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https://github.com/arcan1s/moldyn.git
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Release statgen 1.0.0
+ added messages + added error checking * some bug fix
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arcan1s
279
statgen/coords.c
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279
statgen/coords.c
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/* Library for reading coordinates from input file
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*
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* Usage:
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* reading_coords (filename, type_interaction, labels, cell,
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* &number_of_molecules, &number_of_atoms, true_label_molecule, label_molecule,
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* type_atoms, coords)
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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int reading_coords (char *filename, int type_inter, const int *label_atom,
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const float *cell, int *num_mol, int *num_atoms,
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int *true_label_mol, int *label_mol,
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int *type_atoms, float *coords)
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/* filename - name of file with coordinates
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* type_inter - type interaction (number of molecules for interaction)
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* label_atom - types of atom for interaction
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* cell - cell dimension
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* num_mol - number of molecules for writing coordinates
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* num_atoms - number of atoms for writing coordinates
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* true_label_mol - massive of true numbers of molecule for atoms
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* label_mol - massive of numbers of molecule for atoms
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* type_atoms - massive of atom types for atoms
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* coords - massive of coordinates
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*/
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{
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char file_string[256];
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int atoms, i, j, tr_num_atoms, ref_mol, x, y;
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float not_tr_coords[750000], ref[3];
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FILE *inp;
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/* file_string - temp string variable
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* atoms - total number of atoms in system
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* tr_num_atoms - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
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* ref_mol - number of molecule for reference
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* not_tr_coords - not translated coordinates
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* ref - coordinates of reference molecule
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* inp - file with input data
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*/
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*num_atoms = 0;
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*num_mol = 0;
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// Reading file
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inp = fopen (filename, "r");
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if (inp == NULL)
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return 1;
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ref_mol = -1;
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fscanf (inp, "%i", &atoms);
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for (i=0; i<atoms; i++)
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{
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fgets (file_string, 256, inp);
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for (j=0; j<type_inter; j++)
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if (atoi (&file_string[47]) == label_atom[j])
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{
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not_tr_coords[3**num_atoms+0] = atof (&file_string[10]);
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not_tr_coords[3**num_atoms+1] = atof (&file_string[23]);
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not_tr_coords[3**num_atoms+2] = atof (&file_string[35]);
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if (ref_mol != atoi (&file_string[53]))
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{
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ref_mol = atoi (&file_string[53]);
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true_label_mol[*num_mol] = ref_mol;
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*num_mol = *num_mol + 1;
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}
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label_mol[*num_atoms] = *num_mol - 1;
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type_atoms[*num_atoms] = j;
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*num_atoms = *num_atoms + 1;
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}
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}
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fclose (inp);
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// Translation
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tr_num_atoms = *num_atoms;
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for (i=0; i<*num_atoms; i++)
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for (j=0; j<3; j++)
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coords[3*i+j] = not_tr_coords[3*i+j];
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// Assign initial value to reference coordinates
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ref_mol = label_mol[0];
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for (i=0; i<3; i++)
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ref[i] = coords[i];
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for (i=0; i<*num_atoms; i++)
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{
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if (label_mol[i] != ref_mol)
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{
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ref_mol = label_mol[i];
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for (j=0; j<3; j++)
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ref[j] = not_tr_coords[3*i+j];
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}
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for (x=0; x<3; x++)
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{
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if (ref[x] >= 0.0)
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// if xyz >= 0.0 A
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{
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for (j=0; j<3; j++)
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if (j == x)
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
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else
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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else
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// if xyz < 0.0 A
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{
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for (j=0; j<3; j++)
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if (j == x)
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
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else
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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}
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for (x=0; x<3; x++)
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{
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for (y=x+1; y<3; y++)
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{
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if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
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// if xyz and xyz >= 0.0 A
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{
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for (j=0; j<3; j++)
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if ((j == x) || (j == y))
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
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else
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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if ((ref[x] < 0.0) && (ref[y] < 0.0))
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// if xyz and xyz < 0.0 A
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{
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for (j=0; j<3; j++)
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if ((j == x) || (j == y))
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
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else
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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}
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for (y=0; y<3; y++)
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if ((ref[x] < 0.0) && (ref[y] >= 0.0))
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// if xyz OR xyz >= 0.0
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{
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for (j=0; j<3; j++)
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{
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if (j == x)
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
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if (j == y)
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
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if ((j != x) && (j != y))
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coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
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}
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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}
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if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
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// if x and y and z >= 0.0 A
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{
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coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
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coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
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coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
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// if x and y >= 0.0 A and z < 0.0 A
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{
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coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
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coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
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coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
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// if x and z >= 0.0 A and y < 0.0 A
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{
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coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
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coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
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coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
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// if y and z >= 0.0 A and x < 0.0 A
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{
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coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
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coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
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coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
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// if x and y < 0.0 A and z >= 0.0 A
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{
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coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
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coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
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coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
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// if x and z < 0.0 A and y >= 0.0 A
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{
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coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
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coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
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coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
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// if x >= 0.0 A and y and z < 0.0 A
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{
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coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
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coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
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coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
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// if x and y and z < 0.0 A
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{
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coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
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coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
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coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
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label_mol[tr_num_atoms] = label_mol[i];
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type_atoms[tr_num_atoms] = type_atoms[i];
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tr_num_atoms++;
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}
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}
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return 0;
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}
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