mirror of
https://github.com/arcan1s/moldyn.git
synced 2025-06-28 06:41:42 +00:00
279 lines
8.8 KiB
C
279 lines
8.8 KiB
C
/* Library for reading coordinates from input file
|
|
*
|
|
* Usage:
|
|
* reading_coords (filename, type_interaction, labels, cell,
|
|
* &number_of_molecules, &number_of_atoms, true_label_molecule, label_molecule,
|
|
* type_atoms, coords)
|
|
*/
|
|
|
|
#include <stdio.h>
|
|
#include <stdlib.h>
|
|
#include <string.h>
|
|
|
|
|
|
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,
|
|
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 dimension
|
|
* num_mol - number of molecules for writing coordinates
|
|
* num_atoms - number of atoms for writing coordinates
|
|
* true_label_mol - massive of true numbers of molecule for atoms
|
|
* 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;
|
|
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++)
|
|
{
|
|
fgets (file_string, 256, inp);
|
|
|
|
for (j=0; j<type_inter; j++)
|
|
if (atoi (&file_string[47]) == label_atom[j])
|
|
{
|
|
not_tr_coords[3**num_atoms+0] = atof (&file_string[10]);
|
|
not_tr_coords[3**num_atoms+1] = atof (&file_string[23]);
|
|
not_tr_coords[3**num_atoms+2] = atof (&file_string[35]);
|
|
|
|
if (ref_mol != atoi (&file_string[53]))
|
|
{
|
|
ref_mol = atoi (&file_string[53]);
|
|
true_label_mol[*num_mol] = ref_mol;
|
|
*num_mol = *num_mol + 1;
|
|
}
|
|
label_mol[*num_atoms] = *num_mol - 1;
|
|
type_atoms[*num_atoms] = j;
|
|
|
|
*num_atoms = *num_atoms + 1;
|
|
}
|
|
}
|
|
fclose (inp);
|
|
|
|
// Translation
|
|
tr_num_atoms = *num_atoms;
|
|
for (i=0; i<*num_atoms; i++)
|
|
for (j=0; j<3; j++)
|
|
coords[3*i+j] = not_tr_coords[3*i+j];
|
|
|
|
// Assign initial value to reference coordinates
|
|
ref_mol = label_mol[0];
|
|
for (i=0; i<3; i++)
|
|
ref[i] = coords[i];
|
|
|
|
for (i=0; i<*num_atoms; i++)
|
|
{
|
|
if (label_mol[i] != ref_mol)
|
|
{
|
|
ref_mol = label_mol[i];
|
|
for (j=0; j<3; j++)
|
|
ref[j] = not_tr_coords[3*i+j];
|
|
}
|
|
|
|
for (x=0; x<3; x++)
|
|
{
|
|
if (ref[x] >= 0.0)
|
|
// if xyz >= 0.0 A
|
|
{
|
|
for (j=0; j<3; j++)
|
|
if (j == x)
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
|
else
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
else
|
|
// if xyz < 0.0 A
|
|
{
|
|
for (j=0; j<3; j++)
|
|
if (j == x)
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
|
else
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
}
|
|
|
|
for (x=0; x<3; x++)
|
|
{
|
|
for (y=x+1; y<3; y++)
|
|
{
|
|
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
|
// if xyz and xyz >= 0.0 A
|
|
{
|
|
for (j=0; j<3; j++)
|
|
if ((j == x) || (j == y))
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
|
else
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
|
|
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
|
// if xyz and xyz < 0.0 A
|
|
{
|
|
for (j=0; j<3; j++)
|
|
if ((j == x) || (j == y))
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
|
else
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
}
|
|
|
|
for (y=0; y<3; y++)
|
|
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
|
// if xyz OR xyz >= 0.0
|
|
{
|
|
for (j=0; j<3; j++)
|
|
{
|
|
if (j == x)
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
|
if (j == y)
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
|
if ((j != x) && (j != y))
|
|
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
|
}
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
}
|
|
|
|
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
|
// if x and y and z >= 0.0 A
|
|
{
|
|
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
|
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
|
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
|
|
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
|
// if x and y >= 0.0 A and z < 0.0 A
|
|
{
|
|
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
|
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
|
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
|
|
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
|
// if x and z >= 0.0 A and y < 0.0 A
|
|
{
|
|
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
|
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
|
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
|
|
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
|
// if y and z >= 0.0 A and x < 0.0 A
|
|
{
|
|
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
|
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
|
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
|
|
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
|
// if x and y < 0.0 A and z >= 0.0 A
|
|
{
|
|
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
|
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
|
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
|
|
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
|
// if x and z < 0.0 A and y >= 0.0 A
|
|
{
|
|
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
|
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
|
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
|
|
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
|
// if x >= 0.0 A and y and z < 0.0 A
|
|
{
|
|
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
|
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
|
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
|
|
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
|
// if x and y and z < 0.0 A
|
|
{
|
|
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
|
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
|
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
|
|
|
label_mol[tr_num_atoms] = label_mol[i];
|
|
type_atoms[tr_num_atoms] = type_atoms[i];
|
|
tr_num_atoms++;
|
|
}
|
|
}
|
|
|
|
return 0;
|
|
} |