2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2008, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
39 #include "pull_rotation.h"
50 #include "gromacs/commandline/filenm.h"
51 #include "gromacs/domdec/dlbtiming.h"
52 #include "gromacs/domdec/domdec_struct.h"
53 #include "gromacs/domdec/ga2la.h"
54 #include "gromacs/domdec/localatomset.h"
55 #include "gromacs/domdec/localatomsetmanager.h"
56 #include "gromacs/fileio/gmxfio.h"
57 #include "gromacs/fileio/xvgr.h"
58 #include "gromacs/gmxlib/network.h"
59 #include "gromacs/linearalgebra/nrjac.h"
60 #include "gromacs/math/functions.h"
61 #include "gromacs/math/utilities.h"
62 #include "gromacs/math/vec.h"
63 #include "gromacs/mdlib/groupcoord.h"
64 #include "gromacs/mdlib/sim_util.h"
65 #include "gromacs/mdtypes/commrec.h"
66 #include "gromacs/mdtypes/inputrec.h"
67 #include "gromacs/mdtypes/md_enums.h"
68 #include "gromacs/mdtypes/mdrunoptions.h"
69 #include "gromacs/mdtypes/state.h"
70 #include "gromacs/pbcutil/pbc.h"
71 #include "gromacs/timing/cyclecounter.h"
72 #include "gromacs/timing/wallcycle.h"
73 #include "gromacs/topology/mtop_lookup.h"
74 #include "gromacs/topology/mtop_util.h"
75 #include "gromacs/utility/basedefinitions.h"
76 #include "gromacs/utility/fatalerror.h"
77 #include "gromacs/utility/pleasecite.h"
78 #include "gromacs/utility/smalloc.h"
80 static char const *RotStr = {"Enforced rotation:"};
82 /* Set the minimum weight for the determination of the slab centers */
83 #define WEIGHT_MIN (10*GMX_FLOAT_MIN)
85 //! Helper structure for sorting positions along rotation vector
86 struct sort_along_vec_t
88 //! Projection of xc on the rotation vector
96 //! Reference position
101 //! Enforced rotation / flexible: determine the angle of each slab
104 //! Number of atoms belonging to this slab
106 /*! \brief The positions belonging to this slab.
108 * In general, this should be all positions of the whole
109 * rotation group, but we leave those away that have a small
112 //! Same for reference
114 //! The weight for each atom
119 //! Helper structure for potential fitting
122 /*! \brief Set of angles for which the potential is calculated.
124 * The optimum fit is determined as the angle for with the
125 * potential is minimal. */
127 //! Potential for the different angles
129 //! Rotation matrix corresponding to the angles
134 //! Enforced rotation data for a single rotation group
137 //! Input parameters for this group
138 const t_rotgrp *rotg = nullptr;
139 //! Index of this group within the set of groups
141 //! Rotation angle in degrees
145 //! The atoms subject to enforced rotation
146 std::unique_ptr<gmx::LocalAtomSet> atomSet;
148 //! The normalized rotation vector
150 //! Rotation potential for this rotation group
152 //! Array to store the forces on the local atoms resulting from enforced rotation potential
155 /* Collective coordinates for the whole rotation group */
156 //! Length of each x_rotref vector after x_rotref has been put into origin
158 //! Center of the rotation group positions, may be mass weighted
160 //! Center of the rotation group reference positions
162 //! Current (collective) positions
164 //! Current (collective) shifts
166 //! Extra shifts since last DD step
168 //! Old (collective) positions
170 //! Normalized form of the current positions
172 //! Reference positions (sorted in the same order as xc when sorted)
174 //! Where is a position found after sorting?
176 //! Collective masses
178 //! Collective masses sorted
180 //! one over the total mass of the rotation group
183 //! Torque in the direction of rotation vector
185 //! Actual angle of the whole rotation group
187 /* Fixed rotation only */
188 //! Weights for angle determination
190 //! Local reference coords, correctly rotated
192 //! Local current coords, correct PBC image
194 //! Masses of the current local atoms
197 /* Flexible rotation only */
198 //! For this many slabs memory is allocated
200 //! Lowermost slab for that the calculation needs to be performed at a given time step
202 //! Uppermost slab ...
204 //! First slab for which ref. center is stored
208 //! Slab buffer region around reference slabs
210 //! First relevant atom for a slab
212 //! Last relevant atom for a slab
214 //! Gaussian-weighted slab center
216 //! Gaussian-weighted slab center for the reference positions
217 rvec *slab_center_ref;
218 //! Sum of gaussian weights in a slab
220 //! Torque T = r x f for each slab. torque_v = m.v = angular momentum in the direction of v
222 //! 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
224 //! Precalculated gaussians for a single atom
226 //! Tells to which slab each precalculated gaussian belongs
228 //! Inner sum of the flexible2 potential per slab; this is precalculated for optimization reasons
229 rvec *slab_innersumvec;
230 //! Holds atom positions and gaussian weights of atoms belonging to a slab
231 gmx_slabdata *slab_data;
233 /* For potential fits with varying angle: */
234 //! Used for fit type 'potential'
235 gmx_potfit *PotAngleFit;
239 //! Enforced rotation data for all groups
242 //! Input parameters.
243 const t_rot *rot = nullptr;
244 //! Output period for main rotation outfile
246 //! Output period for per-slab data
248 //! Output file for rotation data
249 FILE *out_rot = nullptr;
250 //! Output file for torque data
251 FILE *out_torque = nullptr;
252 //! Output file for slab angles for flexible type
253 FILE *out_angles = nullptr;
254 //! Output file for slab centers
255 FILE *out_slabs = nullptr;
256 //! Allocation size of buf
258 //! Coordinate buffer variable for sorting
259 rvec *xbuf = nullptr;
260 //! Masses buffer variable for sorting
261 real *mbuf = nullptr;
262 //! Buffer variable needed for position sorting
263 sort_along_vec_t *data = nullptr;
265 real *mpi_inbuf = nullptr;
267 real *mpi_outbuf = nullptr;
268 //! Allocation size of in & outbuf
270 //! If true, append output files
271 gmx_bool appendFiles = false;
272 //! Used to skip first output when appending to avoid duplicate entries in rotation outfiles
273 gmx_bool bOut = false;
274 //! Stores working data per group
275 std::vector<gmx_enfrotgrp> enfrotgrp;
279 gmx_enfrot::~gmx_enfrot()
283 gmx_fio_fclose(out_rot);
287 gmx_fio_fclose(out_slabs);
291 gmx_fio_fclose(out_angles);
295 gmx_fio_fclose(out_torque);
302 class EnforcedRotation::Impl
305 gmx_enfrot enforcedRotation_;
308 EnforcedRotation::EnforcedRotation() : impl_(new Impl)
312 EnforcedRotation::~EnforcedRotation() = default;
314 gmx_enfrot *EnforcedRotation::getLegacyEnfrot()
316 return &impl_->enforcedRotation_;
321 /* Activate output of forces for correctness checks */
322 /* #define PRINT_FORCES */
324 #define PRINT_FORCE_J fprintf(stderr, "f%d = %15.8f %15.8f %15.8f\n", erg->xc_ref_ind[j], erg->f_rot_loc[j][XX], erg->f_rot_loc[j][YY], erg->f_rot_loc[j][ZZ]);
325 #define PRINT_POT_TAU if (MASTER(cr)) { \
326 fprintf(stderr, "potential = %15.8f\n" "torque = %15.8f\n", erg->V, erg->torque_v); \
329 #define PRINT_FORCE_J
330 #define PRINT_POT_TAU
333 /* Shortcuts for often used queries */
334 #define ISFLEX(rg) ( ((rg)->eType == erotgFLEX) || ((rg)->eType == erotgFLEXT) || ((rg)->eType == erotgFLEX2) || ((rg)->eType == erotgFLEX2T) )
335 #define ISCOLL(rg) ( ((rg)->eType == erotgFLEX) || ((rg)->eType == erotgFLEXT) || ((rg)->eType == erotgFLEX2) || ((rg)->eType == erotgFLEX2T) || ((rg)->eType == erotgRMPF) || ((rg)->eType == erotgRM2PF) )
338 /* Does any of the rotation groups use slab decomposition? */
339 static gmx_bool HaveFlexibleGroups(const t_rot *rot)
341 for (int g = 0; g < rot->ngrp; g++)
343 if (ISFLEX(&rot->grp[g]))
353 /* Is for any group the fit angle determined by finding the minimum of the
354 * rotation potential? */
355 static gmx_bool HavePotFitGroups(const t_rot *rot)
357 for (int g = 0; g < rot->ngrp; g++)
359 if (erotgFitPOT == rot->grp[g].eFittype)
369 static double** allocate_square_matrix(int dim)
372 double** mat = nullptr;
376 for (i = 0; i < dim; i++)
385 static void free_square_matrix(double** mat, int dim)
390 for (i = 0; i < dim; i++)
398 /* Return the angle for which the potential is minimal */
399 static real get_fitangle(const gmx_enfrotgrp *erg)
402 real fitangle = -999.9;
403 real pot_min = GMX_FLOAT_MAX;
407 fit = erg->PotAngleFit;
409 for (i = 0; i < erg->rotg->PotAngle_nstep; i++)
411 if (fit->V[i] < pot_min)
414 fitangle = fit->degangle[i];
422 /* Reduce potential angle fit data for this group at this time step? */
423 static inline gmx_bool bPotAngle(const gmx_enfrot *er, const t_rotgrp *rotg, int64_t step)
425 return ( (erotgFitPOT == rotg->eFittype) && (do_per_step(step, er->nstsout) || do_per_step(step, er->nstrout)) );
428 /* Reduce slab torqe data for this group at this time step? */
429 static inline gmx_bool bSlabTau(const gmx_enfrot *er, const t_rotgrp *rotg, int64_t step)
431 return ( (ISFLEX(rotg)) && do_per_step(step, er->nstsout) );
434 /* Output rotation energy, torques, etc. for each rotation group */
435 static void reduce_output(const t_commrec *cr,
436 gmx_enfrot *er, real t, int64_t step)
438 int i, islab, nslabs = 0;
439 int count; /* MPI element counter */
443 /* Fill the MPI buffer with stuff to reduce. If items are added for reduction
444 * here, the MPI buffer size has to be enlarged also in calc_mpi_bufsize() */
448 for (auto &ergRef : er->enfrotgrp)
450 gmx_enfrotgrp *erg = &ergRef;
451 const t_rotgrp *rotg = erg->rotg;
452 nslabs = erg->slab_last - erg->slab_first + 1;
453 er->mpi_inbuf[count++] = erg->V;
454 er->mpi_inbuf[count++] = erg->torque_v;
455 er->mpi_inbuf[count++] = erg->angle_v;
456 er->mpi_inbuf[count++] = erg->weight_v; /* weights are not needed for flex types, but this is just a single value */
458 if (bPotAngle(er, rotg, step))
460 for (i = 0; i < rotg->PotAngle_nstep; i++)
462 er->mpi_inbuf[count++] = erg->PotAngleFit->V[i];
465 if (bSlabTau(er, rotg, step))
467 for (i = 0; i < nslabs; i++)
469 er->mpi_inbuf[count++] = erg->slab_torque_v[i];
473 if (count > er->mpi_bufsize)
475 gmx_fatal(FARGS, "%s MPI buffer overflow, please report this error.", RotStr);
479 MPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REAL, MPI_SUM, MASTERRANK(cr), cr->mpi_comm_mygroup);
482 /* Copy back the reduced data from the buffer on the master */
486 for (auto &ergRef : er->enfrotgrp)
488 gmx_enfrotgrp *erg = &ergRef;
489 const t_rotgrp *rotg = erg->rotg;
490 nslabs = erg->slab_last - erg->slab_first + 1;
491 erg->V = er->mpi_outbuf[count++];
492 erg->torque_v = er->mpi_outbuf[count++];
493 erg->angle_v = er->mpi_outbuf[count++];
494 erg->weight_v = er->mpi_outbuf[count++];
496 if (bPotAngle(er, rotg, step))
498 for (int i = 0; i < rotg->PotAngle_nstep; i++)
500 erg->PotAngleFit->V[i] = er->mpi_outbuf[count++];
503 if (bSlabTau(er, rotg, step))
505 for (int i = 0; i < nslabs; i++)
507 erg->slab_torque_v[i] = er->mpi_outbuf[count++];
517 /* Angle and torque for each rotation group */
518 for (auto &ergRef : er->enfrotgrp)
520 gmx_enfrotgrp *erg = &ergRef;
521 const t_rotgrp *rotg = erg->rotg;
522 bFlex = ISFLEX(rotg);
524 /* Output to main rotation output file: */
525 if (do_per_step(step, er->nstrout) )
527 if (erotgFitPOT == rotg->eFittype)
529 fitangle = get_fitangle(erg);
535 fitangle = erg->angle_v; /* RMSD fit angle */
539 fitangle = (erg->angle_v/erg->weight_v)*180.0*M_1_PI;
542 fprintf(er->out_rot, "%12.4f", fitangle);
543 fprintf(er->out_rot, "%12.3e", erg->torque_v);
544 fprintf(er->out_rot, "%12.3e", erg->V);
547 if (do_per_step(step, er->nstsout) )
549 /* Output to torque log file: */
552 fprintf(er->out_torque, "%12.3e%6d", t, erg->groupIndex);
553 for (int i = erg->slab_first; i <= erg->slab_last; i++)
555 islab = i - erg->slab_first; /* slab index */
556 /* Only output if enough weight is in slab */
557 if (erg->slab_weights[islab] > rotg->min_gaussian)
559 fprintf(er->out_torque, "%6d%12.3e", i, erg->slab_torque_v[islab]);
562 fprintf(er->out_torque, "\n");
565 /* Output to angles log file: */
566 if (erotgFitPOT == rotg->eFittype)
568 fprintf(er->out_angles, "%12.3e%6d%12.4f", t, erg->groupIndex, erg->degangle);
569 /* Output energies at a set of angles around the reference angle */
570 for (int i = 0; i < rotg->PotAngle_nstep; i++)
572 fprintf(er->out_angles, "%12.3e", erg->PotAngleFit->V[i]);
574 fprintf(er->out_angles, "\n");
578 if (do_per_step(step, er->nstrout) )
580 fprintf(er->out_rot, "\n");
586 /* Add the forces from enforced rotation potential to the local forces.
587 * Should be called after the SR forces have been evaluated */
588 real add_rot_forces(gmx_enfrot *er,
589 rvec f[], const t_commrec *cr, int64_t step, real t)
591 real Vrot = 0.0; /* If more than one rotation group is present, Vrot
592 assembles the local parts from all groups */
594 /* Loop over enforced rotation groups (usually 1, though)
595 * Apply the forces from rotation potentials */
596 for (auto &ergRef : er->enfrotgrp)
598 gmx_enfrotgrp *erg = &ergRef;
599 Vrot += erg->V; /* add the local parts from the nodes */
600 const auto &localRotationGroupIndex = erg->atomSet->localIndex();
601 for (gmx::index l = 0; l < localRotationGroupIndex.ssize(); l++)
603 /* Get the right index of the local force */
604 int ii = localRotationGroupIndex[l];
606 rvec_inc(f[ii], erg->f_rot_loc[l]);
610 /* Reduce energy,torque, angles etc. to get the sum values (per rotation group)
611 * on the master and output these values to file. */
612 if ( (do_per_step(step, er->nstrout) || do_per_step(step, er->nstsout)) && er->bOut)
614 reduce_output(cr, er, t, step);
617 /* When appending, er->bOut is FALSE the first time to avoid duplicate entries */
626 /* The Gaussian norm is chosen such that the sum of the gaussian functions
627 * over the slabs is approximately 1.0 everywhere */
628 #define GAUSS_NORM 0.569917543430618
631 /* Calculate the maximum beta that leads to a gaussian larger min_gaussian,
632 * also does some checks
634 static double calc_beta_max(real min_gaussian, real slab_dist)
640 /* Actually the next two checks are already made in grompp */
643 gmx_fatal(FARGS, "Slab distance of flexible rotation groups must be >=0 !");
645 if (min_gaussian <= 0)
647 gmx_fatal(FARGS, "Cutoff value for Gaussian must be > 0. (You requested %f)", min_gaussian);
650 /* Define the sigma value */
651 sigma = 0.7*slab_dist;
653 /* Calculate the argument for the logarithm and check that the log() result is negative or 0 */
654 arg = min_gaussian/GAUSS_NORM;
657 gmx_fatal(FARGS, "min_gaussian of flexible rotation groups must be <%g", GAUSS_NORM);
660 return std::sqrt(-2.0*sigma*sigma*log(min_gaussian/GAUSS_NORM));
664 static inline real calc_beta(rvec curr_x, const gmx_enfrotgrp *erg, int n)
666 return iprod(curr_x, erg->vec) - erg->rotg->slab_dist * n;
670 static inline real gaussian_weight(rvec curr_x, const gmx_enfrotgrp *erg, int n)
672 const real norm = GAUSS_NORM;
676 /* Define the sigma value */
677 sigma = 0.7*erg->rotg->slab_dist;
678 /* Calculate the Gaussian value of slab n for position curr_x */
679 return norm * exp( -0.5 * gmx::square( calc_beta(curr_x, erg, n)/sigma ) );
683 /* Returns the weight in a single slab, also calculates the Gaussian- and mass-
684 * weighted sum of positions for that slab */
685 static real get_slab_weight(int j, const gmx_enfrotgrp *erg,
686 rvec xc[], const real mc[], rvec *x_weighted_sum)
688 rvec curr_x; /* The position of an atom */
689 rvec curr_x_weighted; /* The gaussian-weighted position */
690 real gaussian; /* A single gaussian weight */
691 real wgauss; /* gaussian times current mass */
692 real slabweight = 0.0; /* The sum of weights in the slab */
694 clear_rvec(*x_weighted_sum);
696 /* Loop over all atoms in the rotation group */
697 for (int i = 0; i < erg->rotg->nat; i++)
699 copy_rvec(xc[i], curr_x);
700 gaussian = gaussian_weight(curr_x, erg, j);
701 wgauss = gaussian * mc[i];
702 svmul(wgauss, curr_x, curr_x_weighted);
703 rvec_add(*x_weighted_sum, curr_x_weighted, *x_weighted_sum);
704 slabweight += wgauss;
705 } /* END of loop over rotation group atoms */
711 static void get_slab_centers(
712 gmx_enfrotgrp *erg, /* Enforced rotation group working data */
713 rvec *xc, /* The rotation group positions; will
714 typically be enfrotgrp->xc, but at first call
715 it is enfrotgrp->xc_ref */
716 real *mc, /* The masses of the rotation group atoms */
717 real time, /* Used for output only */
718 FILE *out_slabs, /* For outputting center per slab information */
719 gmx_bool bOutStep, /* Is this an output step? */
720 gmx_bool bReference) /* If this routine is called from
721 init_rot_group we need to store
722 the reference slab centers */
724 /* Loop over slabs */
725 for (int j = erg->slab_first; j <= erg->slab_last; j++)
727 int slabIndex = j - erg->slab_first;
728 erg->slab_weights[slabIndex] = get_slab_weight(j, erg, xc, mc, &erg->slab_center[slabIndex]);
730 /* We can do the calculations ONLY if there is weight in the slab! */
731 if (erg->slab_weights[slabIndex] > WEIGHT_MIN)
733 svmul(1.0/erg->slab_weights[slabIndex], erg->slab_center[slabIndex], erg->slab_center[slabIndex]);
737 /* We need to check this here, since we divide through slab_weights
738 * in the flexible low-level routines! */
739 gmx_fatal(FARGS, "Not enough weight in slab %d. Slab center cannot be determined!", j);
742 /* At first time step: save the centers of the reference structure */
745 copy_rvec(erg->slab_center[slabIndex], erg->slab_center_ref[slabIndex]);
747 } /* END of loop over slabs */
749 /* Output on the master */
750 if ( (nullptr != out_slabs) && bOutStep)
752 fprintf(out_slabs, "%12.3e%6d", time, erg->groupIndex);
753 for (int j = erg->slab_first; j <= erg->slab_last; j++)
755 int slabIndex = j - erg->slab_first;
756 fprintf(out_slabs, "%6d%12.3e%12.3e%12.3e",
757 j, erg->slab_center[slabIndex][XX], erg->slab_center[slabIndex][YY], erg->slab_center[slabIndex][ZZ]);
759 fprintf(out_slabs, "\n");
764 static void calc_rotmat(
766 real degangle, /* Angle alpha of rotation at time t in degrees */
767 matrix rotmat) /* Rotation matrix */
769 real radangle; /* Rotation angle in radians */
770 real cosa; /* cosine alpha */
771 real sina; /* sine alpha */
772 real OMcosa; /* 1 - cos(alpha) */
773 real dumxy, dumxz, dumyz; /* save computations */
774 rvec rot_vec; /* Rotate around rot_vec ... */
777 radangle = degangle * M_PI/180.0;
778 copy_rvec(vec, rot_vec );
780 /* Precompute some variables: */
781 cosa = cos(radangle);
782 sina = sin(radangle);
784 dumxy = rot_vec[XX]*rot_vec[YY]*OMcosa;
785 dumxz = rot_vec[XX]*rot_vec[ZZ]*OMcosa;
786 dumyz = rot_vec[YY]*rot_vec[ZZ]*OMcosa;
788 /* Construct the rotation matrix for this rotation group: */
790 rotmat[XX][XX] = cosa + rot_vec[XX]*rot_vec[XX]*OMcosa;
791 rotmat[YY][XX] = dumxy + rot_vec[ZZ]*sina;
792 rotmat[ZZ][XX] = dumxz - rot_vec[YY]*sina;
794 rotmat[XX][YY] = dumxy - rot_vec[ZZ]*sina;
795 rotmat[YY][YY] = cosa + rot_vec[YY]*rot_vec[YY]*OMcosa;
796 rotmat[ZZ][YY] = dumyz + rot_vec[XX]*sina;
798 rotmat[XX][ZZ] = dumxz + rot_vec[YY]*sina;
799 rotmat[YY][ZZ] = dumyz - rot_vec[XX]*sina;
800 rotmat[ZZ][ZZ] = cosa + rot_vec[ZZ]*rot_vec[ZZ]*OMcosa;
805 for (iii = 0; iii < 3; iii++)
807 for (jjj = 0; jjj < 3; jjj++)
809 fprintf(stderr, " %10.8f ", rotmat[iii][jjj]);
811 fprintf(stderr, "\n");
817 /* Calculates torque on the rotation axis tau = position x force */
818 static inline real torque(const rvec rotvec, /* rotation vector; MUST be normalized! */
819 rvec force, /* force */
820 rvec x, /* position of atom on which the force acts */
821 rvec pivot) /* pivot point of rotation axis */
826 /* Subtract offset */
827 rvec_sub(x, pivot, vectmp);
829 /* position x force */
830 cprod(vectmp, force, tau);
832 /* Return the part of the torque which is parallel to the rotation vector */
833 return iprod(tau, rotvec);
837 /* Right-aligned output of value with standard width */
838 static void print_aligned(FILE *fp, char const *str)
840 fprintf(fp, "%12s", str);
844 /* Right-aligned output of value with standard short width */
845 static void print_aligned_short(FILE *fp, char const *str)
847 fprintf(fp, "%6s", str);
851 static FILE *open_output_file(const char *fn, int steps, const char what[])
856 fp = gmx_ffopen(fn, "w");
858 fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n",
859 what, steps, steps > 1 ? "s" : "");
865 /* Open output file for slab center data. Call on master only */
866 static FILE *open_slab_out(const char *fn,
873 fp = gmx_fio_fopen(fn, "a");
877 fp = open_output_file(fn, er->nstsout, "gaussian weighted slab centers");
879 for (auto &ergRef : er->enfrotgrp)
881 gmx_enfrotgrp *erg = &ergRef;
882 if (ISFLEX(erg->rotg))
884 fprintf(fp, "# Rotation group %d (%s), slab distance %f nm, %s.\n",
885 erg->groupIndex, erotg_names[erg->rotg->eType], erg->rotg->slab_dist,
886 erg->rotg->bMassW ? "centers of mass" : "geometrical centers");
890 fprintf(fp, "# Reference centers are listed first (t=-1).\n");
891 fprintf(fp, "# The following columns have the syntax:\n");
893 print_aligned_short(fp, "t");
894 print_aligned_short(fp, "grp");
895 /* Print legend for the first two entries only ... */
896 for (int i = 0; i < 2; i++)
898 print_aligned_short(fp, "slab");
899 print_aligned(fp, "X center");
900 print_aligned(fp, "Y center");
901 print_aligned(fp, "Z center");
903 fprintf(fp, " ...\n");
911 /* Adds 'buf' to 'str' */
912 static void add_to_string(char **str, char *buf)
917 len = strlen(*str) + strlen(buf) + 1;
923 static void add_to_string_aligned(char **str, char *buf)
925 char buf_aligned[STRLEN];
927 sprintf(buf_aligned, "%12s", buf);
928 add_to_string(str, buf_aligned);
932 /* Open output file and print some general information about the rotation groups.
933 * Call on master only */
934 static FILE *open_rot_out(const char *fn,
935 const gmx_output_env_t *oenv,
940 const char **setname;
941 char buf[50], buf2[75];
943 char *LegendStr = nullptr;
944 const t_rot *rot = er->rot;
948 fp = gmx_fio_fopen(fn, "a");
952 fp = xvgropen(fn, "Rotation angles and energy", "Time (ps)", "angles (degrees) and energies (kJ/mol)", oenv);
953 fprintf(fp, "# Output of enforced rotation data is written in intervals of %d time step%s.\n#\n", er->nstrout, er->nstrout > 1 ? "s" : "");
954 fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector v.\n");
955 fprintf(fp, "# To obtain the vectorial torque, multiply tau with the group's rot-vec.\n");
956 fprintf(fp, "# For flexible groups, tau(t,n) from all slabs n have been summed in a single value tau(t) here.\n");
957 fprintf(fp, "# The torques tau(t,n) are found in the rottorque.log (-rt) output file\n");
959 for (int g = 0; g < rot->ngrp; g++)
961 const t_rotgrp *rotg = &rot->grp[g];
962 const gmx_enfrotgrp *erg = &er->enfrotgrp[g];
963 bFlex = ISFLEX(rotg);
966 fprintf(fp, "# ROTATION GROUP %d, potential type '%s':\n", g, erotg_names[rotg->eType]);
967 fprintf(fp, "# rot-massw%d %s\n", g, yesno_names[rotg->bMassW]);
968 fprintf(fp, "# rot-vec%d %12.5e %12.5e %12.5e\n", g, erg->vec[XX], erg->vec[YY], erg->vec[ZZ]);
969 fprintf(fp, "# rot-rate%d %12.5e degrees/ps\n", g, rotg->rate);
970 fprintf(fp, "# rot-k%d %12.5e kJ/(mol*nm^2)\n", g, rotg->k);
971 if (rotg->eType == erotgISO || rotg->eType == erotgPM || rotg->eType == erotgRM || rotg->eType == erotgRM2)
973 fprintf(fp, "# rot-pivot%d %12.5e %12.5e %12.5e nm\n", g, rotg->pivot[XX], rotg->pivot[YY], rotg->pivot[ZZ]);
978 fprintf(fp, "# rot-slab-distance%d %f nm\n", g, rotg->slab_dist);
979 fprintf(fp, "# rot-min-gaussian%d %12.5e\n", g, rotg->min_gaussian);
982 /* Output the centers of the rotation groups for the pivot-free potentials */
983 if ((rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) || (rotg->eType == erotgRMPF) || (rotg->eType == erotgRM2PF
984 || (rotg->eType == erotgFLEXT) || (rotg->eType == erotgFLEX2T)) )
986 fprintf(fp, "# ref. grp. %d center %12.5e %12.5e %12.5e\n", g,
987 erg->xc_ref_center[XX], erg->xc_ref_center[YY], erg->xc_ref_center[ZZ]);
989 fprintf(fp, "# grp. %d init.center %12.5e %12.5e %12.5e\n", g,
990 erg->xc_center[XX], erg->xc_center[YY], erg->xc_center[ZZ]);
993 if ( (rotg->eType == erotgRM2) || (rotg->eType == erotgFLEX2) || (rotg->eType == erotgFLEX2T) )
995 fprintf(fp, "# rot-eps%d %12.5e nm^2\n", g, rotg->eps);
997 if (erotgFitPOT == rotg->eFittype)
1000 fprintf(fp, "# theta_fit%d is determined by first evaluating the potential for %d angles around theta_ref%d.\n",
1001 g, rotg->PotAngle_nstep, g);
1002 fprintf(fp, "# The fit angle is the one with the smallest potential. It is given as the deviation\n");
1003 fprintf(fp, "# from the reference angle, i.e. if theta_ref=X and theta_fit=Y, then the angle with\n");
1004 fprintf(fp, "# minimal value of the potential is X+Y. Angular resolution is %g degrees.\n", rotg->PotAngle_step);
1008 /* Print a nice legend */
1010 LegendStr[0] = '\0';
1011 sprintf(buf, "# %6s", "time");
1012 add_to_string_aligned(&LegendStr, buf);
1015 snew(setname, 4*rot->ngrp);
1017 for (int g = 0; g < rot->ngrp; g++)
1019 sprintf(buf, "theta_ref%d", g);
1020 add_to_string_aligned(&LegendStr, buf);
1022 sprintf(buf2, "%s (degrees)", buf);
1023 setname[nsets] = gmx_strdup(buf2);
1026 for (int g = 0; g < rot->ngrp; g++)
1028 const t_rotgrp *rotg = &rot->grp[g];
1029 bFlex = ISFLEX(rotg);
1031 /* For flexible axis rotation we use RMSD fitting to determine the
1032 * actual angle of the rotation group */
1033 if (bFlex || erotgFitPOT == rotg->eFittype)
1035 sprintf(buf, "theta_fit%d", g);
1039 sprintf(buf, "theta_av%d", g);
1041 add_to_string_aligned(&LegendStr, buf);
1042 sprintf(buf2, "%s (degrees)", buf);
1043 setname[nsets] = gmx_strdup(buf2);
1046 sprintf(buf, "tau%d", g);
1047 add_to_string_aligned(&LegendStr, buf);
1048 sprintf(buf2, "%s (kJ/mol)", buf);
1049 setname[nsets] = gmx_strdup(buf2);
1052 sprintf(buf, "energy%d", g);
1053 add_to_string_aligned(&LegendStr, buf);
1054 sprintf(buf2, "%s (kJ/mol)", buf);
1055 setname[nsets] = gmx_strdup(buf2);
1062 xvgr_legend(fp, nsets, setname, oenv);
1066 fprintf(fp, "#\n# Legend for the following data columns:\n");
1067 fprintf(fp, "%s\n", LegendStr);
1077 /* Call on master only */
1078 static FILE *open_angles_out(const char *fn,
1083 const t_rot *rot = er->rot;
1085 if (er->appendFiles)
1087 fp = gmx_fio_fopen(fn, "a");
1091 /* Open output file and write some information about it's structure: */
1092 fp = open_output_file(fn, er->nstsout, "rotation group angles");
1093 fprintf(fp, "# All angles given in degrees, time in ps.\n");
1094 for (int g = 0; g < rot->ngrp; g++)
1096 const t_rotgrp *rotg = &rot->grp[g];
1097 const gmx_enfrotgrp *erg = &er->enfrotgrp[g];
1099 /* Output for this group happens only if potential type is flexible or
1100 * if fit type is potential! */
1101 if (ISFLEX(rotg) || (erotgFitPOT == rotg->eFittype) )
1105 sprintf(buf, " slab distance %f nm, ", rotg->slab_dist);
1112 fprintf(fp, "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n",
1113 g, erotg_names[rotg->eType], buf, erotg_fitnames[rotg->eFittype]);
1115 /* Special type of fitting using the potential minimum. This is
1116 * done for the whole group only, not for the individual slabs. */
1117 if (erotgFitPOT == rotg->eFittype)
1119 fprintf(fp, "# To obtain theta_fit%d, the potential is evaluated for %d angles around theta_ref%d\n", g, rotg->PotAngle_nstep, g);
1120 fprintf(fp, "# The fit angle in the rotation standard outfile is the one with minimal energy E(theta_fit) [kJ/mol].\n");
1124 fprintf(fp, "# Legend for the group %d data columns:\n", g);
1126 print_aligned_short(fp, "time");
1127 print_aligned_short(fp, "grp");
1128 print_aligned(fp, "theta_ref");
1130 if (erotgFitPOT == rotg->eFittype)
1132 /* Output the set of angles around the reference angle */
1133 for (int i = 0; i < rotg->PotAngle_nstep; i++)
1135 sprintf(buf, "E(%g)", erg->PotAngleFit->degangle[i]);
1136 print_aligned(fp, buf);
1141 /* Output fit angle for each slab */
1142 print_aligned_short(fp, "slab");
1143 print_aligned_short(fp, "atoms");
1144 print_aligned(fp, "theta_fit");
1145 print_aligned_short(fp, "slab");
1146 print_aligned_short(fp, "atoms");
1147 print_aligned(fp, "theta_fit");
1148 fprintf(fp, " ...");
1160 /* Open torque output file and write some information about it's structure.
1161 * Call on master only */
1162 static FILE *open_torque_out(const char *fn,
1166 const t_rot *rot = er->rot;
1168 if (er->appendFiles)
1170 fp = gmx_fio_fopen(fn, "a");
1174 fp = open_output_file(fn, er->nstsout, "torques");
1176 for (int g = 0; g < rot->ngrp; g++)
1178 const t_rotgrp *rotg = &rot->grp[g];
1179 const gmx_enfrotgrp *erg = &er->enfrotgrp[g];
1182 fprintf(fp, "# Rotation group %d (%s), slab distance %f nm.\n", g, erotg_names[rotg->eType], rotg->slab_dist);
1183 fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector.\n");
1184 fprintf(fp, "# To obtain the vectorial torque, multiply tau with\n");
1185 fprintf(fp, "# rot-vec%d %10.3e %10.3e %10.3e\n", g, erg->vec[XX], erg->vec[YY], erg->vec[ZZ]);
1189 fprintf(fp, "# Legend for the following data columns: (tau=torque for that slab):\n");
1191 print_aligned_short(fp, "t");
1192 print_aligned_short(fp, "grp");
1193 print_aligned_short(fp, "slab");
1194 print_aligned(fp, "tau");
1195 print_aligned_short(fp, "slab");
1196 print_aligned(fp, "tau");
1197 fprintf(fp, " ...\n");
1205 static void swap_val(double* vec, int i, int j)
1207 double tmp = vec[j];
1215 static void swap_col(double **mat, int i, int j)
1217 double tmp[3] = {mat[0][j], mat[1][j], mat[2][j]};
1220 mat[0][j] = mat[0][i];
1221 mat[1][j] = mat[1][i];
1222 mat[2][j] = mat[2][i];
1230 /* Eigenvectors are stored in columns of eigen_vec */
1231 static void diagonalize_symmetric(
1239 jacobi(matrix, 3, eigenval, eigen_vec, &n_rot);
1241 /* sort in ascending order */
1242 if (eigenval[0] > eigenval[1])
1244 swap_val(eigenval, 0, 1);
1245 swap_col(eigen_vec, 0, 1);
1247 if (eigenval[1] > eigenval[2])
1249 swap_val(eigenval, 1, 2);
1250 swap_col(eigen_vec, 1, 2);
1252 if (eigenval[0] > eigenval[1])
1254 swap_val(eigenval, 0, 1);
1255 swap_col(eigen_vec, 0, 1);
1260 static void align_with_z(
1261 rvec* s, /* Structure to align */
1266 rvec zet = {0.0, 0.0, 1.0};
1267 rvec rot_axis = {0.0, 0.0, 0.0};
1268 rvec *rotated_str = nullptr;
1274 snew(rotated_str, natoms);
1276 /* Normalize the axis */
1277 ooanorm = 1.0/norm(axis);
1278 svmul(ooanorm, axis, axis);
1280 /* Calculate the angle for the fitting procedure */
1281 cprod(axis, zet, rot_axis);
1282 angle = acos(axis[2]);
1288 /* Calculate the rotation matrix */
1289 calc_rotmat(rot_axis, angle*180.0/M_PI, rotmat);
1291 /* Apply the rotation matrix to s */
1292 for (i = 0; i < natoms; i++)
1294 for (j = 0; j < 3; j++)
1296 for (k = 0; k < 3; k++)
1298 rotated_str[i][j] += rotmat[j][k]*s[i][k];
1303 /* Rewrite the rotated structure to s */
1304 for (i = 0; i < natoms; i++)
1306 for (j = 0; j < 3; j++)
1308 s[i][j] = rotated_str[i][j];
1316 static void calc_correl_matrix(rvec* Xstr, rvec* Ystr, double** Rmat, int natoms)
1321 for (i = 0; i < 3; i++)
1323 for (j = 0; j < 3; j++)
1329 for (i = 0; i < 3; i++)
1331 for (j = 0; j < 3; j++)
1333 for (k = 0; k < natoms; k++)
1335 Rmat[i][j] += Ystr[k][i] * Xstr[k][j];
1342 static void weigh_coords(rvec* str, real* weight, int natoms)
1347 for (i = 0; i < natoms; i++)
1349 for (j = 0; j < 3; j++)
1351 str[i][j] *= std::sqrt(weight[i]);
1357 static real opt_angle_analytic(
1367 rvec *ref_s_1 = nullptr;
1368 rvec *act_s_1 = nullptr;
1370 double **Rmat, **RtR, **eigvec;
1372 double V[3][3], WS[3][3];
1373 double rot_matrix[3][3];
1377 /* Do not change the original coordinates */
1378 snew(ref_s_1, natoms);
1379 snew(act_s_1, natoms);
1380 for (i = 0; i < natoms; i++)
1382 copy_rvec(ref_s[i], ref_s_1[i]);
1383 copy_rvec(act_s[i], act_s_1[i]);
1386 /* Translate the structures to the origin */
1387 shift[XX] = -ref_com[XX];
1388 shift[YY] = -ref_com[YY];
1389 shift[ZZ] = -ref_com[ZZ];
1390 translate_x(ref_s_1, natoms, shift);
1392 shift[XX] = -act_com[XX];
1393 shift[YY] = -act_com[YY];
1394 shift[ZZ] = -act_com[ZZ];
1395 translate_x(act_s_1, natoms, shift);
1397 /* Align rotation axis with z */
1398 align_with_z(ref_s_1, natoms, axis);
1399 align_with_z(act_s_1, natoms, axis);
1401 /* Correlation matrix */
1402 Rmat = allocate_square_matrix(3);
1404 for (i = 0; i < natoms; i++)
1406 ref_s_1[i][2] = 0.0;
1407 act_s_1[i][2] = 0.0;
1410 /* Weight positions with sqrt(weight) */
1411 if (nullptr != weight)
1413 weigh_coords(ref_s_1, weight, natoms);
1414 weigh_coords(act_s_1, weight, natoms);
1417 /* Calculate correlation matrices R=YXt (X=ref_s; Y=act_s) */
1418 calc_correl_matrix(ref_s_1, act_s_1, Rmat, natoms);
1421 RtR = allocate_square_matrix(3);
1422 for (i = 0; i < 3; i++)
1424 for (j = 0; j < 3; j++)
1426 for (k = 0; k < 3; k++)
1428 RtR[i][j] += Rmat[k][i] * Rmat[k][j];
1432 /* Diagonalize RtR */
1434 for (i = 0; i < 3; i++)
1439 diagonalize_symmetric(RtR, eigvec, eigval);
1440 swap_col(eigvec, 0, 1);
1441 swap_col(eigvec, 1, 2);
1442 swap_val(eigval, 0, 1);
1443 swap_val(eigval, 1, 2);
1446 for (i = 0; i < 3; i++)
1448 for (j = 0; j < 3; j++)
1455 for (i = 0; i < 2; i++)
1457 for (j = 0; j < 2; j++)
1459 WS[i][j] = eigvec[i][j] / std::sqrt(eigval[j]);
1463 for (i = 0; i < 3; i++)
1465 for (j = 0; j < 3; j++)
1467 for (k = 0; k < 3; k++)
1469 V[i][j] += Rmat[i][k]*WS[k][j];
1473 free_square_matrix(Rmat, 3);
1475 /* Calculate optimal rotation matrix */
1476 for (i = 0; i < 3; i++)
1478 for (j = 0; j < 3; j++)
1480 rot_matrix[i][j] = 0.0;
1484 for (i = 0; i < 3; i++)
1486 for (j = 0; j < 3; j++)
1488 for (k = 0; k < 3; k++)
1490 rot_matrix[i][j] += eigvec[i][k]*V[j][k];
1494 rot_matrix[2][2] = 1.0;
1496 /* In some cases abs(rot_matrix[0][0]) can be slighly larger
1497 * than unity due to numerical inacurracies. To be able to calculate
1498 * the acos function, we put these values back in range. */
1499 if (rot_matrix[0][0] > 1.0)
1501 rot_matrix[0][0] = 1.0;
1503 else if (rot_matrix[0][0] < -1.0)
1505 rot_matrix[0][0] = -1.0;
1508 /* Determine the optimal rotation angle: */
1509 opt_angle = (-1.0)*acos(rot_matrix[0][0])*180.0/M_PI;
1510 if (rot_matrix[0][1] < 0.0)
1512 opt_angle = (-1.0)*opt_angle;
1515 /* Give back some memory */
1516 free_square_matrix(RtR, 3);
1519 for (i = 0; i < 3; i++)
1525 return static_cast<real>(opt_angle);
1529 /* Determine angle of the group by RMSD fit to the reference */
1530 /* Not parallelized, call this routine only on the master */
1531 static real flex_fit_angle(gmx_enfrotgrp *erg)
1533 rvec *fitcoords = nullptr;
1534 rvec center; /* Center of positions passed to the fit routine */
1535 real fitangle; /* Angle of the rotation group derived by fitting */
1539 /* Get the center of the rotation group.
1540 * Note, again, erg->xc has been sorted in do_flexible */
1541 get_center(erg->xc, erg->mc_sorted, erg->rotg->nat, center);
1543 /* === Determine the optimal fit angle for the rotation group === */
1544 if (erg->rotg->eFittype == erotgFitNORM)
1546 /* Normalize every position to it's reference length */
1547 for (int i = 0; i < erg->rotg->nat; i++)
1549 /* Put the center of the positions into the origin */
1550 rvec_sub(erg->xc[i], center, coord);
1551 /* Determine the scaling factor for the length: */
1552 scal = erg->xc_ref_length[erg->xc_sortind[i]] / norm(coord);
1553 /* Get position, multiply with the scaling factor and save */
1554 svmul(scal, coord, erg->xc_norm[i]);
1556 fitcoords = erg->xc_norm;
1560 fitcoords = erg->xc;
1562 /* From the point of view of the current positions, the reference has rotated
1563 * backwards. Since we output the angle relative to the fixed reference,
1564 * we need the minus sign. */
1565 fitangle = -opt_angle_analytic(erg->xc_ref_sorted, fitcoords, erg->mc_sorted,
1566 erg->rotg->nat, erg->xc_ref_center, center, erg->vec);
1572 /* Determine actual angle of each slab by RMSD fit to the reference */
1573 /* Not parallelized, call this routine only on the master */
1574 static void flex_fit_angle_perslab(
1581 rvec act_center; /* Center of actual positions that are passed to the fit routine */
1582 rvec ref_center; /* Same for the reference positions */
1583 real fitangle; /* Angle of a slab derived from an RMSD fit to
1584 * the reference structure at t=0 */
1586 real OOm_av; /* 1/average_mass of a rotation group atom */
1587 real m_rel; /* Relative mass of a rotation group atom */
1590 /* Average mass of a rotation group atom: */
1591 OOm_av = erg->invmass*erg->rotg->nat;
1593 /**********************************/
1594 /* First collect the data we need */
1595 /**********************************/
1597 /* Collect the data for the individual slabs */
1598 for (int n = erg->slab_first; n <= erg->slab_last; n++)
1600 int slabIndex = n - erg->slab_first; /* slab index */
1601 sd = &(erg->slab_data[slabIndex]);
1602 sd->nat = erg->lastatom[slabIndex]-erg->firstatom[slabIndex]+1;
1605 /* Loop over the relevant atoms in the slab */
1606 for (int l = erg->firstatom[slabIndex]; l <= erg->lastatom[slabIndex]; l++)
1608 /* Current position of this atom: x[ii][XX/YY/ZZ] */
1609 copy_rvec(erg->xc[l], curr_x);
1611 /* The (unrotated) reference position of this atom is copied to ref_x.
1612 * Beware, the xc coords have been sorted in do_flexible */
1613 copy_rvec(erg->xc_ref_sorted[l], ref_x);
1615 /* Save data for doing angular RMSD fit later */
1616 /* Save the current atom position */
1617 copy_rvec(curr_x, sd->x[ind]);
1618 /* Save the corresponding reference position */
1619 copy_rvec(ref_x, sd->ref[ind]);
1621 /* Maybe also mass-weighting was requested. If yes, additionally
1622 * multiply the weights with the relative mass of the atom. If not,
1623 * multiply with unity. */
1624 m_rel = erg->mc_sorted[l]*OOm_av;
1626 /* Save the weight for this atom in this slab */
1627 sd->weight[ind] = gaussian_weight(curr_x, erg, n) * m_rel;
1629 /* Next atom in this slab */
1634 /******************************/
1635 /* Now do the fit calculation */
1636 /******************************/
1638 fprintf(fp, "%12.3e%6d%12.3f", t, erg->groupIndex, degangle);
1640 /* === Now do RMSD fitting for each slab === */
1641 /* We require at least SLAB_MIN_ATOMS in a slab, such that the fit makes sense. */
1642 #define SLAB_MIN_ATOMS 4
1644 for (int n = erg->slab_first; n <= erg->slab_last; n++)
1646 int slabIndex = n - erg->slab_first; /* slab index */
1647 sd = &(erg->slab_data[slabIndex]);
1648 if (sd->nat >= SLAB_MIN_ATOMS)
1650 /* Get the center of the slabs reference and current positions */
1651 get_center(sd->ref, sd->weight, sd->nat, ref_center);
1652 get_center(sd->x, sd->weight, sd->nat, act_center);
1653 if (erg->rotg->eFittype == erotgFitNORM)
1655 /* Normalize every position to it's reference length
1656 * prior to performing the fit */
1657 for (int i = 0; i < sd->nat; i++) /* Center */
1659 rvec_dec(sd->ref[i], ref_center);
1660 rvec_dec(sd->x[i], act_center);
1661 /* Normalize x_i such that it gets the same length as ref_i */
1662 svmul( norm(sd->ref[i])/norm(sd->x[i]), sd->x[i], sd->x[i] );
1664 /* We already subtracted the centers */
1665 clear_rvec(ref_center);
1666 clear_rvec(act_center);
1668 fitangle = -opt_angle_analytic(sd->ref, sd->x, sd->weight, sd->nat,
1669 ref_center, act_center, erg->vec);
1670 fprintf(fp, "%6d%6d%12.3f", n, sd->nat, fitangle);
1675 #undef SLAB_MIN_ATOMS
1679 /* Shift x with is */
1680 static inline void shift_single_coord(const matrix box, rvec x, const ivec is)
1691 x[XX] += tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
1692 x[YY] += ty*box[YY][YY]+tz*box[ZZ][YY];
1693 x[ZZ] += tz*box[ZZ][ZZ];
1697 x[XX] += tx*box[XX][XX];
1698 x[YY] += ty*box[YY][YY];
1699 x[ZZ] += tz*box[ZZ][ZZ];
1704 /* Determine the 'home' slab of this atom which is the
1705 * slab with the highest Gaussian weight of all */
1706 static inline int get_homeslab(
1707 rvec curr_x, /* The position for which the home slab shall be determined */
1708 const rvec rotvec, /* The rotation vector */
1709 real slabdist) /* The slab distance */
1714 /* The distance of the atom to the coordinate center (where the
1715 * slab with index 0) is */
1716 dist = iprod(rotvec, curr_x);
1718 return gmx::roundToInt(dist / slabdist);
1722 /* For a local atom determine the relevant slabs, i.e. slabs in
1723 * which the gaussian is larger than min_gaussian
1725 static int get_single_atom_gaussians(
1730 /* Determine the 'home' slab of this atom: */
1731 int homeslab = get_homeslab(curr_x, erg->vec, erg->rotg->slab_dist);
1733 /* First determine the weight in the atoms home slab: */
1734 real g = gaussian_weight(curr_x, erg, homeslab);
1736 erg->gn_atom[count] = g;
1737 erg->gn_slabind[count] = homeslab;
1741 /* Determine the max slab */
1742 int slab = homeslab;
1743 while (g > erg->rotg->min_gaussian)
1746 g = gaussian_weight(curr_x, erg, slab);
1747 erg->gn_slabind[count] = slab;
1748 erg->gn_atom[count] = g;
1753 /* Determine the min slab */
1758 g = gaussian_weight(curr_x, erg, slab);
1759 erg->gn_slabind[count] = slab;
1760 erg->gn_atom[count] = g;
1763 while (g > erg->rotg->min_gaussian);
1770 static void flex2_precalc_inner_sum(const gmx_enfrotgrp *erg)
1772 rvec xi; /* positions in the i-sum */
1773 rvec xcn, ycn; /* the current and the reference slab centers */
1776 rvec rin; /* Helper variables */
1779 real OOpsii, OOpsiistar;
1780 real sin_rin; /* s_ii.r_ii */
1781 rvec s_in, tmpvec, tmpvec2;
1782 real mi, wi; /* Mass-weighting of the positions */
1786 N_M = erg->rotg->nat * erg->invmass;
1788 /* Loop over all slabs that contain something */
1789 for (int n = erg->slab_first; n <= erg->slab_last; n++)
1791 int slabIndex = n - erg->slab_first; /* slab index */
1793 /* The current center of this slab is saved in xcn: */
1794 copy_rvec(erg->slab_center[slabIndex], xcn);
1795 /* ... and the reference center in ycn: */
1796 copy_rvec(erg->slab_center_ref[slabIndex+erg->slab_buffer], ycn);
1798 /*** D. Calculate the whole inner sum used for second and third sum */
1799 /* For slab n, we need to loop over all atoms i again. Since we sorted
1800 * the atoms with respect to the rotation vector, we know that it is sufficient
1801 * to calculate from firstatom to lastatom only. All other contributions will
1803 clear_rvec(innersumvec);
1804 for (int i = erg->firstatom[slabIndex]; i <= erg->lastatom[slabIndex]; i++)
1806 /* Coordinate xi of this atom */
1807 copy_rvec(erg->xc[i], xi);
1810 gaussian_xi = gaussian_weight(xi, erg, n);
1811 mi = erg->mc_sorted[i]; /* need the sorted mass here */
1815 copy_rvec(erg->xc_ref_sorted[i], yi0); /* Reference position yi0 */
1816 rvec_sub(yi0, ycn, tmpvec2); /* tmpvec2 = yi0 - ycn */
1817 mvmul(erg->rotmat, tmpvec2, rin); /* rin = Omega.(yi0 - ycn) */
1819 /* Calculate psi_i* and sin */
1820 rvec_sub(xi, xcn, tmpvec2); /* tmpvec2 = xi - xcn */
1822 /* In rare cases, when an atom position coincides with a slab center
1823 * (tmpvec2 == 0) we cannot compute the vector product for s_in.
1824 * However, since the atom is located directly on the pivot, this
1825 * slab's contribution to the force on that atom will be zero
1826 * anyway. Therefore, we continue with the next atom. */
1827 if (gmx_numzero(norm(tmpvec2))) /* 0 == norm(xi - xcn) */
1832 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xi - xcn) */
1833 OOpsiistar = norm2(tmpvec)+erg->rotg->eps; /* OOpsii* = 1/psii* = |v x (xi-xcn)|^2 + eps */
1834 OOpsii = norm(tmpvec); /* OOpsii = 1 / psii = |v x (xi - xcn)| */
1836 /* * v x (xi - xcn) */
1837 unitv(tmpvec, s_in); /* sin = ---------------- */
1838 /* |v x (xi - xcn)| */
1840 sin_rin = iprod(s_in, rin); /* sin_rin = sin . rin */
1842 /* Now the whole sum */
1843 fac = OOpsii/OOpsiistar;
1844 svmul(fac, rin, tmpvec);
1845 fac2 = fac*fac*OOpsii;
1846 svmul(fac2*sin_rin, s_in, tmpvec2);
1847 rvec_dec(tmpvec, tmpvec2);
1849 svmul(wi*gaussian_xi*sin_rin, tmpvec, tmpvec2);
1851 rvec_inc(innersumvec, tmpvec2);
1852 } /* now we have the inner sum, used both for sum2 and sum3 */
1854 /* Save it to be used in do_flex2_lowlevel */
1855 copy_rvec(innersumvec, erg->slab_innersumvec[slabIndex]);
1856 } /* END of loop over slabs */
1860 static void flex_precalc_inner_sum(const gmx_enfrotgrp *erg)
1862 rvec xi; /* position */
1863 rvec xcn, ycn; /* the current and the reference slab centers */
1864 rvec qin, rin; /* q_i^n and r_i^n */
1867 rvec innersumvec; /* Inner part of sum_n2 */
1868 real gaussian_xi; /* Gaussian weight gn(xi) */
1869 real mi, wi; /* Mass-weighting of the positions */
1872 N_M = erg->rotg->nat * erg->invmass;
1874 /* Loop over all slabs that contain something */
1875 for (int n = erg->slab_first; n <= erg->slab_last; n++)
1877 int slabIndex = n - erg->slab_first; /* slab index */
1879 /* The current center of this slab is saved in xcn: */
1880 copy_rvec(erg->slab_center[slabIndex], xcn);
1881 /* ... and the reference center in ycn: */
1882 copy_rvec(erg->slab_center_ref[slabIndex+erg->slab_buffer], ycn);
1884 /* For slab n, we need to loop over all atoms i again. Since we sorted
1885 * the atoms with respect to the rotation vector, we know that it is sufficient
1886 * to calculate from firstatom to lastatom only. All other contributions will
1888 clear_rvec(innersumvec);
1889 for (int i = erg->firstatom[slabIndex]; i <= erg->lastatom[slabIndex]; i++)
1891 /* Coordinate xi of this atom */
1892 copy_rvec(erg->xc[i], xi);
1895 gaussian_xi = gaussian_weight(xi, erg, n);
1896 mi = erg->mc_sorted[i]; /* need the sorted mass here */
1899 /* Calculate rin and qin */
1900 rvec_sub(erg->xc_ref_sorted[i], ycn, tmpvec); /* tmpvec = yi0-ycn */
1902 /* In rare cases, when an atom position coincides with a slab center
1903 * (tmpvec == 0) we cannot compute the vector product for qin.
1904 * However, since the atom is located directly on the pivot, this
1905 * slab's contribution to the force on that atom will be zero
1906 * anyway. Therefore, we continue with the next atom. */
1907 if (gmx_numzero(norm(tmpvec))) /* 0 == norm(yi0 - ycn) */
1912 mvmul(erg->rotmat, tmpvec, rin); /* rin = Omega.(yi0 - ycn) */
1913 cprod(erg->vec, rin, tmpvec); /* tmpvec = v x Omega*(yi0-ycn) */
1915 /* * v x Omega*(yi0-ycn) */
1916 unitv(tmpvec, qin); /* qin = --------------------- */
1917 /* |v x Omega*(yi0-ycn)| */
1920 rvec_sub(xi, xcn, tmpvec); /* tmpvec = xi-xcn */
1921 bin = iprod(qin, tmpvec); /* bin = qin*(xi-xcn) */
1923 svmul(wi*gaussian_xi*bin, qin, tmpvec);
1925 /* Add this contribution to the inner sum: */
1926 rvec_add(innersumvec, tmpvec, innersumvec);
1927 } /* now we have the inner sum vector S^n for this slab */
1928 /* Save it to be used in do_flex_lowlevel */
1929 copy_rvec(innersumvec, erg->slab_innersumvec[slabIndex]);
1934 static real do_flex2_lowlevel(
1936 real sigma, /* The Gaussian width sigma */
1938 gmx_bool bOutstepRot,
1939 gmx_bool bOutstepSlab,
1942 int count, ii, iigrp;
1943 rvec xj; /* position in the i-sum */
1944 rvec yj0; /* the reference position in the j-sum */
1945 rvec xcn, ycn; /* the current and the reference slab centers */
1946 real V; /* This node's part of the rotation pot. energy */
1947 real gaussian_xj; /* Gaussian weight */
1950 real numerator, fit_numerator;
1951 rvec rjn, fit_rjn; /* Helper variables */
1954 real OOpsij, OOpsijstar;
1955 real OOsigma2; /* 1/(sigma^2) */
1958 rvec sjn, tmpvec, tmpvec2, yj0_ycn;
1959 rvec sum1vec_part, sum1vec, sum2vec_part, sum2vec, sum3vec, sum4vec, innersumvec;
1961 real mj, wj; /* Mass-weighting of the positions */
1963 real Wjn; /* g_n(x_j) m_j / Mjn */
1964 gmx_bool bCalcPotFit;
1966 /* To calculate the torque per slab */
1967 rvec slab_force; /* Single force from slab n on one atom */
1968 rvec slab_sum1vec_part;
1969 real slab_sum3part, slab_sum4part;
1970 rvec slab_sum1vec, slab_sum2vec, slab_sum3vec, slab_sum4vec;
1972 /* Pre-calculate the inner sums, so that we do not have to calculate
1973 * them again for every atom */
1974 flex2_precalc_inner_sum(erg);
1976 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
1978 /********************************************************/
1979 /* Main loop over all local atoms of the rotation group */
1980 /********************************************************/
1981 N_M = erg->rotg->nat * erg->invmass;
1983 OOsigma2 = 1.0 / (sigma*sigma);
1984 const auto &localRotationGroupIndex = erg->atomSet->localIndex();
1985 const auto &collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
1987 for (gmx::index j = 0; j < localRotationGroupIndex.ssize(); j++)
1989 /* Local index of a rotation group atom */
1990 ii = localRotationGroupIndex[j];
1991 /* Position of this atom in the collective array */
1992 iigrp = collectiveRotationGroupIndex[j];
1993 /* Mass-weighting */
1994 mj = erg->mc[iigrp]; /* need the unsorted mass here */
1997 /* Current position of this atom: x[ii][XX/YY/ZZ]
1998 * Note that erg->xc_center contains the center of mass in case the flex2-t
1999 * potential was chosen. For the flex2 potential erg->xc_center must be
2001 rvec_sub(x[ii], erg->xc_center, xj);
2003 /* Shift this atom such that it is near its reference */
2004 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2006 /* Determine the slabs to loop over, i.e. the ones with contributions
2007 * larger than min_gaussian */
2008 count = get_single_atom_gaussians(xj, erg);
2010 clear_rvec(sum1vec_part);
2011 clear_rvec(sum2vec_part);
2014 /* Loop over the relevant slabs for this atom */
2015 for (int ic = 0; ic < count; ic++)
2017 int n = erg->gn_slabind[ic];
2019 /* Get the precomputed Gaussian value of curr_slab for curr_x */
2020 gaussian_xj = erg->gn_atom[ic];
2022 int slabIndex = n - erg->slab_first; /* slab index */
2024 /* The (unrotated) reference position of this atom is copied to yj0: */
2025 copy_rvec(erg->rotg->x_ref[iigrp], yj0);
2027 beta = calc_beta(xj, erg, n);
2029 /* The current center of this slab is saved in xcn: */
2030 copy_rvec(erg->slab_center[slabIndex], xcn);
2031 /* ... and the reference center in ycn: */
2032 copy_rvec(erg->slab_center_ref[slabIndex+erg->slab_buffer], ycn);
2034 rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
2037 mvmul(erg->rotmat, yj0_ycn, rjn); /* rjn = Omega.(yj0 - ycn) */
2039 /* Subtract the slab center from xj */
2040 rvec_sub(xj, xcn, tmpvec2); /* tmpvec2 = xj - xcn */
2042 /* In rare cases, when an atom position coincides with a slab center
2043 * (tmpvec2 == 0) we cannot compute the vector product for sjn.
2044 * However, since the atom is located directly on the pivot, this
2045 * slab's contribution to the force on that atom will be zero
2046 * anyway. Therefore, we directly move on to the next slab. */
2047 if (gmx_numzero(norm(tmpvec2))) /* 0 == norm(xj - xcn) */
2053 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xj - xcn) */
2055 OOpsijstar = norm2(tmpvec)+erg->rotg->eps; /* OOpsij* = 1/psij* = |v x (xj-xcn)|^2 + eps */
2057 numerator = gmx::square(iprod(tmpvec, rjn));
2059 /*********************************/
2060 /* Add to the rotation potential */
2061 /*********************************/
2062 V += 0.5*erg->rotg->k*wj*gaussian_xj*numerator/OOpsijstar;
2064 /* If requested, also calculate the potential for a set of angles
2065 * near the current reference angle */
2068 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2070 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, fit_rjn);
2071 fit_numerator = gmx::square(iprod(tmpvec, fit_rjn));
2072 erg->PotAngleFit->V[ifit] += 0.5*erg->rotg->k*wj*gaussian_xj*fit_numerator/OOpsijstar;
2076 /*************************************/
2077 /* Now calculate the force on atom j */
2078 /*************************************/
2080 OOpsij = norm(tmpvec); /* OOpsij = 1 / psij = |v x (xj - xcn)| */
2082 /* * v x (xj - xcn) */
2083 unitv(tmpvec, sjn); /* sjn = ---------------- */
2084 /* |v x (xj - xcn)| */
2086 sjn_rjn = iprod(sjn, rjn); /* sjn_rjn = sjn . rjn */
2089 /*** A. Calculate the first of the four sum terms: ****************/
2090 fac = OOpsij/OOpsijstar;
2091 svmul(fac, rjn, tmpvec);
2092 fac2 = fac*fac*OOpsij;
2093 svmul(fac2*sjn_rjn, sjn, tmpvec2);
2094 rvec_dec(tmpvec, tmpvec2);
2095 fac2 = wj*gaussian_xj; /* also needed for sum4 */
2096 svmul(fac2*sjn_rjn, tmpvec, slab_sum1vec_part);
2097 /********************/
2098 /*** Add to sum1: ***/
2099 /********************/
2100 rvec_inc(sum1vec_part, slab_sum1vec_part); /* sum1 still needs to vector multiplied with v */
2102 /*** B. Calculate the forth of the four sum terms: ****************/
2103 betasigpsi = beta*OOsigma2*OOpsij; /* this is also needed for sum3 */
2104 /********************/
2105 /*** Add to sum4: ***/
2106 /********************/
2107 slab_sum4part = fac2*betasigpsi*fac*sjn_rjn*sjn_rjn; /* Note that fac is still valid from above */
2108 sum4 += slab_sum4part;
2110 /*** C. Calculate Wjn for second and third sum */
2111 /* Note that we can safely divide by slab_weights since we check in
2112 * get_slab_centers that it is non-zero. */
2113 Wjn = gaussian_xj*mj/erg->slab_weights[slabIndex];
2115 /* We already have precalculated the inner sum for slab n */
2116 copy_rvec(erg->slab_innersumvec[slabIndex], innersumvec);
2118 /* Weigh the inner sum vector with Wjn */
2119 svmul(Wjn, innersumvec, innersumvec);
2121 /*** E. Calculate the second of the four sum terms: */
2122 /********************/
2123 /*** Add to sum2: ***/
2124 /********************/
2125 rvec_inc(sum2vec_part, innersumvec); /* sum2 still needs to be vector crossproduct'ed with v */
2127 /*** F. Calculate the third of the four sum terms: */
2128 slab_sum3part = betasigpsi * iprod(sjn, innersumvec);
2129 sum3 += slab_sum3part; /* still needs to be multiplied with v */
2131 /*** G. Calculate the torque on the local slab's axis: */
2135 cprod(slab_sum1vec_part, erg->vec, slab_sum1vec);
2137 cprod(innersumvec, erg->vec, slab_sum2vec);
2139 svmul(slab_sum3part, erg->vec, slab_sum3vec);
2141 svmul(slab_sum4part, erg->vec, slab_sum4vec);
2143 /* The force on atom ii from slab n only: */
2144 for (int m = 0; m < DIM; m++)
2146 slab_force[m] = erg->rotg->k * (-slab_sum1vec[m] + slab_sum2vec[m] - slab_sum3vec[m] + 0.5*slab_sum4vec[m]);
2149 erg->slab_torque_v[slabIndex] += torque(erg->vec, slab_force, xj, xcn);
2151 } /* END of loop over slabs */
2153 /* Construct the four individual parts of the vector sum: */
2154 cprod(sum1vec_part, erg->vec, sum1vec); /* sum1vec = { } x v */
2155 cprod(sum2vec_part, erg->vec, sum2vec); /* sum2vec = { } x v */
2156 svmul(sum3, erg->vec, sum3vec); /* sum3vec = { } . v */
2157 svmul(sum4, erg->vec, sum4vec); /* sum4vec = { } . v */
2159 /* Store the additional force so that it can be added to the force
2160 * array after the normal forces have been evaluated */
2161 for (int m = 0; m < DIM; m++)
2163 erg->f_rot_loc[j][m] = erg->rotg->k * (-sum1vec[m] + sum2vec[m] - sum3vec[m] + 0.5*sum4vec[m]);
2167 fprintf(stderr, "sum1: %15.8f %15.8f %15.8f\n", -erg->rotg->k*sum1vec[XX], -erg->rotg->k*sum1vec[YY], -erg->rotg->k*sum1vec[ZZ]);
2168 fprintf(stderr, "sum2: %15.8f %15.8f %15.8f\n", erg->rotg->k*sum2vec[XX], erg->rotg->k*sum2vec[YY], erg->rotg->k*sum2vec[ZZ]);
2169 fprintf(stderr, "sum3: %15.8f %15.8f %15.8f\n", -erg->rotg->k*sum3vec[XX], -erg->rotg->k*sum3vec[YY], -erg->rotg->k*sum3vec[ZZ]);
2170 fprintf(stderr, "sum4: %15.8f %15.8f %15.8f\n", 0.5*erg->rotg->k*sum4vec[XX], 0.5*erg->rotg->k*sum4vec[YY], 0.5*erg->rotg->k*sum4vec[ZZ]);
2175 } /* END of loop over local atoms */
2181 static real do_flex_lowlevel(
2183 real sigma, /* The Gaussian width sigma */
2185 gmx_bool bOutstepRot,
2186 gmx_bool bOutstepSlab,
2190 rvec xj, yj0; /* current and reference position */
2191 rvec xcn, ycn; /* the current and the reference slab centers */
2192 rvec yj0_ycn; /* yj0 - ycn */
2193 rvec xj_xcn; /* xj - xcn */
2194 rvec qjn, fit_qjn; /* q_i^n */
2195 rvec sum_n1, sum_n2; /* Two contributions to the rotation force */
2196 rvec innersumvec; /* Inner part of sum_n2 */
2198 rvec force_n; /* Single force from slab n on one atom */
2199 rvec force_n1, force_n2; /* First and second part of force_n */
2200 rvec tmpvec, tmpvec2, tmp_f; /* Helper variables */
2201 real V; /* The rotation potential energy */
2202 real OOsigma2; /* 1/(sigma^2) */
2203 real beta; /* beta_n(xj) */
2204 real bjn, fit_bjn; /* b_j^n */
2205 real gaussian_xj; /* Gaussian weight gn(xj) */
2206 real betan_xj_sigma2;
2207 real mj, wj; /* Mass-weighting of the positions */
2209 gmx_bool bCalcPotFit;
2211 /* Pre-calculate the inner sums, so that we do not have to calculate
2212 * them again for every atom */
2213 flex_precalc_inner_sum(erg);
2215 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2217 /********************************************************/
2218 /* Main loop over all local atoms of the rotation group */
2219 /********************************************************/
2220 OOsigma2 = 1.0/(sigma*sigma);
2221 N_M = erg->rotg->nat * erg->invmass;
2223 const auto &localRotationGroupIndex = erg->atomSet->localIndex();
2224 const auto &collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2226 for (gmx::index j = 0; j < localRotationGroupIndex.ssize(); j++)
2228 /* Local index of a rotation group atom */
2229 int ii = localRotationGroupIndex[j];
2230 /* Position of this atom in the collective array */
2231 iigrp = collectiveRotationGroupIndex[j];
2232 /* Mass-weighting */
2233 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2236 /* Current position of this atom: x[ii][XX/YY/ZZ]
2237 * Note that erg->xc_center contains the center of mass in case the flex-t
2238 * potential was chosen. For the flex potential erg->xc_center must be
2240 rvec_sub(x[ii], erg->xc_center, xj);
2242 /* Shift this atom such that it is near its reference */
2243 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2245 /* Determine the slabs to loop over, i.e. the ones with contributions
2246 * larger than min_gaussian */
2247 count = get_single_atom_gaussians(xj, erg);
2252 /* Loop over the relevant slabs for this atom */
2253 for (int ic = 0; ic < count; ic++)
2255 int n = erg->gn_slabind[ic];
2257 /* Get the precomputed Gaussian for xj in slab n */
2258 gaussian_xj = erg->gn_atom[ic];
2260 int slabIndex = n - erg->slab_first; /* slab index */
2262 /* The (unrotated) reference position of this atom is saved in yj0: */
2263 copy_rvec(erg->rotg->x_ref[iigrp], yj0);
2265 beta = calc_beta(xj, erg, n);
2267 /* The current center of this slab is saved in xcn: */
2268 copy_rvec(erg->slab_center[slabIndex], xcn);
2269 /* ... and the reference center in ycn: */
2270 copy_rvec(erg->slab_center_ref[slabIndex+erg->slab_buffer], ycn);
2272 rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
2274 /* In rare cases, when an atom position coincides with a reference slab
2275 * center (yj0_ycn == 0) we cannot compute the normal vector qjn.
2276 * However, since the atom is located directly on the pivot, this
2277 * slab's contribution to the force on that atom will be zero
2278 * anyway. Therefore, we directly move on to the next slab. */
2279 if (gmx_numzero(norm(yj0_ycn))) /* 0 == norm(yj0 - ycn) */
2285 mvmul(erg->rotmat, yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2287 /* Subtract the slab center from xj */
2288 rvec_sub(xj, xcn, xj_xcn); /* xj_xcn = xj - xcn */
2291 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2293 /* * v x Omega.(yj0-ycn) */
2294 unitv(tmpvec, qjn); /* qjn = --------------------- */
2295 /* |v x Omega.(yj0-ycn)| */
2297 bjn = iprod(qjn, xj_xcn); /* bjn = qjn * (xj - xcn) */
2299 /*********************************/
2300 /* Add to the rotation potential */
2301 /*********************************/
2302 V += 0.5*erg->rotg->k*wj*gaussian_xj*gmx::square(bjn);
2304 /* If requested, also calculate the potential for a set of angles
2305 * near the current reference angle */
2308 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2310 /* As above calculate Omega.(yj0-ycn), now for the other angles */
2311 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2312 /* As above calculate qjn */
2313 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2314 /* * v x Omega.(yj0-ycn) */
2315 unitv(tmpvec, fit_qjn); /* fit_qjn = --------------------- */
2316 /* |v x Omega.(yj0-ycn)| */
2317 fit_bjn = iprod(fit_qjn, xj_xcn); /* fit_bjn = fit_qjn * (xj - xcn) */
2318 /* Add to the rotation potential for this angle */
2319 erg->PotAngleFit->V[ifit] += 0.5*erg->rotg->k*wj*gaussian_xj*gmx::square(fit_bjn);
2323 /****************************************************************/
2324 /* sum_n1 will typically be the main contribution to the force: */
2325 /****************************************************************/
2326 betan_xj_sigma2 = beta*OOsigma2; /* beta_n(xj)/sigma^2 */
2328 /* The next lines calculate
2329 * qjn - (bjn*beta(xj)/(2sigma^2))v */
2330 svmul(bjn*0.5*betan_xj_sigma2, erg->vec, tmpvec2);
2331 rvec_sub(qjn, tmpvec2, tmpvec);
2333 /* Multiply with gn(xj)*bjn: */
2334 svmul(gaussian_xj*bjn, tmpvec, tmpvec2);
2337 rvec_inc(sum_n1, tmpvec2);
2339 /* We already have precalculated the Sn term for slab n */
2340 copy_rvec(erg->slab_innersumvec[slabIndex], s_n);
2342 svmul(betan_xj_sigma2*iprod(s_n, xj_xcn), erg->vec, tmpvec); /* tmpvec = ---------- s_n (xj-xcn) */
2345 rvec_sub(s_n, tmpvec, innersumvec);
2347 /* We can safely divide by slab_weights since we check in get_slab_centers
2348 * that it is non-zero. */
2349 svmul(gaussian_xj/erg->slab_weights[slabIndex], innersumvec, innersumvec);
2351 rvec_add(sum_n2, innersumvec, sum_n2);
2353 /* Calculate the torque: */
2356 /* The force on atom ii from slab n only: */
2357 svmul(-erg->rotg->k*wj, tmpvec2, force_n1); /* part 1 */
2358 svmul( erg->rotg->k*mj, innersumvec, force_n2); /* part 2 */
2359 rvec_add(force_n1, force_n2, force_n);
2360 erg->slab_torque_v[slabIndex] += torque(erg->vec, force_n, xj, xcn);
2362 } /* END of loop over slabs */
2364 /* Put both contributions together: */
2365 svmul(wj, sum_n1, sum_n1);
2366 svmul(mj, sum_n2, sum_n2);
2367 rvec_sub(sum_n2, sum_n1, tmp_f); /* F = -grad V */
2369 /* Store the additional force so that it can be added to the force
2370 * array after the normal forces have been evaluated */
2371 for (int m = 0; m < DIM; m++)
2373 erg->f_rot_loc[j][m] = erg->rotg->k*tmp_f[m];
2378 } /* END of loop over local atoms */
2383 static void sort_collective_coordinates(
2385 sort_along_vec_t *data) /* Buffer for sorting the positions */
2387 /* The projection of the position vector on the rotation vector is
2388 * the relevant value for sorting. Fill the 'data' structure */
2389 for (int i = 0; i < erg->rotg->nat; i++)
2391 data[i].xcproj = iprod(erg->xc[i], erg->vec); /* sort criterium */
2392 data[i].m = erg->mc[i];
2394 copy_rvec(erg->xc[i], data[i].x );
2395 copy_rvec(erg->rotg->x_ref[i], data[i].x_ref);
2397 /* Sort the 'data' structure */
2398 std::sort(data, data+erg->rotg->nat,
2399 [](const sort_along_vec_t &a, const sort_along_vec_t &b)
2401 return a.xcproj < b.xcproj;
2404 /* Copy back the sorted values */
2405 for (int i = 0; i < erg->rotg->nat; i++)
2407 copy_rvec(data[i].x, erg->xc[i] );
2408 copy_rvec(data[i].x_ref, erg->xc_ref_sorted[i]);
2409 erg->mc_sorted[i] = data[i].m;
2410 erg->xc_sortind[i] = data[i].ind;
2415 /* For each slab, get the first and the last index of the sorted atom
2417 static void get_firstlast_atom_per_slab(const gmx_enfrotgrp *erg)
2421 /* Find the first atom that needs to enter the calculation for each slab */
2422 int n = erg->slab_first; /* slab */
2423 int i = 0; /* start with the first atom */
2426 /* Find the first atom that significantly contributes to this slab */
2427 do /* move forward in position until a large enough beta is found */
2429 beta = calc_beta(erg->xc[i], erg, n);
2432 while ((beta < -erg->max_beta) && (i < erg->rotg->nat));
2434 int slabIndex = n - erg->slab_first; /* slab index */
2435 erg->firstatom[slabIndex] = i;
2436 /* Proceed to the next slab */
2439 while (n <= erg->slab_last);
2441 /* Find the last atom for each slab */
2442 n = erg->slab_last; /* start with last slab */
2443 i = erg->rotg->nat-1; /* start with the last atom */
2446 do /* move backward in position until a large enough beta is found */
2448 beta = calc_beta(erg->xc[i], erg, n);
2451 while ((beta > erg->max_beta) && (i > -1));
2453 int slabIndex = n - erg->slab_first; /* slab index */
2454 erg->lastatom[slabIndex] = i;
2455 /* Proceed to the next slab */
2458 while (n >= erg->slab_first);
2462 /* Determine the very first and very last slab that needs to be considered
2463 * For the first slab that needs to be considered, we have to find the smallest
2466 * x_first * v - n*Delta_x <= beta_max
2468 * slab index n, slab distance Delta_x, rotation vector v. For the last slab we
2469 * have to find the largest n that obeys
2471 * x_last * v - n*Delta_x >= -beta_max
2474 static inline int get_first_slab(
2475 const gmx_enfrotgrp *erg,
2476 rvec firstatom) /* First atom after sorting along the rotation vector v */
2478 /* Find the first slab for the first atom */
2479 return static_cast<int>(ceil(static_cast<double>((iprod(firstatom, erg->vec) - erg->max_beta)/erg->rotg->slab_dist)));
2483 static inline int get_last_slab(
2484 const gmx_enfrotgrp *erg,
2485 rvec lastatom) /* Last atom along v */
2487 /* Find the last slab for the last atom */
2488 return static_cast<int>(floor(static_cast<double>((iprod(lastatom, erg->vec) + erg->max_beta)/erg->rotg->slab_dist)));
2492 static void get_firstlast_slab_check(
2493 gmx_enfrotgrp *erg, /* The rotation group (data only accessible in this file) */
2494 rvec firstatom, /* First atom after sorting along the rotation vector v */
2495 rvec lastatom) /* Last atom along v */
2497 erg->slab_first = get_first_slab(erg, firstatom);
2498 erg->slab_last = get_last_slab(erg, lastatom);
2500 /* Calculate the slab buffer size, which changes when slab_first changes */
2501 erg->slab_buffer = erg->slab_first - erg->slab_first_ref;
2503 /* Check whether we have reference data to compare against */
2504 if (erg->slab_first < erg->slab_first_ref)
2506 gmx_fatal(FARGS, "%s No reference data for first slab (n=%d), unable to proceed.",
2507 RotStr, erg->slab_first);
2510 /* Check whether we have reference data to compare against */
2511 if (erg->slab_last > erg->slab_last_ref)
2513 gmx_fatal(FARGS, "%s No reference data for last slab (n=%d), unable to proceed.",
2514 RotStr, erg->slab_last);
2519 /* Enforced rotation with a flexible axis */
2520 static void do_flexible(
2522 gmx_enfrot *enfrot, /* Other rotation data */
2524 rvec x[], /* The local positions */
2526 double t, /* Time in picoseconds */
2527 gmx_bool bOutstepRot, /* Output to main rotation output file */
2528 gmx_bool bOutstepSlab) /* Output per-slab data */
2531 real sigma; /* The Gaussian width sigma */
2533 /* Define the sigma value */
2534 sigma = 0.7*erg->rotg->slab_dist;
2536 /* Sort the collective coordinates erg->xc along the rotation vector. This is
2537 * an optimization for the inner loop. */
2538 sort_collective_coordinates(erg, enfrot->data);
2540 /* Determine the first relevant slab for the first atom and the last
2541 * relevant slab for the last atom */
2542 get_firstlast_slab_check(erg, erg->xc[0], erg->xc[erg->rotg->nat-1]);
2544 /* Determine for each slab depending on the min_gaussian cutoff criterium,
2545 * a first and a last atom index inbetween stuff needs to be calculated */
2546 get_firstlast_atom_per_slab(erg);
2548 /* Determine the gaussian-weighted center of positions for all slabs */
2549 get_slab_centers(erg, erg->xc, erg->mc_sorted, t, enfrot->out_slabs, bOutstepSlab, FALSE);
2551 /* Clear the torque per slab from last time step: */
2552 nslabs = erg->slab_last - erg->slab_first + 1;
2553 for (int l = 0; l < nslabs; l++)
2555 erg->slab_torque_v[l] = 0.0;
2558 /* Call the rotational forces kernel */
2559 if (erg->rotg->eType == erotgFLEX || erg->rotg->eType == erotgFLEXT)
2561 erg->V = do_flex_lowlevel(erg, sigma, x, bOutstepRot, bOutstepSlab, box);
2563 else if (erg->rotg->eType == erotgFLEX2 || erg->rotg->eType == erotgFLEX2T)
2565 erg->V = do_flex2_lowlevel(erg, sigma, x, bOutstepRot, bOutstepSlab, box);
2569 gmx_fatal(FARGS, "Unknown flexible rotation type");
2572 /* Determine angle by RMSD fit to the reference - Let's hope this */
2573 /* only happens once in a while, since this is not parallelized! */
2574 if (bMaster && (erotgFitPOT != erg->rotg->eFittype) )
2578 /* Fit angle of the whole rotation group */
2579 erg->angle_v = flex_fit_angle(erg);
2583 /* Fit angle of each slab */
2584 flex_fit_angle_perslab(erg, t, erg->degangle, enfrot->out_angles);
2588 /* Lump together the torques from all slabs: */
2589 erg->torque_v = 0.0;
2590 for (int l = 0; l < nslabs; l++)
2592 erg->torque_v += erg->slab_torque_v[l];
2597 /* Calculate the angle between reference and actual rotation group atom,
2598 * both projected into a plane perpendicular to the rotation vector: */
2599 static void angle(const gmx_enfrotgrp *erg,
2603 real *weight) /* atoms near the rotation axis should count less than atoms far away */
2605 rvec xp, xrp; /* current and reference positions projected on a plane perpendicular to pg->vec */
2609 /* Project x_ref and x into a plane through the origin perpendicular to rot_vec: */
2610 /* Project x_ref: xrp = x_ref - (vec * x_ref) * vec */
2611 svmul(iprod(erg->vec, x_ref), erg->vec, dum);
2612 rvec_sub(x_ref, dum, xrp);
2613 /* Project x_act: */
2614 svmul(iprod(erg->vec, x_act), erg->vec, dum);
2615 rvec_sub(x_act, dum, xp);
2617 /* Retrieve information about which vector precedes. gmx_angle always
2618 * returns a positive angle. */
2619 cprod(xp, xrp, dum); /* if reference precedes, this is pointing into the same direction as vec */
2621 if (iprod(erg->vec, dum) >= 0)
2623 *alpha = -gmx_angle(xrp, xp);
2627 *alpha = +gmx_angle(xrp, xp);
2630 /* Also return the weight */
2635 /* Project first vector onto a plane perpendicular to the second vector
2637 * Note that v must be of unit length.
2639 static inline void project_onto_plane(rvec dr, const rvec v)
2644 svmul(iprod(dr, v), v, tmp); /* tmp = (dr.v)v */
2645 rvec_dec(dr, tmp); /* dr = dr - (dr.v)v */
2649 /* Fixed rotation: The rotation reference group rotates around the v axis. */
2650 /* The atoms of the actual rotation group are attached with imaginary */
2651 /* springs to the reference atoms. */
2652 static void do_fixed(
2654 gmx_bool bOutstepRot, /* Output to main rotation output file */
2655 gmx_bool bOutstepSlab) /* Output per-slab data */
2658 rvec tmp_f; /* Force */
2659 real alpha; /* a single angle between an actual and a reference position */
2660 real weight; /* single weight for a single angle */
2661 rvec xi_xc; /* xi - xc */
2662 gmx_bool bCalcPotFit;
2665 /* for mass weighting: */
2666 real wi; /* Mass-weighting of the positions */
2668 real k_wi; /* k times wi */
2672 bProject = (erg->rotg->eType == erotgPM) || (erg->rotg->eType == erotgPMPF);
2673 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2675 N_M = erg->rotg->nat * erg->invmass;
2676 const auto &collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2677 /* Each process calculates the forces on its local atoms */
2678 for (size_t j = 0; j < erg->atomSet->numAtomsLocal(); j++)
2680 /* Calculate (x_i-x_c) resp. (x_i-u) */
2681 rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xi_xc);
2683 /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
2684 rvec_sub(erg->xr_loc[j], xi_xc, dr);
2688 project_onto_plane(dr, erg->vec);
2691 /* Mass-weighting */
2692 wi = N_M*erg->m_loc[j];
2694 /* Store the additional force so that it can be added to the force
2695 * array after the normal forces have been evaluated */
2696 k_wi = erg->rotg->k*wi;
2697 for (int m = 0; m < DIM; m++)
2699 tmp_f[m] = k_wi*dr[m];
2700 erg->f_rot_loc[j][m] = tmp_f[m];
2701 erg->V += 0.5*k_wi*gmx::square(dr[m]);
2704 /* If requested, also calculate the potential for a set of angles
2705 * near the current reference angle */
2708 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2710 /* Index of this rotation group atom with respect to the whole rotation group */
2711 int jj = collectiveRotationGroupIndex[j];
2713 /* Rotate with the alternative angle. Like rotate_local_reference(),
2714 * just for a single local atom */
2715 mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[jj], fit_xr_loc); /* fit_xr_loc = Omega*(y_i-y_c) */
2717 /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
2718 rvec_sub(fit_xr_loc, xi_xc, dr);
2722 project_onto_plane(dr, erg->vec);
2725 /* Add to the rotation potential for this angle: */
2726 erg->PotAngleFit->V[ifit] += 0.5*k_wi*norm2(dr);
2732 /* Add to the torque of this rotation group */
2733 erg->torque_v += torque(erg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2735 /* Calculate the angle between reference and actual rotation group atom. */
2736 angle(erg, xi_xc, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2737 erg->angle_v += alpha * weight;
2738 erg->weight_v += weight;
2740 /* If you want enforced rotation to contribute to the virial,
2741 * activate the following lines:
2744 Add the rotation contribution to the virial
2745 for(j=0; j<DIM; j++)
2747 vir[j][m] += 0.5*f[ii][j]*dr[m];
2753 } /* end of loop over local rotation group atoms */
2757 /* Calculate the radial motion potential and forces */
2758 static void do_radial_motion(
2760 gmx_bool bOutstepRot, /* Output to main rotation output file */
2761 gmx_bool bOutstepSlab) /* Output per-slab data */
2763 rvec tmp_f; /* Force */
2764 real alpha; /* a single angle between an actual and a reference position */
2765 real weight; /* single weight for a single angle */
2766 rvec xj_u; /* xj - u */
2767 rvec tmpvec, fit_tmpvec;
2768 real fac, fac2, sum = 0.0;
2770 gmx_bool bCalcPotFit;
2772 /* For mass weighting: */
2773 real wj; /* Mass-weighting of the positions */
2776 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2778 N_M = erg->rotg->nat * erg->invmass;
2779 const auto &collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2780 /* Each process calculates the forces on its local atoms */
2781 for (size_t j = 0; j < erg->atomSet->numAtomsLocal(); j++)
2783 /* Calculate (xj-u) */
2784 rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xj_u); /* xj_u = xj-u */
2786 /* Calculate Omega.(yj0-u) */
2787 cprod(erg->vec, erg->xr_loc[j], tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2789 /* * v x Omega.(yj0-u) */
2790 unitv(tmpvec, pj); /* pj = --------------------- */
2791 /* | v x Omega.(yj0-u) | */
2793 fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2796 /* Mass-weighting */
2797 wj = N_M*erg->m_loc[j];
2799 /* Store the additional force so that it can be added to the force
2800 * array after the normal forces have been evaluated */
2801 svmul(-erg->rotg->k*wj*fac, pj, tmp_f);
2802 copy_rvec(tmp_f, erg->f_rot_loc[j]);
2805 /* If requested, also calculate the potential for a set of angles
2806 * near the current reference angle */
2809 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2811 /* Index of this rotation group atom with respect to the whole rotation group */
2812 int jj = collectiveRotationGroupIndex[j];
2814 /* Rotate with the alternative angle. Like rotate_local_reference(),
2815 * just for a single local atom */
2816 mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[jj], fit_tmpvec); /* fit_tmpvec = Omega*(yj0-u) */
2818 /* Calculate Omega.(yj0-u) */
2819 cprod(erg->vec, fit_tmpvec, tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2820 /* * v x Omega.(yj0-u) */
2821 unitv(tmpvec, pj); /* pj = --------------------- */
2822 /* | v x Omega.(yj0-u) | */
2824 fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2827 /* Add to the rotation potential for this angle: */
2828 erg->PotAngleFit->V[ifit] += 0.5*erg->rotg->k*wj*fac2;
2834 /* Add to the torque of this rotation group */
2835 erg->torque_v += torque(erg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2837 /* Calculate the angle between reference and actual rotation group atom. */
2838 angle(erg, xj_u, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2839 erg->angle_v += alpha * weight;
2840 erg->weight_v += weight;
2845 } /* end of loop over local rotation group atoms */
2846 erg->V = 0.5*erg->rotg->k*sum;
2850 /* Calculate the radial motion pivot-free potential and forces */
2851 static void do_radial_motion_pf(
2853 rvec x[], /* The positions */
2854 matrix box, /* The simulation box */
2855 gmx_bool bOutstepRot, /* Output to main rotation output file */
2856 gmx_bool bOutstepSlab) /* Output per-slab data */
2858 rvec xj; /* Current position */
2859 rvec xj_xc; /* xj - xc */
2860 rvec yj0_yc0; /* yj0 - yc0 */
2861 rvec tmp_f; /* Force */
2862 real alpha; /* a single angle between an actual and a reference position */
2863 real weight; /* single weight for a single angle */
2864 rvec tmpvec, tmpvec2;
2865 rvec innersumvec; /* Precalculation of the inner sum */
2867 real fac, fac2, V = 0.0;
2869 gmx_bool bCalcPotFit;
2871 /* For mass weighting: */
2872 real mj, wi, wj; /* Mass-weighting of the positions */
2875 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
2877 N_M = erg->rotg->nat * erg->invmass;
2879 /* Get the current center of the rotation group: */
2880 get_center(erg->xc, erg->mc, erg->rotg->nat, erg->xc_center);
2882 /* Precalculate Sum_i [ wi qi.(xi-xc) qi ] which is needed for every single j */
2883 clear_rvec(innersumvec);
2884 for (int i = 0; i < erg->rotg->nat; i++)
2886 /* Mass-weighting */
2887 wi = N_M*erg->mc[i];
2889 /* Calculate qi. Note that xc_ref_center has already been subtracted from
2890 * x_ref in init_rot_group.*/
2891 mvmul(erg->rotmat, erg->rotg->x_ref[i], tmpvec); /* tmpvec = Omega.(yi0-yc0) */
2893 cprod(erg->vec, tmpvec, tmpvec2); /* tmpvec2 = v x Omega.(yi0-yc0) */
2895 /* * v x Omega.(yi0-yc0) */
2896 unitv(tmpvec2, qi); /* qi = ----------------------- */
2897 /* | v x Omega.(yi0-yc0) | */
2899 rvec_sub(erg->xc[i], erg->xc_center, tmpvec); /* tmpvec = xi-xc */
2901 svmul(wi*iprod(qi, tmpvec), qi, tmpvec2);
2903 rvec_inc(innersumvec, tmpvec2);
2905 svmul(erg->rotg->k*erg->invmass, innersumvec, innersumveckM);
2907 /* Each process calculates the forces on its local atoms */
2908 const auto &localRotationGroupIndex = erg->atomSet->localIndex();
2909 const auto &collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
2910 for (gmx::index j = 0; j < localRotationGroupIndex.ssize(); j++)
2912 /* Local index of a rotation group atom */
2913 int ii = localRotationGroupIndex[j];
2914 /* Position of this atom in the collective array */
2915 int iigrp = collectiveRotationGroupIndex[j];
2916 /* Mass-weighting */
2917 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2920 /* Current position of this atom: x[ii][XX/YY/ZZ] */
2921 copy_rvec(x[ii], xj);
2923 /* Shift this atom such that it is near its reference */
2924 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2926 /* The (unrotated) reference position is yj0. yc0 has already
2927 * been subtracted in init_rot_group */
2928 copy_rvec(erg->rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
2930 /* Calculate Omega.(yj0-yc0) */
2931 mvmul(erg->rotmat, yj0_yc0, tmpvec2); /* tmpvec2 = Omega.(yj0 - yc0) */
2933 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
2935 /* * v x Omega.(yj0-yc0) */
2936 unitv(tmpvec, qj); /* qj = ----------------------- */
2937 /* | v x Omega.(yj0-yc0) | */
2939 /* Calculate (xj-xc) */
2940 rvec_sub(xj, erg->xc_center, xj_xc); /* xj_xc = xj-xc */
2942 fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
2945 /* Store the additional force so that it can be added to the force
2946 * array after the normal forces have been evaluated */
2947 svmul(-erg->rotg->k*wj*fac, qj, tmp_f); /* part 1 of force */
2948 svmul(mj, innersumveckM, tmpvec); /* part 2 of force */
2949 rvec_inc(tmp_f, tmpvec);
2950 copy_rvec(tmp_f, erg->f_rot_loc[j]);
2953 /* If requested, also calculate the potential for a set of angles
2954 * near the current reference angle */
2957 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
2959 /* Rotate with the alternative angle. Like rotate_local_reference(),
2960 * just for a single local atom */
2961 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, tmpvec2); /* tmpvec2 = Omega*(yj0-yc0) */
2963 /* Calculate Omega.(yj0-u) */
2964 cprod(erg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
2965 /* * v x Omega.(yj0-yc0) */
2966 unitv(tmpvec, qj); /* qj = ----------------------- */
2967 /* | v x Omega.(yj0-yc0) | */
2969 fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
2972 /* Add to the rotation potential for this angle: */
2973 erg->PotAngleFit->V[ifit] += 0.5*erg->rotg->k*wj*fac2;
2979 /* Add to the torque of this rotation group */
2980 erg->torque_v += torque(erg->vec, tmp_f, xj, erg->xc_center);
2982 /* Calculate the angle between reference and actual rotation group atom. */
2983 angle(erg, xj_xc, yj0_yc0, &alpha, &weight); /* angle in rad, weighted */
2984 erg->angle_v += alpha * weight;
2985 erg->weight_v += weight;
2990 } /* end of loop over local rotation group atoms */
2991 erg->V = 0.5*erg->rotg->k*V;
2995 /* Precalculate the inner sum for the radial motion 2 forces */
2996 static void radial_motion2_precalc_inner_sum(const gmx_enfrotgrp *erg,
3000 rvec xi_xc; /* xj - xc */
3001 rvec tmpvec, tmpvec2;
3005 rvec v_xi_xc; /* v x (xj - u) */
3006 real psii, psiistar;
3007 real wi; /* Mass-weighting of the positions */
3011 N_M = erg->rotg->nat * erg->invmass;
3013 /* Loop over the collective set of positions */
3015 for (i = 0; i < erg->rotg->nat; i++)
3017 /* Mass-weighting */
3018 wi = N_M*erg->mc[i];
3020 rvec_sub(erg->xc[i], erg->xc_center, xi_xc); /* xi_xc = xi-xc */
3022 /* Calculate ri. Note that xc_ref_center has already been subtracted from
3023 * x_ref in init_rot_group.*/
3024 mvmul(erg->rotmat, erg->rotg->x_ref[i], ri); /* ri = Omega.(yi0-yc0) */
3026 cprod(erg->vec, xi_xc, v_xi_xc); /* v_xi_xc = v x (xi-u) */
3028 fac = norm2(v_xi_xc);
3030 psiistar = 1.0/(fac + erg->rotg->eps); /* psiistar = --------------------- */
3031 /* |v x (xi-xc)|^2 + eps */
3033 psii = gmx::invsqrt(fac); /* 1 */
3034 /* psii = ------------- */
3037 svmul(psii, v_xi_xc, si); /* si = psii * (v x (xi-xc) ) */
3039 siri = iprod(si, ri); /* siri = si.ri */
3041 svmul(psiistar/psii, ri, tmpvec);
3042 svmul(psiistar*psiistar/(psii*psii*psii) * siri, si, tmpvec2);
3043 rvec_dec(tmpvec, tmpvec2);
3044 cprod(tmpvec, erg->vec, tmpvec2);
3046 svmul(wi*siri, tmpvec2, tmpvec);
3048 rvec_inc(sumvec, tmpvec);
3050 svmul(erg->rotg->k*erg->invmass, sumvec, innersumvec);
3054 /* Calculate the radial motion 2 potential and forces */
3055 static void do_radial_motion2(
3057 rvec x[], /* The positions */
3058 matrix box, /* The simulation box */
3059 gmx_bool bOutstepRot, /* Output to main rotation output file */
3060 gmx_bool bOutstepSlab) /* Output per-slab data */
3062 rvec xj; /* Position */
3063 real alpha; /* a single angle between an actual and a reference position */
3064 real weight; /* single weight for a single angle */
3065 rvec xj_u; /* xj - u */
3066 rvec yj0_yc0; /* yj0 -yc0 */
3067 rvec tmpvec, tmpvec2;
3068 real fac, fit_fac, fac2, Vpart = 0.0;
3069 rvec rj, fit_rj, sj;
3071 rvec v_xj_u; /* v x (xj - u) */
3072 real psij, psijstar;
3073 real mj, wj; /* For mass-weighting of the positions */
3077 gmx_bool bCalcPotFit;
3079 bPF = erg->rotg->eType == erotgRM2PF;
3080 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == erg->rotg->eFittype);
3082 clear_rvec(yj0_yc0); /* Make the compiler happy */
3084 clear_rvec(innersumvec);
3087 /* For the pivot-free variant we have to use the current center of
3088 * mass of the rotation group instead of the pivot u */
3089 get_center(erg->xc, erg->mc, erg->rotg->nat, erg->xc_center);
3091 /* Also, we precalculate the second term of the forces that is identical
3092 * (up to the weight factor mj) for all forces */
3093 radial_motion2_precalc_inner_sum(erg, innersumvec);
3096 N_M = erg->rotg->nat * erg->invmass;
3098 /* Each process calculates the forces on its local atoms */
3099 const auto &localRotationGroupIndex = erg->atomSet->localIndex();
3100 const auto &collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
3101 for (gmx::index j = 0; j < localRotationGroupIndex.ssize(); j++)
3105 /* Local index of a rotation group atom */
3106 int ii = localRotationGroupIndex[j];
3107 /* Position of this atom in the collective array */
3108 int iigrp = collectiveRotationGroupIndex[j];
3109 /* Mass-weighting */
3110 mj = erg->mc[iigrp];
3112 /* Current position of this atom: x[ii] */
3113 copy_rvec(x[ii], xj);
3115 /* Shift this atom such that it is near its reference */
3116 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
3118 /* The (unrotated) reference position is yj0. yc0 has already
3119 * been subtracted in init_rot_group */
3120 copy_rvec(erg->rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
3122 /* Calculate Omega.(yj0-yc0) */
3123 mvmul(erg->rotmat, yj0_yc0, rj); /* rj = Omega.(yj0-yc0) */
3128 copy_rvec(erg->x_loc_pbc[j], xj);
3129 copy_rvec(erg->xr_loc[j], rj); /* rj = Omega.(yj0-u) */
3131 /* Mass-weighting */
3134 /* Calculate (xj-u) resp. (xj-xc) */
3135 rvec_sub(xj, erg->xc_center, xj_u); /* xj_u = xj-u */
3137 cprod(erg->vec, xj_u, v_xj_u); /* v_xj_u = v x (xj-u) */
3139 fac = norm2(v_xj_u);
3141 psijstar = 1.0/(fac + erg->rotg->eps); /* psistar = -------------------- */
3142 /* * |v x (xj-u)|^2 + eps */
3144 psij = gmx::invsqrt(fac); /* 1 */
3145 /* psij = ------------ */
3148 svmul(psij, v_xj_u, sj); /* sj = psij * (v x (xj-u) ) */
3150 fac = iprod(v_xj_u, rj); /* fac = (v x (xj-u)).rj */
3153 sjrj = iprod(sj, rj); /* sjrj = sj.rj */
3155 svmul(psijstar/psij, rj, tmpvec);
3156 svmul(psijstar*psijstar/(psij*psij*psij) * sjrj, sj, tmpvec2);
3157 rvec_dec(tmpvec, tmpvec2);
3158 cprod(tmpvec, erg->vec, tmpvec2);
3160 /* Store the additional force so that it can be added to the force
3161 * array after the normal forces have been evaluated */
3162 svmul(-erg->rotg->k*wj*sjrj, tmpvec2, tmpvec);
3163 svmul(mj, innersumvec, tmpvec2); /* This is != 0 only for the pivot-free variant */
3165 rvec_add(tmpvec2, tmpvec, erg->f_rot_loc[j]);
3166 Vpart += wj*psijstar*fac2;
3168 /* If requested, also calculate the potential for a set of angles
3169 * near the current reference angle */
3172 for (int ifit = 0; ifit < erg->rotg->PotAngle_nstep; ifit++)
3176 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, fit_rj); /* fit_rj = Omega.(yj0-yc0) */
3180 /* Position of this atom in the collective array */
3181 int iigrp = collectiveRotationGroupIndex[j];
3182 /* Rotate with the alternative angle. Like rotate_local_reference(),
3183 * just for a single local atom */
3184 mvmul(erg->PotAngleFit->rotmat[ifit], erg->rotg->x_ref[iigrp], fit_rj); /* fit_rj = Omega*(yj0-u) */
3186 fit_fac = iprod(v_xj_u, fit_rj); /* fac = (v x (xj-u)).fit_rj */
3187 /* Add to the rotation potential for this angle: */
3188 erg->PotAngleFit->V[ifit] += 0.5*erg->rotg->k*wj*psijstar*fit_fac*fit_fac;
3194 /* Add to the torque of this rotation group */
3195 erg->torque_v += torque(erg->vec, erg->f_rot_loc[j], xj, erg->xc_center);
3197 /* Calculate the angle between reference and actual rotation group atom. */
3198 angle(erg, xj_u, rj, &alpha, &weight); /* angle in rad, weighted */
3199 erg->angle_v += alpha * weight;
3200 erg->weight_v += weight;
3205 } /* end of loop over local rotation group atoms */
3206 erg->V = 0.5*erg->rotg->k*Vpart;
3210 /* Determine the smallest and largest position vector (with respect to the
3211 * rotation vector) for the reference group */
3212 static void get_firstlast_atom_ref(
3213 const gmx_enfrotgrp *erg,
3218 real xcproj; /* The projection of a reference position on the
3220 real minproj, maxproj; /* Smallest and largest projection on v */
3222 /* Start with some value */
3223 minproj = iprod(erg->rotg->x_ref[0], erg->vec);
3226 /* This is just to ensure that it still works if all the atoms of the
3227 * reference structure are situated in a plane perpendicular to the rotation
3230 *lastindex = erg->rotg->nat-1;
3232 /* Loop over all atoms of the reference group,
3233 * project them on the rotation vector to find the extremes */
3234 for (i = 0; i < erg->rotg->nat; i++)
3236 xcproj = iprod(erg->rotg->x_ref[i], erg->vec);
3237 if (xcproj < minproj)
3242 if (xcproj > maxproj)
3251 /* Allocate memory for the slabs */
3252 static void allocate_slabs(
3257 /* More slabs than are defined for the reference are never needed */
3258 int nslabs = erg->slab_last_ref - erg->slab_first_ref + 1;
3260 /* Remember how many we allocated */
3261 erg->nslabs_alloc = nslabs;
3263 if ( (nullptr != fplog) && bVerbose)
3265 fprintf(fplog, "%s allocating memory to store data for %d slabs (rotation group %d).\n",
3266 RotStr, nslabs, erg->groupIndex);
3268 snew(erg->slab_center, nslabs);
3269 snew(erg->slab_center_ref, nslabs);
3270 snew(erg->slab_weights, nslabs);
3271 snew(erg->slab_torque_v, nslabs);
3272 snew(erg->slab_data, nslabs);
3273 snew(erg->gn_atom, nslabs);
3274 snew(erg->gn_slabind, nslabs);
3275 snew(erg->slab_innersumvec, nslabs);
3276 for (int i = 0; i < nslabs; i++)
3278 snew(erg->slab_data[i].x, erg->rotg->nat);
3279 snew(erg->slab_data[i].ref, erg->rotg->nat);
3280 snew(erg->slab_data[i].weight, erg->rotg->nat);
3282 snew(erg->xc_ref_sorted, erg->rotg->nat);
3283 snew(erg->xc_sortind, erg->rotg->nat);
3284 snew(erg->firstatom, nslabs);
3285 snew(erg->lastatom, nslabs);
3289 /* From the extreme positions of the reference group, determine the first
3290 * and last slab of the reference. We can never have more slabs in the real
3291 * simulation than calculated here for the reference.
3293 static void get_firstlast_slab_ref(gmx_enfrotgrp *erg,
3294 real mc[], int ref_firstindex, int ref_lastindex)
3298 int first = get_first_slab(erg, erg->rotg->x_ref[ref_firstindex]);
3299 int last = get_last_slab(erg, erg->rotg->x_ref[ref_lastindex ]);
3301 while (get_slab_weight(first, erg, erg->rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
3305 erg->slab_first_ref = first+1;
3306 while (get_slab_weight(last, erg, erg->rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
3310 erg->slab_last_ref = last-1;
3314 /* Special version of copy_rvec:
3315 * During the copy procedure of xcurr to b, the correct PBC image is chosen
3316 * such that the copied vector ends up near its reference position xref */
3317 static inline void copy_correct_pbc_image(
3318 const rvec xcurr, /* copy vector xcurr ... */
3319 rvec b, /* ... to b ... */
3320 const rvec xref, /* choosing the PBC image such that b ends up near xref */
3329 /* Shortest PBC distance between the atom and its reference */
3330 rvec_sub(xcurr, xref, dx);
3332 /* Determine the shift for this atom */
3334 for (m = npbcdim-1; m >= 0; m--)
3336 while (dx[m] < -0.5*box[m][m])
3338 for (d = 0; d < DIM; d++)
3344 while (dx[m] >= 0.5*box[m][m])
3346 for (d = 0; d < DIM; d++)
3354 /* Apply the shift to the position */
3355 copy_rvec(xcurr, b);
3356 shift_single_coord(box, b, shift);
3360 static void init_rot_group(FILE *fplog, const t_commrec *cr,
3362 rvec *x, gmx_mtop_t *mtop, gmx_bool bVerbose, FILE *out_slabs, const matrix box,
3363 t_inputrec *ir, gmx_bool bOutputCenters)
3365 rvec coord, xref, *xdum;
3366 gmx_bool bFlex, bColl;
3367 int ref_firstindex, ref_lastindex;
3368 real mass, totalmass;
3371 const t_rotgrp *rotg = erg->rotg;
3374 /* Do we have a flexible axis? */
3375 bFlex = ISFLEX(rotg);
3376 /* Do we use a global set of coordinates? */
3377 bColl = ISCOLL(rotg);
3379 /* Allocate space for collective coordinates if needed */
3382 snew(erg->xc, erg->rotg->nat);
3383 snew(erg->xc_shifts, erg->rotg->nat);
3384 snew(erg->xc_eshifts, erg->rotg->nat);
3385 snew(erg->xc_old, erg->rotg->nat);
3387 if (erg->rotg->eFittype == erotgFitNORM)
3389 snew(erg->xc_ref_length, erg->rotg->nat); /* in case fit type NORM is chosen */
3390 snew(erg->xc_norm, erg->rotg->nat);
3395 snew(erg->xr_loc, erg->rotg->nat);
3396 snew(erg->x_loc_pbc, erg->rotg->nat);
3399 copy_rvec(erg->rotg->inputVec, erg->vec);
3400 snew(erg->f_rot_loc, erg->rotg->nat);
3402 /* Make space for the calculation of the potential at other angles (used
3403 * for fitting only) */
3404 if (erotgFitPOT == erg->rotg->eFittype)
3406 snew(erg->PotAngleFit, 1);
3407 snew(erg->PotAngleFit->degangle, erg->rotg->PotAngle_nstep);
3408 snew(erg->PotAngleFit->V, erg->rotg->PotAngle_nstep);
3409 snew(erg->PotAngleFit->rotmat, erg->rotg->PotAngle_nstep);
3411 /* Get the set of angles around the reference angle */
3412 start = -0.5 * (erg->rotg->PotAngle_nstep - 1)*erg->rotg->PotAngle_step;
3413 for (int i = 0; i < erg->rotg->PotAngle_nstep; i++)
3415 erg->PotAngleFit->degangle[i] = start + i*erg->rotg->PotAngle_step;
3420 erg->PotAngleFit = nullptr;
3423 /* Copy the masses so that the center can be determined. For all types of
3424 * enforced rotation, we store the masses in the erg->mc array. */
3425 snew(erg->mc, erg->rotg->nat);
3428 snew(erg->mc_sorted, erg->rotg->nat);
3432 snew(erg->m_loc, erg->rotg->nat);
3436 for (int i = 0; i < erg->rotg->nat; i++)
3438 if (erg->rotg->bMassW)
3440 mass = mtopGetAtomMass(mtop, erg->rotg->ind[i], &molb);
3449 erg->invmass = 1.0/totalmass;
3451 /* Set xc_ref_center for any rotation potential */
3452 if ((erg->rotg->eType == erotgISO) || (erg->rotg->eType == erotgPM) || (erg->rotg->eType == erotgRM) || (erg->rotg->eType == erotgRM2))
3454 /* Set the pivot point for the fixed, stationary-axis potentials. This
3455 * won't change during the simulation */
3456 copy_rvec(erg->rotg->pivot, erg->xc_ref_center);
3457 copy_rvec(erg->rotg->pivot, erg->xc_center );
3461 /* Center of the reference positions */
3462 get_center(erg->rotg->x_ref, erg->mc, erg->rotg->nat, erg->xc_ref_center);
3464 /* Center of the actual positions */
3467 snew(xdum, erg->rotg->nat);
3468 for (int i = 0; i < erg->rotg->nat; i++)
3470 int ii = erg->rotg->ind[i];
3471 copy_rvec(x[ii], xdum[i]);
3473 get_center(xdum, erg->mc, erg->rotg->nat, erg->xc_center);
3479 gmx_bcast(sizeof(erg->xc_center), erg->xc_center, cr);
3486 /* Save the original (whole) set of positions in xc_old such that at later
3487 * steps the rotation group can always be made whole again. If the simulation is
3488 * restarted, we compute the starting reference positions (given the time)
3489 * and assume that the correct PBC image of each position is the one nearest
3490 * to the current reference */
3493 /* Calculate the rotation matrix for this angle: */
3494 t_start = ir->init_t + ir->init_step*ir->delta_t;
3495 erg->degangle = erg->rotg->rate * t_start;
3496 calc_rotmat(erg->vec, erg->degangle, erg->rotmat);
3498 for (int i = 0; i < erg->rotg->nat; i++)
3500 int ii = erg->rotg->ind[i];
3502 /* Subtract pivot, rotate, and add pivot again. This will yield the
3503 * reference position for time t */
3504 rvec_sub(erg->rotg->x_ref[i], erg->xc_ref_center, coord);
3505 mvmul(erg->rotmat, coord, xref);
3506 rvec_inc(xref, erg->xc_ref_center);
3508 copy_correct_pbc_image(x[ii], erg->xc_old[i], xref, box, 3);
3514 gmx_bcast(erg->rotg->nat*sizeof(erg->xc_old[0]), erg->xc_old, cr);
3519 if ( (erg->rotg->eType != erotgFLEX) && (erg->rotg->eType != erotgFLEX2) )
3521 /* Put the reference positions into origin: */
3522 for (int i = 0; i < erg->rotg->nat; i++)
3524 rvec_dec(erg->rotg->x_ref[i], erg->xc_ref_center);
3528 /* Enforced rotation with flexible axis */
3531 /* Calculate maximum beta value from minimum gaussian (performance opt.) */
3532 erg->max_beta = calc_beta_max(erg->rotg->min_gaussian, erg->rotg->slab_dist);
3534 /* Determine the smallest and largest coordinate with respect to the rotation vector */
3535 get_firstlast_atom_ref(erg, &ref_firstindex, &ref_lastindex);
3537 /* From the extreme positions of the reference group, determine the first
3538 * and last slab of the reference. */
3539 get_firstlast_slab_ref(erg, erg->mc, ref_firstindex, ref_lastindex);
3541 /* Allocate memory for the slabs */
3542 allocate_slabs(erg, fplog, bVerbose);
3544 /* Flexible rotation: determine the reference centers for the rest of the simulation */
3545 erg->slab_first = erg->slab_first_ref;
3546 erg->slab_last = erg->slab_last_ref;
3547 get_slab_centers(erg, erg->rotg->x_ref, erg->mc, -1, out_slabs, bOutputCenters, TRUE);
3549 /* Length of each x_rotref vector from center (needed if fit routine NORM is chosen): */
3550 if (erg->rotg->eFittype == erotgFitNORM)
3552 for (int i = 0; i < erg->rotg->nat; i++)
3554 rvec_sub(erg->rotg->x_ref[i], erg->xc_ref_center, coord);
3555 erg->xc_ref_length[i] = norm(coord);
3561 /* Calculate the size of the MPI buffer needed in reduce_output() */
3562 static int calc_mpi_bufsize(const gmx_enfrot *er)
3565 int count_total = 0;
3566 for (int g = 0; g < er->rot->ngrp; g++)
3568 const t_rotgrp *rotg = &er->rot->grp[g];
3569 const gmx_enfrotgrp *erg = &er->enfrotgrp[g];
3571 /* Count the items that are transferred for this group: */
3572 int count_group = 4; /* V, torque, angle, weight */
3574 /* Add the maximum number of slabs for flexible groups */
3577 count_group += erg->slab_last_ref - erg->slab_first_ref + 1;
3580 /* Add space for the potentials at different angles: */
3581 if (erotgFitPOT == erg->rotg->eFittype)
3583 count_group += erg->rotg->PotAngle_nstep;
3586 /* Add to the total number: */
3587 count_total += count_group;
3594 std::unique_ptr<gmx::EnforcedRotation>
3595 init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
3596 const t_commrec *cr, gmx::LocalAtomSetManager * atomSets, const t_state *globalState, gmx_mtop_t *mtop, const gmx_output_env_t *oenv,
3597 const gmx::MdrunOptions &mdrunOptions)
3599 int nat_max = 0; /* Size of biggest rotation group */
3600 rvec *x_pbc = nullptr; /* Space for the pbc-correct atom positions */
3602 if (MASTER(cr) && mdrunOptions.verbose)
3604 fprintf(stdout, "%s Initializing ...\n", RotStr);
3607 auto enforcedRotation = std::make_unique<gmx::EnforcedRotation>();
3608 gmx_enfrot *er = enforcedRotation->getLegacyEnfrot();
3609 // TODO When this module implements IMdpOptions, the ownership will become more clear.
3611 er->appendFiles = mdrunOptions.continuationOptions.appendFiles;
3613 /* When appending, skip first output to avoid duplicate entries in the data files */
3614 if (er->appendFiles)
3623 if (MASTER(cr) && er->bOut)
3625 please_cite(fplog, "Kutzner2011");
3628 /* Output every step for reruns */
3629 if (mdrunOptions.rerun)
3631 if (nullptr != fplog)
3633 fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
3640 er->nstrout = er->rot->nstrout;
3641 er->nstsout = er->rot->nstsout;
3644 er->out_slabs = nullptr;
3645 if (MASTER(cr) && HaveFlexibleGroups(er->rot) )
3647 er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), er);
3652 /* Remove pbc, make molecule whole.
3653 * When ir->bContinuation=TRUE this has already been done, but ok. */
3654 snew(x_pbc, mtop->natoms);
3655 copy_rvecn(globalState->x.rvec_array(), x_pbc, 0, mtop->natoms);
3656 do_pbc_first_mtop(nullptr, ir->ePBC, globalState->box, mtop, x_pbc);
3657 /* All molecules will be whole now, but not necessarily in the home box.
3658 * Additionally, if a rotation group consists of more than one molecule
3659 * (e.g. two strands of DNA), each one of them can end up in a different
3660 * periodic box. This is taken care of in init_rot_group. */
3663 /* Allocate space for the per-rotation-group data: */
3664 er->enfrotgrp.resize(er->rot->ngrp);
3666 for (auto &ergRef : er->enfrotgrp)
3668 gmx_enfrotgrp *erg = &ergRef;
3669 erg->rotg = &er->rot->grp[groupIndex];
3670 erg->atomSet = std::make_unique<gmx::LocalAtomSet>(atomSets->add({erg->rotg->ind, erg->rotg->ind + erg->rotg->nat}));
3671 erg->groupIndex = groupIndex;
3673 if (nullptr != fplog)
3675 fprintf(fplog, "%s group %d type '%s'\n", RotStr, groupIndex, erotg_names[erg->rotg->eType]);
3678 if (erg->rotg->nat > 0)
3680 nat_max = std::max(nat_max, erg->rotg->nat);
3682 init_rot_group(fplog, cr, erg, x_pbc, mtop, mdrunOptions.verbose, er->out_slabs, MASTER(cr) ? globalState->box : nullptr, ir,
3683 !er->appendFiles); /* Do not output the reference centers
3684 * again if we are appending */
3689 /* Allocate space for enforced rotation buffer variables */
3690 er->bufsize = nat_max;
3691 snew(er->data, nat_max);
3692 snew(er->xbuf, nat_max);
3693 snew(er->mbuf, nat_max);
3695 /* Buffers for MPI reducing torques, angles, weights (for each group), and V */
3698 er->mpi_bufsize = calc_mpi_bufsize(er) + 100; /* larger to catch errors */
3699 snew(er->mpi_inbuf, er->mpi_bufsize);
3700 snew(er->mpi_outbuf, er->mpi_bufsize);
3704 er->mpi_bufsize = 0;
3705 er->mpi_inbuf = nullptr;
3706 er->mpi_outbuf = nullptr;
3709 /* Only do I/O on the MASTER */
3710 er->out_angles = nullptr;
3711 er->out_rot = nullptr;
3712 er->out_torque = nullptr;
3715 er->out_rot = open_rot_out(opt2fn("-ro", nfile, fnm), oenv, er);
3717 if (er->nstsout > 0)
3719 if (HaveFlexibleGroups(er->rot) || HavePotFitGroups(er->rot) )
3721 er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), er);
3723 if (HaveFlexibleGroups(er->rot) )
3725 er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), er);
3731 return enforcedRotation;
3734 /* Rotate the local reference positions and store them in
3735 * erg->xr_loc[0...(nat_loc-1)]
3737 * Note that we already subtracted u or y_c from the reference positions
3738 * in init_rot_group().
3740 static void rotate_local_reference(gmx_enfrotgrp *erg)
3742 const auto &collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
3743 for (size_t i = 0; i < erg->atomSet->numAtomsLocal(); i++)
3745 /* Index of this rotation group atom with respect to the whole rotation group */
3746 int ii = collectiveRotationGroupIndex[i];
3748 mvmul(erg->rotmat, erg->rotg->x_ref[ii], erg->xr_loc[i]);
3753 /* Select the PBC representation for each local x position and store that
3754 * for later usage. We assume the right PBC image of an x is the one nearest to
3755 * its rotated reference */
3756 static void choose_pbc_image(rvec x[],
3758 matrix box, int npbcdim)
3760 const auto &localRotationGroupIndex = erg->atomSet->localIndex();
3761 for (gmx::index i = 0; i < localRotationGroupIndex.ssize(); i++)
3763 /* Index of a rotation group atom */
3764 int ii = localRotationGroupIndex[i];
3766 /* Get the correctly rotated reference position. The pivot was already
3767 * subtracted in init_rot_group() from the reference positions. Also,
3768 * the reference positions have already been rotated in
3769 * rotate_local_reference(). For the current reference position we thus
3770 * only need to add the pivot again. */
3772 copy_rvec(erg->xr_loc[i], xref);
3773 rvec_inc(xref, erg->xc_ref_center);
3775 copy_correct_pbc_image(x[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
3780 void do_rotation(const t_commrec *cr,
3788 gmx_bool outstep_slab, outstep_rot;
3791 gmx_potfit *fit = nullptr; /* For fit type 'potential' determine the fit
3792 angle via the potential minimum */
3798 /* When to output in main rotation output file */
3799 outstep_rot = do_per_step(step, er->nstrout) && er->bOut;
3800 /* When to output per-slab data */
3801 outstep_slab = do_per_step(step, er->nstsout) && er->bOut;
3803 /* Output time into rotation output file */
3804 if (outstep_rot && MASTER(cr))
3806 fprintf(er->out_rot, "%12.3e", t);
3809 /**************************************************************************/
3810 /* First do ALL the communication! */
3811 for (auto &ergRef : er->enfrotgrp)
3813 gmx_enfrotgrp *erg = &ergRef;
3814 const t_rotgrp *rotg = erg->rotg;
3816 /* Do we use a collective (global) set of coordinates? */
3817 bColl = ISCOLL(rotg);
3819 /* Calculate the rotation matrix for this angle: */
3820 erg->degangle = rotg->rate * t;
3821 calc_rotmat(erg->vec, erg->degangle, erg->rotmat);
3825 /* Transfer the rotation group's positions such that every node has
3826 * all of them. Every node contributes its local positions x and stores
3827 * it in the collective erg->xc array. */
3828 communicate_group_positions(cr, erg->xc, erg->xc_shifts, erg->xc_eshifts, bNS,
3829 x, rotg->nat, erg->atomSet->numAtomsLocal(), erg->atomSet->localIndex().data(), erg->atomSet->collectiveIndex().data(), erg->xc_old, box);
3833 /* Fill the local masses array;
3834 * this array changes in DD/neighborsearching steps */
3837 const auto &collectiveRotationGroupIndex = erg->atomSet->collectiveIndex();
3838 for (gmx::index i = 0; i < collectiveRotationGroupIndex.ssize(); i++)
3840 /* Index of local atom w.r.t. the collective rotation group */
3841 int ii = collectiveRotationGroupIndex[i];
3842 erg->m_loc[i] = erg->mc[ii];
3846 /* Calculate Omega*(y_i-y_c) for the local positions */
3847 rotate_local_reference(erg);
3849 /* Choose the nearest PBC images of the group atoms with respect
3850 * to the rotated reference positions */
3851 choose_pbc_image(x, erg, box, 3);
3853 /* Get the center of the rotation group */
3854 if ( (rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) )
3856 get_center_comm(cr, erg->x_loc_pbc, erg->m_loc, erg->atomSet->numAtomsLocal(), rotg->nat, erg->xc_center);
3860 } /* End of loop over rotation groups */
3862 /**************************************************************************/
3863 /* Done communicating, we can start to count cycles for the load balancing now ... */
3864 if (DOMAINDECOMP(cr))
3866 ddReopenBalanceRegionCpu(cr->dd);
3873 for (auto &ergRef : er->enfrotgrp)
3875 gmx_enfrotgrp *erg = &ergRef;
3876 const t_rotgrp *rotg = erg->rotg;
3878 if (outstep_rot && MASTER(cr))
3880 fprintf(er->out_rot, "%12.4f", erg->degangle);
3883 /* Calculate angles and rotation matrices for potential fitting: */
3884 if ( (outstep_rot || outstep_slab) && (erotgFitPOT == rotg->eFittype) )
3886 fit = erg->PotAngleFit;
3887 for (int i = 0; i < rotg->PotAngle_nstep; i++)
3889 calc_rotmat(erg->vec, erg->degangle + fit->degangle[i], fit->rotmat[i]);
3891 /* Clear value from last step */
3892 erg->PotAngleFit->V[i] = 0.0;
3896 /* Clear values from last time step */
3898 erg->torque_v = 0.0;
3900 erg->weight_v = 0.0;
3902 switch (rotg->eType)
3908 do_fixed(erg, outstep_rot, outstep_slab);
3911 do_radial_motion(erg, outstep_rot, outstep_slab);
3914 do_radial_motion_pf(erg, x, box, outstep_rot, outstep_slab);
3918 do_radial_motion2(erg, x, box, outstep_rot, outstep_slab);
3922 /* Subtract the center of the rotation group from the collective positions array
3923 * Also store the center in erg->xc_center since it needs to be subtracted
3924 * in the low level routines from the local coordinates as well */
3925 get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
3926 svmul(-1.0, erg->xc_center, transvec);
3927 translate_x(erg->xc, rotg->nat, transvec);
3928 do_flexible(MASTER(cr), er, erg, x, box, t, outstep_rot, outstep_slab);
3932 /* Do NOT subtract the center of mass in the low level routines! */
3933 clear_rvec(erg->xc_center);
3934 do_flexible(MASTER(cr), er, erg, x, box, t, outstep_rot, outstep_slab);
3937 gmx_fatal(FARGS, "No such rotation potential.");
3944 fprintf(stderr, "%s calculation (step %d) took %g seconds.\n", RotStr, step, MPI_Wtime()-t0);