197 lines
7.0 KiB
C
197 lines
7.0 KiB
C
#include <stdio.h>
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#include <string.h>
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//---
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#include <likwid-marker.h>
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//---
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#include <timing.h>
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#include <allocate.h>
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#include <neighbor.h>
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#include <parameter.h>
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#include <atom.h>
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#include <thermo.h>
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#include <pbc.h>
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#define HLINE "----------------------------------------------------------------------------\n"
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#define LATTICE_DISTANCE 10.0
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#define NEIGH_DISTANCE 1.0
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extern double computeForce( Parameter*, Atom*, Neighbor*, int);
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void init(Parameter *param) {
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param->epsilon = 1.0;
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param->sigma6 = 1.0;
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param->rho = 0.8442;
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param->ntimes = 200;
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param->nx = 4;
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param->ny = 4;
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param->nz = 2;
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param->lattice = LATTICE_DISTANCE;
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param->cutforce = 5.0;
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param->cutneigh = param->cutforce;
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param->mass = 1.0;
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// Unused
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param->dt = 0.005;
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param->dtforce = 0.5 * param->dt;
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param->nstat = 100;
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param->temp = 1.44;
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param->every = 20;
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}
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// Show debug messages
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//#define DEBUG(msg) printf(msg)
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// Do not show debug messages
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#define DEBUG(msg)
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#define ADD_ATOM(x, y, z, vx, vy, vz) atom_x(atom->Nlocal) = base_x + x * NEIGH_DISTANCE; \
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atom_y(atom->Nlocal) = base_y + y * NEIGH_DISTANCE; \
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atom_z(atom->Nlocal) = base_z + z * NEIGH_DISTANCE; \
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atom->vx[atom->Nlocal] = vy; \
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atom->vy[atom->Nlocal] = vy; \
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atom->vz[atom->Nlocal] = vz; \
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atom->Nlocal++
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int main(int argc, const char *argv[]) {
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Atom atom_data;
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Atom *atom = (Atom *)(&atom_data);
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Neighbor neighbor;
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Parameter param;
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LIKWID_MARKER_INIT;
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LIKWID_MARKER_REGISTER("force");
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DEBUG("Initializing parameters...\n");
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init(¶m);
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for(int i = 0; i < argc; i++)
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{
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if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0))
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{
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param.ntimes = atoi(argv[++i]);
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continue;
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}
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if((strcmp(argv[i], "-nx") == 0))
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{
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param.nx = atoi(argv[++i]);
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continue;
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}
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if((strcmp(argv[i], "-ny") == 0))
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{
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param.ny = atoi(argv[++i]);
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continue;
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}
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if((strcmp(argv[i], "-nz") == 0))
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{
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param.nz = atoi(argv[++i]);
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continue;
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}
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if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0))
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{
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printf("MD Bench: A minimalistic re-implementation of miniMD\n");
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printf(HLINE);
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printf("-n / --nsteps <int>: set number of timesteps for simulation\n");
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printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n");
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printf(HLINE);
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exit(EXIT_SUCCESS);
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}
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}
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param.xprd = param.nx * LATTICE_DISTANCE;
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param.yprd = param.ny * LATTICE_DISTANCE;
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param.zprd = param.nz * LATTICE_DISTANCE;
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DEBUG("Initializing atoms...\n");
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initAtom(atom);
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DEBUG("Creating atoms...\n");
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const int atoms_per_unit_cell = 8;
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for(int i = 0; i < param.nx; ++i) {
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for(int j = 0; j < param.ny; ++j) {
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for(int k = 0; k < param.nz; ++k) {
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MD_FLOAT base_x = i * LATTICE_DISTANCE;
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MD_FLOAT base_y = j * LATTICE_DISTANCE;
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MD_FLOAT base_z = k * LATTICE_DISTANCE;
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MD_FLOAT vx = 0.0;
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MD_FLOAT vy = 0.0;
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MD_FLOAT vz = 0.0;
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while(atom->Nlocal > atom->Nmax - atoms_per_unit_cell) {
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growAtom(atom);
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}
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if(atoms_per_unit_cell == 4) {
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ADD_ATOM(0.0, 0.0, 0.0, vx, vy, vz);
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ADD_ATOM(1.0, 0.0, 0.0, vx, vy, vz);
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ADD_ATOM(0.0, 1.0, 0.0, vx, vy, vz);
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ADD_ATOM(0.0, 0.0, 1.0, vx, vy, vz);
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} else if(atoms_per_unit_cell == 8) {
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ADD_ATOM(0.0, 0.0, 0.0, vx, vy, vz);
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ADD_ATOM(1.0, 0.0, 0.0, vx, vy, vz);
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ADD_ATOM(0.0, 1.0, 0.0, vx, vy, vz);
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ADD_ATOM(0.0, 0.0, 1.0, vx, vy, vz);
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ADD_ATOM(1.0, 1.0, 0.0, vx, vy, vz);
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ADD_ATOM(1.0, 0.0, 1.0, vx, vy, vz);
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ADD_ATOM(0.0, 1.0, 1.0, vx, vy, vz);
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ADD_ATOM(1.0, 1.0, 1.0, vx, vy, vz);
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} else if(atoms_per_unit_cell == 16) {
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ADD_ATOM(0.0, 0.0, 0.0, vx, vy, vz);
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ADD_ATOM(1.0, 0.0, 0.0, vx, vy, vz);
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ADD_ATOM(0.0, 1.0, 0.0, vx, vy, vz);
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ADD_ATOM(0.0, 0.0, 1.0, vx, vy, vz);
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ADD_ATOM(1.0, 1.0, 0.0, vx, vy, vz);
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ADD_ATOM(1.0, 0.0, 1.0, vx, vy, vz);
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ADD_ATOM(0.0, 1.0, 1.0, vx, vy, vz);
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ADD_ATOM(1.0, 1.0, 1.0, vx, vy, vz);
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ADD_ATOM(0.5, 0.5, 0.5, vx, vy, vz);
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ADD_ATOM(1.5, 0.5, 0.5, vx, vy, vz);
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ADD_ATOM(0.5, 1.5, 0.5, vx, vy, vz);
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ADD_ATOM(0.5, 0.5, 1.5, vx, vy, vz);
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ADD_ATOM(1.5, 1.5, 0.5, vx, vy, vz);
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ADD_ATOM(1.5, 0.5, 1.5, vx, vy, vz);
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ADD_ATOM(0.5, 1.5, 1.5, vx, vy, vz);
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ADD_ATOM(1.5, 1.5, 1.5, vx, vy, vz);
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} else {
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printf("Invalid number of atoms per unit cell, must be: 4, 8 or 16\n");
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return EXIT_FAILURE;
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}
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}
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}
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}
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const double estim_volume = (double)
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(atom->Nlocal * 6 * sizeof(MD_FLOAT) +
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atom->Nlocal * (atoms_per_unit_cell - 1 + 2) * sizeof(int)) / 1000.0;
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printf("System size (unit cells): %dx%dx%d\n", param.nx, param.ny, param.nz);
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printf("Atoms per unit cell: %d\n", atoms_per_unit_cell);
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printf("Total number of atoms: %d\n", atom->Nlocal);
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printf("Estimated total data volume (kB): %.4f\n", estim_volume );
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printf("Estimated atom data volume (kB): %.4f\n",
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(double)(atom->Nlocal * 3 * sizeof(MD_FLOAT) / 1000.0));
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printf("Estimated neighborlist data volume (kB): %.4f\n",
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(double)(atom->Nlocal * (atoms_per_unit_cell - 1 + 2) * sizeof(int)) / 1000.0);
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DEBUG("Initializing neighbor lists...\n");
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initNeighbor(&neighbor, ¶m);
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DEBUG("Setting up neighbor lists...\n");
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setupNeighbor();
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DEBUG("Building neighbor lists...\n");
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buildNeighbor(atom, &neighbor);
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DEBUG("Computing forces...\n");
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computeForce(¶m, atom, &neighbor, 0);
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double S, E;
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S = getTimeStamp();
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LIKWID_MARKER_START("force");
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for(int i = 0; i < param.ntimes; i++) {
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computeForce(¶m, atom, &neighbor, 1);
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}
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LIKWID_MARKER_STOP("force");
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E = getTimeStamp();
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double T_accum = E-S;
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printf("Total time: %.4f, Mega atom updates/s: %.4f\n",
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T_accum, atom->Nlocal * param.ntimes/T_accum/1.E6);
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LIKWID_MARKER_CLOSE;
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return EXIT_SUCCESS;
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}
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