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51d31d0a2f750b6bfa3a061686375a820f654d87
moldyn/statgen/coords.c
arcan1s 51d31d0a2f + added CMakeLists.txt 
+ added headers
+ added library 'add_main.c'
+ some optimization
2013-07-22 06:06:01 +04:00

282 lines
9.0 KiB
C
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/* 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>
int reading_coords (const char *filename, const 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 at_symb[32], file_string[256];
int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
float cur_coords[3], not_tr_coords[750000], ref[3];
FILE *inp;
/* cur_*, at_symb - temp variables
* 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);
fgets (file_string, 256, inp);
for (i=0; i<atoms; i++)
{
fgets (file_string, 256, inp);
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
for (j=0; j<type_inter; j++)
if (cur_at_type == label_atom[j])
{
not_tr_coords[3**num_atoms+0] = cur_coords[0];
not_tr_coords[3**num_atoms+1] = cur_coords[1];
not_tr_coords[3**num_atoms+2] = cur_coords[2];
if (ref_mol != cur_mol)
{
ref_mol = cur_mol;
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;
}
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