MD-Bench/clusterpair/xtc.c

/*
 * Copyright (C)  NHR@FAU, University Erlangen-Nuremberg.
 * All rights reserved. This file is part of MD-Bench.
 * Use of this source code is governed by a LGPL-3.0
 * license that can be found in the LICENSE file.
 */
#include <stdlib.h>
//---
#include <atom.h>
#include <allocate.h>
#include <xtc.h>

#ifdef XTC_OUTPUT
#include <gromacs/fileio/xtcio.h>

static struct t_fileio *xtc_file = NULL;
static rvec *x_buf = NULL;
static rvec basis[3];

void xtc_init(const char *filename, Atom *atom, int timestep) {
    basis[0][XX] = 1.0;
    basis[0][YY] = 0.0;
    basis[0][ZZ] = 0.0;
    basis[1][XX] = 0.0;
    basis[1][YY] = 1.0;
    basis[1][ZZ] = 0.0;
    basis[2][XX] = 0.0;
    basis[2][YY] = 0.0;
    basis[2][ZZ] = 1.0;

    xtc_file = open_xtc(filename, "w");
    x_buf = (rvec *) allocate(ALIGNMENT, sizeof(rvec) * (atom->Nlocal + 1));
    xtc_write(atom, timestep, 1, 1);
}

void xtc_write(Atom *atom, int timestep, int write_pos, int write_vel) {
    int i = 0;
    for(int ci = 0; ci < atom->Nclusters_local; ++ci) {
        int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
        MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
        for(int cii = 0; cii < atom->clusters[ci].natoms; ++cii) {
            x_buf[i][XX] = ci_x[CL_X_OFFSET + cii];
            x_buf[i][YY] = ci_x[CL_Y_OFFSET + cii];
            x_buf[i][ZZ] = ci_x[CL_Z_OFFSET + cii];
            i++;
        }
    }

    write_xtc(xtc_file, atom->Nlocal, timestep, 0.0, (const rvec *) basis, (const rvec *) x_buf, 1000);
}

void xtc_end() {
    free(x_buf);
    close_xtc(xtc_file);
}
#endif