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32 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
42 #include "gmx_wallcycle.h"
43 #include "gmx_cyclecounter.h"
44 #include "gromacs/fileio/trnio.h"
48 #include "gromacs/fileio/futil.h"
52 #include "mtop_util.h"
56 #include "gmx_ga2la.h"
58 #include "gromacs/fileio/gmxfio.h"
59 #include "groupcoord.h"
60 #include "pull_rotation.h"
66 static char *RotStr = {"Enforced rotation:"};
69 /* Set the minimum weight for the determination of the slab centers */
70 #define WEIGHT_MIN (10*GMX_FLOAT_MIN)
72 /* Helper structure for sorting positions along rotation vector */
74 real xcproj; /* Projection of xc on the rotation vector */
75 int ind; /* Index of xc */
77 rvec x; /* Position */
78 rvec x_ref; /* Reference position */
82 /* Enforced rotation / flexible: determine the angle of each slab */
83 typedef struct gmx_slabdata
85 int nat; /* Number of atoms belonging to this slab */
86 rvec *x; /* The positions belonging to this slab. In
87 general, this should be all positions of the
88 whole rotation group, but we leave those away
89 that have a small enough weight */
90 rvec *ref; /* Same for reference */
91 real *weight; /* The weight for each atom */
95 /* Helper structure for potential fitting */
96 typedef struct gmx_potfit
98 real *degangle; /* Set of angles for which the potential is
99 calculated. The optimum fit is determined as
100 the angle for with the potential is minimal */
101 real *V; /* Potential for the different angles */
102 matrix *rotmat; /* Rotation matrix corresponding to the angles */
106 /* Enforced rotation data for all groups */
107 typedef struct gmx_enfrot
109 FILE *out_rot; /* Output file for rotation data */
110 FILE *out_torque; /* Output file for torque data */
111 FILE *out_angles; /* Output file for slab angles for flexible type */
112 FILE *out_slabs; /* Output file for slab centers */
113 int bufsize; /* Allocation size of buf */
114 rvec *xbuf; /* Coordinate buffer variable for sorting */
115 real *mbuf; /* Masses buffer variable for sorting */
116 sort_along_vec_t *data; /* Buffer variable needed for position sorting */
117 real *mpi_inbuf; /* MPI buffer */
118 real *mpi_outbuf; /* MPI buffer */
119 int mpi_bufsize; /* Allocation size of in & outbuf */
120 unsigned long Flags; /* mdrun flags */
121 gmx_bool bOut; /* Used to skip first output when appending to
122 * avoid duplicate entries in rotation outfiles */
126 /* Global enforced rotation data for a single rotation group */
127 typedef struct gmx_enfrotgrp
129 real degangle; /* Rotation angle in degrees */
130 matrix rotmat; /* Rotation matrix */
131 atom_id *ind_loc; /* Local rotation indices */
132 int nat_loc; /* Number of local group atoms */
133 int nalloc_loc; /* Allocation size for ind_loc and weight_loc */
135 real V; /* Rotation potential for this rotation group */
136 rvec *f_rot_loc; /* Array to store the forces on the local atoms
137 resulting from enforced rotation potential */
139 /* Collective coordinates for the whole rotation group */
140 real *xc_ref_length; /* Length of each x_rotref vector after x_rotref
141 has been put into origin */
142 int *xc_ref_ind; /* Position of each local atom in the collective
144 rvec xc_center; /* Center of the rotation group positions, may
146 rvec xc_ref_center; /* dito, for the reference positions */
147 rvec *xc; /* Current (collective) positions */
148 ivec *xc_shifts; /* Current (collective) shifts */
149 ivec *xc_eshifts; /* Extra shifts since last DD step */
150 rvec *xc_old; /* Old (collective) positions */
151 rvec *xc_norm; /* Normalized form of the current positions */
152 rvec *xc_ref_sorted; /* Reference positions (sorted in the same order
153 as xc when sorted) */
154 int *xc_sortind; /* Where is a position found after sorting? */
155 real *mc; /* Collective masses */
157 real invmass; /* one over the total mass of the rotation group */
159 real torque_v; /* Torque in the direction of rotation vector */
160 real angle_v; /* Actual angle of the whole rotation group */
161 /* Fixed rotation only */
162 real weight_v; /* Weights for angle determination */
163 rvec *xr_loc; /* Local reference coords, correctly rotated */
164 rvec *x_loc_pbc; /* Local current coords, correct PBC image */
165 real *m_loc; /* Masses of the current local atoms */
167 /* Flexible rotation only */
168 int nslabs_alloc; /* For this many slabs memory is allocated */
169 int slab_first; /* Lowermost slab for that the calculation needs
170 to be performed at a given time step */
171 int slab_last; /* Uppermost slab ... */
172 int slab_first_ref; /* First slab for which ref. center is stored */
173 int slab_last_ref; /* Last ... */
174 int slab_buffer; /* Slab buffer region around reference slabs */
175 int *firstatom; /* First relevant atom for a slab */
176 int *lastatom; /* Last relevant atom for a slab */
177 rvec *slab_center; /* Gaussian-weighted slab center */
178 rvec *slab_center_ref; /* Gaussian-weighted slab center for the
179 reference positions */
180 real *slab_weights; /* Sum of gaussian weights in a slab */
181 real *slab_torque_v; /* Torque T = r x f for each slab. */
182 /* torque_v = m.v = angular momentum in the
184 real max_beta; /* min_gaussian from inputrec->rotgrp is the
185 minimum value the gaussian must have so that
186 the force is actually evaluated max_beta is
187 just another way to put it */
188 real *gn_atom; /* Precalculated gaussians for a single atom */
189 int *gn_slabind; /* Tells to which slab each precalculated gaussian
191 rvec *slab_innersumvec; /* Inner sum of the flexible2 potential per slab;
192 this is precalculated for optimization reasons */
193 t_gmx_slabdata *slab_data; /* Holds atom positions and gaussian weights
194 of atoms belonging to a slab */
196 /* For potential fits with varying angle: */
197 t_gmx_potfit *PotAngleFit; /* Used for fit type 'potential' */
201 /* Activate output of forces for correctness checks */
202 /* #define PRINT_FORCES */
204 #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]);
205 #define PRINT_POT_TAU if (MASTER(cr)) { \
206 fprintf(stderr, "potential = %15.8f\n" "torque = %15.8f\n", erg->V, erg->torque_v); \
209 #define PRINT_FORCE_J
210 #define PRINT_POT_TAU
213 /* Shortcuts for often used queries */
214 #define ISFLEX(rg) ( (rg->eType == erotgFLEX) || (rg->eType == erotgFLEXT) || (rg->eType == erotgFLEX2) || (rg->eType == erotgFLEX2T) )
215 #define ISCOLL(rg) ( (rg->eType == erotgFLEX) || (rg->eType == erotgFLEXT) || (rg->eType == erotgFLEX2) || (rg->eType == erotgFLEX2T) || (rg->eType == erotgRMPF) || (rg->eType == erotgRM2PF) )
218 /* Does any of the rotation groups use slab decomposition? */
219 static gmx_bool HaveFlexibleGroups(t_rot *rot)
225 for (g = 0; g < rot->ngrp; g++)
238 /* Is for any group the fit angle determined by finding the minimum of the
239 * rotation potential? */
240 static gmx_bool HavePotFitGroups(t_rot *rot)
246 for (g = 0; g < rot->ngrp; g++)
249 if (erotgFitPOT == rotg->eFittype)
259 static double** allocate_square_matrix(int dim)
266 for (i = 0; i < dim; i++)
275 static void free_square_matrix(double** mat, int dim)
280 for (i = 0; i < dim; i++)
288 /* Return the angle for which the potential is minimal */
289 static real get_fitangle(t_rotgrp *rotg, gmx_enfrotgrp_t erg)
292 real fitangle = -999.9;
293 real pot_min = GMX_FLOAT_MAX;
297 fit = erg->PotAngleFit;
299 for (i = 0; i < rotg->PotAngle_nstep; i++)
301 if (fit->V[i] < pot_min)
304 fitangle = fit->degangle[i];
312 /* Reduce potential angle fit data for this group at this time step? */
313 static gmx_inline gmx_bool bPotAngle(t_rot *rot, t_rotgrp *rotg, gmx_large_int_t step)
315 return ( (erotgFitPOT == rotg->eFittype) && (do_per_step(step, rot->nstsout) || do_per_step(step, rot->nstrout)) );
318 /* Reduce slab torqe data for this group at this time step? */
319 static gmx_inline gmx_bool bSlabTau(t_rot *rot, t_rotgrp *rotg, gmx_large_int_t step)
321 return ( (ISFLEX(rotg)) && do_per_step(step, rot->nstsout) );
324 /* Output rotation energy, torques, etc. for each rotation group */
325 static void reduce_output(t_commrec *cr, t_rot *rot, real t, gmx_large_int_t step)
327 int g, i, islab, nslabs = 0;
328 int count; /* MPI element counter */
330 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
331 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
338 /* Fill the MPI buffer with stuff to reduce. If items are added for reduction
339 * here, the MPI buffer size has to be enlarged also in calc_mpi_bufsize() */
343 for (g = 0; g < rot->ngrp; g++)
346 erg = rotg->enfrotgrp;
347 nslabs = erg->slab_last - erg->slab_first + 1;
348 er->mpi_inbuf[count++] = erg->V;
349 er->mpi_inbuf[count++] = erg->torque_v;
350 er->mpi_inbuf[count++] = erg->angle_v;
351 er->mpi_inbuf[count++] = erg->weight_v; /* weights are not needed for flex types, but this is just a single value */
353 if (bPotAngle(rot, rotg, step))
355 for (i = 0; i < rotg->PotAngle_nstep; i++)
357 er->mpi_inbuf[count++] = erg->PotAngleFit->V[i];
360 if (bSlabTau(rot, rotg, step))
362 for (i = 0; i < nslabs; i++)
364 er->mpi_inbuf[count++] = erg->slab_torque_v[i];
368 if (count > er->mpi_bufsize)
370 gmx_fatal(FARGS, "%s MPI buffer overflow, please report this error.", RotStr);
374 MPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REAL, MPI_SUM, MASTERRANK(cr), cr->mpi_comm_mygroup);
377 /* Copy back the reduced data from the buffer on the master */
381 for (g = 0; g < rot->ngrp; g++)
384 erg = rotg->enfrotgrp;
385 nslabs = erg->slab_last - erg->slab_first + 1;
386 erg->V = er->mpi_outbuf[count++];
387 erg->torque_v = er->mpi_outbuf[count++];
388 erg->angle_v = er->mpi_outbuf[count++];
389 erg->weight_v = er->mpi_outbuf[count++];
391 if (bPotAngle(rot, rotg, step))
393 for (i = 0; i < rotg->PotAngle_nstep; i++)
395 erg->PotAngleFit->V[i] = er->mpi_outbuf[count++];
398 if (bSlabTau(rot, rotg, step))
400 for (i = 0; i < nslabs; i++)
402 erg->slab_torque_v[i] = er->mpi_outbuf[count++];
412 /* Angle and torque for each rotation group */
413 for (g = 0; g < rot->ngrp; g++)
416 bFlex = ISFLEX(rotg);
418 erg = rotg->enfrotgrp;
420 /* Output to main rotation output file: */
421 if (do_per_step(step, rot->nstrout) )
423 if (erotgFitPOT == rotg->eFittype)
425 fitangle = get_fitangle(rotg, erg);
431 fitangle = erg->angle_v; /* RMSD fit angle */
435 fitangle = (erg->angle_v/erg->weight_v)*180.0*M_1_PI;
438 fprintf(er->out_rot, "%12.4f", fitangle);
439 fprintf(er->out_rot, "%12.3e", erg->torque_v);
440 fprintf(er->out_rot, "%12.3e", erg->V);
443 if (do_per_step(step, rot->nstsout) )
445 /* Output to torque log file: */
448 fprintf(er->out_torque, "%12.3e%6d", t, g);
449 for (i = erg->slab_first; i <= erg->slab_last; i++)
451 islab = i - erg->slab_first; /* slab index */
452 /* Only output if enough weight is in slab */
453 if (erg->slab_weights[islab] > rotg->min_gaussian)
455 fprintf(er->out_torque, "%6d%12.3e", i, erg->slab_torque_v[islab]);
458 fprintf(er->out_torque, "\n");
461 /* Output to angles log file: */
462 if (erotgFitPOT == rotg->eFittype)
464 fprintf(er->out_angles, "%12.3e%6d%12.4f", t, g, erg->degangle);
465 /* Output energies at a set of angles around the reference angle */
466 for (i = 0; i < rotg->PotAngle_nstep; i++)
468 fprintf(er->out_angles, "%12.3e", erg->PotAngleFit->V[i]);
470 fprintf(er->out_angles, "\n");
474 if (do_per_step(step, rot->nstrout) )
476 fprintf(er->out_rot, "\n");
482 /* Add the forces from enforced rotation potential to the local forces.
483 * Should be called after the SR forces have been evaluated */
484 extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, gmx_large_int_t step, real t)
488 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
489 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
490 real Vrot = 0.0; /* If more than one rotation group is present, Vrot
491 assembles the local parts from all groups */
496 /* Loop over enforced rotation groups (usually 1, though)
497 * Apply the forces from rotation potentials */
498 for (g = 0; g < rot->ngrp; g++)
501 erg = rotg->enfrotgrp;
502 Vrot += erg->V; /* add the local parts from the nodes */
503 for (l = 0; l < erg->nat_loc; l++)
505 /* Get the right index of the local force */
506 ii = erg->ind_loc[l];
508 rvec_inc(f[ii], erg->f_rot_loc[l]);
512 /* Reduce energy,torque, angles etc. to get the sum values (per rotation group)
513 * on the master and output these values to file. */
514 if ( (do_per_step(step, rot->nstrout) || do_per_step(step, rot->nstsout)) && er->bOut)
516 reduce_output(cr, rot, t, step);
519 /* When appending, er->bOut is FALSE the first time to avoid duplicate entries */
528 /* The Gaussian norm is chosen such that the sum of the gaussian functions
529 * over the slabs is approximately 1.0 everywhere */
530 #define GAUSS_NORM 0.569917543430618
533 /* Calculate the maximum beta that leads to a gaussian larger min_gaussian,
534 * also does some checks
536 static double calc_beta_max(real min_gaussian, real slab_dist)
542 /* Actually the next two checks are already made in grompp */
545 gmx_fatal(FARGS, "Slab distance of flexible rotation groups must be >=0 !");
547 if (min_gaussian <= 0)
549 gmx_fatal(FARGS, "Cutoff value for Gaussian must be > 0. (You requested %f)");
552 /* Define the sigma value */
553 sigma = 0.7*slab_dist;
555 /* Calculate the argument for the logarithm and check that the log() result is negative or 0 */
556 arg = min_gaussian/GAUSS_NORM;
559 gmx_fatal(FARGS, "min_gaussian of flexible rotation groups must be <%g", GAUSS_NORM);
562 return sqrt(-2.0*sigma*sigma*log(min_gaussian/GAUSS_NORM));
566 static gmx_inline real calc_beta(rvec curr_x, t_rotgrp *rotg, int n)
568 return iprod(curr_x, rotg->vec) - rotg->slab_dist * n;
572 static gmx_inline real gaussian_weight(rvec curr_x, t_rotgrp *rotg, int n)
574 const real norm = GAUSS_NORM;
578 /* Define the sigma value */
579 sigma = 0.7*rotg->slab_dist;
580 /* Calculate the Gaussian value of slab n for position curr_x */
581 return norm * exp( -0.5 * sqr( calc_beta(curr_x, rotg, n)/sigma ) );
585 /* Returns the weight in a single slab, also calculates the Gaussian- and mass-
586 * weighted sum of positions for that slab */
587 static real get_slab_weight(int j, t_rotgrp *rotg, rvec xc[], real mc[], rvec *x_weighted_sum)
589 rvec curr_x; /* The position of an atom */
590 rvec curr_x_weighted; /* The gaussian-weighted position */
591 real gaussian; /* A single gaussian weight */
592 real wgauss; /* gaussian times current mass */
593 real slabweight = 0.0; /* The sum of weights in the slab */
595 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
598 erg = rotg->enfrotgrp;
599 clear_rvec(*x_weighted_sum);
602 islab = j - erg->slab_first;
604 /* Loop over all atoms in the rotation group */
605 for (i = 0; i < rotg->nat; i++)
607 copy_rvec(xc[i], curr_x);
608 gaussian = gaussian_weight(curr_x, rotg, j);
609 wgauss = gaussian * mc[i];
610 svmul(wgauss, curr_x, curr_x_weighted);
611 rvec_add(*x_weighted_sum, curr_x_weighted, *x_weighted_sum);
612 slabweight += wgauss;
613 } /* END of loop over rotation group atoms */
619 static void get_slab_centers(
620 t_rotgrp *rotg, /* The rotation group information */
621 rvec *xc, /* The rotation group positions; will
622 typically be enfrotgrp->xc, but at first call
623 it is enfrotgrp->xc_ref */
624 real *mc, /* The masses of the rotation group atoms */
625 int g, /* The number of the rotation group */
626 real time, /* Used for output only */
627 FILE *out_slabs, /* For outputting center per slab information */
628 gmx_bool bOutStep, /* Is this an output step? */
629 gmx_bool bReference) /* If this routine is called from
630 init_rot_group we need to store
631 the reference slab centers */
634 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
637 erg = rotg->enfrotgrp;
639 /* Loop over slabs */
640 for (j = erg->slab_first; j <= erg->slab_last; j++)
642 islab = j - erg->slab_first;
643 erg->slab_weights[islab] = get_slab_weight(j, rotg, xc, mc, &erg->slab_center[islab]);
645 /* We can do the calculations ONLY if there is weight in the slab! */
646 if (erg->slab_weights[islab] > WEIGHT_MIN)
648 svmul(1.0/erg->slab_weights[islab], erg->slab_center[islab], erg->slab_center[islab]);
652 /* We need to check this here, since we divide through slab_weights
653 * in the flexible low-level routines! */
654 gmx_fatal(FARGS, "Not enough weight in slab %d. Slab center cannot be determined!", j);
657 /* At first time step: save the centers of the reference structure */
660 copy_rvec(erg->slab_center[islab], erg->slab_center_ref[islab]);
662 } /* END of loop over slabs */
664 /* Output on the master */
665 if ( (NULL != out_slabs) && bOutStep)
667 fprintf(out_slabs, "%12.3e%6d", time, g);
668 for (j = erg->slab_first; j <= erg->slab_last; j++)
670 islab = j - erg->slab_first;
671 fprintf(out_slabs, "%6d%12.3e%12.3e%12.3e",
672 j, erg->slab_center[islab][XX], erg->slab_center[islab][YY], erg->slab_center[islab][ZZ]);
674 fprintf(out_slabs, "\n");
679 static void calc_rotmat(
681 real degangle, /* Angle alpha of rotation at time t in degrees */
682 matrix rotmat) /* Rotation matrix */
684 real radangle; /* Rotation angle in radians */
685 real cosa; /* cosine alpha */
686 real sina; /* sine alpha */
687 real OMcosa; /* 1 - cos(alpha) */
688 real dumxy, dumxz, dumyz; /* save computations */
689 rvec rot_vec; /* Rotate around rot_vec ... */
692 radangle = degangle * M_PI/180.0;
693 copy_rvec(vec, rot_vec );
695 /* Precompute some variables: */
696 cosa = cos(radangle);
697 sina = sin(radangle);
699 dumxy = rot_vec[XX]*rot_vec[YY]*OMcosa;
700 dumxz = rot_vec[XX]*rot_vec[ZZ]*OMcosa;
701 dumyz = rot_vec[YY]*rot_vec[ZZ]*OMcosa;
703 /* Construct the rotation matrix for this rotation group: */
705 rotmat[XX][XX] = cosa + rot_vec[XX]*rot_vec[XX]*OMcosa;
706 rotmat[YY][XX] = dumxy + rot_vec[ZZ]*sina;
707 rotmat[ZZ][XX] = dumxz - rot_vec[YY]*sina;
709 rotmat[XX][YY] = dumxy - rot_vec[ZZ]*sina;
710 rotmat[YY][YY] = cosa + rot_vec[YY]*rot_vec[YY]*OMcosa;
711 rotmat[ZZ][YY] = dumyz + rot_vec[XX]*sina;
713 rotmat[XX][ZZ] = dumxz + rot_vec[YY]*sina;
714 rotmat[YY][ZZ] = dumyz - rot_vec[XX]*sina;
715 rotmat[ZZ][ZZ] = cosa + rot_vec[ZZ]*rot_vec[ZZ]*OMcosa;
720 for (iii = 0; iii < 3; iii++)
722 for (jjj = 0; jjj < 3; jjj++)
724 fprintf(stderr, " %10.8f ", rotmat[iii][jjj]);
726 fprintf(stderr, "\n");
732 /* Calculates torque on the rotation axis tau = position x force */
733 static gmx_inline real torque(
734 rvec rotvec, /* rotation vector; MUST be normalized! */
735 rvec force, /* force */
736 rvec x, /* position of atom on which the force acts */
737 rvec pivot) /* pivot point of rotation axis */
742 /* Subtract offset */
743 rvec_sub(x, pivot, vectmp);
745 /* position x force */
746 cprod(vectmp, force, tau);
748 /* Return the part of the torque which is parallel to the rotation vector */
749 return iprod(tau, rotvec);
753 /* Right-aligned output of value with standard width */
754 static void print_aligned(FILE *fp, char *str)
756 fprintf(fp, "%12s", str);
760 /* Right-aligned output of value with standard short width */
761 static void print_aligned_short(FILE *fp, char *str)
763 fprintf(fp, "%6s", str);
767 static FILE *open_output_file(const char *fn, int steps, const char what[])
772 fp = ffopen(fn, "w");
774 fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n",
775 what, steps, steps > 1 ? "s" : "");
781 /* Open output file for slab center data. Call on master only */
782 static FILE *open_slab_out(const char *fn, t_rot *rot)
789 if (rot->enfrot->Flags & MD_APPENDFILES)
791 fp = gmx_fio_fopen(fn, "a");
795 fp = open_output_file(fn, rot->nstsout, "gaussian weighted slab centers");
797 for (g = 0; g < rot->ngrp; g++)
802 fprintf(fp, "# Rotation group %d (%s), slab distance %f nm, %s.\n",
803 g, erotg_names[rotg->eType], rotg->slab_dist,
804 rotg->bMassW ? "centers of mass" : "geometrical centers");
808 fprintf(fp, "# Reference centers are listed first (t=-1).\n");
809 fprintf(fp, "# The following columns have the syntax:\n");
811 print_aligned_short(fp, "t");
812 print_aligned_short(fp, "grp");
813 /* Print legend for the first two entries only ... */
814 for (i = 0; i < 2; i++)
816 print_aligned_short(fp, "slab");
817 print_aligned(fp, "X center");
818 print_aligned(fp, "Y center");
819 print_aligned(fp, "Z center");
821 fprintf(fp, " ...\n");
829 /* Adds 'buf' to 'str' */
830 static void add_to_string(char **str, char *buf)
835 len = strlen(*str) + strlen(buf) + 1;
841 static void add_to_string_aligned(char **str, char *buf)
843 char buf_aligned[STRLEN];
845 sprintf(buf_aligned, "%12s", buf);
846 add_to_string(str, buf_aligned);
850 /* Open output file and print some general information about the rotation groups.
851 * Call on master only */
852 static FILE *open_rot_out(const char *fn, t_rot *rot, const output_env_t oenv)
857 const char **setname;
858 char buf[50], buf2[75];
859 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
861 char *LegendStr = NULL;
864 if (rot->enfrot->Flags & MD_APPENDFILES)
866 fp = gmx_fio_fopen(fn, "a");
870 fp = xvgropen(fn, "Rotation angles and energy", "Time (ps)", "angles (degrees) and energies (kJ/mol)", oenv);
871 fprintf(fp, "# Output of enforced rotation data is written in intervals of %d time step%s.\n#\n", rot->nstrout, rot->nstrout > 1 ? "s" : "");
872 fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector v.\n");
873 fprintf(fp, "# To obtain the vectorial torque, multiply tau with the group's rot_vec.\n");
874 fprintf(fp, "# For flexible groups, tau(t,n) from all slabs n have been summed in a single value tau(t) here.\n");
875 fprintf(fp, "# The torques tau(t,n) are found in the rottorque.log (-rt) output file\n");
877 for (g = 0; g < rot->ngrp; g++)
880 erg = rotg->enfrotgrp;
881 bFlex = ISFLEX(rotg);
884 fprintf(fp, "# ROTATION GROUP %d, potential type '%s':\n", g, erotg_names[rotg->eType]);
885 fprintf(fp, "# rot_massw%d %s\n", g, yesno_names[rotg->bMassW]);
886 fprintf(fp, "# rot_vec%d %12.5e %12.5e %12.5e\n", g, rotg->vec[XX], rotg->vec[YY], rotg->vec[ZZ]);
887 fprintf(fp, "# rot_rate%d %12.5e degrees/ps\n", g, rotg->rate);
888 fprintf(fp, "# rot_k%d %12.5e kJ/(mol*nm^2)\n", g, rotg->k);
889 if (rotg->eType == erotgISO || rotg->eType == erotgPM || rotg->eType == erotgRM || rotg->eType == erotgRM2)
891 fprintf(fp, "# rot_pivot%d %12.5e %12.5e %12.5e nm\n", g, rotg->pivot[XX], rotg->pivot[YY], rotg->pivot[ZZ]);
896 fprintf(fp, "# rot_slab_distance%d %f nm\n", g, rotg->slab_dist);
897 fprintf(fp, "# rot_min_gaussian%d %12.5e\n", g, rotg->min_gaussian);
900 /* Output the centers of the rotation groups for the pivot-free potentials */
901 if ((rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) || (rotg->eType == erotgRMPF) || (rotg->eType == erotgRM2PF
902 || (rotg->eType == erotgFLEXT) || (rotg->eType == erotgFLEX2T)) )
904 fprintf(fp, "# ref. grp. %d center %12.5e %12.5e %12.5e\n", g,
905 erg->xc_ref_center[XX], erg->xc_ref_center[YY], erg->xc_ref_center[ZZ]);
907 fprintf(fp, "# grp. %d init.center %12.5e %12.5e %12.5e\n", g,
908 erg->xc_center[XX], erg->xc_center[YY], erg->xc_center[ZZ]);
911 if ( (rotg->eType == erotgRM2) || (rotg->eType == erotgFLEX2) || (rotg->eType == erotgFLEX2T) )
913 fprintf(fp, "# rot_eps%d %12.5e nm^2\n", g, rotg->eps);
915 if (erotgFitPOT == rotg->eFittype)
918 fprintf(fp, "# theta_fit%d is determined by first evaluating the potential for %d angles around theta_ref%d.\n",
919 g, rotg->PotAngle_nstep, g);
920 fprintf(fp, "# The fit angle is the one with the smallest potential. It is given as the deviation\n");
921 fprintf(fp, "# from the reference angle, i.e. if theta_ref=X and theta_fit=Y, then the angle with\n");
922 fprintf(fp, "# minimal value of the potential is X+Y. Angular resolution is %g degrees.\n", rotg->PotAngle_step);
926 /* Print a nice legend */
929 sprintf(buf, "# %6s", "time");
930 add_to_string_aligned(&LegendStr, buf);
933 snew(setname, 4*rot->ngrp);
935 for (g = 0; g < rot->ngrp; g++)
938 sprintf(buf, "theta_ref%d", g);
939 add_to_string_aligned(&LegendStr, buf);
941 sprintf(buf2, "%s (degrees)", buf);
942 setname[nsets] = strdup(buf2);
945 for (g = 0; g < rot->ngrp; g++)
948 bFlex = ISFLEX(rotg);
950 /* For flexible axis rotation we use RMSD fitting to determine the
951 * actual angle of the rotation group */
952 if (bFlex || erotgFitPOT == rotg->eFittype)
954 sprintf(buf, "theta_fit%d", g);
958 sprintf(buf, "theta_av%d", g);
960 add_to_string_aligned(&LegendStr, buf);
961 sprintf(buf2, "%s (degrees)", buf);
962 setname[nsets] = strdup(buf2);
965 sprintf(buf, "tau%d", g);
966 add_to_string_aligned(&LegendStr, buf);
967 sprintf(buf2, "%s (kJ/mol)", buf);
968 setname[nsets] = strdup(buf2);
971 sprintf(buf, "energy%d", g);
972 add_to_string_aligned(&LegendStr, buf);
973 sprintf(buf2, "%s (kJ/mol)", buf);
974 setname[nsets] = strdup(buf2);
981 xvgr_legend(fp, nsets, setname, oenv);
985 fprintf(fp, "#\n# Legend for the following data columns:\n");
986 fprintf(fp, "%s\n", LegendStr);
996 /* Call on master only */
997 static FILE *open_angles_out(const char *fn, t_rot *rot)
1002 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1006 if (rot->enfrot->Flags & MD_APPENDFILES)
1008 fp = gmx_fio_fopen(fn, "a");
1012 /* Open output file and write some information about it's structure: */
1013 fp = open_output_file(fn, rot->nstsout, "rotation group angles");
1014 fprintf(fp, "# All angles given in degrees, time in ps.\n");
1015 for (g = 0; g < rot->ngrp; g++)
1017 rotg = &rot->grp[g];
1018 erg = rotg->enfrotgrp;
1020 /* Output for this group happens only if potential type is flexible or
1021 * if fit type is potential! */
1022 if (ISFLEX(rotg) || (erotgFitPOT == rotg->eFittype) )
1026 sprintf(buf, " slab distance %f nm, ", rotg->slab_dist);
1033 fprintf(fp, "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n",
1034 g, erotg_names[rotg->eType], buf, erotg_fitnames[rotg->eFittype]);
1036 /* Special type of fitting using the potential minimum. This is
1037 * done for the whole group only, not for the individual slabs. */
1038 if (erotgFitPOT == rotg->eFittype)
1040 fprintf(fp, "# To obtain theta_fit%d, the potential is evaluated for %d angles around theta_ref%d\n", g, rotg->PotAngle_nstep, g);
1041 fprintf(fp, "# The fit angle in the rotation standard outfile is the one with minimal energy E(theta_fit) [kJ/mol].\n");
1045 fprintf(fp, "# Legend for the group %d data columns:\n", g);
1047 print_aligned_short(fp, "time");
1048 print_aligned_short(fp, "grp");
1049 print_aligned(fp, "theta_ref");
1051 if (erotgFitPOT == rotg->eFittype)
1053 /* Output the set of angles around the reference angle */
1054 for (i = 0; i < rotg->PotAngle_nstep; i++)
1056 sprintf(buf, "E(%g)", erg->PotAngleFit->degangle[i]);
1057 print_aligned(fp, buf);
1062 /* Output fit angle for each slab */
1063 print_aligned_short(fp, "slab");
1064 print_aligned_short(fp, "atoms");
1065 print_aligned(fp, "theta_fit");
1066 print_aligned_short(fp, "slab");
1067 print_aligned_short(fp, "atoms");
1068 print_aligned(fp, "theta_fit");
1069 fprintf(fp, " ...");
1081 /* Open torque output file and write some information about it's structure.
1082 * Call on master only */
1083 static FILE *open_torque_out(const char *fn, t_rot *rot)
1090 if (rot->enfrot->Flags & MD_APPENDFILES)
1092 fp = gmx_fio_fopen(fn, "a");
1096 fp = open_output_file(fn, rot->nstsout, "torques");
1098 for (g = 0; g < rot->ngrp; g++)
1100 rotg = &rot->grp[g];
1103 fprintf(fp, "# Rotation group %d (%s), slab distance %f nm.\n", g, erotg_names[rotg->eType], rotg->slab_dist);
1104 fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector.\n");
1105 fprintf(fp, "# To obtain the vectorial torque, multiply tau with\n");
1106 fprintf(fp, "# rot_vec%d %10.3e %10.3e %10.3e\n", g, rotg->vec[XX], rotg->vec[YY], rotg->vec[ZZ]);
1110 fprintf(fp, "# Legend for the following data columns: (tau=torque for that slab):\n");
1112 print_aligned_short(fp, "t");
1113 print_aligned_short(fp, "grp");
1114 print_aligned_short(fp, "slab");
1115 print_aligned(fp, "tau");
1116 print_aligned_short(fp, "slab");
1117 print_aligned(fp, "tau");
1118 fprintf(fp, " ...\n");
1126 static void swap_val(double* vec, int i, int j)
1128 double tmp = vec[j];
1136 static void swap_col(double **mat, int i, int j)
1138 double tmp[3] = {mat[0][j], mat[1][j], mat[2][j]};
1141 mat[0][j] = mat[0][i];
1142 mat[1][j] = mat[1][i];
1143 mat[2][j] = mat[2][i];
1151 /* Eigenvectors are stored in columns of eigen_vec */
1152 static void diagonalize_symmetric(
1160 jacobi(matrix, 3, eigenval, eigen_vec, &n_rot);
1162 /* sort in ascending order */
1163 if (eigenval[0] > eigenval[1])
1165 swap_val(eigenval, 0, 1);
1166 swap_col(eigen_vec, 0, 1);
1168 if (eigenval[1] > eigenval[2])
1170 swap_val(eigenval, 1, 2);
1171 swap_col(eigen_vec, 1, 2);
1173 if (eigenval[0] > eigenval[1])
1175 swap_val(eigenval, 0, 1);
1176 swap_col(eigen_vec, 0, 1);
1181 static void align_with_z(
1182 rvec* s, /* Structure to align */
1187 rvec zet = {0.0, 0.0, 1.0};
1188 rvec rot_axis = {0.0, 0.0, 0.0};
1189 rvec *rotated_str = NULL;
1195 snew(rotated_str, natoms);
1197 /* Normalize the axis */
1198 ooanorm = 1.0/norm(axis);
1199 svmul(ooanorm, axis, axis);
1201 /* Calculate the angle for the fitting procedure */
1202 cprod(axis, zet, rot_axis);
1203 angle = acos(axis[2]);
1209 /* Calculate the rotation matrix */
1210 calc_rotmat(rot_axis, angle*180.0/M_PI, rotmat);
1212 /* Apply the rotation matrix to s */
1213 for (i = 0; i < natoms; i++)
1215 for (j = 0; j < 3; j++)
1217 for (k = 0; k < 3; k++)
1219 rotated_str[i][j] += rotmat[j][k]*s[i][k];
1224 /* Rewrite the rotated structure to s */
1225 for (i = 0; i < natoms; i++)
1227 for (j = 0; j < 3; j++)
1229 s[i][j] = rotated_str[i][j];
1237 static void calc_correl_matrix(rvec* Xstr, rvec* Ystr, double** Rmat, int natoms)
1242 for (i = 0; i < 3; i++)
1244 for (j = 0; j < 3; j++)
1250 for (i = 0; i < 3; i++)
1252 for (j = 0; j < 3; j++)
1254 for (k = 0; k < natoms; k++)
1256 Rmat[i][j] += Ystr[k][i] * Xstr[k][j];
1263 static void weigh_coords(rvec* str, real* weight, int natoms)
1268 for (i = 0; i < natoms; i++)
1270 for (j = 0; j < 3; j++)
1272 str[i][j] *= sqrt(weight[i]);
1278 static real opt_angle_analytic(
1288 rvec *ref_s_1 = NULL;
1289 rvec *act_s_1 = NULL;
1291 double **Rmat, **RtR, **eigvec;
1293 double V[3][3], WS[3][3];
1294 double rot_matrix[3][3];
1298 /* Do not change the original coordinates */
1299 snew(ref_s_1, natoms);
1300 snew(act_s_1, natoms);
1301 for (i = 0; i < natoms; i++)
1303 copy_rvec(ref_s[i], ref_s_1[i]);
1304 copy_rvec(act_s[i], act_s_1[i]);
1307 /* Translate the structures to the origin */
1308 shift[XX] = -ref_com[XX];
1309 shift[YY] = -ref_com[YY];
1310 shift[ZZ] = -ref_com[ZZ];
1311 translate_x(ref_s_1, natoms, shift);
1313 shift[XX] = -act_com[XX];
1314 shift[YY] = -act_com[YY];
1315 shift[ZZ] = -act_com[ZZ];
1316 translate_x(act_s_1, natoms, shift);
1318 /* Align rotation axis with z */
1319 align_with_z(ref_s_1, natoms, axis);
1320 align_with_z(act_s_1, natoms, axis);
1322 /* Correlation matrix */
1323 Rmat = allocate_square_matrix(3);
1325 for (i = 0; i < natoms; i++)
1327 ref_s_1[i][2] = 0.0;
1328 act_s_1[i][2] = 0.0;
1331 /* Weight positions with sqrt(weight) */
1334 weigh_coords(ref_s_1, weight, natoms);
1335 weigh_coords(act_s_1, weight, natoms);
1338 /* Calculate correlation matrices R=YXt (X=ref_s; Y=act_s) */
1339 calc_correl_matrix(ref_s_1, act_s_1, Rmat, natoms);
1342 RtR = allocate_square_matrix(3);
1343 for (i = 0; i < 3; i++)
1345 for (j = 0; j < 3; j++)
1347 for (k = 0; k < 3; k++)
1349 RtR[i][j] += Rmat[k][i] * Rmat[k][j];
1353 /* Diagonalize RtR */
1355 for (i = 0; i < 3; i++)
1360 diagonalize_symmetric(RtR, eigvec, eigval);
1361 swap_col(eigvec, 0, 1);
1362 swap_col(eigvec, 1, 2);
1363 swap_val(eigval, 0, 1);
1364 swap_val(eigval, 1, 2);
1367 for (i = 0; i < 3; i++)
1369 for (j = 0; j < 3; j++)
1376 for (i = 0; i < 2; i++)
1378 for (j = 0; j < 2; j++)
1380 WS[i][j] = eigvec[i][j] / sqrt(eigval[j]);
1384 for (i = 0; i < 3; i++)
1386 for (j = 0; j < 3; j++)
1388 for (k = 0; k < 3; k++)
1390 V[i][j] += Rmat[i][k]*WS[k][j];
1394 free_square_matrix(Rmat, 3);
1396 /* Calculate optimal rotation matrix */
1397 for (i = 0; i < 3; i++)
1399 for (j = 0; j < 3; j++)
1401 rot_matrix[i][j] = 0.0;
1405 for (i = 0; i < 3; i++)
1407 for (j = 0; j < 3; j++)
1409 for (k = 0; k < 3; k++)
1411 rot_matrix[i][j] += eigvec[i][k]*V[j][k];
1415 rot_matrix[2][2] = 1.0;
1417 /* In some cases abs(rot_matrix[0][0]) can be slighly larger
1418 * than unity due to numerical inacurracies. To be able to calculate
1419 * the acos function, we put these values back in range. */
1420 if (rot_matrix[0][0] > 1.0)
1422 rot_matrix[0][0] = 1.0;
1424 else if (rot_matrix[0][0] < -1.0)
1426 rot_matrix[0][0] = -1.0;
1429 /* Determine the optimal rotation angle: */
1430 opt_angle = (-1.0)*acos(rot_matrix[0][0])*180.0/M_PI;
1431 if (rot_matrix[0][1] < 0.0)
1433 opt_angle = (-1.0)*opt_angle;
1436 /* Give back some memory */
1437 free_square_matrix(RtR, 3);
1440 for (i = 0; i < 3; i++)
1446 return (real) opt_angle;
1450 /* Determine angle of the group by RMSD fit to the reference */
1451 /* Not parallelized, call this routine only on the master */
1452 static real flex_fit_angle(t_rotgrp *rotg)
1455 rvec *fitcoords = NULL;
1456 rvec center; /* Center of positions passed to the fit routine */
1457 real fitangle; /* Angle of the rotation group derived by fitting */
1460 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1463 erg = rotg->enfrotgrp;
1465 /* Get the center of the rotation group.
1466 * Note, again, erg->xc has been sorted in do_flexible */
1467 get_center(erg->xc, erg->mc_sorted, rotg->nat, center);
1469 /* === Determine the optimal fit angle for the rotation group === */
1470 if (rotg->eFittype == erotgFitNORM)
1472 /* Normalize every position to it's reference length */
1473 for (i = 0; i < rotg->nat; i++)
1475 /* Put the center of the positions into the origin */
1476 rvec_sub(erg->xc[i], center, coord);
1477 /* Determine the scaling factor for the length: */
1478 scal = erg->xc_ref_length[erg->xc_sortind[i]] / norm(coord);
1479 /* Get position, multiply with the scaling factor and save */
1480 svmul(scal, coord, erg->xc_norm[i]);
1482 fitcoords = erg->xc_norm;
1486 fitcoords = erg->xc;
1488 /* From the point of view of the current positions, the reference has rotated
1489 * backwards. Since we output the angle relative to the fixed reference,
1490 * we need the minus sign. */
1491 fitangle = -opt_angle_analytic(erg->xc_ref_sorted, fitcoords, erg->mc_sorted,
1492 rotg->nat, erg->xc_ref_center, center, rotg->vec);
1498 /* Determine actual angle of each slab by RMSD fit to the reference */
1499 /* Not parallelized, call this routine only on the master */
1500 static void flex_fit_angle_perslab(
1507 int i, l, n, islab, ind;
1509 rvec act_center; /* Center of actual positions that are passed to the fit routine */
1510 rvec ref_center; /* Same for the reference positions */
1511 real fitangle; /* Angle of a slab derived from an RMSD fit to
1512 * the reference structure at t=0 */
1514 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1515 real OOm_av; /* 1/average_mass of a rotation group atom */
1516 real m_rel; /* Relative mass of a rotation group atom */
1519 erg = rotg->enfrotgrp;
1521 /* Average mass of a rotation group atom: */
1522 OOm_av = erg->invmass*rotg->nat;
1524 /**********************************/
1525 /* First collect the data we need */
1526 /**********************************/
1528 /* Collect the data for the individual slabs */
1529 for (n = erg->slab_first; n <= erg->slab_last; n++)
1531 islab = n - erg->slab_first; /* slab index */
1532 sd = &(rotg->enfrotgrp->slab_data[islab]);
1533 sd->nat = erg->lastatom[islab]-erg->firstatom[islab]+1;
1536 /* Loop over the relevant atoms in the slab */
1537 for (l = erg->firstatom[islab]; l <= erg->lastatom[islab]; l++)
1539 /* Current position of this atom: x[ii][XX/YY/ZZ] */
1540 copy_rvec(erg->xc[l], curr_x);
1542 /* The (unrotated) reference position of this atom is copied to ref_x.
1543 * Beware, the xc coords have been sorted in do_flexible */
1544 copy_rvec(erg->xc_ref_sorted[l], ref_x);
1546 /* Save data for doing angular RMSD fit later */
1547 /* Save the current atom position */
1548 copy_rvec(curr_x, sd->x[ind]);
1549 /* Save the corresponding reference position */
1550 copy_rvec(ref_x, sd->ref[ind]);
1552 /* Maybe also mass-weighting was requested. If yes, additionally
1553 * multiply the weights with the relative mass of the atom. If not,
1554 * multiply with unity. */
1555 m_rel = erg->mc_sorted[l]*OOm_av;
1557 /* Save the weight for this atom in this slab */
1558 sd->weight[ind] = gaussian_weight(curr_x, rotg, n) * m_rel;
1560 /* Next atom in this slab */
1565 /******************************/
1566 /* Now do the fit calculation */
1567 /******************************/
1569 fprintf(fp, "%12.3e%6d%12.3f", t, g, degangle);
1571 /* === Now do RMSD fitting for each slab === */
1572 /* We require at least SLAB_MIN_ATOMS in a slab, such that the fit makes sense. */
1573 #define SLAB_MIN_ATOMS 4
1575 for (n = erg->slab_first; n <= erg->slab_last; n++)
1577 islab = n - erg->slab_first; /* slab index */
1578 sd = &(rotg->enfrotgrp->slab_data[islab]);
1579 if (sd->nat >= SLAB_MIN_ATOMS)
1581 /* Get the center of the slabs reference and current positions */
1582 get_center(sd->ref, sd->weight, sd->nat, ref_center);
1583 get_center(sd->x, sd->weight, sd->nat, act_center);
1584 if (rotg->eFittype == erotgFitNORM)
1586 /* Normalize every position to it's reference length
1587 * prior to performing the fit */
1588 for (i = 0; i < sd->nat; i++) /* Center */
1590 rvec_dec(sd->ref[i], ref_center);
1591 rvec_dec(sd->x[i], act_center);
1592 /* Normalize x_i such that it gets the same length as ref_i */
1593 svmul( norm(sd->ref[i])/norm(sd->x[i]), sd->x[i], sd->x[i] );
1595 /* We already subtracted the centers */
1596 clear_rvec(ref_center);
1597 clear_rvec(act_center);
1599 fitangle = -opt_angle_analytic(sd->ref, sd->x, sd->weight, sd->nat,
1600 ref_center, act_center, rotg->vec);
1601 fprintf(fp, "%6d%6d%12.3f", n, sd->nat, fitangle);
1606 #undef SLAB_MIN_ATOMS
1610 /* Shift x with is */
1611 static gmx_inline void shift_single_coord(matrix box, rvec x, const ivec is)
1622 x[XX] += tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
1623 x[YY] += ty*box[YY][YY]+tz*box[ZZ][YY];
1624 x[ZZ] += tz*box[ZZ][ZZ];
1628 x[XX] += tx*box[XX][XX];
1629 x[YY] += ty*box[YY][YY];
1630 x[ZZ] += tz*box[ZZ][ZZ];
1635 /* Determine the 'home' slab of this atom which is the
1636 * slab with the highest Gaussian weight of all */
1637 #define round(a) (int)(a+0.5)
1638 static gmx_inline int get_homeslab(
1639 rvec curr_x, /* The position for which the home slab shall be determined */
1640 rvec rotvec, /* The rotation vector */
1641 real slabdist) /* The slab distance */
1646 /* The distance of the atom to the coordinate center (where the
1647 * slab with index 0) is */
1648 dist = iprod(rotvec, curr_x);
1650 return round(dist / slabdist);
1654 /* For a local atom determine the relevant slabs, i.e. slabs in
1655 * which the gaussian is larger than min_gaussian
1657 static int get_single_atom_gaussians(
1664 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1667 erg = rotg->enfrotgrp;
1669 /* Determine the 'home' slab of this atom: */
1670 homeslab = get_homeslab(curr_x, rotg->vec, rotg->slab_dist);
1672 /* First determine the weight in the atoms home slab: */
1673 g = gaussian_weight(curr_x, rotg, homeslab);
1675 erg->gn_atom[count] = g;
1676 erg->gn_slabind[count] = homeslab;
1680 /* Determine the max slab */
1682 while (g > rotg->min_gaussian)
1685 g = gaussian_weight(curr_x, rotg, slab);
1686 erg->gn_slabind[count] = slab;
1687 erg->gn_atom[count] = g;
1692 /* Determine the min slab */
1697 g = gaussian_weight(curr_x, rotg, slab);
1698 erg->gn_slabind[count] = slab;
1699 erg->gn_atom[count] = g;
1702 while (g > rotg->min_gaussian);
1709 static void flex2_precalc_inner_sum(t_rotgrp *rotg)
1712 rvec xi; /* positions in the i-sum */
1713 rvec xcn, ycn; /* the current and the reference slab centers */
1716 rvec rin; /* Helper variables */
1719 real OOpsii, OOpsiistar;
1720 real sin_rin; /* s_ii.r_ii */
1721 rvec s_in, tmpvec, tmpvec2;
1722 real mi, wi; /* Mass-weighting of the positions */
1724 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1727 erg = rotg->enfrotgrp;
1728 N_M = rotg->nat * erg->invmass;
1730 /* Loop over all slabs that contain something */
1731 for (n = erg->slab_first; n <= erg->slab_last; n++)
1733 islab = n - erg->slab_first; /* slab index */
1735 /* The current center of this slab is saved in xcn: */
1736 copy_rvec(erg->slab_center[islab], xcn);
1737 /* ... and the reference center in ycn: */
1738 copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1740 /*** D. Calculate the whole inner sum used for second and third sum */
1741 /* For slab n, we need to loop over all atoms i again. Since we sorted
1742 * the atoms with respect to the rotation vector, we know that it is sufficient
1743 * to calculate from firstatom to lastatom only. All other contributions will
1745 clear_rvec(innersumvec);
1746 for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
1748 /* Coordinate xi of this atom */
1749 copy_rvec(erg->xc[i], xi);
1752 gaussian_xi = gaussian_weight(xi, rotg, n);
1753 mi = erg->mc_sorted[i]; /* need the sorted mass here */
1757 copy_rvec(erg->xc_ref_sorted[i], yi0); /* Reference position yi0 */
1758 rvec_sub(yi0, ycn, tmpvec2); /* tmpvec2 = yi0 - ycn */
1759 mvmul(erg->rotmat, tmpvec2, rin); /* rin = Omega.(yi0 - ycn) */
1761 /* Calculate psi_i* and sin */
1762 rvec_sub(xi, xcn, tmpvec2); /* tmpvec2 = xi - xcn */
1763 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xi - xcn) */
1764 OOpsiistar = norm2(tmpvec)+rotg->eps; /* OOpsii* = 1/psii* = |v x (xi-xcn)|^2 + eps */
1765 OOpsii = norm(tmpvec); /* OOpsii = 1 / psii = |v x (xi - xcn)| */
1767 /* * v x (xi - xcn) */
1768 unitv(tmpvec, s_in); /* sin = ---------------- */
1769 /* |v x (xi - xcn)| */
1771 sin_rin = iprod(s_in, rin); /* sin_rin = sin . rin */
1773 /* Now the whole sum */
1774 fac = OOpsii/OOpsiistar;
1775 svmul(fac, rin, tmpvec);
1776 fac2 = fac*fac*OOpsii;
1777 svmul(fac2*sin_rin, s_in, tmpvec2);
1778 rvec_dec(tmpvec, tmpvec2);
1780 svmul(wi*gaussian_xi*sin_rin, tmpvec, tmpvec2);
1782 rvec_inc(innersumvec, tmpvec2);
1783 } /* now we have the inner sum, used both for sum2 and sum3 */
1785 /* Save it to be used in do_flex2_lowlevel */
1786 copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
1787 } /* END of loop over slabs */
1791 static void flex_precalc_inner_sum(t_rotgrp *rotg)
1794 rvec xi; /* position */
1795 rvec xcn, ycn; /* the current and the reference slab centers */
1796 rvec qin, rin; /* q_i^n and r_i^n */
1799 rvec innersumvec; /* Inner part of sum_n2 */
1800 real gaussian_xi; /* Gaussian weight gn(xi) */
1801 real mi, wi; /* Mass-weighting of the positions */
1804 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1807 erg = rotg->enfrotgrp;
1808 N_M = rotg->nat * erg->invmass;
1810 /* Loop over all slabs that contain something */
1811 for (n = erg->slab_first; n <= erg->slab_last; n++)
1813 islab = n - erg->slab_first; /* slab index */
1815 /* The current center of this slab is saved in xcn: */
1816 copy_rvec(erg->slab_center[islab], xcn);
1817 /* ... and the reference center in ycn: */
1818 copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1820 /* For slab n, we need to loop over all atoms i again. Since we sorted
1821 * the atoms with respect to the rotation vector, we know that it is sufficient
1822 * to calculate from firstatom to lastatom only. All other contributions will
1824 clear_rvec(innersumvec);
1825 for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
1827 /* Coordinate xi of this atom */
1828 copy_rvec(erg->xc[i], xi);
1831 gaussian_xi = gaussian_weight(xi, rotg, n);
1832 mi = erg->mc_sorted[i]; /* need the sorted mass here */
1835 /* Calculate rin and qin */
1836 rvec_sub(erg->xc_ref_sorted[i], ycn, tmpvec); /* tmpvec = yi0-ycn */
1837 mvmul(erg->rotmat, tmpvec, rin); /* rin = Omega.(yi0 - ycn) */
1838 cprod(rotg->vec, rin, tmpvec); /* tmpvec = v x Omega*(yi0-ycn) */
1840 /* * v x Omega*(yi0-ycn) */
1841 unitv(tmpvec, qin); /* qin = --------------------- */
1842 /* |v x Omega*(yi0-ycn)| */
1845 rvec_sub(xi, xcn, tmpvec); /* tmpvec = xi-xcn */
1846 bin = iprod(qin, tmpvec); /* bin = qin*(xi-xcn) */
1848 svmul(wi*gaussian_xi*bin, qin, tmpvec);
1850 /* Add this contribution to the inner sum: */
1851 rvec_add(innersumvec, tmpvec, innersumvec);
1852 } /* now we have the inner sum vector S^n for this slab */
1853 /* Save it to be used in do_flex_lowlevel */
1854 copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
1859 static real do_flex2_lowlevel(
1861 real sigma, /* The Gaussian width sigma */
1863 gmx_bool bOutstepRot,
1864 gmx_bool bOutstepSlab,
1867 int count, ic, ii, j, m, n, islab, iigrp, ifit;
1868 rvec xj; /* position in the i-sum */
1869 rvec yj0; /* the reference position in the j-sum */
1870 rvec xcn, ycn; /* the current and the reference slab centers */
1871 real V; /* This node's part of the rotation pot. energy */
1872 real gaussian_xj; /* Gaussian weight */
1875 real numerator, fit_numerator;
1876 rvec rjn, fit_rjn; /* Helper variables */
1879 real OOpsij, OOpsijstar;
1880 real OOsigma2; /* 1/(sigma^2) */
1883 rvec sjn, tmpvec, tmpvec2, yj0_ycn;
1884 rvec sum1vec_part, sum1vec, sum2vec_part, sum2vec, sum3vec, sum4vec, innersumvec;
1886 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1887 real mj, wj; /* Mass-weighting of the positions */
1889 real Wjn; /* g_n(x_j) m_j / Mjn */
1890 gmx_bool bCalcPotFit;
1892 /* To calculate the torque per slab */
1893 rvec slab_force; /* Single force from slab n on one atom */
1894 rvec slab_sum1vec_part;
1895 real slab_sum3part, slab_sum4part;
1896 rvec slab_sum1vec, slab_sum2vec, slab_sum3vec, slab_sum4vec;
1899 erg = rotg->enfrotgrp;
1901 /* Pre-calculate the inner sums, so that we do not have to calculate
1902 * them again for every atom */
1903 flex2_precalc_inner_sum(rotg);
1905 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
1907 /********************************************************/
1908 /* Main loop over all local atoms of the rotation group */
1909 /********************************************************/
1910 N_M = rotg->nat * erg->invmass;
1912 OOsigma2 = 1.0 / (sigma*sigma);
1913 for (j = 0; j < erg->nat_loc; j++)
1915 /* Local index of a rotation group atom */
1916 ii = erg->ind_loc[j];
1917 /* Position of this atom in the collective array */
1918 iigrp = erg->xc_ref_ind[j];
1919 /* Mass-weighting */
1920 mj = erg->mc[iigrp]; /* need the unsorted mass here */
1923 /* Current position of this atom: x[ii][XX/YY/ZZ]
1924 * Note that erg->xc_center contains the center of mass in case the flex2-t
1925 * potential was chosen. For the flex2 potential erg->xc_center must be
1927 rvec_sub(x[ii], erg->xc_center, xj);
1929 /* Shift this atom such that it is near its reference */
1930 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
1932 /* Determine the slabs to loop over, i.e. the ones with contributions
1933 * larger than min_gaussian */
1934 count = get_single_atom_gaussians(xj, rotg);
1936 clear_rvec(sum1vec_part);
1937 clear_rvec(sum2vec_part);
1940 /* Loop over the relevant slabs for this atom */
1941 for (ic = 0; ic < count; ic++)
1943 n = erg->gn_slabind[ic];
1945 /* Get the precomputed Gaussian value of curr_slab for curr_x */
1946 gaussian_xj = erg->gn_atom[ic];
1948 islab = n - erg->slab_first; /* slab index */
1950 /* The (unrotated) reference position of this atom is copied to yj0: */
1951 copy_rvec(rotg->x_ref[iigrp], yj0);
1953 beta = calc_beta(xj, rotg, n);
1955 /* The current center of this slab is saved in xcn: */
1956 copy_rvec(erg->slab_center[islab], xcn);
1957 /* ... and the reference center in ycn: */
1958 copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1960 rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
1963 mvmul(erg->rotmat, yj0_ycn, rjn); /* rjn = Omega.(yj0 - ycn) */
1965 /* Subtract the slab center from xj */
1966 rvec_sub(xj, xcn, tmpvec2); /* tmpvec2 = xj - xcn */
1968 /* In rare cases, when an atom position coincides with a slab center
1969 * (tmpvec2 == 0) we cannot compute the vector product for sjn.
1970 * However, since the atom is located directly on the pivot, this
1971 * slab's contribution to the force on that atom will be zero
1972 * anyway. Therefore, we directly move on to the next slab. */
1973 if ( 0 == norm(tmpvec2) )
1979 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xj - xcn) */
1981 OOpsijstar = norm2(tmpvec)+rotg->eps; /* OOpsij* = 1/psij* = |v x (xj-xcn)|^2 + eps */
1983 numerator = sqr(iprod(tmpvec, rjn));
1985 /*********************************/
1986 /* Add to the rotation potential */
1987 /*********************************/
1988 V += 0.5*rotg->k*wj*gaussian_xj*numerator/OOpsijstar;
1990 /* If requested, also calculate the potential for a set of angles
1991 * near the current reference angle */
1994 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
1996 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, fit_rjn);
1997 fit_numerator = sqr(iprod(tmpvec, fit_rjn));
1998 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*gaussian_xj*fit_numerator/OOpsijstar;
2002 /*************************************/
2003 /* Now calculate the force on atom j */
2004 /*************************************/
2006 OOpsij = norm(tmpvec); /* OOpsij = 1 / psij = |v x (xj - xcn)| */
2008 /* * v x (xj - xcn) */
2009 unitv(tmpvec, sjn); /* sjn = ---------------- */
2010 /* |v x (xj - xcn)| */
2012 sjn_rjn = iprod(sjn, rjn); /* sjn_rjn = sjn . rjn */
2015 /*** A. Calculate the first of the four sum terms: ****************/
2016 fac = OOpsij/OOpsijstar;
2017 svmul(fac, rjn, tmpvec);
2018 fac2 = fac*fac*OOpsij;
2019 svmul(fac2*sjn_rjn, sjn, tmpvec2);
2020 rvec_dec(tmpvec, tmpvec2);
2021 fac2 = wj*gaussian_xj; /* also needed for sum4 */
2022 svmul(fac2*sjn_rjn, tmpvec, slab_sum1vec_part);
2023 /********************/
2024 /*** Add to sum1: ***/
2025 /********************/
2026 rvec_inc(sum1vec_part, slab_sum1vec_part); /* sum1 still needs to vector multiplied with v */
2028 /*** B. Calculate the forth of the four sum terms: ****************/
2029 betasigpsi = beta*OOsigma2*OOpsij; /* this is also needed for sum3 */
2030 /********************/
2031 /*** Add to sum4: ***/
2032 /********************/
2033 slab_sum4part = fac2*betasigpsi*fac*sjn_rjn*sjn_rjn; /* Note that fac is still valid from above */
2034 sum4 += slab_sum4part;
2036 /*** C. Calculate Wjn for second and third sum */
2037 /* Note that we can safely divide by slab_weights since we check in
2038 * get_slab_centers that it is non-zero. */
2039 Wjn = gaussian_xj*mj/erg->slab_weights[islab];
2041 /* We already have precalculated the inner sum for slab n */
2042 copy_rvec(erg->slab_innersumvec[islab], innersumvec);
2044 /* Weigh the inner sum vector with Wjn */
2045 svmul(Wjn, innersumvec, innersumvec);
2047 /*** E. Calculate the second of the four sum terms: */
2048 /********************/
2049 /*** Add to sum2: ***/
2050 /********************/
2051 rvec_inc(sum2vec_part, innersumvec); /* sum2 still needs to be vector crossproduct'ed with v */
2053 /*** F. Calculate the third of the four sum terms: */
2054 slab_sum3part = betasigpsi * iprod(sjn, innersumvec);
2055 sum3 += slab_sum3part; /* still needs to be multiplied with v */
2057 /*** G. Calculate the torque on the local slab's axis: */
2061 cprod(slab_sum1vec_part, rotg->vec, slab_sum1vec);
2063 cprod(innersumvec, rotg->vec, slab_sum2vec);
2065 svmul(slab_sum3part, rotg->vec, slab_sum3vec);
2067 svmul(slab_sum4part, rotg->vec, slab_sum4vec);
2069 /* The force on atom ii from slab n only: */
2070 for (m = 0; m < DIM; m++)
2072 slab_force[m] = rotg->k * (-slab_sum1vec[m] + slab_sum2vec[m] - slab_sum3vec[m] + 0.5*slab_sum4vec[m]);
2075 erg->slab_torque_v[islab] += torque(rotg->vec, slab_force, xj, xcn);
2077 } /* END of loop over slabs */
2079 /* Construct the four individual parts of the vector sum: */
2080 cprod(sum1vec_part, rotg->vec, sum1vec); /* sum1vec = { } x v */
2081 cprod(sum2vec_part, rotg->vec, sum2vec); /* sum2vec = { } x v */
2082 svmul(sum3, rotg->vec, sum3vec); /* sum3vec = { } . v */
2083 svmul(sum4, rotg->vec, sum4vec); /* sum4vec = { } . v */
2085 /* Store the additional force so that it can be added to the force
2086 * array after the normal forces have been evaluated */
2087 for (m = 0; m < DIM; m++)
2089 erg->f_rot_loc[j][m] = rotg->k * (-sum1vec[m] + sum2vec[m] - sum3vec[m] + 0.5*sum4vec[m]);
2093 fprintf(stderr, "sum1: %15.8f %15.8f %15.8f\n", -rotg->k*sum1vec[XX], -rotg->k*sum1vec[YY], -rotg->k*sum1vec[ZZ]);
2094 fprintf(stderr, "sum2: %15.8f %15.8f %15.8f\n", rotg->k*sum2vec[XX], rotg->k*sum2vec[YY], rotg->k*sum2vec[ZZ]);
2095 fprintf(stderr, "sum3: %15.8f %15.8f %15.8f\n", -rotg->k*sum3vec[XX], -rotg->k*sum3vec[YY], -rotg->k*sum3vec[ZZ]);
2096 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]);
2101 } /* END of loop over local atoms */
2107 static real do_flex_lowlevel(
2109 real sigma, /* The Gaussian width sigma */
2111 gmx_bool bOutstepRot,
2112 gmx_bool bOutstepSlab,
2115 int count, ic, ifit, ii, j, m, n, islab, iigrp;
2116 rvec xj, yj0; /* current and reference position */
2117 rvec xcn, ycn; /* the current and the reference slab centers */
2118 rvec yj0_ycn; /* yj0 - ycn */
2119 rvec xj_xcn; /* xj - xcn */
2120 rvec qjn, fit_qjn; /* q_i^n */
2121 rvec sum_n1, sum_n2; /* Two contributions to the rotation force */
2122 rvec innersumvec; /* Inner part of sum_n2 */
2124 rvec force_n; /* Single force from slab n on one atom */
2125 rvec force_n1, force_n2; /* First and second part of force_n */
2126 rvec tmpvec, tmpvec2, tmp_f; /* Helper variables */
2127 real V; /* The rotation potential energy */
2128 real OOsigma2; /* 1/(sigma^2) */
2129 real beta; /* beta_n(xj) */
2130 real bjn, fit_bjn; /* b_j^n */
2131 real gaussian_xj; /* Gaussian weight gn(xj) */
2132 real betan_xj_sigma2;
2133 real mj, wj; /* Mass-weighting of the positions */
2135 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2136 gmx_bool bCalcPotFit;
2139 erg = rotg->enfrotgrp;
2141 /* Pre-calculate the inner sums, so that we do not have to calculate
2142 * them again for every atom */
2143 flex_precalc_inner_sum(rotg);
2145 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2147 /********************************************************/
2148 /* Main loop over all local atoms of the rotation group */
2149 /********************************************************/
2150 OOsigma2 = 1.0/(sigma*sigma);
2151 N_M = rotg->nat * erg->invmass;
2153 for (j = 0; j < erg->nat_loc; j++)
2155 /* Local index of a rotation group atom */
2156 ii = erg->ind_loc[j];
2157 /* Position of this atom in the collective array */
2158 iigrp = erg->xc_ref_ind[j];
2159 /* Mass-weighting */
2160 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2163 /* Current position of this atom: x[ii][XX/YY/ZZ]
2164 * Note that erg->xc_center contains the center of mass in case the flex-t
2165 * potential was chosen. For the flex potential erg->xc_center must be
2167 rvec_sub(x[ii], erg->xc_center, xj);
2169 /* Shift this atom such that it is near its reference */
2170 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2172 /* Determine the slabs to loop over, i.e. the ones with contributions
2173 * larger than min_gaussian */
2174 count = get_single_atom_gaussians(xj, rotg);
2179 /* Loop over the relevant slabs for this atom */
2180 for (ic = 0; ic < count; ic++)
2182 n = erg->gn_slabind[ic];
2184 /* Get the precomputed Gaussian for xj in slab n */
2185 gaussian_xj = erg->gn_atom[ic];
2187 islab = n - erg->slab_first; /* slab index */
2189 /* The (unrotated) reference position of this atom is saved in yj0: */
2190 copy_rvec(rotg->x_ref[iigrp], yj0);
2192 beta = calc_beta(xj, rotg, n);
2194 /* The current center of this slab is saved in xcn: */
2195 copy_rvec(erg->slab_center[islab], xcn);
2196 /* ... and the reference center in ycn: */
2197 copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
2199 rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
2202 mvmul(erg->rotmat, yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2204 /* Subtract the slab center from xj */
2205 rvec_sub(xj, xcn, xj_xcn); /* xj_xcn = xj - xcn */
2207 /* In rare cases, when an atom position coincides with a slab center
2208 * (xj_xcn == 0) we cannot compute the vector product for qjn.
2209 * However, since the atom is located directly on the pivot, this
2210 * slab's contribution to the force on that atom will be zero
2211 * anyway. Therefore, we directly move on to the next slab. */
2212 if ( 0 == norm(xj_xcn) )
2218 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2220 /* * v x Omega.(yj0-ycn) */
2221 unitv(tmpvec, qjn); /* qjn = --------------------- */
2222 /* |v x Omega.(yj0-ycn)| */
2224 bjn = iprod(qjn, xj_xcn); /* bjn = qjn * (xj - xcn) */
2226 /*********************************/
2227 /* Add to the rotation potential */
2228 /*********************************/
2229 V += 0.5*rotg->k*wj*gaussian_xj*sqr(bjn);
2231 /* If requested, also calculate the potential for a set of angles
2232 * near the current reference angle */
2235 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2237 /* As above calculate Omega.(yj0-ycn), now for the other angles */
2238 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2239 /* As above calculate qjn */
2240 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2241 /* * v x Omega.(yj0-ycn) */
2242 unitv(tmpvec, fit_qjn); /* fit_qjn = --------------------- */
2243 /* |v x Omega.(yj0-ycn)| */
2244 fit_bjn = iprod(fit_qjn, xj_xcn); /* fit_bjn = fit_qjn * (xj - xcn) */
2245 /* Add to the rotation potential for this angle */
2246 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*gaussian_xj*sqr(fit_bjn);
2250 /****************************************************************/
2251 /* sum_n1 will typically be the main contribution to the force: */
2252 /****************************************************************/
2253 betan_xj_sigma2 = beta*OOsigma2; /* beta_n(xj)/sigma^2 */
2255 /* The next lines calculate
2256 * qjn - (bjn*beta(xj)/(2sigma^2))v */
2257 svmul(bjn*0.5*betan_xj_sigma2, rotg->vec, tmpvec2);
2258 rvec_sub(qjn, tmpvec2, tmpvec);
2260 /* Multiply with gn(xj)*bjn: */
2261 svmul(gaussian_xj*bjn, tmpvec, tmpvec2);
2264 rvec_inc(sum_n1, tmpvec2);
2266 /* We already have precalculated the Sn term for slab n */
2267 copy_rvec(erg->slab_innersumvec[islab], s_n);
2269 svmul(betan_xj_sigma2*iprod(s_n, xj_xcn), rotg->vec, tmpvec); /* tmpvec = ---------- s_n (xj-xcn) */
2272 rvec_sub(s_n, tmpvec, innersumvec);
2274 /* We can safely divide by slab_weights since we check in get_slab_centers
2275 * that it is non-zero. */
2276 svmul(gaussian_xj/erg->slab_weights[islab], innersumvec, innersumvec);
2278 rvec_add(sum_n2, innersumvec, sum_n2);
2280 /* Calculate the torque: */
2283 /* The force on atom ii from slab n only: */
2284 svmul(-rotg->k*wj, tmpvec2, force_n1); /* part 1 */
2285 svmul( rotg->k*mj, innersumvec, force_n2); /* part 2 */
2286 rvec_add(force_n1, force_n2, force_n);
2287 erg->slab_torque_v[islab] += torque(rotg->vec, force_n, xj, xcn);
2289 } /* END of loop over slabs */
2291 /* Put both contributions together: */
2292 svmul(wj, sum_n1, sum_n1);
2293 svmul(mj, sum_n2, sum_n2);
2294 rvec_sub(sum_n2, sum_n1, tmp_f); /* F = -grad V */
2296 /* Store the additional force so that it can be added to the force
2297 * array after the normal forces have been evaluated */
2298 for (m = 0; m < DIM; m++)
2300 erg->f_rot_loc[j][m] = rotg->k*tmp_f[m];
2305 } /* END of loop over local atoms */
2311 static void print_coordinates(t_rotgrp *rotg, rvec x[], matrix box, int step)
2315 static char buf[STRLEN];
2316 static gmx_bool bFirst = 1;
2321 sprintf(buf, "coords%d.txt", cr->nodeid);
2322 fp = fopen(buf, "w");
2326 fprintf(fp, "\nStep %d\n", step);
2327 fprintf(fp, "box: %f %f %f %f %f %f %f %f %f\n",
2328 box[XX][XX], box[XX][YY], box[XX][ZZ],
2329 box[YY][XX], box[YY][YY], box[YY][ZZ],
2330 box[ZZ][XX], box[ZZ][ZZ], box[ZZ][ZZ]);
2331 for (i = 0; i < rotg->nat; i++)
2333 fprintf(fp, "%4d %f %f %f\n", i,
2334 erg->xc[i][XX], erg->xc[i][YY], erg->xc[i][ZZ]);
2342 static int projection_compare(const void *a, const void *b)
2344 sort_along_vec_t *xca, *xcb;
2347 xca = (sort_along_vec_t *)a;
2348 xcb = (sort_along_vec_t *)b;
2350 if (xca->xcproj < xcb->xcproj)
2354 else if (xca->xcproj > xcb->xcproj)
2365 static void sort_collective_coordinates(
2366 t_rotgrp *rotg, /* Rotation group */
2367 sort_along_vec_t *data) /* Buffer for sorting the positions */
2370 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2373 erg = rotg->enfrotgrp;
2375 /* The projection of the position vector on the rotation vector is
2376 * the relevant value for sorting. Fill the 'data' structure */
2377 for (i = 0; i < rotg->nat; i++)
2379 data[i].xcproj = iprod(erg->xc[i], rotg->vec); /* sort criterium */
2380 data[i].m = erg->mc[i];
2382 copy_rvec(erg->xc[i], data[i].x );
2383 copy_rvec(rotg->x_ref[i], data[i].x_ref);
2385 /* Sort the 'data' structure */
2386 gmx_qsort(data, rotg->nat, sizeof(sort_along_vec_t), projection_compare);
2388 /* Copy back the sorted values */
2389 for (i = 0; i < rotg->nat; i++)
2391 copy_rvec(data[i].x, erg->xc[i] );
2392 copy_rvec(data[i].x_ref, erg->xc_ref_sorted[i]);
2393 erg->mc_sorted[i] = data[i].m;
2394 erg->xc_sortind[i] = data[i].ind;
2399 /* For each slab, get the first and the last index of the sorted atom
2401 static void get_firstlast_atom_per_slab(t_rotgrp *rotg)
2405 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2408 erg = rotg->enfrotgrp;
2410 /* Find the first atom that needs to enter the calculation for each slab */
2411 n = erg->slab_first; /* slab */
2412 i = 0; /* start with the first atom */
2415 /* Find the first atom that significantly contributes to this slab */
2416 do /* move forward in position until a large enough beta is found */
2418 beta = calc_beta(erg->xc[i], rotg, n);
2421 while ((beta < -erg->max_beta) && (i < rotg->nat));
2423 islab = n - erg->slab_first; /* slab index */
2424 erg->firstatom[islab] = i;
2425 /* Proceed to the next slab */
2428 while (n <= erg->slab_last);
2430 /* Find the last atom for each slab */
2431 n = erg->slab_last; /* start with last slab */
2432 i = rotg->nat-1; /* start with the last atom */
2435 do /* move backward in position until a large enough beta is found */
2437 beta = calc_beta(erg->xc[i], rotg, n);
2440 while ((beta > erg->max_beta) && (i > -1));
2442 islab = n - erg->slab_first; /* slab index */
2443 erg->lastatom[islab] = i;
2444 /* Proceed to the next slab */
2447 while (n >= erg->slab_first);
2451 /* Determine the very first and very last slab that needs to be considered
2452 * For the first slab that needs to be considered, we have to find the smallest
2455 * x_first * v - n*Delta_x <= beta_max
2457 * slab index n, slab distance Delta_x, rotation vector v. For the last slab we
2458 * have to find the largest n that obeys
2460 * x_last * v - n*Delta_x >= -beta_max
2463 static gmx_inline int get_first_slab(
2464 t_rotgrp *rotg, /* The rotation group (inputrec data) */
2465 real max_beta, /* The max_beta value, instead of min_gaussian */
2466 rvec firstatom) /* First atom after sorting along the rotation vector v */
2468 /* Find the first slab for the first atom */
2469 return ceil((iprod(firstatom, rotg->vec) - max_beta)/rotg->slab_dist);
2473 static gmx_inline int get_last_slab(
2474 t_rotgrp *rotg, /* The rotation group (inputrec data) */
2475 real max_beta, /* The max_beta value, instead of min_gaussian */
2476 rvec lastatom) /* Last atom along v */
2478 /* Find the last slab for the last atom */
2479 return floor((iprod(lastatom, rotg->vec) + max_beta)/rotg->slab_dist);
2483 static void get_firstlast_slab_check(
2484 t_rotgrp *rotg, /* The rotation group (inputrec data) */
2485 t_gmx_enfrotgrp *erg, /* The rotation group (data only accessible in this file) */
2486 rvec firstatom, /* First atom after sorting along the rotation vector v */
2487 rvec lastatom) /* Last atom along v */
2489 erg->slab_first = get_first_slab(rotg, erg->max_beta, firstatom);
2490 erg->slab_last = get_last_slab(rotg, erg->max_beta, lastatom);
2492 /* Calculate the slab buffer size, which changes when slab_first changes */
2493 erg->slab_buffer = erg->slab_first - erg->slab_first_ref;
2495 /* Check whether we have reference data to compare against */
2496 if (erg->slab_first < erg->slab_first_ref)
2498 gmx_fatal(FARGS, "%s No reference data for first slab (n=%d), unable to proceed.",
2499 RotStr, erg->slab_first);
2502 /* Check whether we have reference data to compare against */
2503 if (erg->slab_last > erg->slab_last_ref)
2505 gmx_fatal(FARGS, "%s No reference data for last slab (n=%d), unable to proceed.",
2506 RotStr, erg->slab_last);
2511 /* Enforced rotation with a flexible axis */
2512 static void do_flexible(
2514 gmx_enfrot_t enfrot, /* Other rotation data */
2515 t_rotgrp *rotg, /* The rotation group */
2516 int g, /* Group number */
2517 rvec x[], /* The local positions */
2519 double t, /* Time in picoseconds */
2520 gmx_bool bOutstepRot, /* Output to main rotation output file */
2521 gmx_bool bOutstepSlab) /* Output per-slab data */
2524 real sigma; /* The Gaussian width sigma */
2525 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2528 erg = rotg->enfrotgrp;
2530 /* Define the sigma value */
2531 sigma = 0.7*rotg->slab_dist;
2533 /* Sort the collective coordinates erg->xc along the rotation vector. This is
2534 * an optimization for the inner loop. */
2535 sort_collective_coordinates(rotg, enfrot->data);
2537 /* Determine the first relevant slab for the first atom and the last
2538 * relevant slab for the last atom */
2539 get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1]);
2541 /* Determine for each slab depending on the min_gaussian cutoff criterium,
2542 * a first and a last atom index inbetween stuff needs to be calculated */
2543 get_firstlast_atom_per_slab(rotg);
2545 /* Determine the gaussian-weighted center of positions for all slabs */
2546 get_slab_centers(rotg, erg->xc, erg->mc_sorted, g, t, enfrot->out_slabs, bOutstepSlab, FALSE);
2548 /* Clear the torque per slab from last time step: */
2549 nslabs = erg->slab_last - erg->slab_first + 1;
2550 for (l = 0; l < nslabs; l++)
2552 erg->slab_torque_v[l] = 0.0;
2555 /* Call the rotational forces kernel */
2556 if (rotg->eType == erotgFLEX || rotg->eType == erotgFLEXT)
2558 erg->V = do_flex_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
2560 else if (rotg->eType == erotgFLEX2 || rotg->eType == erotgFLEX2T)
2562 erg->V = do_flex2_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
2566 gmx_fatal(FARGS, "Unknown flexible rotation type");
2569 /* Determine angle by RMSD fit to the reference - Let's hope this */
2570 /* only happens once in a while, since this is not parallelized! */
2571 if (bMaster && (erotgFitPOT != rotg->eFittype) )
2575 /* Fit angle of the whole rotation group */
2576 erg->angle_v = flex_fit_angle(rotg);
2580 /* Fit angle of each slab */
2581 flex_fit_angle_perslab(g, rotg, t, erg->degangle, enfrot->out_angles);
2585 /* Lump together the torques from all slabs: */
2586 erg->torque_v = 0.0;
2587 for (l = 0; l < nslabs; l++)
2589 erg->torque_v += erg->slab_torque_v[l];
2594 /* Calculate the angle between reference and actual rotation group atom,
2595 * both projected into a plane perpendicular to the rotation vector: */
2596 static void angle(t_rotgrp *rotg,
2600 real *weight) /* atoms near the rotation axis should count less than atoms far away */
2602 rvec xp, xrp; /* current and reference positions projected on a plane perpendicular to pg->vec */
2606 /* Project x_ref and x into a plane through the origin perpendicular to rot_vec: */
2607 /* Project x_ref: xrp = x_ref - (vec * x_ref) * vec */
2608 svmul(iprod(rotg->vec, x_ref), rotg->vec, dum);
2609 rvec_sub(x_ref, dum, xrp);
2610 /* Project x_act: */
2611 svmul(iprod(rotg->vec, x_act), rotg->vec, dum);
2612 rvec_sub(x_act, dum, xp);
2614 /* Retrieve information about which vector precedes. gmx_angle always
2615 * returns a positive angle. */
2616 cprod(xp, xrp, dum); /* if reference precedes, this is pointing into the same direction as vec */
2618 if (iprod(rotg->vec, dum) >= 0)
2620 *alpha = -gmx_angle(xrp, xp);
2624 *alpha = +gmx_angle(xrp, xp);
2627 /* Also return the weight */
2632 /* Project first vector onto a plane perpendicular to the second vector
2634 * Note that v must be of unit length.
2636 static gmx_inline void project_onto_plane(rvec dr, const rvec v)
2641 svmul(iprod(dr, v), v, tmp); /* tmp = (dr.v)v */
2642 rvec_dec(dr, tmp); /* dr = dr - (dr.v)v */
2646 /* Fixed rotation: The rotation reference group rotates around the v axis. */
2647 /* The atoms of the actual rotation group are attached with imaginary */
2648 /* springs to the reference atoms. */
2649 static void do_fixed(
2650 t_rotgrp *rotg, /* The rotation group */
2651 gmx_bool bOutstepRot, /* Output to main rotation output file */
2652 gmx_bool bOutstepSlab) /* Output per-slab data */
2656 rvec tmp_f; /* Force */
2657 real alpha; /* a single angle between an actual and a reference position */
2658 real weight; /* single weight for a single angle */
2659 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2660 rvec xi_xc; /* xi - xc */
2661 gmx_bool bCalcPotFit;
2664 /* for mass weighting: */
2665 real wi; /* Mass-weighting of the positions */
2667 real k_wi; /* k times wi */
2672 erg = rotg->enfrotgrp;
2673 bProject = (rotg->eType == erotgPM) || (rotg->eType == erotgPMPF);
2674 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2676 N_M = rotg->nat * erg->invmass;
2678 /* Each process calculates the forces on its local atoms */
2679 for (j = 0; j < erg->nat_loc; j++)
2681 /* Calculate (x_i-x_c) resp. (x_i-u) */
2682 rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xi_xc);
2684 /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
2685 rvec_sub(erg->xr_loc[j], xi_xc, dr);
2689 project_onto_plane(dr, rotg->vec);
2692 /* Mass-weighting */
2693 wi = N_M*erg->m_loc[j];
2695 /* Store the additional force so that it can be added to the force
2696 * array after the normal forces have been evaluated */
2698 for (m = 0; m < DIM; m++)
2700 tmp_f[m] = k_wi*dr[m];
2701 erg->f_rot_loc[j][m] = tmp_f[m];
2702 erg->V += 0.5*k_wi*sqr(dr[m]);
2705 /* If requested, also calculate the potential for a set of angles
2706 * near the current reference angle */
2709 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2711 /* Index of this rotation group atom with respect to the whole rotation group */
2712 jj = erg->xc_ref_ind[j];
2714 /* Rotate with the alternative angle. Like rotate_local_reference(),
2715 * just for a single local atom */
2716 mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_xr_loc); /* fit_xr_loc = Omega*(y_i-y_c) */
2718 /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
2719 rvec_sub(fit_xr_loc, xi_xc, dr);
2723 project_onto_plane(dr, rotg->vec);
2726 /* Add to the rotation potential for this angle: */
2727 erg->PotAngleFit->V[ifit] += 0.5*k_wi*norm2(dr);
2733 /* Add to the torque of this rotation group */
2734 erg->torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2736 /* Calculate the angle between reference and actual rotation group atom. */
2737 angle(rotg, xi_xc, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2738 erg->angle_v += alpha * weight;
2739 erg->weight_v += weight;
2741 /* If you want enforced rotation to contribute to the virial,
2742 * activate the following lines:
2745 Add the rotation contribution to the virial
2746 for(j=0; j<DIM; j++)
2748 vir[j][m] += 0.5*f[ii][j]*dr[m];
2754 } /* end of loop over local rotation group atoms */
2758 /* Calculate the radial motion potential and forces */
2759 static void do_radial_motion(
2760 t_rotgrp *rotg, /* The rotation group */
2761 gmx_bool bOutstepRot, /* Output to main rotation output file */
2762 gmx_bool bOutstepSlab) /* Output per-slab data */
2765 rvec tmp_f; /* Force */
2766 real alpha; /* a single angle between an actual and a reference position */
2767 real weight; /* single weight for a single angle */
2768 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2769 rvec xj_u; /* xj - u */
2770 rvec tmpvec, fit_tmpvec;
2771 real fac, fac2, sum = 0.0;
2773 gmx_bool bCalcPotFit;
2775 /* For mass weighting: */
2776 real wj; /* Mass-weighting of the positions */
2780 erg = rotg->enfrotgrp;
2781 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2783 N_M = rotg->nat * erg->invmass;
2785 /* Each process calculates the forces on its local atoms */
2786 for (j = 0; j < erg->nat_loc; j++)
2788 /* Calculate (xj-u) */
2789 rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xj_u); /* xj_u = xj-u */
2791 /* Calculate Omega.(yj0-u) */
2792 cprod(rotg->vec, erg->xr_loc[j], tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2794 /* * v x Omega.(yj0-u) */
2795 unitv(tmpvec, pj); /* pj = --------------------- */
2796 /* | v x Omega.(yj0-u) | */
2798 fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2801 /* Mass-weighting */
2802 wj = N_M*erg->m_loc[j];
2804 /* Store the additional force so that it can be added to the force
2805 * array after the normal forces have been evaluated */
2806 svmul(-rotg->k*wj*fac, pj, tmp_f);
2807 copy_rvec(tmp_f, erg->f_rot_loc[j]);
2810 /* If requested, also calculate the potential for a set of angles
2811 * near the current reference angle */
2814 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2816 /* Index of this rotation group atom with respect to the whole rotation group */
2817 jj = erg->xc_ref_ind[j];
2819 /* Rotate with the alternative angle. Like rotate_local_reference(),
2820 * just for a single local atom */
2821 mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_tmpvec); /* fit_tmpvec = Omega*(yj0-u) */
2823 /* Calculate Omega.(yj0-u) */
2824 cprod(rotg->vec, fit_tmpvec, tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2825 /* * v x Omega.(yj0-u) */
2826 unitv(tmpvec, pj); /* pj = --------------------- */
2827 /* | v x Omega.(yj0-u) | */
2829 fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2832 /* Add to the rotation potential for this angle: */
2833 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*fac2;
2839 /* Add to the torque of this rotation group */
2840 erg->torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2842 /* Calculate the angle between reference and actual rotation group atom. */
2843 angle(rotg, xj_u, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2844 erg->angle_v += alpha * weight;
2845 erg->weight_v += weight;
2850 } /* end of loop over local rotation group atoms */
2851 erg->V = 0.5*rotg->k*sum;
2855 /* Calculate the radial motion pivot-free potential and forces */
2856 static void do_radial_motion_pf(
2857 t_rotgrp *rotg, /* The rotation group */
2858 rvec x[], /* The positions */
2859 matrix box, /* The simulation box */
2860 gmx_bool bOutstepRot, /* Output to main rotation output file */
2861 gmx_bool bOutstepSlab) /* Output per-slab data */
2863 int i, ii, iigrp, ifit, j;
2864 rvec xj; /* Current position */
2865 rvec xj_xc; /* xj - xc */
2866 rvec yj0_yc0; /* yj0 - yc0 */
2867 rvec tmp_f; /* Force */
2868 real alpha; /* a single angle between an actual and a reference position */
2869 real weight; /* single weight for a single angle */
2870 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2871 rvec tmpvec, tmpvec2;
2872 rvec innersumvec; /* Precalculation of the inner sum */
2874 real fac, fac2, V = 0.0;
2876 gmx_bool bCalcPotFit;
2878 /* For mass weighting: */
2879 real mj, wi, wj; /* Mass-weighting of the positions */
2883 erg = rotg->enfrotgrp;
2884 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2886 N_M = rotg->nat * erg->invmass;
2888 /* Get the current center of the rotation group: */
2889 get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
2891 /* Precalculate Sum_i [ wi qi.(xi-xc) qi ] which is needed for every single j */
2892 clear_rvec(innersumvec);
2893 for (i = 0; i < rotg->nat; i++)
2895 /* Mass-weighting */
2896 wi = N_M*erg->mc[i];
2898 /* Calculate qi. Note that xc_ref_center has already been subtracted from
2899 * x_ref in init_rot_group.*/
2900 mvmul(erg->rotmat, rotg->x_ref[i], tmpvec); /* tmpvec = Omega.(yi0-yc0) */
2902 cprod(rotg->vec, tmpvec, tmpvec2); /* tmpvec2 = v x Omega.(yi0-yc0) */
2904 /* * v x Omega.(yi0-yc0) */
2905 unitv(tmpvec2, qi); /* qi = ----------------------- */
2906 /* | v x Omega.(yi0-yc0) | */
2908 rvec_sub(erg->xc[i], erg->xc_center, tmpvec); /* tmpvec = xi-xc */
2910 svmul(wi*iprod(qi, tmpvec), qi, tmpvec2);
2912 rvec_inc(innersumvec, tmpvec2);
2914 svmul(rotg->k*erg->invmass, innersumvec, innersumveckM);
2916 /* Each process calculates the forces on its local atoms */
2917 for (j = 0; j < erg->nat_loc; j++)
2919 /* Local index of a rotation group atom */
2920 ii = erg->ind_loc[j];
2921 /* Position of this atom in the collective array */
2922 iigrp = erg->xc_ref_ind[j];
2923 /* Mass-weighting */
2924 mj = erg->mc[iigrp]; /* need the unsorted mass here */
2927 /* Current position of this atom: x[ii][XX/YY/ZZ] */
2928 copy_rvec(x[ii], xj);
2930 /* Shift this atom such that it is near its reference */
2931 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2933 /* The (unrotated) reference position is yj0. yc0 has already
2934 * been subtracted in init_rot_group */
2935 copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
2937 /* Calculate Omega.(yj0-yc0) */
2938 mvmul(erg->rotmat, yj0_yc0, tmpvec2); /* tmpvec2 = Omega.(yj0 - yc0) */
2940 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
2942 /* * v x Omega.(yj0-yc0) */
2943 unitv(tmpvec, qj); /* qj = ----------------------- */
2944 /* | v x Omega.(yj0-yc0) | */
2946 /* Calculate (xj-xc) */
2947 rvec_sub(xj, erg->xc_center, xj_xc); /* xj_xc = xj-xc */
2949 fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
2952 /* Store the additional force so that it can be added to the force
2953 * array after the normal forces have been evaluated */
2954 svmul(-rotg->k*wj*fac, qj, tmp_f); /* part 1 of force */
2955 svmul(mj, innersumveckM, tmpvec); /* part 2 of force */
2956 rvec_inc(tmp_f, tmpvec);
2957 copy_rvec(tmp_f, erg->f_rot_loc[j]);
2960 /* If requested, also calculate the potential for a set of angles
2961 * near the current reference angle */
2964 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2966 /* Rotate with the alternative angle. Like rotate_local_reference(),
2967 * just for a single local atom */
2968 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, tmpvec2); /* tmpvec2 = Omega*(yj0-yc0) */
2970 /* Calculate Omega.(yj0-u) */
2971 cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
2972 /* * v x Omega.(yj0-yc0) */
2973 unitv(tmpvec, qj); /* qj = ----------------------- */
2974 /* | v x Omega.(yj0-yc0) | */
2976 fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
2979 /* Add to the rotation potential for this angle: */
2980 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*fac2;
2986 /* Add to the torque of this rotation group */
2987 erg->torque_v += torque(rotg->vec, tmp_f, xj, erg->xc_center);
2989 /* Calculate the angle between reference and actual rotation group atom. */
2990 angle(rotg, xj_xc, yj0_yc0, &alpha, &weight); /* angle in rad, weighted */
2991 erg->angle_v += alpha * weight;
2992 erg->weight_v += weight;
2997 } /* end of loop over local rotation group atoms */
2998 erg->V = 0.5*rotg->k*V;
3002 /* Precalculate the inner sum for the radial motion 2 forces */
3003 static void radial_motion2_precalc_inner_sum(t_rotgrp *rotg, rvec innersumvec)
3006 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3007 rvec xi_xc; /* xj - xc */
3008 rvec tmpvec, tmpvec2;
3012 rvec v_xi_xc; /* v x (xj - u) */
3013 real psii, psiistar;
3014 real wi; /* Mass-weighting of the positions */
3018 erg = rotg->enfrotgrp;
3019 N_M = rotg->nat * erg->invmass;
3021 /* Loop over the collective set of positions */
3023 for (i = 0; i < rotg->nat; i++)
3025 /* Mass-weighting */
3026 wi = N_M*erg->mc[i];
3028 rvec_sub(erg->xc[i], erg->xc_center, xi_xc); /* xi_xc = xi-xc */
3030 /* Calculate ri. Note that xc_ref_center has already been subtracted from
3031 * x_ref in init_rot_group.*/
3032 mvmul(erg->rotmat, rotg->x_ref[i], ri); /* ri = Omega.(yi0-yc0) */
3034 cprod(rotg->vec, xi_xc, v_xi_xc); /* v_xi_xc = v x (xi-u) */
3036 fac = norm2(v_xi_xc);
3038 psiistar = 1.0/(fac + rotg->eps); /* psiistar = --------------------- */
3039 /* |v x (xi-xc)|^2 + eps */
3041 psii = gmx_invsqrt(fac); /* 1 */
3042 /* psii = ------------- */
3045 svmul(psii, v_xi_xc, si); /* si = psii * (v x (xi-xc) ) */
3047 fac = iprod(v_xi_xc, ri); /* fac = (v x (xi-xc)).ri */
3050 siri = iprod(si, ri); /* siri = si.ri */
3052 svmul(psiistar/psii, ri, tmpvec);
3053 svmul(psiistar*psiistar/(psii*psii*psii) * siri, si, tmpvec2);
3054 rvec_dec(tmpvec, tmpvec2);
3055 cprod(tmpvec, rotg->vec, tmpvec2);
3057 svmul(wi*siri, tmpvec2, tmpvec);
3059 rvec_inc(sumvec, tmpvec);
3061 svmul(rotg->k*erg->invmass, sumvec, innersumvec);
3065 /* Calculate the radial motion 2 potential and forces */
3066 static void do_radial_motion2(
3067 t_rotgrp *rotg, /* The rotation group */
3068 rvec x[], /* The positions */
3069 matrix box, /* The simulation box */
3070 gmx_bool bOutstepRot, /* Output to main rotation output file */
3071 gmx_bool bOutstepSlab) /* Output per-slab data */
3073 int ii, iigrp, ifit, j;
3074 rvec xj; /* Position */
3075 real alpha; /* a single angle between an actual and a reference position */
3076 real weight; /* single weight for a single angle */
3077 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3078 rvec xj_u; /* xj - u */
3079 rvec yj0_yc0; /* yj0 -yc0 */
3080 rvec tmpvec, tmpvec2;
3081 real fac, fit_fac, fac2, Vpart = 0.0;
3082 rvec rj, fit_rj, sj;
3084 rvec v_xj_u; /* v x (xj - u) */
3085 real psij, psijstar;
3086 real mj, wj; /* For mass-weighting of the positions */
3090 gmx_bool bCalcPotFit;
3093 erg = rotg->enfrotgrp;
3095 bPF = rotg->eType == erotgRM2PF;
3096 bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
3099 clear_rvec(yj0_yc0); /* Make the compiler happy */
3101 clear_rvec(innersumvec);
3104 /* For the pivot-free variant we have to use the current center of
3105 * mass of the rotation group instead of the pivot u */
3106 get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
3108 /* Also, we precalculate the second term of the forces that is identical
3109 * (up to the weight factor mj) for all forces */
3110 radial_motion2_precalc_inner_sum(rotg, innersumvec);
3113 N_M = rotg->nat * erg->invmass;
3115 /* Each process calculates the forces on its local atoms */
3116 for (j = 0; j < erg->nat_loc; j++)
3120 /* Local index of a rotation group atom */
3121 ii = erg->ind_loc[j];
3122 /* Position of this atom in the collective array */
3123 iigrp = erg->xc_ref_ind[j];
3124 /* Mass-weighting */
3125 mj = erg->mc[iigrp];
3127 /* Current position of this atom: x[ii] */
3128 copy_rvec(x[ii], xj);
3130 /* Shift this atom such that it is near its reference */
3131 shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
3133 /* The (unrotated) reference position is yj0. yc0 has already
3134 * been subtracted in init_rot_group */
3135 copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
3137 /* Calculate Omega.(yj0-yc0) */
3138 mvmul(erg->rotmat, yj0_yc0, rj); /* rj = Omega.(yj0-yc0) */
3143 copy_rvec(erg->x_loc_pbc[j], xj);
3144 copy_rvec(erg->xr_loc[j], rj); /* rj = Omega.(yj0-u) */
3146 /* Mass-weighting */
3149 /* Calculate (xj-u) resp. (xj-xc) */
3150 rvec_sub(xj, erg->xc_center, xj_u); /* xj_u = xj-u */
3152 cprod(rotg->vec, xj_u, v_xj_u); /* v_xj_u = v x (xj-u) */
3154 fac = norm2(v_xj_u);
3156 psijstar = 1.0/(fac + rotg->eps); /* psistar = -------------------- */
3157 /* |v x (xj-u)|^2 + eps */
3159 psij = gmx_invsqrt(fac); /* 1 */
3160 /* psij = ------------ */
3163 svmul(psij, v_xj_u, sj); /* sj = psij * (v x (xj-u) ) */
3165 fac = iprod(v_xj_u, rj); /* fac = (v x (xj-u)).rj */
3168 sjrj = iprod(sj, rj); /* sjrj = sj.rj */
3170 svmul(psijstar/psij, rj, tmpvec);
3171 svmul(psijstar*psijstar/(psij*psij*psij) * sjrj, sj, tmpvec2);
3172 rvec_dec(tmpvec, tmpvec2);
3173 cprod(tmpvec, rotg->vec, tmpvec2);
3175 /* Store the additional force so that it can be added to the force
3176 * array after the normal forces have been evaluated */
3177 svmul(-rotg->k*wj*sjrj, tmpvec2, tmpvec);
3178 svmul(mj, innersumvec, tmpvec2); /* This is != 0 only for the pivot-free variant */
3180 rvec_add(tmpvec2, tmpvec, erg->f_rot_loc[j]);
3181 Vpart += wj*psijstar*fac2;
3183 /* If requested, also calculate the potential for a set of angles
3184 * near the current reference angle */
3187 for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
3191 mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, fit_rj); /* fit_rj = Omega.(yj0-yc0) */
3195 /* Position of this atom in the collective array */
3196 iigrp = erg->xc_ref_ind[j];
3197 /* Rotate with the alternative angle. Like rotate_local_reference(),
3198 * just for a single local atom */
3199 mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[iigrp], fit_rj); /* fit_rj = Omega*(yj0-u) */
3201 fit_fac = iprod(v_xj_u, fit_rj); /* fac = (v x (xj-u)).fit_rj */
3202 /* Add to the rotation potential for this angle: */
3203 erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*psijstar*fit_fac*fit_fac;
3209 /* Add to the torque of this rotation group */
3210 erg->torque_v += torque(rotg->vec, erg->f_rot_loc[j], xj, erg->xc_center);
3212 /* Calculate the angle between reference and actual rotation group atom. */
3213 angle(rotg, xj_u, rj, &alpha, &weight); /* angle in rad, weighted */
3214 erg->angle_v += alpha * weight;
3215 erg->weight_v += weight;
3220 } /* end of loop over local rotation group atoms */
3221 erg->V = 0.5*rotg->k*Vpart;
3225 /* Determine the smallest and largest position vector (with respect to the
3226 * rotation vector) for the reference group */
3227 static void get_firstlast_atom_ref(
3232 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3234 real xcproj; /* The projection of a reference position on the
3236 real minproj, maxproj; /* Smallest and largest projection on v */
3240 erg = rotg->enfrotgrp;
3242 /* Start with some value */
3243 minproj = iprod(rotg->x_ref[0], rotg->vec);
3246 /* This is just to ensure that it still works if all the atoms of the
3247 * reference structure are situated in a plane perpendicular to the rotation
3250 *lastindex = rotg->nat-1;
3252 /* Loop over all atoms of the reference group,
3253 * project them on the rotation vector to find the extremes */
3254 for (i = 0; i < rotg->nat; i++)
3256 xcproj = iprod(rotg->x_ref[i], rotg->vec);
3257 if (xcproj < minproj)
3262 if (xcproj > maxproj)
3271 /* Allocate memory for the slabs */
3272 static void allocate_slabs(
3278 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3282 erg = rotg->enfrotgrp;
3284 /* More slabs than are defined for the reference are never needed */
3285 nslabs = erg->slab_last_ref - erg->slab_first_ref + 1;
3287 /* Remember how many we allocated */
3288 erg->nslabs_alloc = nslabs;
3290 if ( (NULL != fplog) && bVerbose)
3292 fprintf(fplog, "%s allocating memory to store data for %d slabs (rotation group %d).\n",
3295 snew(erg->slab_center, nslabs);
3296 snew(erg->slab_center_ref, nslabs);
3297 snew(erg->slab_weights, nslabs);
3298 snew(erg->slab_torque_v, nslabs);
3299 snew(erg->slab_data, nslabs);
3300 snew(erg->gn_atom, nslabs);
3301 snew(erg->gn_slabind, nslabs);
3302 snew(erg->slab_innersumvec, nslabs);
3303 for (i = 0; i < nslabs; i++)
3305 snew(erg->slab_data[i].x, rotg->nat);
3306 snew(erg->slab_data[i].ref, rotg->nat);
3307 snew(erg->slab_data[i].weight, rotg->nat);
3309 snew(erg->xc_ref_sorted, rotg->nat);
3310 snew(erg->xc_sortind, rotg->nat);
3311 snew(erg->firstatom, nslabs);
3312 snew(erg->lastatom, nslabs);
3316 /* From the extreme positions of the reference group, determine the first
3317 * and last slab of the reference. We can never have more slabs in the real
3318 * simulation than calculated here for the reference.
3320 static void get_firstlast_slab_ref(t_rotgrp *rotg, real mc[], int ref_firstindex, int ref_lastindex)
3322 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3327 erg = rotg->enfrotgrp;
3328 first = get_first_slab(rotg, erg->max_beta, rotg->x_ref[ref_firstindex]);
3329 last = get_last_slab( rotg, erg->max_beta, rotg->x_ref[ref_lastindex ]);
3331 while (get_slab_weight(first, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
3335 erg->slab_first_ref = first+1;
3336 while (get_slab_weight(last, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
3340 erg->slab_last_ref = last-1;
3344 /* Special version of copy_rvec:
3345 * During the copy procedure of xcurr to b, the correct PBC image is chosen
3346 * such that the copied vector ends up near its reference position xref */
3347 static inline void copy_correct_pbc_image(
3348 const rvec xcurr, /* copy vector xcurr ... */
3349 rvec b, /* ... to b ... */
3350 const rvec xref, /* choosing the PBC image such that b ends up near xref */
3359 /* Shortest PBC distance between the atom and its reference */
3360 rvec_sub(xcurr, xref, dx);
3362 /* Determine the shift for this atom */
3364 for (m = npbcdim-1; m >= 0; m--)
3366 while (dx[m] < -0.5*box[m][m])
3368 for (d = 0; d < DIM; d++)
3374 while (dx[m] >= 0.5*box[m][m])
3376 for (d = 0; d < DIM; d++)
3384 /* Apply the shift to the position */
3385 copy_rvec(xcurr, b);
3386 shift_single_coord(box, b, shift);
3390 static void init_rot_group(FILE *fplog, t_commrec *cr, int g, t_rotgrp *rotg,
3391 rvec *x, gmx_mtop_t *mtop, gmx_bool bVerbose, FILE *out_slabs, matrix box,
3392 t_inputrec *ir, gmx_bool bOutputCenters)
3395 rvec coord, xref, *xdum;
3396 gmx_bool bFlex, bColl;
3398 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3399 int ref_firstindex, ref_lastindex;
3400 gmx_mtop_atomlookup_t alook = NULL;
3401 real mass, totalmass;
3406 /* Do we have a flexible axis? */
3407 bFlex = ISFLEX(rotg);
3408 /* Do we use a global set of coordinates? */
3409 bColl = ISCOLL(rotg);
3411 erg = rotg->enfrotgrp;
3413 /* Allocate space for collective coordinates if needed */
3416 snew(erg->xc, rotg->nat);
3417 snew(erg->xc_shifts, rotg->nat);
3418 snew(erg->xc_eshifts, rotg->nat);
3419 snew(erg->xc_old, rotg->nat);
3421 if (rotg->eFittype == erotgFitNORM)
3423 snew(erg->xc_ref_length, rotg->nat); /* in case fit type NORM is chosen */
3424 snew(erg->xc_norm, rotg->nat);
3429 snew(erg->xr_loc, rotg->nat);
3430 snew(erg->x_loc_pbc, rotg->nat);
3433 snew(erg->f_rot_loc, rotg->nat);
3434 snew(erg->xc_ref_ind, rotg->nat);
3436 /* Make space for the calculation of the potential at other angles (used
3437 * for fitting only) */
3438 if (erotgFitPOT == rotg->eFittype)
3440 snew(erg->PotAngleFit, 1);
3441 snew(erg->PotAngleFit->degangle, rotg->PotAngle_nstep);
3442 snew(erg->PotAngleFit->V, rotg->PotAngle_nstep);
3443 snew(erg->PotAngleFit->rotmat, rotg->PotAngle_nstep);
3445 /* Get the set of angles around the reference angle */
3446 start = -0.5 * (rotg->PotAngle_nstep - 1)*rotg->PotAngle_step;
3447 for (i = 0; i < rotg->PotAngle_nstep; i++)
3449 erg->PotAngleFit->degangle[i] = start + i*rotg->PotAngle_step;
3454 erg->PotAngleFit = NULL;
3457 /* xc_ref_ind needs to be set to identity in the serial case */
3460 for (i = 0; i < rotg->nat; i++)
3462 erg->xc_ref_ind[i] = i;
3466 /* Copy the masses so that the center can be determined. For all types of
3467 * enforced rotation, we store the masses in the erg->mc array. */
3470 alook = gmx_mtop_atomlookup_init(mtop);
3472 snew(erg->mc, rotg->nat);
3475 snew(erg->mc_sorted, rotg->nat);
3479 snew(erg->m_loc, rotg->nat);
3482 for (i = 0; i < rotg->nat; i++)
3486 gmx_mtop_atomnr_to_atom(alook, rotg->ind[i], &atom);
3496 erg->invmass = 1.0/totalmass;
3500 gmx_mtop_atomlookup_destroy(alook);
3503 /* Set xc_ref_center for any rotation potential */
3504 if ((rotg->eType == erotgISO) || (rotg->eType == erotgPM) || (rotg->eType == erotgRM) || (rotg->eType == erotgRM2))
3506 /* Set the pivot point for the fixed, stationary-axis potentials. This
3507 * won't change during the simulation */
3508 copy_rvec(rotg->pivot, erg->xc_ref_center);
3509 copy_rvec(rotg->pivot, erg->xc_center );
3513 /* Center of the reference positions */
3514 get_center(rotg->x_ref, erg->mc, rotg->nat, erg->xc_ref_center);
3516 /* Center of the actual positions */
3519 snew(xdum, rotg->nat);
3520 for (i = 0; i < rotg->nat; i++)
3523 copy_rvec(x[ii], xdum[i]);
3525 get_center(xdum, erg->mc, rotg->nat, erg->xc_center);
3531 gmx_bcast(sizeof(erg->xc_center), erg->xc_center, cr);
3538 /* Save the original (whole) set of positions in xc_old such that at later
3539 * steps the rotation group can always be made whole again. If the simulation is
3540 * restarted, we compute the starting reference positions (given the time)
3541 * and assume that the correct PBC image of each position is the one nearest
3542 * to the current reference */
3545 /* Calculate the rotation matrix for this angle: */
3546 t_start = ir->init_t + ir->init_step*ir->delta_t;
3547 erg->degangle = rotg->rate * t_start;
3548 calc_rotmat(rotg->vec, erg->degangle, erg->rotmat);
3550 for (i = 0; i < rotg->nat; i++)
3554 /* Subtract pivot, rotate, and add pivot again. This will yield the
3555 * reference position for time t */
3556 rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
3557 mvmul(erg->rotmat, coord, xref);
3558 rvec_inc(xref, erg->xc_ref_center);
3560 copy_correct_pbc_image(x[ii], erg->xc_old[i], xref, box, 3);
3566 gmx_bcast(rotg->nat*sizeof(erg->xc_old[0]), erg->xc_old, cr);
3571 if ( (rotg->eType != erotgFLEX) && (rotg->eType != erotgFLEX2) )
3573 /* Put the reference positions into origin: */
3574 for (i = 0; i < rotg->nat; i++)
3576 rvec_dec(rotg->x_ref[i], erg->xc_ref_center);
3580 /* Enforced rotation with flexible axis */
3583 /* Calculate maximum beta value from minimum gaussian (performance opt.) */
3584 erg->max_beta = calc_beta_max(rotg->min_gaussian, rotg->slab_dist);
3586 /* Determine the smallest and largest coordinate with respect to the rotation vector */
3587 get_firstlast_atom_ref(rotg, &ref_firstindex, &ref_lastindex);
3589 /* From the extreme positions of the reference group, determine the first
3590 * and last slab of the reference. */
3591 get_firstlast_slab_ref(rotg, erg->mc, ref_firstindex, ref_lastindex);
3593 /* Allocate memory for the slabs */
3594 allocate_slabs(rotg, fplog, g, bVerbose);
3596 /* Flexible rotation: determine the reference centers for the rest of the simulation */
3597 erg->slab_first = erg->slab_first_ref;
3598 erg->slab_last = erg->slab_last_ref;
3599 get_slab_centers(rotg, rotg->x_ref, erg->mc, g, -1, out_slabs, bOutputCenters, TRUE);
3601 /* Length of each x_rotref vector from center (needed if fit routine NORM is chosen): */
3602 if (rotg->eFittype == erotgFitNORM)
3604 for (i = 0; i < rotg->nat; i++)
3606 rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
3607 erg->xc_ref_length[i] = norm(coord);
3614 extern void dd_make_local_rotation_groups(gmx_domdec_t *dd, t_rot *rot)
3619 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3623 for (g = 0; g < rot->ngrp; g++)
3625 rotg = &rot->grp[g];
3626 erg = rotg->enfrotgrp;
3629 dd_make_local_group_indices(ga2la, rotg->nat, rotg->ind,
3630 &erg->nat_loc, &erg->ind_loc, &erg->nalloc_loc, erg->xc_ref_ind);
3635 /* Calculate the size of the MPI buffer needed in reduce_output() */
3636 static int calc_mpi_bufsize(t_rot *rot)
3639 int count_group, count_total;
3641 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3645 for (g = 0; g < rot->ngrp; g++)
3647 rotg = &rot->grp[g];
3648 erg = rotg->enfrotgrp;
3650 /* Count the items that are transferred for this group: */
3651 count_group = 4; /* V, torque, angle, weight */
3653 /* Add the maximum number of slabs for flexible groups */
3656 count_group += erg->slab_last_ref - erg->slab_first_ref + 1;
3659 /* Add space for the potentials at different angles: */
3660 if (erotgFitPOT == rotg->eFittype)
3662 count_group += rotg->PotAngle_nstep;
3665 /* Add to the total number: */
3666 count_total += count_group;
3673 extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
3674 t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
3675 gmx_bool bVerbose, unsigned long Flags)
3680 int nat_max = 0; /* Size of biggest rotation group */
3681 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3682 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3683 rvec *x_pbc = NULL; /* Space for the pbc-correct atom positions */
3686 if ( (PAR(cr)) && !DOMAINDECOMP(cr) )
3688 gmx_fatal(FARGS, "Enforced rotation is only implemented for domain decomposition!");
3691 if (MASTER(cr) && bVerbose)
3693 fprintf(stdout, "%s Initializing ...\n", RotStr);
3697 snew(rot->enfrot, 1);
3701 /* When appending, skip first output to avoid duplicate entries in the data files */
3702 if (er->Flags & MD_APPENDFILES)
3711 if (MASTER(cr) && er->bOut)
3713 please_cite(fplog, "Kutzner2011");
3716 /* Output every step for reruns */
3717 if (er->Flags & MD_RERUN)
3721 fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
3727 er->out_slabs = NULL;
3728 if (MASTER(cr) && HaveFlexibleGroups(rot) )
3730 er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), rot);
3735 /* Remove pbc, make molecule whole.
3736 * When ir->bContinuation=TRUE this has already been done, but ok. */
3737 snew(x_pbc, mtop->natoms);
3738 m_rveccopy(mtop->natoms, x, x_pbc);
3739 do_pbc_first_mtop(NULL, ir->ePBC, box, mtop, x_pbc);
3740 /* All molecules will be whole now, but not necessarily in the home box.
3741 * Additionally, if a rotation group consists of more than one molecule
3742 * (e.g. two strands of DNA), each one of them can end up in a different
3743 * periodic box. This is taken care of in init_rot_group. */
3746 for (g = 0; g < rot->ngrp; g++)
3748 rotg = &rot->grp[g];
3752 fprintf(fplog, "%s group %d type '%s'\n", RotStr, g, erotg_names[rotg->eType]);
3757 /* Allocate space for the rotation group's data: */
3758 snew(rotg->enfrotgrp, 1);
3759 erg = rotg->enfrotgrp;
3761 nat_max = max(nat_max, rotg->nat);
3766 erg->nalloc_loc = 0;
3767 erg->ind_loc = NULL;
3771 erg->nat_loc = rotg->nat;
3772 erg->ind_loc = rotg->ind;
3774 init_rot_group(fplog, cr, g, rotg, x_pbc, mtop, bVerbose, er->out_slabs, box, ir,
3775 !(er->Flags & MD_APPENDFILES) ); /* Do not output the reference centers
3776 * again if we are appending */
3780 /* Allocate space for enforced rotation buffer variables */
3781 er->bufsize = nat_max;
3782 snew(er->data, nat_max);
3783 snew(er->xbuf, nat_max);
3784 snew(er->mbuf, nat_max);
3786 /* Buffers for MPI reducing torques, angles, weights (for each group), and V */
3789 er->mpi_bufsize = calc_mpi_bufsize(rot) + 100; /* larger to catch errors */
3790 snew(er->mpi_inbuf, er->mpi_bufsize);
3791 snew(er->mpi_outbuf, er->mpi_bufsize);
3795 er->mpi_bufsize = 0;
3796 er->mpi_inbuf = NULL;
3797 er->mpi_outbuf = NULL;
3800 /* Only do I/O on the MASTER */
3801 er->out_angles = NULL;
3803 er->out_torque = NULL;
3806 er->out_rot = open_rot_out(opt2fn("-ro", nfile, fnm), rot, oenv);
3808 if (rot->nstsout > 0)
3810 if (HaveFlexibleGroups(rot) || HavePotFitGroups(rot) )
3812 er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), rot);
3814 if (HaveFlexibleGroups(rot) )
3816 er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), rot);
3825 extern void finish_rot(t_rot *rot)
3827 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3833 gmx_fio_fclose(er->out_rot);
3837 gmx_fio_fclose(er->out_slabs);
3841 gmx_fio_fclose(er->out_angles);
3845 gmx_fio_fclose(er->out_torque);
3850 /* Rotate the local reference positions and store them in
3851 * erg->xr_loc[0...(nat_loc-1)]
3853 * Note that we already subtracted u or y_c from the reference positions
3854 * in init_rot_group().
3856 static void rotate_local_reference(t_rotgrp *rotg)
3858 gmx_enfrotgrp_t erg;
3862 erg = rotg->enfrotgrp;
3864 for (i = 0; i < erg->nat_loc; i++)
3866 /* Index of this rotation group atom with respect to the whole rotation group */
3867 ii = erg->xc_ref_ind[i];
3869 mvmul(erg->rotmat, rotg->x_ref[ii], erg->xr_loc[i]);
3874 /* Select the PBC representation for each local x position and store that
3875 * for later usage. We assume the right PBC image of an x is the one nearest to
3876 * its rotated reference */
3877 static void choose_pbc_image(rvec x[], t_rotgrp *rotg, matrix box, int npbcdim)
3880 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3884 erg = rotg->enfrotgrp;
3886 for (i = 0; i < erg->nat_loc; i++)
3888 /* Index of a rotation group atom */
3889 ii = erg->ind_loc[i];
3891 /* Get the correctly rotated reference position. The pivot was already
3892 * subtracted in init_rot_group() from the reference positions. Also,
3893 * the reference positions have already been rotated in
3894 * rotate_local_reference(). For the current reference position we thus
3895 * only need to add the pivot again. */
3896 copy_rvec(erg->xr_loc[i], xref);
3897 rvec_inc(xref, erg->xc_ref_center);
3899 copy_correct_pbc_image(x[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
3904 extern void do_rotation(
3910 gmx_large_int_t step,
3911 gmx_wallcycle_t wcycle,
3917 gmx_bool outstep_slab, outstep_rot;
3918 gmx_bool bFlex, bColl;
3919 gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3920 gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3922 t_gmx_potfit *fit = NULL; /* For fit type 'potential' determine the fit
3923 angle via the potential minimum */
3925 /* Enforced rotation cycle counting: */
3926 gmx_cycles_t cycles_comp; /* Cycles for the enf. rotation computation
3927 only, does not count communication. This
3928 counter is used for load-balancing */
3937 /* When to output in main rotation output file */
3938 outstep_rot = do_per_step(step, rot->nstrout) && er->bOut;
3939 /* When to output per-slab data */
3940 outstep_slab = do_per_step(step, rot->nstsout) && er->bOut;
3942 /* Output time into rotation output file */
3943 if (outstep_rot && MASTER(cr))
3945 fprintf(er->out_rot, "%12.3e", t);
3948 /**************************************************************************/
3949 /* First do ALL the communication! */
3950 for (g = 0; g < rot->ngrp; g++)
3952 rotg = &rot->grp[g];
3953 erg = rotg->enfrotgrp;
3955 /* Do we have a flexible axis? */
3956 bFlex = ISFLEX(rotg);
3957 /* Do we use a collective (global) set of coordinates? */
3958 bColl = ISCOLL(rotg);
3960 /* Calculate the rotation matrix for this angle: */
3961 erg->degangle = rotg->rate * t;
3962 calc_rotmat(rotg->vec, erg->degangle, erg->rotmat);
3966 /* Transfer the rotation group's positions such that every node has
3967 * all of them. Every node contributes its local positions x and stores
3968 * it in the collective erg->xc array. */
3969 communicate_group_positions(cr, erg->xc, erg->xc_shifts, erg->xc_eshifts, bNS,
3970 x, rotg->nat, erg->nat_loc, erg->ind_loc, erg->xc_ref_ind, erg->xc_old, box);
3974 /* Fill the local masses array;
3975 * this array changes in DD/neighborsearching steps */
3978 for (i = 0; i < erg->nat_loc; i++)
3980 /* Index of local atom w.r.t. the collective rotation group */
3981 ii = erg->xc_ref_ind[i];
3982 erg->m_loc[i] = erg->mc[ii];
3986 /* Calculate Omega*(y_i-y_c) for the local positions */
3987 rotate_local_reference(rotg);
3989 /* Choose the nearest PBC images of the group atoms with respect
3990 * to the rotated reference positions */
3991 choose_pbc_image(x, rotg, box, 3);
3993 /* Get the center of the rotation group */
3994 if ( (rotg->eType == erotgISOPF) || (rotg->eType == erotgPMPF) )
3996 get_center_comm(cr, erg->x_loc_pbc, erg->m_loc, erg->nat_loc, rotg->nat, erg->xc_center);
4000 } /* End of loop over rotation groups */
4002 /**************************************************************************/
4003 /* Done communicating, we can start to count cycles for the load balancing now ... */
4004 cycles_comp = gmx_cycles_read();
4011 for (g = 0; g < rot->ngrp; g++)
4013 rotg = &rot->grp[g];
4014 erg = rotg->enfrotgrp;
4016 bFlex = ISFLEX(rotg);
4017 bColl = ISCOLL(rotg);
4019 if (outstep_rot && MASTER(cr))
4021 fprintf(er->out_rot, "%12.4f", erg->degangle);
4024 /* Calculate angles and rotation matrices for potential fitting: */
4025 if ( (outstep_rot || outstep_slab) && (erotgFitPOT == rotg->eFittype) )
4027 fit = erg->PotAngleFit;
4028 for (i = 0; i < rotg->PotAngle_nstep; i++)
4030 calc_rotmat(rotg->vec, erg->degangle + fit->degangle[i], fit->rotmat[i]);
4032 /* Clear value from last step */
4033 erg->PotAngleFit->V[i] = 0.0;
4037 /* Clear values from last time step */
4039 erg->torque_v = 0.0;
4041 erg->weight_v = 0.0;
4043 switch (rotg->eType)
4049 do_fixed(rotg, outstep_rot, outstep_slab);
4052 do_radial_motion(rotg, outstep_rot, outstep_slab);
4055 do_radial_motion_pf(rotg, x, box, outstep_rot, outstep_slab);
4059 do_radial_motion2(rotg, x, box, outstep_rot, outstep_slab);
4063 /* Subtract the center of the rotation group from the collective positions array
4064 * Also store the center in erg->xc_center since it needs to be subtracted
4065 * in the low level routines from the local coordinates as well */
4066 get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
4067 svmul(-1.0, erg->xc_center, transvec);
4068 translate_x(erg->xc, rotg->nat, transvec);
4069 do_flexible(MASTER(cr), er, rotg, g, x, box, t, outstep_rot, outstep_slab);
4073 /* Do NOT subtract the center of mass in the low level routines! */
4074 clear_rvec(erg->xc_center);
4075 do_flexible(MASTER(cr), er, rotg, g, x, box, t, outstep_rot, outstep_slab);
4078 gmx_fatal(FARGS, "No such rotation potential.");
4086 fprintf(stderr, "%s calculation (step %d) took %g seconds.\n", RotStr, step, MPI_Wtime()-t0);
4090 /* Stop the enforced rotation cycle counter and add the computation-only
4091 * cycles to the force cycles for load balancing */
4092 cycles_comp = gmx_cycles_read() - cycles_comp;
4094 if (DOMAINDECOMP(cr) && wcycle)
4096 dd_cycles_add(cr->dd, cycles_comp, ddCyclF);