Edited documentation

statgen/README

@@ -1,4 +1,4 @@
-statgen - program for analyze molecular dynamic trajectories
+statgen - program that analyzes molecular dynamic trajectories using topological analysis
 Version: 1.0.1
 License: GPL
 

statgen/about.dox

@@ -1,6 +1,13 @@
-/*! @mainpage statgen
+/*! 
+ * @mainpage statgen 
+ * @image latex ./logo.png
  *
  * @section intro_sec Introduction
+ * 
+ * <b>About this program</b>:
+ * <ul>
+ * <li>Program that analyzes molecular dynamic trajectories using topological analysis
+ * </ul>
  *
  * <b>Developer</b>:
  * <ul>

statgen/src/add_main.c

@@ -119,6 +119,7 @@ int printing_head (const char *output, const int log, const int quiet,
   return 0;
 }
 
+
 /**
  * @fn print_message
  */
@@ -139,7 +140,7 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
  * 
  * @return 0              - exit without errors
  */
-{  
+{
   if ((quiet != 1) && (std_output != stderr))
     message (0, mode, str, std_output);
   if (log == 1)

statgen/src/coords.c

@@ -15,9 +15,8 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
 /**
  * @brief function that reads coordinates from special file format
  * @code
- * reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, 
- *                 &num_atoms, true_label_mol, label_mol, type_atoms, 
- *                 coords, ch_type_atoms);
+ * reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms, 
+ *                 true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
  * @endcode
  * 
  * @param mode            mode of reading; '1' is statgen, '2' is envir or 

statgen/src/graph.c

@@ -23,6 +23,7 @@ int check_cycle (const int N, const int *pn)
  */
 {
   int cycle, i;
+  
 /* cycle                  number of cycle
  */
   
@@ -58,6 +59,7 @@ int check_cycle_size (const int N, const int *matrix, const int depth, int *n_cy
  */
 {
   int cur_N, cycle, i, j, k, n, p, *vertex;
+  
 /* cur_N                  current number of elements in submatrix
  * cycle                  if (cycle == 1) that cycle exist
  * n                      number of samples
@@ -147,6 +149,7 @@ int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso
  */
 {
   int depth, i, j, *n_cycle, p, *pn;
+  
 /* depth                  depth of search for check_cycle_size
  * n_cycle                number of cycle
  * p                      current weight

statgen/src/main.c

@@ -18,7 +18,16 @@
 #include "summary_stat.h"
 
 
+/**
+ * @fn main
+ */
 int main (int argc, char *argv[])
+/**
+ * @return 1              - error in error_checking
+ * @return 2              - input file does not exist
+ * @return 3              - memory error
+ * @return 0              - exit without errors
+ */
 {
   char filename[256], tmp_str[2048];
   int error, i, index, j, k, label[2];
@@ -30,6 +39,7 @@ int main (int argc, char *argv[])
   int *agl, *connect, from, *label_atom, *label_mol, log, max_depth, num_atoms, 
       num_mol, *num_mol_agl, num_of_inter, *stat, *stat_all, step, to, 
       *true_label_mol, *type_agl, *type_atoms, type_inter, quiet;
+  
 /* input                  mask of trajectory files
  * logfile                log file name
  * output                 output file name
@@ -232,7 +242,7 @@ int main (int argc, char *argv[])
   if (f_inp == NULL)
   {
     print_message (quiet, stderr, log, f_log, 18, filename);
-    return 1;
+    return 2;
   }
   fscanf (f_inp, "%i", &num_atoms);
   fclose (f_inp);
@@ -260,7 +270,7 @@ int main (int argc, char *argv[])
     (stat_all == NULL))
   {
     print_message (quiet, stderr, log, f_log, 19, argv[0]);
-    return 17;
+    return 3;
   }
 // set type_agl to zero
   for (i=0; i<max_depth+2; i++)
@@ -327,7 +337,7 @@ int main (int argc, char *argv[])
       (stat_all == NULL))
     {
       print_message (quiet, stderr, log, f_log, 19, argv[0]);
-      return 18;
+      return 3;
     }
     print_message (quiet, stdout, log, f_log, 9, argv[0]);
     

statgen/src/stat_print.c

@@ -17,9 +17,9 @@ int printing_agl (const char *input, const char *output, const int *connect,
 /**
  * @brief function that prints aglomerates to output file
  * @code
- * printing_agl (input_file, output_file, number_of_molecules, 
- *          true_label_molecules, num_of_molecules_in_aglomerates, aglomerates, 
- *                                    statistic, max_depth, type_of_aglomerate);
+ * printing_agl (input_file, output_file, number_of_molecules, true_label_molecules, 
+ *               num_of_molecules_in_aglomerates, aglomerates, statistic, max_depth, 
+ *               type_of_aglomerate);
  * @endcode
  * 
  * @param input           input file name
@@ -39,6 +39,7 @@ int printing_agl (const char *input, const char *output, const int *connect,
 {
   int error, i, *iso, j, k, *label_matrix, *matrix;
   FILE *f_out;
+  
 /* iso                    isomorphic graph in database
  * label_matrix           massive of indexes of molecule
  * matrix                 connectivity graph

statgen/src/stat_select.c

@@ -15,8 +15,8 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
 /**
  * @brief function that creates connectivity matrix
  * @code
- * create_matrix (number_of_molecules, number_of_atoms, label_molecule,
- *        type_atoms, coords, number_of_interactions, criteria, connect_matrix);
+ * create_matrix (number_of_molecules, number_of_atoms, label_molecule, type_atoms, 
+ *                coords, number_of_interactions, criteria, connect_matrix);
  * @endcode
  * 
  * @param num_mol         number of molecules
@@ -34,6 +34,7 @@ int create_matrix (const int num_mol, const int num_atoms, const int *label_mol,
 {
   float r;
   int cur_num_inter, i, j, k, l, num_inter, ***label_inter;
+  
 /* r                      radius
  * cur_num_inter          current number of true interactions
  * num_inter              needed number of true interactions

statgen/src/stat_sort.c

@@ -13,8 +13,8 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
 /**
  * @brief function that processes connectivity matrix
  * @code
- * proc_matrix (number_of_molecules, connect_matrix, 
- *  num_of_molecules_in_aglomerates, aglomerates, statistic, summary_statistic);
+ * proc_matrix (number_of_molecules, connect_matrix, num_of_molecules_in_aglomerates, 
+ *              aglomerates, statistic, summary_statistic);
  * @endcode
  * 
  * @param num_mol         number of molecules
@@ -29,6 +29,7 @@ int proc_matrix (const int num_mol, const int *connect, int *num_mol_agl, int *a
  */
 {
   int i, j, k, p, *bin;
+  
   /* p                    weight / graph index
    * bin                  binary massive of labels
    */

statgen/src/summary_stat.c

@@ -14,7 +14,7 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
  * @brief function that prints summary statistic
  * @code
  * summary_statistic (filename, number_of_step, number_of_molecules, max_depth, 
- *                                       type_of_aglomerate, summary_statistic);
+ *                    type_of_aglomerate, summary_statistic);
  * @endcode
  * 
  * @param filename        output file name
@@ -30,6 +30,7 @@ int summary_statistic (const char *filename, const int step, const int num_mol,
   float conc, p, pn, type[2], x, y;
   int i, index;
   FILE *f_out;
+  
 /* conc                   concentrate of aglomerates
  * p                      probability of aglomerates
  * pn                     weight probability of aglomerates

statgen/statgen.doxygen

@@ -38,7 +38,7 @@ PROJECT_NUMBER         = V.1.0.1
 # for a project that appears at the top of each page and should give viewer 
 # a quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "Program for analyze molecular dynamic trajectories"
+PROJECT_BRIEF          = "Program that analyzes molecular dynamic trajectories using topological analysis"
 
 # With the PROJECT_LOGO tag one can specify an logo or icon that is 
 # included in the documentation. The maximum height of the logo should not 
@@ -52,7 +52,7 @@ PROJECT_LOGO           = /home/arcanis/Documents/github/moldyn/statgen/logo.png
 # If a relative path is entered, it will be relative to the location 
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = /home/arcanis/Documents/github/moldyn/statgen/docs
+OUTPUT_DIRECTORY       = ./docs
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
 # 4096 sub-directories (in 2 levels) under the output directory of each output 
@@ -680,7 +680,6 @@ INPUT_ENCODING         = UTF-8
 # *.f90 *.f *.for *.vhd *.vhdl
 
 FILE_PATTERNS          = *.c \
-                         *.h \
                          *.dox
 
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories