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Merge branch 'master' into stub

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Rafael Ravedutti
2021-04-12 23:10:36 +02:00
parent 706f1c38f2 35273c491b
commit a0699dde4c
10 changed files with 15 additions and 25 deletions
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src/main-stub.c Normal file
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#include <stdio.h>
#include <string.h>
//---
#include <likwid-marker.h>
//---
#include <timing.h>
#include <allocate.h>
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
#include <thermo.h>
#include <pbc.h>
#define HLINE "----------------------------------------------------------------------------\n"
#define LATTICE_DISTANCE 10.0
#define NEIGH_DISTANCE 1.0
extern double computeForce( Parameter*, Atom*, Neighbor*, int, int);
void init(Parameter *param) {
param->epsilon = 1.0;
param->sigma6 = 1.0;
param->rho = 0.8442;
param->ntimes = 200;
param->nx = 4;
param->ny = 4;
param->nz = 2;
param->lattice = LATTICE_DISTANCE;
param->cutforce = 5.0;
param->cutneigh = param->cutforce;
param->mass = 1.0;
// Unused
param->dt = 0.005;
param->dtforce = 0.5 * param->dt;
param->nstat = 100;
param->temp = 1.44;
param->every = 20;
}
// Show debug messages
//#define DEBUG(msg) printf(msg)
// Do not show debug messages
#define DEBUG(msg)
#define ADD_ATOM(x, y, z, vx, vy, vz) atom_x(atom->Nlocal) = base_x + x * NEIGH_DISTANCE; \
atom_y(atom->Nlocal) = base_y + y * NEIGH_DISTANCE; \
atom_z(atom->Nlocal) = base_z + z * NEIGH_DISTANCE; \
atom->vx[atom->Nlocal] = vy; \
atom->vy[atom->Nlocal] = vy; \
atom->vz[atom->Nlocal] = vz; \
atom->Nlocal++
int main(int argc, const char *argv[]) {
Atom atom_data;
Atom *atom = (Atom *)(&atom_data);
Neighbor neighbor;
Parameter param;
LIKWID_MARKER_INIT;
LIKWID_MARKER_REGISTER("force");
DEBUG("Initializing parameters...\n");
init(&param);
for(int i = 0; i < argc; i++)
{
if((strcmp(argv[i], "-n") == 0) || (strcmp(argv[i], "--nsteps") == 0))
{
param.ntimes = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-nx") == 0))
{
param.nx = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-ny") == 0))
{
param.ny = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-nz") == 0))
{
param.nz = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-h") == 0) || (strcmp(argv[i], "--help") == 0))
{
printf("MD Bench: A minimalistic re-implementation of miniMD\n");
printf(HLINE);
printf("-n / --nsteps <int>: set number of timesteps for simulation\n");
printf("-nx/-ny/-nz <int>: set linear dimension of systembox in x/y/z direction\n");
printf(HLINE);
exit(EXIT_SUCCESS);
}
}
param.xprd = param.nx * LATTICE_DISTANCE;
param.yprd = param.ny * LATTICE_DISTANCE;
param.zprd = param.nz * LATTICE_DISTANCE;
DEBUG("Initializing atoms...\n");
initAtom(atom);
DEBUG("Creating atoms...\n");
const int atoms_per_unit_cell = 8;
for(int i = 0; i < param.nx; ++i) {
for(int j = 0; j < param.ny; ++j) {
for(int k = 0; k < param.nz; ++k) {
MD_FLOAT base_x = i * LATTICE_DISTANCE;
MD_FLOAT base_y = j * LATTICE_DISTANCE;
MD_FLOAT base_z = k * LATTICE_DISTANCE;
MD_FLOAT vx = 0.0;
MD_FLOAT vy = 0.0;
MD_FLOAT vz = 0.0;
while(atom->Nlocal > atom->Nmax - atoms_per_unit_cell) {
growAtom(atom);
}
if(atoms_per_unit_cell == 4) {
ADD_ATOM(0.0, 0.0, 0.0, vx, vy, vz);
ADD_ATOM(1.0, 0.0, 0.0, vx, vy, vz);
ADD_ATOM(0.0, 1.0, 0.0, vx, vy, vz);
ADD_ATOM(0.0, 0.0, 1.0, vx, vy, vz);
} else if(atoms_per_unit_cell == 8) {
ADD_ATOM(0.0, 0.0, 0.0, vx, vy, vz);
ADD_ATOM(1.0, 0.0, 0.0, vx, vy, vz);
ADD_ATOM(0.0, 1.0, 0.0, vx, vy, vz);
ADD_ATOM(0.0, 0.0, 1.0, vx, vy, vz);
ADD_ATOM(1.0, 1.0, 0.0, vx, vy, vz);
ADD_ATOM(1.0, 0.0, 1.0, vx, vy, vz);
ADD_ATOM(0.0, 1.0, 1.0, vx, vy, vz);
ADD_ATOM(1.0, 1.0, 1.0, vx, vy, vz);
} else if(atoms_per_unit_cell == 16) {
ADD_ATOM(0.0, 0.0, 0.0, vx, vy, vz);
ADD_ATOM(1.0, 0.0, 0.0, vx, vy, vz);
ADD_ATOM(0.0, 1.0, 0.0, vx, vy, vz);
ADD_ATOM(0.0, 0.0, 1.0, vx, vy, vz);
ADD_ATOM(1.0, 1.0, 0.0, vx, vy, vz);
ADD_ATOM(1.0, 0.0, 1.0, vx, vy, vz);
ADD_ATOM(0.0, 1.0, 1.0, vx, vy, vz);
ADD_ATOM(1.0, 1.0, 1.0, vx, vy, vz);
ADD_ATOM(0.5, 0.5, 0.5, vx, vy, vz);
ADD_ATOM(1.5, 0.5, 0.5, vx, vy, vz);
ADD_ATOM(0.5, 1.5, 0.5, vx, vy, vz);
ADD_ATOM(0.5, 0.5, 1.5, vx, vy, vz);
ADD_ATOM(1.5, 1.5, 0.5, vx, vy, vz);
ADD_ATOM(1.5, 0.5, 1.5, vx, vy, vz);
ADD_ATOM(0.5, 1.5, 1.5, vx, vy, vz);
ADD_ATOM(1.5, 1.5, 1.5, vx, vy, vz);
} else {
printf("Invalid number of atoms per unit cell, must be: 4, 8 or 16\n");
return EXIT_FAILURE;
}
}
}
}
const double estim_volume = (double)(atom->Nlocal * 6 * sizeof(MD_FLOAT) + atom->Nlocal * (atoms_per_unit_cell - 1 + 2) * sizeof(int)) / 1000.0;
printf("System size (unit cells): %dx%dx%d\n", param.nx, param.ny, param.nz);
printf("Atoms per unit cell: %d\n", atoms_per_unit_cell);
printf("Total number of atoms: %d\n", atom->Nlocal);
printf("Estimated memory volume (kB): %.4f\n", estim_volume);
DEBUG("Initializing neighbor lists...\n");
initNeighbor(&neighbor, &param);
DEBUG("Setting up neighbor lists...\n");
setupNeighbor();
DEBUG("Building neighbor lists...\n");
buildNeighbor(atom, &neighbor);
DEBUG("Computing forces...\n");
computeForce(&param, atom, &neighbor, 0, 1);
double T_accum = computeForce(&param, atom, &neighbor, 1, param.ntimes);
printf("Total time: %.4f, Time/force: %.4f\n", T_accum, T_accum / param.ntimes);
LIKWID_MARKER_CLOSE;
return EXIT_SUCCESS;
}