moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Put force kernel in separate compilation unit

Browse Source
This commit is contained in:
Jan Eitzinger 2021-03-25 06:49:28 +01:00
parent dcfa1c4135
commit 2bc3120112
2 changed files with 90 additions and 59 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

89
src/force.c Normal file
View File

@ -0,0 +1,89 @@
/*
* =======================================================================================
*
* Author: Jan Eitzinger (je), jan.eitzinger@fau.de
* Copyright (c) 2021 RRZE, University Erlangen-Nuremberg
*
* This file is part of MD-Bench.
*
* MD-Bench is free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MD-Bench is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
* PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License along
* with MD-Bench. If not, see <https://www.gnu.org/licenses/>.
* =======================================================================================
*/
#include <likwid-marker.h>
#include <timing.h>
#include <neighbor.h>
#include <parameter.h>
#include <atom.h>
double computeForce(
Parameter *param,
Atom *atom,
Neighbor *neighbor)
{
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT S, E;
S = getTimeStamp();
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
fz[i] = 0.0;
}
LIKWID_MARKER_START("force");
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT 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;
}
LIKWID_MARKER_STOP("force");
E = getTimeStamp();
return E-S;
}

60
src/main.c
View File

@ -47,6 +47,7 @@ typedef enum {
NUMTIMER NUMTIMER
} timertype; } timertype;
extern double computeForce( Parameter*, Atom*, Neighbor*);
void init(Parameter *param) void init(Parameter *param)
{ {
@ -141,65 +142,6 @@ void finalIntegrate(Parameter *param, Atom *atom)
} }
} }
double computeForce(Parameter *param, Atom *atom, Neighbor *neighbor)
{
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
MD_FLOAT sigma6 = param->sigma6;
MD_FLOAT epsilon = param->epsilon;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz;
MD_FLOAT S, E;
S = getTimeStamp();
for(int i = 0; i < Nlocal; i++) {
fx[i] = 0.0;
fy[i] = 0.0;
fz[i] = 0.0;
}
LIKWID_MARKER_START("force");
#pragma omp parallel for
for(int i = 0; i < Nlocal; i++) {
neighs = &neighbor->neighbors[i * neighbor->maxneighs];
int numneighs = neighbor->numneigh[i];
MD_FLOAT xtmp = atom_x(i);
MD_FLOAT ytmp = atom_y(i);
MD_FLOAT ztmp = atom_z(i);
MD_FLOAT fix = 0;
MD_FLOAT fiy = 0;
MD_FLOAT fiz = 0;
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT 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;
}
LIKWID_MARKER_STOP("force");
E = getTimeStamp();
return E-S;
}
void printAtomState(Atom *atom) void printAtomState(Atom *atom)
{ {
printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n", printf("Atom counts: Natoms=%d Nlocal=%d Nghost=%d Nmax=%d\n",