Added documentation for statgen

envir/src/CMakeLists.txt

@@ -9,16 +9,16 @@ message (STATUS ${${PROJECT}_VERSION})
 # main files
 set (MAIN_SOURCES main)
 # not public srcs
-set (PRIVATE_CLASSES)
+set (PRIVATE_CLASSES add_main 
+                     coords 
+                     envir_search 
+                     messages 
+                     print_struct 
+                     set_center)
 # headers only files
 SET (HEADERS_ONLY)
 # public srcs
-set (PUBLIC_CLASSES add_main 
-                    coords 
-                    envir_search 
-                    messages 
-                    print_struct 
-                    set_center)
+set (PUBLIC_CLASSES)
 # public headers
 set (PUBLIC_HEADERS)
 # shared libraries

envir/src/add_main.c

@@ -3,7 +3,7 @@
 
 #include <stdio.h>
 
-// #include "messages.h"
+#include "messages.h"
 
 
 int error_checking (const float *cell, const char *input, const char *output)

envir/src/add_main.h

@@ -0,0 +1,8 @@
+#ifndef ADD_MAIN_H
+#define ADD_MAIN_H
+
+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 */

envir/src/coords.c

@@ -15,8 +15,10 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
                     int *num_atoms, int *true_label_mol, int *label_mol, 
                     int *type_atoms, float *coords, char *ch_type_atoms)
 /* filename         - name of file with coordinates
- * type_inter       - type interaction (number of molecules for interaction)
- * label_atom       - types of atom for interaction
+ * type_inter       - type interaction (number of molecules for interaction) 
+ *                    (number of molecules in aglomerate for agl)
+ * label_atom       - types of atom for interaction 
+ *                    (molecules in aglomerate for agl)
  * cell             - cell dimension
  * num_mol          - number of molecules for writing coordinates
  * num_atoms        - number of atoms for writing coordinates
@@ -83,7 +85,7 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
           }
         break;
       case 1:
-//         for envir
+//         for envir and frad
         not_tr_coords[3**num_atoms+0] = cur_coords[0];
         not_tr_coords[3**num_atoms+1] = cur_coords[1];
         not_tr_coords[3**num_atoms+2] = cur_coords[2];
@@ -101,6 +103,29 @@ int reading_coords (const int mode, const char *filename, const int type_inter,
         
         *num_atoms = *num_atoms + 1;
         break;
+      case 2:
+//         for agl
+        for (j=0; j<type_inter; j++)
+          if (cur_mol == label_atom[j])
+          {
+            not_tr_coords[3**num_atoms+0] = cur_coords[0];
+            not_tr_coords[3**num_atoms+1] = cur_coords[1];
+            not_tr_coords[3**num_atoms+2] = cur_coords[2];
+            ch_type_atoms[2**num_atoms+0] = at_symb[0];
+            ch_type_atoms[2**num_atoms+1] = at_symb[1];
+            
+            if (ref_mol != cur_mol)
+            {
+              ref_mol = cur_mol;
+              true_label_mol[*num_mol] = ref_mol;
+              *num_mol = *num_mol + 1;
+            }
+            label_mol[*num_atoms] = *num_mol - 1;
+            type_atoms[*num_atoms] = j;
+            
+            *num_atoms = *num_atoms + 1;
+          }
+        break;
       default: return 1;
     }
   }

envir/src/coords.h

@@ -0,0 +1,8 @@
+#ifndef COORDS_H
+#define COORDS_H
+
+int reading_coords (const int, const char *, const int, const int *, 
+                    const float *, int *, int *, int *, int *, int *, float *, 
+                    char *);
+
+#endif /* COORDS_H */

envir/src/envir_search.c

@@ -22,6 +22,7 @@ int search_envir (const int num_of_mol, const int num_mol, const float *centr_co
   int i;
 /* r                - radius
  */
+  
   *num_needed_mol = 0;
   
   for (i=0; i<8*num_mol; i++)

envir/src/envir_search.h

@@ -0,0 +1,6 @@
+#ifndef ENVIR_SEARCH_H
+#define ENVIR_SEARCH_H
+
+int search_envir (const int, const int, const float *, const double, int *, int *);
+
+#endif /* ENVIR_SEARCH_H */

envir/src/main.c

@@ -3,12 +3,12 @@
 #include <stdlib.h>
 #include <string.h>
 
-// #include "add_main.h"
-// #include "coords.h"
-// #include "envir_search.h"
-// #include "messages.h"
-// #include "print_struct.h"
-// #include "set_center.h"
+#include "add_main.h"
+#include "coords.h"
+#include "envir_search.h"
+#include "messages.h"
+#include "print_struct.h"
+#include "set_center.h"
 
 
 int main(int argc, char *argv[])

envir/src/messages.h

@@ -0,0 +1,6 @@
+#ifndef MESSAGES_H
+#define MESSAGES_H
+
+int message (const int, const int, const char *, FILE *);
+
+#endif /* MESSAGES_H */

envir/src/print_struct.h

@@ -0,0 +1,7 @@
+#ifndef PRINT_STRUCTURE_H
+#define PRINT_STRUCTURE_H
+
+int print_structure (const char *, const int, const int *, const int, const int *, 
+                     const char *, const float *);
+
+#endif /* PRINT_STRUCTURE_H */

envir/src/set_center.h

@@ -0,0 +1,6 @@
+#ifndef SET_CENTER_H
+#define SET_CENTER_H
+
+int set_center (const int, const int, const int *, const float *, float *);
+
+#endif /* SET_CENTER_H */