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40 #include "pull_rotation.h"
51 #include "gromacs/commandline/filenm.h"
52 #include "gromacs/domdec/dlbtiming.h"
53 #include "gromacs/domdec/domdec_struct.h"
54 #include "gromacs/domdec/ga2la.h"
55 #include "gromacs/domdec/localatomset.h"
56 #include "gromacs/domdec/localatomsetmanager.h"
57 #include "gromacs/fileio/gmxfio.h"
58 #include "gromacs/fileio/xvgr.h"
59 #include "gromacs/gmxlib/network.h"
60 #include "gromacs/linearalgebra/nrjac.h"
61 #include "gromacs/math/functions.h"
62 #include "gromacs/math/utilities.h"
63 #include "gromacs/math/vec.h"
64 #include "gromacs/mdlib/groupcoord.h"
65 #include "gromacs/mdlib/stat.h"
66 #include "gromacs/mdrunutility/handlerestart.h"
67 #include "gromacs/mdtypes/commrec.h"
68 #include "gromacs/mdtypes/inputrec.h"
69 #include "gromacs/mdtypes/md_enums.h"
70 #include "gromacs/mdtypes/mdrunoptions.h"
71 #include "gromacs/mdtypes/state.h"
72 #include "gromacs/pbcutil/pbc.h"
73 #include "gromacs/timing/cyclecounter.h"
74 #include "gromacs/timing/wallcycle.h"
75 #include "gromacs/topology/mtop_lookup.h"
76 #include "gromacs/topology/mtop_util.h"
77 #include "gromacs/utility/basedefinitions.h"
78 #include "gromacs/utility/fatalerror.h"
79 #include "gromacs/utility/pleasecite.h"
80 #include "gromacs/utility/smalloc.h"
82 static char const* RotStr = { "Enforced rotation:" };
84 /* Set the minimum weight for the determination of the slab centers */
85 #define WEIGHT_MIN (10 * GMX_FLOAT_MIN)
87 //! Helper structure for sorting positions along rotation vector
88 struct sort_along_vec_t
90 //! Projection of xc on the rotation vector
98 //! Reference position
103 //! Enforced rotation / flexible: determine the angle of each slab
106 //! Number of atoms belonging to this slab
108 /*! \brief The positions belonging to this slab.
110 * In general, this should be all positions of the whole
111 * rotation group, but we leave those away that have a small
114 //! Same for reference
116 //! The weight for each atom
121 //! Helper structure for potential fitting
124 /*! \brief Set of angles for which the potential is calculated.
126 * The optimum fit is determined as the angle for with the
127 * potential is minimal. */
129 //! Potential for the different angles
131 //! Rotation matrix corresponding to the angles
136 //! Enforced rotation data for a single rotation group
139 //! Input parameters for this group
140 const t_rotgrp* rotg = nullptr;
141 //! Index of this group within the set of groups
143 //! Rotation angle in degrees
147 //! The atoms subject to enforced rotation
148 std::unique_ptr<gmx::LocalAtomSet> atomSet;
150 //! The normalized rotation vector
152 //! Rotation potential for this rotation group
154 //! Array to store the forces on the local atoms resulting from enforced rotation potential
157 /* Collective coordinates for the whole rotation group */
158 //! Length of each x_rotref vector after x_rotref has been put into origin
160 //! Center of the rotation group positions, may be mass weighted
162 //! Center of the rotation group reference positions
164 //! Current (collective) positions
166 //! Current (collective) shifts
168 //! Extra shifts since last DD step
170 //! Old (collective) positions
172 //! Normalized form of the current positions
174 //! Reference positions (sorted in the same order as xc when sorted)
176 //! Where is a position found after sorting?
178 //! Collective masses
180 //! Collective masses sorted
182 //! one over the total mass of the rotation group
185 //! Torque in the direction of rotation vector
187 //! Actual angle of the whole rotation group
189 /* Fixed rotation only */
190 //! Weights for angle determination
192 //! Local reference coords, correctly rotated
194 //! Local current coords, correct PBC image
196 //! Masses of the current local atoms
199 /* Flexible rotation only */
200 //! For this many slabs memory is allocated
202 //! Lowermost slab for that the calculation needs to be performed at a given time step
204 //! Uppermost slab ...
206 //! First slab for which ref. center is stored
210 //! Slab buffer region around reference slabs
212 //! First relevant atom for a slab
214 //! Last relevant atom for a slab
216 //! Gaussian-weighted slab center
218 //! Gaussian-weighted slab center for the reference positions
219 rvec* slab_center_ref;
220 //! Sum of gaussian weights in a slab
222 //! Torque T = r x f for each slab. torque_v = m.v = angular momentum in the direction of v
224 //! min_gaussian from t_rotgrp is the minimum value the gaussian must have so that the force is actually evaluated. max_beta is just another way to put it
226 //! Precalculated gaussians for a single atom
228 //! Tells to which slab each precalculated gaussian belongs
230 //! Inner sum of the flexible2 potential per slab; this is precalculated for optimization reasons
231 rvec* slab_innersumvec;
232 //! Holds atom positions and gaussian weights of atoms belonging to a slab
233 gmx_slabdata* slab_data;
235 /* For potential fits with varying angle: */
236 //! Used for fit type 'potential'
237 gmx_potfit* PotAngleFit;
241 //! Enforced rotation data for all groups
244 //! Input parameters.
245 const t_rot* rot = nullptr;
246 //! Output period for main rotation outfile
248 //! Output period for per-slab data
250 //! Output file for rotation data
251 FILE* out_rot = nullptr;
252 //! Output file for torque data
253 FILE* out_torque = nullptr;
254 //! Output file for slab angles for flexible type
255 FILE* out_angles = nullptr;
256 //! Output file for slab centers
257 FILE* out_slabs = nullptr;
258 //! Allocation size of buf
260 //! Coordinate buffer variable for sorting
261 rvec* xbuf = nullptr;
262 //! Masses buffer variable for sorting
263 real* mbuf = nullptr;
264 //! Buffer variable needed for position sorting
265 sort_along_vec_t* data = nullptr;
267 real* mpi_inbuf = nullptr;
269 real* mpi_outbuf = nullptr;
270 //! Allocation size of in & outbuf
272 //! If true, append output files
273 gmx_bool restartWithAppending = false;
274 //! Used to skip first output when appending to avoid duplicate entries in rotation outfiles
275 gmx_bool bOut = false;
276 //! Stores working data per group
277 std::vector<gmx_enfrotgrp> enfrotgrp;
281 gmx_enfrot::~gmx_enfrot()
285 gmx_fio_fclose(out_rot);
289 gmx_fio_fclose(out_slabs);
293 gmx_fio_fclose(out_angles);
297 gmx_fio_fclose(out_torque);
304 extern template LocalAtomSet LocalAtomSetManager::add<void, void>(ArrayRef<const int> globalAtomIndex);
306 class EnforcedRotation::Impl
309 gmx_enfrot enforcedRotation_;
312 EnforcedRotation::EnforcedRotation() : impl_(new Impl) {}
314 EnforcedRotation::~EnforcedRotation() = default;
316 gmx_enfrot* EnforcedRotation::getLegacyEnfrot()
318 return &impl_->enforcedRotation_;
323 /* Activate output of forces for correctness checks */
324 /* #define PRINT_FORCES */
326 # define PRINT_FORCE_J \
328 "f%d = %15.8f %15.8f %15.8f\n", \
329 erg->xc_ref_ind[j], \
330 erg->f_rot_loc[j][XX], \
331 erg->f_rot_loc[j][YY], \
332 erg->f_rot_loc[j][ZZ]);
333 # define PRINT_POT_TAU \
337 "potential = %15.8f\n" \
338 "torque = %15.8f\n", \
343 # define PRINT_FORCE_J
344 # define PRINT_POT_TAU
347 /* Shortcuts for often used queries */
349 (((rg)->eType == erotgFLEX) || ((rg)->eType == erotgFLEXT) || ((rg)->eType == erotgFLEX2) \
350 || ((rg)->eType == erotgFLEX2T))
352 (((rg)->eType == erotgFLEX) || ((rg)->eType == erotgFLEXT) || ((rg)->eType == erotgFLEX2) \
353 || ((rg)->eType == erotgFLEX2T) || ((rg)->eType == erotgRMPF) || ((rg)->eType == erotgRM2PF))
356 /* Does any of the rotation groups use slab decomposition? */
357 static gmx_bool HaveFlexibleGroups(const t_rot* rot)
359 for (int g = 0; g < rot->ngrp; g++)
361 if (ISFLEX(&rot->grp[g]))
371 /* Is for any group the fit angle determined by finding the minimum of the
372 * rotation potential? */
373 static gmx_bool HavePotFitGroups(const t_rot* rot)
375 for (int g = 0; g < rot->ngrp; g++)
377 if (erotgFitPOT == rot->grp[g].eFittype)
387 static double** allocate_square_matrix(int dim)
390 double** mat = nullptr;
394 for (i = 0; i < dim; i++)
403 static void free_square_matrix(double** mat, int dim)
408 for (i = 0; i < dim; i++)
416 /* Return the angle for which the potential is minimal */
417 static real get_fitangle(const gmx_enfrotgrp* erg)
420 real fitangle = -999.9;
421 real pot_min = GMX_FLOAT_MAX;
425 fit = erg->PotAngleFit;
427 for (i = 0; i < erg->rotg->PotAngle_nstep; i++)
429 if (fit->V[i] < pot_min)
432 fitangle = fit->degangle[i];
440 /* Reduce potential angle fit data for this group at this time step? */
441 static inline gmx_bool bPotAngle(const gmx_enfrot* er, const t_rotgrp* rotg, int64_t step)
443 return ((erotgFitPOT == rotg->eFittype)
444 && (do_per_step(step, er->nstsout) || do_per_step(step, er->nstrout)));
447 /* Reduce slab torqe data for this group at this time step? */
448 static inline gmx_bool bSlabTau(const gmx_enfrot* er, const t_rotgrp* rotg, int64_t step)
450 return ((ISFLEX(rotg)) && do_per_step(step, er->nstsout));
453 /* Output rotation energy, torques, etc. for each rotation group */
454 static void reduce_output(const t_commrec* cr, gmx_enfrot* er, real t, int64_t step)
456 int i, islab, nslabs = 0;
457 int count; /* MPI element counter */
461 /* Fill the MPI buffer with stuff to reduce. If items are added for reduction
462 * here, the MPI buffer size has to be enlarged also in calc_mpi_bufsize() */
466 for (auto& ergRef : er->enfrotgrp)
468 gmx_enfrotgrp* erg = &ergRef;
469 const t_rotgrp* rotg = erg->rotg;
470 nslabs = erg->slab_last - erg->slab_first + 1;
471 er->mpi_inbuf[count++] = erg->V;
472 er->mpi_inbuf[count++] = erg->torque_v;
473 er->mpi_inbuf[count++] = erg->angle_v;
474 er->mpi_inbuf[count++] =
475 erg->weight_v; /* weights are not needed for flex types, but this is just a single value */
477 if (bPotAngle(er, rotg, step))
479 for (i = 0; i < rotg->PotAngle_nstep; i++)
481 er->mpi_inbuf[count++] = erg->PotAngleFit->V[i];
484 if (bSlabTau(er, rotg, step))
486 for (i = 0; i < nslabs; i++)
488 er->mpi_inbuf[count++] = erg->slab_torque_v[i];
492 if (count > er->mpi_bufsize)
494 gmx_fatal(FARGS, "%s MPI buffer overflow, please report this error.", RotStr);
498 MPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REAL, MPI_SUM, MASTERRANK(cr), cr->mpi_comm_mygroup);
501 /* Copy back the reduced data from the buffer on the master */
505 for (auto& ergRef : er->enfrotgrp)
507 gmx_enfrotgrp* erg = &ergRef;
508 const t_rotgrp* rotg = erg->rotg;
509 nslabs = erg->slab_last - erg->slab_first + 1;
510 erg->V = er->mpi_outbuf[count++];
511 erg->torque_v = er->mpi_outbuf[count++];
512 erg->angle_v = er->mpi_outbuf[count++];
513 erg->weight_v = er->mpi_outbuf[count++];
515 if (bPotAngle(er, rotg, step))
517 for (int i = 0; i < rotg->PotAngle_nstep; i++)
519 erg->PotAngleFit->V[i] = er->mpi_outbuf[count++];
522 if (bSlabTau(er, rotg, step))
524 for (int i = 0; i < nslabs; i++)
526 erg->slab_torque_v[i] = er->mpi_outbuf[count++];
536 /* Angle and torque for each rotation group */
537 for (auto& ergRef : er->enfrotgrp)
539 gmx_enfrotgrp* erg = &ergRef;
540 const t_rotgrp* rotg = erg->rotg;
541 bFlex = ISFLEX(rotg);
543 /* Output to main rotation output file: */
544 if (do_per_step(step, er->nstrout))
546 if (erotgFitPOT == rotg->eFittype)
548 fitangle = get_fitangle(erg);
554 fitangle = erg->angle_v; /* RMSD fit angle */
558 fitangle = (erg->angle_v / erg->weight_v) * 180.0 * M_1_PI;
561 fprintf(er->out_rot, "%12.4f", fitangle);
562 fprintf(er->out_rot, "%12.3e", erg->torque_v);
563 fprintf(er->out_rot, "%12.3e", erg->V);
566 if (do_per_step(step, er->nstsout))
568 /* Output to torque log file: */
571 fprintf(er->out_torque, "%12.3e%6d", t, erg->groupIndex);
572 for (int i = erg->slab_first; i <= erg->slab_last; i++)
574 islab = i - erg->slab_first; /* slab index */
575 /* Only output if enough weight is in slab */
576 if (erg->slab_weights[islab] > rotg->min_gaussian)
578 fprintf(er->out_torque, "%6d%12.3e", i, erg->slab_torque_v[islab]);
581 fprintf(er->out_torque, "\n");
584 /* Output to angles log file: */
585 if (erotgFitPOT == rotg->eFittype)
587 fprintf(er->out_angles, "%12.3e%6d%12.4f", t, erg->groupIndex, erg->degangle);
588 /* Output energies at a set of angles around the reference angle */
589 for (int i = 0; i < rotg->PotAngle_nstep; i++)
591 fprintf(er->out_angles, "%12.3e", erg->PotAngleFit->V[i]);
593 fprintf(er->out_angles, "\n");
597 if (do_per_step(step, er->nstrout))
599 fprintf(er->out_rot, "\n");
605 /* Add the forces from enforced rotation potential to the local forces.
606 * Should be called after the SR forces have been evaluated */
607 real add_rot_forces(gmx_enfrot* er, rvec f[], const t_commrec* cr, int64_t step, real t)
609 real Vrot = 0.0; /* If more than one rotation group is present, Vrot
610 assembles the local parts from all groups */
612 /* Loop over enforced rotation groups (usually 1, though)
613 * Apply the forces from rotation potentials */
614 for (auto& ergRef : er->enfrotgrp)
616 gmx_enfrotgrp* erg = &ergRef;
617 Vrot += erg->V; /* add the local parts from the nodes */
618 const auto& localRotationGroupIndex = erg->atomSet->localIndex();
619 for (gmx::index l = 0; l < localRotationGroupIndex.ssize(); l++)
621 /* Get the right index of the local force */
622 int ii = localRotationGroupIndex[l];
624 rvec_inc(f[ii], erg->f_rot_loc[l]);
628 /* Reduce energy,torque, angles etc. to get the sum values (per rotation group)
629 * on the master and output these values to file. */
630 if ((do_per_step(step, er->nstrout) || do_per_step(step, er->nstsout)) && er->bOut)
632 reduce_output(cr, er, t, step);
635 /* When appending, er->bOut is FALSE the first time to avoid duplicate entries */
644 /* The Gaussian norm is chosen such that the sum of the gaussian functions
645 * over the slabs is approximately 1.0 everywhere */
646 #define GAUSS_NORM 0.569917543430618
649 /* Calculate the maximum beta that leads to a gaussian larger min_gaussian,
650 * also does some checks
652 static double calc_beta_max(real min_gaussian, real slab_dist)
658 /* Actually the next two checks are already made in grompp */
661 gmx_fatal(FARGS, "Slab distance of flexible rotation groups must be >=0 !");
663 if (min_gaussian <= 0)
665 gmx_fatal(FARGS, "Cutoff value for Gaussian must be > 0. (You requested %f)", min_gaussian);
668 /* Define the sigma value */
669 sigma = 0.7 * slab_dist;
671 /* Calculate the argument for the logarithm and check that the log() result is negative or 0 */
672 arg = min_gaussian / GAUSS_NORM;
675 gmx_fatal(FARGS, "min_gaussian of flexible rotation groups must be <%g", GAUSS_NORM);
678 return std::sqrt(-2.0 * sigma * sigma * log(min_gaussian / GAUSS_NORM));
682 static inline real calc_beta(rvec curr_x, const gmx_enfrotgrp* erg, int n)
684 return iprod(curr_x, erg->vec) - erg->rotg->slab_dist * n;
688 static inline real gaussian_weight(rvec curr_x, const gmx_enfrotgrp* erg, int n)
690 const real norm = GAUSS_NORM;
694 /* Define the sigma value */
695 sigma = 0.7 * erg->rotg->slab_dist;
696 /* Calculate the Gaussian value of slab n for position curr_x */
697 return norm * exp(-0.5 * gmx::square(calc_beta(curr_x, erg, n) / sigma));
701 /* Returns the weight in a single slab, also calculates the Gaussian- and mass-
702 * weighted sum of positions for that slab */
703 static real get_slab_weight(int j, const gmx_enfrotgrp* erg, rvec xc[], const real mc[], rvec* x_weighted_sum)
705 rvec curr_x; /* The position of an atom */
706 rvec curr_x_weighted; /* The gaussian-weighted position */
707 real gaussian; /* A single gaussian weight */
708 real wgauss; /* gaussian times current mass */
709 real slabweight = 0.0; /* The sum of weights in the slab */
711 clear_rvec(*x_weighted_sum);
713 /* Loop over all atoms in the rotation group */
714 for (int i = 0; i < erg->rotg->nat; i++)
716 copy_rvec(xc[i], curr_x);
717 gaussian = gaussian_weight(curr_x, erg, j);
718 wgauss = gaussian * mc[i];
719 svmul(wgauss, curr_x, curr_x_weighted);
720 rvec_add(*x_weighted_sum, curr_x_weighted, *x_weighted_sum);
721 slabweight += wgauss;
722 } /* END of loop over rotation group atoms */
728 static void get_slab_centers(gmx_enfrotgrp* erg, /* Enforced rotation group working data */
729 rvec* xc, /* The rotation group positions; will
730 typically be enfrotgrp->xc, but at first call
731 it is enfrotgrp->xc_ref */
732 real* mc, /* The masses of the rotation group atoms */
733 real time, /* Used for output only */
734 FILE* out_slabs, /* For outputting center per slab information */
735 gmx_bool bOutStep, /* Is this an output step? */
736 gmx_bool bReference) /* If this routine is called from
737 init_rot_group we need to store
738 the reference slab centers */
740 /* Loop over slabs */
741 for (int j = erg->slab_first; j <= erg->slab_last; j++)
743 int slabIndex = j - erg->slab_first;
744 erg->slab_weights[slabIndex] = get_slab_weight(j, erg, xc, mc, &erg->slab_center[slabIndex]);
746 /* We can do the calculations ONLY if there is weight in the slab! */
747 if (erg->slab_weights[slabIndex] > WEIGHT_MIN)
749 svmul(1.0 / erg->slab_weights[slabIndex], erg->slab_center[slabIndex], erg->slab_center[slabIndex]);
753 /* We need to check this here, since we divide through slab_weights
754 * in the flexible low-level routines! */
755 gmx_fatal(FARGS, "Not enough weight in slab %d. Slab center cannot be determined!", j);
758 /* At first time step: save the centers of the reference structure */
761 copy_rvec(erg->slab_center[slabIndex], erg->slab_center_ref[slabIndex]);
763 } /* END of loop over slabs */
765 /* Output on the master */
766 if ((nullptr != out_slabs) && bOutStep)
768 fprintf(out_slabs, "%12.3e%6d", time, erg->groupIndex);
769 for (int j = erg->slab_first; j <= erg->slab_last; j++)
771 int slabIndex = j - erg->slab_first;
773 "%6d%12.3e%12.3e%12.3e",
775 erg->slab_center[slabIndex][XX],
776 erg->slab_center[slabIndex][YY],
777 erg->slab_center[slabIndex][ZZ]);
779 fprintf(out_slabs, "\n");
784 static void calc_rotmat(const rvec vec,
785 real degangle, /* Angle alpha of rotation at time t in degrees */
786 matrix rotmat) /* Rotation matrix */
788 real radangle; /* Rotation angle in radians */
789 real cosa; /* cosine alpha */
790 real sina; /* sine alpha */
791 real OMcosa; /* 1 - cos(alpha) */
792 real dumxy, dumxz, dumyz; /* save computations */
793 rvec rot_vec; /* Rotate around rot_vec ... */
796 radangle = degangle * M_PI / 180.0;
797 copy_rvec(vec, rot_vec);
799 /* Precompute some variables: */
800 cosa = cos(radangle);
801 sina = sin(radangle);
803 dumxy = rot_vec[XX] * rot_vec[YY] * OMcosa;
804 dumxz = rot_vec[XX] * rot_vec[ZZ] * OMcosa;
805 dumyz = rot_vec[YY] * rot_vec[ZZ] * OMcosa;
807 /* Construct the rotation matrix for this rotation group: */
809 rotmat[XX][XX] = cosa + rot_vec[XX] * rot_vec[XX] * OMcosa;
810 rotmat[YY][XX] = dumxy + rot_vec[ZZ] * sina;
811 rotmat[ZZ][XX] = dumxz - rot_vec[YY] * sina;
813 rotmat[XX][YY] = dumxy - rot_vec[ZZ] * sina;
814 rotmat[YY][YY] = cosa + rot_vec[YY] * rot_vec[YY] * OMcosa;
815 rotmat[ZZ][YY] = dumyz + rot_vec[XX] * sina;
817 rotmat[XX][ZZ] = dumxz + rot_vec[YY] * sina;
818 rotmat[YY][ZZ] = dumyz - rot_vec[XX] * sina;
819 rotmat[ZZ][ZZ] = cosa + rot_vec[ZZ] * rot_vec[ZZ] * OMcosa;
824 for (iii = 0; iii < 3; iii++)
826 for (jjj = 0; jjj < 3; jjj++)
828 fprintf(stderr, " %10.8f ", rotmat[iii][jjj]);
830 fprintf(stderr, "\n");
836 /* Calculates torque on the rotation axis tau = position x force */
837 static inline real torque(const rvec rotvec, /* rotation vector; MUST be normalized! */
838 rvec force, /* force */
839 rvec x, /* position of atom on which the force acts */
840 rvec pivot) /* pivot point of rotation axis */
845 /* Subtract offset */
846 rvec_sub(x, pivot, vectmp);
848 /* position x force */
849 cprod(vectmp, force, tau);
851 /* Return the part of the torque which is parallel to the rotation vector */
852 return iprod(tau, rotvec);
856 /* Right-aligned output of value with standard width */
857 static void print_aligned(FILE* fp, char const* str)
859 fprintf(fp, "%12s", str);
863 /* Right-aligned output of value with standard short width */
864 static void print_aligned_short(FILE* fp, char const* str)
866 fprintf(fp, "%6s", str);
870 static FILE* open_output_file(const char* fn, int steps, const char what[])
875 fp = gmx_ffopen(fn, "w");
877 fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n", what, steps, steps > 1 ? "s" : "");
883 /* Open output file for slab center data. Call on master only */
884 static FILE* open_slab_out(const char* fn, gmx_enfrot* er)
888 if (er->restartWithAppending)
890 fp = gmx_fio_fopen(fn, "a");
894 fp = open_output_file(fn, er->nstsout, "gaussian weighted slab centers");
896 for (auto& ergRef : er->enfrotgrp)
898 gmx_enfrotgrp* erg = &ergRef;
899 if (ISFLEX(erg->rotg))
902 "# Rotation group %d (%s), slab distance %f nm, %s.\n",
904 erotg_names[erg->rotg->eType],
905 erg->rotg->slab_dist,
906 erg->rotg->bMassW ? "centers of mass" : "geometrical centers");
910 fprintf(fp, "# Reference centers are listed first (t=-1).\n");
911 fprintf(fp, "# The following columns have the syntax:\n");
913 print_aligned_short(fp, "t");
914 print_aligned_short(fp, "grp");
915 /* Print legend for the first two entries only ... */
916 for (int i = 0; i < 2; i++)
918 print_aligned_short(fp, "slab");
919 print_aligned(fp, "X center");
920 print_aligned(fp, "Y center");
921 print_aligned(fp, "Z center");
923 fprintf(fp, " ...\n");
931 /* Adds 'buf' to 'str' */
932 static void add_to_string(char** str, char* buf)
937 len = strlen(*str) + strlen(buf) + 1;
943 static void add_to_string_aligned(char** str, char* buf)
945 char buf_aligned[STRLEN];
947 sprintf(buf_aligned, "%12s", buf);
948 add_to_string(str, buf_aligned);
952 /* Open output file and print some general information about the rotation groups.
953 * Call on master only */
954 static FILE* open_rot_out(const char* fn, const gmx_output_env_t* oenv, gmx_enfrot* er)
958 const char** setname;
959 char buf[50], buf2[75];
961 char* LegendStr = nullptr;
962 const t_rot* rot = er->rot;
964 if (er->restartWithAppending)
966 fp = gmx_fio_fopen(fn, "a");
971 "Rotation angles and energy",
973 "angles (degrees) and energies (kJ/mol)",
976 "# Output of enforced rotation data is written in intervals of %d time "
979 er->nstrout > 1 ? "s" : "");
981 "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector "
983 fprintf(fp, "# To obtain the vectorial torque, multiply tau with the group's rot-vec.\n");
985 "# For flexible groups, tau(t,n) from all slabs n have been summed in a single "
986 "value tau(t) here.\n");
987 fprintf(fp, "# The torques tau(t,n) are found in the rottorque.log (-rt) output file\n");
989 for (int g = 0; g < rot->ngrp; g++)
991 const t_rotgrp* rotg = &rot->grp[g];
992 const gmx_enfrotgrp* erg = &er->enfrotgrp[g];
993 bFlex = ISFLEX(rotg);
996 fprintf(fp, "# ROTATION GROUP %d, potential type '%s':\n", g, erotg_names[rotg->eType]);
997 fprintf(fp, "# rot-massw%d %s\n", g, yesno_names[rotg->bMassW]);
999 "# rot-vec%d %12.5e %12.5e %12.5e\n",
1004 fprintf(fp, "# rot-rate%d %12.5e degrees/ps\n", g, rotg->rate);
1005 fprintf(fp, "# rot-k%d %12.5e kJ/(mol*nm^2)\n", g, rotg->k);
1006 if (rotg->eType == erotgISO || rotg->eType == erotgPM || rotg->eType == erotgRM
1007 || rotg->eType == erotgRM2)
1010 "# rot-pivot%d %12.5e %12.5e %12.5e nm\n",
1019 fprintf(fp, "# rot-slab-distance%d %f nm\n", g, rotg->slab_dist);
1020 fprintf(fp, "# rot-min-gaussian%d %12.5e\n", g, rotg->min_gaussian);
1023 /* Output the centers of the rotation groups for the pivot-free potentials */
1024 if ((rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) || (rotg->eType == erotgRMPF)
1025 || (rotg->eType == erotgRM2PF || (rotg->eType == erotgFLEXT) || (rotg->eType == erotgFLEX2T)))
1028 "# ref. grp. %d center %12.5e %12.5e %12.5e\n",
1030 erg->xc_ref_center[XX],
1031 erg->xc_ref_center[YY],
1032 erg->xc_ref_center[ZZ]);
1035 "# grp. %d init.center %12.5e %12.5e %12.5e\n",
1039 erg->xc_center[ZZ]);
1042 if ((rotg->eType == erotgRM2) || (rotg->eType == erotgFLEX2) || (rotg->eType == erotgFLEX2T))
1044 fprintf(fp, "# rot-eps%d %12.5e nm^2\n", g, rotg->eps);
1046 if (erotgFitPOT == rotg->eFittype)
1050 "# theta_fit%d is determined by first evaluating the potential for %d "
1051 "angles around theta_ref%d.\n",
1053 rotg->PotAngle_nstep,
1056 "# The fit angle is the one with the smallest potential. It is given as "
1059 "# from the reference angle, i.e. if theta_ref=X and theta_fit=Y, then the "
1062 "# minimal value of the potential is X+Y. Angular resolution is %g "
1064 rotg->PotAngle_step);
1068 /* Print a nice legend */
1070 LegendStr[0] = '\0';
1071 sprintf(buf, "# %6s", "time");
1072 add_to_string_aligned(&LegendStr, buf);
1075 snew(setname, 4 * rot->ngrp);
1077 for (int g = 0; g < rot->ngrp; g++)
1079 sprintf(buf, "theta_ref%d", g);
1080 add_to_string_aligned(&LegendStr, buf);
1082 sprintf(buf2, "%s (degrees)", buf);
1083 setname[nsets] = gmx_strdup(buf2);
1086 for (int g = 0; g < rot->ngrp; g++)
1088 const t_rotgrp* rotg = &rot->grp[g];
1089 bFlex = ISFLEX(rotg);
1091 /* For flexible axis rotation we use RMSD fitting to determine the
1092 * actual angle of the rotation group */
1093 if (bFlex || erotgFitPOT == rotg->eFittype)
1095 sprintf(buf, "theta_fit%d", g);
1099 sprintf(buf, "theta_av%d", g);
1101 add_to_string_aligned(&LegendStr, buf);
1102 sprintf(buf2, "%s (degrees)", buf);
1103 setname[nsets] = gmx_strdup(buf2);
1106 sprintf(buf, "tau%d", g);
1107 add_to_string_aligned(&LegendStr, buf);
1108 sprintf(buf2, "%s (kJ/mol)", buf);
1109 setname[nsets] = gmx_strdup(buf2);
1112 sprintf(buf, "energy%d", g);
1113 add_to_string_aligned(&LegendStr, buf);
1114 sprintf(buf2, "%s (kJ/mol)", buf);
1115 setname[nsets] = gmx_strdup(buf2);
1122 xvgr_legend(fp, nsets, setname, oenv);
1126 fprintf(fp, "#\n# Legend for the following data columns:\n");
1127 fprintf(fp, "%s\n", LegendStr);
1137 /* Call on master only */
1138 static FILE* open_angles_out(const char* fn, gmx_enfrot* er)
1142 const t_rot* rot = er->rot;
1144 if (er->restartWithAppending)
1146 fp = gmx_fio_fopen(fn, "a");
1150 /* Open output file and write some information about it's structure: */
1151 fp = open_output_file(fn, er->nstsout, "rotation group angles");
1152 fprintf(fp, "# All angles given in degrees, time in ps.\n");
1153 for (int g = 0; g < rot->ngrp; g++)
1155 const t_rotgrp* rotg = &rot->grp[g];
1156 const gmx_enfrotgrp* erg = &er->enfrotgrp[g];
1158 /* Output for this group happens only if potential type is flexible or
1159 * if fit type is potential! */
1160 if (ISFLEX(rotg) || (erotgFitPOT == rotg->eFittype))
1164 sprintf(buf, " slab distance %f nm, ", rotg->slab_dist);
1172 "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n",
1174 erotg_names[rotg->eType],
1176 erotg_fitnames[rotg->eFittype]);
1178 /* Special type of fitting using the potential minimum. This is
1179 * done for the whole group only, not for the individual slabs. */
1180 if (erotgFitPOT == rotg->eFittype)
1183 "# To obtain theta_fit%d, the potential is evaluated for %d angles "
1184 "around theta_ref%d\n",
1186 rotg->PotAngle_nstep,
1189 "# The fit angle in the rotation standard outfile is the one with "
1190 "minimal energy E(theta_fit) [kJ/mol].\n");
1194 fprintf(fp, "# Legend for the group %d data columns:\n", g);
1196 print_aligned_short(fp, "time");
1197 print_aligned_short(fp, "grp");
1198 print_aligned(fp, "theta_ref");
1200 if (erotgFitPOT == rotg->eFittype)
1202 /* Output the set of angles around the reference angle */
1203 for (int i = 0; i < rotg->PotAngle_nstep; i++)
1205 sprintf(buf, "E(%g)", erg->PotAngleFit->degangle[i]);
1206 print_aligned(fp, buf);
1211 /* Output fit angle for each slab */
1212 print_aligned_short(fp, "slab");
1213 print_aligned_short(fp, "atoms");
1214 print_aligned(fp, "theta_fit");
1215 print_aligned_short(fp, "slab");
1216 print_aligned_short(fp, "atoms");
1217 print_aligned(fp, "theta_fit");
1218 fprintf(fp, " ...");
1230 /* Open torque output file and write some information about it's structure.
1231 * Call on master only */
1232 static FILE* open_torque_out(const char* fn, gmx_enfrot* er)
1235 const t_rot* rot = er->rot;
1237 if (er->restartWithAppending)
1239 fp = gmx_fio_fopen(fn, "a");
1243 fp = open_output_file(fn, er->nstsout, "torques");
1245 for (int g = 0; g < rot->ngrp; g++)
1247 const t_rotgrp* rotg = &rot->grp[g];
1248 const gmx_enfrotgrp* erg = &er->enfrotgrp[g];
1252 "# Rotation group %d (%s), slab distance %f nm.\n",
1254 erotg_names[rotg->eType],
1257 "# The scalar tau is the torque (kJ/mol) in the direction of the rotation "
1259 fprintf(fp, "# To obtain the vectorial torque, multiply tau with\n");
1261 "# rot-vec%d %10.3e %10.3e %10.3e\n",
1269 fprintf(fp, "# Legend for the following data columns: (tau=torque for that slab):\n");
1271 print_aligned_short(fp, "t");
1272 print_aligned_short(fp, "grp");
1273 print_aligned_short(fp, "slab");
1274 print_aligned(fp, "tau");
1275 print_aligned_short(fp, "slab");
1276 print_aligned(fp, "tau");
1277 fprintf(fp, " ...\n");
1285 static void swap_val(double* vec, int i, int j)
1287 double tmp = vec[j];
1295 static void swap_col(double** mat, int i, int j)
1297 double tmp[3] = { mat[0][j], mat[1][j], mat[2][j] };
1300 mat[0][j] = mat[0][i];
1301 mat[1][j] = mat[1][i];
1302 mat[2][j] = mat[2][i];
1310 /* Eigenvectors are stored in columns of eigen_vec */
1311 static void diagonalize_symmetric(double** matrix, double** eigen_vec, double eigenval[3])
1316 jacobi(matrix, 3, eigenval, eigen_vec, &n_rot);
1318 /* sort in ascending order */
1319 if (eigenval[0] > eigenval[1])
1321 swap_val(eigenval, 0, 1);
1322 swap_col(eigen_vec, 0, 1);
1324 if (eigenval[1] > eigenval[2])
1326 swap_val(eigenval, 1, 2);
1327 swap_col(eigen_vec, 1, 2);
1329 if (eigenval[0] > eigenval[1])
1331 swap_val(eigenval, 0, 1);
1332 swap_col(eigen_vec, 0, 1);
1337 static void align_with_z(rvec* s, /* Structure to align */
1342 rvec zet = { 0.0, 0.0, 1.0 };
1343 rvec rot_axis = { 0.0, 0.0, 0.0 };
1344 rvec* rotated_str = nullptr;
1350 snew(rotated_str, natoms);
1352 /* Normalize the axis */
1353 ooanorm = 1.0 / norm(axis);
1354 svmul(ooanorm, axis, axis);
1356 /* Calculate the angle for the fitting procedure */
1357 cprod(axis, zet, rot_axis);
1358 angle = acos(axis[2]);
1364 /* Calculate the rotation matrix */
1365 calc_rotmat(rot_axis, angle * 180.0 / M_PI, rotmat);
1367 /* Apply the rotation matrix to s */
1368 for (i = 0; i < natoms; i++)
1370 for (j = 0; j < 3; j++)
1372 for (k = 0; k < 3; k++)
1374 rotated_str[i][j] += rotmat[j][k] * s[i][k];
1379 /* Rewrite the rotated structure to s */
1380 for (i = 0; i < natoms; i++)
1382 for (j = 0; j < 3; j++)
1384 s[i][j] = rotated_str[i][j];
1392 static void calc_correl_matrix(rvec* Xstr, rvec* Ystr, double** Rmat, int natoms)
1397 for (i = 0; i < 3; i++)
1399 for (j = 0; j < 3; j++)
1405 for (i = 0; i < 3; i++)
1407 for (j = 0; j < 3; j++)
1409 for (k = 0; k < natoms; k++)
1411 Rmat[i][j] += Ystr[k][i] * Xstr[k][j];
1418 static void weigh_coords(rvec* str, real* weight, int natoms)
1423 for (i = 0; i < natoms; i++)
1425 for (j = 0; j < 3; j++)
1427 str[i][j] *= std::sqrt(weight[i]);
1433 static real opt_angle_analytic(rvec* ref_s,
1442 rvec* ref_s_1 = nullptr;
1443 rvec* act_s_1 = nullptr;
1445 double **Rmat, **RtR, **eigvec;
1447 double V[3][3], WS[3][3];
1448 double rot_matrix[3][3];
1452 /* Do not change the original coordinates */
1453 snew(ref_s_1, natoms);
1454 snew(act_s_1, natoms);
1455 for (i = 0; i < natoms; i++)
1457 copy_rvec(ref_s[i], ref_s_1[i]);
1458 copy_rvec(act_s[i], act_s_1[i]);
1461 /* Translate the structures to the origin */
1462 shift[XX] = -ref_com[XX];
1463 shift[YY] = -ref_com[YY];
1464 shift[ZZ] = -ref_com[ZZ];
1465 translate_x(ref_s_1, natoms, shift);
1467 shift[XX] = -act_com[XX];
1468 shift[YY] = -act_com[YY];
1469 shift[ZZ] = -act_com[ZZ];
1470 translate_x(act_s_1, natoms, shift);
1472 /* Align rotation axis with z */
1473 align_with_z(ref_s_1, natoms, axis);
1474 align_with_z(act_s_1, natoms, axis);
1476 /* Correlation matrix */
1477 Rmat = allocate_square_matrix(3);
1479 for (i = 0; i < natoms; i++)
1481 ref_s_1[i][2] = 0.0;
1482 act_s_1[i][2] = 0.0;
1485 /* Weight positions with sqrt(weight) */
1486 if (nullptr != weight)
1488 weigh_coords(ref_s_1, weight, natoms);
1489 weigh_coords(act_s_1, weight, natoms);
1492 /* Calculate correlation matrices R=YXt (X=ref_s; Y=act_s) */
1493 calc_correl_matrix(ref_s_1, act_s_1, Rmat, natoms);
1496 RtR = allocate_square_matrix(3);
1497 for (i = 0; i < 3; i++)
1499 for (j = 0; j < 3; j++)
1501 for (k = 0; k < 3; k++)
1503 RtR[i][j] += Rmat[k][i] * Rmat[k][j];
1507 /* Diagonalize RtR */
1509 for (i = 0; i < 3; i++)
1514 diagonalize_symmetric(RtR, eigvec, eigval);
1515 swap_col(eigvec, 0, 1);
1516 swap_col(eigvec, 1, 2);
1517 swap_val(eigval, 0, 1);
1518 swap_val(eigval, 1, 2);
1521 for (i = 0; i < 3; i++)
1523 for (j = 0; j < 3; j++)
1530 for (i = 0; i < 2; i++)
1532 for (j = 0; j < 2; j++)
1534 WS[i][j] = eigvec[i][j] / std::sqrt(eigval[j]);
1538 for (i = 0; i < 3; i++)
1540 for (j = 0; j < 3; j++)
1542 for (k = 0; k < 3; k++)
1544 V[i][j] += Rmat[i][k] * WS[k][j];
1548 free_square_matrix(Rmat, 3);
1550 /* Calculate optimal rotation matrix */
1551 for (i = 0; i < 3; i++)
1553 for (j = 0; j < 3; j++)
1555 rot_matrix[i][j] = 0.0;
1559 for (i = 0; i < 3; i++)
1561 for (j = 0; j < 3; j++)
1563 for (k = 0; k < 3; k++)
1565 rot_matrix[i][j] += eigvec[i][k] * V[j][k];
1569 rot_matrix[2][2] = 1.0;
1571 /* In some cases abs(rot_matrix[0][0]) can be slighly larger
1572 * than unity due to numerical inacurracies. To be able to calculate
1573 * the acos function, we put these values back in range. */
1574 if (rot_matrix[0][0] > 1.0)
1576 rot_matrix[0][0] = 1.0;
1578 else if (rot_matrix[0][0] < -1.0)
1580 rot_matrix[0][0] = -1.0;
1583 /* Determine the optimal rotation angle: */
1584 opt_angle = (-1.0) * acos(rot_matrix[0][0]) * 180.0 / M_PI;
1585 if (rot_matrix[0][1] < 0.0)
1587 opt_angle = (-1.0) * opt_angle;
1590 /* Give back some memory */
1591 free_square_matrix(RtR, 3);
1594 for (i = 0; i < 3; i++)
1600 return static_cast<real>(opt_angle);
1604 /* Determine angle of the group by RMSD fit to the reference */
1605 /* Not parallelized, call this routine only on the master */
1606 static real flex_fit_angle(gmx_enfrotgrp* erg)
1608 rvec* fitcoords = nullptr;
1609 rvec center; /* Center of positions passed to the fit routine */
1610 real fitangle; /* Angle of the rotation group derived by fitting */
1614 /* Get the center of the rotation group.
1615 * Note, again, erg->xc has been sorted in do_flexible */
1616 get_center(erg->xc, erg->mc_sorted, erg->rotg->nat, center);
1618 /* === Determine the optimal fit angle for the rotation group === */
1619 if (erg->rotg->eFittype == erotgFitNORM)
1621 /* Normalize every position to it's reference length */
1622 for (int i = 0; i < erg->rotg->nat; i++)
1624 /* Put the center of the positions into the origin */
1625 rvec_sub(erg->xc[i], center, coord);
1626 /* Determine the scaling factor for the length: */
1627 scal = erg->xc_ref_length[erg->xc_sortind[i]] / norm(coord);
1628 /* Get position, multiply with the scaling factor and save */
1629 svmul(scal, coord, erg->xc_norm[i]);
1631 fitcoords = erg->xc_norm;
1635 fitcoords = erg->xc;
1637 /* From the point of view of the current positions, the reference has rotated
1638 * backwards. Since we output the angle relative to the fixed reference,
1639 * we need the minus sign. */
1640 fitangle = -opt_angle_analytic(
1641 erg->xc_ref_sorted, fitcoords, erg->mc_sorted, erg->rotg->nat, erg->xc_ref_center, center, erg->vec);
1647 /* Determine actual angle of each slab by RMSD fit to the reference */
1648 /* Not parallelized, call this routine only on the master */
1649 static void flex_fit_angle_perslab(gmx_enfrotgrp* erg, double t, real degangle, FILE* fp)
1652 rvec act_center; /* Center of actual positions that are passed to the fit routine */
1653 rvec ref_center; /* Same for the reference positions */
1654 real fitangle; /* Angle of a slab derived from an RMSD fit to
1655 * the reference structure at t=0 */
1657 real OOm_av; /* 1/average_mass of a rotation group atom */
1658 real m_rel; /* Relative mass of a rotation group atom */
1661 /* Average mass of a rotation group atom: */
1662 OOm_av = erg->invmass * erg->rotg->nat;
1664 /**********************************/
1665 /* First collect the data we need */
1666 /**********************************/
1668 /* Collect the data for the individual slabs */
1669 for (int n = erg->slab_first; n <= erg->slab_last; n++)
1671 int slabIndex = n - erg->slab_first; /* slab index */
1672 sd = &(erg->slab_data[slabIndex]);
1673 sd->nat = erg->lastatom[slabIndex] - erg->firstatom[slabIndex] + 1;
1676 /* Loop over the relevant atoms in the slab */
1677 for (int l = erg->firstatom[slabIndex]; l <= erg->lastatom[slabIndex]; l++)
1679 /* Current position of this atom: x[ii][XX/YY/ZZ] */
1680 copy_rvec(erg->xc[l], curr_x);
1682 /* The (unrotated) reference position of this atom is copied to ref_x.
1683 * Beware, the xc coords have been sorted in do_flexible */
1684 copy_rvec(erg->xc_ref_sorted[l], ref_x);
1686 /* Save data for doing angular RMSD fit later */
1687 /* Save the current atom position */
1688 copy_rvec(curr_x, sd->x[ind]);
1689 /* Save the corresponding reference position */
1690 copy_rvec(ref_x, sd->ref[ind]);
1692 /* Maybe also mass-weighting was requested. If yes, additionally
1693 * multiply the weights with the relative mass of the atom. If not,
1694 * multiply with unity. */
1695 m_rel = erg->mc_sorted[l] * OOm_av;
1697 /* Save the weight for this atom in this slab */
1698 sd->weight[ind] = gaussian_weight(curr_x, erg, n) * m_rel;
1700 /* Next atom in this slab */
1705 /******************************/
1706 /* Now do the fit calculation */
1707 /******************************/
1709 fprintf(fp, "%12.3e%6d%12.3f", t, erg->groupIndex, degangle);
1711 /* === Now do RMSD fitting for each slab === */
1712 /* We require at least SLAB_MIN_ATOMS in a slab, such that the fit makes sense. */
1713 #define SLAB_MIN_ATOMS 4
1715 for (int n = erg->slab_first; n <= erg->slab_last; n++)
1717 int slabIndex = n - erg->slab_first; /* slab index */
1718 sd = &(erg->slab_data[slabIndex]);
1719 if (sd->nat >= SLAB_MIN_ATOMS)
1721 /* Get the center of the slabs reference and current positions */
1722 get_center(sd->ref, sd->weight, sd->nat, ref_center);
1723 get_center(sd->x, sd->weight, sd->nat, act_center);
1724 if (erg->rotg->eFittype == erotgFitNORM)
1726 /* Normalize every position to it's reference length
1727 * prior to performing the fit */
1728 for (int i = 0; i < sd->nat; i++) /* Center */
1730 rvec_dec(sd->ref[i], ref_center);
1731 rvec_dec(sd->x[i], act_center);
1732 /* Normalize x_i such that it gets the same length as ref_i */
1733 svmul(norm(sd->ref[i]) / norm(sd->x[i]), sd->x[i], sd->x[i]);
1735 /* We already subtracted the centers */
1736 clear_rvec(ref_center);
1737 clear_rvec(act_center);
1739 fitangle = -opt_angle_analytic(
1740 sd->ref, sd->x, sd->weight, sd->nat, ref_center, act_center, erg->vec);
1741 fprintf(fp, "%6d%6d%12.3f", n, sd->nat, fitangle);
1746 #undef SLAB_MIN_ATOMS
1750 /* Shift x with is */
1751 static inline void shift_single_coord(const matrix box, rvec x, const ivec is)
1762 x[XX] += tx * box[XX][XX] + ty * box[YY][XX] + tz * box[ZZ][XX];
1763 x[YY] += ty * box[YY][YY] + tz * box[ZZ][YY];
1764 x[ZZ] += tz * box[ZZ][ZZ];
1768 x[XX] += tx * box[XX][XX];
1769 x[YY] += ty * box[YY][YY];
1770 x[ZZ] += tz * box[ZZ][ZZ];
1775 /* Determine the 'home' slab of this atom which is the
1776 * slab with the highest Gaussian weight of all */
1777 static inline int get_homeslab(rvec curr_x, /* The position for which the home slab shall be determined */
1778 const rvec rotvec, /* The rotation vector */
1779 real slabdist) /* The slab distance */
1784 /* The distance of the atom to the coordinate center (where the
1785 * slab with index 0) is */
1786 dist = iprod(rotvec, curr_x);
1788 return gmx::roundToInt(dist / slabdist);
1792 /* For a local atom determine the relevant slabs, i.e. slabs in
1793 * which the gaussian is larger than min_gaussian
1795 static int get_single_atom_gaussians(rvec curr_x, gmx_enfrotgrp* erg)
1798 /* Determine the 'home' slab of this atom: */
1799 int homeslab = get_homeslab(curr_x, erg->vec, erg->rotg->slab_dist);
1801 /* First determine the weight in the atoms home slab: */
1802 real g = gaussian_weight(curr_x, erg, homeslab);
1804 erg->gn_atom[count] = g;
1805 erg->gn_slabind[count] = homeslab;
1809 /* Determine the max slab */
1810 int slab = homeslab;
1811 while (g > erg->rotg->min_gaussian)
1814 g = gaussian_weight(curr_x, erg, slab);
1815 erg->gn_slabind[count] = slab;
1816 erg->gn_atom[count] = g;
1821 /* Determine the min slab */
1826 g = gaussian_weight(curr_x, erg, slab);
1827 erg->gn_slabind[count] = slab;
1828 erg->gn_atom[count] = g;
1830 } while (g > erg->rotg->min_gaussian);
1837 static void flex2_precalc_inner_sum(const gmx_enfrotgrp* erg)
1839 rvec xi; /* positions in the i-sum */
1840 rvec xcn, ycn; /* the current and the reference slab centers */
1843 rvec rin; /* Helper variables */
1846 real OOpsii, OOpsiistar;
1847 real sin_rin; /* s_ii.r_ii */
1848 rvec s_in, tmpvec, tmpvec2;
1849 real mi, wi; /* Mass-weighting of the positions */
1853 N_M = erg->rotg->nat * erg->invmass;
1855 /* Loop over all slabs that contain something */
1856 for (int n = erg->slab_first; n <= erg->slab_last; n++)
1858 int slabIndex = n - erg->slab_first; /* slab index */
1860 /* The current center of this slab is saved in xcn: */
1861 copy_rvec(erg->slab_center[slabIndex], xcn);
1862 /* ... and the reference center in ycn: */
1863 copy_rvec(erg->slab_center_ref[slabIndex + erg->slab_buffer], ycn);
1865 /*** D. Calculate the whole inner sum used for second and third sum */
1866 /* For slab n, we need to loop over all atoms i again. Since we sorted
1867 * the atoms with respect to the rotation vector, we know that it is sufficient
1868 * to calculate from firstatom to lastatom only. All other contributions will
1870 clear_rvec(innersumvec);
1871 for (int i = erg->firstatom[slabIndex]; i <= erg->lastatom[slabIndex]; i++)
1873 /* Coordinate xi of this atom */
1874 copy_rvec(erg->xc[i], xi);
1877 gaussian_xi = gaussian_weight(xi, erg, n);
1878 mi = erg->mc_sorted[i]; /* need the sorted mass here */
1882 copy_rvec(erg->xc_ref_sorted[i], yi0); /* Reference position yi0 */
1883 rvec_sub(yi0, ycn, tmpvec2); /* tmpvec2 = yi0 - ycn */
1884 mvmul(erg->rotmat, tmpvec2, rin); /* rin = Omega.(yi0 - ycn) */
1886 /* Calculate psi_i* and sin */
1887 rvec_sub(xi, xcn, tmpvec2); /* tmpvec2 = xi - xcn */
1889 /* In rare cases, when an atom position coincides with a slab center
1890 * (tmpvec2 == 0) we cannot compute the vector product for s_in.
1891 * However, since the atom is located directly on the pivot, this
1892 * slab's contribution to the force on that atom will be zero
1893 * anyway. Therefore, we continue with the next atom. */
1894 if (gmx_numzero(norm(tmpvec2))) /* 0 == norm(xi - xcn) */
1899 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xi - xcn) */
1900 OOpsiistar = norm2(tmpvec) + erg->rotg->eps; /* OOpsii* = 1/psii* = |v x (xi-xcn)|^2 + eps */
1901 OOpsii = norm(tmpvec); /* OOpsii = 1 / psii = |v x (xi - xcn)| */
1903 /* * v x (xi - xcn) */
1904 unitv(tmpvec, s_in); /* sin = ---------------- */
1905 /* |v x (xi - xcn)| */
1907 sin_rin = iprod(s_in, rin); /* sin_rin = sin . rin */
1909 /* Now the whole sum */
1910 fac = OOpsii / OOpsiistar;
1911 svmul(fac, rin, tmpvec);
1912 fac2 = fac * fac * OOpsii;
1913 svmul(fac2 * sin_rin, s_in, tmpvec2);
1914 rvec_dec(tmpvec, tmpvec2);
1916 svmul(wi * gaussian_xi * sin_rin, tmpvec, tmpvec2);
1918 rvec_inc(innersumvec, tmpvec2);
1919 } /* now we have the inner sum, used both for sum2 and sum3 */
1921 /* Save it to be used in do_flex2_lowlevel */
1922 copy_rvec(innersumvec, erg->slab_innersumvec[slabIndex]);
1923 } /* END of loop over slabs */
1927 static void flex_precalc_inner_sum(const gmx_enfrotgrp* erg)
1929 rvec xi; /* position */
1930 rvec xcn, ycn; /* the current and the reference slab centers */
1931 rvec qin, rin; /* q_i^n and r_i^n */
1934 rvec innersumvec; /* Inner part of sum_n2 */
1935 real gaussian_xi; /* Gaussian weight gn(xi) */
1936 real mi, wi; /* Mass-weighting of the positions */
1939 N_M = erg->rotg->nat * erg->invmass;
1941 /* Loop over all slabs that contain something */
1942 for (int n = erg->slab_first; n <= erg->slab_last; n++)
1944 int slabIndex = n - erg->slab_first; /* slab index */
1946 /* The current center of this slab is saved in xcn: */
1947 copy_rvec(erg->slab_center[slabIndex], xcn);
1948 /* ... and the reference center in ycn: */
1949 copy_rvec(erg->slab_center_ref[slabIndex + erg->slab_buffer], ycn);
1951 /* For slab n, we need to loop over all atoms i again. Since we sorted
1952 * the atoms with respect to the rotation vector, we know that it is sufficient
1953 * to calculate from firstatom to lastatom only. All other contributions will
1955 clear_rvec(innersumvec);
1956 for (int i = erg->firstatom[slabIndex]; i <= erg->lastatom[slabIndex]; i++)
1958 /* Coordinate xi of this atom */
1959 copy_rvec(erg->xc[i], xi);
1962 gaussian_xi = gaussian_weight(xi, erg, n);
1963 mi = erg->mc_sorted[i]; /* need the sorted mass here */
1966 /* Calculate rin and qin */
1967 rvec_sub(erg->xc_ref_sorted[i], ycn, tmpvec); /* tmpvec = yi0-ycn */
1969 /* In rare cases, when an atom position coincides with a slab center
1970 * (tmpvec == 0) we cannot compute the vector product for qin.
1971 * However, since the atom is located directly on the pivot, this
1972 * slab's contribution to the force on that atom will be zero
1973 * anyway. Therefore, we continue with the next atom. */
1974 if (gmx_numzero(norm(tmpvec))) /* 0 == norm(yi0 - ycn) */
1979 mvmul(erg->rotmat, tmpvec, rin); /* rin = Omega.(yi0 - ycn) */
1980 cprod(erg->vec, rin, tmpvec); /* tmpvec = v x Omega*(yi0-ycn) */
1982 /* * v x Omega*(yi0-ycn) */
1983 unitv(tmpvec, qin); /* qin = --------------------- */
1984 /* |v x Omega*(yi0-ycn)| */
1987 rvec_sub(xi, xcn, tmpvec); /* tmpvec = xi-xcn */
1988 bin = iprod(qin, tmpvec); /* bin = qin*(xi-xcn) */
1990 svmul(wi * gaussian_xi * bin, qin, tmpvec);
1992 /* Add this contribution to the inner sum: */
1993 rvec_add(innersumvec, tmpvec, innersumvec);
1994 } /* now we have the inner sum vector S^n for this slab */
1995 /* Save it to be used in do_flex_lowlevel */
1996 copy_rvec(innersumvec, erg->slab_innersumvec[slabIndex]);
2001 static real do_flex2_lowlevel(gmx_enfrotgrp* erg,
2002 real sigma, /* The Gaussian width sigma */
2004 gmx_bool bOutstepRot,
2005 gmx_bool bOutstepSlab,
2008 int count, ii, iigrp;
2009 rvec xj; /* position in the i-sum */
2010 rvec yj0; /* the reference position in the j-sum */
2011 rvec xcn, ycn; /* the current and the reference slab centers */
2012 real V; /* This node's part of the rotation pot. energy */
2013 real gaussian_xj; /* Gaussian weight */
2016 real numerator, fit_numerator;
2017 rvec rjn, fit_rjn; /* Helper variables */
2020 real OOpsij, OOpsijstar;
2021 real OOsigma2; /* 1/(sigma^2) */
2024 rvec sjn, tmpvec, tmpvec2, yj0_ycn;
2025 rvec sum1vec_part, sum1vec, sum2vec_part, sum2vec, sum3vec, sum4vec, innersumvec;
2027 real mj, wj; /* Mass-weighting of the positions */
2029 real Wjn; /* g_n(x_j) m_j / Mjn */
2030 gmx_bool bCalcPotFit;
2032 /* To calculate the torque per slab */
2033 rvec slab_force; /* Single force from slab n on one atom */
2034 rvec slab_sum1vec_part;
2035 real slab_sum3part, slab_sum4part;
2036 rvec slab_sum1vec, slab_sum2vec, slab_sum3vec, slab_sum4vec;
2038 /* Pre-calculate the inner sums, so that we do not have to calculate
2039 * them again for every atom */
2040 flex2_precalc_inner_sum(erg);
2042 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2044 /********************************************************/
2045 /* Main loop over all local atoms of the rotation group */
2046 /********************************************************/
2047 N_M = erg->rotg->nat * erg->invmass;
2049 OOsigma2 = 1.0 / (sigma * sigma);
2050 const auto& localRotationGroupIndex = erg->atomSet->localIndex();
2051 const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2053 for (gmx::index j = 0; j < localRotationGroupIndex.ssize(); j++)
2055 /* Local index of a rotation group atom */
2056 ii = localRotationGroupIndex[j];
2057 /* Position of this atom in the collective array */
2058 iigrp = collectiveRotationGroupIndex[j];
2059 /* Mass-weighting */
2060 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2063 /* Current position of this atom: x[ii][XX/YY/ZZ]
2064 * Note that erg->xc_center contains the center of mass in case the flex2-t
2065 * potential was chosen. For the flex2 potential erg->xc_center must be
2067 rvec_sub(x[ii], erg->xc_center, xj);
2069 /* Shift this atom such that it is near its reference */
2070 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2072 /* Determine the slabs to loop over, i.e. the ones with contributions
2073 * larger than min_gaussian */
2074 count = get_single_atom_gaussians(xj, erg);
2076 clear_rvec(sum1vec_part);
2077 clear_rvec(sum2vec_part);
2080 /* Loop over the relevant slabs for this atom */
2081 for (int ic = 0; ic < count; ic++)
2083 int n = erg->gn_slabind[ic];
2085 /* Get the precomputed Gaussian value of curr_slab for curr_x */
2086 gaussian_xj = erg->gn_atom[ic];
2088 int slabIndex = n - erg->slab_first; /* slab index */
2090 /* The (unrotated) reference position of this atom is copied to yj0: */
2091 copy_rvec(erg->rotg->x_ref[iigrp], yj0);
2093 beta = calc_beta(xj, erg, n);
2095 /* The current center of this slab is saved in xcn: */
2096 copy_rvec(erg->slab_center[slabIndex], xcn);
2097 /* ... and the reference center in ycn: */
2098 copy_rvec(erg->slab_center_ref[slabIndex + erg->slab_buffer], ycn);
2100 rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
2103 mvmul(erg->rotmat, yj0_ycn, rjn); /* rjn = Omega.(yj0 - ycn) */
2105 /* Subtract the slab center from xj */
2106 rvec_sub(xj, xcn, tmpvec2); /* tmpvec2 = xj - xcn */
2108 /* In rare cases, when an atom position coincides with a slab center
2109 * (tmpvec2 == 0) we cannot compute the vector product for sjn.
2110 * However, since the atom is located directly on the pivot, this
2111 * slab's contribution to the force on that atom will be zero
2112 * anyway. Therefore, we directly move on to the next slab. */
2113 if (gmx_numzero(norm(tmpvec2))) /* 0 == norm(xj - xcn) */
2119 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xj - xcn) */
2121 OOpsijstar = norm2(tmpvec) + erg->rotg->eps; /* OOpsij* = 1/psij* = |v x (xj-xcn)|^2 + eps */
2123 numerator = gmx::square(iprod(tmpvec, rjn));
2125 /*********************************/
2126 /* Add to the rotation potential */
2127 /*********************************/
2128 V += 0.5 * erg->rotg->k * wj * gaussian_xj * numerator / OOpsijstar;
2130 /* If requested, also calculate the potential for a set of angles
2131 * near the current reference angle */
2134 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2136 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, fit_rjn);
2137 fit_numerator = gmx::square(iprod(tmpvec, fit_rjn));
2138 erg->PotAngleFit->V[ifit] +=
2139 0.5 * erg->rotg->k * wj * gaussian_xj * fit_numerator / OOpsijstar;
2143 /*************************************/
2144 /* Now calculate the force on atom j */
2145 /*************************************/
2147 OOpsij = norm(tmpvec); /* OOpsij = 1 / psij = |v x (xj - xcn)| */
2149 /* * v x (xj - xcn) */
2150 unitv(tmpvec, sjn); /* sjn = ---------------- */
2151 /* |v x (xj - xcn)| */
2153 sjn_rjn = iprod(sjn, rjn); /* sjn_rjn = sjn . rjn */
2156 /*** A. Calculate the first of the four sum terms: ****************/
2157 fac = OOpsij / OOpsijstar;
2158 svmul(fac, rjn, tmpvec);
2159 fac2 = fac * fac * OOpsij;
2160 svmul(fac2 * sjn_rjn, sjn, tmpvec2);
2161 rvec_dec(tmpvec, tmpvec2);
2162 fac2 = wj * gaussian_xj; /* also needed for sum4 */
2163 svmul(fac2 * sjn_rjn, tmpvec, slab_sum1vec_part);
2164 /********************/
2165 /*** Add to sum1: ***/
2166 /********************/
2167 rvec_inc(sum1vec_part, slab_sum1vec_part); /* sum1 still needs to vector multiplied with v */
2169 /*** B. Calculate the forth of the four sum terms: ****************/
2170 betasigpsi = beta * OOsigma2 * OOpsij; /* this is also needed for sum3 */
2171 /********************/
2172 /*** Add to sum4: ***/
2173 /********************/
2174 slab_sum4part = fac2 * betasigpsi * fac * sjn_rjn
2175 * sjn_rjn; /* Note that fac is still valid from above */
2176 sum4 += slab_sum4part;
2178 /*** C. Calculate Wjn for second and third sum */
2179 /* Note that we can safely divide by slab_weights since we check in
2180 * get_slab_centers that it is non-zero. */
2181 Wjn = gaussian_xj * mj / erg->slab_weights[slabIndex];
2183 /* We already have precalculated the inner sum for slab n */
2184 copy_rvec(erg->slab_innersumvec[slabIndex], innersumvec);
2186 /* Weigh the inner sum vector with Wjn */
2187 svmul(Wjn, innersumvec, innersumvec);
2189 /*** E. Calculate the second of the four sum terms: */
2190 /********************/
2191 /*** Add to sum2: ***/
2192 /********************/
2193 rvec_inc(sum2vec_part, innersumvec); /* sum2 still needs to be vector crossproduct'ed with v */
2195 /*** F. Calculate the third of the four sum terms: */
2196 slab_sum3part = betasigpsi * iprod(sjn, innersumvec);
2197 sum3 += slab_sum3part; /* still needs to be multiplied with v */
2199 /*** G. Calculate the torque on the local slab's axis: */
2203 cprod(slab_sum1vec_part, erg->vec, slab_sum1vec);
2205 cprod(innersumvec, erg->vec, slab_sum2vec);
2207 svmul(slab_sum3part, erg->vec, slab_sum3vec);
2209 svmul(slab_sum4part, erg->vec, slab_sum4vec);
2211 /* The force on atom ii from slab n only: */
2212 for (int m = 0; m < DIM; m++)
2214 slab_force[m] = erg->rotg->k
2215 * (-slab_sum1vec[m] + slab_sum2vec[m] - slab_sum3vec[m]
2216 + 0.5 * slab_sum4vec[m]);
2219 erg->slab_torque_v[slabIndex] += torque(erg->vec, slab_force, xj, xcn);
2221 } /* END of loop over slabs */
2223 /* Construct the four individual parts of the vector sum: */
2224 cprod(sum1vec_part, erg->vec, sum1vec); /* sum1vec = { } x v */
2225 cprod(sum2vec_part, erg->vec, sum2vec); /* sum2vec = { } x v */
2226 svmul(sum3, erg->vec, sum3vec); /* sum3vec = { } . v */
2227 svmul(sum4, erg->vec, sum4vec); /* sum4vec = { } . v */
2229 /* Store the additional force so that it can be added to the force
2230 * array after the normal forces have been evaluated */
2231 for (int m = 0; m < DIM; m++)
2233 erg->f_rot_loc[j][m] =
2234 erg->rotg->k * (-sum1vec[m] + sum2vec[m] - sum3vec[m] + 0.5 * sum4vec[m]);
2239 "sum1: %15.8f %15.8f %15.8f\n",
2240 -erg->rotg->k * sum1vec[XX],
2241 -erg->rotg->k * sum1vec[YY],
2242 -erg->rotg->k * sum1vec[ZZ]);
2244 "sum2: %15.8f %15.8f %15.8f\n",
2245 erg->rotg->k * sum2vec[XX],
2246 erg->rotg->k * sum2vec[YY],
2247 erg->rotg->k * sum2vec[ZZ]);
2249 "sum3: %15.8f %15.8f %15.8f\n",
2250 -erg->rotg->k * sum3vec[XX],
2251 -erg->rotg->k * sum3vec[YY],
2252 -erg->rotg->k * sum3vec[ZZ]);
2254 "sum4: %15.8f %15.8f %15.8f\n",
2255 0.5 * erg->rotg->k * sum4vec[XX],
2256 0.5 * erg->rotg->k * sum4vec[YY],
2257 0.5 * erg->rotg->k * sum4vec[ZZ]);
2262 } /* END of loop over local atoms */
2268 static real do_flex_lowlevel(gmx_enfrotgrp* erg,
2269 real sigma, /* The Gaussian width sigma */
2271 gmx_bool bOutstepRot,
2272 gmx_bool bOutstepSlab,
2276 rvec xj, yj0; /* current and reference position */
2277 rvec xcn, ycn; /* the current and the reference slab centers */
2278 rvec yj0_ycn; /* yj0 - ycn */
2279 rvec xj_xcn; /* xj - xcn */
2280 rvec qjn, fit_qjn; /* q_i^n */
2281 rvec sum_n1, sum_n2; /* Two contributions to the rotation force */
2282 rvec innersumvec; /* Inner part of sum_n2 */
2284 rvec force_n; /* Single force from slab n on one atom */
2285 rvec force_n1, force_n2; /* First and second part of force_n */
2286 rvec tmpvec, tmpvec2, tmp_f; /* Helper variables */
2287 real V; /* The rotation potential energy */
2288 real OOsigma2; /* 1/(sigma^2) */
2289 real beta; /* beta_n(xj) */
2290 real bjn, fit_bjn; /* b_j^n */
2291 real gaussian_xj; /* Gaussian weight gn(xj) */
2292 real betan_xj_sigma2;
2293 real mj, wj; /* Mass-weighting of the positions */
2295 gmx_bool bCalcPotFit;
2297 /* Pre-calculate the inner sums, so that we do not have to calculate
2298 * them again for every atom */
2299 flex_precalc_inner_sum(erg);
2301 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2303 /********************************************************/
2304 /* Main loop over all local atoms of the rotation group */
2305 /********************************************************/
2306 OOsigma2 = 1.0 / (sigma * sigma);
2307 N_M = erg->rotg->nat * erg->invmass;
2309 const auto& localRotationGroupIndex = erg->atomSet->localIndex();
2310 const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2312 for (gmx::index j = 0; j < localRotationGroupIndex.ssize(); j++)
2314 /* Local index of a rotation group atom */
2315 int ii = localRotationGroupIndex[j];
2316 /* Position of this atom in the collective array */
2317 iigrp = collectiveRotationGroupIndex[j];
2318 /* Mass-weighting */
2319 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2322 /* Current position of this atom: x[ii][XX/YY/ZZ]
2323 * Note that erg->xc_center contains the center of mass in case the flex-t
2324 * potential was chosen. For the flex potential erg->xc_center must be
2326 rvec_sub(x[ii], erg->xc_center, xj);
2328 /* Shift this atom such that it is near its reference */
2329 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2331 /* Determine the slabs to loop over, i.e. the ones with contributions
2332 * larger than min_gaussian */
2333 count = get_single_atom_gaussians(xj, erg);
2338 /* Loop over the relevant slabs for this atom */
2339 for (int ic = 0; ic < count; ic++)
2341 int n = erg->gn_slabind[ic];
2343 /* Get the precomputed Gaussian for xj in slab n */
2344 gaussian_xj = erg->gn_atom[ic];
2346 int slabIndex = n - erg->slab_first; /* slab index */
2348 /* The (unrotated) reference position of this atom is saved in yj0: */
2349 copy_rvec(erg->rotg->x_ref[iigrp], yj0);
2351 beta = calc_beta(xj, erg, n);
2353 /* The current center of this slab is saved in xcn: */
2354 copy_rvec(erg->slab_center[slabIndex], xcn);
2355 /* ... and the reference center in ycn: */
2356 copy_rvec(erg->slab_center_ref[slabIndex + erg->slab_buffer], ycn);
2358 rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
2360 /* In rare cases, when an atom position coincides with a reference slab
2361 * center (yj0_ycn == 0) we cannot compute the normal vector qjn.
2362 * However, since the atom is located directly on the pivot, this
2363 * slab's contribution to the force on that atom will be zero
2364 * anyway. Therefore, we directly move on to the next slab. */
2365 if (gmx_numzero(norm(yj0_ycn))) /* 0 == norm(yj0 - ycn) */
2371 mvmul(erg->rotmat, yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2373 /* Subtract the slab center from xj */
2374 rvec_sub(xj, xcn, xj_xcn); /* xj_xcn = xj - xcn */
2377 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2379 /* * v x Omega.(yj0-ycn) */
2380 unitv(tmpvec, qjn); /* qjn = --------------------- */
2381 /* |v x Omega.(yj0-ycn)| */
2383 bjn = iprod(qjn, xj_xcn); /* bjn = qjn * (xj - xcn) */
2385 /*********************************/
2386 /* Add to the rotation potential */
2387 /*********************************/
2388 V += 0.5 * erg->rotg->k * wj * gaussian_xj * gmx::square(bjn);
2390 /* If requested, also calculate the potential for a set of angles
2391 * near the current reference angle */
2394 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2396 /* As above calculate Omega.(yj0-ycn), now for the other angles */
2397 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2398 /* As above calculate qjn */
2399 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2400 /* * v x Omega.(yj0-ycn) */
2401 unitv(tmpvec, fit_qjn); /* fit_qjn = --------------------- */
2402 /* |v x Omega.(yj0-ycn)| */
2403 fit_bjn = iprod(fit_qjn, xj_xcn); /* fit_bjn = fit_qjn * (xj - xcn) */
2404 /* Add to the rotation potential for this angle */
2405 erg->PotAngleFit->V[ifit] +=
2406 0.5 * erg->rotg->k * wj * gaussian_xj * gmx::square(fit_bjn);
2410 /****************************************************************/
2411 /* sum_n1 will typically be the main contribution to the force: */
2412 /****************************************************************/
2413 betan_xj_sigma2 = beta * OOsigma2; /* beta_n(xj)/sigma^2 */
2415 /* The next lines calculate
2416 * qjn - (bjn*beta(xj)/(2sigma^2))v */
2417 svmul(bjn * 0.5 * betan_xj_sigma2, erg->vec, tmpvec2);
2418 rvec_sub(qjn, tmpvec2, tmpvec);
2420 /* Multiply with gn(xj)*bjn: */
2421 svmul(gaussian_xj * bjn, tmpvec, tmpvec2);
2424 rvec_inc(sum_n1, tmpvec2);
2426 /* We already have precalculated the Sn term for slab n */
2427 copy_rvec(erg->slab_innersumvec[slabIndex], s_n);
2429 svmul(betan_xj_sigma2 * iprod(s_n, xj_xcn), erg->vec, tmpvec); /* tmpvec = ---------- s_n (xj-xcn) */
2432 rvec_sub(s_n, tmpvec, innersumvec);
2434 /* We can safely divide by slab_weights since we check in get_slab_centers
2435 * that it is non-zero. */
2436 svmul(gaussian_xj / erg->slab_weights[slabIndex], innersumvec, innersumvec);
2438 rvec_add(sum_n2, innersumvec, sum_n2);
2440 /* Calculate the torque: */
2443 /* The force on atom ii from slab n only: */
2444 svmul(-erg->rotg->k * wj, tmpvec2, force_n1); /* part 1 */
2445 svmul(erg->rotg->k * mj, innersumvec, force_n2); /* part 2 */
2446 rvec_add(force_n1, force_n2, force_n);
2447 erg->slab_torque_v[slabIndex] += torque(erg->vec, force_n, xj, xcn);
2449 } /* END of loop over slabs */
2451 /* Put both contributions together: */
2452 svmul(wj, sum_n1, sum_n1);
2453 svmul(mj, sum_n2, sum_n2);
2454 rvec_sub(sum_n2, sum_n1, tmp_f); /* F = -grad V */
2456 /* Store the additional force so that it can be added to the force
2457 * array after the normal forces have been evaluated */
2458 for (int m = 0; m < DIM; m++)
2460 erg->f_rot_loc[j][m] = erg->rotg->k * tmp_f[m];
2465 } /* END of loop over local atoms */
2470 static void sort_collective_coordinates(gmx_enfrotgrp* erg,
2471 sort_along_vec_t* data) /* Buffer for sorting the positions */
2473 /* The projection of the position vector on the rotation vector is
2474 * the relevant value for sorting. Fill the 'data' structure */
2475 for (int i = 0; i < erg->rotg->nat; i++)
2477 data[i].xcproj = iprod(erg->xc[i], erg->vec); /* sort criterium */
2478 data[i].m = erg->mc[i];
2480 copy_rvec(erg->xc[i], data[i].x);
2481 copy_rvec(erg->rotg->x_ref[i], data[i].x_ref);
2483 /* Sort the 'data' structure */
2484 std::sort(data, data + erg->rotg->nat, [](const sort_along_vec_t& a, const sort_along_vec_t& b) {
2485 return a.xcproj < b.xcproj;
2488 /* Copy back the sorted values */
2489 for (int i = 0; i < erg->rotg->nat; i++)
2491 copy_rvec(data[i].x, erg->xc[i]);
2492 copy_rvec(data[i].x_ref, erg->xc_ref_sorted[i]);
2493 erg->mc_sorted[i] = data[i].m;
2494 erg->xc_sortind[i] = data[i].ind;
2499 /* For each slab, get the first and the last index of the sorted atom
2501 static void get_firstlast_atom_per_slab(const gmx_enfrotgrp* erg)
2505 /* Find the first atom that needs to enter the calculation for each slab */
2506 int n = erg->slab_first; /* slab */
2507 int i = 0; /* start with the first atom */
2510 /* Find the first atom that significantly contributes to this slab */
2511 do /* move forward in position until a large enough beta is found */
2513 beta = calc_beta(erg->xc[i], erg, n);
2515 } while ((beta < -erg->max_beta) && (i < erg->rotg->nat));
2517 int slabIndex = n - erg->slab_first; /* slab index */
2518 erg->firstatom[slabIndex] = i;
2519 /* Proceed to the next slab */
2521 } while (n <= erg->slab_last);
2523 /* Find the last atom for each slab */
2524 n = erg->slab_last; /* start with last slab */
2525 i = erg->rotg->nat - 1; /* start with the last atom */
2528 do /* move backward in position until a large enough beta is found */
2530 beta = calc_beta(erg->xc[i], erg, n);
2532 } while ((beta > erg->max_beta) && (i > -1));
2534 int slabIndex = n - erg->slab_first; /* slab index */
2535 erg->lastatom[slabIndex] = i;
2536 /* Proceed to the next slab */
2538 } while (n >= erg->slab_first);
2542 /* Determine the very first and very last slab that needs to be considered
2543 * For the first slab that needs to be considered, we have to find the smallest
2546 * x_first * v - n*Delta_x <= beta_max
2548 * slab index n, slab distance Delta_x, rotation vector v. For the last slab we
2549 * have to find the largest n that obeys
2551 * x_last * v - n*Delta_x >= -beta_max
2554 static inline int get_first_slab(const gmx_enfrotgrp* erg,
2555 rvec firstatom) /* First atom after sorting along the rotation vector v */
2557 /* Find the first slab for the first atom */
2558 return static_cast<int>(ceil(
2559 static_cast<double>((iprod(firstatom, erg->vec) - erg->max_beta) / erg->rotg->slab_dist)));
2563 static inline int get_last_slab(const gmx_enfrotgrp* erg, rvec lastatom) /* Last atom along v */
2565 /* Find the last slab for the last atom */
2566 return static_cast<int>(floor(
2567 static_cast<double>((iprod(lastatom, erg->vec) + erg->max_beta) / erg->rotg->slab_dist)));
2571 static void get_firstlast_slab_check(gmx_enfrotgrp* erg, /* The rotation group (data only accessible in this file) */
2572 rvec firstatom, /* First atom after sorting along the rotation vector v */
2573 rvec lastatom) /* Last atom along v */
2575 erg->slab_first = get_first_slab(erg, firstatom);
2576 erg->slab_last = get_last_slab(erg, lastatom);
2578 /* Calculate the slab buffer size, which changes when slab_first changes */
2579 erg->slab_buffer = erg->slab_first - erg->slab_first_ref;
2581 /* Check whether we have reference data to compare against */
2582 if (erg->slab_first < erg->slab_first_ref)
2584 gmx_fatal(FARGS, "%s No reference data for first slab (n=%d), unable to proceed.", RotStr, erg->slab_first);
2587 /* Check whether we have reference data to compare against */
2588 if (erg->slab_last > erg->slab_last_ref)
2590 gmx_fatal(FARGS, "%s No reference data for last slab (n=%d), unable to proceed.", RotStr, erg->slab_last);
2595 /* Enforced rotation with a flexible axis */
2596 static void do_flexible(gmx_bool bMaster,
2597 gmx_enfrot* enfrot, /* Other rotation data */
2599 rvec x[], /* The local positions */
2601 double t, /* Time in picoseconds */
2602 gmx_bool bOutstepRot, /* Output to main rotation output file */
2603 gmx_bool bOutstepSlab) /* Output per-slab data */
2606 real sigma; /* The Gaussian width sigma */
2608 /* Define the sigma value */
2609 sigma = 0.7 * erg->rotg->slab_dist;
2611 /* Sort the collective coordinates erg->xc along the rotation vector. This is
2612 * an optimization for the inner loop. */
2613 sort_collective_coordinates(erg, enfrot->data);
2615 /* Determine the first relevant slab for the first atom and the last
2616 * relevant slab for the last atom */
2617 get_firstlast_slab_check(erg, erg->xc[0], erg->xc[erg->rotg->nat - 1]);
2619 /* Determine for each slab depending on the min_gaussian cutoff criterium,
2620 * a first and a last atom index inbetween stuff needs to be calculated */
2621 get_firstlast_atom_per_slab(erg);
2623 /* Determine the gaussian-weighted center of positions for all slabs */
2624 get_slab_centers(erg, erg->xc, erg->mc_sorted, t, enfrot->out_slabs, bOutstepSlab, FALSE);
2626 /* Clear the torque per slab from last time step: */
2627 nslabs = erg->slab_last - erg->slab_first + 1;
2628 for (int l = 0; l < nslabs; l++)
2630 erg->slab_torque_v[l] = 0.0;
2633 /* Call the rotational forces kernel */
2634 if (erg->rotg->eType == erotgFLEX || erg->rotg->eType == erotgFLEXT)
2636 erg->V = do_flex_lowlevel(erg, sigma, x, bOutstepRot, bOutstepSlab, box);
2638 else if (erg->rotg->eType == erotgFLEX2 || erg->rotg->eType == erotgFLEX2T)
2640 erg->V = do_flex2_lowlevel(erg, sigma, x, bOutstepRot, bOutstepSlab, box);
2644 gmx_fatal(FARGS, "Unknown flexible rotation type");
2647 /* Determine angle by RMSD fit to the reference - Let's hope this */
2648 /* only happens once in a while, since this is not parallelized! */
2649 if (bMaster && (erotgFitPOT != erg->rotg->eFittype))
2653 /* Fit angle of the whole rotation group */
2654 erg->angle_v = flex_fit_angle(erg);
2658 /* Fit angle of each slab */
2659 flex_fit_angle_perslab(erg, t, erg->degangle, enfrot->out_angles);
2663 /* Lump together the torques from all slabs: */
2664 erg->torque_v = 0.0;
2665 for (int l = 0; l < nslabs; l++)
2667 erg->torque_v += erg->slab_torque_v[l];
2672 /* Calculate the angle between reference and actual rotation group atom,
2673 * both projected into a plane perpendicular to the rotation vector: */
2674 static void angle(const gmx_enfrotgrp* erg,
2678 real* weight) /* atoms near the rotation axis should count less than atoms far away */
2680 rvec xp, xrp; /* current and reference positions projected on a plane perpendicular to pg->vec */
2684 /* Project x_ref and x into a plane through the origin perpendicular to rot_vec: */
2685 /* Project x_ref: xrp = x_ref - (vec * x_ref) * vec */
2686 svmul(iprod(erg->vec, x_ref), erg->vec, dum);
2687 rvec_sub(x_ref, dum, xrp);
2688 /* Project x_act: */
2689 svmul(iprod(erg->vec, x_act), erg->vec, dum);
2690 rvec_sub(x_act, dum, xp);
2692 /* Retrieve information about which vector precedes. gmx_angle always
2693 * returns a positive angle. */
2694 cprod(xp, xrp, dum); /* if reference precedes, this is pointing into the same direction as vec */
2696 if (iprod(erg->vec, dum) >= 0)
2698 *alpha = -gmx_angle(xrp, xp);
2702 *alpha = +gmx_angle(xrp, xp);
2705 /* Also return the weight */
2710 /* Project first vector onto a plane perpendicular to the second vector
2712 * Note that v must be of unit length.
2714 static inline void project_onto_plane(rvec dr, const rvec v)
2719 svmul(iprod(dr, v), v, tmp); /* tmp = (dr.v)v */
2720 rvec_dec(dr, tmp); /* dr = dr - (dr.v)v */
2724 /* Fixed rotation: The rotation reference group rotates around the v axis. */
2725 /* The atoms of the actual rotation group are attached with imaginary */
2726 /* springs to the reference atoms. */
2727 static void do_fixed(gmx_enfrotgrp* erg,
2728 gmx_bool bOutstepRot, /* Output to main rotation output file */
2729 gmx_bool bOutstepSlab) /* Output per-slab data */
2732 rvec tmp_f; /* Force */
2733 real alpha; /* a single angle between an actual and a reference position */
2734 real weight; /* single weight for a single angle */
2735 rvec xi_xc; /* xi - xc */
2736 gmx_bool bCalcPotFit;
2739 /* for mass weighting: */
2740 real wi; /* Mass-weighting of the positions */
2742 real k_wi; /* k times wi */
2746 bProject = (erg->rotg->eType == erotgPM) || (erg->rotg->eType == erotgPMPF);
2747 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2749 N_M = erg->rotg->nat * erg->invmass;
2750 const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2751 /* Each process calculates the forces on its local atoms */
2752 for (size_t j = 0; j < erg->atomSet->numAtomsLocal(); j++)
2754 /* Calculate (x_i-x_c) resp. (x_i-u) */
2755 rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xi_xc);
2757 /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
2758 rvec_sub(erg->xr_loc[j], xi_xc, dr);
2762 project_onto_plane(dr, erg->vec);
2765 /* Mass-weighting */
2766 wi = N_M * erg->m_loc[j];
2768 /* Store the additional force so that it can be added to the force
2769 * array after the normal forces have been evaluated */
2770 k_wi = erg->rotg->k * wi;
2771 for (int m = 0; m < DIM; m++)
2773 tmp_f[m] = k_wi * dr[m];
2774 erg->f_rot_loc[j][m] = tmp_f[m];
2775 erg->V += 0.5 * k_wi * gmx::square(dr[m]);
2778 /* If requested, also calculate the potential for a set of angles
2779 * near the current reference angle */
2782 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2784 /* Index of this rotation group atom with respect to the whole rotation group */
2785 int jj = collectiveRotationGroupIndex[j];
2787 /* Rotate with the alternative angle. Like rotate_local_reference(),
2788 * just for a single local atom */
2789 mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[jj], fit_xr_loc); /* fit_xr_loc = Omega*(y_i-y_c) */
2791 /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
2792 rvec_sub(fit_xr_loc, xi_xc, dr);
2796 project_onto_plane(dr, erg->vec);
2799 /* Add to the rotation potential for this angle: */
2800 erg->PotAngleFit->V[ifit] += 0.5 * k_wi * norm2(dr);
2806 /* Add to the torque of this rotation group */
2807 erg->torque_v += torque(erg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2809 /* Calculate the angle between reference and actual rotation group atom. */
2810 angle(erg, xi_xc, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2811 erg->angle_v += alpha * weight;
2812 erg->weight_v += weight;
2814 /* If you want enforced rotation to contribute to the virial,
2815 * activate the following lines:
2818 Add the rotation contribution to the virial
2819 for(j=0; j<DIM; j++)
2821 vir[j][m] += 0.5*f[ii][j]*dr[m];
2827 } /* end of loop over local rotation group atoms */
2831 /* Calculate the radial motion potential and forces */
2832 static void do_radial_motion(gmx_enfrotgrp* erg,
2833 gmx_bool bOutstepRot, /* Output to main rotation output file */
2834 gmx_bool bOutstepSlab) /* Output per-slab data */
2836 rvec tmp_f; /* Force */
2837 real alpha; /* a single angle between an actual and a reference position */
2838 real weight; /* single weight for a single angle */
2839 rvec xj_u; /* xj - u */
2840 rvec tmpvec, fit_tmpvec;
2841 real fac, fac2, sum = 0.0;
2843 gmx_bool bCalcPotFit;
2845 /* For mass weighting: */
2846 real wj; /* Mass-weighting of the positions */
2849 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2851 N_M = erg->rotg->nat * erg->invmass;
2852 const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2853 /* Each process calculates the forces on its local atoms */
2854 for (size_t j = 0; j < erg->atomSet->numAtomsLocal(); j++)
2856 /* Calculate (xj-u) */
2857 rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xj_u); /* xj_u = xj-u */
2859 /* Calculate Omega.(yj0-u) */
2860 cprod(erg->vec, erg->xr_loc[j], tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2862 /* * v x Omega.(yj0-u) */
2863 unitv(tmpvec, pj); /* pj = --------------------- */
2864 /* | v x Omega.(yj0-u) | */
2866 fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2869 /* Mass-weighting */
2870 wj = N_M * erg->m_loc[j];
2872 /* Store the additional force so that it can be added to the force
2873 * array after the normal forces have been evaluated */
2874 svmul(-erg->rotg->k * wj * fac, pj, tmp_f);
2875 copy_rvec(tmp_f, erg->f_rot_loc[j]);
2878 /* If requested, also calculate the potential for a set of angles
2879 * near the current reference angle */
2882 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2884 /* Index of this rotation group atom with respect to the whole rotation group */
2885 int jj = collectiveRotationGroupIndex[j];
2887 /* Rotate with the alternative angle. Like rotate_local_reference(),
2888 * just for a single local atom */
2889 mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[jj], fit_tmpvec); /* fit_tmpvec = Omega*(yj0-u) */
2891 /* Calculate Omega.(yj0-u) */
2892 cprod(erg->vec, fit_tmpvec, tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2893 /* * v x Omega.(yj0-u) */
2894 unitv(tmpvec, pj); /* pj = --------------------- */
2895 /* | v x Omega.(yj0-u) | */
2897 fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2900 /* Add to the rotation potential for this angle: */
2901 erg->PotAngleFit->V[ifit] += 0.5 * erg->rotg->k * wj * fac2;
2907 /* Add to the torque of this rotation group */
2908 erg->torque_v += torque(erg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2910 /* Calculate the angle between reference and actual rotation group atom. */
2911 angle(erg, xj_u, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2912 erg->angle_v += alpha * weight;
2913 erg->weight_v += weight;
2918 } /* end of loop over local rotation group atoms */
2919 erg->V = 0.5 * erg->rotg->k * sum;
2923 /* Calculate the radial motion pivot-free potential and forces */
2924 static void do_radial_motion_pf(gmx_enfrotgrp* erg,
2925 rvec x[], /* The positions */
2926 const matrix box, /* The simulation box */
2927 gmx_bool bOutstepRot, /* Output to main rotation output file */
2928 gmx_bool bOutstepSlab) /* Output per-slab data */
2930 rvec xj; /* Current position */
2931 rvec xj_xc; /* xj - xc */
2932 rvec yj0_yc0; /* yj0 - yc0 */
2933 rvec tmp_f; /* Force */
2934 real alpha; /* a single angle between an actual and a reference position */
2935 real weight; /* single weight for a single angle */
2936 rvec tmpvec, tmpvec2;
2937 rvec innersumvec; /* Precalculation of the inner sum */
2939 real fac, fac2, V = 0.0;
2941 gmx_bool bCalcPotFit;
2943 /* For mass weighting: */
2944 real mj, wi, wj; /* Mass-weighting of the positions */
2947 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2949 N_M = erg->rotg->nat * erg->invmass;
2951 /* Get the current center of the rotation group: */
2952 get_center(erg->xc, erg->mc, erg->rotg->nat, erg->xc_center);
2954 /* Precalculate Sum_i [ wi qi.(xi-xc) qi ] which is needed for every single j */
2955 clear_rvec(innersumvec);
2956 for (int i = 0; i < erg->rotg->nat; i++)
2958 /* Mass-weighting */
2959 wi = N_M * erg->mc[i];
2961 /* Calculate qi. Note that xc_ref_center has already been subtracted from
2962 * x_ref in init_rot_group.*/
2963 mvmul(erg->rotmat, erg->rotg->x_ref[i], tmpvec); /* tmpvec = Omega.(yi0-yc0) */
2965 cprod(erg->vec, tmpvec, tmpvec2); /* tmpvec2 = v x Omega.(yi0-yc0) */
2967 /* * v x Omega.(yi0-yc0) */
2968 unitv(tmpvec2, qi); /* qi = ----------------------- */
2969 /* | v x Omega.(yi0-yc0) | */
2971 rvec_sub(erg->xc[i], erg->xc_center, tmpvec); /* tmpvec = xi-xc */
2973 svmul(wi * iprod(qi, tmpvec), qi, tmpvec2);
2975 rvec_inc(innersumvec, tmpvec2);
2977 svmul(erg->rotg->k * erg->invmass, innersumvec, innersumveckM);
2979 /* Each process calculates the forces on its local atoms */
2980 const auto& localRotationGroupIndex = erg->atomSet->localIndex();
2981 const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2982 for (gmx::index j = 0; j < localRotationGroupIndex.ssize(); j++)
2984 /* Local index of a rotation group atom */
2985 int ii = localRotationGroupIndex[j];
2986 /* Position of this atom in the collective array */
2987 int iigrp = collectiveRotationGroupIndex[j];
2988 /* Mass-weighting */
2989 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2992 /* Current position of this atom: x[ii][XX/YY/ZZ] */
2993 copy_rvec(x[ii], xj);
2995 /* Shift this atom such that it is near its reference */
2996 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2998 /* The (unrotated) reference position is yj0. yc0 has already
2999 * been subtracted in init_rot_group */
3000 copy_rvec(erg->rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
3002 /* Calculate Omega.(yj0-yc0) */
3003 mvmul(erg->rotmat, yj0_yc0, tmpvec2); /* tmpvec2 = Omega.(yj0 - yc0) */
3005 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
3007 /* * v x Omega.(yj0-yc0) */
3008 unitv(tmpvec, qj); /* qj = ----------------------- */
3009 /* | v x Omega.(yj0-yc0) | */
3011 /* Calculate (xj-xc) */
3012 rvec_sub(xj, erg->xc_center, xj_xc); /* xj_xc = xj-xc */
3014 fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
3017 /* Store the additional force so that it can be added to the force
3018 * array after the normal forces have been evaluated */
3019 svmul(-erg->rotg->k * wj * fac, qj, tmp_f); /* part 1 of force */
3020 svmul(mj, innersumveckM, tmpvec); /* part 2 of force */
3021 rvec_inc(tmp_f, tmpvec);
3022 copy_rvec(tmp_f, erg->f_rot_loc[j]);
3025 /* If requested, also calculate the potential for a set of angles
3026 * near the current reference angle */
3029 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
3031 /* Rotate with the alternative angle. Like rotate_local_reference(),
3032 * just for a single local atom */
3033 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, tmpvec2); /* tmpvec2 = Omega*(yj0-yc0) */
3035 /* Calculate Omega.(yj0-u) */
3036 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
3037 /* * v x Omega.(yj0-yc0) */
3038 unitv(tmpvec, qj); /* qj = ----------------------- */
3039 /* | v x Omega.(yj0-yc0) | */
3041 fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
3044 /* Add to the rotation potential for this angle: */
3045 erg->PotAngleFit->V[ifit] += 0.5 * erg->rotg->k * wj * fac2;
3051 /* Add to the torque of this rotation group */
3052 erg->torque_v += torque(erg->vec, tmp_f, xj, erg->xc_center);
3054 /* Calculate the angle between reference and actual rotation group atom. */
3055 angle(erg, xj_xc, yj0_yc0, &alpha, &weight); /* angle in rad, weighted */
3056 erg->angle_v += alpha * weight;
3057 erg->weight_v += weight;
3062 } /* end of loop over local rotation group atoms */
3063 erg->V = 0.5 * erg->rotg->k * V;
3067 /* Precalculate the inner sum for the radial motion 2 forces */
3068 static void radial_motion2_precalc_inner_sum(const gmx_enfrotgrp* erg, rvec innersumvec)
3071 rvec xi_xc; /* xj - xc */
3072 rvec tmpvec, tmpvec2;
3076 rvec v_xi_xc; /* v x (xj - u) */
3077 real psii, psiistar;
3078 real wi; /* Mass-weighting of the positions */
3082 N_M = erg->rotg->nat * erg->invmass;
3084 /* Loop over the collective set of positions */
3086 for (i = 0; i < erg->rotg->nat; i++)
3088 /* Mass-weighting */
3089 wi = N_M * erg->mc[i];
3091 rvec_sub(erg->xc[i], erg->xc_center, xi_xc); /* xi_xc = xi-xc */
3093 /* Calculate ri. Note that xc_ref_center has already been subtracted from
3094 * x_ref in init_rot_group.*/
3095 mvmul(erg->rotmat, erg->rotg->x_ref[i], ri); /* ri = Omega.(yi0-yc0) */
3097 cprod(erg->vec, xi_xc, v_xi_xc); /* v_xi_xc = v x (xi-u) */
3099 fac = norm2(v_xi_xc);
3101 psiistar = 1.0 / (fac + erg->rotg->eps); /* psiistar = --------------------- */
3102 /* |v x (xi-xc)|^2 + eps */
3104 psii = gmx::invsqrt(fac); /* 1 */
3105 /* psii = ------------- */
3108 svmul(psii, v_xi_xc, si); /* si = psii * (v x (xi-xc) ) */
3110 siri = iprod(si, ri); /* siri = si.ri */
3112 svmul(psiistar / psii, ri, tmpvec);
3113 svmul(psiistar * psiistar / (psii * psii * psii) * siri, si, tmpvec2);
3114 rvec_dec(tmpvec, tmpvec2);
3115 cprod(tmpvec, erg->vec, tmpvec2);
3117 svmul(wi * siri, tmpvec2, tmpvec);
3119 rvec_inc(sumvec, tmpvec);
3121 svmul(erg->rotg->k * erg->invmass, sumvec, innersumvec);
3125 /* Calculate the radial motion 2 potential and forces */
3126 static void do_radial_motion2(gmx_enfrotgrp* erg,
3127 rvec x[], /* The positions */
3128 const matrix box, /* The simulation box */
3129 gmx_bool bOutstepRot, /* Output to main rotation output file */
3130 gmx_bool bOutstepSlab) /* Output per-slab data */
3132 rvec xj; /* Position */
3133 real alpha; /* a single angle between an actual and a reference position */
3134 real weight; /* single weight for a single angle */
3135 rvec xj_u; /* xj - u */
3136 rvec yj0_yc0; /* yj0 -yc0 */
3137 rvec tmpvec, tmpvec2;
3138 real fac, fit_fac, fac2, Vpart = 0.0;
3139 rvec rj, fit_rj, sj;
3141 rvec v_xj_u; /* v x (xj - u) */
3142 real psij, psijstar;
3143 real mj, wj; /* For mass-weighting of the positions */
3147 gmx_bool bCalcPotFit;
3149 bPF = erg->rotg->eType == erotgRM2PF;
3150 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
3152 clear_rvec(yj0_yc0); /* Make the compiler happy */
3154 clear_rvec(innersumvec);
3157 /* For the pivot-free variant we have to use the current center of
3158 * mass of the rotation group instead of the pivot u */
3159 get_center(erg->xc, erg->mc, erg->rotg->nat, erg->xc_center);
3161 /* Also, we precalculate the second term of the forces that is identical
3162 * (up to the weight factor mj) for all forces */
3163 radial_motion2_precalc_inner_sum(erg, innersumvec);
3166 N_M = erg->rotg->nat * erg->invmass;
3168 /* Each process calculates the forces on its local atoms */
3169 const auto& localRotationGroupIndex = erg->atomSet->localIndex();
3170 const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
3171 for (gmx::index j = 0; j < localRotationGroupIndex.ssize(); j++)
3175 /* Local index of a rotation group atom */
3176 int ii = localRotationGroupIndex[j];
3177 /* Position of this atom in the collective array */
3178 int iigrp = collectiveRotationGroupIndex[j];
3179 /* Mass-weighting */
3180 mj = erg->mc[iigrp];
3182 /* Current position of this atom: x[ii] */
3183 copy_rvec(x[ii], xj);
3185 /* Shift this atom such that it is near its reference */
3186 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
3188 /* The (unrotated) reference position is yj0. yc0 has already
3189 * been subtracted in init_rot_group */
3190 copy_rvec(erg->rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
3192 /* Calculate Omega.(yj0-yc0) */
3193 mvmul(erg->rotmat, yj0_yc0, rj); /* rj = Omega.(yj0-yc0) */
3198 copy_rvec(erg->x_loc_pbc[j], xj);
3199 copy_rvec(erg->xr_loc[j], rj); /* rj = Omega.(yj0-u) */
3201 /* Mass-weighting */
3204 /* Calculate (xj-u) resp. (xj-xc) */
3205 rvec_sub(xj, erg->xc_center, xj_u); /* xj_u = xj-u */
3207 cprod(erg->vec, xj_u, v_xj_u); /* v_xj_u = v x (xj-u) */
3209 fac = norm2(v_xj_u);
3211 psijstar = 1.0 / (fac + erg->rotg->eps); /* psistar = -------------------- */
3212 /* * |v x (xj-u)|^2 + eps */
3214 psij = gmx::invsqrt(fac); /* 1 */
3215 /* psij = ------------ */
3218 svmul(psij, v_xj_u, sj); /* sj = psij * (v x (xj-u) ) */
3220 fac = iprod(v_xj_u, rj); /* fac = (v x (xj-u)).rj */
3223 sjrj = iprod(sj, rj); /* sjrj = sj.rj */
3225 svmul(psijstar / psij, rj, tmpvec);
3226 svmul(psijstar * psijstar / (psij * psij * psij) * sjrj, sj, tmpvec2);
3227 rvec_dec(tmpvec, tmpvec2);
3228 cprod(tmpvec, erg->vec, tmpvec2);
3230 /* Store the additional force so that it can be added to the force
3231 * array after the normal forces have been evaluated */
3232 svmul(-erg->rotg->k * wj * sjrj, tmpvec2, tmpvec);
3233 svmul(mj, innersumvec, tmpvec2); /* This is != 0 only for the pivot-free variant */
3235 rvec_add(tmpvec2, tmpvec, erg->f_rot_loc[j]);
3236 Vpart += wj * psijstar * fac2;
3238 /* If requested, also calculate the potential for a set of angles
3239 * near the current reference angle */
3242 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
3246 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, fit_rj); /* fit_rj = Omega.(yj0-yc0) */
3250 /* Position of this atom in the collective array */
3251 int iigrp = collectiveRotationGroupIndex[j];
3252 /* Rotate with the alternative angle. Like rotate_local_reference(),
3253 * just for a single local atom */
3254 mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[iigrp], fit_rj); /* fit_rj = Omega*(yj0-u) */
3256 fit_fac = iprod(v_xj_u, fit_rj); /* fac = (v x (xj-u)).fit_rj */
3257 /* Add to the rotation potential for this angle: */
3258 erg->PotAngleFit->V[ifit] += 0.5 * erg->rotg->k * wj * psijstar * fit_fac * fit_fac;
3264 /* Add to the torque of this rotation group */
3265 erg->torque_v += torque(erg->vec, erg->f_rot_loc[j], xj, erg->xc_center);
3267 /* Calculate the angle between reference and actual rotation group atom. */
3268 angle(erg, xj_u, rj, &alpha, &weight); /* angle in rad, weighted */
3269 erg->angle_v += alpha * weight;
3270 erg->weight_v += weight;
3275 } /* end of loop over local rotation group atoms */
3276 erg->V = 0.5 * erg->rotg->k * Vpart;
3280 /* Determine the smallest and largest position vector (with respect to the
3281 * rotation vector) for the reference group */
3282 static void get_firstlast_atom_ref(const gmx_enfrotgrp* erg, int* firstindex, int* lastindex)
3285 real xcproj; /* The projection of a reference position on the
3287 real minproj, maxproj; /* Smallest and largest projection on v */
3289 /* Start with some value */
3290 minproj = iprod(erg->rotg->x_ref[0], erg->vec);
3293 /* This is just to ensure that it still works if all the atoms of the
3294 * reference structure are situated in a plane perpendicular to the rotation
3297 *lastindex = erg->rotg->nat - 1;
3299 /* Loop over all atoms of the reference group,
3300 * project them on the rotation vector to find the extremes */
3301 for (i = 0; i < erg->rotg->nat; i++)
3303 xcproj = iprod(erg->rotg->x_ref[i], erg->vec);
3304 if (xcproj < minproj)
3309 if (xcproj > maxproj)
3318 /* Allocate memory for the slabs */
3319 static void allocate_slabs(gmx_enfrotgrp* erg, FILE* fplog, gmx_bool bVerbose)
3321 /* More slabs than are defined for the reference are never needed */
3322 int nslabs = erg->slab_last_ref - erg->slab_first_ref + 1;
3324 /* Remember how many we allocated */
3325 erg->nslabs_alloc = nslabs;
3327 if ((nullptr != fplog) && bVerbose)
3330 "%s allocating memory to store data for %d slabs (rotation group %d).\n",
3335 snew(erg->slab_center, nslabs);
3336 snew(erg->slab_center_ref, nslabs);
3337 snew(erg->slab_weights, nslabs);
3338 snew(erg->slab_torque_v, nslabs);
3339 snew(erg->slab_data, nslabs);
3340 snew(erg->gn_atom, nslabs);
3341 snew(erg->gn_slabind, nslabs);
3342 snew(erg->slab_innersumvec, nslabs);
3343 for (int i = 0; i < nslabs; i++)
3345 snew(erg->slab_data[i].x, erg->rotg->nat);
3346 snew(erg->slab_data[i].ref, erg->rotg->nat);
3347 snew(erg->slab_data[i].weight, erg->rotg->nat);
3349 snew(erg->xc_ref_sorted, erg->rotg->nat);
3350 snew(erg->xc_sortind, erg->rotg->nat);
3351 snew(erg->firstatom, nslabs);
3352 snew(erg->lastatom, nslabs);
3356 /* From the extreme positions of the reference group, determine the first
3357 * and last slab of the reference. We can never have more slabs in the real
3358 * simulation than calculated here for the reference.
3360 static void get_firstlast_slab_ref(gmx_enfrotgrp* erg, real mc[], int ref_firstindex, int ref_lastindex)
3364 int first = get_first_slab(erg, erg->rotg->x_ref[ref_firstindex]);
3365 int last = get_last_slab(erg, erg->rotg->x_ref[ref_lastindex]);
3367 while (get_slab_weight(first, erg, erg->rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
3371 erg->slab_first_ref = first + 1;
3372 while (get_slab_weight(last, erg, erg->rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
3376 erg->slab_last_ref = last - 1;
3380 /* Special version of copy_rvec:
3381 * During the copy procedure of xcurr to b, the correct PBC image is chosen
3382 * such that the copied vector ends up near its reference position xref */
3383 static inline void copy_correct_pbc_image(const rvec xcurr, /* copy vector xcurr ... */
3384 rvec b, /* ... to b ... */
3385 const rvec xref, /* choosing the PBC image such that b ends up near xref */
3394 /* Shortest PBC distance between the atom and its reference */
3395 rvec_sub(xcurr, xref, dx);
3397 /* Determine the shift for this atom */
3399 for (m = npbcdim - 1; m >= 0; m--)
3401 while (dx[m] < -0.5 * box[m][m])
3403 for (d = 0; d < DIM; d++)
3409 while (dx[m] >= 0.5 * box[m][m])
3411 for (d = 0; d < DIM; d++)
3419 /* Apply the shift to the position */
3420 copy_rvec(xcurr, b);
3421 shift_single_coord(box, b, shift);
3425 static void init_rot_group(FILE* fplog,
3426 const t_commrec* cr,
3434 gmx_bool bOutputCenters)
3436 rvec coord, xref, *xdum;
3437 gmx_bool bFlex, bColl;
3438 int ref_firstindex, ref_lastindex;
3439 real mass, totalmass;
3442 const t_rotgrp* rotg = erg->rotg;
3445 /* Do we have a flexible axis? */
3446 bFlex = ISFLEX(rotg);
3447 /* Do we use a global set of coordinates? */
3448 bColl = ISCOLL(rotg);
3450 /* Allocate space for collective coordinates if needed */
3453 snew(erg->xc, erg->rotg->nat);
3454 snew(erg->xc_shifts, erg->rotg->nat);
3455 snew(erg->xc_eshifts, erg->rotg->nat);
3456 snew(erg->xc_old, erg->rotg->nat);
3458 if (erg->rotg->eFittype == erotgFitNORM)
3460 snew(erg->xc_ref_length, erg->rotg->nat); /* in case fit type NORM is chosen */
3461 snew(erg->xc_norm, erg->rotg->nat);
3466 snew(erg->xr_loc, erg->rotg->nat);
3467 snew(erg->x_loc_pbc, erg->rotg->nat);
3470 copy_rvec(erg->rotg->inputVec, erg->vec);
3471 snew(erg->f_rot_loc, erg->rotg->nat);
3473 /* Make space for the calculation of the potential at other angles (used
3474 * for fitting only) */
3475 if (erotgFitPOT == erg->rotg->eFittype)
3477 snew(erg->PotAngleFit, 1);
3478 snew(erg->PotAngleFit->degangle, erg->rotg->PotAngle_nstep);
3479 snew(erg->PotAngleFit->V, erg->rotg->PotAngle_nstep);
3480 snew(erg->PotAngleFit->rotmat, erg->rotg->PotAngle_nstep);
3482 /* Get the set of angles around the reference angle */
3483 start = -0.5 * (erg->rotg->PotAngle_nstep - 1) * erg->rotg->PotAngle_step;
3484 for (int i = 0; i < erg->rotg->PotAngle_nstep; i++)
3486 erg->PotAngleFit->degangle[i] = start + i * erg->rotg->PotAngle_step;
3491 erg->PotAngleFit = nullptr;
3494 /* Copy the masses so that the center can be determined. For all types of
3495 * enforced rotation, we store the masses in the erg->mc array. */
3496 snew(erg->mc, erg->rotg->nat);
3499 snew(erg->mc_sorted, erg->rotg->nat);
3503 snew(erg->m_loc, erg->rotg->nat);
3507 for (int i = 0; i < erg->rotg->nat; i++)
3509 if (erg->rotg->bMassW)
3511 mass = mtopGetAtomMass(mtop, erg->rotg->ind[i], &molb);
3520 erg->invmass = 1.0 / totalmass;
3522 /* Set xc_ref_center for any rotation potential */
3523 if ((erg->rotg->eType == erotgISO) || (erg->rotg->eType == erotgPM)
3524 || (erg->rotg->eType == erotgRM) || (erg->rotg->eType == erotgRM2))
3526 /* Set the pivot point for the fixed, stationary-axis potentials. This
3527 * won't change during the simulation */
3528 copy_rvec(erg->rotg->pivot, erg->xc_ref_center);
3529 copy_rvec(erg->rotg->pivot, erg->xc_center);
3533 /* Center of the reference positions */
3534 get_center(erg->rotg->x_ref, erg->mc, erg->rotg->nat, erg->xc_ref_center);
3536 /* Center of the actual positions */
3539 snew(xdum, erg->rotg->nat);
3540 for (int i = 0; i < erg->rotg->nat; i++)
3542 int ii = erg->rotg->ind[i];
3543 copy_rvec(x[ii], xdum[i]);
3545 get_center(xdum, erg->mc, erg->rotg->nat, erg->xc_center);
3551 gmx_bcast(sizeof(erg->xc_center), erg->xc_center, cr->mpi_comm_mygroup);
3558 /* Save the original (whole) set of positions in xc_old such that at later
3559 * steps the rotation group can always be made whole again. If the simulation is
3560 * restarted, we compute the starting reference positions (given the time)
3561 * and assume that the correct PBC image of each position is the one nearest
3562 * to the current reference */
3565 /* Calculate the rotation matrix for this angle: */
3566 t_start = ir->init_t + ir->init_step * ir->delta_t;
3567 erg->degangle = erg->rotg->rate * t_start;
3568 calc_rotmat(erg->vec, erg->degangle, erg->rotmat);
3570 for (int i = 0; i < erg->rotg->nat; i++)
3572 int ii = erg->rotg->ind[i];
3574 /* Subtract pivot, rotate, and add pivot again. This will yield the
3575 * reference position for time t */
3576 rvec_sub(erg->rotg->x_ref[i], erg->xc_ref_center, coord);
3577 mvmul(erg->rotmat, coord, xref);
3578 rvec_inc(xref, erg->xc_ref_center);
3580 copy_correct_pbc_image(x[ii], erg->xc_old[i], xref, box, 3);
3586 gmx_bcast(erg->rotg->nat * sizeof(erg->xc_old[0]), erg->xc_old, cr->mpi_comm_mygroup);
3591 if ((erg->rotg->eType != erotgFLEX) && (erg->rotg->eType != erotgFLEX2))
3593 /* Put the reference positions into origin: */
3594 for (int i = 0; i < erg->rotg->nat; i++)
3596 rvec_dec(erg->rotg->x_ref[i], erg->xc_ref_center);
3600 /* Enforced rotation with flexible axis */
3603 /* Calculate maximum beta value from minimum gaussian (performance opt.) */
3604 erg->max_beta = calc_beta_max(erg->rotg->min_gaussian, erg->rotg->slab_dist);
3606 /* Determine the smallest and largest coordinate with respect to the rotation vector */
3607 get_firstlast_atom_ref(erg, &ref_firstindex, &ref_lastindex);
3609 /* From the extreme positions of the reference group, determine the first
3610 * and last slab of the reference. */
3611 get_firstlast_slab_ref(erg, erg->mc, ref_firstindex, ref_lastindex);
3613 /* Allocate memory for the slabs */
3614 allocate_slabs(erg, fplog, bVerbose);
3616 /* Flexible rotation: determine the reference centers for the rest of the simulation */
3617 erg->slab_first = erg->slab_first_ref;
3618 erg->slab_last = erg->slab_last_ref;
3619 get_slab_centers(erg, erg->rotg->x_ref, erg->mc, -1, out_slabs, bOutputCenters, TRUE);
3621 /* Length of each x_rotref vector from center (needed if fit routine NORM is chosen): */
3622 if (erg->rotg->eFittype == erotgFitNORM)
3624 for (int i = 0; i < erg->rotg->nat; i++)
3626 rvec_sub(erg->rotg->x_ref[i], erg->xc_ref_center, coord);
3627 erg->xc_ref_length[i] = norm(coord);
3633 /* Calculate the size of the MPI buffer needed in reduce_output() */
3634 static int calc_mpi_bufsize(const gmx_enfrot* er)
3637 int count_total = 0;
3638 for (int g = 0; g < er->rot->ngrp; g++)
3640 const t_rotgrp* rotg = &er->rot->grp[g];
3641 const gmx_enfrotgrp* erg = &er->enfrotgrp[g];
3643 /* Count the items that are transferred for this group: */
3644 int count_group = 4; /* V, torque, angle, weight */
3646 /* Add the maximum number of slabs for flexible groups */
3649 count_group += erg->slab_last_ref - erg->slab_first_ref + 1;
3652 /* Add space for the potentials at different angles: */
3653 if (erotgFitPOT == erg->rotg->eFittype)
3655 count_group += erg->rotg->PotAngle_nstep;
3658 /* Add to the total number: */
3659 count_total += count_group;
3666 std::unique_ptr<gmx::EnforcedRotation> init_rot(FILE* fplog,
3669 const t_filenm fnm[],
3670 const t_commrec* cr,
3671 gmx::LocalAtomSetManager* atomSets,
3672 const t_state* globalState,
3674 const gmx_output_env_t* oenv,
3675 const gmx::MdrunOptions& mdrunOptions,
3676 const gmx::StartingBehavior startingBehavior)
3678 int nat_max = 0; /* Size of biggest rotation group */
3679 rvec* x_pbc = nullptr; /* Space for the pbc-correct atom positions */
3681 if (MASTER(cr) && mdrunOptions.verbose)
3683 fprintf(stdout, "%s Initializing ...\n", RotStr);
3686 auto enforcedRotation = std::make_unique<gmx::EnforcedRotation>();
3687 gmx_enfrot* er = enforcedRotation->getLegacyEnfrot();
3688 // TODO When this module implements IMdpOptions, the ownership will become more clear.
3690 er->restartWithAppending = (startingBehavior == gmx::StartingBehavior::RestartWithAppending);
3692 /* When appending, skip first output to avoid duplicate entries in the data files */
3693 er->bOut = er->restartWithAppending;
3695 if (MASTER(cr) && er->bOut)
3697 please_cite(fplog, "Kutzner2011");
3700 /* Output every step for reruns */
3701 if (mdrunOptions.rerun)
3703 if (nullptr != fplog)
3705 fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
3712 er->nstrout = er->rot->nstrout;
3713 er->nstsout = er->rot->nstsout;
3716 er->out_slabs = nullptr;
3717 if (MASTER(cr) && HaveFlexibleGroups(er->rot))
3719 er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), er);
3724 /* Remove pbc, make molecule whole.
3725 * When ir->bContinuation=TRUE this has already been done, but ok. */
3726 snew(x_pbc, mtop->natoms);
3727 copy_rvecn(globalState->x.rvec_array(), x_pbc, 0, mtop->natoms);
3728 do_pbc_first_mtop(nullptr, ir->pbcType, globalState->box, mtop, x_pbc);
3729 /* All molecules will be whole now, but not necessarily in the home box.
3730 * Additionally, if a rotation group consists of more than one molecule
3731 * (e.g. two strands of DNA), each one of them can end up in a different
3732 * periodic box. This is taken care of in init_rot_group. */
3735 /* Allocate space for the per-rotation-group data: */
3736 er->enfrotgrp.resize(er->rot->ngrp);
3738 for (auto& ergRef : er->enfrotgrp)
3740 gmx_enfrotgrp* erg = &ergRef;
3741 erg->rotg = &er->rot->grp[groupIndex];
3742 erg->atomSet = std::make_unique<gmx::LocalAtomSet>(
3743 atomSets->add({ erg->rotg->ind, erg->rotg->ind + erg->rotg->nat }));
3744 erg->groupIndex = groupIndex;
3746 if (nullptr != fplog)
3748 fprintf(fplog, "%s group %d type '%s'\n", RotStr, groupIndex, erotg_names[erg->rotg->eType]);
3751 if (erg->rotg->nat > 0)
3753 nat_max = std::max(nat_max, erg->rotg->nat);
3755 init_rot_group(fplog,
3760 mdrunOptions.verbose,
3762 MASTER(cr) ? globalState->box : nullptr,
3764 !er->restartWithAppending); /* Do not output the reference centers
3765 * again if we are appending */
3770 /* Allocate space for enforced rotation buffer variables */
3771 er->bufsize = nat_max;
3772 snew(er->data, nat_max);
3773 snew(er->xbuf, nat_max);
3774 snew(er->mbuf, nat_max);
3776 /* Buffers for MPI reducing torques, angles, weights (for each group), and V */
3779 er->mpi_bufsize = calc_mpi_bufsize(er) + 100; /* larger to catch errors */
3780 snew(er->mpi_inbuf, er->mpi_bufsize);
3781 snew(er->mpi_outbuf, er->mpi_bufsize);
3785 er->mpi_bufsize = 0;
3786 er->mpi_inbuf = nullptr;
3787 er->mpi_outbuf = nullptr;
3790 /* Only do I/O on the MASTER */
3791 er->out_angles = nullptr;
3792 er->out_rot = nullptr;
3793 er->out_torque = nullptr;
3796 er->out_rot = open_rot_out(opt2fn("-ro", nfile, fnm), oenv, er);
3798 if (er->nstsout > 0)
3800 if (HaveFlexibleGroups(er->rot) || HavePotFitGroups(er->rot))
3802 er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), er);
3804 if (HaveFlexibleGroups(er->rot))
3806 er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), er);
3812 return enforcedRotation;
3815 /* Rotate the local reference positions and store them in
3816 * erg->xr_loc[0...(nat_loc-1)]
3818 * Note that we already subtracted u or y_c from the reference positions
3819 * in init_rot_group().
3821 static void rotate_local_reference(gmx_enfrotgrp* erg)
3823 const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
3824 for (size_t i = 0; i < erg->atomSet->numAtomsLocal(); i++)
3826 /* Index of this rotation group atom with respect to the whole rotation group */
3827 int ii = collectiveRotationGroupIndex[i];
3829 mvmul(erg->rotmat, erg->rotg->x_ref[ii], erg->xr_loc[i]);
3834 /* Select the PBC representation for each local x position and store that
3835 * for later usage. We assume the right PBC image of an x is the one nearest to
3836 * its rotated reference */
3837 static void choose_pbc_image(rvec x[], gmx_enfrotgrp* erg, const matrix box, int npbcdim)
3839 const auto& localRotationGroupIndex = erg->atomSet->localIndex();
3840 for (gmx::index i = 0; i < localRotationGroupIndex.ssize(); i++)
3842 /* Index of a rotation group atom */
3843 int ii = localRotationGroupIndex[i];
3845 /* Get the correctly rotated reference position. The pivot was already
3846 * subtracted in init_rot_group() from the reference positions. Also,
3847 * the reference positions have already been rotated in
3848 * rotate_local_reference(). For the current reference position we thus
3849 * only need to add the pivot again. */
3851 copy_rvec(erg->xr_loc[i], xref);
3852 rvec_inc(xref, erg->xc_ref_center);
3854 copy_correct_pbc_image(x[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
3859 void do_rotation(const t_commrec* cr, gmx_enfrot* er, const matrix box, rvec x[], real t, int64_t step, gmx_bool bNS)
3861 gmx_bool outstep_slab, outstep_rot;
3864 gmx_potfit* fit = nullptr; /* For fit type 'potential' determine the fit
3865 angle via the potential minimum */
3871 /* When to output in main rotation output file */
3872 outstep_rot = do_per_step(step, er->nstrout) && er->bOut;
3873 /* When to output per-slab data */
3874 outstep_slab = do_per_step(step, er->nstsout) && er->bOut;
3876 /* Output time into rotation output file */
3877 if (outstep_rot && MASTER(cr))
3879 fprintf(er->out_rot, "%12.3e", t);
3882 /**************************************************************************/
3883 /* First do ALL the communication! */
3884 for (auto& ergRef : er->enfrotgrp)
3886 gmx_enfrotgrp* erg = &ergRef;
3887 const t_rotgrp* rotg = erg->rotg;
3889 /* Do we use a collective (global) set of coordinates? */
3890 bColl = ISCOLL(rotg);
3892 /* Calculate the rotation matrix for this angle: */
3893 erg->degangle = rotg->rate * t;
3894 calc_rotmat(erg->vec, erg->degangle, erg->rotmat);
3898 /* Transfer the rotation group's positions such that every node has
3899 * all of them. Every node contributes its local positions x and stores
3900 * it in the collective erg->xc array. */
3901 communicate_group_positions(cr,
3908 erg->atomSet->numAtomsLocal(),
3909 erg->atomSet->localIndex().data(),
3910 erg->atomSet->collectiveIndex().data(),
3916 /* Fill the local masses array;
3917 * this array changes in DD/neighborsearching steps */
3920 const auto& collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
3921 for (gmx::index i = 0; i < collectiveRotationGroupIndex.ssize(); i++)
3923 /* Index of local atom w.r.t. the collective rotation group */
3924 int ii = collectiveRotationGroupIndex[i];
3925 erg->m_loc[i] = erg->mc[ii];
3929 /* Calculate Omega*(y_i-y_c) for the local positions */
3930 rotate_local_reference(erg);
3932 /* Choose the nearest PBC images of the group atoms with respect
3933 * to the rotated reference positions */
3934 choose_pbc_image(x, erg, box, 3);
3936 /* Get the center of the rotation group */
3937 if ((rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF))
3940 cr, erg->x_loc_pbc, erg->m_loc, erg->atomSet->numAtomsLocal(), rotg->nat, erg->xc_center);
3944 } /* End of loop over rotation groups */
3946 /**************************************************************************/
3947 /* Done communicating, we can start to count cycles for the load balancing now ... */
3948 if (DOMAINDECOMP(cr))
3950 ddReopenBalanceRegionCpu(cr->dd);
3957 for (auto& ergRef : er->enfrotgrp)
3959 gmx_enfrotgrp* erg = &ergRef;
3960 const t_rotgrp* rotg = erg->rotg;
3962 if (outstep_rot && MASTER(cr))
3964 fprintf(er->out_rot, "%12.4f", erg->degangle);
3967 /* Calculate angles and rotation matrices for potential fitting: */
3968 if ((outstep_rot || outstep_slab) && (erotgFitPOT == rotg->eFittype))
3970 fit = erg->PotAngleFit;
3971 for (int i = 0; i < rotg->PotAngle_nstep; i++)
3973 calc_rotmat(erg->vec, erg->degangle + fit->degangle[i], fit->rotmat[i]);
3975 /* Clear value from last step */
3976 erg->PotAngleFit->V[i] = 0.0;
3980 /* Clear values from last time step */
3982 erg->torque_v = 0.0;
3984 erg->weight_v = 0.0;
3986 switch (rotg->eType)
3991 case erotgPMPF: do_fixed(erg, outstep_rot, outstep_slab); break;
3992 case erotgRM: do_radial_motion(erg, outstep_rot, outstep_slab); break;
3993 case erotgRMPF: do_radial_motion_pf(erg, x, box, outstep_rot, outstep_slab); break;
3995 case erotgRM2PF: do_radial_motion2(erg, x, box, outstep_rot, outstep_slab); break;
3998 /* Subtract the center of the rotation group from the collective positions array
3999 * Also store the center in erg->xc_center since it needs to be subtracted
4000 * in the low level routines from the local coordinates as well */
4001 get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
4002 svmul(-1.0, erg->xc_center, transvec);
4003 translate_x(erg->xc, rotg->nat, transvec);
4004 do_flexible(MASTER(cr), er, erg, x, box, t, outstep_rot, outstep_slab);
4008 /* Do NOT subtract the center of mass in the low level routines! */
4009 clear_rvec(erg->xc_center);
4010 do_flexible(MASTER(cr), er, erg, x, box, t, outstep_rot, outstep_slab);
4012 default: gmx_fatal(FARGS, "No such rotation potential.");
4019 fprintf(stderr, "%s calculation (step %d) took %g seconds.\n", RotStr, step, MPI_Wtime() - t0);