From 0714cb654176e2716704a5d766ff8a66b8ffe4a4 Mon Sep 17 00:00:00 2001
From: arcan1s <esalexeev@gmail.com>
Date: Tue, 28 Jan 2014 03:45:36 +0400
Subject: [PATCH] fixed agl

---
 mathmech/agl/src/add_main.c | 57 +++--------------------------
 mathmech/agl/src/add_main.h | 73 +++++++++++++++++++++++++++++++++++--
 mathmech/agl/src/main.c     | 67 +++++++++++++++-------------------
 3 files changed, 104 insertions(+), 93 deletions(-)

diff --git a/mathmech/agl/src/add_main.c b/mathmech/agl/src/add_main.c
index 5f3c9f5..253f4b3 100644
--- a/mathmech/agl/src/add_main.c
+++ b/mathmech/agl/src/add_main.c
@@ -5,32 +5,16 @@
 #include <stdio.h>
 
 #include <mathmech/messages.h>
+#include <mathmech/var_types.h>
 
 
 /**
  * @fn error_checking
  */
-int error_checking (const char *aglinp, const float *cell, const char *input, 
+int error_checking (const char *aglinp, const system_info _system_info, const char *input, 
                     const char *output)
-/**
- * @brief function that checks errors in input variables
- * @code
- * error_checking (aglinp, cell, input, output);
- * @endcode
- * 
- * @param aglinp          agglomerate file name
- * @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 14             - error in 'aglinp'
- * @return 0              - exit without errors
- */
 {
-  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;
@@ -48,21 +32,6 @@ int error_checking (const char *aglinp, const float *cell, 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);
@@ -76,28 +45,14 @@ int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log
 /**
  * @fn set_defaults
  */
-int set_defaults (char *aglinp, float *cell, char *input, int *log, char *output, int *quiet)
-/**
- * @brief function that sets default values of variables
- * @code
- * set_defaults (aglinp, cell, input, &log, output, &quiet);
- * @endcode
- * 
- * @param aglinp          agglomerate file name
- * @param cell            massive of cell size
- * @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 set_defaults (char *aglinp, system_info *_system_info, char *input, int *log, 
+                  char *output, int *quiet)
 {
   int i;
   
   aglinp[0] = '#';
   for (i=0; i<3; i++)
-    cell[i] = 0.0;
+    (*_system_info).cell[i] = 0.0;
   input[0] = '#';
   *log = 0;
   output[0] = '#';
diff --git a/mathmech/agl/src/add_main.h b/mathmech/agl/src/add_main.h
index ba8e3ec..e016db5 100644
--- a/mathmech/agl/src/add_main.h
+++ b/mathmech/agl/src/add_main.h
@@ -5,18 +5,83 @@
 #ifndef ADD_MAIN_H
 #define ADD_MAIN_H
 
+
+/**
+ * @file
+ */
+
+#include <stdio.h>
+
+#include <mathmech/messages.h>
+#include <mathmech/var_types.h>
+
+
 /**
  * @fn error_checking
  */
+int error_checking (const char *aglinp, const system_info _system_info, 
+                    const char *input, const char *output);
+/**
+ * @brief function that checks errors in input variables
+ * @code
+ * error_checking (aglinp, _system_info, input, output);
+ * @endcode
+ * 
+ * @param aglinp          agglomerate file name
+ * @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 14             - error in 'aglinp'
+ * @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 *aglinp, system_info *_system_info, char *input, int *log, char *output, 
+                  int *quiet);
+/**
+ * @brief function that sets default values of variables
+ * @code
+ * set_defaults (aglinp, &_system_info, input, &log, output, &quiet);
+ * @endcode
+ * 
+ * @param aglinp          agglomerate file name
+ * @param _system_info    system 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 char *, const float *, const char *, const char *);
-int print_message (const int, FILE *, const int, FILE *, const int, const char *);
-int set_defaults (char *, float *, char *, int *, char *, int *);
 
-#endif /* ADD_MAIN_H */
\ No newline at end of file
+#endif /* ADD_MAIN_H */
diff --git a/mathmech/agl/src/main.c b/mathmech/agl/src/main.c
index 4039f7f..580c13e 100644
--- a/mathmech/agl/src/main.c
+++ b/mathmech/agl/src/main.c
@@ -15,6 +15,7 @@
 #include <mathmech/read_agl.h>
 #include <mathmech/select_mol.h>
 #include <mathmech/set_center.h>
+#include <mathmech/var_types.h>
 
 
 /**
@@ -30,35 +31,33 @@ int main(int argc, char *argv[])
  */
 {
   char tmp_str[2048];
-  int error, i, *tmp_int;
+  int error, i;
   FILE *f_inp, *f_log;
   
-  char aglinp[256], *ch_type_atoms, input[256], logfile[256], output[256];
-  float cell[3], *centr_coords, *coords;
-  int *label_mol, log, num_atoms, num_mol, num_needed_mol, *needed_mol, quiet, 
-      *true_label_mol;
+  char aglinp[256], input[256], logfile[256], output[256];
+  float *centr_coords;
+  int log, num_needed_mol, *needed_mol, quiet, *true_label_mol;
+  atom_info *_atom_info;
+  system_info _system_info;
   
 /* aglinp                 agglomerate file name
- * ch_type_atoms          massive of char atom types
  * 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
  * 
- * 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
  * 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 structure
+ * _system_info           system information structure
  */
   
-  set_defaults (aglinp, cell, input, &log, output, &quiet);
+  set_defaults (aglinp, &_system_info, input, &log, output, &quiet);
   
   for (i=1; i<argc; i++)
   {
@@ -97,7 +96,8 @@ 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'))
@@ -132,7 +132,7 @@ int main(int argc, char *argv[])
   print_message (quiet, stdout, log, f_log, 1, argv[0]);
   
 // error check
-  error = error_checking (aglinp, cell, input, output);
+  error = error_checking (aglinp, _system_info, input, output);
   if (error != 0)
   {
     print_message (quiet, stderr, log, f_log, 17, argv[0]);
@@ -150,20 +150,14 @@ 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));
-  needed_mol = (int *) malloc (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));
+  needed_mol = (int *) malloc (_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) ||
      (needed_mol == NULL) || 
-     (tmp_int == NULL) || 
      (true_label_mol == NULL))
   {
     print_message (quiet, stderr, log, f_log, 19, argv[0]);
@@ -171,7 +165,8 @@ int main(int argc, char *argv[])
   }
   sprintf (tmp_str, "%6cAglomerate file: '%s';\n%6cInput file: '%s';\n\
 %6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f\n", 
-' ', aglinp, ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0], cell[1], cell[2]);
+' ', aglinp, ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', _system_info.cell[0], 
+_system_info.cell[1], _system_info.cell[2]);
   print_message (quiet, stdout, log, f_log, 5, tmp_str);
   
   print_message (quiet, stdout, log, f_log, 6, argv[0]);
@@ -187,10 +182,9 @@ int main(int argc, char *argv[])
 // reading coordinates
     print_message (quiet, stdout, log, f_log, 7, input);
     error = 1;
-    error = reading_coords (2, input, num_needed_mol, needed_mol, 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));
+    error = reading_coords (2, input, num_needed_mol, needed_mol, &_system_info, 
+                            true_label_mol, _atom_info);
+    centr_coords = (float *) malloc (3 * 8 * _system_info.num_mol * sizeof (float));
     if (centr_coords == NULL)
     {
       print_message (quiet, stderr, log, f_log, 19, argv[0]);
@@ -202,10 +196,10 @@ int main(int argc, char *argv[])
   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;
-    error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
+    error = set_center (_system_info, _atom_info, centr_coords);
   }
   if (error == 0)
   {
@@ -217,8 +211,8 @@ int main(int argc, char *argv[])
   {
     print_message (quiet, stderr, log, f_log, 4, 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);
@@ -227,12 +221,9 @@ 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);
   
   print_message (quiet, stdout, log, f_log, 16, argv[0]);