moebiusband/MD-Bench
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Add version with stubbed force calculation

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2021-03-30 01:54:56 +02:00
parent 2bc3120112
commit 7efd30791a
12 changed files with 174 additions and 13 deletions
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28
Makefile
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@ -1,10 +1,12 @@
#CONFIGURE BUILD SYSTEM
TARGET = MDBench-$(TAG)
BUILD_DIR = ./$(TAG)
SRC_DIR = ./src
SRC_DIR = ./src/core
MAKE_DIR = ./
Q ?= @
TARGET_MDBENCH = MDBench-$(TAG)
TARGET_STUB = stub
#DO NOT EDIT BELOW
include $(MAKE_DIR)/config.mk
include $(MAKE_DIR)/include_$(TAG).mk
@ -24,12 +26,28 @@ ASM = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.s,$(wildcard $(SRC_DIR)/*.
OBJ = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.o,$(wildcard $(SRC_DIR)/*.c))
CPPFLAGS := $(CPPFLAGS) $(DEFINES) $(OPTIONS) $(INCLUDES)
${TARGET}: $(BUILD_DIR) $(OBJ)
@echo "===> LINKING $(TARGET)"
$(Q)${LINKER} ${LFLAGS} -o $(TARGET) $(OBJ) $(LIBS)
all: ${TARGET_MDBENCH} ${TARGET_STUB}
${TARGET_MDBENCH}: $(BUILD_DIR) $(OBJ) $(BUILD_DIR)/main.o
@echo "===> LINKING $(TARGET_MDBENCH)"
$(Q)${LINKER} ${LFLAGS} -o $(TARGET_MDBENCH) $(OBJ) $(BUILD_DIR)/main.o $(LIBS)
${TARGET_STUB}: $(BUILD_DIR) $(OBJ) $(BUILD_DIR)/stub.o
@echo "===> LINKING $(TARGET_STUB)"
$(Q)${LINKER} ${LFLAGS} -o $(TARGET_STUB) $(OBJ) $(BUILD_DIR)/stub.o $(LIBS)
asm: $(BUILD_DIR) $(ASM)
$(BUILD_DIR)/main.o: ./src/main.c
@echo "===> COMPILE $@"
$(Q)$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
$(Q)$(CC) $(CPPFLAGS) -MT $(@:.d=.o) -MM $< > $(BUILD_DIR)/main.d
$(BUILD_DIR)/stub.o: ./src/stub.c
@echo "===> COMPILE $@"
$(Q)$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
$(Q)$(CC) $(CPPFLAGS) -MT $(@:.d=.o) -MM $< > $(BUILD_DIR)/stub.d
$(BUILD_DIR)/%.o: %.c
@echo "===> COMPILE $@"
$(Q)$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@

0
src/allocate.c → src/core/allocate.c
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0
src/atom.c → src/core/atom.c
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0
src/force.c → src/core/force.c
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7
src/neighbor.c → src/core/neighbor.c
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@ -53,11 +53,10 @@ static MD_FLOAT bindist(int, int, int);
/* exported subroutines */
void initNeighbor(Neighbor *neighbor, Parameter *param)
{
MD_FLOAT lattice = pow((4.0 / param->rho), (1.0 / 3.0));
MD_FLOAT neighscale = 5.0 / 6.0;
xprd = param->nx * lattice;
yprd = param->ny * lattice;
zprd = param->nz * lattice;
xprd = param->nx * param->lattice;
yprd = param->ny * param->lattice;
zprd = param->nz * param->lattice;
cutneigh = param->cutneigh;
nbinx = neighscale * param->nx;
nbiny = neighscale * param->ny;

0
src/pbc.c → src/core/pbc.c
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0
src/thermo.c → src/core/thermo.c
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0
src/timing.c → src/core/timing.c
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0
src/util.c → src/core/util.c
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1
src/includes/parameter.h
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@ -43,6 +43,7 @@ typedef struct {
MD_FLOAT cutforce;
MD_FLOAT cutneigh;
int nx, ny, nz;
MD_FLOAT lattice;
MD_FLOAT xprd, yprd, zprd;
} Parameter;
#endif

8
src/main.c
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@ -74,10 +74,10 @@ double setup(
Neighbor *neighbor)
{
double S, E;
double lattice = pow((4.0 / param->rho), (1.0 / 3.0));
param->xprd = param->nx * lattice;
param->yprd = param->ny * lattice;
param->zprd = param->nz * lattice;
param->lattice = pow((4.0 / param->rho), (1.0 / 3.0));
param->xprd = param->nx * param->lattice;
param->yprd = param->ny * param->lattice;
param->zprd = param->nz * param->lattice;
S = getTimeStamp();
initAtom(atom);

143
src/stub.c Normal file
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@ -0,0 +1,143 @@
#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
#define NX 4
#define NY 4
#define NZ 2
extern double computeForce( Parameter*, Atom*, Neighbor*);
void init(Parameter *param) {
param->epsilon = 1.0;
param->sigma6 = 1.0;
param->rho = 0.8442;
param->ntimes = 200;
param->nx = NX;
param->ny = NY;
param->nz = NZ;
param->lattice = LATTICE_DISTANCE;
param->xprd = NX * LATTICE_DISTANCE;
param->yprd = NY * LATTICE_DISTANCE;
param->zprd = NZ * 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;
}
#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");
printf("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);
}
}
printf("Initializing atoms...\n");
initAtom(atom);
printf("Creating atoms...\n");
// Neighbors per atom
// Total atoms: NX * NY * NZ * atoms_per_unit_cell
const int atoms_per_unit_cell = 8;
for(int i = 0; i < NX; ++i) {
for(int j = 0; j < NY; ++j) {
for(int k = 0; k < 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);
}
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);
}
}
}
printf("Initializing neighbor lists...\n");
initNeighbor(&neighbor, &param);
printf("Setting up neighbor lists...\n");
setupNeighbor();
printf("Building neighbor lists...\n");
buildNeighbor(atom, &neighbor);
printf("Computing forces...\n");
computeForce(&param, atom, &neighbor);
LIKWID_MARKER_CLOSE;
return EXIT_SUCCESS;
}