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moldyn/mathmech/mm/src/coords.c
arcan1s 2c44b229ee rewrite trajectory format to store coordinates
2015-11-01 00:10:42 +03:00

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/*
* ----------------------------------------------------------------------------
* "THE BEER-WARE LICENSE" (Revision 42):
* Evgeniy Alekseev wrote this file. As long as you retain this notice you
* can do whatever you want with this stuff. If we meet some day, and you think
* this stuff is worth it, you can buy me a beer in return
* ----------------------------------------------------------------------------
*/
/**
* @file coords.c
* Source code of mathmech library
* @author Evgeniy Alekseev (arcanis)
* @copyright Beerware
* @bug No known bugs
*/
#include <stdio.h>
#include <stdlib.h>
#include <mathmech/coords.h>
/**
* @fn reading_coords
*/
int reading_coords (const int mode, const char *filename, const int type_inter,
const int *label_atom, system_info *_system_info,
int *true_label_mol, atom_info *_atom_info)
{
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], ref[3], cur_cell[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(*_system_info).num_atoms)
* ref_mol number of molecule for reference in translation
* ref massive of coordinates of reference molecule
* inp input file
*/
/// <b>Work blocks</b>
(*_system_info).num_atoms = 0;
(*_system_info).num_mol = 0;
/// <pre> reading file </pre>
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);
// 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])
{
_atom_info[(*_system_info).num_atoms].coords[0] = cur_coords[0];
_atom_info[(*_system_info).num_atoms].coords[1] = cur_coords[1];
_atom_info[(*_system_info).num_atoms].coords[2] = cur_coords[2];
_atom_info[(*_system_info).num_atoms].ch_type_atoms[0] = at_symb[0];
_atom_info[(*_system_info).num_atoms].ch_type_atoms[1] = at_symb[1];
if (ref_mol != cur_mol)
{
ref_mol = cur_mol;
true_label_mol[(*_system_info).num_mol] = ref_mol;
(*_system_info).num_mol = (*_system_info).num_mol + 1;
}
_atom_info[(*_system_info).num_atoms].label_mol = (*_system_info).num_mol - 1;
_atom_info[(*_system_info).num_atoms].type_atoms = j;
(*_system_info).num_atoms = (*_system_info).num_atoms + 1;
}
break;
case 1:
// mode == 1 (all atoms)
_atom_info[(*_system_info).num_atoms].coords[0] = cur_coords[0];
_atom_info[(*_system_info).num_atoms].coords[1] = cur_coords[1];
_atom_info[(*_system_info).num_atoms].coords[2] = cur_coords[2];
_atom_info[(*_system_info).num_atoms].ch_type_atoms[0] = at_symb[0];
_atom_info[(*_system_info).num_atoms].ch_type_atoms[1] = at_symb[1];
if (ref_mol != cur_mol)
{
ref_mol = cur_mol;
true_label_mol[(*_system_info).num_mol] = ref_mol;
(*_system_info).num_mol = (*_system_info).num_mol + 1;
}
_atom_info[(*_system_info).num_atoms].label_mol = (*_system_info).num_mol - 1;
_atom_info[(*_system_info).num_atoms].type_atoms = j;
(*_system_info).num_atoms = (*_system_info).num_atoms + 1;
break;
case 2:
// mode == 2 (selected molecules)
for (j=0; j<type_inter; j++)
if (cur_mol == label_atom[j])
{
_atom_info[(*_system_info).num_atoms].coords[0] = cur_coords[0];
_atom_info[(*_system_info).num_atoms].coords[1] = cur_coords[1];
_atom_info[(*_system_info).num_atoms].coords[2] = cur_coords[2];
_atom_info[(*_system_info).num_atoms].ch_type_atoms[0] = at_symb[0];
_atom_info[(*_system_info).num_atoms].ch_type_atoms[1] = at_symb[1];
if (ref_mol != cur_mol)
{
ref_mol = cur_mol;
true_label_mol[(*_system_info).num_mol] = ref_mol;
(*_system_info).num_mol = (*_system_info).num_mol + 1;
}
_atom_info[(*_system_info).num_atoms].label_mol = (*_system_info).num_mol - 1;
_atom_info[(*_system_info).num_atoms].type_atoms = j;
(*_system_info).num_atoms = (*_system_info).num_atoms + 1;
}
break;
default: return 2;
}
}
// cell sizes
fgets (file_string, 256, inp);
sscanf (file_string, "%f,%f,%f", &cur_cell[0], &cur_cell[1],
&cur_cell[2]);
(*_system_info).cell[0] = cur_cell[0];
(*_system_info).cell[1] = cur_cell[1];
(*_system_info).cell[2] = cur_cell[2];
fclose (inp);
/// <pre> translation </pre>
tr_num_atoms = (*_system_info).num_atoms;
// assign initial value to reference coordinates
ref_mol = _atom_info[0].label_mol;
for (i=0; i<3; i++)
ref[i] = _atom_info[0].coords[i];
for (i=0; i<(*_system_info).num_atoms; i++)
{
if (_atom_info[i].label_mol != ref_mol)
{
ref_mol = _atom_info[i].label_mol;
for (j=0; j<3; j++)
ref[j] = _atom_info[i].coords[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)
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j] - (*_system_info).cell[j];
else
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
tr_num_atoms++;
}
else
// if xyz < 0.0 A
{
for (j=0; j<3; j++)
if (j == x)
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j] + (*_system_info).cell[j];
else
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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))
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j] - (*_system_info).cell[j];
else
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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))
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j] + (*_system_info).cell[j];
else
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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)
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j] + (*_system_info).cell[j];
if (j == y)
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j] - (*_system_info).cell[j];
if ((j != x) && (j != y))
_atom_info[tr_num_atoms].coords[j] = _atom_info[i].coords[j];
}
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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
{
_atom_info[tr_num_atoms].coords[0] = _atom_info[i].coords[0] - (*_system_info).cell[0];
_atom_info[tr_num_atoms].coords[1] = _atom_info[i].coords[1] - (*_system_info).cell[1];
_atom_info[tr_num_atoms].coords[2] = _atom_info[i].coords[2] - (*_system_info).cell[2];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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
{
_atom_info[tr_num_atoms].coords[0] = _atom_info[i].coords[0] - (*_system_info).cell[0];
_atom_info[tr_num_atoms].coords[1] = _atom_info[i].coords[1] - (*_system_info).cell[1];
_atom_info[tr_num_atoms].coords[2] = _atom_info[i].coords[2] + (*_system_info).cell[2];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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
{
_atom_info[tr_num_atoms].coords[0] = _atom_info[i].coords[0] - (*_system_info).cell[0];
_atom_info[tr_num_atoms].coords[1] = _atom_info[i].coords[1] + (*_system_info).cell[1];
_atom_info[tr_num_atoms].coords[2] = _atom_info[i].coords[2] - (*_system_info).cell[2];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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
{
_atom_info[tr_num_atoms].coords[0] = _atom_info[i].coords[0] + (*_system_info).cell[0];
_atom_info[tr_num_atoms].coords[1] = _atom_info[i].coords[1] - (*_system_info).cell[1];
_atom_info[tr_num_atoms].coords[2] = _atom_info[i].coords[2] - (*_system_info).cell[2];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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
{
_atom_info[tr_num_atoms].coords[0] = _atom_info[i].coords[0] + (*_system_info).cell[0];
_atom_info[tr_num_atoms].coords[1] = _atom_info[i].coords[1] + (*_system_info).cell[1];
_atom_info[tr_num_atoms].coords[2] = _atom_info[i].coords[2] - (*_system_info).cell[2];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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
{
_atom_info[tr_num_atoms].coords[0] = _atom_info[i].coords[0] + (*_system_info).cell[0];
_atom_info[tr_num_atoms].coords[1] = _atom_info[i].coords[1] - (*_system_info).cell[1];
_atom_info[tr_num_atoms].coords[2] = _atom_info[i].coords[2] + (*_system_info).cell[2];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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
{
_atom_info[tr_num_atoms].coords[0] = _atom_info[i].coords[0] - (*_system_info).cell[0];
_atom_info[tr_num_atoms].coords[1] = _atom_info[i].coords[1] + (*_system_info).cell[1];
_atom_info[tr_num_atoms].coords[2] = _atom_info[i].coords[2] + (*_system_info).cell[2];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
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
{
_atom_info[tr_num_atoms].coords[0] = _atom_info[i].coords[0] + (*_system_info).cell[0];
_atom_info[tr_num_atoms].coords[1] = _atom_info[i].coords[1] + (*_system_info).cell[1];
_atom_info[tr_num_atoms].coords[2] = _atom_info[i].coords[2] + (*_system_info).cell[2];
_atom_info[tr_num_atoms].label_mol = _atom_info[i].label_mol;
_atom_info[tr_num_atoms].type_atoms = _atom_info[i].type_atoms;
_atom_info[tr_num_atoms].ch_type_atoms[0] = _atom_info[i].ch_type_atoms[0];
_atom_info[tr_num_atoms].ch_type_atoms[1] = _atom_info[i].ch_type_atoms[1];
tr_num_atoms++;
}
}
return 0;
}
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