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start moving to another architecture
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arcan1s
354
mathmech/mm/src/coords.c
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354
mathmech/mm/src/coords.c
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@ -0,0 +1,354 @@
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/**
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* @file
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*/
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#include <stdio.h>
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#include <stdlib.h>
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/**
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* @fn reading_coords
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*/
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int reading_coords (const int mode, const char *filename, const int type_inter,
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const int *label_atom, const float *cell, int *num_mol,
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int *num_atoms, int *true_label_mol, int *label_mol,
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int *type_atoms, float *coords, char *ch_type_atoms)
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/**
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* @brief function that reads coordinates from special file format
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* @code
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* reading_coords (0, filename, type_inter, label_atom, cell, &num_mol, &num_atoms,
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* true_label_mol, label_mol, type_atoms, coords, ch_type_atoms);
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* @endcode
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*
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* @param mode mode of reading; '1' is statgen, '2' is envir or
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* frad, '3' is agl
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* @param filename input file name
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* @param type_inter number of needed atoms
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* (number of needed molecules)
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* @param label_atom massive of needed atom types
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* (massive of needed molecules)
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* @param cell massive of cell size
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* @param num_mol number of molecules
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* @param num_atoms number of atoms
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* @param true_label_mol massive of true numbers of molecule for atoms
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* @param label_mol massive of numbers of molecule for atoms
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* @param type_atoms massive of atom types
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* @param coords massive of coordinates
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* @param ch_type_atoms massive of char atom types
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*
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* @return 1 - file $filename does not exist
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* @return 2 - unknown mode
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* @return 0 - exit without errors
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*/
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{
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char at_symb[32], file_string[256];
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int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
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float cur_coords[3], *not_tr_coords, ref[3];
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FILE *inp;
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/* cur_* temp variables
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* at_symb temp variable
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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 (must be 8*num_atoms)
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* ref_mol number of molecule for reference in translation
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* not_tr_coords massive of not translated coordinates
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* ref massive of coordinates of reference molecule
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* inp input file
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*/
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/// <b>Work blocks</b>
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*num_atoms = 0;
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*num_mol = 0;
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/// <pre> reading file </pre>
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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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not_tr_coords = (float *) malloc (3 * atoms * sizeof (float));
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fgets (file_string, 256, inp);
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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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sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
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&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
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// reading variables according to selected mode
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switch (mode)
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{
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case 0:
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// mode == 0 (selected atoms)
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for (j=0; j<type_inter; j++)
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if (cur_at_type == label_atom[j])
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{
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not_tr_coords[3**num_atoms+0] = cur_coords[0];
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not_tr_coords[3**num_atoms+1] = cur_coords[1];
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not_tr_coords[3**num_atoms+2] = cur_coords[2];
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if (ref_mol != cur_mol)
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{
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ref_mol = cur_mol;
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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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break;
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case 1:
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// mode == 1 (all atoms)
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not_tr_coords[3**num_atoms+0] = cur_coords[0];
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not_tr_coords[3**num_atoms+1] = cur_coords[1];
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not_tr_coords[3**num_atoms+2] = cur_coords[2];
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ch_type_atoms[2**num_atoms+0] = at_symb[0];
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ch_type_atoms[2**num_atoms+1] = at_symb[1];
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if (ref_mol != cur_mol)
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{
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ref_mol = cur_mol;
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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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break;
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case 2:
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// mode == 2 (selected molecules)
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for (j=0; j<type_inter; j++)
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if (cur_mol == label_atom[j])
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{
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not_tr_coords[3**num_atoms+0] = cur_coords[0];
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not_tr_coords[3**num_atoms+1] = cur_coords[1];
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not_tr_coords[3**num_atoms+2] = cur_coords[2];
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ch_type_atoms[2**num_atoms+0] = at_symb[0];
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ch_type_atoms[2**num_atoms+1] = at_symb[1];
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if (ref_mol != cur_mol)
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{
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ref_mol = cur_mol;
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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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break;
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default: return 2;
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}
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}
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fclose (inp);
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/// <pre> translation </pre>
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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[3*0+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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/// <pre> free memory </pre>
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free (not_tr_coords);
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return 0;
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}
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