Release mm_trj-1.0.1

mm_trj/README

@@ -3,22 +3,16 @@ Version : 1.0.1
 License : GPL
 
 Usage:
-mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
+mm_trj -i INPUT_TRJ -t INPUT_TYPE -s NUMBER -a INPUT_ATOMS -o OUTPUT [ -tt TOTAL_TYPES ]
-                   [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
+                                                            [ -l LOGFILE ] [ -q ] [ -h ]
 
 Parametrs:
-  -i          - mask of input files
+  -i          - input file name
-  -s          - trajectory steps (integer)
+  -t          - type of trajectory. Supported formats: gmx, puma
-  -c          - cell size (float), A
+  -s          - number of trajectory steps (integer)
-  -a          - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' 
+  -a          - input file with atom types. See file format in manual
-                (will enable RDF calculation for center mass automaticaly)
+  -o          - mask of output files
-  -o          - output file name
+  -tt         - number of different atom types. Default is 1024
-  -r          - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0'
-  -rs         - radius step for analyze (float), A. Default is '0.2'
-  -a          - minimal and maximal angles for analyze (float), deg. Default is '0.0,90.0'
-  -as         - angle step for analyze (float), deg. This option will enable RADF 
-                calculation automaticaly
-  -m          - matrix output enable
   -l          - log enable
   -q          - quiet enable
   -h          - show this help and exit

mm_trj/src/main.c

@@ -24,21 +24,15 @@
  * @section How-To-Use How to use
  * Usage:
  * <pre>
- * mm_radf -i INPUT -s FIRST,LAST -c X,Y,Z -a ... -o OUTPUT [ -r MIN,MAX ] [ -rs R_STEP ] 
+ * mm_trj -i INPUT_TRJ -t INPUT_TYPE -s NUMBER -a INPUT_ATOMS -o OUTPUT [ -tt TOTAL_TYPES ]
- *                    [ -a MIN,MAX ] [ -as ANG_STEP ] [ -m ] [ -l LOGFILE ] [ -q ] [ -h ]
+ *                                                             [ -l LOGFILE ] [ -q ] [ -h ]
  * Parametrs:
- *    -i          - mask of input files
+ *    -i          - input file name
- *    -s          - trajectory steps (integer)
+ *    -t          - type of trajectory. Supported formats: gmx, puma
- *    -c          - cell size (float), A
+ *    -s          - number of trajectory steps (integer)
- *    -a          - atom types (integer). Format: 'ATOM1-ATOM2' or 'A1,A2,A3-B1,B2,B3' 
+ *    -a          - input file with atom types. See file format in manual
- *                  (will enable RDF calculation for center mass automaticaly)
+ *    -o          - mask of output files
- *    -o          - output file name
+ *    -tt         - number of different atom types. Default is 1024
- *    -r          - minimal and maximal radii for analyze (float), A. Default is '2.0,15.0'
- *    -rs         - radius step for analyze (float), A. Default is '0.2'
- *    -a          - minimal and maximal angles for analyze (float), deg. Default is '0.0,90.0'
- *    -as         - angle step for analyze (float), deg. This option will enable RADF 
- *                  calculation automaticaly
- *    -m          - matrix output enable
  *    -l          - log enable
  *    -q          - quiet enable
  *    -h          - show this help and exit
@@ -269,6 +263,7 @@ int main(int argc, char *argv[])
   error = 1;
   error = reading_atoms (input_at, &num_types, num_mol, num_atoms, ch_atom_types, 
                          atom_types, total_types);
+  
   if (error == 0)
   {
     sprintf (tmp_str, "%6cLog: %i;\n%6cQuiet: %i;\n%6cInput file: %s;\n%6cTrajectory type: %i;\n\

mm_trj/src/read_gmx.c

@@ -2,11 +2,37 @@
  * @file
  */
 
+#include <math.h>
 #include <stdio.h>
 
 #include "print_trj.h"
 
 
+/**
+ * @fn translate_coords
+ */
+int translate_coords (const float coords, const float cell, float *trans)
+/**
+ * @brief funtion that translates coordinate
+ * @code
+ * 
+ * @endcode
+ * 
+ * @param coords          coordinate
+ * @param cell            cell size
+ * @param trans           massive of translated coordinates
+ * 
+ * @return 0              - exit without errors
+ */
+{
+    trans[0] = coords;
+    trans[1] = coords - cell;
+    trans[2] = coords + cell;
+   
+  return 0;
+}
+
+
 /**
  * @fn rw_gmx
  */
@@ -34,5 +60,95 @@ int rw_gmx (const char *input, const int step, const char *output, const int num
  * @return 0              - exit without errors
  */
 {
+  char filename[256], tmp_str[256];
+  float cell[3], trans[3], r_min;
+  int atoms, i, j, k, l, m, n;
+  FILE *f_inp;
+  
+/* filename               output file name
+ * cell                   cell size
+ * trans                  translated coordinates
+ * r_min                  minimal radius
+ * atom                   number of atoms
+ * f_inp                  input file
+ */
+  
+  f_inp = fopen (input, "r");
+  if (f_inp == NULL)
+    return 1;
+  
+  for (i=0; i<step; i++)
+  {
+// initial variables
+    sprintf (filename, "%s.%03i", output, i+1);
+    fgets (tmp_str, 256, f_inp);
+    fgets (tmp_str, 256, f_inp);
+    sscanf (tmp_str, "   natoms=%i%s", &atoms, tmp_str);
+    fgets (tmp_str, 256, f_inp);
+    fgets (tmp_str, 256, f_inp);
+    sscanf (tmp_str, "      box[    0]={%f%s", &cell[0], tmp_str);
+    fgets (tmp_str, 256, f_inp);
+    sscanf (tmp_str, "      box[    1]={%f,%f%s", &cell[1], &cell[1], tmp_str);
+    fgets (tmp_str, 256, f_inp);
+    sscanf (tmp_str, "      box[    2]={%f,%f,%f%s", &cell[2], &cell[2], &cell[2], tmp_str);
+    fgets (tmp_str, 256, f_inp);
+    for (j=0; j<3; j++)
+      cell[j] = 10 * cell[j];
+// coordinates
+    for (j=0; j<atoms; j++)
+    {
+      fgets (tmp_str, 256, f_inp);
+      sscanf (tmp_str, "      x[%i]={%f,%f,%f%s", &k, &coords[3*j+0], &coords[3*j+1], 
+              &coords[3*j+2], tmp_str);
+      for (k=0; k<3; k++)
+        coords[3*j+k] = 10 * coords[3*j+k];
+    }
+// velocities
+    fgets (tmp_str, 256, f_inp);
+    for (j=0; j<atoms; j++)
+      fgets (tmp_str, 256, f_inp);
+    
+// processing coordinates
+    j = 0;
+    while (j < atoms)
+      for (k=0; k<num_types; k++)
+        for (l=0; l<num_mol[k]; l++)
+        {
+          for (m=1; m<num_atoms[k]; m++)
+            for (n=0; n<3; n++)
+            {
+              r_min = fabs (coords[3*(j+m)+n] - coords[3*j+n]);
+              translate_coords (coords[3*(j+m)+n], cell[n], trans);
+              if (fabs (trans[1] - coords[3*j+n]) < r_min)
+                coords[3*(j+m)+n] = trans[1];
+              if (fabs (trans[2] - coords[3*j+n]) < r_min)
+                coords[3*(j+m)+n] = trans[2];
+            }
+          j += num_atoms[k];
+        }
+    j = 0;
+    while (j < atoms)
+      for (k=0; k<num_types; k++)
+        for (l=0; l<num_mol[k]; l++)
+        {
+          for (m=0; m<3; m++)
+          {
+            while (coords[3*j+m] > cell[m]/2)
+              for (n=j; n<j+num_atoms[k]; n++)
+                coords[3*n+m] -= cell[m];
+            while (coords[3*j+m] < -cell[m]/2)
+              for (n=j; n<j+num_atoms[k]; n++)
+                coords[3*n+m] += cell[m];
+          }
+          j += num_atoms[k];
+        }
+    
+// write to output
+    printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types, 
+                  atom_types, coords);
+  }
+  
+  fclose (f_inp);
+  
   return 0;
 }

mm_trj/src/read_gmx.h

@@ -5,10 +5,14 @@
 #ifndef READ_GMX_H
 #define READ_GMX_H
 
+/**
+ * @fn translate_coords
+ */
 /**
  * @fn rw_gmx
  */
 
+int translate_coords (const float, const float, float *);
 int rw_gmx (const char *, const int, const char *, const int, const int *, 
             const int *, const char *, const int *, float *);
 

mm_trj/src/read_puma.c

@@ -39,6 +39,12 @@ int rw_puma (const char *input, const int step, const char *output, const int nu
   int atoms, i, j, k, l, m, n;
   FILE *f_inp;
   
+/* filename               output file name
+ * cell                   cell size
+ * atom                   number of atoms
+ * f_inp                  input file
+ */
+  
   f_inp = fopen (input, "r");
   if (f_inp == NULL)
     return 1;
@@ -51,7 +57,7 @@ int rw_puma (const char *input, const int step, const char *output, const int nu
     sscanf (tmp_str, "%s%s%i%s", tmp_str, tmp_str, &atoms, tmp_str);
     fgets (tmp_str, 256, f_inp);
     sscanf (tmp_str, "%f%f%f", &cell[0], &cell[1], &cell[2]);
-
+// coordinates
     for (j=0; j<atoms; j++)
     {
       fgets (tmp_str, 256, f_inp);
@@ -76,6 +82,7 @@ int rw_puma (const char *input, const int step, const char *output, const int nu
           }
           j += num_atoms[k];
         }
+    
 // write to output
     printing_trj (filename, atoms, num_types, num_mol, num_atoms, ch_atom_types, 
                   atom_types, coords);

mm_trj/src/types

@@ -1,32 +0,0 @@
-NUMTYPES=2
-NUMMOL=3
-NUMAT=12
-CL=5
-CA=2
-CA=2
-CA=2
-CA=2
-CA=2
-CA=2
-HC=3
-HC=3
-HC=3
-HC=3
-HC=3
-NUMMOL=97
-NUMAT=15
-CL=1
-CT=4
-CA=2
-CA=2
-CA=2
-CA=2
-CA=2
-CA=2
-HC=3
-HC=3
-HC=3
-HC=3
-HC=3
-HC=3
-HC=3