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Setup first DEM example with input file from lecture

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-07-07 02:11:50 +02:00
parent 9ffc09f497
commit 32836eebcb
6 changed files with 86 additions and 1 deletions
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3
data/dem/collision.in Normal file
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@ -0,0 +1,3 @@
2
1 0.1 0.166 0.55 0 1 0 0
1 0.1 0.833 0.45 0 -1 0 0

5
data/dem/mdbench_params.conf Normal file
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@ -0,0 +1,5 @@
ntimes 200
dt 0.001
reneigh_every 20
k_s 100
k_dn 10

64
lammps/atom.c
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@ -174,7 +174,8 @@ int readAtom(Atom* atom, Parameter* param) {
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, gro, dmp\n", param->input_file);
if(strncmp(&param->input_file[len - 3], ".in", 3) == 0) { return readAtom_in(atom, param); }
fprintf(stderr, "Invalid input file extension: %s\nValid choices are: pdb, gro, dmp, in\n", param->input_file);
exit(-1);
return -1;
}
@ -435,6 +436,67 @@ int readAtom_dmp(Atom* atom, Parameter* param) {
return natoms;
}
int readAtom_in(Atom* atom, Parameter* param) {
FILE *fp = fopen(param->input_file, "r");
char line[MAXLINE];
int natoms = 0;
int atom_id = 0;
if(!fp) {
fprintf(stderr, "Could not open input file: %s\n", param->input_file);
exit(-1);
return -1;
}
atom->ntypes = 1;
while(!feof(fp)) {
fgets(line, MAXLINE, fp);
natoms = atoi(line);
for(int i = 0; i < natoms; i++) {
fgets(line, MAXLINE, fp);
// TODO: store mass per atom
char *s_mass = strtok(line, " ");
if(strncmp(s_mass, "inf", 3) == 0) {
// Set atom's mass to INFINITY
} else {
param->mass = atof(s_mass);
}
atom->radius[atom_id] = atof(strtok(NULL, " "));
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->type[atom_id] = 0;
atom->ntypes = MAX(atom->type[atom_id], atom->ntypes);
atom_id++;
}
}
if(!natoms) {
fprintf(stderr, "Input error: atom data was not read!\n");
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", natoms, param->input_file);
return natoms;
}
void growAtom(Atom *atom) {
int nold = atom->Nmax;
atom->Nmax += DELTA;

1
lammps/includes/atom.h
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@ -49,6 +49,7 @@ extern int readAtom(Atom*, Parameter*);
extern int readAtom_pdb(Atom*, Parameter*);
extern int readAtom_gro(Atom*, Parameter*);
extern int readAtom_dmp(Atom*, Parameter*);
extern int readAtom_in(Atom*, Parameter*);
extern void growAtom(Atom*);
#ifdef AOS

1
lammps/includes/parameter.h
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@ -62,6 +62,7 @@ typedef struct {
MD_FLOAT k_s;
MD_FLOAT k_dn;
MD_FLOAT gx, gy, gz;
MD_FLOAT reflect_x, reflect_y, reflect_z;
} Parameter;
void initParameter(Parameter*);

13
lammps/parameter.c
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@ -60,6 +60,9 @@ void initParameter(Parameter *param) {
param->gx = 0.0;
param->gy = 0.0;
param->gz = 0.0;
param->reflect_x = 0.0;
param->reflect_y = 0.0;
param->reflect_z = 0.0;
}
void readParameter(Parameter *param, const char *filename) {
@ -93,6 +96,14 @@ void readParameter(Parameter *param, const char *filename) {
PARSE_STRING(vtk_file);
PARSE_REAL(epsilon);
PARSE_REAL(sigma);
PARSE_REAL(k_s);
PARSE_REAL(k_dn);
PARSE_REAL(reflect_x);
PARSE_REAL(reflect_y);
PARSE_REAL(reflect_z);
PARSE_REAL(gx);
PARSE_REAL(gy);
PARSE_REAL(gz);
PARSE_REAL(rho);
PARSE_REAL(dt);
PARSE_REAL(cutforce);
@ -139,6 +150,8 @@ void printParameter(Parameter *param) {
printf("\tLattice size: %e\n", param->lattice);
printf("\tEpsilon: %e\n", param->epsilon);
printf("\tSigma: %e\n", param->sigma);
printf("\tSpring constant: %e\n", param->k_s);
printf("\tDamping constant: %e\n", param->k_dn);
printf("\tTemperature: %e\n", param->temp);
printf("\tRHO: %e\n", param->rho);
printf("\tMass: %e\n", param->mass);