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MD-Bench/util/mdBench.c

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Introduce modular version.
2020-08-18 14:27:28 +02:00
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2019 RRZE, University Erlangen-Nuremberg
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* =======================================================================================
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <limits.h>
#include <math.h>
#include <float.h>
#define HLINE "----------------------------------------------------------------------------\n"
#define FACTOR 0.999
#define SMALL 1.0e-6
#define DELTA 20000
#ifndef MIN
#define MIN(x,y) ((x)<(y)?(x):(y))
#endif
#ifndef MAX
#define MAX(x,y) ((x)>(y)?(x):(y))
#endif
#ifndef ABS
#define ABS(a) ((a) >= 0 ? (a) : -(a))
#endif
static int Natoms, Nlocal, Nghost, Nmax;
static double Cutneigh; // neighbor cutoff
static double xprd, yprd, zprd;
static double xlo, xhi;
static double ylo, yhi;
static double zlo, zhi;
static double *x, *y, *z;
static double *vx, *vy, *vz;
static double *fx, *fy, *fz;
static int NmaxGhost;
static int *BorderMap;
static int *PBCx, *PBCy, *PBCz;
typedef struct {
int* numneigh;
int* neighbors;
int maxneighs;
int nbinx, nbiny, nbinz;
/* double cutneigh; // neighbor cutoff */
double cutneighsq; // neighbor cutoff squared
int every;
int ncalls;
int max_totalneigh;
int *bincount;
int *bins;
int nmax;
int nstencil; // # of bins in stencil
int* stencil; // stencil list of bin offsets
int mbins; //total number of bins
int atoms_per_bin; // max atoms per bin
int mbinx, mbiny, mbinz; // n bins in x, y, z
int mbinxlo, mbinylo, mbinzlo;
double binsizex, binsizey, binsizez;
double bininvx, bininvy, bininvz;
} Neighbor;
typedef struct {
double epsilon;
double sigma6;
double temp;
double rho;
double mass;
int ntimes;
int nstat;
double dt;
double dtforce;
double cutforce;
int nx, ny, nz;
} Parameter;
typedef struct {
int *steparr;
double *tmparr;
double *engarr;
double *prsarr;
double mvv2e;
int dof_boltz;
double t_scale;
double p_scale;
double e_scale;
double t_act;
double p_act;
double e_act;
int mstat;
} Thermo;
/* Park/Miller RNG w/out MASKING, so as to be like f90s version */
#define IA 16807
#define IM 2147483647
#define AM (1.0/IM)
#define IQ 127773
#define IR 2836
#define MASK 123459876
double myrandom(int* idum)
{
int k= (*idum) / IQ;
double ans;
*idum = IA * (*idum - k * IQ) - IR * k;
if(*idum < 0) *idum += IM;
ans = AM * (*idum);
return ans;
}
int coord2bin(Neighbor* neighbor, double xin, double yin, double zin)
{
int ix, iy, iz;
double bininvx = neighbor->bininvx;
double bininvy = neighbor->bininvy;
double bininvz = neighbor->bininvz;
int mbinxlo = neighbor->mbinxlo;
int mbinylo = neighbor->mbinylo;
int mbinzlo = neighbor->mbinzlo;
if(xin >= xprd) {
ix = (int)((xin - xprd) * bininvx) + neighbor->nbinx - mbinxlo;
} else if(xin >= 0.0) {
ix = (int)(xin * bininvx) - mbinxlo;
} else {
ix = (int)(xin * bininvx) - mbinxlo - 1;
}
if(yin >= yprd) {
iy = (int)((yin - yprd) * bininvy) + neighbor->nbiny - mbinylo;
} else if(yin >= 0.0) {
iy = (int)(yin * bininvy) - mbinylo;
} else {
iy = (int)(yin * bininvy) - mbinylo - 1;
}
if(zin >= zprd) {
iz = (int)((zin - zprd) * bininvz) + neighbor->nbinz - mbinzlo;
} else if(zin >= 0.0) {
iz = (int)(zin * bininvz) - mbinzlo;
} else {
iz = (int)(zin * bininvz) - mbinzlo - 1;
}
return (iz * neighbor->mbiny * neighbor->mbinx + iy * neighbor->mbinx + ix + 1);
}
void binatoms(Neighbor *neighbor)
{
int* bincount = neighbor->bincount;
int mbins = neighbor->mbins;
int nall = Nlocal + Nghost;
int resize = 1;
while(resize > 0) {
resize = 0;
for(int i = 0; i < mbins; i++) {
bincount[i] = 0;
}
for(int i = 0; i < nall; i++) {
int ibin = coord2bin(neighbor, x[i], y[i], z[i]);
if(bincount[ibin] < neighbor->atoms_per_bin) {
int ac = neighbor->bincount[ibin]++;
neighbor->bins[ibin * neighbor->atoms_per_bin + ac] = i;
} else {
resize = 1;
}
}
if(resize) {
free(neighbor->bins);
neighbor->atoms_per_bin *= 2;
neighbor->bins = (int*) malloc(mbins * neighbor->atoms_per_bin * sizeof(int));
}
}
}
double bindist(Neighbor *neighbor, int i, int j, int k)
{
double delx, dely, delz;
if(i > 0) {
delx = (i - 1) * neighbor->binsizex;
} else if(i == 0) {
delx = 0.0;
} else {
delx = (i + 1) * neighbor->binsizex;
}
if(j > 0) {
dely = (j - 1) * neighbor->binsizey;
} else if(j == 0) {
dely = 0.0;
} else {
dely = (j + 1) * neighbor->binsizey;
}
if(k > 0) {
delz = (k - 1) * neighbor->binsizez;
} else if(k == 0) {
delz = 0.0;
} else {
delz = (k + 1) * neighbor->binsizez;
}
return (delx * delx + dely * dely + delz * delz);
}
void buildNeighborlist(Neighbor *neighbor)
{
neighbor->ncalls++;
int nall = Nlocal + Nghost;
/* extend atom arrays if necessary */
if(nall > neighbor->nmax) {
neighbor->nmax = nall;
if(neighbor->numneigh) free(neighbor->numneigh);
if(neighbor->neighbors) free(neighbor->neighbors);
neighbor->numneigh = (int*) malloc(neighbor->nmax * sizeof(int));
neighbor->neighbors = (int*) malloc(neighbor->nmax * neighbor->maxneighs * sizeof(int*));
}
/* bin local & ghost atoms */
binatoms(neighbor);
int resize = 1;
/* loop over each atom, storing neighbors */
while(resize) {
int new_maxneighs = neighbor->maxneighs;
resize = 0;
for(int i = 0; i < Nlocal; i++) {
int* neighptr = &neighbor->neighbors[i * neighbor->maxneighs];
int n = 0;
double xtmp = x[i];
double ytmp = y[i];
double ztmp = z[i];
int ibin = coord2bin(neighbor, xtmp, ytmp, ztmp);
for(int k = 0; k < neighbor->nstencil; k++) {
int jbin = ibin + neighbor->stencil[k];
int* loc_bin = &neighbor->bins[jbin * neighbor->atoms_per_bin];
for(int m = 0; m < neighbor->bincount[jbin]; m++) {
int j = loc_bin[m];
if ( j == i ){
continue;
}
double delx = xtmp - x[j];
double dely = ytmp - y[j];
double delz = ztmp - z[j];
double rsq = delx * delx + dely * dely + delz * delz;
if( rsq <= neighbor->cutneighsq ) {
neighptr[n++] = j;
}
}
}
neighbor->numneigh[i] = n;
if(n >= neighbor->maxneighs) {
resize = 1;
if(n >= new_maxneighs) {
new_maxneighs = n;
}
}
}
if(resize) {
neighbor->maxneighs = new_maxneighs * 1.2;
free(neighbor->neighbors);
neighbor->neighbors = (int*) malloc(Nmax* neighbor->maxneighs * sizeof(int));
}
}
}
void init(Neighbor *neighbor, Parameter *param)
{
x = NULL; y = NULL; z = NULL;
vx = NULL; vy = NULL; vz = NULL;
fx = NULL; fy = NULL; fz = NULL;
NmaxGhost = 0;
BorderMap = NULL;
PBCx = NULL; PBCy = NULL; PBCz = NULL;
param->epsilon = 1.0;
param->sigma6 = 1.0;
param->rho = 0.8442;
param->ntimes = 200;
param->dt = 0.005;
param->nx = 32;
param->ny = 32;
param->nz = 32;
param->cutforce = 2.5;
param->temp = 1.44;
param->nstat = 100;
param->mass = 1.0;
param->dtforce = 0.5 * param->dt;
Cutneigh = param->cutforce + 0.30;
double neighscale = 5.0 / 6.0;
neighbor->nbinx = neighscale * param->nx;
neighbor->nbiny = neighscale * param->ny;
neighbor->nbinz = neighscale * param->nz;
neighbor->every = 20;
neighbor->ncalls = 0;
neighbor->nmax = 0;
neighbor->atoms_per_bin = 8;
neighbor->maxneighs = 100;
/* neighbor->cutneigh = param->cutforce + 0.30; */
neighbor->numneigh = NULL;
neighbor->neighbors = NULL;
neighbor->stencil = NULL;
neighbor->bins = NULL;
neighbor->bincount = NULL;
}
void setup(Neighbor *neighbor, Parameter *param)
{
double lattice = pow((4.0 / param->rho), (1.0 / 3.0));
double coord;
int mbinxhi, mbinyhi, mbinzhi;
int nextx, nexty, nextz;
xprd = param->nx * lattice;
yprd = param->ny * lattice;
zprd = param->nz * lattice;
xlo = 0.0; xhi = xprd;
ylo = 0.0; yhi = yprd;
zlo = 0.0; zhi = zprd;
neighbor->cutneighsq = Cutneigh * Cutneigh;
neighbor->binsizex = xprd / neighbor->nbinx;
neighbor->binsizey = yprd / neighbor->nbiny;
neighbor->binsizez = zprd / neighbor->nbinz;
neighbor->bininvx = 1.0 / neighbor->binsizex;
neighbor->bininvy = 1.0 / neighbor->binsizey;
neighbor->bininvz = 1.0 / neighbor->binsizez;
coord = xlo - Cutneigh - SMALL * xprd;
neighbor->mbinxlo = (int) (coord * neighbor->bininvx);
if (coord < 0.0) {
neighbor->mbinxlo = neighbor->mbinxlo - 1;
}
coord = xhi + Cutneigh + SMALL * xprd;
mbinxhi = (int) (coord * neighbor->bininvx);
coord = ylo - Cutneigh - SMALL * yprd;
neighbor->mbinylo = (int) (coord * neighbor->bininvy);
if (coord < 0.0) {
neighbor->mbinylo = neighbor->mbinylo - 1;
}
coord = yhi + Cutneigh + SMALL * yprd;
mbinyhi = (int) (coord * neighbor->bininvy);
coord = zlo - Cutneigh - SMALL * zprd;
neighbor->mbinzlo = (int) (coord * neighbor->bininvz);
if (coord < 0.0) {
neighbor->mbinzlo = neighbor->mbinzlo - 1;
}
coord = zhi + Cutneigh + SMALL * zprd;
mbinzhi = (int) (coord * neighbor->bininvz);
neighbor->mbinxlo = neighbor->mbinxlo - 1;
mbinxhi = mbinxhi + 1;
neighbor->mbinx = mbinxhi - neighbor->mbinxlo + 1;
neighbor->mbinylo = neighbor->mbinylo - 1;
mbinyhi = mbinyhi + 1;
neighbor->mbiny = mbinyhi - neighbor->mbinylo + 1;
neighbor->mbinzlo = neighbor->mbinzlo - 1;
mbinzhi = mbinzhi + 1;
neighbor->mbinz = mbinzhi - neighbor->mbinzlo + 1;
nextx = (int) (Cutneigh * neighbor->bininvx);
if(nextx * neighbor->binsizex < FACTOR * Cutneigh) nextx++;
nexty = (int) (Cutneigh * neighbor->bininvy);
if(nexty * neighbor->binsizey < FACTOR * Cutneigh) nexty++;
nextz = (int) (Cutneigh * neighbor->bininvz);
if(nextz * neighbor->binsizez < FACTOR * Cutneigh) nextz++;
if (neighbor->stencil) {
free(neighbor->stencil);
}
neighbor->stencil = (int*) malloc(
(2 * nextz + 1) * (2 * nexty + 1) * (2 * nextx + 1) * sizeof(int));
neighbor->nstencil = 0;
int kstart = -nextz;
for(int k = kstart; k <= nextz; k++) {
for(int j = -nexty; j <= nexty; j++) {
for(int i = -nextx; i <= nextx; i++) {
if(bindist(neighbor, i, j, k) < neighbor->cutneighsq) {
neighbor->stencil[neighbor->nstencil++] =
k * neighbor->mbiny * neighbor->mbinx + j * neighbor->mbinx + i;
}
}
}
}
neighbor->mbins = neighbor->mbinx * neighbor->mbiny * neighbor->mbinz;
if (neighbor->bincount) {
free(neighbor->bincount);
}
neighbor->bincount = (int*) malloc(neighbor->mbins * sizeof(int));
if (neighbor->bins) {
free(neighbor->bins);
}
neighbor->bins = (int*) malloc(neighbor->mbins * neighbor->atoms_per_bin * sizeof(int));
}
double* myrealloc(double *ptr, int n, int nold) {
double* newarray;
newarray = (double*) malloc(n * sizeof(double));
if(nold) {
memcpy(newarray, ptr, nold * sizeof(double));
}
if(ptr) {
free(ptr);
}
return newarray;
}
int* myreallocInt(int *ptr, int n, int nold) {
int* newarray;
newarray = (int*) malloc(n * sizeof(int));
if(nold) {
memcpy(newarray, ptr, nold * sizeof(int));
}
if(ptr) {
free(ptr);
}
return newarray;
}
void growBoundary()
{
int nold = NmaxGhost;
NmaxGhost += DELTA;
BorderMap = myreallocInt(BorderMap, NmaxGhost, nold);
PBCx = myreallocInt(PBCx, NmaxGhost, nold);
PBCy = myreallocInt(PBCy, NmaxGhost, nold);
PBCz = myreallocInt(PBCz, NmaxGhost, nold);
if(BorderMap == NULL || PBCx == NULL || PBCy == NULL || PBCz == NULL ) {
printf("ERROR: No memory for Boundary\n");
}
}
void growarray()
{
int nold = Nmax;
Nmax += DELTA;
x = myrealloc(x, Nmax, nold); y = myrealloc(y, Nmax, nold); z = myrealloc(z, Nmax, nold);
vx = myrealloc(vx, Nmax, nold); vy = myrealloc(vy, Nmax, nold); vz = myrealloc(vz, Nmax, nold);
fx = myrealloc(fx, Nmax, nold); fy = myrealloc(fy, Nmax, nold); fz = myrealloc(fz, Nmax, nold);
if(x == NULL || y == NULL || z == NULL ||
vx == NULL || vy == NULL || vz == NULL ||
fx == NULL || fy == NULL || fz == NULL ) {
printf("ERROR: No memory for atoms\n");
}
}
void updateBorders()
{
for(int i = 0; i < Nghost; i++) {
x[Nlocal + i] = x[BorderMap[i]] + PBCx[i] * xprd;
y[Nlocal + i] = y[BorderMap[i]] + PBCy[i] * yprd;
z[Nlocal + i] = z[BorderMap[i]] + PBCz[i] * zprd;
}
}
void updateAtomLocations()
{
for(int i = 0; i < Nlocal; i++) {
if(x[i] < 0.0) {
x[i] += xprd;
} else if(x[i] >= xprd) {
x[i] -= xprd;
}
if(y[i] < 0.0) {
y[i] += yprd;
} else if(y[i] >= yprd) {
y[i] -= yprd;
}
if(z[i] < 0.0) {
z[i] += zprd;
} else if(z[i] >= zprd) {
z[i] -= zprd;
}
}
}
void setupBordersNew()
{
int lastidx = 0;
int nghostprev = 0;
Nghost = 0;
for (int i = 0; i < Nlocal; i++) {
if (Nlocal + Nghost + 1 >= Nmax) {
growarray();
}
if (x[i] < Cutneigh) {
Nghost++;
x[i+lastidx] = x[i] + xprd;
y[i+lastidx] = y[i];
z[i+lastidx] = z[i];
lastidx++;
} else if (x[i] >= xprd - Cutneigh) {
Nghost++;
x[i+lastidx] = x[i] - xprd;
y[i+lastidx] = y[i];
z[i+lastidx] = z[i];
lastidx++;
}
}
nghostprev = Nghost+1;
for (int i = 0; i < Nlocal + nghostprev ; i++) {
if (Nlocal + Nghost + 1 >= Nmax) {
growarray();
}
if (y[i] < Cutneigh) {
Nghost++;
x[i+lastidx] = x[i];
y[i+lastidx] = y[i] + yprd;
z[i+lastidx] = z[i];
lastidx++;
} else if (y[i] >= yprd - Cutneigh) {
Nghost++;
x[i+lastidx] = x[i];
y[i+lastidx] = y[i] - yprd;
z[i+lastidx] = z[i];
lastidx++;
}
}
nghostprev = Nghost+1;
for (int i = 0; i < Nlocal + nghostprev; i++) {
if (Nlocal + Nghost + 1 >= Nmax) {
growarray();
}
if (z[i] < Cutneigh) {
Nghost++;
x[i+lastidx] = x[i];
y[i+lastidx] = y[i];
z[i+lastidx] = z[i] + zprd;
lastidx++;
} else if(z[i] >= zprd - Cutneigh) {
Nghost++;
x[i+lastidx] = x[i];
y[i+lastidx] = y[i];
z[i+lastidx] = z[i] - zprd;
lastidx++;
}
}
Nghost++;
}
#define ADDGHOST(dx,dy,dz) Nghost++; BorderMap[Nghost] = i; PBCx[Nghost] = dx; PBCy[Nghost] = dy; PBCz[Nghost] = dz;
void setupBorders()
{
Nghost = -1;
for(int i = 0; i < Nlocal; i++) {
if (Nlocal + Nghost + 7 >= Nmax) {
growarray();
}
if (Nghost + 7 >= NmaxGhost) {
growBoundary();
}
/* Setup ghost atoms */
/* 6 planes */
if (x[i] < Cutneigh) { ADDGHOST(+1,0,0); }
if (x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,0,0); }
if (y[i] < Cutneigh) { ADDGHOST(0,+1,0); }
if (y[i] >= (yprd-Cutneigh)) { ADDGHOST(0,-1,0); }
if (z[i] < Cutneigh) { ADDGHOST(0,0,+1); }
if (z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,0,-1); }
/* 8 corners */
if (x[i] < Cutneigh && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,+1,+1); }
if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(+1,-1,+1); }
if (x[i] < Cutneigh && y[i] >= Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,+1,-1); }
if (x[i] < Cutneigh && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,-1,-1); }
if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(-1,+1,+1); }
if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,-1,+1); }
if (x[i] >= (xprd-Cutneigh) && y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,+1,-1); }
if (x[i] >= (xprd-Cutneigh) && y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,-1,-1); }
/* 12 edges */
if (x[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(+1,0,+1); }
if (x[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(+1,0,-1); }
if (x[i] >= (xprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(-1,0,+1); }
if (x[i] >= (xprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(-1,0,-1); }
if (y[i] < Cutneigh && z[i] < Cutneigh) { ADDGHOST(0,+1,+1); }
if (y[i] < Cutneigh && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,+1,-1); }
if (y[i] >= (yprd-Cutneigh) && z[i] < Cutneigh) { ADDGHOST(0,-1,+1); }
if (y[i] >= (yprd-Cutneigh) && z[i] >= (zprd-Cutneigh)) { ADDGHOST(0,-1,-1); }
if (y[i] < Cutneigh && x[i] < Cutneigh) { ADDGHOST(+1,+1,0); }
if (y[i] < Cutneigh && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,+1,0); }
if (y[i] >= (yprd-Cutneigh) && x[i] < Cutneigh) { ADDGHOST(+1,-1,0); }
if (y[i] >= (yprd-Cutneigh) && x[i] >= (xprd-Cutneigh)) { ADDGHOST(-1,-1,0); }
}
// increase by one to make it the ghost atom count
Nghost++;
}
void sortAtoms(Neighbor *neighbor)
{
binatoms(neighbor);
int* binpos = neighbor->bincount;
int* bins = neighbor->bins;
int mbins = neighbor->mbins;
int atoms_per_bin = neighbor->atoms_per_bin;
for(int i=1; i<mbins; i++) {
binpos[i] += binpos[i-1];
}
double* new_x = (double*) malloc(Nmax * sizeof(double));
double* new_y = (double*) malloc(Nmax * sizeof(double));
double* new_z = (double*) malloc(Nmax * sizeof(double));
double* new_vx = (double*) malloc(Nmax * sizeof(double));
double* new_vy = (double*) malloc(Nmax * sizeof(double));
double* new_vz = (double*) malloc(Nmax * sizeof(double));
double* old_x = x; double* old_y = y; double* old_z = z;
double* old_vx = vx; double* old_vy = vy; double* old_vz = vz;
for(int mybin = 0; mybin<mbins; mybin++) {
int start = mybin>0?binpos[mybin-1]:0;
int count = binpos[mybin] - start;
for(int k=0; k<count; k++) {
int new_i = start + k;
int old_i = bins[mybin * atoms_per_bin + k];
new_x[new_i] = old_x[old_i];
new_y[new_i] = old_y[old_i];
new_z[new_i] = old_z[old_i];
new_vx[new_i] = old_vx[old_i];
new_vy[new_i] = old_vy[old_i];
new_vz[new_i] = old_vz[old_i];
}
}
free(x); free(y); free(z);
free(vx); free(vy); free(vz);
x = new_x; y = new_y; z = new_z;
vx = new_vx; vy = new_vy; vz = new_vz;
}
void create_atoms(Parameter *param)
{
Natoms = 4 * param->nx * param->ny * param->nz;
Nlocal = 0;
double alat = pow((4.0 / param->rho), (1.0 / 3.0));
int ilo = (int) (xlo / (0.5 * alat) - 1);
int ihi = (int) (xhi / (0.5 * alat) + 1);
int jlo = (int) (ylo / (0.5 * alat) - 1);
int jhi = (int) (yhi / (0.5 * alat) + 1);
int klo = (int) (zlo / (0.5 * alat) - 1);
int khi = (int) (zhi / (0.5 * alat) + 1);
ilo = MAX(ilo, 0);
ihi = MIN(ihi, 2 * param->nx - 1);
jlo = MAX(jlo, 0);
jhi = MIN(jhi, 2 * param->ny - 1);
klo = MAX(klo, 0);
khi = MIN(khi, 2 * param->nz - 1);
double xtmp, ytmp, ztmp, vxtmp, vytmp, vztmp;
int i, j, k, m, n;
int sx = 0; int sy = 0; int sz = 0;
int ox = 0; int oy = 0; int oz = 0;
int subboxdim = 8;
while(oz * subboxdim <= khi) {
k = oz * subboxdim + sz;
j = oy * subboxdim + sy;
i = ox * subboxdim + sx;
if(((i + j + k) % 2 == 0) &&
(i >= ilo) && (i <= ihi) &&
(j >= jlo) && (j <= jhi) &&
(k >= klo) && (k <= khi)) {
xtmp = 0.5 * alat * i;
ytmp = 0.5 * alat * j;
ztmp = 0.5 * alat * k;
if( xtmp >= xlo && xtmp < xhi &&
ytmp >= ylo && ytmp < yhi &&
ztmp >= zlo && ztmp < zhi ) {
n = k * (2 * param->ny) * (2 * param->nx) +
j * (2 * param->nx) +
i + 1;
for(m = 0; m < 5; m++) {
myrandom(&n);
}
vxtmp = myrandom(&n);
for(m = 0; m < 5; m++){
myrandom(&n);
}
vytmp = myrandom(&n);
for(m = 0; m < 5; m++) {
myrandom(&n);
}
vztmp = myrandom(&n);
if(Nlocal == Nmax) {
growarray();
}
x[Nlocal] = xtmp; y[Nlocal] = ytmp; z[Nlocal] = ztmp;
vx[Nlocal] = vxtmp; vy[Nlocal] = vytmp; vz[Nlocal] = vztmp;
Nlocal++;
}
}
sx++;
if(sx == subboxdim) { sx = 0; sy++; }
if(sy == subboxdim) { sy = 0; sz++; }
if(sz == subboxdim) { sz = 0; ox++; }
if(ox * subboxdim > ihi) { ox = 0; oy++; }
if(oy * subboxdim > jhi) { oy = 0; oz++; }
}
}
void adjustVelocity(Parameter *param, Thermo *thermo)
{
/* zero center-of-mass motion */
double vxtot = 0.0;
double vytot = 0.0;
double vztot = 0.0;
for(int i = 0; i < Nlocal; i++) {
vxtot += vx[i];
vytot += vy[i];
vztot += vz[i];
}
vxtot = vxtot / Natoms;
vytot = vytot / Natoms;
vztot = vztot / Natoms;
for(int i = 0; i < Nlocal; i++) {
vx[i] -= vxtot;
vy[i] -= vytot;
vz[i] -= vztot;
}
thermo->t_act = 0;
double t = 0.0;
for(int i = 0; i < Nlocal; i++) {
t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
}
t *= thermo->t_scale;
double factor = sqrt(param->temp / t);
for(int i = 0; i < Nlocal; i++) {
vx[i] *= factor;
vy[i] *= factor;
vz[i] *= factor;
}
}
void thermoSetup(Parameter *param, Thermo *thermo)
{
int maxstat = param->ntimes / param->nstat + 2;
thermo->steparr = (int*) malloc(maxstat * sizeof(int));
thermo->tmparr = (double*) malloc(maxstat * sizeof(double));
thermo->engarr = (double*) malloc(maxstat * sizeof(double));
thermo->prsarr = (double*) malloc(maxstat * sizeof(double));
thermo->mvv2e = 1.0;
thermo->dof_boltz = (Natoms * 3 - 3);
thermo->t_scale = thermo->mvv2e / thermo->dof_boltz;
thermo->p_scale = 1.0 / 3 / xprd / yprd / zprd;
thermo->e_scale = 0.5;
printf("step\ttemp\t\tpressure\n");
}
void thermoCompute(int iflag, Parameter *param, Thermo *thermo)
{
double t = 0.0, p;
for(int i = 0; i < Nlocal; i++) {
t += (vx[i] * vx[i] + vy[i] * vy[i] + vz[i] * vz[i]) * param->mass;
}
t = t * thermo->t_scale;
p = (t * thermo->dof_boltz) * thermo->p_scale;
int istep = iflag;
if(iflag == -1){
istep = param->ntimes;
}
if(iflag == 0){
thermo->mstat = 0;
}
thermo->steparr[thermo->mstat] = istep;
thermo->tmparr[thermo->mstat] = t;
thermo->prsarr[thermo->mstat] = p;
thermo->mstat++;
fprintf(stdout, "%i\t%e\t%e\n", istep, t, p);
}
void initialIntegrate(Parameter *param)
{
for(int i = 0; i < Nlocal; i++) {
vx[i] += param->dtforce * fx[i];
vy[i] += param->dtforce * fy[i];
vz[i] += param->dtforce * fz[i];
x[i] += param->dt * vx[i];
y[i] += param->dt * vy[i];
z[i] += param->dt * vz[i];
}
}
void finalIntegrate(Parameter *param)
{
for(int i = 0; i < Nlocal; i++) {
vx[i] += param->dtforce * fx[i];
vy[i] += param->dtforce * fy[i];
vz[i] += param->dtforce * fz[i];
}
}
void computeForce(Neighbor *neighbor, Parameter *param)
{
int* neighs;
double cutforcesq = param->cutforce * param->cutforce;
double sigma6 = param->sigma6;
double epsilon = param->epsilon;
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
fz[i] = 0.0;
}
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
double xtmp = x[i];
double ytmp = y[i];
double ztmp = z[i];
double fix = 0;
double fiy = 0;
double fiz = 0;
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
double delx = xtmp - x[j];
double dely = ytmp - y[j];
double delz = ztmp - z[j];
double rsq = delx * delx + dely * dely + delz * delz;
if(rsq < cutforcesq) {
double sr2 = 1.0 / rsq;
double sr6 = sr2 * sr2 * sr2 * sigma6;
double force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix += delx * force;
fiy += dely * force;
fiz += delz * force;
}
}
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
}
}
int main (int argc, char** argv)
{
Neighbor neighbor;
Parameter param;
Thermo thermo;
init(&neighbor, &param);
setup(&neighbor, &param);
create_atoms(&param);
thermoSetup(&param, &thermo);
adjustVelocity(&param, &thermo);
setupBorders();
updateBorders();
buildNeighborlist(&neighbor);
thermoCompute(0, &param, &thermo);
computeForce(&neighbor, &param);
for(int n = 0; n < param.ntimes; n++) {
initialIntegrate(&param);
if((n + 1) % neighbor.every) {
updateBorders();
} else {
updateAtomLocations();
setupBorders();
updateBorders();
/* sortAtoms(&neighbor); */
buildNeighborlist(&neighbor);
}
computeForce(&neighbor, &param);
finalIntegrate(&param);
if(!((n + 1) % param.nstat) && (n+1) < param.ntimes) {
thermoCompute(n + 1, &param, &thermo);
}
}
thermoCompute(-1, &param, &thermo);
return EXIT_SUCCESS;
}
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