static void insert_mols(int nmol_insrt, int ntry, int seed,
t_atoms *atoms, rvec **x, real **exclusionDistances,
t_atoms *atoms_insrt, rvec *x_insrt, real *exclusionDistances_insrt,
int ePBC, matrix box,
const char* posfn, const rvec deltaR, int enum_rot)
{
t_pbc pbc;
rvec *x_n;
int mol;
int trial;
double **rpos;
const real maxInsertRadius
= *std::max_element(exclusionDistances_insrt,
exclusionDistances_insrt + atoms_insrt->nr);
real maxRadius = maxInsertRadius;
if (atoms->nr > 0)
{
const real maxExistingRadius
= *std::max_element(*exclusionDistances,
*exclusionDistances + atoms->nr);
maxRadius = std::max(maxInsertRadius, maxExistingRadius);
}
// TODO: Make all of this exception-safe.
gmx::AnalysisNeighborhood nb;
nb.setCutoff(maxInsertRadius + maxRadius);
gmx_rng_t rng = gmx_rng_init(seed);
set_pbc(&pbc, ePBC, box);
snew(x_n, atoms_insrt->nr);
/* With -ip, take nmol_insrt from file posfn */
if (posfn != NULL)
{
int ncol;
nmol_insrt = read_xvg(posfn, &rpos, &ncol);
if (ncol != 3)
{
gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n", ncol, posfn);
}
fprintf(stderr, "Read %d positions from file %s\n\n", nmol_insrt, posfn);
}
{
const int finalAtomCount = atoms->nr + nmol_insrt * atoms_insrt->nr;
const int finalResidueCount = atoms->nres + nmol_insrt * atoms_insrt->nres;
srenew(atoms->resinfo, finalResidueCount);
srenew(atoms->atomname, finalAtomCount);
srenew(atoms->atom, finalAtomCount);
srenew(*x, finalAtomCount);
srenew(*exclusionDistances, finalAtomCount);
}
trial = mol = 0;
while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
{
fprintf(stderr, "\rTry %d", trial++);
rvec offset_x;
if (posfn == NULL)
{
/* insert at random positions */
offset_x[XX] = box[XX][XX] * gmx_rng_uniform_real(rng);
offset_x[YY] = box[YY][YY] * gmx_rng_uniform_real(rng);
offset_x[ZZ] = box[ZZ][ZZ] * gmx_rng_uniform_real(rng);
}
else
{
/* Insert at positions taken from option -ip file */
offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2 * gmx_rng_uniform_real(rng)-1);
offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2 * gmx_rng_uniform_real(rng)-1);
offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2 * gmx_rng_uniform_real(rng)-1);
}
generate_trial_conf(atoms_insrt->nr, x_insrt, offset_x, enum_rot, rng,
x_n);
gmx::AnalysisNeighborhoodPositions pos(*x, atoms->nr);
gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, pos);
if (is_insertion_allowed(&search, *exclusionDistances, atoms_insrt->nr,
x_n, exclusionDistances_insrt))
{
const int firstIndex = atoms->nr;
for (int i = 0; i < atoms_insrt->nr; ++i)
{
copy_rvec(x_n[i], (*x)[firstIndex + i]);
(*exclusionDistances)[firstIndex + i] = exclusionDistances_insrt[i];
}
merge_atoms_noalloc(atoms, atoms_insrt);
++mol;
fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
}
}
gmx_rng_destroy(rng);
srenew(atoms->resinfo, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
srenew(*exclusionDistances, atoms->nr);
fprintf(stderr, "\n");
/* print number of molecules added */
fprintf(stderr, "Added %d molecules (out of %d requested) of %s\n",
mol, nmol_insrt, *atoms_insrt->resinfo[0].name);
sfree(x_n);
}
static void insert_mols(int nmol_insrt, int ntry, int seed,
real defaultDistance, real scaleFactor,
t_atoms *atoms, rvec **x,
const t_atoms *atoms_insrt, const rvec *x_insrt,
int ePBC, matrix box,
const std::string &posfn, const rvec deltaR, int enum_rot)
{
t_pbc pbc;
rvec *x_n;
fprintf(stderr, "Initialising inter-atomic distances...\n");
gmx_atomprop_t aps = gmx_atomprop_init();
real *exclusionDistances
= makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor);
real *exclusionDistances_insrt
= makeExclusionDistances(atoms_insrt, aps, defaultDistance, scaleFactor);
gmx_atomprop_destroy(aps);
const real maxInsertRadius
= *std::max_element(exclusionDistances_insrt,
exclusionDistances_insrt + atoms_insrt->nr);
real maxRadius = maxInsertRadius;
if (atoms->nr > 0)
{
const real maxExistingRadius
= *std::max_element(exclusionDistances,
exclusionDistances + atoms->nr);
maxRadius = std::max(maxInsertRadius, maxExistingRadius);
}
// TODO: Make all of this exception-safe.
gmx::AnalysisNeighborhood nb;
nb.setCutoff(maxInsertRadius + maxRadius);
gmx_rng_t rng = gmx_rng_init(seed);
set_pbc(&pbc, ePBC, box);
snew(x_n, atoms_insrt->nr);
/* With -ip, take nmol_insrt from file posfn */
double **rpos = NULL;
if (!posfn.empty())
{
int ncol;
nmol_insrt = read_xvg(posfn.c_str(), &rpos, &ncol);
if (ncol != 3)
{
gmx_fatal(FARGS, "Expected 3 columns (x/y/z coordinates) in file %s\n",
posfn.c_str());
}
fprintf(stderr, "Read %d positions from file %s\n\n",
nmol_insrt, posfn.c_str());
}
{
const int finalAtomCount = atoms->nr + nmol_insrt * atoms_insrt->nr;
const int finalResidueCount = atoms->nres + nmol_insrt * atoms_insrt->nres;
srenew(atoms->resinfo, finalResidueCount);
srenew(atoms->atomname, finalAtomCount);
srenew(atoms->atom, finalAtomCount);
srenew(*x, finalAtomCount);
srenew(exclusionDistances, finalAtomCount);
}
int mol = 0;
int trial = 0;
int firstTrial = 0;
int failed = 0;
while ((mol < nmol_insrt) && (trial < ntry*nmol_insrt))
{
rvec offset_x;
if (posfn.empty())
{
// Insert at random positions.
offset_x[XX] = box[XX][XX] * gmx_rng_uniform_real(rng);
offset_x[YY] = box[YY][YY] * gmx_rng_uniform_real(rng);
offset_x[ZZ] = box[ZZ][ZZ] * gmx_rng_uniform_real(rng);
}
else
{
// Skip a position if ntry trials were not successful.
if (trial >= firstTrial + ntry)
{
fprintf(stderr, " skipped position (%.3f, %.3f, %.3f)\n",
rpos[XX][mol], rpos[YY][mol], rpos[ZZ][mol]);
++mol;
++failed;
}
// Insert at positions taken from option -ip file.
offset_x[XX] = rpos[XX][mol] + deltaR[XX]*(2 * gmx_rng_uniform_real(rng)-1);
offset_x[YY] = rpos[YY][mol] + deltaR[YY]*(2 * gmx_rng_uniform_real(rng)-1);
offset_x[ZZ] = rpos[ZZ][mol] + deltaR[ZZ]*(2 * gmx_rng_uniform_real(rng)-1);
}
fprintf(stderr, "\rTry %d", ++trial);
generate_trial_conf(atoms_insrt->nr, x_insrt, offset_x, enum_rot, rng,
x_n);
gmx::AnalysisNeighborhoodPositions pos(*x, atoms->nr);
gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, pos);
if (is_insertion_allowed(&search, exclusionDistances, atoms_insrt->nr,
x_n, exclusionDistances_insrt))
{
const int firstIndex = atoms->nr;
for (int i = 0; i < atoms_insrt->nr; ++i)
{
copy_rvec(x_n[i], (*x)[firstIndex + i]);
exclusionDistances[firstIndex + i] = exclusionDistances_insrt[i];
}
merge_atoms_noalloc(atoms, atoms_insrt);
++mol;
firstTrial = trial;
fprintf(stderr, " success (now %d atoms)!\n", atoms->nr);
}
}
gmx_rng_destroy(rng);
srenew(atoms->resinfo, atoms->nres);
srenew(atoms->atomname, atoms->nr);
srenew(atoms->atom, atoms->nr);
srenew(*x, atoms->nr);
fprintf(stderr, "\n");
/* print number of molecules added */
fprintf(stderr, "Added %d molecules (out of %d requested)\n",
mol - failed, nmol_insrt);
sfree(x_n);
sfree(exclusionDistances);
sfree(exclusionDistances_insrt);
if (rpos != NULL)
{
for (int i = 0; i < DIM; ++i)
{
sfree(rpos[i]);
}
sfree(rpos);
}
}