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

Add first working version of EAM

Browse Source 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2021-10-26 13:55:14 +02:00
parent 7db14b2ffe
commit 70cc6aeb19
5 changed files with 22 additions and 28 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

28
src/eam_utils.c
View File

@ -34,28 +34,24 @@
#define MAXLINE 4096
#endif
void initEam(Eam* eam, const char* input_file, int ntypes) {
void initEam(Eam* eam, Parameter* param) {
int ntypes = param->ntypes;
eam->nmax = 0;
eam->fp = NULL;
eam->ntypes = ntypes;
eam->cutforcesq = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * sizeof(MD_FLOAT));
coeff(eam, input_file);
init_style(eam);
coeff(eam, param);
init_style(eam, param);
}
void coeff(Eam* eam, const char* arg) {
read_file(&eam->file, arg);
int n = strlen(arg) + 1;
int ntypes = eam->ntypes;
double cutmax = eam->file.cut;
for(int i=0; i<ntypes*ntypes; i++)
eam->cutforcesq[i] = cutmax * cutmax;
void coeff(Eam* eam, Parameter* param) {
read_file(&eam->file, param->input_file);
param->cutforce = eam->file.cut;
param->cutneigh = param->cutforce + 0.3;
}
void init_style(Eam* eam) {
void init_style(Eam* eam, Parameter* param) {
// convert read-in file(s) to arrays and spline them
file2array(eam);
array2spline(eam);
array2spline(eam, param);
}
void read_file(Funcfl* file, const char* filename) {
@ -214,7 +210,7 @@ void file2array(Eam* eam) {
}
}
void array2spline(Eam* eam) {
void array2spline(Eam* eam, Parameter* param) {
eam->rdr = 1.0 / eam->dr;
eam->rdrho = 1.0 / eam->drho;
eam->nrho_tot = (eam->nrho + 1) * 7 + 64;
@ -222,7 +218,7 @@ void array2spline(Eam* eam) {
eam->nrho_tot -= eam->nrho_tot%64;
eam->nr_tot -= eam->nr_tot%64;
int ntypes = eam->ntypes;
int ntypes = param->ntypes;
eam->frho_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nrho_tot * sizeof(MD_FLOAT));
eam->rhor_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nr_tot * sizeof(MD_FLOAT));
eam->z2r_spline = (MD_FLOAT *) allocate(ALIGNMENT, ntypes * ntypes * eam->nr_tot * sizeof(MD_FLOAT));

8
src/force_eam.c
View File

@ -41,10 +41,10 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i
int Nlocal = atom->Nlocal;
int* neighs;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz; MD_FLOAT* fp = eam->fp;
MD_FLOAT* fx = atom->fx; MD_FLOAT* fy = atom->fy; MD_FLOAT* fz = atom->fz; int ntypes = atom->ntypes; MD_FLOAT* fp = eam->fp;
MD_FLOAT* rhor_spline = eam->rhor_spline; MD_FLOAT* frho_spline = eam->frho_spline; MD_FLOAT* z2r_spline = eam->z2r_spline;
int rdr = eam->rdr; int nr = eam->nr; int nr_tot = eam->nr_tot; int rdrho = eam->rdrho;
int nrho = eam->nrho; int nrho_tot = eam->nrho_tot; int ntypes = eam->ntypes;
int nrho = eam->nrho; int nrho_tot = eam->nrho_tot;
double S = getTimeStamp();
LIKWID_MARKER_START("force_eam_fp");
@ -67,7 +67,7 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
const int type_j = atom->type[j];
const int type_ij = type_i * ntypes + type_j;
const MD_FLOAT cutforcesq = eam->cutforcesq[type_ij];
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
if(rsq < cutforcesq) {
MD_FLOAT p = sqrt(rsq) * rdr + 1.0;
@ -115,7 +115,7 @@ double computeForceEam(Eam* eam, Atom *atom, Neighbor *neighbor, Stats *stats, i
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
const int type_j = atom->type[j];
const int type_ij = type_i * ntypes + type_j;
const MD_FLOAT cutforcesq = eam->cutforcesq[type_ij];
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
if(rsq < cutforcesq) {
MD_FLOAT r = sqrt(rsq);

10
src/includes/eam.h
View File

@ -36,22 +36,20 @@ typedef struct {
typedef struct {
MD_FLOAT* fp;
int nmax;
int ntypes;
int nrho, nr;
int nrho_tot, nr_tot;
MD_FLOAT dr, rdr, drho, rdrho;
MD_FLOAT *frho, *rhor, *z2r;
MD_FLOAT *rhor_spline, *frho_spline, *z2r_spline;
MD_FLOAT *cutforcesq;
Funcfl file;
} Eam;
void initEam(Eam* eam, const char* input_file, int ntypes);
void coeff(Eam* eam, const char* arg);
void init_style(Eam* eam);
void initEam(Eam* eam, Parameter* param);
void coeff(Eam* eam, Parameter* param);
void init_style(Eam* eam, Parameter *param);
void read_file(Funcfl* file, const char* filename);
void file2array(Eam* eam);
void array2spline(Eam* eam);
void array2spline(Eam* eam, Parameter* param);
void interpolate(int n, MD_FLOAT delta, MD_FLOAT* f, MD_FLOAT* spline);
void grab(FILE* fptr, int n, MD_FLOAT* list);
#endif

2
src/main.c
View File

@ -84,7 +84,7 @@ double setup(
param->zprd = param->nz * param->lattice;
S = getTimeStamp();
if(param->force_field == FF_EAM) { initEam(eam, param->input_file, param->ntypes); }
if(param->force_field == FF_EAM) { initEam(eam, param); }
initAtom(atom);
initNeighbor(neighbor, param);
initPbc();

2
src/stats.c
View File

@ -17,7 +17,7 @@ void displayStatistics(Atom *atom, Parameter *param, Stats *stats, double *timer
double avg_neigh = stats->total_force_neighs / (double)(atom->Nlocal * (param->ntimes + 1));
double avg_simd = stats->total_force_iters / (double)(atom->Nlocal * (param->ntimes + 1));
#ifdef EXPLICIT_TYPES
force_useful_volume += 1e-9 * (double)((atom.Nlocal * (param.ntimes + 1)) + stats.total_force_neighs) * sizeof(int);
force_useful_volume += 1e-9 * (double)((atom->Nlocal * (param->ntimes + 1)) + stats->total_force_neighs) * sizeof(int);
#endif
printf("Statistics:\n");
printf("\tVector width: %d, Processor frequency: %.4f GHz\n", VECTOR_WIDTH, param->proc_freq);