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moldyn/mathmech/mm/src/coords.c
arcan1s 7c874ca96d start moving to another architecture
2014-01-26 03:49:43 +04:00

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/**
* @file
*/
#include <stdio.h>
#include <stdlib.h>
/**
* @fn reading_coords
*/
int reading_coords (const int mode, 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, char *ch_type_atoms)
/**
* @brief function that reads coordinates from special file format
* @code
* reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms,
* true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
* @endcode
*
* @param mode mode of reading; '1' is statgen, '2' is envir or
* frad, '3' is agl
* @param filename input file name
* @param type_inter number of needed atoms
* (number of needed molecules)
* @param label_atom massive of needed atom types
* (massive of needed molecules)
* @param cell massive of cell size
* @param num_mol number of molecules
* @param num_atoms number of atoms
* @param true_label_mol massive of true numbers of molecule for atoms
* @param label_mol massive of numbers of molecule for atoms
* @param type_atoms massive of atom types
* @param coords massive of coordinates
* @param ch_type_atoms massive of char atom types
*
* @return 1 - file $filename does not exist
* @return 2 - unknown mode
* @return 0 - exit without errors
*/
{
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, ref[3];
FILE *inp;
/* cur_* temp variables
* at_symb temp variable
* file_string temp string variable
* atoms total number of atoms in system
* tr_num_atoms number of translated atoms (must be 8*num_atoms)
* ref_mol number of molecule for reference in translation
* not_tr_coords massive of not translated coordinates
* ref massive of coordinates of reference molecule
* inp input file
*/
/// <b>Work blocks</b>
*num_atoms = 0;
*num_mol = 0;
/// <pre> reading file </pre>
inp = fopen (filename, "r");
if (inp == NULL)
return 1;
ref_mol = -1;
fscanf (inp, "%i", &atoms);
not_tr_coords = (float *) malloc (3 * atoms * sizeof (float));
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);
// reading variables according to selected mode
switch (mode)
{
case 0:
// mode == 0 (selected atoms)
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;
}
break;
case 1:
// mode == 1 (all atoms)
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];
ch_type_atoms[2**num_atoms+0] = at_symb[0];
ch_type_atoms[2**num_atoms+1] = at_symb[1];
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;
break;
case 2:
// mode == 2 (selected molecules)
for (j=0; j<type_inter; j++)
if (cur_mol == 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];
ch_type_atoms[2**num_atoms+0] = at_symb[0];
ch_type_atoms[2**num_atoms+1] = at_symb[1];
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;
}
break;
default: return 2;
}
}
fclose (inp);
/// <pre> translation </pre>
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[3*0+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++;
}
}
/// <pre> free memory </pre>
free (not_tr_coords);
return 0;
}
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