]);
     return 3;
@@ -270,7 +254,9 @@ int main(int argc, char *argv[])
   sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cMatrix mode: %i;\n\
 %6cMask: %s;\n%6cFirst step: %i;\n%6cLast step: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cMode: %i;\n\
 %6cR_MIN: %6.3f; R_MAX: %6.3f; R_STEP: %6.3f;\n", ' ', output, ' ', log, ' ', quiet, ' ', matrix, 
-' ', input, ' ', from, ' ', to, ' ', cell[0], cell[1], cell[2], ' ', mode, ' ', r_min, r_max, r_step);
+' ', input, ' ', _system_info.from, ' ', _system_info.to, ' ', _system_info.cell[0], 
+_system_info.cell[1], _system_info.cell[2], ' ', mode, ' ', _radf_info.r_min, 
+_radf_info.r_max, _radf_info.r_step);
   switch (mode)
   {
     case 0:
@@ -282,44 +268,41 @@ needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
       break;
     case 2:
       sprintf (tmp_str, "%s%6cANG_MIN: %6.2f; ANG_MAX: %6.2f; ANG_STEP: %6.2f;\n\
-%6cATOM TYPES: %i,%i,%i-%i,%i,%i\n", tmp_str, ' ', ang_min, ang_max, ang_step, ' ', needed_at[0], 
-needed_at[1], needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
+%6cATOM TYPES: %i,%i,%i-%i,%i,%i\n", tmp_str, ' ', _radf_info.ang_min, _radf_info.ang_max, 
+_radf_info.ang_step, ' ', needed_at[0], needed_at[1], needed_at[2], needed_at[3], 
+needed_at[4], needed_at[5]);
       break;
   }
   print_message (quiet, stdout, log, f_log, 5, tmp_str);
   
 // head
-  printing_head (output, log, quiet, matrix, input, from, to, cell, mode, r_min, 
-                 r_max, r_step, ang_min, ang_max, ang_step, needed_at);
+  printing_head (output, log, quiet, matrix, input, _system_info, mode, _radf_info, 
+                 needed_at);
   
   print_message (quiet, stdout, log, f_log, 6, argv[0]);
 // main cycle
-  for (i=from; i<to+1; i++)
+  for (i=_system_info.from; i<_system_info.to+1; i++)
   {
     sprintf (filename, "%s.%03i", input, i);
     print_message (quiet, stdout, log, f_log, 7, filename);
-    error = reading_coords (0, filename, num_needed_at, needed_at, cell, &num_mol, 
-                            &num_atoms, true_label_mol, label_mol, type_atoms, 
-                            coords, tmp_str);
+    error = reading_coords (0, filename, num_needed_at, needed_at, &_system_info, 
+                            true_label_mol, _atom_info);
     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;
       switch (mode)
       {
         case 0:
-          error = search_rdf (num_atoms, type_atoms, label_mol, coords, r_min, 
-                              r_max, r_step, radf);
+          error = search_rdf (_system_info, _atom_info, _radf_info, radf);
           break;
         case 1:
-          error = search_rdf_centr (num_atoms, type_atoms, label_mol, coords, r_min, 
-                                    r_max, r_step, radf);
+          error = search_rdf_centr (_system_info, _atom_info, _radf_info, radf);
           if (error == 0)
         case 2:
-          error = search_radf (num_atoms, type_atoms, label_mol, coords, r_min, r_max, 
-                               r_step, ang_min, ang_max, ang_step, radf);
+          error = search_radf (_system_info, _atom_info, _radf_info, radf);
           break;
       }
     }
@@ -330,15 +313,12 @@ needed_at[1], needed_at[2], needed_at[3], needed_at[4], needed_at[5]);
   print_message (quiet, stdout, log, f_log, 13, argv[0]);
   print_message (quiet, stdout, log, f_log, 14, output);
 // tail
-  print_result (output, matrix, mode, step, num_atoms, r_min, r_max, r_step, ang_min, 
-                ang_max, ang_step, cell, radf);
+  print_result (output, matrix, mode, _system_info, _radf_info, radf);
   
   print_message (quiet, stdout, log, f_log, 15, argv[0]);
 // free memory
-  free (coords);
-  free (label_mol);
+  free (_atom_info);
   free (radf);
-  free (type_atoms);
   free (true_label_mol);
   
   print_message (quiet, stdout, log, f_log, 16, argv[0]);