From 9957e98086b9c1567ff69771f3e66f96efccd2ea Mon Sep 17 00:00:00 2001
From: arcan1s <esalexeev@gmail.com>
Date: Tue, 16 Jul 2013 04:01:37 +0400
Subject: [PATCH] Added lib 'stat_select.c'

---
 stat_new/coords        | Bin 13538 -> 13854 bytes
 stat_new/coords.c      |  49 ++++++++++++++-----
 stat_new/stat          | Bin 0 -> 9319 bytes
 stat_new/stat_select.c | 107 +++++++++++++++++++++++++++++++++++++++++
 stat_new/stat_sort.c   |  49 +++++++++++++++++++
 5 files changed, 194 insertions(+), 11 deletions(-)
 create mode 100755 stat_new/stat
 create mode 100644 stat_new/stat_select.c
 create mode 100644 stat_new/stat_sort.c

diff --git a/stat_new/coords b/stat_new/coords
index f11c8150e70ea181ab5eb51127681a164f312793..82e3cb9c679f9095cc7150703ede2da451a60a40 100755
GIT binary patch
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diff --git a/stat_new/coords.c b/stat_new/coords.c
index 555d4bf..df4dbfd 100644
--- a/stat_new/coords.c
+++ b/stat_new/coords.c
@@ -1,8 +1,10 @@
-/* Usage:
- *                    reading_coords(filename, label, coords)
+/* Library for reading coordinates from input file
+ * 
+ * Usage:
+ *                    reading_coords (filename, type_interaction, labels, cell, 
+ *   &number_of_molecules, &number_of_atoms, label_molecule, type_atoms, coords)
  */
 
-#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -24,29 +26,42 @@ char conv (int fnumb, int dig_pos)
 }
 
 
-int reading_coords (char *filename, int type_inter, int *label_atom, float *cell, int *label_mol, int *num_atoms, float *coords, int *type_atoms)
+int reading_coords (char *filename, int type_inter, const int *label_atom, 
+                    const float *cell, int *num_mol, int *num_atoms, 
+                    int *label_mol, int *type_atoms, float *coords)
 /* filename         - name of file with coordinates
  * type_inter       - type interaction (number of molecules for interaction)
  * label_atom       - types of atom for interaction
- * cell             - cell dimention
- * label_mol        - massive of numbers of molecule for atoms
+ * cell             - cell dimension
+ * num_mol          - number of molecules for writing coordinates
  * num_atoms        - number of atoms for writing coordinates
- * coords           - massive of coordinates
+ * label_mol        - massive of numbers of molecule for atoms
  * type_atoms       - massive of atom types for atoms
+ * coords           - massive of coordinates
  */
 {
   char file_string[256];
   int atoms, i, j, tr_num_atoms, ref_mol, x, y, z;
   float not_tr_coords[750000], ref[3];
   FILE *inp;
+/* file_string      - temp string variable
+ * atoms            - total number of atoms in system
+ * tr_num_atoms     - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
+ * ref_mol          - number of molecule for reference
+ * not_tr_coords    - not translated coordinates
+ * ref              - coordinates of reference molecule
+ * inp              - file with input data
+ */
   
   *num_atoms = 0;
+  *num_mol = 0;
   
 //   Reading file
   inp = fopen (filename, "r+");
   if (inp == NULL)
     return 1;
   
+  ref_mol = -1;
   fscanf (inp, "%i", &atoms);
   for (i=0; i<atoms; i++)
   {
@@ -59,7 +74,12 @@ int reading_coords (char *filename, int type_inter, int *label_atom, float *cell
         not_tr_coords[3**num_atoms+1] = atof (&file_string[23]);
         not_tr_coords[3**num_atoms+2] = atof (&file_string[35]);
         
-        label_mol[*num_atoms] = atoi (&file_string[53]);
+        if (ref_mol != atoi (&file_string[53]))
+        {
+          ref_mol = atoi (&file_string[53]);
+          *num_mol = *num_mol + 1;
+        }
+        label_mol[*num_atoms] = num_mol - 1;
         type_atoms[*num_atoms] = j;
         
         *num_atoms = *num_atoms + 1;
@@ -267,13 +287,20 @@ int reading_coords (char *filename, int type_inter, int *label_atom, float *cell
     }
   }
   
+//   Reading number of molecules
+//   *num_mol = 1;
+//   ref_mol = label_mol[0];
+//   for (i=0; i<*num_atoms; i++)
+//     if (ref_mol != label_mol[i])
+//       *num_mol = *num_mol + 1;
+//   
   return 0;
 }
 
 
 int main (int argc, char *argv[])
 {
-//   int i, label_atom[5], label_mol[200000], num_atoms, type_atoms[200000];
+//   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++)
@@ -283,7 +310,7 @@ int main (int argc, char *argv[])
 //   cell[1] = 34.7930;
 //   cell[2] = 34.7925;
 // 
-//   reading_coords ("oct.001", 1, label_atom, cell, label_mol, &num_atoms, a, type_atoms);
-  
+//   reading_coords ("oct.001", 1, label_atom, cell, &num_mol, &num_atoms, label_mol, type_atoms, a);
+//   
   return 0;
 }
\ No newline at end of file
diff --git a/stat_new/stat b/stat_new/stat
new file mode 100755
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diff --git a/stat_new/stat_select.c b/stat_new/stat_select.c
new file mode 100644
index 0000000..af74ce8
--- /dev/null
+++ b/stat_new/stat_select.c
@@ -0,0 +1,107 @@
+/* Library for creating connectivity matrix
+ * 
+ * Usage:
+ *          create_matrix (number_of_molecules, number_of_atoms, label_molecule,
+ *         type_atoms, coords, number_of_interactions, criteria, connect_matrix)
+ */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+
+float radii (const float *a, const float *b)
+{
+  return sqrt (pow((a[0]-b[0]), 2) + pow((a[1]-b[1]), 2) + pow((a[2]-b[2]), 2));
+}
+
+
+int create_matrix (int num_mol, int num_atoms, const int *label_mol, 
+                   const int *type_atoms, const float *coords, int num_of_inter, 
+                   const float *crit, int *connect, int *num_bonds)
+{
+  float x[2][3];
+  int cur_num_inter, i, j, k, l, num_inter, ***label_inter;
+  
+  label_inter = (int ***) malloc (num_mol * sizeof (int **));
+  for (i=0; i<num_mol; i++)
+  {
+    label_inter[i] = (int **) malloc (num_mol * sizeof (int *));
+    for (j=0; j<num_mol; j++)
+    {
+      label_inter[i][j] = (int *) malloc (16 * sizeof (int));
+      for (k=0; k<16; k++)
+        label_inter[i][j][k] = 0;
+    }
+  }
+  
+//   creating initial connectivity matrix
+  for (i=0; i<num_atoms*8; i++)
+    for (j=i+1; j<num_atoms*8; j++)
+//       if atoms from different molecules
+      if (label_mol[i] != label_mol[j])
+      {
+        for (k=0; k<3; k++)
+        {
+          x[0][k] = coords[3*i+k];
+          x[1][k] = coords[3*j+k];
+        }
+        for (k=0; k<num_of_inter; k++)
+          if (crit[16*k+4*type_atoms[i]+type_atoms[j]] != 0.0)
+            if (radii (x[0], x[1]) <= crit[16*k+4*type_atoms[i]+type_atoms[j]])
+            {
+              label_inter[label_mol[i]][label_mol[j]][4*type_atoms[i]+type_atoms[j]] = 1;
+              label_inter[label_mol[j]][label_mol[i]][4*type_atoms[i]+type_atoms[j]] = 1;
+            }
+      }
+  
+  for (i=0; i<num_mol; i++)
+  {
+    num_bonds[i] = 0;
+    for (j=0; j<num_mol; j++)
+      connect[i*num_mol+j] = 0;
+  }
+  
+//   processing of initial connectivity matrix
+  for (k=0; k<num_of_inter; k++)
+  {
+//     determination of the number of interactions
+    num_inter = 0;
+    for (l=0; l<16; l++)
+      if (crit[16*k+l] != 0.0)
+        num_inter++;
+    
+    for (i=0; i<num_mol; i++)
+      for (j=0; j<num_mol; j++)
+      {
+        cur_num_inter = 0;
+        for (l=0; l<16; l++)
+          cur_num_inter += label_inter[i][j][l];
+        
+        if (cur_num_inter == num_inter)
+        {
+          connect[i*num_mol+j] = 1;
+          connect[j*num_mol+i] = 1;
+          num_bonds[i]++;
+          num_bonds[j]++;
+        }
+      }
+  }
+  
+//   free memory
+  for (i=0; i<num_mol; i++)
+  {
+    for (j=0; j<num_mol; j++)
+      free (label_inter[i][j]);
+    free (label_inter[i]);
+  }
+  free (label_inter);
+  
+  return 0;
+}
+
+
+int main (int argc, char *argv[])
+{
+  return 0;
+}
\ No newline at end of file
diff --git a/stat_new/stat_sort.c b/stat_new/stat_sort.c
new file mode 100644
index 0000000..6e6baef
--- /dev/null
+++ b/stat_new/stat_sort.c
@@ -0,0 +1,49 @@
+/* Library for processing connectivity matrix
+ * 
+ * Usage:
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+
+
+int proc_matrix (int num_mol, const int *connect, const int *num_bond, int *num_mol_agl, int *agl, int *stat)
+{
+  int i, j, p, *bin;
+  
+//   definition and zeroing
+  bin = (int *) malloc (num_mol * sizeof (int));
+  for (i=0; i<num_mol; i++)
+    bin[i] = 0;
+  for (i=0; i<5000; i++)
+  {
+    stat[i] = 0;
+    num_mol_agl[i] = 0;
+    for (j=0; j<5000; j++)
+      agl[5000*i+j] = 0;
+  }
+  
+  p = num_mol;
+  for (i=0; i<num_mol; i++)
+    if (num_bond[i] == 0)
+    {
+      bin[i] = 0;
+      stat[0]++;
+      p--;
+    }
+  
+  while (p > 0)
+  {
+    
+  }
+  
+  free (bin);
+  
+  return 0;
+}
+
+
+int main (int argc, char *argv[])
+{
+  return 0;
+}
\ No newline at end of file