#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/pbcmethods.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-enum {
- euSel, euRect, euTric, euCompact, euNR
-};
-
-
-static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC,
- rvec x[], const int index[], matrix box)
-{
- int m, i, j, j0, j1, jj, ai, aj;
- int imin, jmin;
- real fac, min_dist2;
- rvec dx, xtest, box_center;
- int nmol, imol_center;
- int *molind;
- gmx_bool *bMol, *bTmp;
- rvec *m_com, *m_shift;
- t_pbc pbc;
- int *cluster;
- int *added;
- int ncluster, nadded;
- real tmp_r2;
-
- calc_box_center(ecenter, box, box_center);
-
- /* Initiate the pbc structure */
- std::memset(&pbc, 0, sizeof(pbc));
- set_pbc(&pbc, ePBC, box);
-
- /* Convert atom index to molecular */
- nmol = top->mols.nr;
- molind = top->mols.index;
- snew(bMol, nmol);
- snew(m_com, nmol);
- snew(m_shift, nmol);
- snew(cluster, nmol);
- snew(added, nmol);
- snew(bTmp, top->atoms.nr);
-
- for (i = 0; (i < nrefat); i++)
- {
- /* Mark all molecules in the index */
- ai = index[i];
- bTmp[ai] = TRUE;
- /* Binary search assuming the molecules are sorted */
- j0 = 0;
- j1 = nmol-1;
- while (j0 < j1)
- {
- if (ai < molind[j0+1])
- {
- j1 = j0;
- }
- else if (ai >= molind[j1])
- {
- j0 = j1;
- }
- else
- {
- jj = (j0+j1)/2;
- if (ai < molind[jj+1])
- {
- j1 = jj;
- }
- else
- {
- j0 = jj;
- }
- }
- }
- bMol[j0] = TRUE;
- }
- /* Double check whether all atoms in all molecules that are marked are part
- * of the cluster. Simultaneously compute the center of geometry.
- */
- min_dist2 = 10*gmx::square(trace(box));
- imol_center = -1;
- ncluster = 0;
- for (i = 0; i < nmol; i++)
- {
- for (j = molind[i]; j < molind[i+1]; j++)
- {
- if (bMol[i] && !bTmp[j])
- {
- gmx_fatal(FARGS, "Molecule %d marked for clustering but not atom %d in it - check your index!", i+1, j+1);
- }
- else if (!bMol[i] && bTmp[j])
- {
- gmx_fatal(FARGS, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j+1, i+1);
- }
- else if (bMol[i])
- {
- /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
- if (j > molind[i])
- {
- pbc_dx(&pbc, x[j], x[j-1], dx);
- rvec_add(x[j-1], dx, x[j]);
- }
- /* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
- rvec_inc(m_com[i], x[j]);
- }
- }
- if (bMol[i])
- {
- /* Normalize center of geometry */
- fac = 1.0/(molind[i+1]-molind[i]);
- for (m = 0; (m < DIM); m++)
- {
- m_com[i][m] *= fac;
- }
- /* Determine which molecule is closest to the center of the box */
- pbc_dx(&pbc, box_center, m_com[i], dx);
- tmp_r2 = iprod(dx, dx);
-
- if (tmp_r2 < min_dist2)
- {
- min_dist2 = tmp_r2;
- imol_center = i;
- }
- cluster[ncluster++] = i;
- }
- }
- sfree(bTmp);
-
- if (ncluster <= 0)
- {
- fprintf(stderr, "No molecules selected in the cluster\n");
- return;
- }
- else if (imol_center == -1)
- {
- fprintf(stderr, "No central molecules could be found\n");
- return;
- }
-
- nadded = 0;
- added[nadded++] = imol_center;
- bMol[imol_center] = FALSE;
-
- while (nadded < ncluster)
- {
- /* Find min distance between cluster molecules and those remaining to be added */
- min_dist2 = 10*gmx::square(trace(box));
- imin = -1;
- jmin = -1;
- /* Loop over added mols */
- for (i = 0; i < nadded; i++)
- {
- ai = added[i];
- /* Loop over all mols */
- for (j = 0; j < ncluster; j++)
- {
- aj = cluster[j];
- /* check those remaining to be added */
- if (bMol[aj])
- {
- pbc_dx(&pbc, m_com[aj], m_com[ai], dx);
- tmp_r2 = iprod(dx, dx);
- if (tmp_r2 < min_dist2)
- {
- min_dist2 = tmp_r2;
- imin = ai;
- jmin = aj;
- }
- }
- }
- }
-
- /* Add the best molecule */
- added[nadded++] = jmin;
- bMol[jmin] = FALSE;
- /* Calculate the shift from the ai molecule */
- pbc_dx(&pbc, m_com[jmin], m_com[imin], dx);
- rvec_add(m_com[imin], dx, xtest);
- rvec_sub(xtest, m_com[jmin], m_shift[jmin]);
- rvec_inc(m_com[jmin], m_shift[jmin]);
-
- for (j = molind[jmin]; j < molind[jmin+1]; j++)
- {
- rvec_inc(x[j], m_shift[jmin]);
- }
- fprintf(stdout, "\rClustering iteration %d of %d...", nadded, ncluster);
- fflush(stdout);
- }
-
- sfree(added);
- sfree(cluster);
- sfree(bMol);
- sfree(m_com);
- sfree(m_shift);
-
- fprintf(stdout, "\n");
-}
-
-static void put_molecule_com_in_box(int unitcell_enum, int ecenter,
- t_block *mols,
- int natoms, t_atom atom[],
- int ePBC, matrix box, rvec x[])
-{
- int i, j;
- int d;
- rvec com, shift, box_center;
- real m;
- double mtot;
- t_pbc pbc;
-
- calc_box_center(ecenter, box, box_center);
- set_pbc(&pbc, ePBC, box);
- if (mols->nr <= 0)
- {
- gmx_fatal(FARGS, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
- }
- for (i = 0; (i < mols->nr); i++)
- {
- /* calc COM */
- clear_rvec(com);
- mtot = 0;
- for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
- {
- m = atom[j].m;
- for (d = 0; d < DIM; d++)
- {
- com[d] += m*x[j][d];
- }
- mtot += m;
- }
- /* calculate final COM */
- svmul(1.0/mtot, com, com);
-
- /* check if COM is outside box */
- gmx::RVec newCom;
- copy_rvec(com, newCom);
- auto newComArrayRef = gmx::arrayRefFromArray(&newCom, 1);
- switch (unitcell_enum)
- {
- case euRect:
- put_atoms_in_box(ePBC, box, newComArrayRef);
- break;
- case euTric:
- put_atoms_in_triclinic_unitcell(ecenter, box, newComArrayRef);
- break;
- case euCompact:
- put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
- break;
- }
- rvec_sub(newCom, com, shift);
- if (norm2(shift) > 0)
- {
- if (debug)
- {
- fprintf(debug, "\nShifting position of molecule %d "
- "by %8.3f %8.3f %8.3f\n", i+1,
- shift[XX], shift[YY], shift[ZZ]);
- }
- for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
- {
- rvec_inc(x[j], shift);
- }
- }
- }
-}
-
-static void put_residue_com_in_box(int unitcell_enum, int ecenter,
- int natoms, t_atom atom[],
- int ePBC, matrix box, rvec x[])
-{
- int i, j, res_start, res_end;
- int d, presnr;
- real m;
- double mtot;
- rvec box_center, com, shift;
- static const int NOTSET = -12347;
- calc_box_center(ecenter, box, box_center);
-
- presnr = NOTSET;
- res_start = 0;
- clear_rvec(com);
- mtot = 0;
- for (i = 0; i < natoms+1; i++)
- {
- if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET))
- {
- /* calculate final COM */
- res_end = i;
- svmul(1.0/mtot, com, com);
-
- /* check if COM is outside box */
- gmx::RVec newCom;
- copy_rvec(com, newCom);
- auto newComArrayRef = gmx::arrayRefFromArray(&newCom, 1);
- switch (unitcell_enum)
- {
- case euRect:
- put_atoms_in_box(ePBC, box, newComArrayRef);
- break;
- case euTric:
- put_atoms_in_triclinic_unitcell(ecenter, box, newComArrayRef);
- break;
- case euCompact:
- put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
- break;
- }
- rvec_sub(newCom, com, shift);
- if (norm2(shift) != 0.0f)
- {
- if (debug)
- {
- fprintf(debug, "\nShifting position of residue %d (atoms %d-%d) "
- "by %g,%g,%g\n", atom[res_start].resind+1,
- res_start+1, res_end+1, shift[XX], shift[YY], shift[ZZ]);
- }
- for (j = res_start; j < res_end; j++)
- {
- rvec_inc(x[j], shift);
- }
- }
- clear_rvec(com);
- mtot = 0;
-
- /* remember start of new residue */
- res_start = i;
- }
- if (i < natoms)
- {
- /* calc COM */
- m = atom[i].m;
- for (d = 0; d < DIM; d++)
- {
- com[d] += m*x[i][d];
- }
- mtot += m;
-
- presnr = atom[i].resind;
- }
- }
-}
-
-static void center_x(int ecenter, rvec x[], matrix box, int n, int nc, const int ci[])
-{
- int i, m, ai;
- rvec cmin, cmax, box_center, dx;
-
- if (nc > 0)
- {
- copy_rvec(x[ci[0]], cmin);
- copy_rvec(x[ci[0]], cmax);
- for (i = 0; i < nc; i++)
- {
- ai = ci[i];
- for (m = 0; m < DIM; m++)
- {
- if (x[ai][m] < cmin[m])
- {
- cmin[m] = x[ai][m];
- }
- else if (x[ai][m] > cmax[m])
- {
- cmax[m] = x[ai][m];
- }
- }
- }
- calc_box_center(ecenter, box, box_center);
- for (m = 0; m < DIM; m++)
- {
- dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
- }
-
- for (i = 0; i < n; i++)
- {
- rvec_inc(x[i], dx);
- }
- }
-}
-
static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
char out_file[])
{
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