537 lines
19 KiB
C
537 lines
19 KiB
C
/*
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* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
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* All rights reserved. This file is part of MD-Bench.
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* Use of this source code is governed by a LGPL-3.0
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* license that can be found in the LICENSE file.
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <math.h>
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#include <atom.h>
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#include <allocate.h>
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#include <device.h>
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#include <util.h>
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#define DELTA 20000
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#ifndef MAXLINE
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#define MAXLINE 4096
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#endif
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#ifndef MAX
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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#endif
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void initAtom(Atom *atom) {
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atom->x = NULL; atom->y = NULL; atom->z = NULL;
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atom->vx = NULL; atom->vy = NULL; atom->vz = NULL;
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atom->fx = NULL; atom->fy = NULL; atom->fz = NULL;
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atom->Natoms = 0;
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atom->Nlocal = 0;
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atom->Nghost = 0;
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atom->Nmax = 0;
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atom->type = NULL;
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atom->ntypes = 0;
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atom->epsilon = NULL;
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atom->sigma6 = NULL;
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atom->cutforcesq = NULL;
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atom->cutneighsq = NULL;
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atom->radius = NULL;
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atom->av = NULL;
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atom->r = NULL;
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DeviceAtom *d_atom = &(atom->d_atom);
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d_atom->x = NULL; d_atom->y = NULL; d_atom->z = NULL;
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d_atom->vx = NULL; d_atom->vy = NULL; d_atom->vz = NULL;
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d_atom->fx = NULL; d_atom->fy = NULL; d_atom->fz = NULL;
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d_atom->border_map = NULL;
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d_atom->type = NULL;
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d_atom->epsilon = NULL;
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d_atom->sigma6 = NULL;
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d_atom->cutforcesq = NULL;
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d_atom->cutneighsq = NULL;
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}
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void createAtom(Atom *atom, Parameter *param) {
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MD_FLOAT xlo = 0.0; MD_FLOAT xhi = param->xprd;
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MD_FLOAT ylo = 0.0; MD_FLOAT yhi = param->yprd;
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MD_FLOAT zlo = 0.0; MD_FLOAT zhi = param->zprd;
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atom->Natoms = 4 * param->nx * param->ny * param->nz;
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atom->Nlocal = 0;
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atom->ntypes = param->ntypes;
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atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
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atom->epsilon[i] = param->epsilon;
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atom->sigma6[i] = param->sigma6;
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atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
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atom->cutforcesq[i] = param->cutforce * param->cutforce;
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}
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MD_FLOAT alat = pow((4.0 / param->rho), (1.0 / 3.0));
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int ilo = (int) (xlo / (0.5 * alat) - 1);
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int ihi = (int) (xhi / (0.5 * alat) + 1);
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int jlo = (int) (ylo / (0.5 * alat) - 1);
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int jhi = (int) (yhi / (0.5 * alat) + 1);
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int klo = (int) (zlo / (0.5 * alat) - 1);
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int khi = (int) (zhi / (0.5 * alat) + 1);
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ilo = MAX(ilo, 0);
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ihi = MIN(ihi, 2 * param->nx - 1);
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jlo = MAX(jlo, 0);
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jhi = MIN(jhi, 2 * param->ny - 1);
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klo = MAX(klo, 0);
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khi = MIN(khi, 2 * param->nz - 1);
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MD_FLOAT xtmp, ytmp, ztmp, vxtmp, vytmp, vztmp;
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int i, j, k, m, n;
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int sx = 0; int sy = 0; int sz = 0;
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int ox = 0; int oy = 0; int oz = 0;
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int subboxdim = 8;
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while(oz * subboxdim <= khi) {
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k = oz * subboxdim + sz;
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j = oy * subboxdim + sy;
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i = ox * subboxdim + sx;
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if(((i + j + k) % 2 == 0) &&
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(i >= ilo) && (i <= ihi) &&
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(j >= jlo) && (j <= jhi) &&
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(k >= klo) && (k <= khi)) {
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xtmp = 0.5 * alat * i;
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ytmp = 0.5 * alat * j;
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ztmp = 0.5 * alat * k;
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if( xtmp >= xlo && xtmp < xhi &&
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ytmp >= ylo && ytmp < yhi &&
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ztmp >= zlo && ztmp < zhi ) {
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n = k * (2 * param->ny) * (2 * param->nx) +
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j * (2 * param->nx) +
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i + 1;
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for(m = 0; m < 5; m++) {
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myrandom(&n);
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}
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vxtmp = myrandom(&n);
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for(m = 0; m < 5; m++){
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myrandom(&n);
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}
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vytmp = myrandom(&n);
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for(m = 0; m < 5; m++) {
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myrandom(&n);
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}
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vztmp = myrandom(&n);
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if(atom->Nlocal == atom->Nmax) {
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growAtom(atom);
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}
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atom_x(atom->Nlocal) = xtmp;
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atom_y(atom->Nlocal) = ytmp;
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atom_z(atom->Nlocal) = ztmp;
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atom_vx(atom->Nlocal) = vxtmp;
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atom_vy(atom->Nlocal) = vytmp;
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atom_vz(atom->Nlocal) = vztmp;
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atom->type[atom->Nlocal] = rand() % atom->ntypes;
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atom->Nlocal++;
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}
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}
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sx++;
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if(sx == subboxdim) { sx = 0; sy++; }
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if(sy == subboxdim) { sy = 0; sz++; }
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if(sz == subboxdim) { sz = 0; ox++; }
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if(ox * subboxdim > ihi) { ox = 0; oy++; }
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if(oy * subboxdim > jhi) { oy = 0; oz++; }
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}
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}
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int type_str2int(const char *type) {
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if(strncmp(type, "Ar", 2) == 0) { return 0; } // Argon
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fprintf(stderr, "Invalid atom type: %s\n", type);
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exit(-1);
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return -1;
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}
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int readAtom(Atom* atom, Parameter* param) {
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int len = strlen(param->input_file);
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if(strncmp(¶m->input_file[len - 4], ".pdb", 4) == 0) { return readAtom_pdb(atom, param); }
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if(strncmp(¶m->input_file[len - 4], ".gro", 4) == 0) { return readAtom_gro(atom, param); }
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if(strncmp(¶m->input_file[len - 4], ".dmp", 4) == 0) { return readAtom_dmp(atom, param); }
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if(strncmp(¶m->input_file[len - 3], ".in", 3) == 0) { return readAtom_in(atom, param); }
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fprintf(stderr, "Invalid input file extension: %s\nValid choices are: pdb, gro, dmp, in\n", param->input_file);
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exit(-1);
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return -1;
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}
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int readAtom_pdb(Atom* atom, Parameter* param) {
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FILE *fp = fopen(param->input_file, "r");
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char line[MAXLINE];
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int read_atoms = 0;
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if(!fp) {
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fprintf(stderr, "Could not open input file: %s\n", param->input_file);
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exit(-1);
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return -1;
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}
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while(!feof(fp)) {
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readline(line, fp);
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char *item = strtok(line, " ");
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if(strncmp(item, "CRYST1", 6) == 0) {
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param->xlo = 0.0;
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param->xhi = atof(strtok(NULL, " "));
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param->ylo = 0.0;
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param->yhi = atof(strtok(NULL, " "));
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param->zlo = 0.0;
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param->zhi = atof(strtok(NULL, " "));
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param->xprd = param->xhi - param->xlo;
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param->yprd = param->yhi - param->ylo;
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param->zprd = param->zhi - param->zlo;
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// alpha, beta, gamma, sGroup, z
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} else if(strncmp(item, "ATOM", 4) == 0) {
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char *label;
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int atom_id, comp_id;
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MD_FLOAT occupancy, charge;
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atom_id = atoi(strtok(NULL, " ")) - 1;
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while(atom_id + 1 >= atom->Nmax) {
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growAtom(atom);
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}
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atom->type[atom_id] = type_str2int(strtok(NULL, " "));
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label = strtok(NULL, " ");
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comp_id = atoi(strtok(NULL, " "));
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atom_x(atom_id) = atof(strtok(NULL, " "));
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atom_y(atom_id) = atof(strtok(NULL, " "));
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atom_z(atom_id) = atof(strtok(NULL, " "));
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atom_vx(atom_id) = 0.0;
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atom_vy(atom_id) = 0.0;
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atom_vz(atom_id) = 0.0;
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occupancy = atof(strtok(NULL, " "));
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charge = atof(strtok(NULL, " "));
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atom->ntypes = MAX(atom->type[atom_id] + 1, atom->ntypes);
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atom->Natoms++;
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atom->Nlocal++;
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read_atoms++;
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} else if(strncmp(item, "HEADER", 6) == 0 ||
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strncmp(item, "REMARK", 6) == 0 ||
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strncmp(item, "MODEL", 5) == 0 ||
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strncmp(item, "TER", 3) == 0 ||
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strncmp(item, "ENDMDL", 6) == 0) {
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// Do nothing
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} else {
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fprintf(stderr, "Invalid item: %s\n", item);
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exit(-1);
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return -1;
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}
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}
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if(!read_atoms) {
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fprintf(stderr, "Input error: No atoms read!\n");
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exit(-1);
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return -1;
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}
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atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
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atom->epsilon[i] = param->epsilon;
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atom->sigma6[i] = param->sigma6;
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atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
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atom->cutforcesq[i] = param->cutforce * param->cutforce;
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}
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fprintf(stdout, "Read %d atoms from %s\n", read_atoms, param->input_file);
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fclose(fp);
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return read_atoms;
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}
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int readAtom_gro(Atom* atom, Parameter* param) {
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FILE *fp = fopen(param->input_file, "r");
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char line[MAXLINE];
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char desc[MAXLINE];
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int read_atoms = 0;
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int atoms_to_read = 0;
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int i = 0;
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if(!fp) {
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fprintf(stderr, "Could not open input file: %s\n", param->input_file);
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exit(-1);
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return -1;
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}
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readline(desc, fp);
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for(i = 0; desc[i] != '\n'; i++);
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desc[i] = '\0';
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readline(line, fp);
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atoms_to_read = atoi(strtok(line, " "));
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fprintf(stdout, "System: %s with %d atoms\n", desc, atoms_to_read);
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while(!feof(fp) && read_atoms < atoms_to_read) {
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readline(line, fp);
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char *label = strtok(line, " ");
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int type = type_str2int(strtok(NULL, " "));
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int atom_id = atoi(strtok(NULL, " ")) - 1;
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atom_id = read_atoms;
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while(atom_id + 1 >= atom->Nmax) {
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growAtom(atom);
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}
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atom->type[atom_id] = type;
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atom_x(atom_id) = atof(strtok(NULL, " "));
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atom_y(atom_id) = atof(strtok(NULL, " "));
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atom_z(atom_id) = atof(strtok(NULL, " "));
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atom_vx(atom_id) = atof(strtok(NULL, " "));
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atom_vy(atom_id) = atof(strtok(NULL, " "));
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atom_vz(atom_id) = atof(strtok(NULL, " "));
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atom->ntypes = MAX(atom->type[atom_id] + 1, atom->ntypes);
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atom->Natoms++;
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atom->Nlocal++;
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read_atoms++;
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}
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if(!feof(fp)) {
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readline(line, fp);
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param->xlo = 0.0;
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param->xhi = atof(strtok(line, " "));
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param->ylo = 0.0;
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param->yhi = atof(strtok(NULL, " "));
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param->zlo = 0.0;
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param->zhi = atof(strtok(NULL, " "));
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param->xprd = param->xhi - param->xlo;
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param->yprd = param->yhi - param->ylo;
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param->zprd = param->zhi - param->zlo;
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}
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if(read_atoms != atoms_to_read) {
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fprintf(stderr, "Input error: Number of atoms read do not match (%d/%d).\n", read_atoms, atoms_to_read);
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exit(-1);
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return -1;
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}
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atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
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atom->epsilon[i] = param->epsilon;
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atom->sigma6[i] = param->sigma6;
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atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
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atom->cutforcesq[i] = param->cutforce * param->cutforce;
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}
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fprintf(stdout, "Read %d atoms from %s\n", read_atoms, param->input_file);
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fclose(fp);
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return read_atoms;
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}
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int readAtom_dmp(Atom* atom, Parameter* param) {
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FILE *fp = fopen(param->input_file, "r");
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char line[MAXLINE];
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int natoms = 0;
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int read_atoms = 0;
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int atom_id = -1;
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int ts = -1;
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if(!fp) {
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fprintf(stderr, "Could not open input file: %s\n", param->input_file);
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exit(-1);
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return -1;
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}
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while(!feof(fp) && ts < 1 && !read_atoms) {
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readline(line, fp);
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if(strncmp(line, "ITEM: ", 6) == 0) {
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char *item = &line[6];
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if(strncmp(item, "TIMESTEP", 8) == 0) {
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readline(line, fp);
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ts = atoi(line);
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} else if(strncmp(item, "NUMBER OF ATOMS", 15) == 0) {
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readline(line, fp);
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natoms = atoi(line);
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atom->Natoms = natoms;
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atom->Nlocal = natoms;
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while(atom->Nlocal >= atom->Nmax) {
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growAtom(atom);
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}
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} else if(strncmp(item, "BOX BOUNDS pp pp pp", 19) == 0) {
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readline(line, fp);
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param->xlo = atof(strtok(line, " "));
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param->xhi = atof(strtok(NULL, " "));
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param->xprd = param->xhi - param->xlo;
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readline(line, fp);
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param->ylo = atof(strtok(line, " "));
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param->yhi = atof(strtok(NULL, " "));
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param->yprd = param->yhi - param->ylo;
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readline(line, fp);
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param->zlo = atof(strtok(line, " "));
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param->zhi = atof(strtok(NULL, " "));
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param->zprd = param->zhi - param->zlo;
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} else if(strncmp(item, "ATOMS id type x y z vx vy vz", 28) == 0) {
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for(int i = 0; i < natoms; i++) {
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readline(line, fp);
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atom_id = atoi(strtok(line, " ")) - 1;
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atom->type[atom_id] = atoi(strtok(NULL, " "));
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atom_x(atom_id) = atof(strtok(NULL, " "));
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atom_y(atom_id) = atof(strtok(NULL, " "));
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atom_z(atom_id) = atof(strtok(NULL, " "));
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atom_vx(atom_id) = atof(strtok(NULL, " "));
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atom_vy(atom_id) = atof(strtok(NULL, " "));
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atom_vz(atom_id) = atof(strtok(NULL, " "));
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atom->ntypes = MAX(atom->type[atom_id], atom->ntypes);
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read_atoms++;
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}
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} else {
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fprintf(stderr, "Invalid item: %s\n", item);
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exit(-1);
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return -1;
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}
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} else {
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fprintf(stderr, "Invalid input from file, expected item reference but got:\n%s\n", line);
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exit(-1);
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return -1;
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}
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}
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if(ts < 0 || !natoms || !read_atoms) {
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fprintf(stderr, "Input error: atom data was not read!\n");
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exit(-1);
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return -1;
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}
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atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
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for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
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atom->epsilon[i] = param->epsilon;
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atom->sigma6[i] = param->sigma6;
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atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
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atom->cutforcesq[i] = param->cutforce * param->cutforce;
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}
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fprintf(stdout, "Read %d atoms from %s\n", natoms, param->input_file);
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return natoms;
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}
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int readAtom_in(Atom* atom, Parameter* param) {
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FILE *fp = fopen(param->input_file, "r");
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char line[MAXLINE];
|
|
int natoms = 0;
|
|
int atom_id = 0;
|
|
|
|
if(!fp) {
|
|
fprintf(stderr, "Could not open input file: %s\n", param->input_file);
|
|
exit(-1);
|
|
return -1;
|
|
}
|
|
|
|
readline(line, fp);
|
|
natoms = atoi(strtok(line, " "));
|
|
param->xlo = atof(strtok(NULL, " "));
|
|
param->xhi = atof(strtok(NULL, " "));
|
|
param->ylo = atof(strtok(NULL, " "));
|
|
param->yhi = atof(strtok(NULL, " "));
|
|
param->zlo = atof(strtok(NULL, " "));
|
|
param->zhi = atof(strtok(NULL, " "));
|
|
atom->Natoms = natoms;
|
|
atom->Nlocal = natoms;
|
|
atom->ntypes = 1;
|
|
|
|
while(atom->Nlocal >= atom->Nmax) {
|
|
growAtom(atom);
|
|
}
|
|
|
|
for(int i = 0; i < natoms; i++) {
|
|
readline(line, fp);
|
|
|
|
// TODO: store mass per atom
|
|
char *s_mass = strtok(line, " ");
|
|
if(strncmp(s_mass, "inf", 3) == 0) {
|
|
// Set atom's mass to INFINITY
|
|
} else {
|
|
param->mass = atof(s_mass);
|
|
}
|
|
|
|
atom->radius[atom_id] = atof(strtok(NULL, " "));
|
|
atom_x(atom_id) = atof(strtok(NULL, " "));
|
|
atom_y(atom_id) = atof(strtok(NULL, " "));
|
|
atom_z(atom_id) = atof(strtok(NULL, " "));
|
|
atom_vx(atom_id) = atof(strtok(NULL, " "));
|
|
atom_vy(atom_id) = atof(strtok(NULL, " "));
|
|
atom_vz(atom_id) = atof(strtok(NULL, " "));
|
|
atom->type[atom_id] = 0;
|
|
atom->ntypes = MAX(atom->type[atom_id], atom->ntypes);
|
|
atom_id++;
|
|
}
|
|
|
|
if(!natoms) {
|
|
fprintf(stderr, "Input error: atom data was not read!\n");
|
|
exit(-1);
|
|
return -1;
|
|
}
|
|
|
|
atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
|
|
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
|
|
atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
|
|
atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
|
|
for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
|
|
atom->epsilon[i] = param->epsilon;
|
|
atom->sigma6[i] = param->sigma6;
|
|
atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
|
|
atom->cutforcesq[i] = param->cutforce * param->cutforce;
|
|
}
|
|
|
|
fprintf(stdout, "Read %d atoms from %s\n", natoms, param->input_file);
|
|
return natoms;
|
|
}
|
|
|
|
void growAtom(Atom *atom) {
|
|
DeviceAtom *d_atom = &(atom->d_atom);
|
|
int nold = atom->Nmax;
|
|
atom->Nmax += DELTA;
|
|
|
|
#undef REALLOC
|
|
#define REALLOC(p,t,ns,os); \
|
|
atom->p = (t *) reallocate(atom->p, ALIGNMENT, ns, os); \
|
|
atom->d_atom.p = (t *) reallocateGPU(atom->d_atom.p, ns);
|
|
|
|
#ifdef AOS
|
|
REALLOC(x, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3);
|
|
REALLOC(vx, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3);
|
|
REALLOC(fx, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3);
|
|
#else
|
|
REALLOC(x, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
REALLOC(y, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
REALLOC(z, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
REALLOC(vx, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
REALLOC(vy, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
REALLOC(vz, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
REALLOC(fx, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
REALLOC(fy, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
REALLOC(fz, MD_FLOAT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
#endif
|
|
REALLOC(type, int, atom->Nmax * sizeof(int), nold * sizeof(int));
|
|
|
|
// DEM
|
|
atom->radius = (MD_FLOAT *) reallocate(atom->radius, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT), nold * sizeof(MD_FLOAT));
|
|
atom->av = (MD_FLOAT*) reallocate(atom->av, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 3, nold * sizeof(MD_FLOAT) * 3);
|
|
atom->r = (MD_FLOAT*) reallocate(atom->r, ALIGNMENT, atom->Nmax * sizeof(MD_FLOAT) * 4, nold * sizeof(MD_FLOAT) * 4);
|
|
}
|