void full_free_atomgrp(struct atomgrp *ag)
{
int i;
for (i = 0; i < ag->natoms; i++)
free_atom(ag->atoms + i); // free bonded pointers of each atom
free(ag->atoms); // free all the atoms in the ag
free(ag->activelist); // free list of active atoms
if (ag->nbact > 0)
free(ag->bact); // free active bond pointers
free(ag->bonds); // free bonds
if (ag->nangact > 0)
free(ag->angact); // free active angle pointers
free(ag->angs); // free angles
if (ag->ntoract > 0)
free(ag->toract); // free active torsion pointers
free(ag->tors); // free torsions
if (ag->nimpact > 0)
free(ag->impact); // free active improper pointers
free(ag->imps); // free impropers
if (ag->idres != NULL) {
for (i = 0; i < ag->nres; i++)
free(ag->idres[i]); //free residue names
}
free(ag->idres); //free pointers to residue names
free(ag->iares); //free array of first atom in residues
free(ag->rot);
free(ag->res_type);
free(ag->atypenn);
free(ag->atom_group_name);
free(ag); // free the ag itself
}
void full_free_atomgrp (struct atomgrp* ag)
{
int i;
for(i=0; i<ag->natoms; i++)
free_atom(ag->atoms+i); // free bonded pointers of each atom
free (ag->atoms); // free all the atoms in the ag
free (ag->activelist);// free list of active atoms
free (ag->bact); // free active bond pointers
free (ag->bonds); // free bonds
free (ag->angact); // free active angle pointers
free (ag->angs); // free angles
free (ag->toract); // free active torsion pointers
free (ag->tors); // free torsions
free (ag->impact); // free active improper pointers
free (ag->imps); // free impropers
for(i=0; i<ag->nres; i++)
free (ag->idres[i]); //free residue names
free (ag->idres); //free pointers to residue names
free (ag->iares); //free array of first atom in residues
free (ag); // free the ag itself
}
int main(int argc, char *argv[]) {
Atoms *atom;
LatticeDim lattice_dim;
Lattice *cpu_lattice;
Vec3 min_ext, max_ext; /* Bounding box of atoms */
Vec3 lo, hi; /* Bounding box with padding */
float h = 0.5f; /* Lattice spacing */
float cutoff = 12.f; /* Cutoff radius */
float exclcutoff = 1.f; /* Radius for exclusion */
float padding = 0.5f; /* Bounding box padding distance */
int n;
struct pb_Parameters *parameters;
struct pb_TimerSet timers;
/* Read input parameters */
parameters = pb_ReadParameters(&argc, argv);
if (parameters == NULL) {
exit(1);
}
/* Expect one input file */
if (pb_Parameters_CountInputs(parameters) != 1) {
fprintf(stderr, "Expecting one input file\n");
exit(1);
}
pb_InitializeTimerSet(&timers);
pb_SwitchToTimer(&timers, pb_TimerID_IO);
{
const char *pqrfilename = parameters->inpFiles[0];
if (!(atom = read_atom_file(pqrfilename))) {
fprintf(stderr, "read_atom_file() failed\n");
exit(1);
}
printf("read %d atoms from file '%s'\n", atom->size, pqrfilename);
}
pb_SwitchToTimer(&timers, pb_TimerID_COMPUTE);
/* find extent of domain */
get_atom_extent(&min_ext, &max_ext, atom);
printf("extent of domain is:\n");
printf(" minimum %g %g %g\n", min_ext.x, min_ext.y, min_ext.z);
printf(" maximum %g %g %g\n", max_ext.x, max_ext.y, max_ext.z);
printf("padding domain by %g Angstroms\n", padding);
lo = (Vec3) {min_ext.x - padding, min_ext.y - padding, min_ext.z - padding};
hi = (Vec3) {max_ext.x + padding, max_ext.y + padding, max_ext.z + padding};
printf("domain lengths are %g by %g by %g\n", hi.x-lo.x, hi.y-lo.y, hi.z-lo.z);
lattice_dim = lattice_from_bounding_box(lo, hi, h);
cpu_lattice = create_lattice(lattice_dim);
printf("\n");
/*
* CPU kernel
*/
if (cpu_compute_cutoff_potential_lattice(cpu_lattice, cutoff, atom)) {
fprintf(stderr, "Computation failed\n");
exit(1);
}
/*
* Zero the lattice points that are too close to an atom. This is
* necessary for numerical stability.
*/
if (remove_exclusions(cpu_lattice, exclcutoff, atom)) {
fprintf(stderr, "remove_exclusions() failed for cpu lattice\n");
exit(1);
}
/* Print output */
pb_SwitchToTimer(&timers, pb_TimerID_IO);
if (parameters->outFile) {
write_lattice_summary(parameters->outFile, cpu_lattice);
}
pb_SwitchToTimer(&timers, pb_TimerID_COMPUTE);
/* Cleanup */
destroy_lattice(cpu_lattice);
free_atom(atom);
pb_SwitchToTimer(&timers, pb_TimerID_NONE);
pb_PrintTimerSet(&timers);
pb_FreeParameters(parameters);
return 0;
}
