Prerelease statgen 1.0.1

stat/input_stat.dat

@@ -1,9 +0,0 @@
-Mask:	meth
-Trajectory step:	1	3	(first; last)
-Cell dimention:	24.42	24.40	24.49	(a; b; c)
-Parametr:	2	(0 - gen.stat; 1 - gen.stat and bonds length; 2 - gen.stat and bonds length and form of agl; 3 - stat for once molecule)
-Interaction:	2	(1 - mono; 2 - di)
-Atom types:	6	21	(1st atom, 2nd atom; or atom)
-Criteria:	3.2	2.4	(1-1 criterion, 1-2 criterion; or 1-1 criterion)
-Num of mol.for stat:	4
-Output:	out_all.dat

statgen/include/statgen/add_main.h

@@ -6,6 +6,7 @@ int error_checking (const float *, 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 *);
 

statgen/src/CMakeLists.txt

@@ -13,15 +13,7 @@ set (PRIVATE_CLASSES)
 # headers only files
 SET (HEADERS_ONLY)
 # public srcs
-set (PUBLIC_CLASSES add_main 
+set (PUBLIC_CLASSES)
-                    coords 
-                    graph 
-                    int2char 
-                    messages 
-                    stat_print 
-                    stat_select 
-                    stat_sort 
-                    summary_stat)
 # public headers
 set (PUBLIC_HEADERS)
 # shared libraries
@@ -31,6 +23,17 @@ else ()
   set (ADDITIONAL_LIB)
 endif()
 set (SOURCES)
+# for library
+set (LIBRARY_NAME stat)
+set (LIB_SOURCES add_main 
+                 coords 
+                 graph 
+                 int2char 
+                 messages 
+                 stat_print 
+                 stat_select 
+                 stat_sort 
+                 summary_stat)
 
 # append list
 foreach (class ${PRIVATE_CLASSES})
@@ -49,12 +52,15 @@ foreach (class ${PUBLIC_CLASSES})
 endforeach ()
 
 # link libraries and compile
+add_library (${LIBRARY_NAME} SHARED ${LIB_SOURCES})
 add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
-target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
+target_link_libraries (${PROJECT} ${ADDITIONAL_LIB} ${LIBRARY_NAME})
 
 # install properties
 INSTALL (TARGETS ${PROJECT} 
          DESTINATION bin)
+INSTALL (TARGETS ${LIBRARY_NAME} 
+         DESTINATION lib${LIB_SUFFIX})
 if (ADD_INCLUDE)
   INSTALL (FILES ${PUBLIC_HEADERS} 
            DESTINATION include/${PROJECT})

statgen/src/add_main.c

@@ -2,6 +2,9 @@
  */
 
 #include <stdio.h>
+#include <string.h>
+
+// #include "messages.h"
 
 
 int error_checking (const float *cell, const int from, const char *input, 
@@ -36,7 +39,7 @@ int printing_head (const char *output, const int log, const int quiet,
   FILE *f_out;
   
   f_out = fopen (output, "w");
-  fprintf (f_out, "statgen ::: V.1.0.0 ::: 2013-07-17\n\n");
+  fprintf (f_out, "statgen ::: V.1.0.1 ::: 2013-07-23\n\n");
   fprintf (f_out, "CONFIGURATION\n");
   
   fprintf (f_out, "LOG=%i\nQUIET=%i\n", log, quiet);
@@ -64,6 +67,18 @@ 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)
+{  
+  if (quiet != 1)
+    message (0, mode, str, std_output);
+  if (log == 1)
+    message (1, mode, str, f_log);
+  
+  return 0;
+}
+
+
 int set_defaults (float *cell, int *from, char *input, int *log, int *max_depth, 
                   int *num_of_inter, char *output, int *to, int *type_inter, int *quiet)
 {

statgen/src/graph.c

@@ -105,6 +105,9 @@ int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso
 //   convert to matrix of weight
   pn = (int *) malloc (N * sizeof (int));
   n_cycle = (int *) malloc ((depth - 2) * sizeof (int));
+  if ((pn == NULL) || 
+    (n_cycle == NULL))
+    return 1;
   for (i=0; i<N; i++)
     pn[i] = 0;
   for (i=0; i<N; i++)
@@ -129,5 +132,5 @@ int graph_analyze (const int N, const int *matrix, const int max_depth, int *iso
   free (n_cycle);
   free (pn);
   
-  return 1;
+  return 0;
 }

statgen/src/main.c

@@ -78,7 +78,7 @@ int main (int argc, char *argv[])
     {
       sprintf (tmp_str, "                                        statgen\n");
       sprintf (tmp_str, "%sProgram for analyze molecular dynamic trajectories\n", tmp_str);
-      sprintf (tmp_str, "%sVersion : 1.0.0                                                    License : GPL\n", tmp_str);
+      sprintf (tmp_str, "%sVersion : 1.0.1                                                    License : GPL\n", tmp_str);
       sprintf (tmp_str, "%s                                                    Evgeniy Alekseev aka arcanis\n", tmp_str);
       sprintf (tmp_str, "%s                                                    E-mail : esalexeev@gmail.com\n\n", tmp_str);
       sprintf (tmp_str, "%sUsage:\n", tmp_str);
@@ -132,6 +132,8 @@ int main (int argc, char *argv[])
           type_inter++;
       
       label_atom = (int *) malloc (type_inter * sizeof (int));
+      if (label_atom == NULL)
+        return 1;
       switch (type_inter)
       {
         case 1:
@@ -198,16 +200,8 @@ int main (int argc, char *argv[])
   if (log == 1)
     f_log = fopen (logfile, "w");
   
-  if (quiet != 1)
+  print_message (quiet, stdout, log, f_log, 0, argv[0]);
-  {
+  print_message (quiet, stdout, log, f_log, 1, argv[0]);
-    message (0, 0, argv[0], stdout);
-    message (0, 1, argv[0], stdout);
-  }
-  if (log == 1)
-  {
-    message (1, 0, argv[0], f_log);
-    message (1, 1, argv[0], f_log);
-  }
   
   //   error checking
   error = error_checking (cell, from, input, max_depth, num_of_inter, output, to, 
@@ -221,10 +215,7 @@ int main (int argc, char *argv[])
     return 1;
   }
   
-  if (quiet != 1)
+  print_message (quiet, stdout, log, f_log, 2, argv[0]);
-    message (0, 2, argv[0], stdout);
-  if (log == 1)
-    message (1, 2, argv[0], f_log);
   
 //   processing
 //   initial variables
@@ -235,10 +226,7 @@ int main (int argc, char *argv[])
   filename[k+2] = conv (from, 2);
   filename[k+3] = conv (from, 1);
   filename[k+4] = '\0';
-  if (quiet != 1)
+  print_message (quiet, stdout, log, f_log, 3, filename);
-    message (0, 3, filename, stdout);
-  if (log == 1)
-    message (1, 3, filename, f_log);
   f_inp = fopen (filename, "r");
   if (f_inp == NULL)
   {
@@ -282,58 +270,31 @@ int main (int argc, char *argv[])
 //   set type_agl to zero
   for (i=0; i<max_depth+2; i++)
     type_agl[i] = 0;
-  if (quiet != 1)
+  sprintf (tmp_str, "%6cOutput file: '%s';\n%6cLog: %i;\n%6cQuiet: %i;\n\
-  {
-    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, 
 ' ' , to, ' ', cell[0], cell[1], cell[2], ' ' , label_atom[0]);
-    for (i=1; i<type_inter; i++)
+  for (i=1; i<type_inter; i++)
-      sprintf (tmp_str, "%s,%i", tmp_str, label_atom[i]);
+    sprintf (tmp_str, "%s,%i", tmp_str, label_atom[i]);
-    sprintf (tmp_str, "%s;\n", tmp_str);
+  sprintf (tmp_str, "%s;\n", tmp_str);
-    for (i=0; i<num_of_inter; i++)
+  for (i=0; i<num_of_inter; i++)
-    {
-      sprintf (tmp_str, "%s%6cInteraction: ", tmp_str, ' ');
-      for (j=0; j<16; j++)
-        if ((crit[16*i+j] != 0.0) && 
-          ((j != 4) && (j != 8) && (j != 9) && (j != 12) && (j != 13) && (j != 14)))
-          sprintf (tmp_str, "%s%i-%i:%4.2f,", tmp_str, j/4, j%4, crit[16*i+j]);
-      sprintf (tmp_str, "%s;\n", tmp_str);
-    }
-    sprintf (tmp_str, "%s%6cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
-    message (0, 5, tmp_str, stdout);
-  }
-  if (log == 1)
   {
-    sprintf (tmp_str, "%34cOutput file: '%s';\n%34cLog: %i;\n%34cQuiet: %i;\n\
+    sprintf (tmp_str, "%s%6cInteraction: ", tmp_str, ' ');
-%34cMask: %s;\n%34cFirst step: %i;\n%34cLast step: %i;\n%34cCell size: %.4f, %.4f, %.4f;\n\
+    for (j=0; j<16; j++)
-%34cSelect atoms: %i", ' ', output, ' ', log, ' ', quiet, ' ', input, ' ', from, 
+      if ((crit[16*i+j] != 0.0) && 
-' ' , to, ' ', cell[0], cell[1], cell[2], ' ' , label_atom[0]);
+        ((j != 4) && (j != 8) && (j != 9) && (j != 12) && (j != 13) && (j != 14)))
-    for (i=1; i<type_inter; i++)
+        sprintf (tmp_str, "%s%i-%i:%4.2f,", tmp_str, j/4, j%4, crit[16*i+j]);
-      sprintf (tmp_str, "%s,%i", tmp_str, label_atom[i]);
     sprintf (tmp_str, "%s;\n", tmp_str);
-    for (i=0; i<num_of_inter; i++)
-    {
-      sprintf (tmp_str, "%s%34cInteraction: ", tmp_str, ' ');
-      for (j=0; j<16; j++)
-        if ((crit[16*i+j] != 0.0) && 
-          ((j != 4) && (j != 8) && (j != 9) && (j != 12) && (j != 13) && (j != 14)))
-          sprintf (tmp_str, "%s%i-%i:%4.2f,", tmp_str, j/4, j%4, crit[16*i+j]);
-      sprintf (tmp_str, "%s;\n", tmp_str);
-    }
-    sprintf (tmp_str, "%s%34cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
-    message (1, 5, tmp_str, f_log);
   }
+  sprintf (tmp_str, "%s%6cIsomorphism check: %i\n", tmp_str, ' ', max_depth);
+  print_message (quiet, stdout, log, f_log, 5, tmp_str);
   
 //   head
   printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom, 
                  num_of_inter, crit, max_depth);
   
 //   main cycle
-  if (quiet != 1)
+  print_message (quiet, stdout, log, f_log, 6, argv[0]);
-    message (0, 6, argv[0], stdout);
-  if (log == 1)
-    message (1, 6, argv[0], f_log);
   for (i=from; i<to+1; i++)
   {
 //     reading coordinates
@@ -341,26 +302,14 @@ int main (int argc, char *argv[])
     filename[k+2] = conv (i, 2);
     filename[k+3] = conv (i, 1);
     filename[k+4] = '\0';
-    if (quiet != 1)
+    print_message (quiet, stdout, log, f_log, 7, filename);
-      message (0, 7, filename, stdout);
-    if (log == 1)
-      message (1, 7, filename, f_log);
     error = reading_coords (filename, type_inter, label_atom, cell, &num_mol, 
                             &num_atoms, true_label_mol, label_mol, type_atoms, coords);
     if (error != 1)
     {
-      if (quiet != 1)
+      sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n", 
-      {
-        sprintf (tmp_str, "%6cNumber of molecules: %i\n%6cNumber of atoms: %i\n", 
                  ' ', num_mol, ' ', num_atoms);
-        message (0, 8, tmp_str, stdout);
+      print_message (quiet, stdout, log, f_log, 8, tmp_str);
-      }
-      if (log == 1)
-      {
-        sprintf (tmp_str, "%6cNumber of molecules: %i\n%34cNumber of atoms: %i\n", 
-                 ' ', num_mol, ' ', num_atoms);
-        message (1, 8, tmp_str, f_log);
-      }
     }
     
 //     resize dynamic arrays
@@ -387,62 +336,37 @@ int main (int argc, char *argv[])
         fputs (tmp_str, f_log);
       return 18;
     }
-    if (quiet != 1)
+    print_message (quiet, stdout, log, f_log, 9, argv[0]);
-      message (0, 9, argv[0], stdout);
-    if (log == 1)
-      message (1, 9, argv[0], f_log);
     
 //     analyze
     if (error == 0)
     {
       error = 1;
       error = create_matrix (num_mol, num_atoms, label_mol, type_atoms, coords, 
-                            num_of_inter, crit, connect);
+                             num_of_inter, crit, connect);
       if (error == 0)
       {
-        if (quiet != 1)
+        print_message (quiet, stdout, log, f_log, 10, argv[0]);
-          message (0, 10, argv[0], stdout);
-        if (log == 1)
-          message (1, 10, argv[0], f_log);
         error = 1;
         error = proc_matrix (num_mol, connect, num_mol_agl, agl, stat, stat_all);
         if (error == 0)
         {
-          if (quiet != 1)
+          print_message (quiet, stdout, log, f_log, 11, argv[0]);
-            message (0, 11, argv[0], stdout);
-          if (log == 1)
-            message (1, 11, argv[0], f_log);
           error = printing_agl (filename, output, connect, num_mol, true_label_mol, 
                                 num_mol_agl, agl, stat, max_depth, type_agl);
           if (error == 0)
-          {
+            print_message (quiet, stdout, log, f_log, 12, output);
-            if (quiet != 1)
-              message (0, 12, output, stdout);
-            if (log == 1)
-              message (1, 12, output, f_log);
-          }
         }
       }
     }
   }
   
-  if (quiet != 1)
+  print_message (quiet, stdout, log, f_log, 13, argv[0]);
-  {
+  print_message (quiet, stdout, log, f_log, 14, output);
-    message (0, 13, argv[0], stdout);
-    message (0, 14, output, stdout);
-  }
-  if (log == 1)
-  {
-    message (1, 13, argv[0], f_log);
-    message (1, 14, output, f_log);
-  }
 //     tail
   summary_statistic (output, step, num_mol, max_depth, type_agl, stat_all);
   
-  if (quiet != 1)
+  print_message (quiet, stdout, log, f_log, 15, argv[0]);
-    message (0, 15, argv[0], stdout);
-  if (log == 1)
-    message (1, 15, argv[0], f_log);
 //   free memory
   free (agl);
   free (connect);
@@ -456,10 +380,7 @@ int main (int argc, char *argv[])
   free (type_agl);
   free (type_atoms);
   
-  if (quiet != 1)
+  print_message (quiet, stdout, log, f_log, 16, argv[0]);
-    message (0, 16, argv[0], stdout);
-  if (log == 1)
-    message (1, 16, argv[0], f_log);
   
   if (log == 1)
     fclose (f_log);

statgen/src/messages.c

@@ -1,14 +1,14 @@
-/* Library for printing messages at stdout
+/* Library for printing messages at output
  *
  * Usage:
- *                                             message (log, mode, text, stdout)
+ *                                             message (log, mode, text, output)
  */
 
 #include <stdio.h>
 #include <time.h>
 
 
-int message (const int log, const int mode, const char *text, FILE *stdout)
+int message (const int log, const int mode, const char *text, FILE *output)
 /* mode             - number of message
  * text             - additional text
  */
@@ -18,17 +18,17 @@ int message (const int log, const int mode, const char *text, FILE *stdout)
   if (log == 1)
   {
     char time_str[256];
-    time_t t = time(NULL);
+    time_t t = time (NULL);
-    struct tm* aTm = localtime(&t);
+    struct tm* aTm = localtime (&t);
-    sprintf(time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900, 
+    sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900, 
             aTm->tm_mon+1, aTm->tm_mday, aTm->tm_hour, aTm->tm_min, aTm->tm_sec, mode);
-    fputs (time_str, stdout);
+    fputs (time_str, output);
   }
   
   switch (mode)
   {
     case 0:
-      sprintf (out, "Starting program: '%s' (Ver.1.0.0)\n", text);
+      sprintf (out, "Starting program: '%s'\n", text);
       break;
     case 1:
       sprintf (out, "Checking errors\n");
@@ -79,6 +79,6 @@ int message (const int log, const int mode, const char *text, FILE *stdout)
       break;
   }
   
-  fputs (out, stdout);
+  fputs (out, output);
   return 0;
 }

statgen/src/stat_print.c

@@ -27,7 +27,7 @@ int printing_agl (const char *input, const char *output, const int *connect,
  * type_agl         - massive of numbers of aglomerate types
  */
 {
-  int i, *iso, j, k, *label_matrix, *matrix;
+  int error, i, *iso, j, k, *label_matrix, *matrix;
   FILE *f_out;
 /* iso              - isomorphic graph in database
  * label_matrix     - massive of indexes of molecule
@@ -36,6 +36,8 @@ int printing_agl (const char *input, const char *output, const int *connect,
  */
   
   iso = (int *) malloc (max_depth * sizeof (int));
+  if (iso == NULL)
+    return 1;
   f_out = fopen (output, "a");
   
 //   head
@@ -50,14 +52,14 @@ int printing_agl (const char *input, const char *output, const int *connect,
     if (num_mol_agl[i] > 0)
     {
 //       creating connectivity graph
-      matrix = (int *) malloc (num_mol_agl[i] * num_mol_agl[i] * sizeof (int));
-      for (j=0; j<num_mol_agl[i]; j++)
-        for (k=0; k<num_mol_agl[i]; k++)
-          matrix[num_mol_agl[i]*j+k] = 0;
       label_matrix = (int *) malloc (num_mol * sizeof (int));
+      matrix = (int *) malloc (num_mol_agl[i] * num_mol_agl[i] * sizeof (int));
       if ((matrix == NULL) ||
         (label_matrix == NULL))
         return 1;
+      for (j=0; j<num_mol_agl[i]; j++)
+        for (k=0; k<num_mol_agl[i]; k++)
+          matrix[num_mol_agl[i]*j+k] = 0;
       
       for (j=0; j<num_mol_agl[i]; j++)
         label_matrix[agl[num_mol*i+j]] = j;
@@ -71,7 +73,9 @@ int printing_agl (const char *input, const char *output, const int *connect,
 
 //       graph topology analyze
       if (max_depth > 0)
-        graph_analyze (num_mol_agl[i], matrix, max_depth, iso);
+        error = graph_analyze (num_mol_agl[i], matrix, max_depth, iso);
+      if (error > 0)
+        return 1;
       
 //       printing class of aglomerate
       fprintf (f_out, "AGL=%i=", num_mol_agl[i]);

statgen/statgen.cmake

@@ -1,13 +1,12 @@
 # set directories
-set ("${PROJECT}_BINARY_DIR"  bin)
+set (${PROJECT}_BINARY_DIR bin)
-set ("${PROJECT}_SOURCE_DIR" src:include)
+set (${PROJECT}_SOURCE_DIR src:include)
-set ("${PROJECT}_LIB_DIR" lib)
+set (${PROJECT}_LIB_DIR lib)
 
 set (CMAKE_INCLUDE_PATH ${${PROJECT}_SOURCE_DIR})
 set (CMAKE_LIBRARY_PATH ${${PROJECT}_LIB_DIR})
 set (EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/${${PROJECT}_BINARY_DIR})
 set (CMAKE_VERBOSE_MAKEFILE ON)
-set (CMAKE_BUILD_TYPE Debug)
 
 if ( WITH_DEBUG_MODE )
   ADD_DEFINITIONS ( -DDEBUG_MODE=1 )
@@ -18,5 +17,5 @@ if ( CMAKE_COMPILER_IS_GNUCXX )
   set (CMAKE_CXX_FLAGS "-O0 ${ADD_CXX_FLAGS}")
   set (CMAKE_CXX_FLAGS_DEBUG "-g -O0")
 else ()
-  message ("not yet")
+  message ("Not enabled")
 endif ()