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Add code to read GRO files

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-03-03 20:03:33 +01:00
parent af92800c64
commit aae29a5b5a
5 changed files with 102 additions and 44 deletions
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6
config.mk
View File

@ -11,7 +11,7 @@ DATA_LAYOUT ?= AOS
# Assembly syntax to generate (ATT/INTEL)
ASM_SYNTAX ?= ATT
# Debug
DEBUG ?= false
DEBUG ?= true
# Number of times to run the atoms loop on stubbed variant
ATOMS_LOOP_RUNS ?= 1
@ -24,9 +24,9 @@ MEM_TRACER ?= false
# Trace indexes and distances for gather-md (true or false)
INDEX_TRACER ?= false
# Vector width (elements) for index and distance tracer
VECTOR_WIDTH ?= 4
VECTOR_WIDTH ?= 8
# When vector width is 4 but AVX2 is not supported (AVX only), set this to true
NO_AVX2 ?= true
NO_AVX2 ?= false
# Compute statistics
COMPUTE_STATS ?= true

131
gromacs/atom.c
View File

@ -41,8 +41,7 @@
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#endif
void initAtom(Atom *atom)
{
void initAtom(Atom *atom) {
atom->x = NULL; atom->y = NULL; atom->z = NULL;
atom->vx = NULL; atom->vy = NULL; atom->vz = NULL;
atom->cl_x = NULL;
@ -65,8 +64,7 @@ void initAtom(Atom *atom)
atom->clusters = NULL;
}
void createAtom(Atom *atom, Parameter *param)
{
void createAtom(Atom *atom, Parameter *param) {
MD_FLOAT xlo = 0.0; MD_FLOAT xhi = param->xprd;
MD_FLOAT ylo = 0.0; MD_FLOAT yhi = param->yprd;
MD_FLOAT zlo = 0.0; MD_FLOAT zhi = param->zprd;
@ -106,47 +104,25 @@ void createAtom(Atom *atom, Parameter *param)
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)) {
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);
}
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);
}
for(m = 0; m < 5; m++){ myrandom(&n); }
vytmp = myrandom(&n);
for(m = 0; m < 5; m++) {
myrandom(&n);
}
for(m = 0; m < 5; m++) { myrandom(&n); }
vztmp = myrandom(&n);
if(atom->Nlocal == atom->Nmax) {
growAtom(atom);
}
if(atom->Nlocal == atom->Nmax) { growAtom(atom); }
atom_x(atom->Nlocal) = xtmp;
atom_y(atom->Nlocal) = ytmp;
atom_z(atom->Nlocal) = ztmp;
@ -159,7 +135,6 @@ void createAtom(Atom *atom, Parameter *param)
}
sx++;
if(sx == subboxdim) { sx = 0; sy++; }
if(sy == subboxdim) { sy = 0; sz++; }
if(sz == subboxdim) { sz = 0; ox++; }
@ -178,8 +153,9 @@ int type_str2int(const char *type) {
int readAtom(Atom* atom, Parameter* param) {
int len = strlen(param->input_file);
if(strncmp(&param->input_file[len - 4], ".pdb", 4) == 0) { return readAtom_pdb(atom, param); }
if(strncmp(&param->input_file[len - 4], ".gro", 4) == 0) { return readAtom_gro(atom, param); }
if(strncmp(&param->input_file[len - 4], ".dmp", 4) == 0) { return readAtom_dmp(atom, param); }
fprintf(stderr, "Invalid input file extension: %s\nValid choices are: pdb, dmp\n", param->input_file);
fprintf(stderr, "Invalid input file extension: %s\nValid choices are: pdb, gro, dmp\n", param->input_file);
exit(-1);
return -1;
}
@ -269,6 +245,85 @@ int readAtom_pdb(Atom* atom, Parameter* param) {
return read_atoms;
}
int readAtom_gro(Atom* atom, Parameter* param) {
FILE *fp = fopen(param->input_file, "r");
char line[MAXLINE];
char desc[MAXLINE];
int read_atoms = 0;
int atoms_to_read = 0;
int i = 0;
if(!fp) {
fprintf(stderr, "Could not open input file: %s\n", param->input_file);
exit(-1);
return -1;
}
fgets(desc, MAXLINE, fp);
for(i = 0; desc[i] != '\n'; i++);
desc[i] = '\0';
fgets(line, MAXLINE, fp);
atoms_to_read = atoi(strtok(line, " "));
fprintf(stdout, "System: %s with %d atoms\n", desc, atoms_to_read);
while(!feof(fp) && read_atoms < atoms_to_read) {
fgets(line, MAXLINE, fp);
char *label = strtok(line, " ");
int type = type_str2int(strtok(NULL, " "));
int atom_id = atoi(strtok(NULL, " ")) - 1;
atom_id = read_atoms;
while(atom_id + 1 >= atom->Nmax) {
growAtom(atom);
}
atom->type[atom_id] = type;
atom_x(atom_id) = atof(strtok(NULL, " "));
atom_y(atom_id) = atof(strtok(NULL, " "));
atom_z(atom_id) = atof(strtok(NULL, " "));
atom->vx[atom_id] = atof(strtok(NULL, " "));
atom->vy[atom_id] = atof(strtok(NULL, " "));
atom->vz[atom_id] = atof(strtok(NULL, " "));
atom->ntypes = MAX(atom->type[atom_id] + 1, atom->ntypes);
atom->Natoms++;
atom->Nlocal++;
read_atoms++;
}
if(!feof(fp)) {
fgets(line, MAXLINE, fp);
param->xlo = 0.0;
param->xhi = atof(strtok(line, " "));
param->ylo = 0.0;
param->yhi = atof(strtok(NULL, " "));
param->zlo = 0.0;
param->zhi = atof(strtok(NULL, " "));
param->xprd = param->xhi - param->xlo;
param->yprd = param->yhi - param->ylo;
param->zprd = param->zhi - param->zlo;
}
if(read_atoms != atoms_to_read) {
fprintf(stderr, "Input error: Number of atoms read do not match (%d/%d).\n", read_atoms, atoms_to_read);
exit(-1);
return -1;
}
atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
atom->epsilon[i] = param->epsilon;
atom->sigma6[i] = param->sigma6;
atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
atom->cutforcesq[i] = param->cutforce * param->cutforce;
}
fprintf(stdout, "Read %d atoms from %s\n", read_atoms, param->input_file);
fclose(fp);
return read_atoms;
}
int readAtom_dmp(Atom* atom, Parameter* param) {
FILE *fp = fopen(param->input_file, "r");
char line[MAXLINE];
@ -362,8 +417,7 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
return natoms;
}
void growAtom(Atom *atom)
{
void growAtom(Atom *atom) {
int nold = atom->Nmax;
atom->Nmax += DELTA;
@ -380,8 +434,7 @@ void growAtom(Atom *atom)
atom->type = (int *) reallocate(atom->type, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int));
}
void growClusters(Atom *atom)
{
void growClusters(Atom *atom) {
int nold = atom->Nclusters_max;
atom->Nclusters_max += DELTA;
atom->clusters = (Cluster*) reallocate(atom->clusters, ALIGNMENT, atom->Nclusters_max * sizeof(Cluster), nold * sizeof(Cluster));

1
gromacs/includes/atom.h
View File

@ -60,6 +60,7 @@ extern void initAtom(Atom*);
extern void createAtom(Atom*, Parameter*);
extern int readAtom(Atom*, Parameter*);
extern int readAtom_pdb(Atom*, Parameter*);
extern int readAtom_gro(Atom*, Parameter*);
extern int readAtom_dmp(Atom*, Parameter*);
extern void growAtom(Atom*);
extern void growClusters(Atom*);

4
gromacs/main.c
View File

@ -229,6 +229,10 @@ int main(int argc, char** argv) {
param.nz = atoi(argv[++i]);
continue;
}
if((strcmp(argv[i], "-m") == 0) || (strcmp(argv[i], "--mass") == 0)) {
param.mass = atof(argv[++i]);
continue;
}
if((strcmp(argv[i], "-r") == 0) || (strcmp(argv[i], "--radius") == 0)) {
param.cutforce = atof(argv[++i]);
continue;

4
include_ICC.mk
View File

@ -4,7 +4,7 @@ LINKER = $(CC)
OPENMP = #-qopenmp
PROFILE = #-profile-functions -g -pg
OPTS = -Ofast -xCORE-AVX512 -qopt-zmm-usage=high $(PROFILE)
#OPTS = -fast -xCORE-AVX2 $(PROFILE)
#OPTS = -Ofast -xCORE-AVX2 $(PROFILE)
#OPTS = -fast -xAVX $(PROFILE)
#OPTS = -fast -xSSE4.2 $(PROFILE)
#OPTS = -fast -no-vec $(PROFILE)
@ -12,6 +12,6 @@ OPTS = -Ofast -xCORE-AVX512 -qopt-zmm-usage=high $(PROFILE)
CFLAGS = $(PROFILE) -restrict $(OPENMP) $(OPTS)
ASFLAGS = #-masm=intel
LFLAGS = $(PROFILE) $(OPTS) $(OPENMP)
DEFINES = -D_GNU_SOURCE #-DLIKWID_PERFMON
DEFINES = -std=c11 -pedantic-errors -D_GNU_SOURCE #-DLIKWID_PERFMON
INCLUDES = #$(LIKWID_INC)
LIBS = -lm #$(LIKWID_LIB) -llikwid