73 lines
2.3 KiB
C
73 lines
2.3 KiB
C
/*
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* =======================================================================================
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*
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* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
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* Copyright (c) 2020 RRZE, University Erlangen-Nuremberg
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*
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* This file is part of MD-Bench.
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*
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* MD-Bench is free software: you can redistribute it and/or modify it
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* under the terms of the GNU Lesser General Public License as published
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* by the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
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* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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* details.
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*
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* You should have received a copy of the GNU Lesser General Public License along
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* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
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* =======================================================================================
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*/
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#include <stdlib.h>
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//---
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#include <atom.h>
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#include <allocate.h>
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#include <xtc.h>
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#ifdef XTC_OUTPUT
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#include <gromacs/fileio/xtcio.h>
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static struct t_fileio *xtc_file = NULL;
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static rvec *x_buf = NULL;
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static rvec basis[3];
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void xtc_init(const char *filename, Atom *atom, int timestep) {
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basis[0][XX] = 1.0;
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basis[0][YY] = 0.0;
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basis[0][ZZ] = 0.0;
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basis[1][XX] = 0.0;
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basis[1][YY] = 1.0;
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basis[1][ZZ] = 0.0;
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basis[2][XX] = 0.0;
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basis[2][YY] = 0.0;
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basis[2][ZZ] = 1.0;
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xtc_file = open_xtc(filename, "w");
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x_buf = (rvec *) allocate(ALIGNMENT, sizeof(rvec) * (atom->Nlocal + 1));
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xtc_write(atom, timestep, 1, 1);
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}
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void xtc_write(Atom *atom, int timestep, int write_pos, int write_vel) {
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int i = 0;
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for(int ci = 0; ci < atom->Nclusters_local; ++ci) {
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int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
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MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
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for(int cii = 0; cii < atom->clusters[ci].natoms; ++cii) {
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x_buf[i][XX] = ci_x[CL_X_OFFSET + cii];
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x_buf[i][YY] = ci_x[CL_Y_OFFSET + cii];
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x_buf[i][ZZ] = ci_x[CL_Z_OFFSET + cii];
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i++;
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}
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}
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write_xtc(xtc_file, atom->Nlocal, timestep, 0.0, (const rvec *) basis, (const rvec *) x_buf, 1000);
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}
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void xtc_end() {
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free(x_buf);
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close_xtc(xtc_file);
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}
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#endif
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