Added Makefile

Added lib 'int2str.c'
Added 'main.c'

stat_new/Makefile

@@ -0,0 +1,20 @@
+PROJECT=STATGEN
+
+CC=gcc
+CFLAGS=-c -Wall -fPIC
+LDFLAGS=-lm
+SOURCES=main.c coords.c int2str.c stat_print.c stat_select.c stat_sort.c summary_stat.c
+OBJECTS=$(SOURCES:.c=.o)
+EXECUTABLE=statgen
+
+$(STATGEN): $(SOURCES) $(EXECUTABLE)
+
+$(EXECUTABLE): $(OBJECTS)
+	$(CC) $(LDFLAGS) $(OBJECTS) -o $@
+
+.c.o:
+	$(CC) $(CFLAGS) $< -o $@
+
+clean:
+	rm -f *.o
+

stat_new/coords.c

@@ -11,22 +11,6 @@
 #include <string.h>
 
 
-char conv (int fnumb, int dig_pos)
-{
-  int d, h, o;
-  char const digit[] = "0123456789";
- 
-  h = fnumb / 100;
-  d = (fnumb % 100) / 10;
-  o = fnumb % 10;
-
-  if (dig_pos == 1) return digit[o];
-  if (dig_pos == 2) return digit[d];
-  if (dig_pos == 3) return digit[h];
-  else return digit[0];
-}
-
-
 int reading_coords (char *filename, int type_inter, const int *label_atom, 
                     const float *cell, int *num_mol, int *num_atoms, 
                     int *true_label_mol, int *label_mol, 
@@ -44,7 +28,7 @@ int reading_coords (char *filename, int type_inter, const int *label_atom,
  */
 {
   char file_string[256];
-  int atoms, i, j, tr_num_atoms, ref_mol, x, y, z;
+  int atoms, i, j, tr_num_atoms, ref_mol, x, y;
   float not_tr_coords[750000], ref[3];
   FILE *inp;
 /* file_string      - temp string variable
@@ -293,21 +277,3 @@ int reading_coords (char *filename, int type_inter, const int *label_atom,
   
   return 0;
 }
-
-
-int main (int argc, char *argv[])
-{
-//   int i, label_atom[5], label_mol[200000], num_atoms, num_mol, type_atoms[200000];
-//   float a[600000], cell[3];
-// 
-//   for (i=0; i<5; i++)
-//     label_atom[i] = 0;
-//   label_atom[0] = 1;
-//   cell[0] = 34.8616;
-//   cell[1] = 34.7930;
-//   cell[2] = 34.7925;
-// 
-//   reading_coords ("oct.001", 1, label_atom, cell, &num_mol, &num_atoms, label_mol, type_atoms, a);
-//   
-  return 0;
-}

stat_new/int2str.c

@@ -0,0 +1,26 @@
+/* Library for converting integer to string
+ * Usage
+ *                                                char = conv (number, position)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+
+
+char conv (int fnumb, int dig_pos)
+/* fnumb            - integer
+ * dig_pos          - position
+ */
+{
+  int d, h, o;
+  char const digit[] = "0123456789";
+ 
+  h = fnumb / 100;
+  d = (fnumb % 100) / 10;
+  o = fnumb % 10;
+
+  if (dig_pos == 1) return digit[o];
+  if (dig_pos == 2) return digit[d];
+  if (dig_pos == 3) return digit[h];
+  else return digit[0];
+}

stat_new/main.c

@@ -0,0 +1,342 @@
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+
+int error_checking (const float *cell, int from, const char *input, 
+                    int num_of_inter, const char *output, int to, int type_inter)
+{
+  if ((type_inter == 0) || (type_inter > 4))
+    return 11;
+  if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
+    return 12;
+  if ((to == -1) || (from == -1))
+    return 13;
+  if (num_of_inter == 0)
+    return 14;
+  if (input[0] == '#')
+    return 15;
+  if (output[0] == '#')
+    return 16;
+  
+  return 0;
+}
+
+
+int printing_head (const char *output, int log, int quiet, const char *input, 
+                   int from, int to, const float *cell, int type_inter, 
+                   const int *label_atom, int num_of_inter, const float *crit)
+{
+  int i;
+  FILE *f_out;
+  
+  f_out = fopen (output, "w");
+  fprintf (f_out, "statgen ::: V.1.0.0 ::: 2013-07-17\n\n");
+  fprintf (f_out, "CONFIGURATION\n");
+  
+  fprintf (f_out, "LOG=%i\nQUIET=%i\n", log, quiet);
+  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, "ATOMS=%i", label_atom[0]);
+  for (i=1; i<type_inter; i++)
+    fprintf (f_out, ",%i", label_atom[i]);
+  fprintf (f_out, "\n");
+  for (i=0; i<num_of_inter; i++)
+  {
+    fprintf (f_out, "INTERACTION=");
+    fprintf (f_out, "0-0:%4.2f,0-1:%4.2f,1-1:%4.2f,", crit[16*i+0], crit[16*i+1], 
+             crit[16*i+5]);
+    fprintf (f_out, "0-2:%4.2f,1-2:%4.2f,2-2:%4.2f,", crit[16*i+2], crit[16*i+6], 
+             crit[16*i+10]);
+    fprintf (f_out, "0-3:%4.2f,1-3:%4.2f,2-3:%4.2f,3-3:%4.2f\n", crit[16*i+3], 
+             crit[16*i+7], crit[16*i+11], crit[16*i+15]);
+  }
+    
+  fprintf (f_out, "END\n\n");
+  fclose (f_out);
+  
+  return 0;
+}
+
+
+int set_defaults (float *cell, int *from, char *input, int *log, int *num_of_inter, 
+                  char *output, int *to, int *type_agl, int *type_inter, int *quiet)
+{
+  int i;
+  
+  for (i=0; i<3; i++)
+    cell[i] = 0.0;
+  *from = -1;
+  input[0] = '#';
+  *log = 0;
+  *num_of_inter = 0;
+  output[0] = '#';
+  *to = -1;
+  type_agl[0] = 0;
+  type_agl[1] = 0;
+  *type_inter = 0;
+  *quiet = 0;
+  
+  return 0;
+}
+
+
+int main (int argc, char *argv[])
+{
+  char filename[256], tmp_str[256];
+  int error, i, index, j, k, label[2];
+  float label_fl;
+  FILE *f_inp;
+  
+  char input[256], logfile[256], output[256];
+  float cell[3], *coords, *crit;
+  int *agl, *connect, from, *label_atom, *label_mol, log, num_atoms, num_mol, 
+      *num_mol_agl, num_of_inter, *stat, *stat_all, step, to, *true_label_mol, 
+      type_agl[2], *type_atoms, type_inter, quiet;
+/* input            - mask of input files
+ * logfile          - log file name
+ * output           - output file name
+ * 
+ * cell             - cell dimension
+ * coords           - massive of coordinates
+ * crit             - massive of criteria
+ * 
+ * agl              - massive of aglomerates
+ * connect          - connectivity graph for all molecules
+ * from             - start point
+ * label_atom       - types of atom for interaction
+ * label_mol        - massive of numbers of molecule for atoms
+ * log              - status of log-mode
+ * num_atoms        - number of atoms for writing coordinates
+ * num_mol          - number of molecules for writing coordinates
+ * num_mol_agl      - massive of numbers of molecule in aglomerates
+ * num_of_inter     - number of different interactions
+ * stat             - massive of statistics
+ * stat_all         - massive of summary statistics
+ * step             - $(to - from + 1)
+ * to               - finish point
+ * true_label_mol   - massive of true numbers of molecule for atoms
+ * type_agl         - massive of numbers of aglomerate types
+ * type_atoms       - massive of atom types for atoms
+ * type_inter       - type interaction (number of molecules for interaction)
+ * quiet            - status of quiet-mode
+ */
+  
+  set_defaults (cell, &from, input, &log, &num_of_inter, output, &to, type_agl, 
+                &type_inter, &quiet);
+  
+//   reading number of interactions
+  for (i=1; i<argc; i++)
+    if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
+      num_of_inter++;
+  if (num_of_inter > 0)
+  {
+    crit = (float *) malloc ( 16 * num_of_inter * sizeof (float));
+    for (i=0; i<16*num_of_inter; i++)
+      crit[i] = 0.0;
+    num_of_inter = 0;
+  }
+  
+//   reading arguments
+  for (i=1; i<argc; i++)
+  {
+    if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
+    {
+      printf ("                                        statgen\n");
+      printf ("Program for analyze molecular dynamic trajectories\n");
+      printf ("Version : 1.0.0                                                    License : GPL\n");
+      printf ("                                                    Alekseev Evgeniy aka arcanis\n");
+      printf ("                                                    E-mail : esalexeev@gmail.com\n\n");
+      printf ("Usage:\n");
+      printf ("statgen -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -r ... -o OUTPUT [ -l LOGFILE ] [ -q ] [ -h ]\n\n");
+      printf ("Parametrs:\n");
+      printf ("  -i          - mask of input files\n");
+      printf ("  -s          - trajectory steps (integer)\n");
+      printf ("  -c          - cell size (float), A\n");
+      printf ("  -a          - atom types (integer). Format: 'ATOM1' or 'ATOM1,ATOM2' or etc\n");
+      printf ("  -r          - criteria (float), A. Format: '0-0:2.4,0-1:3.0' means 0-0-interaction\n");
+      printf ("                (<2.4 A) and 0-1 (<3.0) are needed. This flag can be used multiple times\n");
+      printf ("  -o          - output file name\n");
+      printf ("  -l          - log enable\n");
+      printf ("  -q          - quiet enable\n");
+      printf ("  -h          - show this help and exit\n");
+      return 0;
+    }
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
+//       mask of input files
+    {
+      strcpy (input, argv[i+1]);
+      i++;
+    }
+    else if ((argv[i][0] == '-') && (argv[i][1] == 's'))
+//       steps
+    {
+      sscanf (argv[i+1], "%i,%i", &from, &to);
+      if (from > to)
+      {
+        to += from;
+        from = to - from;
+        to -= from;
+      }
+      step = to - from + 1;
+      i++;
+    }
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
+//       cell size
+    {
+      sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
+      i++;
+    }
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'a'))
+//       atom types
+    {
+      type_inter = 1;
+      for (j=0; j<strlen(argv[i+1]); j++)
+        if (argv[i+1][j] == ',')
+          type_inter++;
+      
+      label_atom = (int *) malloc (type_inter * sizeof (int));
+      switch (type_inter)
+      {
+        case 1:
+          sscanf (argv[i+1], "%i", &label_atom[0]);
+          break;
+        case 2:
+          sscanf (argv[i+1], "%i,%i", &label_atom[0], &label_atom[1]);
+          break;
+        case 3:
+          sscanf (argv[i+1], "%i,%i,%i", &label_atom[0], &label_atom[1], &label_atom[2]);
+          break;
+        case 4:
+          sscanf (argv[i+1], "%i,%i,%i,%i", &label_atom[0], &label_atom[1], &label_atom[2], &label_atom[3]);
+          break;
+      }
+      
+      i++;
+    }
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
+//       criteria
+    {
+      index = 0;
+      sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
+      crit[16*num_of_inter+4*label[0]+label[1]] = label_fl;
+      crit[16*num_of_inter+4*label[1]+label[0]] = label_fl;
+      for (j=index; j<strlen(argv[i+1]); j++)
+        if (argv[i+1][j] == ',')
+        {
+          index = j+1;
+          sscanf (&argv[i+1][index], "%i-%i:%f%s", &label[0], &label[1], &label_fl, tmp_str);
+          crit[16*num_of_inter+4*label[0]+label[1]] = label_fl;
+          crit[16*num_of_inter+4*label[1]+label[0]] = label_fl;
+        }
+      
+      num_of_inter++;
+      i++;
+    }
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
+//       output file
+    {
+      strcpy (output, argv[i+1]);
+      i++;
+    }
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
+//       log mode
+    {
+      log = 1;
+      strcpy (logfile, argv[i+1]);
+      i++;
+    }
+    else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
+//       quiet mode
+    {
+      quiet = 1;
+    }
+  }
+  
+//   error checking
+  error = error_checking (cell, from, input, num_of_inter, output, to, type_inter);
+  if (error > 1)
+  {
+    printf ("Something wrong (error code: %i)!\nSee 'statgen -h' for more details\n", error);
+    return 1;
+  }
+  
+//   processing
+//   initial variables
+  k = strlen (input);
+  strcpy (filename, input);
+  filename[k] = '.';
+  filename[k+1] = conv (from, 3);
+  filename[k+2] = conv (from, 2);
+  filename[k+3] = conv (from, 1);
+  filename[k+4] = '\0';
+  f_inp = fopen (filename, "r");
+  if (f_inp == NULL)
+    return 1;
+  fscanf (f_inp, "%i", &num_atoms);
+  fclose (f_inp);
+  coords = (float *) malloc (3 * num_atoms * sizeof (float));
+  label_mol = (int *) malloc (num_atoms * sizeof (int));
+  true_label_mol = (int *) malloc (num_atoms * sizeof (int));
+  type_atoms = (int *) malloc (num_atoms * sizeof (int));
+  
+//   head
+  printing_head (output, log, quiet, input, from, to, cell, type_inter, label_atom, 
+                 num_of_inter, crit);
+  
+//   main cycle
+  for (i=from; i<to+1; i++)
+  {
+//     reading coordinates
+    filename[k+1] = conv (i, 3);
+    filename[k+2] = conv (i, 2);
+    filename[k+3] = conv (i, 1);
+    filename[k+4] = '\0';
+    error = reading_coords (filename, type_inter, label_atom, cell, &num_mol, 
+                            &num_atoms, true_label_mol, label_mol, type_atoms, coords);
+    
+//     initializate variables
+    if (i == from)
+    {
+      agl = (int *) malloc (num_mol * num_mol * sizeof (int));
+      connect = (int *) malloc (num_mol * num_mol * sizeof (int));
+      num_mol_agl = (int *) malloc (num_mol * sizeof (int));
+      if (num_mol_agl != NULL)
+        printf ("error\n");
+      stat = (int *) malloc (num_mol * sizeof (int));
+      stat_all = (int *) malloc (num_mol * sizeof (int));
+    }
+    
+//     analyze
+    if (error == 0)
+    {
+      error = create_matrix (num_mol, num_atoms, label_mol, type_atoms, coords, 
+                             num_of_inter, crit, connect);
+      if (error == 0)
+      {
+        error = proc_matrix (num_mol, connect, num_mol_agl, agl, stat, stat_all);
+        if (error == 0)
+          printing_agl (filename, output, connect, num_mol, true_label_mol, 
+                        num_mol_agl, agl, stat, type_agl);
+      }
+    }
+    
+//     tail
+    summary_statistic (output, step, num_mol, type_agl, stat_all);
+  }
+
+//   free memory
+  free (agl);
+  free (connect);
+  free (coords);
+  free (crit);
+  free (label_mol);
+  free (num_mol_agl);
+//   free (stat);
+//   free (stat_all);
+  free (true_label_mol);
+  free (type_atoms);
+  
+  return 0;
+}

stat_new/stat_print.c

@@ -33,13 +33,10 @@ int printing_agl (char *input, char *output, const int *connect, int num_mol,
  * f_out            - output file
  */
   
-  type_agl[0] = 0;
-  type_agl[1] = 0;
-  
   f_out = fopen (output, "a");
   
 //   head
-  fprintf (f_out, "FILE=%s\nSTATISTIC:\n|   n   |   N   |\n-----------------", input);
+  fprintf (f_out, "FILE=%s\nSTATISTIC:\n|   n   |   N   |\n-----------------\n", input);
   for (i=0; i<num_mol; i++)
     if (stat[i] != 0)
       fprintf (f_out, " %7i %7i \n", i+1, stat[i]);
@@ -113,9 +110,3 @@ int printing_agl (char *input, char *output, const int *connect, int num_mol,
   fprintf (f_out, "---------------------------------------------------\n");
   return 0;
 }
-
-
-int main (int argc, char *argv[])
-{
-  return 0;
-}

stat_new/stat_select.c

@@ -111,9 +111,3 @@ int create_matrix (int num_mol, int num_atoms, const int *label_mol,
   
   return 0;
 }
-
-
-int main (int argc, char *argv[])
-{
-  return 0;
-}

stat_new/stat_sort.c

@@ -80,9 +80,3 @@ int proc_matrix (int num_mol, const int *connect, int *num_mol_agl, int *agl,
   
   return 0;
 }
-
-
-int main (int argc, char *argv[])
-{
-  return 0;
-}

stat_new/summary_stat.c

@@ -56,15 +56,9 @@ int summary_statistic (char *filename, int step, int num_mol, const int *type_ag
   type[0] = type_agl[0];
   type[1] = type_agl[1];
   fprintf (f_out, "------------------------------------------------\n");
-  fprintf (f_out, "LINEAR=%7.5f\nCYCLE=%7.5f\n", type[0]/x, type[1]/x);
+  fprintf (f_out, "LINEAR=%.5f\nCYCLE=%.5f\n", type[0]/x, type[1]/x);
   
   fclose (f_out);
   
   return 0;
 }
-
-
-int main (int argc, char *argv[])
-{
-  return 0;
-}