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Initial checkin of simplified miniMD port. Does not work yet.

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This commit is contained in:
Jan Eitzinger 2020-08-11 16:34:22 +02:00
parent 0f4be2a9eb
commit ff45b07749
9 changed files with 1288 additions and 0 deletions
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57
Makefile Normal file
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TAG = CLANG
#CONFIGURE BUILD SYSTEM
TARGET = MDBench-$(TAG)
BUILD_DIR = ./$(TAG)
SRC_DIR = ./src
MAKE_DIR = ./
Q ?= @
#DO NOT EDIT BELOW
include $(MAKE_DIR)/include_$(TAG).mk
INCLUDES += -I./src/includes
VPATH = $(SRC_DIR)
ASM = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.s,$(wildcard $(SRC_DIR)/*.c))
OBJ = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.o,$(wildcard $(SRC_DIR)/*.c))
CPPFLAGS := $(CPPFLAGS) $(DEFINES) $(INCLUDES)
${TARGET}: $(BUILD_DIR) $(OBJ)
@echo "===> LINKING $(TARGET)"
$(Q)${LINKER} ${LFLAGS} -o $(TARGET) $(OBJ) $(LIBS)
asm: $(BUILD_DIR) $(ASM)
$(BUILD_DIR)/%.o: %.c
@echo "===> COMPILE $@"
$(Q)$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
$(Q)$(CC) $(CPPFLAGS) -MT $(@:.d=.o) -MM $< > $(BUILD_DIR)/$*.d
$(BUILD_DIR)/%.s: %.c
@echo "===> GENERATE ASM $@"
$(Q)$(CC) -S $(ASFLAGS) $(CPPFLAGS) $(CFLAGS) $< -o $@
tags:
@echo "===> GENERATE TAGS"
$(Q)ctags -R
$(BUILD_DIR):
@mkdir $(BUILD_DIR)
ifeq ($(findstring $(MAKECMDGOALS),clean),)
-include $(OBJ:.o=.d)
endif
.PHONY: clean distclean
clean:
@echo "===> CLEAN"
@rm -rf $(BUILD_DIR)
@rm -f tags
distclean: clean
@echo "===> DIST CLEAN"
@rm -f $(TARGET)
@rm -f tags

17
include_CLANG.mk Normal file
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CC = cc
CXX = cc
LINKER = $(CC)
ANSI_CFLAGS = -ansi
ANSI_CFLAGS += -std=c99
ANSI_CFLAGS += -pedantic
ANSI_CFLAGS += -Wextra
CFLAGS = -O2 -g #$(ANSI_CFLAGS)
ASFLAGS = -masm=intel
CXXFLAGS = $(CFLAGS)
FCFLAGS =
LFLAGS =
DEFINES = -D_GNU_SOURCE
INCLUDES =
LIBS =

21
include_GCC.mk Normal file
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CC = gcc
CXX = g++
FC = gfortran
LINKER = $(CXX)
ANSI_CFLAGS = -ansi
ANSI_CFLAGS += -std=c99
ANSI_CFLAGS += -pedantic
ANSI_CFLAGS += -Wextra
# CFLAGS = -O0 -g -std=c99 -fargument-noalias
CFLAGS = -O3 -march=znver1 -ffast-math -funroll-loops -fopenmp
CXXFLAGS = $(CFLAGS)
ASFLAGS = -masm=intel
FCFLAGS =
LFLAGS =
DEFINES = -D_GNU_SOURCE
INCLUDES =
LIBS =

20
include_ICC.mk Normal file
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CC = icc
CXX = mpiicpc
FC = ifort
LINKER = $(CXX)
PROFILE = #-g -pg
# OPTS = -O3 -xCORE-AVX512 -qopt-zmm-usage=high $(PROFILE)
# OPTS = -O3 -xCORE-AVX2 $(PROFILE)
# OPTS = -O3 -xAVX $(PROFILE)
# OPTS = -O3 -xSSE4.2 $(PROFILE)
OPTS = -O3 -no-vec $(PROFILE)
# OPTS = -O3 -xHost $(PROFILE)
CFLAGS = $(PROFILE) -restrict $(OPTS)
CXXFLAGS = $(CFLAGS)
ASFLAGS = -masm=intel
FCFLAGS =
LFLAGS = $(PROFILE) $(OPTS)
DEFINES = -D_GNU_SOURCE -DNOCHUNK -DUSE_SIMD# -DLIKWID_PERFMON -DPRECISION=1
INCLUDES = $(MPIINC) $(LIKWID_INC)
LIBS = $(LIKWID_LIB) -llikwid

58
src/allocate.c Normal file
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/*
* =======================================================================================
*
* 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 <errno.h>
void* allocate (int alignment, size_t bytesize)
{
int errorCode;
void* ptr;
errorCode = posix_memalign(&ptr, alignment, bytesize);
if (errorCode) {
if (errorCode == EINVAL) {
fprintf(stderr,
"Error: Alignment parameter is not a power of two\n");
exit(EXIT_FAILURE);
}
if (errorCode == ENOMEM) {
fprintf(stderr,
"Error: Insufficient memory to fulfill the request\n");
exit(EXIT_FAILURE);
}
}
if (ptr == NULL) {
fprintf(stderr, "Error: posix_memalign failed!\n");
exit(EXIT_FAILURE);
}
return ptr;
}

33
src/includes/allocate.h Normal file
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/*
* =======================================================================================
*
* 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.
*
* =======================================================================================
*/
#ifndef __ALLOCATE_H_
#define __ALLOCATE_H_
extern void* allocate (int alignment, size_t bytesize);
#endif

35
src/includes/timing.h Normal file
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/*
* =======================================================================================
*
* 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.
*
* =======================================================================================
*/
#ifndef __TIMING_H_
#define __TIMING_H_
extern double getTimeStamp();
extern double getTimeResolution();
extern double getTimeStamp_();
#endif

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src/main.c Normal file
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/*
* =======================================================================================
*
* 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>
#include <timing.h>
#include <allocate.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 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 double eng_vdwl;
static double virial;
typedef enum {
LEFT = 0,
RIGHT,
FRONT,
BACK,
TOP,
BOTTOM,
TOPRIGHTBACK,
TOPLEFTBACK,
TOPRIGHTFRONT,
TOPLEFTFRONT,
BOTTOMRIGHTBACK,
BOTTOMLEFTBACK,
BOTTOMRIGHTFRONT,
BOTTOMLEFTFRONT,
DCOUNT
} direction;
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;
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;
double ans;
k = (*idum) / IQ;
*idum = IA * (*idum - k * IQ) - IR * k;
if(*idum < 0) *idum += IM;
ans = AM * (*idum);
return ans;
}
// Neighbor list related subroutines
// convert atom coordinates in bin index
int coord2bin(Neighbor* neighbor, double x, double y, double z)
{
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(x >= xprd) {
ix = (int)((x - xprd) * bininvx) + neighbor->nbinx - mbinxlo;
} else if(x >= 0.0) {
ix = (int)(x * bininvx) - mbinxlo;
} else {
ix = (int)(x * bininvx) - mbinxlo - 1;
}
if(y >= yprd) {
iy = (int)((y - yprd) * bininvy) + neighbor->nbiny - mbinylo;
} else if(y >= 0.0) {
iy = (int)(y * bininvy) - mbinylo;
} else {
iy = (int)(y * bininvy) - mbinylo - 1;
}
if(z >= zprd) {
iz = (int)((z - zprd) * bininvz) + neighbor->nbinz - mbinzlo;
} else if(z >= 0.0) {
iz = (int)(z * bininvz) - mbinzlo;
} else {
iz = (int)(z * bininvz) - mbinzlo - 1;
}
return (iz * neighbor->mbiny * neighbor->mbinx + iy * neighbor->mbinx + ix + 1);
}
// Sort atoms in bins. All bins can hold the same number of max atoms
// If one bin is exceeded reallocate and start over.
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));
}
}
}
/* compute closest distance between central bin (0,0,0) and bin (i,j,k) */
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 > Nmax) {
Nmax = nall;
if(neighbor->numneigh) free(neighbor->numneigh);
if(neighbor->neighbors) free(neighbor->neighbors);
neighbor->numneigh = (int*) malloc(Nmax * sizeof(int));
neighbor->neighbors = (int*) malloc(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];
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;
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;
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->atoms_per_bin = 8;
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;
double cutneigh = neighbor->cutneigh;
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;
// x coordinate
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);
// y coordinate
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);
// z coordinate
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;
}
}
}
}
/* printf("STENCIL %d \n", neighbor->nstencil); */
/* for (int i=0; i<neighbor->nstencil; i++) { */
/* printf("%d ", neighbor->stencil[i]); */
/* } */
/* printf("\n"); */
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;
}
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");
}
}
/* Enforce periodic boundary conditions
* Relocate atoms that have left domain for
* 6 planes (and 8 corners (diagonal))
* Setup ghost atoms at boundaries*/
void processBorders(double cutneigh)
{
Nghost = 0;
int lastidx = Nlocal;
for(int i = 0; i < Nlocal; i++) {
/* Relocate atoms that have left the domain */
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;
}
if (lastidx+1 >= Nmax) {
growarray();
}
/* Setup ghost atoms */
if (x[i] < cutneigh) { /* left plane */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i];
z[lastidx+1] = z[i];
lastidx++; Nghost++;
/* treat corners */
if (y[i] < cutneigh && z[i] < cutneigh) { /* bottom left front corner */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (y[i] >= (yprd-cutneigh) && z[i] < cutneigh) { /* bottom left back corner */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (y[i] < cutneigh && z[i] >= (zprd-cutneigh)) { /* top left front corner */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
} else if (y[i] >= (yprd-cutneigh) && z[i] >= (zprd-cutneigh)) { /* top left back corner */
x[lastidx+1] = x[i] + xprd;
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
}
} else if (x[i] >= (xprd-cutneigh)) { /* right plane */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i];
z[lastidx+1] = z[i];
lastidx++; Nghost++;
/* treat corners */
if (y[i] < cutneigh && z[i] < cutneigh) { /* bottom right front corner */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (y[i] >= (yprd-cutneigh) && z[i] < cutneigh) { /* bottom right back corner */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (y[i] < cutneigh && z[i] >= (zprd-cutneigh)) { /* top right front corner */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
} else if (y[i] >= (yprd-cutneigh) && z[i] >= (zprd-cutneigh)) { /* top right back corner */
x[lastidx+1] = x[i] - xprd;
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
}
} else if (y[i] < cutneigh) { /* front plane */
x[lastidx+1] = x[i];
y[lastidx+1] = y[i] + yprd;
z[lastidx+1] = z[i];
lastidx++; Nghost++;
} else if (y[i] >= (yprd-cutneigh)) { /* back plane */
x[lastidx+1] = x[i];
y[lastidx+1] = y[i] - yprd;
z[lastidx+1] = z[i];
lastidx++; Nghost++;
} else if (z[i] < cutneigh) { /* bottom plane */
x[lastidx+1] = x[i];
y[lastidx+1] = y[i];
z[lastidx+1] = z[i] + zprd;
lastidx++; Nghost++;
} else if (z[i] >= (zprd-cutneigh)) { /* top plane */
x[lastidx+1] = x[i];
y[lastidx+1] = y[i];
z[lastidx+1] = z[i] - zprd;
lastidx++; Nghost++;
}
}
}
void addatom(double x_in, double y_in, double z_in,
double vx_in, double vy_in, double vz_in)
{
if(Nlocal == Nmax) {
growarray();
}
x[Nlocal] = x_in;
y[Nlocal] = y_in;
z[Nlocal] = z_in;
vx[Nlocal] = vx_in;
vy[Nlocal] = vy_in;
vz[Nlocal] = vz_in;
Nlocal++;
}
/* place atoms in the same bin consecutive in memory */
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)
{
/* total # of atoms */
Natoms = 4 * param->nx * param->ny * param->nz;
Nlocal = 0;
/* determine loop bounds of lattice subsection that overlaps my sub-box
insure loop bounds do not exceed nx,ny,nz */
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);
/* each proc generates positions and velocities of atoms on fcc sublattice
that overlaps its box, only store atoms that fall in my box
use atom # (generated from lattice coords) as unique seed to generate a
unique velocity exercise RNG between calls to avoid correlations in adjacent atoms */
double xtmp, ytmp, ztmp, vx, vy, vz;
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);
}
vx = myrandom(&n);
for(m = 0; m < 5; m++){
myrandom(&n);
}
vy = myrandom(&n);
for(m = 0; m < 5; m++) {
myrandom(&n);
}
vz = myrandom(&n);
addatom(xtmp, ytmp, ztmp, vx, vy, vz);
}
}
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 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;
eng_vdwl = 0.0;
virial = 0.0;
}
void thermoCompute(int iflag, Parameter *param, Thermo *thermo)
{
double t, eng, p;
if(iflag > 0 && iflag % param->nstat){
return;
}
if(iflag == -1 && param->nstat > 0 && param->ntimes % param->nstat == 0)
{
return;
}
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 = t * thermo->t_scale;
eng = eng_vdwl * thermo->e_scale / Natoms;
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->engarr[thermo->mstat] = eng;
thermo->prsarr[thermo->mstat] = p;
thermo->mstat++;
fprintf(stdout, "%i %e %e %e\n", istep, t, eng, 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;
double t_eng_vdwl = 0.0;
double t_virial = 0.0;
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
fz[i] = 0.0;
}
// loop over all neighbors of my atoms
// store force on atom i
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;
t_eng_vdwl += sr6 * (sr6 - 1.0) * epsilon;
t_virial += (delx * delx + dely * dely + delz * delz) * force;
}
}
fx[i] += fix;
fy[i] += fiy;
fz[i] += fiz;
}
eng_vdwl += (4.0 * t_eng_vdwl);
virial += (0.5 * t_virial);
}
void printState()
{
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n",
Natoms, Nlocal, Nghost, Nmax);
}
int main (int argc, char** argv)
{
Neighbor neighbor;
Parameter param;
Thermo thermo;
init(&neighbor, &param);
printState();
setup(&neighbor, &param);
create_atoms(&param);
printState();
thermoSetup(&param, &thermo);
processBorders(neighbor.cutneigh);
buildNeighborlist(&neighbor);
printState();
exit(EXIT_SUCCESS);
for(int n = 0; n < param.ntimes; n++) {
initialIntegrate(&param);
if(!((n + 1) % neighbor.every)) {
processBorders(neighbor.cutneigh);
sortAtoms(&neighbor);
buildNeighborlist(&neighbor);
}
computeForce(&neighbor, &param);
finalIntegrate(&param);
if(param.nstat) {
thermoCompute(n + 1, &param, &thermo);
}
}
return EXIT_SUCCESS;
}

48
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/*
* =======================================================================================
*
* 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 <time.h>
double getTimeStamp()
{
struct timespec ts;
clock_gettime(CLOCK_MONOTONIC, &ts);
return (double)ts.tv_sec + (double)ts.tv_nsec * 1.e-9;
}
double getTimeResolution()
{
struct timespec ts;
clock_getres(CLOCK_MONOTONIC, &ts);
return (double)ts.tv_sec + (double)ts.tv_nsec * 1.e-9;
}
double getTimeStamp_()
{
return getTimeStamp();
}