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39 #include "pull_rotation.h"
49 #include "gromacs/commandline/filenm.h"
50 #include "gromacs/domdec/dlbtiming.h"
51 #include "gromacs/domdec/domdec_struct.h"
52 #include "gromacs/domdec/ga2la.h"
53 #include "gromacs/fileio/gmxfio.h"
54 #include "gromacs/fileio/xvgr.h"
55 #include "gromacs/gmxlib/network.h"
56 #include "gromacs/linearalgebra/nrjac.h"
57 #include "gromacs/math/functions.h"
58 #include "gromacs/math/utilities.h"
59 #include "gromacs/math/vec.h"
60 #include "gromacs/mdlib/groupcoord.h"
61 #include "gromacs/mdlib/mdrun.h"
62 #include "gromacs/mdlib/sim_util.h"
63 #include "gromacs/mdtypes/commrec.h"
64 #include "gromacs/mdtypes/inputrec.h"
65 #include "gromacs/mdtypes/md_enums.h"
66 #include "gromacs/mdtypes/state.h"
67 #include "gromacs/pbcutil/pbc.h"
68 #include "gromacs/timing/cyclecounter.h"
69 #include "gromacs/timing/wallcycle.h"
70 #include "gromacs/topology/mtop_lookup.h"
71 #include "gromacs/topology/mtop_util.h"
72 #include "gromacs/utility/fatalerror.h"
73 #include "gromacs/utility/pleasecite.h"
74 #include "gromacs/utility/qsort_threadsafe.h"
75 #include "gromacs/utility/smalloc.h"
77 static char const *RotStr = {"Enforced rotation:"};
79 /* Set the minimum weight for the determination of the slab centers */
80 #define WEIGHT_MIN (10*GMX_FLOAT_MIN)
82 /* Helper structure for sorting positions along rotation vector */
84 real xcproj; /* Projection of xc on the rotation vector */
85 int ind; /* Index of xc */
87 rvec x; /* Position */
88 rvec x_ref; /* Reference position */
92 /* Enforced rotation / flexible: determine the angle of each slab */
93 typedef struct gmx_slabdata
95 int nat; /* Number of atoms belonging to this slab */
96 rvec *x; /* The positions belonging to this slab. In
97 general, this should be all positions of the
98 whole rotation group, but we leave those away
99 that have a small enough weight */
100 rvec *ref; /* Same for reference */
101 real *weight; /* The weight for each atom */
105 /* Helper structure for potential fitting */
106 typedef struct gmx_potfit
108 real *degangle; /* Set of angles for which the potential is
109 calculated. The optimum fit is determined as
110 the angle for with the potential is minimal */
111 real *V; /* Potential for the different angles */
112 matrix *rotmat; /* Rotation matrix corresponding to the angles */
116 /* Enforced rotation data for all groups */
117 typedef struct gmx_enfrot
119 FILE *out_rot; /* Output file for rotation data */
120 FILE *out_torque; /* Output file for torque data */
121 FILE *out_angles; /* Output file for slab angles for flexible type */
122 FILE *out_slabs; /* Output file for slab centers */
123 int bufsize; /* Allocation size of buf */
124 rvec *xbuf; /* Coordinate buffer variable for sorting */
125 real *mbuf; /* Masses buffer variable for sorting */
126 sort_along_vec_t *data; /* Buffer variable needed for position sorting */
127 real *mpi_inbuf; /* MPI buffer */
128 real *mpi_outbuf; /* MPI buffer */
129 int mpi_bufsize; /* Allocation size of in & outbuf */
130 gmx_bool appendFiles; /* If true, append output files */
131 gmx_bool bOut; /* Used to skip first output when appending to
132 * avoid duplicate entries in rotation outfiles */
136 /* Global enforced rotation data for a single rotation group */
137 typedef struct gmx_enfrotgrp
139 real degangle; /* Rotation angle in degrees */
140 matrix rotmat; /* Rotation matrix */
141 int *ind_loc; /* Local rotation indices */
142 int nat_loc; /* Number of local group atoms */
143 int nalloc_loc; /* Allocation size for ind_loc and weight_loc */
145 real V; /* Rotation potential for this rotation group */
146 rvec *f_rot_loc; /* Array to store the forces on the local atoms
147 resulting from enforced rotation potential */
149 /* Collective coordinates for the whole rotation group */
150 real *xc_ref_length; /* Length of each x_rotref vector after x_rotref
151 has been put into origin */
152 int *xc_ref_ind; /* Position of each local atom in the collective
154 rvec xc_center; /* Center of the rotation group positions, may
156 rvec xc_ref_center; /* dito, for the reference positions */
157 rvec *xc; /* Current (collective) positions */
158 ivec *xc_shifts; /* Current (collective) shifts */
159 ivec *xc_eshifts; /* Extra shifts since last DD step */
160 rvec *xc_old; /* Old (collective) positions */
161 rvec *xc_norm; /* Normalized form of the current positions */
162 rvec *xc_ref_sorted; /* Reference positions (sorted in the same order
163 as xc when sorted) */
164 int *xc_sortind; /* Where is a position found after sorting? */
165 real *mc; /* Collective masses */
167 real invmass; /* one over the total mass of the rotation group */
169 real torque_v; /* Torque in the direction of rotation vector */
170 real angle_v; /* Actual angle of the whole rotation group */
171 /* Fixed rotation only */
172 real weight_v; /* Weights for angle determination */
173 rvec *xr_loc; /* Local reference coords, correctly rotated */
174 rvec *x_loc_pbc; /* Local current coords, correct PBC image */
175 real *m_loc; /* Masses of the current local atoms */
177 /* Flexible rotation only */
178 int nslabs_alloc; /* For this many slabs memory is allocated */
179 int slab_first; /* Lowermost slab for that the calculation needs
180 to be performed at a given time step */
181 int slab_last; /* Uppermost slab ... */
182 int slab_first_ref; /* First slab for which ref. center is stored */
183 int slab_last_ref; /* Last ... */
184 int slab_buffer; /* Slab buffer region around reference slabs */
185 int *firstatom; /* First relevant atom for a slab */
186 int *lastatom; /* Last relevant atom for a slab */
187 rvec *slab_center; /* Gaussian-weighted slab center */
188 rvec *slab_center_ref; /* Gaussian-weighted slab center for the
189 reference positions */
190 real *slab_weights; /* Sum of gaussian weights in a slab */
191 real *slab_torque_v; /* Torque T = r x f for each slab. */
192 /* torque_v = m.v = angular momentum in the
194 real max_beta; /* min_gaussian from inputrec->rotgrp is the
195 minimum value the gaussian must have so that
196 the force is actually evaluated max_beta is
197 just another way to put it */
198 real *gn_atom; /* Precalculated gaussians for a single atom */
199 int *gn_slabind; /* Tells to which slab each precalculated gaussian
201 rvec *slab_innersumvec; /* Inner sum of the flexible2 potential per slab;
202 this is precalculated for optimization reasons */
203 t_gmx_slabdata *slab_data; /* Holds atom positions and gaussian weights
204 of atoms belonging to a slab */
206 /* For potential fits with varying angle: */
207 t_gmx_potfit *PotAngleFit; /* Used for fit type 'potential' */
211 /* Activate output of forces for correctness checks */
212 /* #define PRINT_FORCES */
214 #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]);
215 #define PRINT_POT_TAU if (MASTER(cr)) { \
216 fprintf(stderr, "potential = %15.8f\n" "torque = %15.8f\n", erg->V, erg->torque_v); \
219 #define PRINT_FORCE_J
220 #define PRINT_POT_TAU
223 /* Shortcuts for often used queries */
224 #define ISFLEX(rg) ( ((rg)->eType == erotgFLEX) || ((rg)->eType == erotgFLEXT) || ((rg)->eType == erotgFLEX2) || ((rg)->eType == erotgFLEX2T) )
225 #define ISCOLL(rg) ( ((rg)->eType == erotgFLEX) || ((rg)->eType == erotgFLEXT) || ((rg)->eType == erotgFLEX2) || ((rg)->eType == erotgFLEX2T) || ((rg)->eType == erotgRMPF) || ((rg)->eType == erotgRM2PF) )
228 /* Does any of the rotation groups use slab decomposition? */
229 static gmx_bool HaveFlexibleGroups(t_rot *rot)
235 for (g = 0; g < rot->ngrp; g++)
248 /* Is for any group the fit angle determined by finding the minimum of the
249 * rotation potential? */
250 static gmx_bool HavePotFitGroups(t_rot *rot)
256 for (g = 0; g < rot->ngrp; g++)
259 if (erotgFitPOT == rotg->eFittype)
269 static double** allocate_square_matrix(int dim)
272 double** mat = nullptr;
276 for (i = 0; i < dim; i++)
285 static void free_square_matrix(double** mat, int dim)
290 for (i = 0; i < dim; i++)
298 /* Return the angle for which the potential is minimal */
299 static real get_fitangle(t_rotgrp *rotg, gmx_enfrotgrp_t erg)
302 real fitangle = -999.9;
303 real pot_min = GMX_FLOAT_MAX;
307 fit = erg->PotAngleFit;
309 for (i = 0; i < rotg->PotAngle_nstep; i++)
311 if (fit->V[i] < pot_min)
314 fitangle = fit->degangle[i];
322 /* Reduce potential angle fit data for this group at this time step? */
323 static inline gmx_bool bPotAngle(t_rot *rot, t_rotgrp *rotg, gmx_int64_t step)
325 return ( (erotgFitPOT == rotg->eFittype) && (do_per_step(step, rot->nstsout) || do_per_step(step, rot->nstrout)) );
328 /* Reduce slab torqe data for this group at this time step? */
329 static inline gmx_bool bSlabTau(t_rot *rot, t_rotgrp *rotg, gmx_int64_t step)
331 return ( (ISFLEX(rotg)) && do_per_step(step, rot->nstsout) );
334 /* Output rotation energy, torques, etc. for each rotation group */
335 static void reduce_output(const t_commrec *cr, t_rot *rot, real t, gmx_int64_t step)
337 int g, i, islab, nslabs = 0;
338 int count; /* MPI element counter */
340 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
341 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
348 /* Fill the MPI buffer with stuff to reduce. If items are added for reduction
349 * here, the MPI buffer size has to be enlarged also in calc_mpi_bufsize() */
353 for (g = 0; g < rot->ngrp; g++)
356 erg = rotg->enfrotgrp;
357 nslabs = erg->slab_last - erg->slab_first + 1;
358 er->mpi_inbuf[count++] = erg->V;
359 er->mpi_inbuf[count++] = erg->torque_v;
360 er->mpi_inbuf[count++] = erg->angle_v;
361 er->mpi_inbuf[count++] = erg->weight_v; /* weights are not needed for flex types, but this is just a single value */
363 if (bPotAngle(rot, rotg, step))
365 for (i = 0; i < rotg->PotAngle_nstep; i++)
367 er->mpi_inbuf[count++] = erg->PotAngleFit->V[i];
370 if (bSlabTau(rot, rotg, step))
372 for (i = 0; i < nslabs; i++)
374 er->mpi_inbuf[count++] = erg->slab_torque_v[i];
378 if (count > er->mpi_bufsize)
380 gmx_fatal(FARGS, "%s MPI buffer overflow, please report this error.", RotStr);
384 MPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REAL, MPI_SUM, MASTERRANK(cr), cr->mpi_comm_mygroup);
387 /* Copy back the reduced data from the buffer on the master */
391 for (g = 0; g < rot->ngrp; g++)
394 erg = rotg->enfrotgrp;
395 nslabs = erg->slab_last - erg->slab_first + 1;
396 erg->V = er->mpi_outbuf[count++];
397 erg->torque_v = er->mpi_outbuf[count++];
398 erg->angle_v = er->mpi_outbuf[count++];
399 erg->weight_v = er->mpi_outbuf[count++];
401 if (bPotAngle(rot, rotg, step))
403 for (i = 0; i < rotg->PotAngle_nstep; i++)
405 erg->PotAngleFit->V[i] = er->mpi_outbuf[count++];
408 if (bSlabTau(rot, rotg, step))
410 for (i = 0; i < nslabs; i++)
412 erg->slab_torque_v[i] = er->mpi_outbuf[count++];
422 /* Angle and torque for each rotation group */
423 for (g = 0; g < rot->ngrp; g++)
426 bFlex = ISFLEX(rotg);
428 erg = rotg->enfrotgrp;
430 /* Output to main rotation output file: */
431 if (do_per_step(step, rot->nstrout) )
433 if (erotgFitPOT == rotg->eFittype)
435 fitangle = get_fitangle(rotg, erg);
441 fitangle = erg->angle_v; /* RMSD fit angle */
445 fitangle = (erg->angle_v/erg->weight_v)*180.0*M_1_PI;
448 fprintf(er->out_rot, "%12.4f", fitangle);
449 fprintf(er->out_rot, "%12.3e", erg->torque_v);
450 fprintf(er->out_rot, "%12.3e", erg->V);
453 if (do_per_step(step, rot->nstsout) )
455 /* Output to torque log file: */
458 fprintf(er->out_torque, "%12.3e%6d", t, g);
459 for (i = erg->slab_first; i <= erg->slab_last; i++)
461 islab = i - erg->slab_first; /* slab index */
462 /* Only output if enough weight is in slab */
463 if (erg->slab_weights[islab] > rotg->min_gaussian)
465 fprintf(er->out_torque, "%6d%12.3e", i, erg->slab_torque_v[islab]);
468 fprintf(er->out_torque, "\n");
471 /* Output to angles log file: */
472 if (erotgFitPOT == rotg->eFittype)
474 fprintf(er->out_angles, "%12.3e%6d%12.4f", t, g, erg->degangle);
475 /* Output energies at a set of angles around the reference angle */
476 for (i = 0; i < rotg->PotAngle_nstep; i++)
478 fprintf(er->out_angles, "%12.3e", erg->PotAngleFit->V[i]);
480 fprintf(er->out_angles, "\n");
484 if (do_per_step(step, rot->nstrout) )
486 fprintf(er->out_rot, "\n");
492 /* Add the forces from enforced rotation potential to the local forces.
493 * Should be called after the SR forces have been evaluated */
494 extern real add_rot_forces(t_rot *rot, rvec f[], const t_commrec *cr, gmx_int64_t step, real t)
498 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
499 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
500 real Vrot = 0.0; /* If more than one rotation group is present, Vrot
501 assembles the local parts from all groups */
506 /* Loop over enforced rotation groups (usually 1, though)
507 * Apply the forces from rotation potentials */
508 for (g = 0; g < rot->ngrp; g++)
511 erg = rotg->enfrotgrp;
512 Vrot += erg->V; /* add the local parts from the nodes */
513 for (l = 0; l < erg->nat_loc; l++)
515 /* Get the right index of the local force */
516 ii = erg->ind_loc[l];
518 rvec_inc(f[ii], erg->f_rot_loc[l]);
522 /* Reduce energy,torque, angles etc. to get the sum values (per rotation group)
523 * on the master and output these values to file. */
524 if ( (do_per_step(step, rot->nstrout) || do_per_step(step, rot->nstsout)) && er->bOut)
526 reduce_output(cr, rot, t, step);
529 /* When appending, er->bOut is FALSE the first time to avoid duplicate entries */
538 /* The Gaussian norm is chosen such that the sum of the gaussian functions
539 * over the slabs is approximately 1.0 everywhere */
540 #define GAUSS_NORM 0.569917543430618
543 /* Calculate the maximum beta that leads to a gaussian larger min_gaussian,
544 * also does some checks
546 static double calc_beta_max(real min_gaussian, real slab_dist)
552 /* Actually the next two checks are already made in grompp */
555 gmx_fatal(FARGS, "Slab distance of flexible rotation groups must be >=0 !");
557 if (min_gaussian <= 0)
559 gmx_fatal(FARGS, "Cutoff value for Gaussian must be > 0. (You requested %f)");
562 /* Define the sigma value */
563 sigma = 0.7*slab_dist;
565 /* Calculate the argument for the logarithm and check that the log() result is negative or 0 */
566 arg = min_gaussian/GAUSS_NORM;
569 gmx_fatal(FARGS, "min_gaussian of flexible rotation groups must be <%g", GAUSS_NORM);
572 return std::sqrt(-2.0*sigma*sigma*log(min_gaussian/GAUSS_NORM));
576 static inline real calc_beta(rvec curr_x, t_rotgrp *rotg, int n)
578 return iprod(curr_x, rotg->vec) - rotg->slab_dist * n;
582 static inline real gaussian_weight(rvec curr_x, t_rotgrp *rotg, int n)
584 const real norm = GAUSS_NORM;
588 /* Define the sigma value */
589 sigma = 0.7*rotg->slab_dist;
590 /* Calculate the Gaussian value of slab n for position curr_x */
591 return norm * exp( -0.5 * gmx::square( calc_beta(curr_x, rotg, n)/sigma ) );
595 /* Returns the weight in a single slab, also calculates the Gaussian- and mass-
596 * weighted sum of positions for that slab */
597 static real get_slab_weight(int j, t_rotgrp *rotg, rvec xc[], const real mc[], rvec *x_weighted_sum)
599 rvec curr_x; /* The position of an atom */
600 rvec curr_x_weighted; /* The gaussian-weighted position */
601 real gaussian; /* A single gaussian weight */
602 real wgauss; /* gaussian times current mass */
603 real slabweight = 0.0; /* The sum of weights in the slab */
607 clear_rvec(*x_weighted_sum);
609 /* Loop over all atoms in the rotation group */
610 for (i = 0; i < rotg->nat; i++)
612 copy_rvec(xc[i], curr_x);
613 gaussian = gaussian_weight(curr_x, rotg, j);
614 wgauss = gaussian * mc[i];
615 svmul(wgauss, curr_x, curr_x_weighted);
616 rvec_add(*x_weighted_sum, curr_x_weighted, *x_weighted_sum);
617 slabweight += wgauss;
618 } /* END of loop over rotation group atoms */
624 static void get_slab_centers(
625 t_rotgrp *rotg, /* The rotation group information */
626 rvec *xc, /* The rotation group positions; will
627 typically be enfrotgrp->xc, but at first call
628 it is enfrotgrp->xc_ref */
629 real *mc, /* The masses of the rotation group atoms */
630 int g, /* The number of the rotation group */
631 real time, /* Used for output only */
632 FILE *out_slabs, /* For outputting center per slab information */
633 gmx_bool bOutStep, /* Is this an output step? */
634 gmx_bool bReference) /* If this routine is called from
635 init_rot_group we need to store
636 the reference slab centers */
640 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
643 erg = rotg->enfrotgrp;
645 /* Loop over slabs */
646 for (j = erg->slab_first; j <= erg->slab_last; j++)
648 islab = j - erg->slab_first;
649 erg->slab_weights[islab] = get_slab_weight(j, rotg, xc, mc, &erg->slab_center[islab]);
651 /* We can do the calculations ONLY if there is weight in the slab! */
652 if (erg->slab_weights[islab] > WEIGHT_MIN)
654 svmul(1.0/erg->slab_weights[islab], erg->slab_center[islab], erg->slab_center[islab]);
658 /* We need to check this here, since we divide through slab_weights
659 * in the flexible low-level routines! */
660 gmx_fatal(FARGS, "Not enough weight in slab %d. Slab center cannot be determined!", j);
663 /* At first time step: save the centers of the reference structure */
666 copy_rvec(erg->slab_center[islab], erg->slab_center_ref[islab]);
668 } /* END of loop over slabs */
670 /* Output on the master */
671 if ( (nullptr != out_slabs) && bOutStep)
673 fprintf(out_slabs, "%12.3e%6d", time, g);
674 for (j = erg->slab_first; j <= erg->slab_last; j++)
676 islab = j - erg->slab_first;
677 fprintf(out_slabs, "%6d%12.3e%12.3e%12.3e",
678 j, erg->slab_center[islab][XX], erg->slab_center[islab][YY], erg->slab_center[islab][ZZ]);
680 fprintf(out_slabs, "\n");
685 static void calc_rotmat(
687 real degangle, /* Angle alpha of rotation at time t in degrees */
688 matrix rotmat) /* Rotation matrix */
690 real radangle; /* Rotation angle in radians */
691 real cosa; /* cosine alpha */
692 real sina; /* sine alpha */
693 real OMcosa; /* 1 - cos(alpha) */
694 real dumxy, dumxz, dumyz; /* save computations */
695 rvec rot_vec; /* Rotate around rot_vec ... */
698 radangle = degangle * M_PI/180.0;
699 copy_rvec(vec, rot_vec );
701 /* Precompute some variables: */
702 cosa = cos(radangle);
703 sina = sin(radangle);
705 dumxy = rot_vec[XX]*rot_vec[YY]*OMcosa;
706 dumxz = rot_vec[XX]*rot_vec[ZZ]*OMcosa;
707 dumyz = rot_vec[YY]*rot_vec[ZZ]*OMcosa;
709 /* Construct the rotation matrix for this rotation group: */
711 rotmat[XX][XX] = cosa + rot_vec[XX]*rot_vec[XX]*OMcosa;
712 rotmat[YY][XX] = dumxy + rot_vec[ZZ]*sina;
713 rotmat[ZZ][XX] = dumxz - rot_vec[YY]*sina;
715 rotmat[XX][YY] = dumxy - rot_vec[ZZ]*sina;
716 rotmat[YY][YY] = cosa + rot_vec[YY]*rot_vec[YY]*OMcosa;
717 rotmat[ZZ][YY] = dumyz + rot_vec[XX]*sina;
719 rotmat[XX][ZZ] = dumxz + rot_vec[YY]*sina;
720 rotmat[YY][ZZ] = dumyz - rot_vec[XX]*sina;
721 rotmat[ZZ][ZZ] = cosa + rot_vec[ZZ]*rot_vec[ZZ]*OMcosa;
726 for (iii = 0; iii < 3; iii++)
728 for (jjj = 0; jjj < 3; jjj++)
730 fprintf(stderr, " %10.8f ", rotmat[iii][jjj]);
732 fprintf(stderr, "\n");
738 /* Calculates torque on the rotation axis tau = position x force */
739 static inline real torque(
740 rvec rotvec, /* rotation vector; MUST be normalized! */
741 rvec force, /* force */
742 rvec x, /* position of atom on which the force acts */
743 rvec pivot) /* pivot point of rotation axis */
748 /* Subtract offset */
749 rvec_sub(x, pivot, vectmp);
751 /* position x force */
752 cprod(vectmp, force, tau);
754 /* Return the part of the torque which is parallel to the rotation vector */
755 return iprod(tau, rotvec);
759 /* Right-aligned output of value with standard width */
760 static void print_aligned(FILE *fp, char const *str)
762 fprintf(fp, "%12s", str);
766 /* Right-aligned output of value with standard short width */
767 static void print_aligned_short(FILE *fp, char const *str)
769 fprintf(fp, "%6s", str);
773 static FILE *open_output_file(const char *fn, int steps, const char what[])
778 fp = gmx_ffopen(fn, "w");
780 fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n",
781 what, steps, steps > 1 ? "s" : "");
787 /* Open output file for slab center data. Call on master only */
788 static FILE *open_slab_out(const char *fn, t_rot *rot)
795 if (rot->enfrot->appendFiles)
797 fp = gmx_fio_fopen(fn, "a");
801 fp = open_output_file(fn, rot->nstsout, "gaussian weighted slab centers");
803 for (g = 0; g < rot->ngrp; g++)
808 fprintf(fp, "# Rotation group %d (%s), slab distance %f nm, %s.\n",
809 g, erotg_names[rotg->eType], rotg->slab_dist,
810 rotg->bMassW ? "centers of mass" : "geometrical centers");
814 fprintf(fp, "# Reference centers are listed first (t=-1).\n");
815 fprintf(fp, "# The following columns have the syntax:\n");
817 print_aligned_short(fp, "t");
818 print_aligned_short(fp, "grp");
819 /* Print legend for the first two entries only ... */
820 for (i = 0; i < 2; i++)
822 print_aligned_short(fp, "slab");
823 print_aligned(fp, "X center");
824 print_aligned(fp, "Y center");
825 print_aligned(fp, "Z center");
827 fprintf(fp, " ...\n");
835 /* Adds 'buf' to 'str' */
836 static void add_to_string(char **str, char *buf)
841 len = strlen(*str) + strlen(buf) + 1;
847 static void add_to_string_aligned(char **str, char *buf)
849 char buf_aligned[STRLEN];
851 sprintf(buf_aligned, "%12s", buf);
852 add_to_string(str, buf_aligned);
856 /* Open output file and print some general information about the rotation groups.
857 * Call on master only */
858 static FILE *open_rot_out(const char *fn, t_rot *rot, const gmx_output_env_t *oenv)
863 const char **setname;
864 char buf[50], buf2[75];
865 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
867 char *LegendStr = nullptr;
870 if (rot->enfrot->appendFiles)
872 fp = gmx_fio_fopen(fn, "a");
876 fp = xvgropen(fn, "Rotation angles and energy", "Time (ps)", "angles (degrees) and energies (kJ/mol)", oenv);
877 fprintf(fp, "# Output of enforced rotation data is written in intervals of %d time step%s.\n#\n", rot->nstrout, rot->nstrout > 1 ? "s" : "");
878 fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector v.\n");
879 fprintf(fp, "# To obtain the vectorial torque, multiply tau with the group's rot-vec.\n");
880 fprintf(fp, "# For flexible groups, tau(t,n) from all slabs n have been summed in a single value tau(t) here.\n");
881 fprintf(fp, "# The torques tau(t,n) are found in the rottorque.log (-rt) output file\n");
883 for (g = 0; g < rot->ngrp; g++)
886 erg = rotg->enfrotgrp;
887 bFlex = ISFLEX(rotg);
890 fprintf(fp, "# ROTATION GROUP %d, potential type '%s':\n", g, erotg_names[rotg->eType]);
891 fprintf(fp, "# rot-massw%d %s\n", g, yesno_names[rotg->bMassW]);
892 fprintf(fp, "# rot-vec%d %12.5e %12.5e %12.5e\n", g, rotg->vec[XX], rotg->vec[YY], rotg->vec[ZZ]);
893 fprintf(fp, "# rot-rate%d %12.5e degrees/ps\n", g, rotg->rate);
894 fprintf(fp, "# rot-k%d %12.5e kJ/(mol*nm^2)\n", g, rotg->k);
895 if (rotg->eType == erotgISO || rotg->eType == erotgPM || rotg->eType == erotgRM || rotg->eType == erotgRM2)
897 fprintf(fp, "# rot-pivot%d %12.5e %12.5e %12.5e nm\n", g, rotg->pivot[XX], rotg->pivot[YY], rotg->pivot[ZZ]);
902 fprintf(fp, "# rot-slab-distance%d %f nm\n", g, rotg->slab_dist);
903 fprintf(fp, "# rot-min-gaussian%d %12.5e\n", g, rotg->min_gaussian);
906 /* Output the centers of the rotation groups for the pivot-free potentials */
907 if ((rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) || (rotg->eType == erotgRMPF) || (rotg->eType == erotgRM2PF
908 || (rotg->eType == erotgFLEXT) || (rotg->eType == erotgFLEX2T)) )
910 fprintf(fp, "# ref. grp. %d center %12.5e %12.5e %12.5e\n", g,
911 erg->xc_ref_center[XX], erg->xc_ref_center[YY], erg->xc_ref_center[ZZ]);
913 fprintf(fp, "# grp. %d init.center %12.5e %12.5e %12.5e\n", g,
914 erg->xc_center[XX], erg->xc_center[YY], erg->xc_center[ZZ]);
917 if ( (rotg->eType == erotgRM2) || (rotg->eType == erotgFLEX2) || (rotg->eType == erotgFLEX2T) )
919 fprintf(fp, "# rot-eps%d %12.5e nm^2\n", g, rotg->eps);
921 if (erotgFitPOT == rotg->eFittype)
924 fprintf(fp, "# theta_fit%d is determined by first evaluating the potential for %d angles around theta_ref%d.\n",
925 g, rotg->PotAngle_nstep, g);
926 fprintf(fp, "# The fit angle is the one with the smallest potential. It is given as the deviation\n");
927 fprintf(fp, "# from the reference angle, i.e. if theta_ref=X and theta_fit=Y, then the angle with\n");
928 fprintf(fp, "# minimal value of the potential is X+Y. Angular resolution is %g degrees.\n", rotg->PotAngle_step);
932 /* Print a nice legend */
935 sprintf(buf, "# %6s", "time");
936 add_to_string_aligned(&LegendStr, buf);
939 snew(setname, 4*rot->ngrp);
941 for (g = 0; g < rot->ngrp; g++)
943 sprintf(buf, "theta_ref%d", g);
944 add_to_string_aligned(&LegendStr, buf);
946 sprintf(buf2, "%s (degrees)", buf);
947 setname[nsets] = gmx_strdup(buf2);
950 for (g = 0; g < rot->ngrp; g++)
953 bFlex = ISFLEX(rotg);
955 /* For flexible axis rotation we use RMSD fitting to determine the
956 * actual angle of the rotation group */
957 if (bFlex || erotgFitPOT == rotg->eFittype)
959 sprintf(buf, "theta_fit%d", g);
963 sprintf(buf, "theta_av%d", g);
965 add_to_string_aligned(&LegendStr, buf);
966 sprintf(buf2, "%s (degrees)", buf);
967 setname[nsets] = gmx_strdup(buf2);
970 sprintf(buf, "tau%d", g);
971 add_to_string_aligned(&LegendStr, buf);
972 sprintf(buf2, "%s (kJ/mol)", buf);
973 setname[nsets] = gmx_strdup(buf2);
976 sprintf(buf, "energy%d", g);
977 add_to_string_aligned(&LegendStr, buf);
978 sprintf(buf2, "%s (kJ/mol)", buf);
979 setname[nsets] = gmx_strdup(buf2);
986 xvgr_legend(fp, nsets, setname, oenv);
990 fprintf(fp, "#\n# Legend for the following data columns:\n");
991 fprintf(fp, "%s\n", LegendStr);
1001 /* Call on master only */
1002 static FILE *open_angles_out(const char *fn, t_rot *rot)
1007 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1011 if (rot->enfrot->appendFiles)
1013 fp = gmx_fio_fopen(fn, "a");
1017 /* Open output file and write some information about it's structure: */
1018 fp = open_output_file(fn, rot->nstsout, "rotation group angles");
1019 fprintf(fp, "# All angles given in degrees, time in ps.\n");
1020 for (g = 0; g < rot->ngrp; g++)
1022 rotg = &rot->grp[g];
1023 erg = rotg->enfrotgrp;
1025 /* Output for this group happens only if potential type is flexible or
1026 * if fit type is potential! */
1027 if (ISFLEX(rotg) || (erotgFitPOT == rotg->eFittype) )
1031 sprintf(buf, " slab distance %f nm, ", rotg->slab_dist);
1038 fprintf(fp, "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n",
1039 g, erotg_names[rotg->eType], buf, erotg_fitnames[rotg->eFittype]);
1041 /* Special type of fitting using the potential minimum. This is
1042 * done for the whole group only, not for the individual slabs. */
1043 if (erotgFitPOT == rotg->eFittype)
1045 fprintf(fp, "# To obtain theta_fit%d, the potential is evaluated for %d angles around theta_ref%d\n", g, rotg->PotAngle_nstep, g);
1046 fprintf(fp, "# The fit angle in the rotation standard outfile is the one with minimal energy E(theta_fit) [kJ/mol].\n");
1050 fprintf(fp, "# Legend for the group %d data columns:\n", g);
1052 print_aligned_short(fp, "time");
1053 print_aligned_short(fp, "grp");
1054 print_aligned(fp, "theta_ref");
1056 if (erotgFitPOT == rotg->eFittype)
1058 /* Output the set of angles around the reference angle */
1059 for (i = 0; i < rotg->PotAngle_nstep; i++)
1061 sprintf(buf, "E(%g)", erg->PotAngleFit->degangle[i]);
1062 print_aligned(fp, buf);
1067 /* Output fit angle for each slab */
1068 print_aligned_short(fp, "slab");
1069 print_aligned_short(fp, "atoms");
1070 print_aligned(fp, "theta_fit");
1071 print_aligned_short(fp, "slab");
1072 print_aligned_short(fp, "atoms");
1073 print_aligned(fp, "theta_fit");
1074 fprintf(fp, " ...");
1086 /* Open torque output file and write some information about it's structure.
1087 * Call on master only */
1088 static FILE *open_torque_out(const char *fn, t_rot *rot)
1095 if (rot->enfrot->appendFiles)
1097 fp = gmx_fio_fopen(fn, "a");
1101 fp = open_output_file(fn, rot->nstsout, "torques");
1103 for (g = 0; g < rot->ngrp; g++)
1105 rotg = &rot->grp[g];
1108 fprintf(fp, "# Rotation group %d (%s), slab distance %f nm.\n", g, erotg_names[rotg->eType], rotg->slab_dist);
1109 fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector.\n");
1110 fprintf(fp, "# To obtain the vectorial torque, multiply tau with\n");
1111 fprintf(fp, "# rot-vec%d %10.3e %10.3e %10.3e\n", g, rotg->vec[XX], rotg->vec[YY], rotg->vec[ZZ]);
1115 fprintf(fp, "# Legend for the following data columns: (tau=torque for that slab):\n");
1117 print_aligned_short(fp, "t");
1118 print_aligned_short(fp, "grp");
1119 print_aligned_short(fp, "slab");
1120 print_aligned(fp, "tau");
1121 print_aligned_short(fp, "slab");
1122 print_aligned(fp, "tau");
1123 fprintf(fp, " ...\n");
1131 static void swap_val(double* vec, int i, int j)
1133 double tmp = vec[j];
1141 static void swap_col(double **mat, int i, int j)
1143 double tmp[3] = {mat[0][j], mat[1][j], mat[2][j]};
1146 mat[0][j] = mat[0][i];
1147 mat[1][j] = mat[1][i];
1148 mat[2][j] = mat[2][i];
1156 /* Eigenvectors are stored in columns of eigen_vec */
1157 static void diagonalize_symmetric(
1165 jacobi(matrix, 3, eigenval, eigen_vec, &n_rot);
1167 /* sort in ascending order */
1168 if (eigenval[0] > eigenval[1])
1170 swap_val(eigenval, 0, 1);
1171 swap_col(eigen_vec, 0, 1);
1173 if (eigenval[1] > eigenval[2])
1175 swap_val(eigenval, 1, 2);
1176 swap_col(eigen_vec, 1, 2);
1178 if (eigenval[0] > eigenval[1])
1180 swap_val(eigenval, 0, 1);
1181 swap_col(eigen_vec, 0, 1);
1186 static void align_with_z(
1187 rvec* s, /* Structure to align */
1192 rvec zet = {0.0, 0.0, 1.0};
1193 rvec rot_axis = {0.0, 0.0, 0.0};
1194 rvec *rotated_str = nullptr;
1200 snew(rotated_str, natoms);
1202 /* Normalize the axis */
1203 ooanorm = 1.0/norm(axis);
1204 svmul(ooanorm, axis, axis);
1206 /* Calculate the angle for the fitting procedure */
1207 cprod(axis, zet, rot_axis);
1208 angle = acos(axis[2]);
1214 /* Calculate the rotation matrix */
1215 calc_rotmat(rot_axis, angle*180.0/M_PI, rotmat);
1217 /* Apply the rotation matrix to s */
1218 for (i = 0; i < natoms; i++)
1220 for (j = 0; j < 3; j++)
1222 for (k = 0; k < 3; k++)
1224 rotated_str[i][j] += rotmat[j][k]*s[i][k];
1229 /* Rewrite the rotated structure to s */
1230 for (i = 0; i < natoms; i++)
1232 for (j = 0; j < 3; j++)
1234 s[i][j] = rotated_str[i][j];
1242 static void calc_correl_matrix(rvec* Xstr, rvec* Ystr, double** Rmat, int natoms)
1247 for (i = 0; i < 3; i++)
1249 for (j = 0; j < 3; j++)
1255 for (i = 0; i < 3; i++)
1257 for (j = 0; j < 3; j++)
1259 for (k = 0; k < natoms; k++)
1261 Rmat[i][j] += Ystr[k][i] * Xstr[k][j];
1268 static void weigh_coords(rvec* str, real* weight, int natoms)
1273 for (i = 0; i < natoms; i++)
1275 for (j = 0; j < 3; j++)
1277 str[i][j] *= std::sqrt(weight[i]);
1283 static real opt_angle_analytic(
1293 rvec *ref_s_1 = nullptr;
1294 rvec *act_s_1 = nullptr;
1296 double **Rmat, **RtR, **eigvec;
1298 double V[3][3], WS[3][3];
1299 double rot_matrix[3][3];
1303 /* Do not change the original coordinates */
1304 snew(ref_s_1, natoms);
1305 snew(act_s_1, natoms);
1306 for (i = 0; i < natoms; i++)
1308 copy_rvec(ref_s[i], ref_s_1[i]);
1309 copy_rvec(act_s[i], act_s_1[i]);
1312 /* Translate the structures to the origin */
1313 shift[XX] = -ref_com[XX];
1314 shift[YY] = -ref_com[YY];
1315 shift[ZZ] = -ref_com[ZZ];
1316 translate_x(ref_s_1, natoms, shift);
1318 shift[XX] = -act_com[XX];
1319 shift[YY] = -act_com[YY];
1320 shift[ZZ] = -act_com[ZZ];
1321 translate_x(act_s_1, natoms, shift);
1323 /* Align rotation axis with z */
1324 align_with_z(ref_s_1, natoms, axis);
1325 align_with_z(act_s_1, natoms, axis);
1327 /* Correlation matrix */
1328 Rmat = allocate_square_matrix(3);
1330 for (i = 0; i < natoms; i++)
1332 ref_s_1[i][2] = 0.0;
1333 act_s_1[i][2] = 0.0;
1336 /* Weight positions with sqrt(weight) */
1337 if (nullptr != weight)
1339 weigh_coords(ref_s_1, weight, natoms);
1340 weigh_coords(act_s_1, weight, natoms);
1343 /* Calculate correlation matrices R=YXt (X=ref_s; Y=act_s) */
1344 calc_correl_matrix(ref_s_1, act_s_1, Rmat, natoms);
1347 RtR = allocate_square_matrix(3);
1348 for (i = 0; i < 3; i++)
1350 for (j = 0; j < 3; j++)
1352 for (k = 0; k < 3; k++)
1354 RtR[i][j] += Rmat[k][i] * Rmat[k][j];
1358 /* Diagonalize RtR */
1360 for (i = 0; i < 3; i++)
1365 diagonalize_symmetric(RtR, eigvec, eigval);
1366 swap_col(eigvec, 0, 1);
1367 swap_col(eigvec, 1, 2);
1368 swap_val(eigval, 0, 1);
1369 swap_val(eigval, 1, 2);
1372 for (i = 0; i < 3; i++)
1374 for (j = 0; j < 3; j++)
1381 for (i = 0; i < 2; i++)
1383 for (j = 0; j < 2; j++)
1385 WS[i][j] = eigvec[i][j] / std::sqrt(eigval[j]);
1389 for (i = 0; i < 3; i++)
1391 for (j = 0; j < 3; j++)
1393 for (k = 0; k < 3; k++)
1395 V[i][j] += Rmat[i][k]*WS[k][j];
1399 free_square_matrix(Rmat, 3);
1401 /* Calculate optimal rotation matrix */
1402 for (i = 0; i < 3; i++)
1404 for (j = 0; j < 3; j++)
1406 rot_matrix[i][j] = 0.0;
1410 for (i = 0; i < 3; i++)
1412 for (j = 0; j < 3; j++)
1414 for (k = 0; k < 3; k++)
1416 rot_matrix[i][j] += eigvec[i][k]*V[j][k];
1420 rot_matrix[2][2] = 1.0;
1422 /* In some cases abs(rot_matrix[0][0]) can be slighly larger
1423 * than unity due to numerical inacurracies. To be able to calculate
1424 * the acos function, we put these values back in range. */
1425 if (rot_matrix[0][0] > 1.0)
1427 rot_matrix[0][0] = 1.0;
1429 else if (rot_matrix[0][0] < -1.0)
1431 rot_matrix[0][0] = -1.0;
1434 /* Determine the optimal rotation angle: */
1435 opt_angle = (-1.0)*acos(rot_matrix[0][0])*180.0/M_PI;
1436 if (rot_matrix[0][1] < 0.0)
1438 opt_angle = (-1.0)*opt_angle;
1441 /* Give back some memory */
1442 free_square_matrix(RtR, 3);
1445 for (i = 0; i < 3; i++)
1451 return (real) opt_angle;
1455 /* Determine angle of the group by RMSD fit to the reference */
1456 /* Not parallelized, call this routine only on the master */
1457 static real flex_fit_angle(t_rotgrp *rotg)
1460 rvec *fitcoords = nullptr;
1461 rvec center; /* Center of positions passed to the fit routine */
1462 real fitangle; /* Angle of the rotation group derived by fitting */
1465 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1468 erg = rotg->enfrotgrp;
1470 /* Get the center of the rotation group.
1471 * Note, again, erg->xc has been sorted in do_flexible */
1472 get_center(erg->xc, erg->mc_sorted, rotg->nat, center);
1474 /* === Determine the optimal fit angle for the rotation group === */
1475 if (rotg->eFittype == erotgFitNORM)
1477 /* Normalize every position to it's reference length */
1478 for (i = 0; i < rotg->nat; i++)
1480 /* Put the center of the positions into the origin */
1481 rvec_sub(erg->xc[i], center, coord);
1482 /* Determine the scaling factor for the length: */
1483 scal = erg->xc_ref_length[erg->xc_sortind[i]] / norm(coord);
1484 /* Get position, multiply with the scaling factor and save */
1485 svmul(scal, coord, erg->xc_norm[i]);
1487 fitcoords = erg->xc_norm;
1491 fitcoords = erg->xc;
1493 /* From the point of view of the current positions, the reference has rotated
1494 * backwards. Since we output the angle relative to the fixed reference,
1495 * we need the minus sign. */
1496 fitangle = -opt_angle_analytic(erg->xc_ref_sorted, fitcoords, erg->mc_sorted,
1497 rotg->nat, erg->xc_ref_center, center, rotg->vec);
1503 /* Determine actual angle of each slab by RMSD fit to the reference */
1504 /* Not parallelized, call this routine only on the master */
1505 static void flex_fit_angle_perslab(
1512 int i, l, n, islab, ind;
1514 rvec act_center; /* Center of actual positions that are passed to the fit routine */
1515 rvec ref_center; /* Same for the reference positions */
1516 real fitangle; /* Angle of a slab derived from an RMSD fit to
1517 * the reference structure at t=0 */
1519 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1520 real OOm_av; /* 1/average_mass of a rotation group atom */
1521 real m_rel; /* Relative mass of a rotation group atom */
1524 erg = rotg->enfrotgrp;
1526 /* Average mass of a rotation group atom: */
1527 OOm_av = erg->invmass*rotg->nat;
1529 /**********************************/
1530 /* First collect the data we need */
1531 /**********************************/
1533 /* Collect the data for the individual slabs */
1534 for (n = erg->slab_first; n <= erg->slab_last; n++)
1536 islab = n - erg->slab_first; /* slab index */
1537 sd = &(rotg->enfrotgrp->slab_data[islab]);
1538 sd->nat = erg->lastatom[islab]-erg->firstatom[islab]+1;
1541 /* Loop over the relevant atoms in the slab */
1542 for (l = erg->firstatom[islab]; l <= erg->lastatom[islab]; l++)
1544 /* Current position of this atom: x[ii][XX/YY/ZZ] */
1545 copy_rvec(erg->xc[l], curr_x);
1547 /* The (unrotated) reference position of this atom is copied to ref_x.
1548 * Beware, the xc coords have been sorted in do_flexible */
1549 copy_rvec(erg->xc_ref_sorted[l], ref_x);
1551 /* Save data for doing angular RMSD fit later */
1552 /* Save the current atom position */
1553 copy_rvec(curr_x, sd->x[ind]);
1554 /* Save the corresponding reference position */
1555 copy_rvec(ref_x, sd->ref[ind]);
1557 /* Maybe also mass-weighting was requested. If yes, additionally
1558 * multiply the weights with the relative mass of the atom. If not,
1559 * multiply with unity. */
1560 m_rel = erg->mc_sorted[l]*OOm_av;
1562 /* Save the weight for this atom in this slab */
1563 sd->weight[ind] = gaussian_weight(curr_x, rotg, n) * m_rel;
1565 /* Next atom in this slab */
1570 /******************************/
1571 /* Now do the fit calculation */
1572 /******************************/
1574 fprintf(fp, "%12.3e%6d%12.3f", t, g, degangle);
1576 /* === Now do RMSD fitting for each slab === */
1577 /* We require at least SLAB_MIN_ATOMS in a slab, such that the fit makes sense. */
1578 #define SLAB_MIN_ATOMS 4
1580 for (n = erg->slab_first; n <= erg->slab_last; n++)
1582 islab = n - erg->slab_first; /* slab index */
1583 sd = &(rotg->enfrotgrp->slab_data[islab]);
1584 if (sd->nat >= SLAB_MIN_ATOMS)
1586 /* Get the center of the slabs reference and current positions */
1587 get_center(sd->ref, sd->weight, sd->nat, ref_center);
1588 get_center(sd->x, sd->weight, sd->nat, act_center);
1589 if (rotg->eFittype == erotgFitNORM)
1591 /* Normalize every position to it's reference length
1592 * prior to performing the fit */
1593 for (i = 0; i < sd->nat; i++) /* Center */
1595 rvec_dec(sd->ref[i], ref_center);
1596 rvec_dec(sd->x[i], act_center);
1597 /* Normalize x_i such that it gets the same length as ref_i */
1598 svmul( norm(sd->ref[i])/norm(sd->x[i]), sd->x[i], sd->x[i] );
1600 /* We already subtracted the centers */
1601 clear_rvec(ref_center);
1602 clear_rvec(act_center);
1604 fitangle = -opt_angle_analytic(sd->ref, sd->x, sd->weight, sd->nat,
1605 ref_center, act_center, rotg->vec);
1606 fprintf(fp, "%6d%6d%12.3f", n, sd->nat, fitangle);
1611 #undef SLAB_MIN_ATOMS
1615 /* Shift x with is */
1616 static inline void shift_single_coord(const matrix box, rvec x, const ivec is)
1627 x[XX] += tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
1628 x[YY] += ty*box[YY][YY]+tz*box[ZZ][YY];
1629 x[ZZ] += tz*box[ZZ][ZZ];
1633 x[XX] += tx*box[XX][XX];
1634 x[YY] += ty*box[YY][YY];
1635 x[ZZ] += tz*box[ZZ][ZZ];
1640 /* Determine the 'home' slab of this atom which is the
1641 * slab with the highest Gaussian weight of all */
1642 #define round(a) (int)((a)+0.5)
1643 static inline int get_homeslab(
1644 rvec curr_x, /* The position for which the home slab shall be determined */
1645 rvec rotvec, /* The rotation vector */
1646 real slabdist) /* The slab distance */
1651 /* The distance of the atom to the coordinate center (where the
1652 * slab with index 0) is */
1653 dist = iprod(rotvec, curr_x);
1655 return round(dist / slabdist);
1659 /* For a local atom determine the relevant slabs, i.e. slabs in
1660 * which the gaussian is larger than min_gaussian
1662 static int get_single_atom_gaussians(
1669 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1672 erg = rotg->enfrotgrp;
1674 /* Determine the 'home' slab of this atom: */
1675 homeslab = get_homeslab(curr_x, rotg->vec, rotg->slab_dist);
1677 /* First determine the weight in the atoms home slab: */
1678 g = gaussian_weight(curr_x, rotg, homeslab);
1680 erg->gn_atom[count] = g;
1681 erg->gn_slabind[count] = homeslab;
1685 /* Determine the max slab */
1687 while (g > rotg->min_gaussian)
1690 g = gaussian_weight(curr_x, rotg, slab);
1691 erg->gn_slabind[count] = slab;
1692 erg->gn_atom[count] = g;
1697 /* Determine the min slab */
1702 g = gaussian_weight(curr_x, rotg, slab);
1703 erg->gn_slabind[count] = slab;
1704 erg->gn_atom[count] = g;
1707 while (g > rotg->min_gaussian);
1714 static void flex2_precalc_inner_sum(t_rotgrp *rotg)
1717 rvec xi; /* positions in the i-sum */
1718 rvec xcn, ycn; /* the current and the reference slab centers */
1721 rvec rin; /* Helper variables */
1724 real OOpsii, OOpsiistar;
1725 real sin_rin; /* s_ii.r_ii */
1726 rvec s_in, tmpvec, tmpvec2;
1727 real mi, wi; /* Mass-weighting of the positions */
1729 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1732 erg = rotg->enfrotgrp;
1733 N_M = rotg->nat * erg->invmass;
1735 /* Loop over all slabs that contain something */
1736 for (n = erg->slab_first; n <= erg->slab_last; n++)
1738 islab = n - erg->slab_first; /* slab index */
1740 /* The current center of this slab is saved in xcn: */
1741 copy_rvec(erg->slab_center[islab], xcn);
1742 /* ... and the reference center in ycn: */
1743 copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1745 /*** D. Calculate the whole inner sum used for second and third sum */
1746 /* For slab n, we need to loop over all atoms i again. Since we sorted
1747 * the atoms with respect to the rotation vector, we know that it is sufficient
1748 * to calculate from firstatom to lastatom only. All other contributions will
1750 clear_rvec(innersumvec);
1751 for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
1753 /* Coordinate xi of this atom */
1754 copy_rvec(erg->xc[i], xi);
1757 gaussian_xi = gaussian_weight(xi, rotg, n);
1758 mi = erg->mc_sorted[i]; /* need the sorted mass here */
1762 copy_rvec(erg->xc_ref_sorted[i], yi0); /* Reference position yi0 */
1763 rvec_sub(yi0, ycn, tmpvec2); /* tmpvec2 = yi0 - ycn */
1764 mvmul(erg->rotmat, tmpvec2, rin); /* rin = Omega.(yi0 - ycn) */
1766 /* Calculate psi_i* and sin */
1767 rvec_sub(xi, xcn, tmpvec2); /* tmpvec2 = xi - xcn */
1768 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xi - xcn) */
1769 OOpsiistar = norm2(tmpvec)+rotg->eps; /* OOpsii* = 1/psii* = |v x (xi-xcn)|^2 + eps */
1770 OOpsii = norm(tmpvec); /* OOpsii = 1 / psii = |v x (xi - xcn)| */
1772 /* * v x (xi - xcn) */
1773 unitv(tmpvec, s_in); /* sin = ---------------- */
1774 /* |v x (xi - xcn)| */
1776 sin_rin = iprod(s_in, rin); /* sin_rin = sin . rin */
1778 /* Now the whole sum */
1779 fac = OOpsii/OOpsiistar;
1780 svmul(fac, rin, tmpvec);
1781 fac2 = fac*fac*OOpsii;
1782 svmul(fac2*sin_rin, s_in, tmpvec2);
1783 rvec_dec(tmpvec, tmpvec2);
1785 svmul(wi*gaussian_xi*sin_rin, tmpvec, tmpvec2);
1787 rvec_inc(innersumvec, tmpvec2);
1788 } /* now we have the inner sum, used both for sum2 and sum3 */
1790 /* Save it to be used in do_flex2_lowlevel */
1791 copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
1792 } /* END of loop over slabs */
1796 static void flex_precalc_inner_sum(t_rotgrp *rotg)
1799 rvec xi; /* position */
1800 rvec xcn, ycn; /* the current and the reference slab centers */
1801 rvec qin, rin; /* q_i^n and r_i^n */
1804 rvec innersumvec; /* Inner part of sum_n2 */
1805 real gaussian_xi; /* Gaussian weight gn(xi) */
1806 real mi, wi; /* Mass-weighting of the positions */
1809 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1812 erg = rotg->enfrotgrp;
1813 N_M = rotg->nat * erg->invmass;
1815 /* Loop over all slabs that contain something */
1816 for (n = erg->slab_first; n <= erg->slab_last; n++)
1818 islab = n - erg->slab_first; /* slab index */
1820 /* The current center of this slab is saved in xcn: */
1821 copy_rvec(erg->slab_center[islab], xcn);
1822 /* ... and the reference center in ycn: */
1823 copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1825 /* For slab n, we need to loop over all atoms i again. Since we sorted
1826 * the atoms with respect to the rotation vector, we know that it is sufficient
1827 * to calculate from firstatom to lastatom only. All other contributions will
1829 clear_rvec(innersumvec);
1830 for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
1832 /* Coordinate xi of this atom */
1833 copy_rvec(erg->xc[i], xi);
1836 gaussian_xi = gaussian_weight(xi, rotg, n);
1837 mi = erg->mc_sorted[i]; /* need the sorted mass here */
1840 /* Calculate rin and qin */
1841 rvec_sub(erg->xc_ref_sorted[i], ycn, tmpvec); /* tmpvec = yi0-ycn */
1842 mvmul(erg->rotmat, tmpvec, rin); /* rin = Omega.(yi0 - ycn) */
1843 cprod(rotg->vec, rin, tmpvec); /* tmpvec = v x Omega*(yi0-ycn) */
1845 /* * v x Omega*(yi0-ycn) */
1846 unitv(tmpvec, qin); /* qin = --------------------- */
1847 /* |v x Omega*(yi0-ycn)| */
1850 rvec_sub(xi, xcn, tmpvec); /* tmpvec = xi-xcn */
1851 bin = iprod(qin, tmpvec); /* bin = qin*(xi-xcn) */
1853 svmul(wi*gaussian_xi*bin, qin, tmpvec);
1855 /* Add this contribution to the inner sum: */
1856 rvec_add(innersumvec, tmpvec, innersumvec);
1857 } /* now we have the inner sum vector S^n for this slab */
1858 /* Save it to be used in do_flex_lowlevel */
1859 copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
1864 static real do_flex2_lowlevel(
1866 real sigma, /* The Gaussian width sigma */
1868 gmx_bool bOutstepRot,
1869 gmx_bool bOutstepSlab,
1872 int count, ic, ii, j, m, n, islab, iigrp, ifit;
1873 rvec xj; /* position in the i-sum */
1874 rvec yj0; /* the reference position in the j-sum */
1875 rvec xcn, ycn; /* the current and the reference slab centers */
1876 real V; /* This node's part of the rotation pot. energy */
1877 real gaussian_xj; /* Gaussian weight */
1880 real numerator, fit_numerator;
1881 rvec rjn, fit_rjn; /* Helper variables */
1884 real OOpsij, OOpsijstar;
1885 real OOsigma2; /* 1/(sigma^2) */
1888 rvec sjn, tmpvec, tmpvec2, yj0_ycn;
1889 rvec sum1vec_part, sum1vec, sum2vec_part, sum2vec, sum3vec, sum4vec, innersumvec;
1891 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1892 real mj, wj; /* Mass-weighting of the positions */
1894 real Wjn; /* g_n(x_j) m_j / Mjn */
1895 gmx_bool bCalcPotFit;
1897 /* To calculate the torque per slab */
1898 rvec slab_force; /* Single force from slab n on one atom */
1899 rvec slab_sum1vec_part;
1900 real slab_sum3part, slab_sum4part;
1901 rvec slab_sum1vec, slab_sum2vec, slab_sum3vec, slab_sum4vec;
1904 erg = rotg->enfrotgrp;
1906 /* Pre-calculate the inner sums, so that we do not have to calculate
1907 * them again for every atom */
1908 flex2_precalc_inner_sum(rotg);
1910 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
1912 /********************************************************/
1913 /* Main loop over all local atoms of the rotation group */
1914 /********************************************************/
1915 N_M = rotg->nat * erg->invmass;
1917 OOsigma2 = 1.0 / (sigma*sigma);
1918 for (j = 0; j < erg->nat_loc; j++)
1920 /* Local index of a rotation group atom */
1921 ii = erg->ind_loc[j];
1922 /* Position of this atom in the collective array */
1923 iigrp = erg->xc_ref_ind[j];
1924 /* Mass-weighting */
1925 mj = erg->mc[iigrp]; /* need the unsorted mass here */
1928 /* Current position of this atom: x[ii][XX/YY/ZZ]
1929 * Note that erg->xc_center contains the center of mass in case the flex2-t
1930 * potential was chosen. For the flex2 potential erg->xc_center must be
1932 rvec_sub(x[ii], erg->xc_center, xj);
1934 /* Shift this atom such that it is near its reference */
1935 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
1937 /* Determine the slabs to loop over, i.e. the ones with contributions
1938 * larger than min_gaussian */
1939 count = get_single_atom_gaussians(xj, rotg);
1941 clear_rvec(sum1vec_part);
1942 clear_rvec(sum2vec_part);
1945 /* Loop over the relevant slabs for this atom */
1946 for (ic = 0; ic < count; ic++)
1948 n = erg->gn_slabind[ic];
1950 /* Get the precomputed Gaussian value of curr_slab for curr_x */
1951 gaussian_xj = erg->gn_atom[ic];
1953 islab = n - erg->slab_first; /* slab index */
1955 /* The (unrotated) reference position of this atom is copied to yj0: */
1956 copy_rvec(rotg->x_ref[iigrp], yj0);
1958 beta = calc_beta(xj, rotg, n);
1960 /* The current center of this slab is saved in xcn: */
1961 copy_rvec(erg->slab_center[islab], xcn);
1962 /* ... and the reference center in ycn: */
1963 copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1965 rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
1968 mvmul(erg->rotmat, yj0_ycn, rjn); /* rjn = Omega.(yj0 - ycn) */
1970 /* Subtract the slab center from xj */
1971 rvec_sub(xj, xcn, tmpvec2); /* tmpvec2 = xj - xcn */
1973 /* In rare cases, when an atom position coincides with a slab center
1974 * (tmpvec2 == 0) we cannot compute the vector product for sjn.
1975 * However, since the atom is located directly on the pivot, this
1976 * slab's contribution to the force on that atom will be zero
1977 * anyway. Therefore, we directly move on to the next slab. */
1978 if (gmx_numzero(norm(tmpvec2))) /* 0 == norm(xj - xcn) */
1984 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xj - xcn) */
1986 OOpsijstar = norm2(tmpvec)+rotg->eps; /* OOpsij* = 1/psij* = |v x (xj-xcn)|^2 + eps */
1988 numerator = gmx::square(iprod(tmpvec, rjn));
1990 /*********************************/
1991 /* Add to the rotation potential */
1992 /*********************************/
1993 V += 0.5*rotg->k*wj*gaussian_xj*numerator/OOpsijstar;
1995 /* If requested, also calculate the potential for a set of angles
1996 * near the current reference angle */
1999 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2001 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, fit_rjn);
2002 fit_numerator = gmx::square(iprod(tmpvec, fit_rjn));
2003 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*gaussian_xj*fit_numerator/OOpsijstar;
2007 /*************************************/
2008 /* Now calculate the force on atom j */
2009 /*************************************/
2011 OOpsij = norm(tmpvec); /* OOpsij = 1 / psij = |v x (xj - xcn)| */
2013 /* * v x (xj - xcn) */
2014 unitv(tmpvec, sjn); /* sjn = ---------------- */
2015 /* |v x (xj - xcn)| */
2017 sjn_rjn = iprod(sjn, rjn); /* sjn_rjn = sjn . rjn */
2020 /*** A. Calculate the first of the four sum terms: ****************/
2021 fac = OOpsij/OOpsijstar;
2022 svmul(fac, rjn, tmpvec);
2023 fac2 = fac*fac*OOpsij;
2024 svmul(fac2*sjn_rjn, sjn, tmpvec2);
2025 rvec_dec(tmpvec, tmpvec2);
2026 fac2 = wj*gaussian_xj; /* also needed for sum4 */
2027 svmul(fac2*sjn_rjn, tmpvec, slab_sum1vec_part);
2028 /********************/
2029 /*** Add to sum1: ***/
2030 /********************/
2031 rvec_inc(sum1vec_part, slab_sum1vec_part); /* sum1 still needs to vector multiplied with v */
2033 /*** B. Calculate the forth of the four sum terms: ****************/
2034 betasigpsi = beta*OOsigma2*OOpsij; /* this is also needed for sum3 */
2035 /********************/
2036 /*** Add to sum4: ***/
2037 /********************/
2038 slab_sum4part = fac2*betasigpsi*fac*sjn_rjn*sjn_rjn; /* Note that fac is still valid from above */
2039 sum4 += slab_sum4part;
2041 /*** C. Calculate Wjn for second and third sum */
2042 /* Note that we can safely divide by slab_weights since we check in
2043 * get_slab_centers that it is non-zero. */
2044 Wjn = gaussian_xj*mj/erg->slab_weights[islab];
2046 /* We already have precalculated the inner sum for slab n */
2047 copy_rvec(erg->slab_innersumvec[islab], innersumvec);
2049 /* Weigh the inner sum vector with Wjn */
2050 svmul(Wjn, innersumvec, innersumvec);
2052 /*** E. Calculate the second of the four sum terms: */
2053 /********************/
2054 /*** Add to sum2: ***/
2055 /********************/
2056 rvec_inc(sum2vec_part, innersumvec); /* sum2 still needs to be vector crossproduct'ed with v */
2058 /*** F. Calculate the third of the four sum terms: */
2059 slab_sum3part = betasigpsi * iprod(sjn, innersumvec);
2060 sum3 += slab_sum3part; /* still needs to be multiplied with v */
2062 /*** G. Calculate the torque on the local slab's axis: */
2066 cprod(slab_sum1vec_part, rotg->vec, slab_sum1vec);
2068 cprod(innersumvec, rotg->vec, slab_sum2vec);
2070 svmul(slab_sum3part, rotg->vec, slab_sum3vec);
2072 svmul(slab_sum4part, rotg->vec, slab_sum4vec);
2074 /* The force on atom ii from slab n only: */
2075 for (m = 0; m < DIM; m++)
2077 slab_force[m] = rotg->k * (-slab_sum1vec[m] + slab_sum2vec[m] - slab_sum3vec[m] + 0.5*slab_sum4vec[m]);
2080 erg->slab_torque_v[islab] += torque(rotg->vec, slab_force, xj, xcn);
2082 } /* END of loop over slabs */
2084 /* Construct the four individual parts of the vector sum: */
2085 cprod(sum1vec_part, rotg->vec, sum1vec); /* sum1vec = { } x v */
2086 cprod(sum2vec_part, rotg->vec, sum2vec); /* sum2vec = { } x v */
2087 svmul(sum3, rotg->vec, sum3vec); /* sum3vec = { } . v */
2088 svmul(sum4, rotg->vec, sum4vec); /* sum4vec = { } . v */
2090 /* Store the additional force so that it can be added to the force
2091 * array after the normal forces have been evaluated */
2092 for (m = 0; m < DIM; m++)
2094 erg->f_rot_loc[j][m] = rotg->k * (-sum1vec[m] + sum2vec[m] - sum3vec[m] + 0.5*sum4vec[m]);
2098 fprintf(stderr, "sum1: %15.8f %15.8f %15.8f\n", -rotg->k*sum1vec[XX], -rotg->k*sum1vec[YY], -rotg->k*sum1vec[ZZ]);
2099 fprintf(stderr, "sum2: %15.8f %15.8f %15.8f\n", rotg->k*sum2vec[XX], rotg->k*sum2vec[YY], rotg->k*sum2vec[ZZ]);
2100 fprintf(stderr, "sum3: %15.8f %15.8f %15.8f\n", -rotg->k*sum3vec[XX], -rotg->k*sum3vec[YY], -rotg->k*sum3vec[ZZ]);
2101 fprintf(stderr, "sum4: %15.8f %15.8f %15.8f\n", 0.5*rotg->k*sum4vec[XX], 0.5*rotg->k*sum4vec[YY], 0.5*rotg->k*sum4vec[ZZ]);
2106 } /* END of loop over local atoms */
2112 static real do_flex_lowlevel(
2114 real sigma, /* The Gaussian width sigma */
2116 gmx_bool bOutstepRot,
2117 gmx_bool bOutstepSlab,
2120 int count, ic, ifit, ii, j, m, n, islab, iigrp;
2121 rvec xj, yj0; /* current and reference position */
2122 rvec xcn, ycn; /* the current and the reference slab centers */
2123 rvec yj0_ycn; /* yj0 - ycn */
2124 rvec xj_xcn; /* xj - xcn */
2125 rvec qjn, fit_qjn; /* q_i^n */
2126 rvec sum_n1, sum_n2; /* Two contributions to the rotation force */
2127 rvec innersumvec; /* Inner part of sum_n2 */
2129 rvec force_n; /* Single force from slab n on one atom */
2130 rvec force_n1, force_n2; /* First and second part of force_n */
2131 rvec tmpvec, tmpvec2, tmp_f; /* Helper variables */
2132 real V; /* The rotation potential energy */
2133 real OOsigma2; /* 1/(sigma^2) */
2134 real beta; /* beta_n(xj) */
2135 real bjn, fit_bjn; /* b_j^n */
2136 real gaussian_xj; /* Gaussian weight gn(xj) */
2137 real betan_xj_sigma2;
2138 real mj, wj; /* Mass-weighting of the positions */
2140 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2141 gmx_bool bCalcPotFit;
2144 erg = rotg->enfrotgrp;
2146 /* Pre-calculate the inner sums, so that we do not have to calculate
2147 * them again for every atom */
2148 flex_precalc_inner_sum(rotg);
2150 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2152 /********************************************************/
2153 /* Main loop over all local atoms of the rotation group */
2154 /********************************************************/
2155 OOsigma2 = 1.0/(sigma*sigma);
2156 N_M = rotg->nat * erg->invmass;
2158 for (j = 0; j < erg->nat_loc; j++)
2160 /* Local index of a rotation group atom */
2161 ii = erg->ind_loc[j];
2162 /* Position of this atom in the collective array */
2163 iigrp = erg->xc_ref_ind[j];
2164 /* Mass-weighting */
2165 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2168 /* Current position of this atom: x[ii][XX/YY/ZZ]
2169 * Note that erg->xc_center contains the center of mass in case the flex-t
2170 * potential was chosen. For the flex potential erg->xc_center must be
2172 rvec_sub(x[ii], erg->xc_center, xj);
2174 /* Shift this atom such that it is near its reference */
2175 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2177 /* Determine the slabs to loop over, i.e. the ones with contributions
2178 * larger than min_gaussian */
2179 count = get_single_atom_gaussians(xj, rotg);
2184 /* Loop over the relevant slabs for this atom */
2185 for (ic = 0; ic < count; ic++)
2187 n = erg->gn_slabind[ic];
2189 /* Get the precomputed Gaussian for xj in slab n */
2190 gaussian_xj = erg->gn_atom[ic];
2192 islab = n - erg->slab_first; /* slab index */
2194 /* The (unrotated) reference position of this atom is saved in yj0: */
2195 copy_rvec(rotg->x_ref[iigrp], yj0);
2197 beta = calc_beta(xj, rotg, n);
2199 /* The current center of this slab is saved in xcn: */
2200 copy_rvec(erg->slab_center[islab], xcn);
2201 /* ... and the reference center in ycn: */
2202 copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
2204 rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
2206 /* In rare cases, when an atom position coincides with a reference slab
2207 * center (yj0_ycn == 0) we cannot compute the normal vector qjn.
2208 * However, since the atom is located directly on the pivot, this
2209 * slab's contribution to the force on that atom will be zero
2210 * anyway. Therefore, we directly move on to the next slab. */
2211 if (gmx_numzero(norm(yj0_ycn))) /* 0 == norm(yj0 - ycn) */
2217 mvmul(erg->rotmat, yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2219 /* Subtract the slab center from xj */
2220 rvec_sub(xj, xcn, xj_xcn); /* xj_xcn = xj - xcn */
2223 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2225 /* * v x Omega.(yj0-ycn) */
2226 unitv(tmpvec, qjn); /* qjn = --------------------- */
2227 /* |v x Omega.(yj0-ycn)| */
2229 bjn = iprod(qjn, xj_xcn); /* bjn = qjn * (xj - xcn) */
2231 /*********************************/
2232 /* Add to the rotation potential */
2233 /*********************************/
2234 V += 0.5*rotg->k*wj*gaussian_xj*gmx::square(bjn);
2236 /* If requested, also calculate the potential for a set of angles
2237 * near the current reference angle */
2240 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2242 /* As above calculate Omega.(yj0-ycn), now for the other angles */
2243 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2244 /* As above calculate qjn */
2245 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2246 /* * v x Omega.(yj0-ycn) */
2247 unitv(tmpvec, fit_qjn); /* fit_qjn = --------------------- */
2248 /* |v x Omega.(yj0-ycn)| */
2249 fit_bjn = iprod(fit_qjn, xj_xcn); /* fit_bjn = fit_qjn * (xj - xcn) */
2250 /* Add to the rotation potential for this angle */
2251 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*gaussian_xj*gmx::square(fit_bjn);
2255 /****************************************************************/
2256 /* sum_n1 will typically be the main contribution to the force: */
2257 /****************************************************************/
2258 betan_xj_sigma2 = beta*OOsigma2; /* beta_n(xj)/sigma^2 */
2260 /* The next lines calculate
2261 * qjn - (bjn*beta(xj)/(2sigma^2))v */
2262 svmul(bjn*0.5*betan_xj_sigma2, rotg->vec, tmpvec2);
2263 rvec_sub(qjn, tmpvec2, tmpvec);
2265 /* Multiply with gn(xj)*bjn: */
2266 svmul(gaussian_xj*bjn, tmpvec, tmpvec2);
2269 rvec_inc(sum_n1, tmpvec2);
2271 /* We already have precalculated the Sn term for slab n */
2272 copy_rvec(erg->slab_innersumvec[islab], s_n);
2274 svmul(betan_xj_sigma2*iprod(s_n, xj_xcn), rotg->vec, tmpvec); /* tmpvec = ---------- s_n (xj-xcn) */
2277 rvec_sub(s_n, tmpvec, innersumvec);
2279 /* We can safely divide by slab_weights since we check in get_slab_centers
2280 * that it is non-zero. */
2281 svmul(gaussian_xj/erg->slab_weights[islab], innersumvec, innersumvec);
2283 rvec_add(sum_n2, innersumvec, sum_n2);
2285 /* Calculate the torque: */
2288 /* The force on atom ii from slab n only: */
2289 svmul(-rotg->k*wj, tmpvec2, force_n1); /* part 1 */
2290 svmul( rotg->k*mj, innersumvec, force_n2); /* part 2 */
2291 rvec_add(force_n1, force_n2, force_n);
2292 erg->slab_torque_v[islab] += torque(rotg->vec, force_n, xj, xcn);
2294 } /* END of loop over slabs */
2296 /* Put both contributions together: */
2297 svmul(wj, sum_n1, sum_n1);
2298 svmul(mj, sum_n2, sum_n2);
2299 rvec_sub(sum_n2, sum_n1, tmp_f); /* F = -grad V */
2301 /* Store the additional force so that it can be added to the force
2302 * array after the normal forces have been evaluated */
2303 for (m = 0; m < DIM; m++)
2305 erg->f_rot_loc[j][m] = rotg->k*tmp_f[m];
2310 } /* END of loop over local atoms */
2316 static void print_coordinates(t_rotgrp *rotg, rvec x[], matrix box, int step)
2320 static char buf[STRLEN];
2321 static gmx_bool bFirst = 1;
2326 sprintf(buf, "coords%d.txt", cr->nodeid);
2327 fp = fopen(buf, "w");
2331 fprintf(fp, "\nStep %d\n", step);
2332 fprintf(fp, "box: %f %f %f %f %f %f %f %f %f\n",
2333 box[XX][XX], box[XX][YY], box[XX][ZZ],
2334 box[YY][XX], box[YY][YY], box[YY][ZZ],
2335 box[ZZ][XX], box[ZZ][ZZ], box[ZZ][ZZ]);
2336 for (i = 0; i < rotg->nat; i++)
2338 fprintf(fp, "%4d %f %f %f\n", i,
2339 erg->xc[i][XX], erg->xc[i][YY], erg->xc[i][ZZ]);
2347 static int projection_compare(const void *a, const void *b)
2349 sort_along_vec_t *xca, *xcb;
2352 xca = (sort_along_vec_t *)a;
2353 xcb = (sort_along_vec_t *)b;
2355 if (xca->xcproj < xcb->xcproj)
2359 else if (xca->xcproj > xcb->xcproj)
2370 static void sort_collective_coordinates(
2371 t_rotgrp *rotg, /* Rotation group */
2372 sort_along_vec_t *data) /* Buffer for sorting the positions */
2375 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2378 erg = rotg->enfrotgrp;
2380 /* The projection of the position vector on the rotation vector is
2381 * the relevant value for sorting. Fill the 'data' structure */
2382 for (i = 0; i < rotg->nat; i++)
2384 data[i].xcproj = iprod(erg->xc[i], rotg->vec); /* sort criterium */
2385 data[i].m = erg->mc[i];
2387 copy_rvec(erg->xc[i], data[i].x );
2388 copy_rvec(rotg->x_ref[i], data[i].x_ref);
2390 /* Sort the 'data' structure */
2391 gmx_qsort(data, rotg->nat, sizeof(sort_along_vec_t), projection_compare);
2393 /* Copy back the sorted values */
2394 for (i = 0; i < rotg->nat; i++)
2396 copy_rvec(data[i].x, erg->xc[i] );
2397 copy_rvec(data[i].x_ref, erg->xc_ref_sorted[i]);
2398 erg->mc_sorted[i] = data[i].m;
2399 erg->xc_sortind[i] = data[i].ind;
2404 /* For each slab, get the first and the last index of the sorted atom
2406 static void get_firstlast_atom_per_slab(t_rotgrp *rotg)
2410 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2413 erg = rotg->enfrotgrp;
2415 /* Find the first atom that needs to enter the calculation for each slab */
2416 n = erg->slab_first; /* slab */
2417 i = 0; /* start with the first atom */
2420 /* Find the first atom that significantly contributes to this slab */
2421 do /* move forward in position until a large enough beta is found */
2423 beta = calc_beta(erg->xc[i], rotg, n);
2426 while ((beta < -erg->max_beta) && (i < rotg->nat));
2428 islab = n - erg->slab_first; /* slab index */
2429 erg->firstatom[islab] = i;
2430 /* Proceed to the next slab */
2433 while (n <= erg->slab_last);
2435 /* Find the last atom for each slab */
2436 n = erg->slab_last; /* start with last slab */
2437 i = rotg->nat-1; /* start with the last atom */
2440 do /* move backward in position until a large enough beta is found */
2442 beta = calc_beta(erg->xc[i], rotg, n);
2445 while ((beta > erg->max_beta) && (i > -1));
2447 islab = n - erg->slab_first; /* slab index */
2448 erg->lastatom[islab] = i;
2449 /* Proceed to the next slab */
2452 while (n >= erg->slab_first);
2456 /* Determine the very first and very last slab that needs to be considered
2457 * For the first slab that needs to be considered, we have to find the smallest
2460 * x_first * v - n*Delta_x <= beta_max
2462 * slab index n, slab distance Delta_x, rotation vector v. For the last slab we
2463 * have to find the largest n that obeys
2465 * x_last * v - n*Delta_x >= -beta_max
2468 static inline int get_first_slab(
2469 t_rotgrp *rotg, /* The rotation group (inputrec data) */
2470 real max_beta, /* The max_beta value, instead of min_gaussian */
2471 rvec firstatom) /* First atom after sorting along the rotation vector v */
2473 /* Find the first slab for the first atom */
2474 return static_cast<int>(ceil(static_cast<double>((iprod(firstatom, rotg->vec) - max_beta)/rotg->slab_dist)));
2478 static inline int get_last_slab(
2479 t_rotgrp *rotg, /* The rotation group (inputrec data) */
2480 real max_beta, /* The max_beta value, instead of min_gaussian */
2481 rvec lastatom) /* Last atom along v */
2483 /* Find the last slab for the last atom */
2484 return static_cast<int>(floor(static_cast<double>((iprod(lastatom, rotg->vec) + max_beta)/rotg->slab_dist)));
2488 static void get_firstlast_slab_check(
2489 t_rotgrp *rotg, /* The rotation group (inputrec data) */
2490 t_gmx_enfrotgrp *erg, /* The rotation group (data only accessible in this file) */
2491 rvec firstatom, /* First atom after sorting along the rotation vector v */
2492 rvec lastatom) /* Last atom along v */
2494 erg->slab_first = get_first_slab(rotg, erg->max_beta, firstatom);
2495 erg->slab_last = get_last_slab(rotg, erg->max_beta, lastatom);
2497 /* Calculate the slab buffer size, which changes when slab_first changes */
2498 erg->slab_buffer = erg->slab_first - erg->slab_first_ref;
2500 /* Check whether we have reference data to compare against */
2501 if (erg->slab_first < erg->slab_first_ref)
2503 gmx_fatal(FARGS, "%s No reference data for first slab (n=%d), unable to proceed.",
2504 RotStr, erg->slab_first);
2507 /* Check whether we have reference data to compare against */
2508 if (erg->slab_last > erg->slab_last_ref)
2510 gmx_fatal(FARGS, "%s No reference data for last slab (n=%d), unable to proceed.",
2511 RotStr, erg->slab_last);
2516 /* Enforced rotation with a flexible axis */
2517 static void do_flexible(
2519 gmx_enfrot_t enfrot, /* Other rotation data */
2520 t_rotgrp *rotg, /* The rotation group */
2521 int g, /* Group number */
2522 rvec x[], /* The local positions */
2524 double t, /* Time in picoseconds */
2525 gmx_bool bOutstepRot, /* Output to main rotation output file */
2526 gmx_bool bOutstepSlab) /* Output per-slab data */
2529 real sigma; /* The Gaussian width sigma */
2530 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2533 erg = rotg->enfrotgrp;
2535 /* Define the sigma value */
2536 sigma = 0.7*rotg->slab_dist;
2538 /* Sort the collective coordinates erg->xc along the rotation vector. This is
2539 * an optimization for the inner loop. */
2540 sort_collective_coordinates(rotg, enfrot->data);
2542 /* Determine the first relevant slab for the first atom and the last
2543 * relevant slab for the last atom */
2544 get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1]);
2546 /* Determine for each slab depending on the min_gaussian cutoff criterium,
2547 * a first and a last atom index inbetween stuff needs to be calculated */
2548 get_firstlast_atom_per_slab(rotg);
2550 /* Determine the gaussian-weighted center of positions for all slabs */
2551 get_slab_centers(rotg, erg->xc, erg->mc_sorted, g, t, enfrot->out_slabs, bOutstepSlab, FALSE);
2553 /* Clear the torque per slab from last time step: */
2554 nslabs = erg->slab_last - erg->slab_first + 1;
2555 for (l = 0; l < nslabs; l++)
2557 erg->slab_torque_v[l] = 0.0;
2560 /* Call the rotational forces kernel */
2561 if (rotg->eType == erotgFLEX || rotg->eType == erotgFLEXT)
2563 erg->V = do_flex_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
2565 else if (rotg->eType == erotgFLEX2 || rotg->eType == erotgFLEX2T)
2567 erg->V = do_flex2_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
2571 gmx_fatal(FARGS, "Unknown flexible rotation type");
2574 /* Determine angle by RMSD fit to the reference - Let's hope this */
2575 /* only happens once in a while, since this is not parallelized! */
2576 if (bMaster && (erotgFitPOT != rotg->eFittype) )
2580 /* Fit angle of the whole rotation group */
2581 erg->angle_v = flex_fit_angle(rotg);
2585 /* Fit angle of each slab */
2586 flex_fit_angle_perslab(g, rotg, t, erg->degangle, enfrot->out_angles);
2590 /* Lump together the torques from all slabs: */
2591 erg->torque_v = 0.0;
2592 for (l = 0; l < nslabs; l++)
2594 erg->torque_v += erg->slab_torque_v[l];
2599 /* Calculate the angle between reference and actual rotation group atom,
2600 * both projected into a plane perpendicular to the rotation vector: */
2601 static void angle(t_rotgrp *rotg,
2605 real *weight) /* atoms near the rotation axis should count less than atoms far away */
2607 rvec xp, xrp; /* current and reference positions projected on a plane perpendicular to pg->vec */
2611 /* Project x_ref and x into a plane through the origin perpendicular to rot_vec: */
2612 /* Project x_ref: xrp = x_ref - (vec * x_ref) * vec */
2613 svmul(iprod(rotg->vec, x_ref), rotg->vec, dum);
2614 rvec_sub(x_ref, dum, xrp);
2615 /* Project x_act: */
2616 svmul(iprod(rotg->vec, x_act), rotg->vec, dum);
2617 rvec_sub(x_act, dum, xp);
2619 /* Retrieve information about which vector precedes. gmx_angle always
2620 * returns a positive angle. */
2621 cprod(xp, xrp, dum); /* if reference precedes, this is pointing into the same direction as vec */
2623 if (iprod(rotg->vec, dum) >= 0)
2625 *alpha = -gmx_angle(xrp, xp);
2629 *alpha = +gmx_angle(xrp, xp);
2632 /* Also return the weight */
2637 /* Project first vector onto a plane perpendicular to the second vector
2639 * Note that v must be of unit length.
2641 static inline void project_onto_plane(rvec dr, const rvec v)
2646 svmul(iprod(dr, v), v, tmp); /* tmp = (dr.v)v */
2647 rvec_dec(dr, tmp); /* dr = dr - (dr.v)v */
2651 /* Fixed rotation: The rotation reference group rotates around the v axis. */
2652 /* The atoms of the actual rotation group are attached with imaginary */
2653 /* springs to the reference atoms. */
2654 static void do_fixed(
2655 t_rotgrp *rotg, /* The rotation group */
2656 gmx_bool bOutstepRot, /* Output to main rotation output file */
2657 gmx_bool bOutstepSlab) /* Output per-slab data */
2661 rvec tmp_f; /* Force */
2662 real alpha; /* a single angle between an actual and a reference position */
2663 real weight; /* single weight for a single angle */
2664 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2665 rvec xi_xc; /* xi - xc */
2666 gmx_bool bCalcPotFit;
2669 /* for mass weighting: */
2670 real wi; /* Mass-weighting of the positions */
2672 real k_wi; /* k times wi */
2677 erg = rotg->enfrotgrp;
2678 bProject = (rotg->eType == erotgPM) || (rotg->eType == erotgPMPF);
2679 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2681 N_M = rotg->nat * erg->invmass;
2683 /* Each process calculates the forces on its local atoms */
2684 for (j = 0; j < erg->nat_loc; j++)
2686 /* Calculate (x_i-x_c) resp. (x_i-u) */
2687 rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xi_xc);
2689 /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
2690 rvec_sub(erg->xr_loc[j], xi_xc, dr);
2694 project_onto_plane(dr, rotg->vec);
2697 /* Mass-weighting */
2698 wi = N_M*erg->m_loc[j];
2700 /* Store the additional force so that it can be added to the force
2701 * array after the normal forces have been evaluated */
2703 for (m = 0; m < DIM; m++)
2705 tmp_f[m] = k_wi*dr[m];
2706 erg->f_rot_loc[j][m] = tmp_f[m];
2707 erg->V += 0.5*k_wi*gmx::square(dr[m]);
2710 /* If requested, also calculate the potential for a set of angles
2711 * near the current reference angle */
2714 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2716 /* Index of this rotation group atom with respect to the whole rotation group */
2717 jj = erg->xc_ref_ind[j];
2719 /* Rotate with the alternative angle. Like rotate_local_reference(),
2720 * just for a single local atom */
2721 mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_xr_loc); /* fit_xr_loc = Omega*(y_i-y_c) */
2723 /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
2724 rvec_sub(fit_xr_loc, xi_xc, dr);
2728 project_onto_plane(dr, rotg->vec);
2731 /* Add to the rotation potential for this angle: */
2732 erg->PotAngleFit->V[ifit] += 0.5*k_wi*norm2(dr);
2738 /* Add to the torque of this rotation group */
2739 erg->torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2741 /* Calculate the angle between reference and actual rotation group atom. */
2742 angle(rotg, xi_xc, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2743 erg->angle_v += alpha * weight;
2744 erg->weight_v += weight;
2746 /* If you want enforced rotation to contribute to the virial,
2747 * activate the following lines:
2750 Add the rotation contribution to the virial
2751 for(j=0; j<DIM; j++)
2753 vir[j][m] += 0.5*f[ii][j]*dr[m];
2759 } /* end of loop over local rotation group atoms */
2763 /* Calculate the radial motion potential and forces */
2764 static void do_radial_motion(
2765 t_rotgrp *rotg, /* The rotation group */
2766 gmx_bool bOutstepRot, /* Output to main rotation output file */
2767 gmx_bool bOutstepSlab) /* Output per-slab data */
2770 rvec tmp_f; /* Force */
2771 real alpha; /* a single angle between an actual and a reference position */
2772 real weight; /* single weight for a single angle */
2773 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2774 rvec xj_u; /* xj - u */
2775 rvec tmpvec, fit_tmpvec;
2776 real fac, fac2, sum = 0.0;
2778 gmx_bool bCalcPotFit;
2780 /* For mass weighting: */
2781 real wj; /* Mass-weighting of the positions */
2785 erg = rotg->enfrotgrp;
2786 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2788 N_M = rotg->nat * erg->invmass;
2790 /* Each process calculates the forces on its local atoms */
2791 for (j = 0; j < erg->nat_loc; j++)
2793 /* Calculate (xj-u) */
2794 rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xj_u); /* xj_u = xj-u */
2796 /* Calculate Omega.(yj0-u) */
2797 cprod(rotg->vec, erg->xr_loc[j], tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2799 /* * v x Omega.(yj0-u) */
2800 unitv(tmpvec, pj); /* pj = --------------------- */
2801 /* | v x Omega.(yj0-u) | */
2803 fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2806 /* Mass-weighting */
2807 wj = N_M*erg->m_loc[j];
2809 /* Store the additional force so that it can be added to the force
2810 * array after the normal forces have been evaluated */
2811 svmul(-rotg->k*wj*fac, pj, tmp_f);
2812 copy_rvec(tmp_f, erg->f_rot_loc[j]);
2815 /* If requested, also calculate the potential for a set of angles
2816 * near the current reference angle */
2819 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2821 /* Index of this rotation group atom with respect to the whole rotation group */
2822 jj = erg->xc_ref_ind[j];
2824 /* Rotate with the alternative angle. Like rotate_local_reference(),
2825 * just for a single local atom */
2826 mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_tmpvec); /* fit_tmpvec = Omega*(yj0-u) */
2828 /* Calculate Omega.(yj0-u) */
2829 cprod(rotg->vec, fit_tmpvec, tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2830 /* * v x Omega.(yj0-u) */
2831 unitv(tmpvec, pj); /* pj = --------------------- */
2832 /* | v x Omega.(yj0-u) | */
2834 fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2837 /* Add to the rotation potential for this angle: */
2838 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*fac2;
2844 /* Add to the torque of this rotation group */
2845 erg->torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2847 /* Calculate the angle between reference and actual rotation group atom. */
2848 angle(rotg, xj_u, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2849 erg->angle_v += alpha * weight;
2850 erg->weight_v += weight;
2855 } /* end of loop over local rotation group atoms */
2856 erg->V = 0.5*rotg->k*sum;
2860 /* Calculate the radial motion pivot-free potential and forces */
2861 static void do_radial_motion_pf(
2862 t_rotgrp *rotg, /* The rotation group */
2863 rvec x[], /* The positions */
2864 matrix box, /* The simulation box */
2865 gmx_bool bOutstepRot, /* Output to main rotation output file */
2866 gmx_bool bOutstepSlab) /* Output per-slab data */
2868 int i, ii, iigrp, ifit, j;
2869 rvec xj; /* Current position */
2870 rvec xj_xc; /* xj - xc */
2871 rvec yj0_yc0; /* yj0 - yc0 */
2872 rvec tmp_f; /* Force */
2873 real alpha; /* a single angle between an actual and a reference position */
2874 real weight; /* single weight for a single angle */
2875 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2876 rvec tmpvec, tmpvec2;
2877 rvec innersumvec; /* Precalculation of the inner sum */
2879 real fac, fac2, V = 0.0;
2881 gmx_bool bCalcPotFit;
2883 /* For mass weighting: */
2884 real mj, wi, wj; /* Mass-weighting of the positions */
2888 erg = rotg->enfrotgrp;
2889 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2891 N_M = rotg->nat * erg->invmass;
2893 /* Get the current center of the rotation group: */
2894 get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
2896 /* Precalculate Sum_i [ wi qi.(xi-xc) qi ] which is needed for every single j */
2897 clear_rvec(innersumvec);
2898 for (i = 0; i < rotg->nat; i++)
2900 /* Mass-weighting */
2901 wi = N_M*erg->mc[i];
2903 /* Calculate qi. Note that xc_ref_center has already been subtracted from
2904 * x_ref in init_rot_group.*/
2905 mvmul(erg->rotmat, rotg->x_ref[i], tmpvec); /* tmpvec = Omega.(yi0-yc0) */
2907 cprod(rotg->vec, tmpvec, tmpvec2); /* tmpvec2 = v x Omega.(yi0-yc0) */
2909 /* * v x Omega.(yi0-yc0) */
2910 unitv(tmpvec2, qi); /* qi = ----------------------- */
2911 /* | v x Omega.(yi0-yc0) | */
2913 rvec_sub(erg->xc[i], erg->xc_center, tmpvec); /* tmpvec = xi-xc */
2915 svmul(wi*iprod(qi, tmpvec), qi, tmpvec2);
2917 rvec_inc(innersumvec, tmpvec2);
2919 svmul(rotg->k*erg->invmass, innersumvec, innersumveckM);
2921 /* Each process calculates the forces on its local atoms */
2922 for (j = 0; j < erg->nat_loc; j++)
2924 /* Local index of a rotation group atom */
2925 ii = erg->ind_loc[j];
2926 /* Position of this atom in the collective array */
2927 iigrp = erg->xc_ref_ind[j];
2928 /* Mass-weighting */
2929 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2932 /* Current position of this atom: x[ii][XX/YY/ZZ] */
2933 copy_rvec(x[ii], xj);
2935 /* Shift this atom such that it is near its reference */
2936 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2938 /* The (unrotated) reference position is yj0. yc0 has already
2939 * been subtracted in init_rot_group */
2940 copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
2942 /* Calculate Omega.(yj0-yc0) */
2943 mvmul(erg->rotmat, yj0_yc0, tmpvec2); /* tmpvec2 = Omega.(yj0 - yc0) */
2945 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
2947 /* * v x Omega.(yj0-yc0) */
2948 unitv(tmpvec, qj); /* qj = ----------------------- */
2949 /* | v x Omega.(yj0-yc0) | */
2951 /* Calculate (xj-xc) */
2952 rvec_sub(xj, erg->xc_center, xj_xc); /* xj_xc = xj-xc */
2954 fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
2957 /* Store the additional force so that it can be added to the force
2958 * array after the normal forces have been evaluated */
2959 svmul(-rotg->k*wj*fac, qj, tmp_f); /* part 1 of force */
2960 svmul(mj, innersumveckM, tmpvec); /* part 2 of force */
2961 rvec_inc(tmp_f, tmpvec);
2962 copy_rvec(tmp_f, erg->f_rot_loc[j]);
2965 /* If requested, also calculate the potential for a set of angles
2966 * near the current reference angle */
2969 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2971 /* Rotate with the alternative angle. Like rotate_local_reference(),
2972 * just for a single local atom */
2973 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, tmpvec2); /* tmpvec2 = Omega*(yj0-yc0) */
2975 /* Calculate Omega.(yj0-u) */
2976 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
2977 /* * v x Omega.(yj0-yc0) */
2978 unitv(tmpvec, qj); /* qj = ----------------------- */
2979 /* | v x Omega.(yj0-yc0) | */
2981 fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
2984 /* Add to the rotation potential for this angle: */
2985 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*fac2;
2991 /* Add to the torque of this rotation group */
2992 erg->torque_v += torque(rotg->vec, tmp_f, xj, erg->xc_center);
2994 /* Calculate the angle between reference and actual rotation group atom. */
2995 angle(rotg, xj_xc, yj0_yc0, &alpha, &weight); /* angle in rad, weighted */
2996 erg->angle_v += alpha * weight;
2997 erg->weight_v += weight;
3002 } /* end of loop over local rotation group atoms */
3003 erg->V = 0.5*rotg->k*V;
3007 /* Precalculate the inner sum for the radial motion 2 forces */
3008 static void radial_motion2_precalc_inner_sum(t_rotgrp *rotg, rvec innersumvec)
3011 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3012 rvec xi_xc; /* xj - xc */
3013 rvec tmpvec, tmpvec2;
3017 rvec v_xi_xc; /* v x (xj - u) */
3018 real psii, psiistar;
3019 real wi; /* Mass-weighting of the positions */
3023 erg = rotg->enfrotgrp;
3024 N_M = rotg->nat * erg->invmass;
3026 /* Loop over the collective set of positions */
3028 for (i = 0; i < rotg->nat; i++)
3030 /* Mass-weighting */
3031 wi = N_M*erg->mc[i];
3033 rvec_sub(erg->xc[i], erg->xc_center, xi_xc); /* xi_xc = xi-xc */
3035 /* Calculate ri. Note that xc_ref_center has already been subtracted from
3036 * x_ref in init_rot_group.*/
3037 mvmul(erg->rotmat, rotg->x_ref[i], ri); /* ri = Omega.(yi0-yc0) */
3039 cprod(rotg->vec, xi_xc, v_xi_xc); /* v_xi_xc = v x (xi-u) */
3041 fac = norm2(v_xi_xc);
3043 psiistar = 1.0/(fac + rotg->eps); /* psiistar = --------------------- */
3044 /* |v x (xi-xc)|^2 + eps */
3046 psii = gmx::invsqrt(fac); /* 1 */
3047 /* psii = ------------- */
3050 svmul(psii, v_xi_xc, si); /* si = psii * (v x (xi-xc) ) */
3052 siri = iprod(si, ri); /* siri = si.ri */
3054 svmul(psiistar/psii, ri, tmpvec);
3055 svmul(psiistar*psiistar/(psii*psii*psii) * siri, si, tmpvec2);
3056 rvec_dec(tmpvec, tmpvec2);
3057 cprod(tmpvec, rotg->vec, tmpvec2);
3059 svmul(wi*siri, tmpvec2, tmpvec);
3061 rvec_inc(sumvec, tmpvec);
3063 svmul(rotg->k*erg->invmass, sumvec, innersumvec);
3067 /* Calculate the radial motion 2 potential and forces */
3068 static void do_radial_motion2(
3069 t_rotgrp *rotg, /* The rotation group */
3070 rvec x[], /* The positions */
3071 matrix box, /* The simulation box */
3072 gmx_bool bOutstepRot, /* Output to main rotation output file */
3073 gmx_bool bOutstepSlab) /* Output per-slab data */
3075 int ii, iigrp, ifit, j;
3076 rvec xj; /* Position */
3077 real alpha; /* a single angle between an actual and a reference position */
3078 real weight; /* single weight for a single angle */
3079 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3080 rvec xj_u; /* xj - u */
3081 rvec yj0_yc0; /* yj0 -yc0 */
3082 rvec tmpvec, tmpvec2;
3083 real fac, fit_fac, fac2, Vpart = 0.0;
3084 rvec rj, fit_rj, sj;
3086 rvec v_xj_u; /* v x (xj - u) */
3087 real psij, psijstar;
3088 real mj, wj; /* For mass-weighting of the positions */
3092 gmx_bool bCalcPotFit;
3095 erg = rotg->enfrotgrp;
3097 bPF = rotg->eType == erotgRM2PF;
3098 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
3101 clear_rvec(yj0_yc0); /* Make the compiler happy */
3103 clear_rvec(innersumvec);
3106 /* For the pivot-free variant we have to use the current center of
3107 * mass of the rotation group instead of the pivot u */
3108 get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
3110 /* Also, we precalculate the second term of the forces that is identical
3111 * (up to the weight factor mj) for all forces */
3112 radial_motion2_precalc_inner_sum(rotg, innersumvec);
3115 N_M = rotg->nat * erg->invmass;
3117 /* Each process calculates the forces on its local atoms */
3118 for (j = 0; j < erg->nat_loc; j++)
3122 /* Local index of a rotation group atom */
3123 ii = erg->ind_loc[j];
3124 /* Position of this atom in the collective array */
3125 iigrp = erg->xc_ref_ind[j];
3126 /* Mass-weighting */
3127 mj = erg->mc[iigrp];
3129 /* Current position of this atom: x[ii] */
3130 copy_rvec(x[ii], xj);
3132 /* Shift this atom such that it is near its reference */
3133 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
3135 /* The (unrotated) reference position is yj0. yc0 has already
3136 * been subtracted in init_rot_group */
3137 copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
3139 /* Calculate Omega.(yj0-yc0) */
3140 mvmul(erg->rotmat, yj0_yc0, rj); /* rj = Omega.(yj0-yc0) */
3145 copy_rvec(erg->x_loc_pbc[j], xj);
3146 copy_rvec(erg->xr_loc[j], rj); /* rj = Omega.(yj0-u) */
3148 /* Mass-weighting */
3151 /* Calculate (xj-u) resp. (xj-xc) */
3152 rvec_sub(xj, erg->xc_center, xj_u); /* xj_u = xj-u */
3154 cprod(rotg->vec, xj_u, v_xj_u); /* v_xj_u = v x (xj-u) */
3156 fac = norm2(v_xj_u);
3158 psijstar = 1.0/(fac + rotg->eps); /* psistar = -------------------- */
3159 /* |v x (xj-u)|^2 + eps */
3161 psij = gmx::invsqrt(fac); /* 1 */
3162 /* psij = ------------ */
3165 svmul(psij, v_xj_u, sj); /* sj = psij * (v x (xj-u) ) */
3167 fac = iprod(v_xj_u, rj); /* fac = (v x (xj-u)).rj */
3170 sjrj = iprod(sj, rj); /* sjrj = sj.rj */
3172 svmul(psijstar/psij, rj, tmpvec);
3173 svmul(psijstar*psijstar/(psij*psij*psij) * sjrj, sj, tmpvec2);
3174 rvec_dec(tmpvec, tmpvec2);
3175 cprod(tmpvec, rotg->vec, tmpvec2);
3177 /* Store the additional force so that it can be added to the force
3178 * array after the normal forces have been evaluated */
3179 svmul(-rotg->k*wj*sjrj, tmpvec2, tmpvec);
3180 svmul(mj, innersumvec, tmpvec2); /* This is != 0 only for the pivot-free variant */
3182 rvec_add(tmpvec2, tmpvec, erg->f_rot_loc[j]);
3183 Vpart += wj*psijstar*fac2;
3185 /* If requested, also calculate the potential for a set of angles
3186 * near the current reference angle */
3189 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
3193 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, fit_rj); /* fit_rj = Omega.(yj0-yc0) */
3197 /* Position of this atom in the collective array */
3198 iigrp = erg->xc_ref_ind[j];
3199 /* Rotate with the alternative angle. Like rotate_local_reference(),
3200 * just for a single local atom */
3201 mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[iigrp], fit_rj); /* fit_rj = Omega*(yj0-u) */
3203 fit_fac = iprod(v_xj_u, fit_rj); /* fac = (v x (xj-u)).fit_rj */
3204 /* Add to the rotation potential for this angle: */
3205 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*psijstar*fit_fac*fit_fac;
3211 /* Add to the torque of this rotation group */
3212 erg->torque_v += torque(rotg->vec, erg->f_rot_loc[j], xj, erg->xc_center);
3214 /* Calculate the angle between reference and actual rotation group atom. */
3215 angle(rotg, xj_u, rj, &alpha, &weight); /* angle in rad, weighted */
3216 erg->angle_v += alpha * weight;
3217 erg->weight_v += weight;
3222 } /* end of loop over local rotation group atoms */
3223 erg->V = 0.5*rotg->k*Vpart;
3227 /* Determine the smallest and largest position vector (with respect to the
3228 * rotation vector) for the reference group */
3229 static void get_firstlast_atom_ref(
3235 real xcproj; /* The projection of a reference position on the
3237 real minproj, maxproj; /* Smallest and largest projection on v */
3241 /* Start with some value */
3242 minproj = iprod(rotg->x_ref[0], rotg->vec);
3245 /* This is just to ensure that it still works if all the atoms of the
3246 * reference structure are situated in a plane perpendicular to the rotation
3249 *lastindex = rotg->nat-1;
3251 /* Loop over all atoms of the reference group,
3252 * project them on the rotation vector to find the extremes */
3253 for (i = 0; i < rotg->nat; i++)
3255 xcproj = iprod(rotg->x_ref[i], rotg->vec);
3256 if (xcproj < minproj)
3261 if (xcproj > maxproj)
3270 /* Allocate memory for the slabs */
3271 static void allocate_slabs(
3277 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3281 erg = rotg->enfrotgrp;
3283 /* More slabs than are defined for the reference are never needed */
3284 nslabs = erg->slab_last_ref - erg->slab_first_ref + 1;
3286 /* Remember how many we allocated */
3287 erg->nslabs_alloc = nslabs;
3289 if ( (nullptr != fplog) && bVerbose)
3291 fprintf(fplog, "%s allocating memory to store data for %d slabs (rotation group %d).\n",
3294 snew(erg->slab_center, nslabs);
3295 snew(erg->slab_center_ref, nslabs);
3296 snew(erg->slab_weights, nslabs);
3297 snew(erg->slab_torque_v, nslabs);
3298 snew(erg->slab_data, nslabs);
3299 snew(erg->gn_atom, nslabs);
3300 snew(erg->gn_slabind, nslabs);
3301 snew(erg->slab_innersumvec, nslabs);
3302 for (i = 0; i < nslabs; i++)
3304 snew(erg->slab_data[i].x, rotg->nat);
3305 snew(erg->slab_data[i].ref, rotg->nat);
3306 snew(erg->slab_data[i].weight, rotg->nat);
3308 snew(erg->xc_ref_sorted, rotg->nat);
3309 snew(erg->xc_sortind, rotg->nat);
3310 snew(erg->firstatom, nslabs);
3311 snew(erg->lastatom, nslabs);
3315 /* From the extreme positions of the reference group, determine the first
3316 * and last slab of the reference. We can never have more slabs in the real
3317 * simulation than calculated here for the reference.
3319 static void get_firstlast_slab_ref(t_rotgrp *rotg, real mc[], int ref_firstindex, int ref_lastindex)
3321 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3326 erg = rotg->enfrotgrp;
3327 first = get_first_slab(rotg, erg->max_beta, rotg->x_ref[ref_firstindex]);
3328 last = get_last_slab( rotg, erg->max_beta, rotg->x_ref[ref_lastindex ]);
3330 while (get_slab_weight(first, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
3334 erg->slab_first_ref = first+1;
3335 while (get_slab_weight(last, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
3339 erg->slab_last_ref = last-1;
3343 /* Special version of copy_rvec:
3344 * During the copy procedure of xcurr to b, the correct PBC image is chosen
3345 * such that the copied vector ends up near its reference position xref */
3346 static inline void copy_correct_pbc_image(
3347 const rvec xcurr, /* copy vector xcurr ... */
3348 rvec b, /* ... to b ... */
3349 const rvec xref, /* choosing the PBC image such that b ends up near xref */
3358 /* Shortest PBC distance between the atom and its reference */
3359 rvec_sub(xcurr, xref, dx);
3361 /* Determine the shift for this atom */
3363 for (m = npbcdim-1; m >= 0; m--)
3365 while (dx[m] < -0.5*box[m][m])
3367 for (d = 0; d < DIM; d++)
3373 while (dx[m] >= 0.5*box[m][m])
3375 for (d = 0; d < DIM; d++)
3383 /* Apply the shift to the position */
3384 copy_rvec(xcurr, b);
3385 shift_single_coord(box, b, shift);
3389 static void init_rot_group(FILE *fplog, const t_commrec *cr, int g, t_rotgrp *rotg,
3390 rvec *x, gmx_mtop_t *mtop, gmx_bool bVerbose, FILE *out_slabs, const matrix box,
3391 t_inputrec *ir, gmx_bool bOutputCenters)
3394 rvec coord, xref, *xdum;
3395 gmx_bool bFlex, bColl;
3396 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3397 int ref_firstindex, ref_lastindex;
3398 real mass, totalmass;
3403 /* Do we have a flexible axis? */
3404 bFlex = ISFLEX(rotg);
3405 /* Do we use a global set of coordinates? */
3406 bColl = ISCOLL(rotg);
3408 erg = rotg->enfrotgrp;
3410 /* Allocate space for collective coordinates if needed */
3413 snew(erg->xc, rotg->nat);
3414 snew(erg->xc_shifts, rotg->nat);
3415 snew(erg->xc_eshifts, rotg->nat);
3416 snew(erg->xc_old, rotg->nat);
3418 if (rotg->eFittype == erotgFitNORM)
3420 snew(erg->xc_ref_length, rotg->nat); /* in case fit type NORM is chosen */
3421 snew(erg->xc_norm, rotg->nat);
3426 snew(erg->xr_loc, rotg->nat);
3427 snew(erg->x_loc_pbc, rotg->nat);
3430 snew(erg->f_rot_loc, rotg->nat);
3431 snew(erg->xc_ref_ind, rotg->nat);
3433 /* Make space for the calculation of the potential at other angles (used
3434 * for fitting only) */
3435 if (erotgFitPOT == rotg->eFittype)
3437 snew(erg->PotAngleFit, 1);
3438 snew(erg->PotAngleFit->degangle, rotg->PotAngle_nstep);
3439 snew(erg->PotAngleFit->V, rotg->PotAngle_nstep);
3440 snew(erg->PotAngleFit->rotmat, rotg->PotAngle_nstep);
3442 /* Get the set of angles around the reference angle */
3443 start = -0.5 * (rotg->PotAngle_nstep - 1)*rotg->PotAngle_step;
3444 for (i = 0; i < rotg->PotAngle_nstep; i++)
3446 erg->PotAngleFit->degangle[i] = start + i*rotg->PotAngle_step;
3451 erg->PotAngleFit = nullptr;
3454 /* xc_ref_ind needs to be set to identity in the serial case */
3457 for (i = 0; i < rotg->nat; i++)
3459 erg->xc_ref_ind[i] = i;
3463 /* Copy the masses so that the center can be determined. For all types of
3464 * enforced rotation, we store the masses in the erg->mc array. */
3465 snew(erg->mc, rotg->nat);
3468 snew(erg->mc_sorted, rotg->nat);
3472 snew(erg->m_loc, rotg->nat);
3476 for (i = 0; i < rotg->nat; i++)
3480 mass = mtopGetAtomMass(mtop, rotg->ind[i], &molb);
3489 erg->invmass = 1.0/totalmass;
3491 /* Set xc_ref_center for any rotation potential */
3492 if ((rotg->eType == erotgISO) || (rotg->eType == erotgPM) || (rotg->eType == erotgRM) || (rotg->eType == erotgRM2))
3494 /* Set the pivot point for the fixed, stationary-axis potentials. This
3495 * won't change during the simulation */
3496 copy_rvec(rotg->pivot, erg->xc_ref_center);
3497 copy_rvec(rotg->pivot, erg->xc_center );
3501 /* Center of the reference positions */
3502 get_center(rotg->x_ref, erg->mc, rotg->nat, erg->xc_ref_center);
3504 /* Center of the actual positions */
3507 snew(xdum, rotg->nat);
3508 for (i = 0; i < rotg->nat; i++)
3511 copy_rvec(x[ii], xdum[i]);
3513 get_center(xdum, erg->mc, rotg->nat, erg->xc_center);
3519 gmx_bcast(sizeof(erg->xc_center), erg->xc_center, cr);
3526 /* Save the original (whole) set of positions in xc_old such that at later
3527 * steps the rotation group can always be made whole again. If the simulation is
3528 * restarted, we compute the starting reference positions (given the time)
3529 * and assume that the correct PBC image of each position is the one nearest
3530 * to the current reference */
3533 /* Calculate the rotation matrix for this angle: */
3534 t_start = ir->init_t + ir->init_step*ir->delta_t;
3535 erg->degangle = rotg->rate * t_start;
3536 calc_rotmat(rotg->vec, erg->degangle, erg->rotmat);
3538 for (i = 0; i < rotg->nat; i++)
3542 /* Subtract pivot, rotate, and add pivot again. This will yield the
3543 * reference position for time t */
3544 rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
3545 mvmul(erg->rotmat, coord, xref);
3546 rvec_inc(xref, erg->xc_ref_center);
3548 copy_correct_pbc_image(x[ii], erg->xc_old[i], xref, box, 3);
3554 gmx_bcast(rotg->nat*sizeof(erg->xc_old[0]), erg->xc_old, cr);
3559 if ( (rotg->eType != erotgFLEX) && (rotg->eType != erotgFLEX2) )
3561 /* Put the reference positions into origin: */
3562 for (i = 0; i < rotg->nat; i++)
3564 rvec_dec(rotg->x_ref[i], erg->xc_ref_center);
3568 /* Enforced rotation with flexible axis */
3571 /* Calculate maximum beta value from minimum gaussian (performance opt.) */
3572 erg->max_beta = calc_beta_max(rotg->min_gaussian, rotg->slab_dist);
3574 /* Determine the smallest and largest coordinate with respect to the rotation vector */
3575 get_firstlast_atom_ref(rotg, &ref_firstindex, &ref_lastindex);
3577 /* From the extreme positions of the reference group, determine the first
3578 * and last slab of the reference. */
3579 get_firstlast_slab_ref(rotg, erg->mc, ref_firstindex, ref_lastindex);
3581 /* Allocate memory for the slabs */
3582 allocate_slabs(rotg, fplog, g, bVerbose);
3584 /* Flexible rotation: determine the reference centers for the rest of the simulation */
3585 erg->slab_first = erg->slab_first_ref;
3586 erg->slab_last = erg->slab_last_ref;
3587 get_slab_centers(rotg, rotg->x_ref, erg->mc, g, -1, out_slabs, bOutputCenters, TRUE);
3589 /* Length of each x_rotref vector from center (needed if fit routine NORM is chosen): */
3590 if (rotg->eFittype == erotgFitNORM)
3592 for (i = 0; i < rotg->nat; i++)
3594 rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
3595 erg->xc_ref_length[i] = norm(coord);
3602 extern void dd_make_local_rotation_groups(gmx_domdec_t *dd, t_rot *rot)
3607 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3611 for (g = 0; g < rot->ngrp; g++)
3613 rotg = &rot->grp[g];
3614 erg = rotg->enfrotgrp;
3617 dd_make_local_group_indices(ga2la, rotg->nat, rotg->ind,
3618 &erg->nat_loc, &erg->ind_loc, &erg->nalloc_loc, erg->xc_ref_ind);
3623 /* Calculate the size of the MPI buffer needed in reduce_output() */
3624 static int calc_mpi_bufsize(t_rot *rot)
3627 int count_group, count_total;
3629 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3633 for (g = 0; g < rot->ngrp; g++)
3635 rotg = &rot->grp[g];
3636 erg = rotg->enfrotgrp;
3638 /* Count the items that are transferred for this group: */
3639 count_group = 4; /* V, torque, angle, weight */
3641 /* Add the maximum number of slabs for flexible groups */
3644 count_group += erg->slab_last_ref - erg->slab_first_ref + 1;
3647 /* Add space for the potentials at different angles: */
3648 if (erotgFitPOT == rotg->eFittype)
3650 count_group += rotg->PotAngle_nstep;
3653 /* Add to the total number: */
3654 count_total += count_group;
3661 extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
3662 const t_commrec *cr, const t_state *globalState, gmx_mtop_t *mtop, const gmx_output_env_t *oenv,
3663 const MdrunOptions &mdrunOptions)
3668 int nat_max = 0; /* Size of biggest rotation group */
3669 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3670 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3671 rvec *x_pbc = nullptr; /* Space for the pbc-correct atom positions */
3674 if (MASTER(cr) && mdrunOptions.verbose)
3676 fprintf(stdout, "%s Initializing ...\n", RotStr);
3680 snew(rot->enfrot, 1);
3682 er->appendFiles = mdrunOptions.continuationOptions.appendFiles;
3684 /* When appending, skip first output to avoid duplicate entries in the data files */
3685 if (er->appendFiles)
3694 if (MASTER(cr) && er->bOut)
3696 please_cite(fplog, "Kutzner2011");
3699 /* Output every step for reruns */
3700 if (mdrunOptions.rerun)
3702 if (nullptr != fplog)
3704 fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
3710 er->out_slabs = nullptr;
3711 if (MASTER(cr) && HaveFlexibleGroups(rot) )
3713 er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), rot);
3718 /* Remove pbc, make molecule whole.
3719 * When ir->bContinuation=TRUE this has already been done, but ok. */
3720 snew(x_pbc, mtop->natoms);
3721 copy_rvecn(as_rvec_array(globalState->x.data()), x_pbc, 0, mtop->natoms);
3722 do_pbc_first_mtop(nullptr, ir->ePBC, globalState->box, mtop, x_pbc);
3723 /* All molecules will be whole now, but not necessarily in the home box.
3724 * Additionally, if a rotation group consists of more than one molecule
3725 * (e.g. two strands of DNA), each one of them can end up in a different
3726 * periodic box. This is taken care of in init_rot_group. */
3729 for (g = 0; g < rot->ngrp; g++)
3731 rotg = &rot->grp[g];
3733 if (nullptr != fplog)
3735 fprintf(fplog, "%s group %d type '%s'\n", RotStr, g, erotg_names[rotg->eType]);
3740 /* Allocate space for the rotation group's data: */
3741 snew(rotg->enfrotgrp, 1);
3742 erg = rotg->enfrotgrp;
3744 nat_max = std::max(nat_max, rotg->nat);
3749 erg->nalloc_loc = 0;
3750 erg->ind_loc = nullptr;
3754 erg->nat_loc = rotg->nat;
3755 erg->ind_loc = rotg->ind;
3757 init_rot_group(fplog, cr, g, rotg, x_pbc, mtop, mdrunOptions.verbose, er->out_slabs, MASTER(cr) ? globalState->box : nullptr, ir,
3758 !er->appendFiles); /* Do not output the reference centers
3759 * again if we are appending */
3763 /* Allocate space for enforced rotation buffer variables */
3764 er->bufsize = nat_max;
3765 snew(er->data, nat_max);
3766 snew(er->xbuf, nat_max);
3767 snew(er->mbuf, nat_max);
3769 /* Buffers for MPI reducing torques, angles, weights (for each group), and V */
3772 er->mpi_bufsize = calc_mpi_bufsize(rot) + 100; /* larger to catch errors */
3773 snew(er->mpi_inbuf, er->mpi_bufsize);
3774 snew(er->mpi_outbuf, er->mpi_bufsize);
3778 er->mpi_bufsize = 0;
3779 er->mpi_inbuf = nullptr;
3780 er->mpi_outbuf = nullptr;
3783 /* Only do I/O on the MASTER */
3784 er->out_angles = nullptr;
3785 er->out_rot = nullptr;
3786 er->out_torque = nullptr;
3789 er->out_rot = open_rot_out(opt2fn("-ro", nfile, fnm), rot, oenv);
3791 if (rot->nstsout > 0)
3793 if (HaveFlexibleGroups(rot) || HavePotFitGroups(rot) )
3795 er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), rot);
3797 if (HaveFlexibleGroups(rot) )
3799 er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), rot);
3808 extern void finish_rot(t_rot *rot)
3810 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3816 gmx_fio_fclose(er->out_rot);
3820 gmx_fio_fclose(er->out_slabs);
3824 gmx_fio_fclose(er->out_angles);
3828 gmx_fio_fclose(er->out_torque);
3833 /* Rotate the local reference positions and store them in
3834 * erg->xr_loc[0...(nat_loc-1)]
3836 * Note that we already subtracted u or y_c from the reference positions
3837 * in init_rot_group().
3839 static void rotate_local_reference(t_rotgrp *rotg)
3841 gmx_enfrotgrp_t erg;
3845 erg = rotg->enfrotgrp;
3847 for (i = 0; i < erg->nat_loc; i++)
3849 /* Index of this rotation group atom with respect to the whole rotation group */
3850 ii = erg->xc_ref_ind[i];
3852 mvmul(erg->rotmat, rotg->x_ref[ii], erg->xr_loc[i]);
3857 /* Select the PBC representation for each local x position and store that
3858 * for later usage. We assume the right PBC image of an x is the one nearest to
3859 * its rotated reference */
3860 static void choose_pbc_image(rvec x[], t_rotgrp *rotg, matrix box, int npbcdim)
3863 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3867 erg = rotg->enfrotgrp;
3869 for (i = 0; i < erg->nat_loc; i++)
3871 /* Index of a rotation group atom */
3872 ii = erg->ind_loc[i];
3874 /* Get the correctly rotated reference position. The pivot was already
3875 * subtracted in init_rot_group() from the reference positions. Also,
3876 * the reference positions have already been rotated in
3877 * rotate_local_reference(). For the current reference position we thus
3878 * only need to add the pivot again. */
3879 copy_rvec(erg->xr_loc[i], xref);
3880 rvec_inc(xref, erg->xc_ref_center);
3882 copy_correct_pbc_image(x[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
3887 extern void do_rotation(
3888 const t_commrec *cr,
3889 const t_inputrec *ir,
3899 gmx_bool outstep_slab, outstep_rot;
3901 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3902 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3904 t_gmx_potfit *fit = nullptr; /* For fit type 'potential' determine the fit
3905 angle via the potential minimum */
3914 /* When to output in main rotation output file */
3915 outstep_rot = do_per_step(step, rot->nstrout) && er->bOut;
3916 /* When to output per-slab data */
3917 outstep_slab = do_per_step(step, rot->nstsout) && er->bOut;
3919 /* Output time into rotation output file */
3920 if (outstep_rot && MASTER(cr))
3922 fprintf(er->out_rot, "%12.3e", t);
3925 /**************************************************************************/
3926 /* First do ALL the communication! */
3927 for (g = 0; g < rot->ngrp; g++)
3929 rotg = &rot->grp[g];
3930 erg = rotg->enfrotgrp;
3932 /* Do we use a collective (global) set of coordinates? */
3933 bColl = ISCOLL(rotg);
3935 /* Calculate the rotation matrix for this angle: */
3936 erg->degangle = rotg->rate * t;
3937 calc_rotmat(rotg->vec, erg->degangle, erg->rotmat);
3941 /* Transfer the rotation group's positions such that every node has
3942 * all of them. Every node contributes its local positions x and stores
3943 * it in the collective erg->xc array. */
3944 communicate_group_positions(cr, erg->xc, erg->xc_shifts, erg->xc_eshifts, bNS,
3945 x, rotg->nat, erg->nat_loc, erg->ind_loc, erg->xc_ref_ind, erg->xc_old, box);
3949 /* Fill the local masses array;
3950 * this array changes in DD/neighborsearching steps */
3953 for (i = 0; i < erg->nat_loc; i++)
3955 /* Index of local atom w.r.t. the collective rotation group */
3956 ii = erg->xc_ref_ind[i];
3957 erg->m_loc[i] = erg->mc[ii];
3961 /* Calculate Omega*(y_i-y_c) for the local positions */
3962 rotate_local_reference(rotg);
3964 /* Choose the nearest PBC images of the group atoms with respect
3965 * to the rotated reference positions */
3966 choose_pbc_image(x, rotg, box, 3);
3968 /* Get the center of the rotation group */
3969 if ( (rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) )
3971 get_center_comm(cr, erg->x_loc_pbc, erg->m_loc, erg->nat_loc, rotg->nat, erg->xc_center);
3975 } /* End of loop over rotation groups */
3977 /**************************************************************************/
3978 /* Done communicating, we can start to count cycles for the load balancing now ... */
3979 if (DOMAINDECOMP(cr))
3981 ddReopenBalanceRegionCpu(cr->dd);
3988 for (g = 0; g < rot->ngrp; g++)
3990 rotg = &rot->grp[g];
3991 erg = rotg->enfrotgrp;
3993 if (outstep_rot && MASTER(cr))
3995 fprintf(er->out_rot, "%12.4f", erg->degangle);
3998 /* Calculate angles and rotation matrices for potential fitting: */
3999 if ( (outstep_rot || outstep_slab) && (erotgFitPOT == rotg->eFittype) )
4001 fit = erg->PotAngleFit;
4002 for (i = 0; i < rotg->PotAngle_nstep; i++)
4004 calc_rotmat(rotg->vec, erg->degangle + fit->degangle[i], fit->rotmat[i]);
4006 /* Clear value from last step */
4007 erg->PotAngleFit->V[i] = 0.0;
4011 /* Clear values from last time step */
4013 erg->torque_v = 0.0;
4015 erg->weight_v = 0.0;
4017 switch (rotg->eType)
4023 do_fixed(rotg, outstep_rot, outstep_slab);
4026 do_radial_motion(rotg, outstep_rot, outstep_slab);
4029 do_radial_motion_pf(rotg, x, box, outstep_rot, outstep_slab);
4033 do_radial_motion2(rotg, x, box, outstep_rot, outstep_slab);
4037 /* Subtract the center of the rotation group from the collective positions array
4038 * Also store the center in erg->xc_center since it needs to be subtracted
4039 * in the low level routines from the local coordinates as well */
4040 get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
4041 svmul(-1.0, erg->xc_center, transvec);
4042 translate_x(erg->xc, rotg->nat, transvec);
4043 do_flexible(MASTER(cr), er, rotg, g, x, box, t, outstep_rot, outstep_slab);
4047 /* Do NOT subtract the center of mass in the low level routines! */
4048 clear_rvec(erg->xc_center);
4049 do_flexible(MASTER(cr), er, rotg, g, x, box, t, outstep_rot, outstep_slab);
4052 gmx_fatal(FARGS, "No such rotation potential.");
4060 fprintf(stderr, "%s calculation (step %d) took %g seconds.\n", RotStr, step, MPI_Wtime()-t0);