/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull

Bug Summary

File:	gromacs/pulling/pull_rotation.c
Location:	line 3052, column 9
Description:	Value stored to 'fac2' is never read

Annotated Source Code

1	/*
2	* This file is part of the GROMACS molecular simulation package.
3	*
4	* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5	* Copyright (c) 2001-2008, The GROMACS development team.
6	* Copyright (c) 2013,2014, by the GROMACS development team, led by
7	* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8	* and including many others, as listed in the AUTHORS file in the
9	* top-level source directory and at http://www.gromacs.org.
10	*
11	* GROMACS is free software; you can redistribute it and/or
12	* modify it under the terms of the GNU Lesser General Public License
13	* as published by the Free Software Foundation; either version 2.1
14	* of the License, or (at your option) any later version.
15	*
16	* GROMACS is distributed in the hope that it will be useful,
17	* but WITHOUT ANY WARRANTY; without even the implied warranty of
18	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19	* Lesser General Public License for more details.
20	*
21	* You should have received a copy of the GNU Lesser General Public
22	* License along with GROMACS; if not, see
23	* http://www.gnu.org/licenses, or write to the Free Software Foundation,
24	* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25	*
26	* If you want to redistribute modifications to GROMACS, please
27	* consider that scientific software is very special. Version
28	* control is crucial - bugs must be traceable. We will be happy to
29	* consider code for inclusion in the official distribution, but
30	* derived work must not be called official GROMACS. Details are found
31	* in the README & COPYING files - if they are missing, get the
32	* official version at http://www.gromacs.org.
33	*
34	* To help us fund GROMACS development, we humbly ask that you cite
35	* the research papers on the package. Check out http://www.gromacs.org.
36	*/
37	#ifdef HAVE_CONFIG_H1
38	#include <config.h>
39	#endif
40
41	#include <stdio.h>
42	#include <stdlib.h>
43	#include <string.h>
44
45	#include "domdec.h"
46	#include "gromacs/utility/smalloc.h"
47	#include "network.h"
48	#include "pbc.h"
49	#include "mdrun.h"
50	#include "txtdump.h"
51	#include "names.h"
52	#include "mtop_util.h"
53	#include "names.h"
54	#include "gromacs/math/vec.h"
55	#include "gmx_ga2la.h"
56	#include "gromacs/fileio/xvgr.h"
57	#include "copyrite.h"
58	#include "macros.h"
59
60	#include "gromacs/utility/futil.h"
61	#include "gromacs/fileio/gmxfio.h"
62	#include "gromacs/fileio/trnio.h"
63	#include "gromacs/linearalgebra/nrjac.h"
64	#include "gromacs/timing/cyclecounter.h"
65	#include "gromacs/timing/wallcycle.h"
66	#include "gromacs/utility/qsort_threadsafe.h"
67	#include "gromacs/pulling/pull_rotation.h"
68	#include "gromacs/mdlib/groupcoord.h"
69	#include "gromacs/math/utilities.h"
70
71	static char *RotStr = {"Enforced rotation:"};
72
73	/* Set the minimum weight for the determination of the slab centers */
74	#define WEIGHT_MIN(101.17549435E-38) (10GMX_FLOAT_MIN1.17549435E-38)
75
76	/* Helper structure for sorting positions along rotation vector */
77	typedef struct {
78	real xcproj; /* Projection of xc on the rotation vector */
79	int ind; /* Index of xc */
80	real m; /* Mass */
81	rvec x; /* Position */
82	rvec x_ref; /* Reference position */
83	} sort_along_vec_t;
84
85
86	/* Enforced rotation / flexible: determine the angle of each slab */
87	typedef struct gmx_slabdata
88	{
89	int nat; /* Number of atoms belonging to this slab */
90	rvec x; / The positions belonging to this slab. In
91	general, this should be all positions of the
92	whole rotation group, but we leave those away
93	that have a small enough weight */
94	rvec ref; / Same for reference */
95	real weight; / The weight for each atom */
96	} t_gmx_slabdata;
97
98
99	/* Helper structure for potential fitting */
100	typedef struct gmx_potfit
101	{
102	real degangle; / Set of angles for which the potential is
103	calculated. The optimum fit is determined as
104	the angle for with the potential is minimal */
105	real V; / Potential for the different angles */
106	matrix rotmat; / Rotation matrix corresponding to the angles */
107	} t_gmx_potfit;
108
109
110	/* Enforced rotation data for all groups */
111	typedef struct gmx_enfrot
112	{
113	FILE out_rot; / Output file for rotation data */
114	FILE out_torque; / Output file for torque data */
115	FILE out_angles; / Output file for slab angles for flexible type */
116	FILE out_slabs; / Output file for slab centers */
117	int bufsize; /* Allocation size of buf */
118	rvec xbuf; / Coordinate buffer variable for sorting */
119	real mbuf; / Masses buffer variable for sorting */
120	sort_along_vec_t data; / Buffer variable needed for position sorting */
121	real mpi_inbuf; / MPI buffer */
122	real mpi_outbuf; / MPI buffer */
123	int mpi_bufsize; /* Allocation size of in & outbuf */
124	unsigned long Flags; /* mdrun flags */
125	gmx_bool bOut; /* Used to skip first output when appending to
126	* avoid duplicate entries in rotation outfiles */
127	} t_gmx_enfrot;
128
129
130	/* Global enforced rotation data for a single rotation group */
131	typedef struct gmx_enfrotgrp
132	{
133	real degangle; /* Rotation angle in degrees */
134	matrix rotmat; /* Rotation matrix */
135	atom_id ind_loc; / Local rotation indices */
136	int nat_loc; /* Number of local group atoms */
137	int nalloc_loc; /* Allocation size for ind_loc and weight_loc */
138
139	real V; /* Rotation potential for this rotation group */
140	rvec f_rot_loc; / Array to store the forces on the local atoms
141	resulting from enforced rotation potential */
142
143	/* Collective coordinates for the whole rotation group */
144	real xc_ref_length; / Length of each x_rotref vector after x_rotref
145	has been put into origin */
146	int xc_ref_ind; / Position of each local atom in the collective
147	array */
148	rvec xc_center; /* Center of the rotation group positions, may
149	be mass weighted */
150	rvec xc_ref_center; /* dito, for the reference positions */
151	rvec xc; / Current (collective) positions */
152	ivec xc_shifts; / Current (collective) shifts */
153	ivec xc_eshifts; / Extra shifts since last DD step */
154	rvec xc_old; / Old (collective) positions */
155	rvec xc_norm; / Normalized form of the current positions */
156	rvec xc_ref_sorted; / Reference positions (sorted in the same order
157	as xc when sorted) */
158	int xc_sortind; / Where is a position found after sorting? */
159	real mc; / Collective masses */
160	real *mc_sorted;
161	real invmass; /* one over the total mass of the rotation group */
162
163	real torque_v; /* Torque in the direction of rotation vector */
164	real angle_v; /* Actual angle of the whole rotation group */
165	/* Fixed rotation only */
166	real weight_v; /* Weights for angle determination */
167	rvec xr_loc; / Local reference coords, correctly rotated */
168	rvec x_loc_pbc; / Local current coords, correct PBC image */
169	real m_loc; / Masses of the current local atoms */
170
171	/* Flexible rotation only */
172	int nslabs_alloc; /* For this many slabs memory is allocated */
173	int slab_first; /* Lowermost slab for that the calculation needs
174	to be performed at a given time step */
175	int slab_last; /* Uppermost slab ... */
176	int slab_first_ref; /* First slab for which ref. center is stored */
177	int slab_last_ref; /* Last ... */
178	int slab_buffer; /* Slab buffer region around reference slabs */
179	int firstatom; / First relevant atom for a slab */
180	int lastatom; / Last relevant atom for a slab */
181	rvec slab_center; / Gaussian-weighted slab center */
182	rvec slab_center_ref; / Gaussian-weighted slab center for the
183	reference positions */
184	real slab_weights; / Sum of gaussian weights in a slab */
185	real slab_torque_v; / Torque T = r x f for each slab. */
186	/* torque_v = m.v = angular momentum in the
187	direction of v */
188	real max_beta; /* min_gaussian from inputrec->rotgrp is the
189	minimum value the gaussian must have so that
190	the force is actually evaluated max_beta is
191	just another way to put it */
192	real gn_atom; / Precalculated gaussians for a single atom */
193	int gn_slabind; / Tells to which slab each precalculated gaussian
194	belongs */
195	rvec slab_innersumvec; / Inner sum of the flexible2 potential per slab;
196	this is precalculated for optimization reasons */
197	t_gmx_slabdata slab_data; / Holds atom positions and gaussian weights
198	of atoms belonging to a slab */
199
200	/* For potential fits with varying angle: */
201	t_gmx_potfit PotAngleFit; / Used for fit type 'potential' */
202	} t_gmx_enfrotgrp;
203
204
205	/* Activate output of forces for correctness checks */
206	/* #define PRINT_FORCES */
207	#ifdef PRINT_FORCES
208	#define PRINT_FORCE_J fprintf(stderrstderr, "f%d = %15.8f %15.8f %15.8f\n", erg->xc_ref_ind[j], erg->f_rot_loc[j][XX0], erg->f_rot_loc[j][YY1], erg->f_rot_loc[j][ZZ2]);
209	#define PRINT_POT_TAU if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1))) { \
210	fprintf(stderrstderr, "potential = %15.8f\n" "torque = %15.8f\n", erg->V, erg->torque_v); \
211	}
212	#else
213	#define PRINT_FORCE_J
214	#define PRINT_POT_TAU
215	#endif
216
217	/* Shortcuts for often used queries */
218	#define ISFLEX(rg)( (rg->eType == erotgFLEX) \|\| (rg->eType == erotgFLEXT) \|\| (rg->eType == erotgFLEX2) \|\| (rg->eType == erotgFLEX2T ) ) ( (rg->eType == erotgFLEX) \|\| (rg->eType == erotgFLEXT) \|\| (rg->eType == erotgFLEX2) \|\| (rg->eType == erotgFLEX2T) )
219	#define ISCOLL(rg)( (rg->eType == erotgFLEX) \|\| (rg->eType == erotgFLEXT) \|\| (rg->eType == erotgFLEX2) \|\| (rg->eType == erotgFLEX2T ) \|\| (rg->eType == erotgRMPF) \|\| (rg->eType == erotgRM2PF ) ) ( (rg->eType == erotgFLEX) \|\| (rg->eType == erotgFLEXT) \|\| (rg->eType == erotgFLEX2) \|\| (rg->eType == erotgFLEX2T) \|\| (rg->eType == erotgRMPF) \|\| (rg->eType == erotgRM2PF) )
220
221
222	/* Does any of the rotation groups use slab decomposition? */
223	static gmx_bool HaveFlexibleGroups(t_rot *rot)
224	{
225	int g;
226	t_rotgrp *rotg;
227
228
229	for (g = 0; g < rot->ngrp; g++)
230	{
231	rotg = &rot->grp[g];
232	if (ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) ))
233	{
234	return TRUE1;
235	}
236	}
237
238	return FALSE0;
239	}
240
241
242	/* Is for any group the fit angle determined by finding the minimum of the
243	* rotation potential? */
244	static gmx_bool HavePotFitGroups(t_rot *rot)
245	{
246	int g;
247	t_rotgrp *rotg;
248
249
250	for (g = 0; g < rot->ngrp; g++)
251	{
252	rotg = &rot->grp[g];
253	if (erotgFitPOT == rotg->eFittype)
254	{
255	return TRUE1;
256	}
257	}
258
259	return FALSE0;
260	}
261
262
263	static double** allocate_square_matrix(int dim)
264	{
265	int i;
266	double** mat = NULL((void*)0);
267
268
269	snew(mat, dim)(mat) = save_calloc("mat", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 269, (dim), sizeof(*(mat)));
270	for (i = 0; i < dim; i++)
271	{
272	snew(mat[i], dim)(mat[i]) = save_calloc("mat[i]", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 272, (dim), sizeof(*(mat[i])));
273	}
274
275	return mat;
276	}
277
278
279	static void free_square_matrix(double** mat, int dim)
280	{
281	int i;
282
283
284	for (i = 0; i < dim; i++)
285	{
286	sfree(mat[i])save_free("mat[i]", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 286, (mat[i]));
287	}
288	sfree(mat)save_free("mat", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 288, (mat));
289	}
290
291
292	/* Return the angle for which the potential is minimal */
293	static real get_fitangle(t_rotgrp *rotg, gmx_enfrotgrp_t erg)
294	{
295	int i;
296	real fitangle = -999.9;
297	real pot_min = GMX_FLOAT_MAX3.40282346E+38;
298	t_gmx_potfit *fit;
299
300
301	fit = erg->PotAngleFit;
302
303	for (i = 0; i < rotg->PotAngle_nstep; i++)
304	{
305	if (fit->V[i] < pot_min)
306	{
307	pot_min = fit->V[i];
308	fitangle = fit->degangle[i];
309	}
310	}
311
312	return fitangle;
313	}
314
315
316	/* Reduce potential angle fit data for this group at this time step? */
317	static gmx_inlineinline gmx_bool bPotAngle(t_rot rot, t_rotgrp rotg, gmx_int64_t step)
318	{
319	return ( (erotgFitPOT == rotg->eFittype) && (do_per_step(step, rot->nstsout) \|\| do_per_step(step, rot->nstrout)) );
320	}
321
322	/* Reduce slab torqe data for this group at this time step? */
323	static gmx_inlineinline gmx_bool bSlabTau(t_rot rot, t_rotgrp rotg, gmx_int64_t step)
324	{
325	return ( (ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) )) && do_per_step(step, rot->nstsout) );
326	}
327
328	/* Output rotation energy, torques, etc. for each rotation group */
329	static void reduce_output(t_commrec cr, t_rot rot, real t, gmx_int64_t step)
330	{
331	int g, i, islab, nslabs = 0;
332	int count; /* MPI element counter */
333	t_rotgrp *rotg;
334	gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
335	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
336	real fitangle;
337	gmx_bool bFlex;
338
339
340	er = rot->enfrot;
341
342	/* Fill the MPI buffer with stuff to reduce. If items are added for reduction
343	* here, the MPI buffer size has to be enlarged also in calc_mpi_bufsize() */
344	if (PAR(cr)((cr)->nnodes > 1))
345	{
346	count = 0;
347	for (g = 0; g < rot->ngrp; g++)
348	{
349	rotg = &rot->grp[g];
350	erg = rotg->enfrotgrp;
351	nslabs = erg->slab_last - erg->slab_first + 1;
352	er->mpi_inbuf[count++] = erg->V;
353	er->mpi_inbuf[count++] = erg->torque_v;
354	er->mpi_inbuf[count++] = erg->angle_v;
355	er->mpi_inbuf[count++] = erg->weight_v; /* weights are not needed for flex types, but this is just a single value */
356
357	if (bPotAngle(rot, rotg, step))
358	{
359	for (i = 0; i < rotg->PotAngle_nstep; i++)
360	{
361	er->mpi_inbuf[count++] = erg->PotAngleFit->V[i];
362	}
363	}
364	if (bSlabTau(rot, rotg, step))
365	{
366	for (i = 0; i < nslabs; i++)
367	{
368	er->mpi_inbuf[count++] = erg->slab_torque_v[i];
369	}
370	}
371	}
372	if (count > er->mpi_bufsize)
373	{
374	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 374, "%s MPI buffer overflow, please report this error.", RotStr);
375	}
376
377	#ifdef GMX_MPI
378	MPI_ReducetMPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REALTMPI_FLOAT, MPI_SUMTMPI_SUM, MASTERRANK(cr)(0), cr->mpi_comm_mygroup);
379	#endif
380
381	/* Copy back the reduced data from the buffer on the master */
382	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
383	{
384	count = 0;
385	for (g = 0; g < rot->ngrp; g++)
386	{
387	rotg = &rot->grp[g];
388	erg = rotg->enfrotgrp;
389	nslabs = erg->slab_last - erg->slab_first + 1;
390	erg->V = er->mpi_outbuf[count++];
391	erg->torque_v = er->mpi_outbuf[count++];
392	erg->angle_v = er->mpi_outbuf[count++];
393	erg->weight_v = er->mpi_outbuf[count++];
394
395	if (bPotAngle(rot, rotg, step))
396	{
397	for (i = 0; i < rotg->PotAngle_nstep; i++)
398	{
399	erg->PotAngleFit->V[i] = er->mpi_outbuf[count++];
400	}
401	}
402	if (bSlabTau(rot, rotg, step))
403	{
404	for (i = 0; i < nslabs; i++)
405	{
406	erg->slab_torque_v[i] = er->mpi_outbuf[count++];
407	}
408	}
409	}
410	}
411	}
412
413	/* Output */
414	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
415	{
416	/* Angle and torque for each rotation group */
417	for (g = 0; g < rot->ngrp; g++)
418	{
419	rotg = &rot->grp[g];
420	bFlex = ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) );
421
422	erg = rotg->enfrotgrp;
423
424	/* Output to main rotation output file: */
425	if (do_per_step(step, rot->nstrout) )
426	{
427	if (erotgFitPOT == rotg->eFittype)
428	{
429	fitangle = get_fitangle(rotg, erg);
430	}
431	else
432	{
433	if (bFlex)
434	{
435	fitangle = erg->angle_v; /* RMSD fit angle */
436	}
437	else
438	{
439	fitangle = (erg->angle_v/erg->weight_v)180.0M_1_PI0.31830988618379067154;
440	}
441	}
442	fprintf(er->out_rot, "%12.4f", fitangle);
443	fprintf(er->out_rot, "%12.3e", erg->torque_v);
444	fprintf(er->out_rot, "%12.3e", erg->V);
445	}
446
447	if (do_per_step(step, rot->nstsout) )
448	{
449	/* Output to torque log file: */
450	if (bFlex)
451	{
452	fprintf(er->out_torque, "%12.3e%6d", t, g);
453	for (i = erg->slab_first; i <= erg->slab_last; i++)
454	{
455	islab = i - erg->slab_first; /* slab index */
456	/* Only output if enough weight is in slab */
457	if (erg->slab_weights[islab] > rotg->min_gaussian)
458	{
459	fprintf(er->out_torque, "%6d%12.3e", i, erg->slab_torque_v[islab]);
460	}
461	}
462	fprintf(er->out_torque, "\n");
463	}
464
465	/* Output to angles log file: */
466	if (erotgFitPOT == rotg->eFittype)
467	{
468	fprintf(er->out_angles, "%12.3e%6d%12.4f", t, g, erg->degangle);
469	/* Output energies at a set of angles around the reference angle */
470	for (i = 0; i < rotg->PotAngle_nstep; i++)
471	{
472	fprintf(er->out_angles, "%12.3e", erg->PotAngleFit->V[i]);
473	}
474	fprintf(er->out_angles, "\n");
475	}
476	}
477	}
478	if (do_per_step(step, rot->nstrout) )
479	{
480	fprintf(er->out_rot, "\n");
481	}
482	}
483	}
484
485
486	/* Add the forces from enforced rotation potential to the local forces.
487	* Should be called after the SR forces have been evaluated */
488	extern real add_rot_forces(t_rot rot, rvec f[], t_commrec cr, gmx_int64_t step, real t)
489	{
490	int g, l, ii;
491	t_rotgrp *rotg;
492	gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
493	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
494	real Vrot = 0.0; /* If more than one rotation group is present, Vrot
495	assembles the local parts from all groups */
496
497
498	er = rot->enfrot;
499
500	/* Loop over enforced rotation groups (usually 1, though)
501	* Apply the forces from rotation potentials */
502	for (g = 0; g < rot->ngrp; g++)
503	{
504	rotg = &rot->grp[g];
505	erg = rotg->enfrotgrp;
506	Vrot += erg->V; /* add the local parts from the nodes */
507	for (l = 0; l < erg->nat_loc; l++)
508	{
509	/* Get the right index of the local force */
510	ii = erg->ind_loc[l];
511	/* Add */
512	rvec_inc(f[ii], erg->f_rot_loc[l]);
513	}
514	}
515
516	/* Reduce energy,torque, angles etc. to get the sum values (per rotation group)
517	* on the master and output these values to file. */
518	if ( (do_per_step(step, rot->nstrout) \|\| do_per_step(step, rot->nstsout)) && er->bOut)
519	{
520	reduce_output(cr, rot, t, step);
521	}
522
523	/* When appending, er->bOut is FALSE the first time to avoid duplicate entries */
524	er->bOut = TRUE1;
525
526	PRINT_POT_TAU
527
528	return Vrot;
529	}
530
531
532	/* The Gaussian norm is chosen such that the sum of the gaussian functions
533	* over the slabs is approximately 1.0 everywhere */
534	#define GAUSS_NORM0.569917543430618 0.569917543430618
535
536
537	/* Calculate the maximum beta that leads to a gaussian larger min_gaussian,
538	* also does some checks
539	*/
540	static double calc_beta_max(real min_gaussian, real slab_dist)
541	{
542	double sigma;
543	double arg;
544
545
546	/* Actually the next two checks are already made in grompp */
547	if (slab_dist <= 0)
548	{
549	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 549, "Slab distance of flexible rotation groups must be >=0 !");
550	}
551	if (min_gaussian <= 0)
552	{
553	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 553, "Cutoff value for Gaussian must be > 0. (You requested %f)");
554	}
555
556	/* Define the sigma value */
557	sigma = 0.7*slab_dist;
558
559	/* Calculate the argument for the logarithm and check that the log() result is negative or 0 */
560	arg = min_gaussian/GAUSS_NORM0.569917543430618;
561	if (arg > 1.0)
562	{
563	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 563, "min_gaussian of flexible rotation groups must be <%g", GAUSS_NORM0.569917543430618);
564	}
565
566	return sqrt(-2.0sigmasigma*log(min_gaussian/GAUSS_NORM0.569917543430618));
567	}
568
569
570	static gmx_inlineinline real calc_beta(rvec curr_x, t_rotgrp *rotg, int n)
571	{
572	return iprod(curr_x, rotg->vec) - rotg->slab_dist * n;
573	}
574
575
576	static gmx_inlineinline real gaussian_weight(rvec curr_x, t_rotgrp *rotg, int n)
577	{
578	const real norm = GAUSS_NORM0.569917543430618;
579	real sigma;
580
581
582	/* Define the sigma value */
583	sigma = 0.7*rotg->slab_dist;
584	/* Calculate the Gaussian value of slab n for position curr_x */
585	return norm * exp( -0.5 * sqr( calc_beta(curr_x, rotg, n)/sigma ) );
586	}
587
588
589	/* Returns the weight in a single slab, also calculates the Gaussian- and mass-
590	* weighted sum of positions for that slab */
591	static real get_slab_weight(int j, t_rotgrp rotg, rvec xc[], real mc[], rvec x_weighted_sum)
592	{
593	rvec curr_x; /* The position of an atom */
594	rvec curr_x_weighted; /* The gaussian-weighted position */
595	real gaussian; /* A single gaussian weight */
596	real wgauss; /* gaussian times current mass */
597	real slabweight = 0.0; /* The sum of weights in the slab */
598	int i, islab;
599	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
600
601
602	erg = rotg->enfrotgrp;
603	clear_rvec(*x_weighted_sum);
604
605	/* Slab index */
606	islab = j - erg->slab_first;
607
608	/* Loop over all atoms in the rotation group */
609	for (i = 0; i < rotg->nat; i++)
610	{
611	copy_rvec(xc[i], curr_x);
612	gaussian = gaussian_weight(curr_x, rotg, j);
613	wgauss = gaussian * mc[i];
614	svmul(wgauss, curr_x, curr_x_weighted);
615	rvec_add(x_weighted_sum, curr_x_weighted, x_weighted_sum);
616	slabweight += wgauss;
617	} /* END of loop over rotation group atoms */
618
619	return slabweight;
620	}
621
622
623	static void get_slab_centers(
624	t_rotgrp rotg, / The rotation group information */
625	rvec xc, / The rotation group positions; will
626	typically be enfrotgrp->xc, but at first call
627	it is enfrotgrp->xc_ref */
628	real mc, / The masses of the rotation group atoms */
629	int g, /* The number of the rotation group */
630	real time, /* Used for output only */
631	FILE out_slabs, / For outputting center per slab information */
632	gmx_bool bOutStep, /* Is this an output step? */
633	gmx_bool bReference) /* If this routine is called from
634	init_rot_group we need to store
635	the reference slab centers */
636	{
637	int j, islab;
638	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
639
640
641	erg = rotg->enfrotgrp;
642
643	/* Loop over slabs */
644	for (j = erg->slab_first; j <= erg->slab_last; j++)
645	{
646	islab = j - erg->slab_first;
647	erg->slab_weights[islab] = get_slab_weight(j, rotg, xc, mc, &erg->slab_center[islab]);
648
649	/* We can do the calculations ONLY if there is weight in the slab! */
650	if (erg->slab_weights[islab] > WEIGHT_MIN(10*1.17549435E-38))
651	{
652	svmul(1.0/erg->slab_weights[islab], erg->slab_center[islab], erg->slab_center[islab]);
653	}
654	else
655	{
656	/* We need to check this here, since we divide through slab_weights
657	* in the flexible low-level routines! */
658	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 658, "Not enough weight in slab %d. Slab center cannot be determined!", j);
659	}
660
661	/* At first time step: save the centers of the reference structure */
662	if (bReference)
663	{
664	copy_rvec(erg->slab_center[islab], erg->slab_center_ref[islab]);
665	}
666	} /* END of loop over slabs */
667
668	/* Output on the master */
669	if ( (NULL((void*)0) != out_slabs) && bOutStep)
670	{
671	fprintf(out_slabs, "%12.3e%6d", time, g);
672	for (j = erg->slab_first; j <= erg->slab_last; j++)
673	{
674	islab = j - erg->slab_first;
675	fprintf(out_slabs, "%6d%12.3e%12.3e%12.3e",
676	j, erg->slab_center[islab][XX0], erg->slab_center[islab][YY1], erg->slab_center[islab][ZZ2]);
677	}
678	fprintf(out_slabs, "\n");
679	}
680	}
681
682
683	static void calc_rotmat(
684	rvec vec,
685	real degangle, /* Angle alpha of rotation at time t in degrees */
686	matrix rotmat) /* Rotation matrix */
687	{
688	real radangle; /* Rotation angle in radians */
689	real cosa; /* cosine alpha */
690	real sina; /* sine alpha */
691	real OMcosa; /* 1 - cos(alpha) */
692	real dumxy, dumxz, dumyz; /* save computations */
693	rvec rot_vec; /* Rotate around rot_vec ... */
694
695
696	radangle = degangle * M_PI3.14159265358979323846/180.0;
697	copy_rvec(vec, rot_vec );
698
699	/* Precompute some variables: */
700	cosa = cos(radangle);
701	sina = sin(radangle);
702	OMcosa = 1.0 - cosa;
703	dumxy = rot_vec[XX0]rot_vec[YY1]OMcosa;
704	dumxz = rot_vec[XX0]rot_vec[ZZ2]OMcosa;
705	dumyz = rot_vec[YY1]rot_vec[ZZ2]OMcosa;
706
707	/* Construct the rotation matrix for this rotation group: */
708	/* 1st column: */
709	rotmat[XX0][XX0] = cosa + rot_vec[XX0]rot_vec[XX0]OMcosa;
710	rotmat[YY1][XX0] = dumxy + rot_vec[ZZ2]*sina;
711	rotmat[ZZ2][XX0] = dumxz - rot_vec[YY1]*sina;
712	/* 2nd column: */
713	rotmat[XX0][YY1] = dumxy - rot_vec[ZZ2]*sina;
714	rotmat[YY1][YY1] = cosa + rot_vec[YY1]rot_vec[YY1]OMcosa;
715	rotmat[ZZ2][YY1] = dumyz + rot_vec[XX0]*sina;
716	/* 3rd column: */
717	rotmat[XX0][ZZ2] = dumxz + rot_vec[YY1]*sina;
718	rotmat[YY1][ZZ2] = dumyz - rot_vec[XX0]*sina;
719	rotmat[ZZ2][ZZ2] = cosa + rot_vec[ZZ2]rot_vec[ZZ2]OMcosa;
720
721	#ifdef PRINTMATRIX
722	int iii, jjj;
723
724	for (iii = 0; iii < 3; iii++)
725	{
726	for (jjj = 0; jjj < 3; jjj++)
727	{
728	fprintf(stderrstderr, " %10.8f ", rotmat[iii][jjj]);
729	}
730	fprintf(stderrstderr, "\n");
731	}
732	#endif
733	}
734
735
736	/* Calculates torque on the rotation axis tau = position x force */
737	static gmx_inlineinline real torque(
738	rvec rotvec, /* rotation vector; MUST be normalized! */
739	rvec force, /* force */
740	rvec x, /* position of atom on which the force acts */
741	rvec pivot) /* pivot point of rotation axis */
742	{
743	rvec vectmp, tau;
744
745
746	/* Subtract offset */
747	rvec_sub(x, pivot, vectmp);
748
749	/* position x force */
750	cprod(vectmp, force, tau);
751
752	/* Return the part of the torque which is parallel to the rotation vector */
753	return iprod(tau, rotvec);
754	}
755
756
757	/* Right-aligned output of value with standard width */
758	static void print_aligned(FILE fp, char str)
759	{
760	fprintf(fp, "%12s", str);
761	}
762
763
764	/* Right-aligned output of value with standard short width */
765	static void print_aligned_short(FILE fp, char str)
766	{
767	fprintf(fp, "%6s", str);
768	}
769
770
771	static FILE open_output_file(const char fn, int steps, const char what[])
772	{
773	FILE *fp;
774
775
776	fp = gmx_ffopen(fn, "w");
777
778	fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n",
779	what, steps, steps > 1 ? "s" : "");
780
781	return fp;
782	}
783
784
785	/* Open output file for slab center data. Call on master only */
786	static FILE open_slab_out(const char fn, t_rot *rot)
787	{
788	FILE *fp;
789	int g, i;
790	t_rotgrp *rotg;
791
792
793	if (rot->enfrot->Flags & MD_APPENDFILES(1<<15))
794	{
795	fp = gmx_fio_fopen(fn, "a");
796	}
797	else
798	{
799	fp = open_output_file(fn, rot->nstsout, "gaussian weighted slab centers");
800
801	for (g = 0; g < rot->ngrp; g++)
802	{
803	rotg = &rot->grp[g];
804	if (ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) ))
805	{
806	fprintf(fp, "# Rotation group %d (%s), slab distance %f nm, %s.\n",
807	g, erotg_names[rotg->eType], rotg->slab_dist,
808	rotg->bMassW ? "centers of mass" : "geometrical centers");
809	}
810	}
811
812	fprintf(fp, "# Reference centers are listed first (t=-1).\n");
813	fprintf(fp, "# The following columns have the syntax:\n");
814	fprintf(fp, "# ");
815	print_aligned_short(fp, "t");
816	print_aligned_short(fp, "grp");
817	/* Print legend for the first two entries only ... */
818	for (i = 0; i < 2; i++)
819	{
820	print_aligned_short(fp, "slab");
821	print_aligned(fp, "X center");
822	print_aligned(fp, "Y center");
823	print_aligned(fp, "Z center");
824	}
825	fprintf(fp, " ...\n");
826	fflush(fp);
827	}
828
829	return fp;
830	}
831
832
833	/* Adds 'buf' to 'str' */
834	static void add_to_string(char *str, char buf)
835	{
836	int len;
837
838
839	len = strlen(*str) + strlen(buf) + 1;
840	srenew(str, len)(str) = save_realloc("str", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 840, (str), (len), sizeof((str)));
841	strcat(*str, buf);
842	}
843
844
845	static void add_to_string_aligned(char *str, char buf)
846	{
847	char buf_aligned[STRLEN4096];
848
849	sprintf(buf_aligned, "%12s", buf);
850	add_to_string(str, buf_aligned);
851	}
852
853
854	/* Open output file and print some general information about the rotation groups.
855	* Call on master only */
856	static FILE open_rot_out(const char fn, t_rot *rot, const output_env_t oenv)
857	{
858	FILE *fp;
859	int g, nsets;
860	t_rotgrp *rotg;
861	const char **setname;
862	char buf[50], buf2[75];
863	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
864	gmx_bool bFlex;
865	char LegendStr = NULL((void)0);
866
867
868	if (rot->enfrot->Flags & MD_APPENDFILES(1<<15))
869	{
870	fp = gmx_fio_fopen(fn, "a");
871	}
872	else
873	{
874	fp = xvgropen(fn, "Rotation angles and energy", "Time (ps)", "angles (degrees) and energies (kJ/mol)", oenv);
875	fprintf(fp, "# Output of enforced rotation data is written in intervals of %d time step%s.\n#\n", rot->nstrout, rot->nstrout > 1 ? "s" : "");
876	fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector v.\n");
877	fprintf(fp, "# To obtain the vectorial torque, multiply tau with the group's rot_vec.\n");
878	fprintf(fp, "# For flexible groups, tau(t,n) from all slabs n have been summed in a single value tau(t) here.\n");
879	fprintf(fp, "# The torques tau(t,n) are found in the rottorque.log (-rt) output file\n");
880
881	for (g = 0; g < rot->ngrp; g++)
882	{
883	rotg = &rot->grp[g];
884	erg = rotg->enfrotgrp;
885	bFlex = ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) );
886
887	fprintf(fp, "#\n");
888	fprintf(fp, "# ROTATION GROUP %d, potential type '%s':\n", g, erotg_names[rotg->eType]);
889	fprintf(fp, "# rot_massw%d %s\n", g, yesno_names[rotg->bMassW]);
890	fprintf(fp, "# rot_vec%d %12.5e %12.5e %12.5e\n", g, rotg->vec[XX0], rotg->vec[YY1], rotg->vec[ZZ2]);
891	fprintf(fp, "# rot_rate%d %12.5e degrees/ps\n", g, rotg->rate);
892	fprintf(fp, "# rot_k%d %12.5e kJ/(mol*nm^2)\n", g, rotg->k);
893	if (rotg->eType == erotgISO \|\| rotg->eType == erotgPM \|\| rotg->eType == erotgRM \|\| rotg->eType == erotgRM2)
894	{
895	fprintf(fp, "# rot_pivot%d %12.5e %12.5e %12.5e nm\n", g, rotg->pivot[XX0], rotg->pivot[YY1], rotg->pivot[ZZ2]);
896	}
897
898	if (bFlex)
899	{
900	fprintf(fp, "# rot_slab_distance%d %f nm\n", g, rotg->slab_dist);
901	fprintf(fp, "# rot_min_gaussian%d %12.5e\n", g, rotg->min_gaussian);
902	}
903
904	/* Output the centers of the rotation groups for the pivot-free potentials */
905	if ((rotg->eType == erotgISOPF) \|\| (rotg->eType == erotgPMPF) \|\| (rotg->eType == erotgRMPF) \|\| (rotg->eType == erotgRM2PF
906	\|\| (rotg->eType == erotgFLEXT) \|\| (rotg->eType == erotgFLEX2T)) )
907	{
908	fprintf(fp, "# ref. grp. %d center %12.5e %12.5e %12.5e\n", g,
909	erg->xc_ref_center[XX0], erg->xc_ref_center[YY1], erg->xc_ref_center[ZZ2]);
910
911	fprintf(fp, "# grp. %d init.center %12.5e %12.5e %12.5e\n", g,
912	erg->xc_center[XX0], erg->xc_center[YY1], erg->xc_center[ZZ2]);
913	}
914
915	if ( (rotg->eType == erotgRM2) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T) )
916	{
917	fprintf(fp, "# rot_eps%d %12.5e nm^2\n", g, rotg->eps);
918	}
919	if (erotgFitPOT == rotg->eFittype)
920	{
921	fprintf(fp, "#\n");
922	fprintf(fp, "# theta_fit%d is determined by first evaluating the potential for %d angles around theta_ref%d.\n",
923	g, rotg->PotAngle_nstep, g);
924	fprintf(fp, "# The fit angle is the one with the smallest potential. It is given as the deviation\n");
925	fprintf(fp, "# from the reference angle, i.e. if theta_ref=X and theta_fit=Y, then the angle with\n");
926	fprintf(fp, "# minimal value of the potential is X+Y. Angular resolution is %g degrees.\n", rotg->PotAngle_step);
927	}
928	}
929
930	/* Print a nice legend */
931	snew(LegendStr, 1)(LegendStr) = save_calloc("LegendStr", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 931, (1), sizeof(*(LegendStr)));
932	LegendStr[0] = '\0';
933	sprintf(buf, "# %6s", "time");
934	add_to_string_aligned(&LegendStr, buf);
935
936	nsets = 0;
937	snew(setname, 4rot->ngrp)(setname) = save_calloc("setname", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 937, (4rot->ngrp), sizeof(*(setname)));
938
939	for (g = 0; g < rot->ngrp; g++)
940	{
941	rotg = &rot->grp[g];
942	sprintf(buf, "theta_ref%d", g);
943	add_to_string_aligned(&LegendStr, buf);
944
945	sprintf(buf2, "%s (degrees)", buf);
946	setname[nsets] = strdup(buf2)(__extension__ (__builtin_constant_p (buf2) && ((size_t )(const void )((buf2) + 1) - (size_t)(const void )(buf2) == 1) ? (((const char ) (buf2))[0] == '\0' ? (char ) calloc ( (size_t) 1, (size_t) 1) : ({ size_t __len = strlen (buf2) + 1 ; char __retval = (char ) malloc (__len); if (__retval != ( (void)0)) __retval = (char ) memcpy (__retval, buf2, __len) ; __retval; })) : __strdup (buf2)));
947	nsets++;
948	}
949	for (g = 0; g < rot->ngrp; g++)
950	{
951	rotg = &rot->grp[g];
952	bFlex = ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) );
953
954	/* For flexible axis rotation we use RMSD fitting to determine the
955	* actual angle of the rotation group */
956	if (bFlex \|\| erotgFitPOT == rotg->eFittype)
957	{
958	sprintf(buf, "theta_fit%d", g);
959	}
960	else
961	{
962	sprintf(buf, "theta_av%d", g);
963	}
964	add_to_string_aligned(&LegendStr, buf);
965	sprintf(buf2, "%s (degrees)", buf);
966	setname[nsets] = strdup(buf2)(__extension__ (__builtin_constant_p (buf2) && ((size_t )(const void )((buf2) + 1) - (size_t)(const void )(buf2) == 1) ? (((const char ) (buf2))[0] == '\0' ? (char ) calloc ( (size_t) 1, (size_t) 1) : ({ size_t __len = strlen (buf2) + 1 ; char __retval = (char ) malloc (__len); if (__retval != ( (void)0)) __retval = (char ) memcpy (__retval, buf2, __len) ; __retval; })) : __strdup (buf2)));
967	nsets++;
968
969	sprintf(buf, "tau%d", g);
970	add_to_string_aligned(&LegendStr, buf);
971	sprintf(buf2, "%s (kJ/mol)", buf);
972	setname[nsets] = strdup(buf2)(__extension__ (__builtin_constant_p (buf2) && ((size_t )(const void )((buf2) + 1) - (size_t)(const void )(buf2) == 1) ? (((const char ) (buf2))[0] == '\0' ? (char ) calloc ( (size_t) 1, (size_t) 1) : ({ size_t __len = strlen (buf2) + 1 ; char __retval = (char ) malloc (__len); if (__retval != ( (void)0)) __retval = (char ) memcpy (__retval, buf2, __len) ; __retval; })) : __strdup (buf2)));
973	nsets++;
974
975	sprintf(buf, "energy%d", g);
976	add_to_string_aligned(&LegendStr, buf);
977	sprintf(buf2, "%s (kJ/mol)", buf);
978	setname[nsets] = strdup(buf2)(__extension__ (__builtin_constant_p (buf2) && ((size_t )(const void )((buf2) + 1) - (size_t)(const void )(buf2) == 1) ? (((const char ) (buf2))[0] == '\0' ? (char ) calloc ( (size_t) 1, (size_t) 1) : ({ size_t __len = strlen (buf2) + 1 ; char __retval = (char ) malloc (__len); if (__retval != ( (void)0)) __retval = (char ) memcpy (__retval, buf2, __len) ; __retval; })) : __strdup (buf2)));
979	nsets++;
980	}
981	fprintf(fp, "#\n");
982
983	if (nsets > 1)
984	{
985	xvgr_legend(fp, nsets, setname, oenv);
986	}
987	sfree(setname)save_free("setname", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 987, (setname));
988
989	fprintf(fp, "#\n# Legend for the following data columns:\n");
990	fprintf(fp, "%s\n", LegendStr);
991	sfree(LegendStr)save_free("LegendStr", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 991, (LegendStr));
992
993	fflush(fp);
994	}
995
996	return fp;
997	}
998
999
1000	/* Call on master only */
1001	static FILE open_angles_out(const char fn, t_rot *rot)
1002	{
1003	int g, i;
1004	FILE *fp;
1005	t_rotgrp *rotg;
1006	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1007	char buf[100];
1008
1009
1010	if (rot->enfrot->Flags & MD_APPENDFILES(1<<15))
1011	{
1012	fp = gmx_fio_fopen(fn, "a");
1013	}
1014	else
1015	{
1016	/* Open output file and write some information about it's structure: */
1017	fp = open_output_file(fn, rot->nstsout, "rotation group angles");
1018	fprintf(fp, "# All angles given in degrees, time in ps.\n");
1019	for (g = 0; g < rot->ngrp; g++)
1020	{
1021	rotg = &rot->grp[g];
1022	erg = rotg->enfrotgrp;
1023
1024	/* Output for this group happens only if potential type is flexible or
1025	* if fit type is potential! */
1026	if (ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) ) \|\| (erotgFitPOT == rotg->eFittype) )
1027	{
1028	if (ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) ))
1029	{
1030	sprintf(buf, " slab distance %f nm, ", rotg->slab_dist);
1031	}
1032	else
1033	{
1034	buf[0] = '\0';
1035	}
1036
1037	fprintf(fp, "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n",
1038	g, erotg_names[rotg->eType], buf, erotg_fitnames[rotg->eFittype]);
1039
1040	/* Special type of fitting using the potential minimum. This is
1041	* done for the whole group only, not for the individual slabs. */
1042	if (erotgFitPOT == rotg->eFittype)
1043	{
1044	fprintf(fp, "# To obtain theta_fit%d, the potential is evaluated for %d angles around theta_ref%d\n", g, rotg->PotAngle_nstep, g);
1045	fprintf(fp, "# The fit angle in the rotation standard outfile is the one with minimal energy E(theta_fit) [kJ/mol].\n");
1046	fprintf(fp, "#\n");
1047	}
1048
1049	fprintf(fp, "# Legend for the group %d data columns:\n", g);
1050	fprintf(fp, "# ");
1051	print_aligned_short(fp, "time");
1052	print_aligned_short(fp, "grp");
1053	print_aligned(fp, "theta_ref");
1054
1055	if (erotgFitPOT == rotg->eFittype)
1056	{
1057	/* Output the set of angles around the reference angle */
1058	for (i = 0; i < rotg->PotAngle_nstep; i++)
1059	{
1060	sprintf(buf, "E(%g)", erg->PotAngleFit->degangle[i]);
1061	print_aligned(fp, buf);
1062	}
1063	}
1064	else
1065	{
1066	/* Output fit angle for each slab */
1067	print_aligned_short(fp, "slab");
1068	print_aligned_short(fp, "atoms");
1069	print_aligned(fp, "theta_fit");
1070	print_aligned_short(fp, "slab");
1071	print_aligned_short(fp, "atoms");
1072	print_aligned(fp, "theta_fit");
1073	fprintf(fp, " ...");
1074	}
1075	fprintf(fp, "\n");
1076	}
1077	}
1078	fflush(fp);
1079	}
1080
1081	return fp;
1082	}
1083
1084
1085	/* Open torque output file and write some information about it's structure.
1086	* Call on master only */
1087	static FILE open_torque_out(const char fn, t_rot *rot)
1088	{
1089	FILE *fp;
1090	int g;
1091	t_rotgrp *rotg;
1092
1093
1094	if (rot->enfrot->Flags & MD_APPENDFILES(1<<15))
1095	{
1096	fp = gmx_fio_fopen(fn, "a");
1097	}
1098	else
1099	{
1100	fp = open_output_file(fn, rot->nstsout, "torques");
1101
1102	for (g = 0; g < rot->ngrp; g++)
1103	{
1104	rotg = &rot->grp[g];
1105	if (ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) ))
1106	{
1107	fprintf(fp, "# Rotation group %d (%s), slab distance %f nm.\n", g, erotg_names[rotg->eType], rotg->slab_dist);
1108	fprintf(fp, "# The scalar tau is the torque (kJ/mol) in the direction of the rotation vector.\n");
1109	fprintf(fp, "# To obtain the vectorial torque, multiply tau with\n");
1110	fprintf(fp, "# rot_vec%d %10.3e %10.3e %10.3e\n", g, rotg->vec[XX0], rotg->vec[YY1], rotg->vec[ZZ2]);
1111	fprintf(fp, "#\n");
1112	}
1113	}
1114	fprintf(fp, "# Legend for the following data columns: (tau=torque for that slab):\n");
1115	fprintf(fp, "# ");
1116	print_aligned_short(fp, "t");
1117	print_aligned_short(fp, "grp");
1118	print_aligned_short(fp, "slab");
1119	print_aligned(fp, "tau");
1120	print_aligned_short(fp, "slab");
1121	print_aligned(fp, "tau");
1122	fprintf(fp, " ...\n");
1123	fflush(fp);
1124	}
1125
1126	return fp;
1127	}
1128
1129
1130	static void swap_val(double* vec, int i, int j)
1131	{
1132	double tmp = vec[j];
1133
1134
1135	vec[j] = vec[i];
1136	vec[i] = tmp;
1137	}
1138
1139
1140	static void swap_col(double **mat, int i, int j)
1141	{
1142	double tmp[3] = {mat[0][j], mat[1][j], mat[2][j]};
1143
1144
1145	mat[0][j] = mat[0][i];
1146	mat[1][j] = mat[1][i];
1147	mat[2][j] = mat[2][i];
1148
1149	mat[0][i] = tmp[0];
1150	mat[1][i] = tmp[1];
1151	mat[2][i] = tmp[2];
1152	}
1153
1154
1155	/* Eigenvectors are stored in columns of eigen_vec */
1156	static void diagonalize_symmetric(
1157	double **matrix,
1158	double **eigen_vec,
1159	double eigenval[3])
1160	{
1161	int n_rot;
1162
1163
1164	jacobi(matrix, 3, eigenval, eigen_vec, &n_rot);
1165
1166	/* sort in ascending order */
1167	if (eigenval[0] > eigenval[1])
1168	{
1169	swap_val(eigenval, 0, 1);
1170	swap_col(eigen_vec, 0, 1);
1171	}
1172	if (eigenval[1] > eigenval[2])
1173	{
1174	swap_val(eigenval, 1, 2);
1175	swap_col(eigen_vec, 1, 2);
1176	}
1177	if (eigenval[0] > eigenval[1])
1178	{
1179	swap_val(eigenval, 0, 1);
1180	swap_col(eigen_vec, 0, 1);
1181	}
1182	}
1183
1184
1185	static void align_with_z(
1186	rvec* s, /* Structure to align */
1187	int natoms,
1188	rvec axis)
1189	{
1190	int i, j, k;
1191	rvec zet = {0.0, 0.0, 1.0};
1192	rvec rot_axis = {0.0, 0.0, 0.0};
1193	rvec rotated_str = NULL((void)0);
1194	real ooanorm;
1195	real angle;
1196	matrix rotmat;
1197
1198
1199	snew(rotated_str, natoms)(rotated_str) = save_calloc("rotated_str", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1199, (natoms), sizeof(*(rotated_str)));
1200
1201	/* Normalize the axis */
1202	ooanorm = 1.0/norm(axis);
1203	svmul(ooanorm, axis, axis);
1204
1205	/* Calculate the angle for the fitting procedure */
1206	cprod(axis, zet, rot_axis);
1207	angle = acos(axis[2]);
1208	if (angle < 0.0)
1209	{
1210	angle += M_PI3.14159265358979323846;
1211	}
1212
1213	/* Calculate the rotation matrix */
1214	calc_rotmat(rot_axis, angle*180.0/M_PI3.14159265358979323846, rotmat);
1215
1216	/* Apply the rotation matrix to s */
1217	for (i = 0; i < natoms; i++)
1218	{
1219	for (j = 0; j < 3; j++)
1220	{
1221	for (k = 0; k < 3; k++)
1222	{
1223	rotated_str[i][j] += rotmat[j][k]*s[i][k];
1224	}
1225	}
1226	}
1227
1228	/* Rewrite the rotated structure to s */
1229	for (i = 0; i < natoms; i++)
1230	{
1231	for (j = 0; j < 3; j++)
1232	{
1233	s[i][j] = rotated_str[i][j];
1234	}
1235	}
1236
1237	sfree(rotated_str)save_free("rotated_str", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1237, (rotated_str));
1238	}
1239
1240
1241	static void calc_correl_matrix(rvec* Xstr, rvec* Ystr, double** Rmat, int natoms)
1242	{
1243	int i, j, k;
1244
1245
1246	for (i = 0; i < 3; i++)
1247	{
1248	for (j = 0; j < 3; j++)
1249	{
1250	Rmat[i][j] = 0.0;
1251	}
1252	}
1253
1254	for (i = 0; i < 3; i++)
1255	{
1256	for (j = 0; j < 3; j++)
1257	{
1258	for (k = 0; k < natoms; k++)
1259	{
1260	Rmat[i][j] += Ystr[k][i] * Xstr[k][j];
1261	}
1262	}
1263	}
1264	}
1265
1266
1267	static void weigh_coords(rvec* str, real* weight, int natoms)
1268	{
1269	int i, j;
1270
1271
1272	for (i = 0; i < natoms; i++)
1273	{
1274	for (j = 0; j < 3; j++)
1275	{
1276	str[i][j] *= sqrt(weight[i]);
1277	}
1278	}
1279	}
1280
1281
1282	static real opt_angle_analytic(
1283	rvec* ref_s,
1284	rvec* act_s,
1285	real* weight,
1286	int natoms,
1287	rvec ref_com,
1288	rvec act_com,
1289	rvec axis)
1290	{
1291	int i, j, k;
1292	rvec ref_s_1 = NULL((void)0);
1293	rvec act_s_1 = NULL((void)0);
1294	rvec shift;
1295	double Rmat, RtR, **eigvec;
1296	double eigval[3];
1297	double V[3][3], WS[3][3];
1298	double rot_matrix[3][3];
1299	double opt_angle;
1300
1301
1302	/* Do not change the original coordinates */
1303	snew(ref_s_1, natoms)(ref_s_1) = save_calloc("ref_s_1", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1303, (natoms), sizeof(*(ref_s_1)));
1304	snew(act_s_1, natoms)(act_s_1) = save_calloc("act_s_1", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1304, (natoms), sizeof(*(act_s_1)));
1305	for (i = 0; i < natoms; i++)
1306	{
1307	copy_rvec(ref_s[i], ref_s_1[i]);
1308	copy_rvec(act_s[i], act_s_1[i]);
1309	}
1310
1311	/* Translate the structures to the origin */
1312	shift[XX0] = -ref_com[XX0];
1313	shift[YY1] = -ref_com[YY1];
1314	shift[ZZ2] = -ref_com[ZZ2];
1315	translate_x(ref_s_1, natoms, shift);
1316
1317	shift[XX0] = -act_com[XX0];
1318	shift[YY1] = -act_com[YY1];
1319	shift[ZZ2] = -act_com[ZZ2];
1320	translate_x(act_s_1, natoms, shift);
1321
1322	/* Align rotation axis with z */
1323	align_with_z(ref_s_1, natoms, axis);
1324	align_with_z(act_s_1, natoms, axis);
1325
1326	/* Correlation matrix */
1327	Rmat = allocate_square_matrix(3);
1328
1329	for (i = 0; i < natoms; i++)
1330	{
1331	ref_s_1[i][2] = 0.0;
1332	act_s_1[i][2] = 0.0;
1333	}
1334
1335	/* Weight positions with sqrt(weight) */
1336	if (NULL((void*)0) != weight)
1337	{
1338	weigh_coords(ref_s_1, weight, natoms);
1339	weigh_coords(act_s_1, weight, natoms);
1340	}
1341
1342	/* Calculate correlation matrices R=YXt (X=ref_s; Y=act_s) */
1343	calc_correl_matrix(ref_s_1, act_s_1, Rmat, natoms);
1344
1345	/* Calculate RtR */
1346	RtR = allocate_square_matrix(3);
1347	for (i = 0; i < 3; i++)
1348	{
1349	for (j = 0; j < 3; j++)
1350	{
1351	for (k = 0; k < 3; k++)
1352	{
1353	RtR[i][j] += Rmat[k][i] * Rmat[k][j];
1354	}
1355	}
1356	}
1357	/* Diagonalize RtR */
1358	snew(eigvec, 3)(eigvec) = save_calloc("eigvec", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1358, (3), sizeof(*(eigvec)));
1359	for (i = 0; i < 3; i++)
1360	{
1361	snew(eigvec[i], 3)(eigvec[i]) = save_calloc("eigvec[i]", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1361, (3), sizeof(*(eigvec[i])));
1362	}
1363
1364	diagonalize_symmetric(RtR, eigvec, eigval);
1365	swap_col(eigvec, 0, 1);
1366	swap_col(eigvec, 1, 2);
1367	swap_val(eigval, 0, 1);
1368	swap_val(eigval, 1, 2);
1369
1370	/* Calculate V */
1371	for (i = 0; i < 3; i++)
1372	{
1373	for (j = 0; j < 3; j++)
1374	{
1375	V[i][j] = 0.0;
1376	WS[i][j] = 0.0;
1377	}
1378	}
1379
1380	for (i = 0; i < 2; i++)
1381	{
1382	for (j = 0; j < 2; j++)
1383	{
1384	WS[i][j] = eigvec[i][j] / sqrt(eigval[j]);
1385	}
1386	}
1387
1388	for (i = 0; i < 3; i++)
1389	{
1390	for (j = 0; j < 3; j++)
1391	{
1392	for (k = 0; k < 3; k++)
1393	{
1394	V[i][j] += Rmat[i][k]*WS[k][j];
1395	}
1396	}
1397	}
1398	free_square_matrix(Rmat, 3);
1399
1400	/* Calculate optimal rotation matrix */
1401	for (i = 0; i < 3; i++)
1402	{
1403	for (j = 0; j < 3; j++)
1404	{
1405	rot_matrix[i][j] = 0.0;
1406	}
1407	}
1408
1409	for (i = 0; i < 3; i++)
1410	{
1411	for (j = 0; j < 3; j++)
1412	{
1413	for (k = 0; k < 3; k++)
1414	{
1415	rot_matrix[i][j] += eigvec[i][k]*V[j][k];
1416	}
1417	}
1418	}
1419	rot_matrix[2][2] = 1.0;
1420
1421	/* In some cases abs(rot_matrix[0][0]) can be slighly larger
1422	* than unity due to numerical inacurracies. To be able to calculate
1423	* the acos function, we put these values back in range. */
1424	if (rot_matrix[0][0] > 1.0)
1425	{
1426	rot_matrix[0][0] = 1.0;
1427	}
1428	else if (rot_matrix[0][0] < -1.0)
1429	{
1430	rot_matrix[0][0] = -1.0;
1431	}
1432
1433	/* Determine the optimal rotation angle: */
1434	opt_angle = (-1.0)acos(rot_matrix[0][0])180.0/M_PI3.14159265358979323846;
1435	if (rot_matrix[0][1] < 0.0)
1436	{
1437	opt_angle = (-1.0)*opt_angle;
1438	}
1439
1440	/* Give back some memory */
1441	free_square_matrix(RtR, 3);
1442	sfree(ref_s_1)save_free("ref_s_1", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1442, (ref_s_1));
1443	sfree(act_s_1)save_free("act_s_1", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1443, (act_s_1));
1444	for (i = 0; i < 3; i++)
1445	{
1446	sfree(eigvec[i])save_free("eigvec[i]", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1446, (eigvec[i]));
1447	}
1448	sfree(eigvec)save_free("eigvec", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 1448, (eigvec));
1449
1450	return (real) opt_angle;
1451	}
1452
1453
1454	/* Determine angle of the group by RMSD fit to the reference */
1455	/* Not parallelized, call this routine only on the master */
1456	static real flex_fit_angle(t_rotgrp *rotg)
1457	{
1458	int i;
1459	rvec fitcoords = NULL((void)0);
1460	rvec center; /* Center of positions passed to the fit routine */
1461	real fitangle; /* Angle of the rotation group derived by fitting */
1462	rvec coord;
1463	real scal;
1464	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1465
1466
1467	erg = rotg->enfrotgrp;
1468
1469	/* Get the center of the rotation group.
1470	* Note, again, erg->xc has been sorted in do_flexible */
1471	get_center(erg->xc, erg->mc_sorted, rotg->nat, center);
1472
1473	/* === Determine the optimal fit angle for the rotation group === */
1474	if (rotg->eFittype == erotgFitNORM)
1475	{
1476	/* Normalize every position to it's reference length */
1477	for (i = 0; i < rotg->nat; i++)
1478	{
1479	/* Put the center of the positions into the origin */
1480	rvec_sub(erg->xc[i], center, coord);
1481	/* Determine the scaling factor for the length: */
1482	scal = erg->xc_ref_length[erg->xc_sortind[i]] / norm(coord);
1483	/* Get position, multiply with the scaling factor and save */
1484	svmul(scal, coord, erg->xc_norm[i]);
1485	}
1486	fitcoords = erg->xc_norm;
1487	}
1488	else
1489	{
1490	fitcoords = erg->xc;
1491	}
1492	/* From the point of view of the current positions, the reference has rotated
1493	* backwards. Since we output the angle relative to the fixed reference,
1494	* we need the minus sign. */
1495	fitangle = -opt_angle_analytic(erg->xc_ref_sorted, fitcoords, erg->mc_sorted,
1496	rotg->nat, erg->xc_ref_center, center, rotg->vec);
1497
1498	return fitangle;
1499	}
1500
1501
1502	/* Determine actual angle of each slab by RMSD fit to the reference */
1503	/* Not parallelized, call this routine only on the master */
1504	static void flex_fit_angle_perslab(
1505	int g,
1506	t_rotgrp *rotg,
1507	double t,
1508	real degangle,
1509	FILE *fp)
1510	{
1511	int i, l, n, islab, ind;
1512	rvec curr_x, ref_x;
1513	rvec act_center; /* Center of actual positions that are passed to the fit routine */
1514	rvec ref_center; /* Same for the reference positions */
1515	real fitangle; /* Angle of a slab derived from an RMSD fit to
1516	* the reference structure at t=0 */
1517	t_gmx_slabdata *sd;
1518	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1519	real OOm_av; /* 1/average_mass of a rotation group atom */
1520	real m_rel; /* Relative mass of a rotation group atom */
1521
1522
1523	erg = rotg->enfrotgrp;
1524
1525	/* Average mass of a rotation group atom: */
1526	OOm_av = erg->invmass*rotg->nat;
1527
1528	/**********************************/
1529	/* First collect the data we need */
1530	/**********************************/
1531
1532	/* Collect the data for the individual slabs */
1533	for (n = erg->slab_first; n <= erg->slab_last; n++)
1534	{
1535	islab = n - erg->slab_first; /* slab index */
1536	sd = &(rotg->enfrotgrp->slab_data[islab]);
1537	sd->nat = erg->lastatom[islab]-erg->firstatom[islab]+1;
1538	ind = 0;
1539
1540	/* Loop over the relevant atoms in the slab */
1541	for (l = erg->firstatom[islab]; l <= erg->lastatom[islab]; l++)
1542	{
1543	/* Current position of this atom: x[ii][XX/YY/ZZ] */
1544	copy_rvec(erg->xc[l], curr_x);
1545
1546	/* The (unrotated) reference position of this atom is copied to ref_x.
1547	* Beware, the xc coords have been sorted in do_flexible */
1548	copy_rvec(erg->xc_ref_sorted[l], ref_x);
1549
1550	/* Save data for doing angular RMSD fit later */
1551	/* Save the current atom position */
1552	copy_rvec(curr_x, sd->x[ind]);
1553	/* Save the corresponding reference position */
1554	copy_rvec(ref_x, sd->ref[ind]);
1555
1556	/* Maybe also mass-weighting was requested. If yes, additionally
1557	* multiply the weights with the relative mass of the atom. If not,
1558	* multiply with unity. */
1559	m_rel = erg->mc_sorted[l]*OOm_av;
1560
1561	/* Save the weight for this atom in this slab */
1562	sd->weight[ind] = gaussian_weight(curr_x, rotg, n) * m_rel;
1563
1564	/* Next atom in this slab */
1565	ind++;
1566	}
1567	}
1568
1569	/******************************/
1570	/* Now do the fit calculation */
1571	/******************************/
1572
1573	fprintf(fp, "%12.3e%6d%12.3f", t, g, degangle);
1574
1575	/* === Now do RMSD fitting for each slab === */
1576	/* We require at least SLAB_MIN_ATOMS in a slab, such that the fit makes sense. */
1577	#define SLAB_MIN_ATOMS 4
1578
1579	for (n = erg->slab_first; n <= erg->slab_last; n++)
1580	{
1581	islab = n - erg->slab_first; /* slab index */
1582	sd = &(rotg->enfrotgrp->slab_data[islab]);
1583	if (sd->nat >= SLAB_MIN_ATOMS)
1584	{
1585	/* Get the center of the slabs reference and current positions */
1586	get_center(sd->ref, sd->weight, sd->nat, ref_center);
1587	get_center(sd->x, sd->weight, sd->nat, act_center);
1588	if (rotg->eFittype == erotgFitNORM)
1589	{
1590	/* Normalize every position to it's reference length
1591	* prior to performing the fit */
1592	for (i = 0; i < sd->nat; i++) /* Center */
1593	{
1594	rvec_dec(sd->ref[i], ref_center);
1595	rvec_dec(sd->x[i], act_center);
1596	/* Normalize x_i such that it gets the same length as ref_i */
1597	svmul( norm(sd->ref[i])/norm(sd->x[i]), sd->x[i], sd->x[i] );
1598	}
1599	/* We already subtracted the centers */
1600	clear_rvec(ref_center);
1601	clear_rvec(act_center);
1602	}
1603	fitangle = -opt_angle_analytic(sd->ref, sd->x, sd->weight, sd->nat,
1604	ref_center, act_center, rotg->vec);
1605	fprintf(fp, "%6d%6d%12.3f", n, sd->nat, fitangle);
1606	}
1607	}
1608	fprintf(fp, "\n");
1609
1610	#undef SLAB_MIN_ATOMS
1611	}
1612
1613
1614	/* Shift x with is */
1615	static gmx_inlineinline void shift_single_coord(matrix box, rvec x, const ivec is)
1616	{
1617	int tx, ty, tz;
1618
1619
1620	tx = is[XX0];
1621	ty = is[YY1];
1622	tz = is[ZZ2];
1623
1624	if (TRICLINIC(box)(box[1][0] != 0 \|\| box[2][0] != 0 \|\| box[2][1] != 0))
1625	{
1626	x[XX0] += txbox[XX0][XX0]+tybox[YY1][XX0]+tz*box[ZZ2][XX0];
1627	x[YY1] += tybox[YY1][YY1]+tzbox[ZZ2][YY1];
1628	x[ZZ2] += tz*box[ZZ2][ZZ2];
1629	}
1630	else
1631	{
1632	x[XX0] += tx*box[XX0][XX0];
1633	x[YY1] += ty*box[YY1][YY1];
1634	x[ZZ2] += tz*box[ZZ2][ZZ2];
1635	}
1636	}
1637
1638
1639	/* Determine the 'home' slab of this atom which is the
1640	* slab with the highest Gaussian weight of all */
1641	#define round(a)(int)(a+0.5) (int)(a+0.5)
1642	static gmx_inlineinline int get_homeslab(
1643	rvec curr_x, /* The position for which the home slab shall be determined */
1644	rvec rotvec, /* The rotation vector */
1645	real slabdist) /* The slab distance */
1646	{
1647	real dist;
1648
1649
1650	/* The distance of the atom to the coordinate center (where the
1651	* slab with index 0) is */
1652	dist = iprod(rotvec, curr_x);
1653
1654	return round(dist / slabdist)(int)(dist / slabdist+0.5);
1655	}
1656
1657
1658	/* For a local atom determine the relevant slabs, i.e. slabs in
1659	* which the gaussian is larger than min_gaussian
1660	*/
1661	static int get_single_atom_gaussians(
1662	rvec curr_x,
1663	t_rotgrp *rotg)
1664	{
1665	int slab, homeslab;
1666	real g;
1667	int count = 0;
1668	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1669
1670
1671	erg = rotg->enfrotgrp;
1672
1673	/* Determine the 'home' slab of this atom: */
1674	homeslab = get_homeslab(curr_x, rotg->vec, rotg->slab_dist);
1675
1676	/* First determine the weight in the atoms home slab: */
1677	g = gaussian_weight(curr_x, rotg, homeslab);
1678
1679	erg->gn_atom[count] = g;
1680	erg->gn_slabind[count] = homeslab;
1681	count++;
1682
1683
1684	/* Determine the max slab */
1685	slab = homeslab;
1686	while (g > rotg->min_gaussian)
1687	{
1688	slab++;
1689	g = gaussian_weight(curr_x, rotg, slab);
1690	erg->gn_slabind[count] = slab;
1691	erg->gn_atom[count] = g;
1692	count++;
1693	}
1694	count--;
1695
1696	/* Determine the min slab */
1697	slab = homeslab;
1698	do
1699	{
1700	slab--;
1701	g = gaussian_weight(curr_x, rotg, slab);
1702	erg->gn_slabind[count] = slab;
1703	erg->gn_atom[count] = g;
1704	count++;
1705	}
1706	while (g > rotg->min_gaussian);
1707	count--;
1708
1709	return count;
1710	}
1711
1712
1713	static void flex2_precalc_inner_sum(t_rotgrp *rotg)
1714	{
1715	int i, n, islab;
1716	rvec xi; /* positions in the i-sum */
1717	rvec xcn, ycn; /* the current and the reference slab centers */
1718	real gaussian_xi;
1719	rvec yi0;
1720	rvec rin; /* Helper variables */
1721	real fac, fac2;
1722	rvec innersumvec;
1723	real OOpsii, OOpsiistar;
1724	real sin_rin; /* s_ii.r_ii */
1725	rvec s_in, tmpvec, tmpvec2;
1726	real mi, wi; /* Mass-weighting of the positions */
1727	real N_M; /* N/M */
1728	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1729
1730
1731	erg = rotg->enfrotgrp;
1732	N_M = rotg->nat * erg->invmass;
1733
1734	/* Loop over all slabs that contain something */
1735	for (n = erg->slab_first; n <= erg->slab_last; n++)
1736	{
1737	islab = n - erg->slab_first; /* slab index */
1738
1739	/* The current center of this slab is saved in xcn: */
1740	copy_rvec(erg->slab_center[islab], xcn);
1741	/* ... and the reference center in ycn: */
1742	copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1743
1744	/*** D. Calculate the whole inner sum used for second and third sum */
1745	/* For slab n, we need to loop over all atoms i again. Since we sorted
1746	* the atoms with respect to the rotation vector, we know that it is sufficient
1747	* to calculate from firstatom to lastatom only. All other contributions will
1748	* be very small. */
1749	clear_rvec(innersumvec);
1750	for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
1751	{
1752	/* Coordinate xi of this atom */
1753	copy_rvec(erg->xc[i], xi);
1754
1755	/* The i-weights */
1756	gaussian_xi = gaussian_weight(xi, rotg, n);
1757	mi = erg->mc_sorted[i]; /* need the sorted mass here */
1758	wi = N_M*mi;
1759
1760	/* Calculate rin */
1761	copy_rvec(erg->xc_ref_sorted[i], yi0); /* Reference position yi0 */
1762	rvec_sub(yi0, ycn, tmpvec2); /* tmpvec2 = yi0 - ycn */
1763	mvmul(erg->rotmat, tmpvec2, rin); /* rin = Omega.(yi0 - ycn) */
1764
1765	/* Calculate psi_i* and sin */
1766	rvec_sub(xi, xcn, tmpvec2); /* tmpvec2 = xi - xcn */
1767	cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xi - xcn) */
1768	OOpsiistar = norm2(tmpvec)+rotg->eps; /* OOpsii* = 1/psii* = \|v x (xi-xcn)\|^2 + eps */
1769	OOpsii = norm(tmpvec); /* OOpsii = 1 / psii = \|v x (xi - xcn)\| */
1770
1771	/* * v x (xi - xcn) */
1772	unitv(tmpvec, s_in); /* sin = ---------------- */
1773	/* \|v x (xi - xcn)\| */
1774
1775	sin_rin = iprod(s_in, rin); /* sin_rin = sin . rin */
1776
1777	/* Now the whole sum */
1778	fac = OOpsii/OOpsiistar;
1779	svmul(fac, rin, tmpvec);
1780	fac2 = facfacOOpsii;
1781	svmul(fac2*sin_rin, s_in, tmpvec2);
1782	rvec_dec(tmpvec, tmpvec2);
1783
1784	svmul(wigaussian_xisin_rin, tmpvec, tmpvec2);
1785
1786	rvec_inc(innersumvec, tmpvec2);
1787	} /* now we have the inner sum, used both for sum2 and sum3 */
1788
1789	/* Save it to be used in do_flex2_lowlevel */
1790	copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
1791	} /* END of loop over slabs */
1792	}
1793
1794
1795	static void flex_precalc_inner_sum(t_rotgrp *rotg)
1796	{
1797	int i, n, islab;
1798	rvec xi; /* position */
1799	rvec xcn, ycn; /* the current and the reference slab centers */
1800	rvec qin, rin; /* q_i^n and r_i^n */
1801	real bin;
1802	rvec tmpvec;
1803	rvec innersumvec; /* Inner part of sum_n2 */
1804	real gaussian_xi; /* Gaussian weight gn(xi) */
1805	real mi, wi; /* Mass-weighting of the positions */
1806	real N_M; /* N/M */
1807
1808	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1809
1810
1811	erg = rotg->enfrotgrp;
1812	N_M = rotg->nat * erg->invmass;
1813
1814	/* Loop over all slabs that contain something */
1815	for (n = erg->slab_first; n <= erg->slab_last; n++)
1816	{
1817	islab = n - erg->slab_first; /* slab index */
1818
1819	/* The current center of this slab is saved in xcn: */
1820	copy_rvec(erg->slab_center[islab], xcn);
1821	/* ... and the reference center in ycn: */
1822	copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1823
1824	/* For slab n, we need to loop over all atoms i again. Since we sorted
1825	* the atoms with respect to the rotation vector, we know that it is sufficient
1826	* to calculate from firstatom to lastatom only. All other contributions will
1827	* be very small. */
1828	clear_rvec(innersumvec);
1829	for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
1830	{
1831	/* Coordinate xi of this atom */
1832	copy_rvec(erg->xc[i], xi);
1833
1834	/* The i-weights */
1835	gaussian_xi = gaussian_weight(xi, rotg, n);
1836	mi = erg->mc_sorted[i]; /* need the sorted mass here */
1837	wi = N_M*mi;
1838
1839	/* Calculate rin and qin */
1840	rvec_sub(erg->xc_ref_sorted[i], ycn, tmpvec); /* tmpvec = yi0-ycn */
1841	mvmul(erg->rotmat, tmpvec, rin); /* rin = Omega.(yi0 - ycn) */
1842	cprod(rotg->vec, rin, tmpvec); /* tmpvec = v x Omega(yi0-ycn) /
1843
1844	/* * v x Omega(yi0-ycn) /
1845	unitv(tmpvec, qin); /* qin = --------------------- */
1846	/* \|v x Omega(yi0-ycn)\| /
1847
1848	/* Calculate bin */
1849	rvec_sub(xi, xcn, tmpvec); /* tmpvec = xi-xcn */
1850	bin = iprod(qin, tmpvec); /* bin = qin(xi-xcn) /
1851
1852	svmul(wigaussian_xibin, qin, tmpvec);
1853
1854	/* Add this contribution to the inner sum: */
1855	rvec_add(innersumvec, tmpvec, innersumvec);
1856	} /* now we have the inner sum vector S^n for this slab */
1857	/* Save it to be used in do_flex_lowlevel */
1858	copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
1859	}
1860	}
1861
1862
1863	static real do_flex2_lowlevel(
1864	t_rotgrp *rotg,
1865	real sigma, /* The Gaussian width sigma */
1866	rvec x[],
1867	gmx_bool bOutstepRot,
1868	gmx_bool bOutstepSlab,
1869	matrix box)
1870	{
1871	int count, ic, ii, j, m, n, islab, iigrp, ifit;
1872	rvec xj; /* position in the i-sum */
1873	rvec yj0; /* the reference position in the j-sum */
1874	rvec xcn, ycn; /* the current and the reference slab centers */
1875	real V; /* This node's part of the rotation pot. energy */
1876	real gaussian_xj; /* Gaussian weight */
1877	real beta;
1878
1879	real numerator, fit_numerator;
1880	rvec rjn, fit_rjn; /* Helper variables */
1881	real fac, fac2;
1882
1883	real OOpsij, OOpsijstar;
1884	real OOsigma2; /* 1/(sigma^2) */
1885	real sjn_rjn;
1886	real betasigpsi;
1887	rvec sjn, tmpvec, tmpvec2, yj0_ycn;
1888	rvec sum1vec_part, sum1vec, sum2vec_part, sum2vec, sum3vec, sum4vec, innersumvec;
1889	real sum3, sum4;
1890	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
1891	real mj, wj; /* Mass-weighting of the positions */
1892	real N_M; /* N/M */
1893	real Wjn; /* g_n(x_j) m_j / Mjn */
1894	gmx_bool bCalcPotFit;
1895
1896	/* To calculate the torque per slab */
1897	rvec slab_force; /* Single force from slab n on one atom */
1898	rvec slab_sum1vec_part;
1899	real slab_sum3part, slab_sum4part;
1900	rvec slab_sum1vec, slab_sum2vec, slab_sum3vec, slab_sum4vec;
1901
1902
1903	erg = rotg->enfrotgrp;
1904
1905	/* Pre-calculate the inner sums, so that we do not have to calculate
1906	* them again for every atom */
1907	flex2_precalc_inner_sum(rotg);
1908
1909	bCalcPotFit = (bOutstepRot \|\| bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
1910
1911	/********************************************************/
1912	/* Main loop over all local atoms of the rotation group */
1913	/********************************************************/
1914	N_M = rotg->nat * erg->invmass;
1915	V = 0.0;
1916	OOsigma2 = 1.0 / (sigma*sigma);
1917	for (j = 0; j < erg->nat_loc; j++)
1918	{
1919	/* Local index of a rotation group atom */
1920	ii = erg->ind_loc[j];
1921	/* Position of this atom in the collective array */
1922	iigrp = erg->xc_ref_ind[j];
1923	/* Mass-weighting */
1924	mj = erg->mc[iigrp]; /* need the unsorted mass here */
1925	wj = N_M*mj;
1926
1927	/* Current position of this atom: x[ii][XX/YY/ZZ]
1928	* Note that erg->xc_center contains the center of mass in case the flex2-t
1929	* potential was chosen. For the flex2 potential erg->xc_center must be
1930	* zero. */
1931	rvec_sub(x[ii], erg->xc_center, xj);
1932
1933	/* Shift this atom such that it is near its reference */
1934	shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
1935
1936	/* Determine the slabs to loop over, i.e. the ones with contributions
1937	* larger than min_gaussian */
1938	count = get_single_atom_gaussians(xj, rotg);
1939
1940	clear_rvec(sum1vec_part);
1941	clear_rvec(sum2vec_part);
1942	sum3 = 0.0;
1943	sum4 = 0.0;
1944	/* Loop over the relevant slabs for this atom */
1945	for (ic = 0; ic < count; ic++)
1946	{
1947	n = erg->gn_slabind[ic];
1948
1949	/* Get the precomputed Gaussian value of curr_slab for curr_x */
1950	gaussian_xj = erg->gn_atom[ic];
1951
1952	islab = n - erg->slab_first; /* slab index */
1953
1954	/* The (unrotated) reference position of this atom is copied to yj0: */
1955	copy_rvec(rotg->x_ref[iigrp], yj0);
1956
1957	beta = calc_beta(xj, rotg, n);
1958
1959	/* The current center of this slab is saved in xcn: */
1960	copy_rvec(erg->slab_center[islab], xcn);
1961	/* ... and the reference center in ycn: */
1962	copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
1963
1964	rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
1965
1966	/* Rotate: */
1967	mvmul(erg->rotmat, yj0_ycn, rjn); /* rjn = Omega.(yj0 - ycn) */
1968
1969	/* Subtract the slab center from xj */
1970	rvec_sub(xj, xcn, tmpvec2); /* tmpvec2 = xj - xcn */
1971
1972	/* In rare cases, when an atom position coincides with a slab center
1973	* (tmpvec2 == 0) we cannot compute the vector product for sjn.
1974	* However, since the atom is located directly on the pivot, this
1975	* slab's contribution to the force on that atom will be zero
1976	* anyway. Therefore, we directly move on to the next slab. */
1977	if (gmx_numzero(norm(tmpvec2))) /* 0 == norm(xj - xcn) */
1978	{
1979	continue;
1980	}
1981
1982	/* Calculate sjn */
1983	cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xj - xcn) */
1984
1985	OOpsijstar = norm2(tmpvec)+rotg->eps; /* OOpsij* = 1/psij* = \|v x (xj-xcn)\|^2 + eps */
1986
1987	numerator = sqr(iprod(tmpvec, rjn));
1988
1989	/*********************************/
1990	/* Add to the rotation potential */
1991	/*********************************/
1992	V += 0.5rotg->kwjgaussian_xjnumerator/OOpsijstar;
1993
1994	/* If requested, also calculate the potential for a set of angles
1995	* near the current reference angle */
1996	if (bCalcPotFit)
1997	{
1998	for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
1999	{
2000	mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, fit_rjn);
2001	fit_numerator = sqr(iprod(tmpvec, fit_rjn));
2002	erg->PotAngleFit->V[ifit] += 0.5rotg->kwjgaussian_xjfit_numerator/OOpsijstar;
2003	}
2004	}
2005
2006	/*************************************/
2007	/* Now calculate the force on atom j */
2008	/*************************************/
2009
2010	OOpsij = norm(tmpvec); /* OOpsij = 1 / psij = \|v x (xj - xcn)\| */
2011
2012	/* * v x (xj - xcn) */
2013	unitv(tmpvec, sjn); /* sjn = ---------------- */
2014	/* \|v x (xj - xcn)\| */
2015
2016	sjn_rjn = iprod(sjn, rjn); /* sjn_rjn = sjn . rjn */
2017
2018
2019	/* A. Calculate the first of the four sum terms: **************/
2020	fac = OOpsij/OOpsijstar;
2021	svmul(fac, rjn, tmpvec);
2022	fac2 = facfacOOpsij;
2023	svmul(fac2*sjn_rjn, sjn, tmpvec2);
2024	rvec_dec(tmpvec, tmpvec2);
2025	fac2 = wjgaussian_xj; / also needed for sum4 */
2026	svmul(fac2*sjn_rjn, tmpvec, slab_sum1vec_part);
2027	/********************/
2028	/* Add to sum1: */
2029	/********************/
2030	rvec_inc(sum1vec_part, slab_sum1vec_part); /* sum1 still needs to vector multiplied with v */
2031
2032	/* B. Calculate the forth of the four sum terms: **************/
2033	betasigpsi = betaOOsigma2OOpsij; /* this is also needed for sum3 */
2034	/********************/
2035	/* Add to sum4: */
2036	/********************/
2037	slab_sum4part = fac2betasigpsifacsjn_rjnsjn_rjn; /* Note that fac is still valid from above */
2038	sum4 += slab_sum4part;
2039
2040	/*** C. Calculate Wjn for second and third sum */
2041	/* Note that we can safely divide by slab_weights since we check in
2042	* get_slab_centers that it is non-zero. */
2043	Wjn = gaussian_xj*mj/erg->slab_weights[islab];
2044
2045	/* We already have precalculated the inner sum for slab n */
2046	copy_rvec(erg->slab_innersumvec[islab], innersumvec);
2047
2048	/* Weigh the inner sum vector with Wjn */
2049	svmul(Wjn, innersumvec, innersumvec);
2050
2051	/*** E. Calculate the second of the four sum terms: */
2052	/********************/
2053	/* Add to sum2: */
2054	/********************/
2055	rvec_inc(sum2vec_part, innersumvec); /* sum2 still needs to be vector crossproduct'ed with v */
2056
2057	/*** F. Calculate the third of the four sum terms: */
2058	slab_sum3part = betasigpsi * iprod(sjn, innersumvec);
2059	sum3 += slab_sum3part; /* still needs to be multiplied with v */
2060
2061	/*** G. Calculate the torque on the local slab's axis: */
2062	if (bOutstepRot)
2063	{
2064	/* Sum1 */
2065	cprod(slab_sum1vec_part, rotg->vec, slab_sum1vec);
2066	/* Sum2 */
2067	cprod(innersumvec, rotg->vec, slab_sum2vec);
2068	/* Sum3 */
2069	svmul(slab_sum3part, rotg->vec, slab_sum3vec);
2070	/* Sum4 */
2071	svmul(slab_sum4part, rotg->vec, slab_sum4vec);
2072
2073	/* The force on atom ii from slab n only: */
2074	for (m = 0; m < DIM3; m++)
2075	{
2076	slab_force[m] = rotg->k * (-slab_sum1vec[m] + slab_sum2vec[m] - slab_sum3vec[m] + 0.5*slab_sum4vec[m]);
2077	}
2078
2079	erg->slab_torque_v[islab] += torque(rotg->vec, slab_force, xj, xcn);
2080	}
2081	} /* END of loop over slabs */
2082
2083	/* Construct the four individual parts of the vector sum: */
2084	cprod(sum1vec_part, rotg->vec, sum1vec); /* sum1vec = { } x v */
2085	cprod(sum2vec_part, rotg->vec, sum2vec); /* sum2vec = { } x v */
2086	svmul(sum3, rotg->vec, sum3vec); /* sum3vec = { } . v */
2087	svmul(sum4, rotg->vec, sum4vec); /* sum4vec = { } . v */
2088
2089	/* Store the additional force so that it can be added to the force
2090	* array after the normal forces have been evaluated */
2091	for (m = 0; m < DIM3; m++)
2092	{
2093	erg->f_rot_loc[j][m] = rotg->k * (-sum1vec[m] + sum2vec[m] - sum3vec[m] + 0.5*sum4vec[m]);
2094	}
2095
2096	#ifdef SUM_PARTS
2097	fprintf(stderrstderr, "sum1: %15.8f %15.8f %15.8f\n", -rotg->ksum1vec[XX0], -rotg->ksum1vec[YY1], -rotg->k*sum1vec[ZZ2]);
2098	fprintf(stderrstderr, "sum2: %15.8f %15.8f %15.8f\n", rotg->ksum2vec[XX0], rotg->ksum2vec[YY1], rotg->k*sum2vec[ZZ2]);
2099	fprintf(stderrstderr, "sum3: %15.8f %15.8f %15.8f\n", -rotg->ksum3vec[XX0], -rotg->ksum3vec[YY1], -rotg->k*sum3vec[ZZ2]);
2100	fprintf(stderrstderr, "sum4: %15.8f %15.8f %15.8f\n", 0.5rotg->ksum4vec[XX0], 0.5rotg->ksum4vec[YY1], 0.5rotg->ksum4vec[ZZ2]);
2101	#endif
2102
2103	PRINT_FORCE_J
2104
2105	} /* END of loop over local atoms */
2106
2107	return V;
2108	}
2109
2110
2111	static real do_flex_lowlevel(
2112	t_rotgrp *rotg,
2113	real sigma, /* The Gaussian width sigma */
2114	rvec x[],
2115	gmx_bool bOutstepRot,
2116	gmx_bool bOutstepSlab,
2117	matrix box)
2118	{
2119	int count, ic, ifit, ii, j, m, n, islab, iigrp;
2120	rvec xj, yj0; /* current and reference position */
2121	rvec xcn, ycn; /* the current and the reference slab centers */
2122	rvec yj0_ycn; /* yj0 - ycn */
2123	rvec xj_xcn; /* xj - xcn */
2124	rvec qjn, fit_qjn; /* q_i^n */
2125	rvec sum_n1, sum_n2; /* Two contributions to the rotation force */
2126	rvec innersumvec; /* Inner part of sum_n2 */
2127	rvec s_n;
2128	rvec force_n; /* Single force from slab n on one atom */
2129	rvec force_n1, force_n2; /* First and second part of force_n */
2130	rvec tmpvec, tmpvec2, tmp_f; /* Helper variables */
2131	real V; /* The rotation potential energy */
2132	real OOsigma2; /* 1/(sigma^2) */
2133	real beta; /* beta_n(xj) */
2134	real bjn, fit_bjn; /* b_j^n */
2135	real gaussian_xj; /* Gaussian weight gn(xj) */
2136	real betan_xj_sigma2;
2137	real mj, wj; /* Mass-weighting of the positions */
2138	real N_M; /* N/M */
2139	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2140	gmx_bool bCalcPotFit;
2141
2142
2143	erg = rotg->enfrotgrp;
2144
2145	/* Pre-calculate the inner sums, so that we do not have to calculate
2146	* them again for every atom */
2147	flex_precalc_inner_sum(rotg);
2148
2149	bCalcPotFit = (bOutstepRot \|\| bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2150
2151	/********************************************************/
2152	/* Main loop over all local atoms of the rotation group */
2153	/********************************************************/
2154	OOsigma2 = 1.0/(sigma*sigma);
2155	N_M = rotg->nat * erg->invmass;
2156	V = 0.0;
2157	for (j = 0; j < erg->nat_loc; j++)
2158	{
2159	/* Local index of a rotation group atom */
2160	ii = erg->ind_loc[j];
2161	/* Position of this atom in the collective array */
2162	iigrp = erg->xc_ref_ind[j];
2163	/* Mass-weighting */
2164	mj = erg->mc[iigrp]; /* need the unsorted mass here */
2165	wj = N_M*mj;
2166
2167	/* Current position of this atom: x[ii][XX/YY/ZZ]
2168	* Note that erg->xc_center contains the center of mass in case the flex-t
2169	* potential was chosen. For the flex potential erg->xc_center must be
2170	* zero. */
2171	rvec_sub(x[ii], erg->xc_center, xj);
2172
2173	/* Shift this atom such that it is near its reference */
2174	shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2175
2176	/* Determine the slabs to loop over, i.e. the ones with contributions
2177	* larger than min_gaussian */
2178	count = get_single_atom_gaussians(xj, rotg);
2179
2180	clear_rvec(sum_n1);
2181	clear_rvec(sum_n2);
2182
2183	/* Loop over the relevant slabs for this atom */
2184	for (ic = 0; ic < count; ic++)
2185	{
2186	n = erg->gn_slabind[ic];
2187
2188	/* Get the precomputed Gaussian for xj in slab n */
2189	gaussian_xj = erg->gn_atom[ic];
2190
2191	islab = n - erg->slab_first; /* slab index */
2192
2193	/* The (unrotated) reference position of this atom is saved in yj0: */
2194	copy_rvec(rotg->x_ref[iigrp], yj0);
2195
2196	beta = calc_beta(xj, rotg, n);
2197
2198	/* The current center of this slab is saved in xcn: */
2199	copy_rvec(erg->slab_center[islab], xcn);
2200	/* ... and the reference center in ycn: */
2201	copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
2202
2203	rvec_sub(yj0, ycn, yj0_ycn); /* yj0_ycn = yj0 - ycn */
2204
2205	/* In rare cases, when an atom position coincides with a reference slab
2206	* center (yj0_ycn == 0) we cannot compute the normal vector qjn.
2207	* However, since the atom is located directly on the pivot, this
2208	* slab's contribution to the force on that atom will be zero
2209	* anyway. Therefore, we directly move on to the next slab. */
2210	if (gmx_numzero(norm(yj0_ycn))) /* 0 == norm(yj0 - ycn) */
2211	{
2212	continue;
2213	}
2214
2215	/* Rotate: */
2216	mvmul(erg->rotmat, yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2217
2218	/* Subtract the slab center from xj */
2219	rvec_sub(xj, xcn, xj_xcn); /* xj_xcn = xj - xcn */
2220
2221	/* Calculate qjn */
2222	cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2223
2224	/* * v x Omega.(yj0-ycn) */
2225	unitv(tmpvec, qjn); /* qjn = --------------------- */
2226	/* \|v x Omega.(yj0-ycn)\| */
2227
2228	bjn = iprod(qjn, xj_xcn); /* bjn = qjn * (xj - xcn) */
2229
2230	/*********************************/
2231	/* Add to the rotation potential */
2232	/*********************************/
2233	V += 0.5rotg->kwjgaussian_xjsqr(bjn);
2234
2235	/* If requested, also calculate the potential for a set of angles
2236	* near the current reference angle */
2237	if (bCalcPotFit)
2238	{
2239	for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2240	{
2241	/* As above calculate Omega.(yj0-ycn), now for the other angles */
2242	mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
2243	/* As above calculate qjn */
2244	cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
2245	/* * v x Omega.(yj0-ycn) */
2246	unitv(tmpvec, fit_qjn); /* fit_qjn = --------------------- */
2247	/* \|v x Omega.(yj0-ycn)\| */
2248	fit_bjn = iprod(fit_qjn, xj_xcn); /* fit_bjn = fit_qjn * (xj - xcn) */
2249	/* Add to the rotation potential for this angle */
2250	erg->PotAngleFit->V[ifit] += 0.5rotg->kwjgaussian_xjsqr(fit_bjn);
2251	}
2252	}
2253
2254	/****************************************************************/
2255	/* sum_n1 will typically be the main contribution to the force: */
2256	/****************************************************************/
2257	betan_xj_sigma2 = betaOOsigma2; / beta_n(xj)/sigma^2 */
2258
2259	/* The next lines calculate
2260	* qjn - (bjnbeta(xj)/(2sigma^2))v /
2261	svmul(bjn0.5betan_xj_sigma2, rotg->vec, tmpvec2);
2262	rvec_sub(qjn, tmpvec2, tmpvec);
2263
2264	/* Multiply with gn(xj)bjn: /
2265	svmul(gaussian_xj*bjn, tmpvec, tmpvec2);
2266
2267	/* Sum over n: */
2268	rvec_inc(sum_n1, tmpvec2);
2269
2270	/* We already have precalculated the Sn term for slab n */
2271	copy_rvec(erg->slab_innersumvec[islab], s_n);
2272	/* * beta_n(xj) */
2273	svmul(betan_xj_sigma2iprod(s_n, xj_xcn), rotg->vec, tmpvec); / tmpvec = ---------- s_n (xj-xcn) */
2274	/* sigma^2 */
2275
2276	rvec_sub(s_n, tmpvec, innersumvec);
2277
2278	/* We can safely divide by slab_weights since we check in get_slab_centers
2279	* that it is non-zero. */
2280	svmul(gaussian_xj/erg->slab_weights[islab], innersumvec, innersumvec);
2281
2282	rvec_add(sum_n2, innersumvec, sum_n2);
2283
2284	/* Calculate the torque: */
2285	if (bOutstepRot)
2286	{
2287	/* The force on atom ii from slab n only: */
2288	svmul(-rotg->kwj, tmpvec2, force_n1); / part 1 */
2289	svmul( rotg->kmj, innersumvec, force_n2); / part 2 */
2290	rvec_add(force_n1, force_n2, force_n);
2291	erg->slab_torque_v[islab] += torque(rotg->vec, force_n, xj, xcn);
2292	}
2293	} /* END of loop over slabs */
2294
2295	/* Put both contributions together: */
2296	svmul(wj, sum_n1, sum_n1);
2297	svmul(mj, sum_n2, sum_n2);
2298	rvec_sub(sum_n2, sum_n1, tmp_f); /* F = -grad V */
2299
2300	/* Store the additional force so that it can be added to the force
2301	* array after the normal forces have been evaluated */
2302	for (m = 0; m < DIM3; m++)
2303	{
2304	erg->f_rot_loc[j][m] = rotg->k*tmp_f[m];
2305	}
2306
2307	PRINT_FORCE_J
2308
2309	} /* END of loop over local atoms */
2310
2311	return V;
2312	}
2313
2314	#ifdef PRINT_COORDS
2315	static void print_coordinates(t_rotgrp *rotg, rvec x[], matrix box, int step)
2316	{
2317	int i;
2318	static FILE *fp;
2319	static char buf[STRLEN4096];
2320	static gmx_bool bFirst = 1;
2321
2322
2323	if (bFirst)
2324	{
2325	sprintf(buf, "coords%d.txt", cr->nodeid);
2326	fp = fopen(buf, "w");
2327	bFirst = 0;
2328	}
2329
2330	fprintf(fp, "\nStep %d\n", step);
2331	fprintf(fp, "box: %f %f %f %f %f %f %f %f %f\n",
2332	box[XX0][XX0], box[XX0][YY1], box[XX0][ZZ2],
2333	box[YY1][XX0], box[YY1][YY1], box[YY1][ZZ2],
2334	box[ZZ2][XX0], box[ZZ2][ZZ2], box[ZZ2][ZZ2]);
2335	for (i = 0; i < rotg->nat; i++)
2336	{
2337	fprintf(fp, "%4d %f %f %f\n", i,
2338	erg->xc[i][XX0], erg->xc[i][YY1], erg->xc[i][ZZ2]);
2339	}
2340	fflush(fp);
2341
2342	}
2343	#endif
2344
2345
2346	static int projection_compare(const void a, const void b)
2347	{
2348	sort_along_vec_t xca, xcb;
2349
2350
2351	xca = (sort_along_vec_t *)a;
2352	xcb = (sort_along_vec_t *)b;
2353
2354	if (xca->xcproj < xcb->xcproj)
2355	{
2356	return -1;
2357	}
2358	else if (xca->xcproj > xcb->xcproj)
2359	{
2360	return 1;
2361	}
2362	else
2363	{
2364	return 0;
2365	}
2366	}
2367
2368
2369	static void sort_collective_coordinates(
2370	t_rotgrp rotg, / Rotation group */
2371	sort_along_vec_t data) / Buffer for sorting the positions */
2372	{
2373	int i;
2374	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2375
2376
2377	erg = rotg->enfrotgrp;
2378
2379	/* The projection of the position vector on the rotation vector is
2380	* the relevant value for sorting. Fill the 'data' structure */
2381	for (i = 0; i < rotg->nat; i++)
2382	{
2383	data[i].xcproj = iprod(erg->xc[i], rotg->vec); /* sort criterium */
2384	data[i].m = erg->mc[i];
2385	data[i].ind = i;
2386	copy_rvec(erg->xc[i], data[i].x );
2387	copy_rvec(rotg->x_ref[i], data[i].x_ref);
2388	}
2389	/* Sort the 'data' structure */
2390	gmx_qsort(data, rotg->nat, sizeof(sort_along_vec_t), projection_compare);
2391
2392	/* Copy back the sorted values */
2393	for (i = 0; i < rotg->nat; i++)
2394	{
2395	copy_rvec(data[i].x, erg->xc[i] );
2396	copy_rvec(data[i].x_ref, erg->xc_ref_sorted[i]);
2397	erg->mc_sorted[i] = data[i].m;
2398	erg->xc_sortind[i] = data[i].ind;
2399	}
2400	}
2401
2402
2403	/* For each slab, get the first and the last index of the sorted atom
2404	* indices */
2405	static void get_firstlast_atom_per_slab(t_rotgrp *rotg)
2406	{
2407	int i, islab, n;
2408	real beta;
2409	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2410
2411
2412	erg = rotg->enfrotgrp;
2413
2414	/* Find the first atom that needs to enter the calculation for each slab */
2415	n = erg->slab_first; /* slab */
2416	i = 0; /* start with the first atom */
2417	do
2418	{
2419	/* Find the first atom that significantly contributes to this slab */
2420	do /* move forward in position until a large enough beta is found */
2421	{
2422	beta = calc_beta(erg->xc[i], rotg, n);
2423	i++;
2424	}
2425	while ((beta < -erg->max_beta) && (i < rotg->nat));
2426	i--;
2427	islab = n - erg->slab_first; /* slab index */
2428	erg->firstatom[islab] = i;
2429	/* Proceed to the next slab */
2430	n++;
2431	}
2432	while (n <= erg->slab_last);
2433
2434	/* Find the last atom for each slab */
2435	n = erg->slab_last; /* start with last slab */
2436	i = rotg->nat-1; /* start with the last atom */
2437	do
2438	{
2439	do /* move backward in position until a large enough beta is found */
2440	{
2441	beta = calc_beta(erg->xc[i], rotg, n);
2442	i--;
2443	}
2444	while ((beta > erg->max_beta) && (i > -1));
2445	i++;
2446	islab = n - erg->slab_first; /* slab index */
2447	erg->lastatom[islab] = i;
2448	/* Proceed to the next slab */
2449	n--;
2450	}
2451	while (n >= erg->slab_first);
2452	}
2453
2454
2455	/* Determine the very first and very last slab that needs to be considered
2456	* For the first slab that needs to be considered, we have to find the smallest
2457	* n that obeys:
2458	*
2459	* x_first * v - n*Delta_x <= beta_max
2460	*
2461	* slab index n, slab distance Delta_x, rotation vector v. For the last slab we
2462	* have to find the largest n that obeys
2463	*
2464	* x_last * v - n*Delta_x >= -beta_max
2465	*
2466	*/
2467	static gmx_inlineinline int get_first_slab(
2468	t_rotgrp rotg, / The rotation group (inputrec data) */
2469	real max_beta, /* The max_beta value, instead of min_gaussian */
2470	rvec firstatom) /* First atom after sorting along the rotation vector v */
2471	{
2472	/* Find the first slab for the first atom */
2473	return ceil((iprod(firstatom, rotg->vec) - max_beta)/rotg->slab_dist);
2474	}
2475
2476
2477	static gmx_inlineinline int get_last_slab(
2478	t_rotgrp rotg, / The rotation group (inputrec data) */
2479	real max_beta, /* The max_beta value, instead of min_gaussian */
2480	rvec lastatom) /* Last atom along v */
2481	{
2482	/* Find the last slab for the last atom */
2483	return floor((iprod(lastatom, rotg->vec) + max_beta)/rotg->slab_dist);
2484	}
2485
2486
2487	static void get_firstlast_slab_check(
2488	t_rotgrp rotg, / The rotation group (inputrec data) */
2489	t_gmx_enfrotgrp erg, / The rotation group (data only accessible in this file) */
2490	rvec firstatom, /* First atom after sorting along the rotation vector v */
2491	rvec lastatom) /* Last atom along v */
2492	{
2493	erg->slab_first = get_first_slab(rotg, erg->max_beta, firstatom);
2494	erg->slab_last = get_last_slab(rotg, erg->max_beta, lastatom);
2495
2496	/* Calculate the slab buffer size, which changes when slab_first changes */
2497	erg->slab_buffer = erg->slab_first - erg->slab_first_ref;
2498
2499	/* Check whether we have reference data to compare against */
2500	if (erg->slab_first < erg->slab_first_ref)
2501	{
2502	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 2502, "%s No reference data for first slab (n=%d), unable to proceed.",
2503	RotStr, erg->slab_first);
2504	}
2505
2506	/* Check whether we have reference data to compare against */
2507	if (erg->slab_last > erg->slab_last_ref)
2508	{
2509	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 2509, "%s No reference data for last slab (n=%d), unable to proceed.",
2510	RotStr, erg->slab_last);
2511	}
2512	}
2513
2514
2515	/* Enforced rotation with a flexible axis */
2516	static void do_flexible(
2517	gmx_bool bMaster,
2518	gmx_enfrot_t enfrot, /* Other rotation data */
2519	t_rotgrp rotg, / The rotation group */
2520	int g, /* Group number */
2521	rvec x[], /* The local positions */
2522	matrix box,
2523	double t, /* Time in picoseconds */
2524	gmx_bool bOutstepRot, /* Output to main rotation output file */
2525	gmx_bool bOutstepSlab) /* Output per-slab data */
2526	{
2527	int l, nslabs;
2528	real sigma; /* The Gaussian width sigma */
2529	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2530
2531
2532	erg = rotg->enfrotgrp;
2533
2534	/* Define the sigma value */
2535	sigma = 0.7*rotg->slab_dist;
2536
2537	/* Sort the collective coordinates erg->xc along the rotation vector. This is
2538	* an optimization for the inner loop. */
2539	sort_collective_coordinates(rotg, enfrot->data);
2540
2541	/* Determine the first relevant slab for the first atom and the last
2542	* relevant slab for the last atom */
2543	get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1]);
2544
2545	/* Determine for each slab depending on the min_gaussian cutoff criterium,
2546	* a first and a last atom index inbetween stuff needs to be calculated */
2547	get_firstlast_atom_per_slab(rotg);
2548
2549	/* Determine the gaussian-weighted center of positions for all slabs */
2550	get_slab_centers(rotg, erg->xc, erg->mc_sorted, g, t, enfrot->out_slabs, bOutstepSlab, FALSE0);
2551
2552	/* Clear the torque per slab from last time step: */
2553	nslabs = erg->slab_last - erg->slab_first + 1;
2554	for (l = 0; l < nslabs; l++)
2555	{
2556	erg->slab_torque_v[l] = 0.0;
2557	}
2558
2559	/* Call the rotational forces kernel */
2560	if (rotg->eType == erotgFLEX \|\| rotg->eType == erotgFLEXT)
2561	{
2562	erg->V = do_flex_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
2563	}
2564	else if (rotg->eType == erotgFLEX2 \|\| rotg->eType == erotgFLEX2T)
2565	{
2566	erg->V = do_flex2_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
2567	}
2568	else
2569	{
2570	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 2570, "Unknown flexible rotation type");
2571	}
2572
2573	/* Determine angle by RMSD fit to the reference - Let's hope this */
2574	/* only happens once in a while, since this is not parallelized! */
2575	if (bMaster && (erotgFitPOT != rotg->eFittype) )
2576	{
2577	if (bOutstepRot)
2578	{
2579	/* Fit angle of the whole rotation group */
2580	erg->angle_v = flex_fit_angle(rotg);
2581	}
2582	if (bOutstepSlab)
2583	{
2584	/* Fit angle of each slab */
2585	flex_fit_angle_perslab(g, rotg, t, erg->degangle, enfrot->out_angles);
2586	}
2587	}
2588
2589	/* Lump together the torques from all slabs: */
2590	erg->torque_v = 0.0;
2591	for (l = 0; l < nslabs; l++)
2592	{
2593	erg->torque_v += erg->slab_torque_v[l];
2594	}
2595	}
2596
2597
2598	/* Calculate the angle between reference and actual rotation group atom,
2599	* both projected into a plane perpendicular to the rotation vector: */
2600	static void angle(t_rotgrp *rotg,
2601	rvec x_act,
2602	rvec x_ref,
2603	real *alpha,
2604	real weight) / atoms near the rotation axis should count less than atoms far away */
2605	{
2606	rvec xp, xrp; /* current and reference positions projected on a plane perpendicular to pg->vec */
2607	rvec dum;
2608
2609
2610	/* Project x_ref and x into a plane through the origin perpendicular to rot_vec: */
2611	/* Project x_ref: xrp = x_ref - (vec * x_ref) * vec */
2612	svmul(iprod(rotg->vec, x_ref), rotg->vec, dum);
2613	rvec_sub(x_ref, dum, xrp);
2614	/* Project x_act: */
2615	svmul(iprod(rotg->vec, x_act), rotg->vec, dum);
2616	rvec_sub(x_act, dum, xp);
2617
2618	/* Retrieve information about which vector precedes. gmx_angle always
2619	* returns a positive angle. */
2620	cprod(xp, xrp, dum); /* if reference precedes, this is pointing into the same direction as vec */
2621
2622	if (iprod(rotg->vec, dum) >= 0)
2623	{
2624	*alpha = -gmx_angle(xrp, xp);
2625	}
2626	else
2627	{
2628	*alpha = +gmx_angle(xrp, xp);
2629	}
2630
2631	/* Also return the weight */
2632	*weight = norm(xp);
2633	}
2634
2635
2636	/* Project first vector onto a plane perpendicular to the second vector
2637	* dr = dr - (dr.v)v
2638	* Note that v must be of unit length.
2639	*/
2640	static gmx_inlineinline void project_onto_plane(rvec dr, const rvec v)
2641	{
2642	rvec tmp;
2643
2644
2645	svmul(iprod(dr, v), v, tmp); /* tmp = (dr.v)v */
2646	rvec_dec(dr, tmp); /* dr = dr - (dr.v)v */
2647	}
2648
2649
2650	/* Fixed rotation: The rotation reference group rotates around the v axis. */
2651	/* The atoms of the actual rotation group are attached with imaginary */
2652	/* springs to the reference atoms. */
2653	static void do_fixed(
2654	t_rotgrp rotg, / The rotation group */
2655	gmx_bool bOutstepRot, /* Output to main rotation output file */
2656	gmx_bool bOutstepSlab) /* Output per-slab data */
2657	{
2658	int ifit, j, jj, m;
2659	rvec dr;
2660	rvec tmp_f; /* Force */
2661	real alpha; /* a single angle between an actual and a reference position */
2662	real weight; /* single weight for a single angle */
2663	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2664	rvec xi_xc; /* xi - xc */
2665	gmx_bool bCalcPotFit;
2666	rvec fit_xr_loc;
2667
2668	/* for mass weighting: */
2669	real wi; /* Mass-weighting of the positions */
2670	real N_M; /* N/M */
2671	real k_wi; /* k times wi */
2672
2673	gmx_bool bProject;
2674
2675
2676	erg = rotg->enfrotgrp;
2677	bProject = (rotg->eType == erotgPM) \|\| (rotg->eType == erotgPMPF);
2678	bCalcPotFit = (bOutstepRot \|\| bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2679
2680	N_M = rotg->nat * erg->invmass;
2681
2682	/* Each process calculates the forces on its local atoms */
2683	for (j = 0; j < erg->nat_loc; j++)
2684	{
2685	/* Calculate (x_i-x_c) resp. (x_i-u) */
2686	rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xi_xc);
2687
2688	/* Calculate Omega(y_i-y_c)-(x_i-x_c) /
2689	rvec_sub(erg->xr_loc[j], xi_xc, dr);
2690
2691	if (bProject)
2692	{
2693	project_onto_plane(dr, rotg->vec);
2694	}
2695
2696	/* Mass-weighting */
2697	wi = N_M*erg->m_loc[j];
2698
2699	/* Store the additional force so that it can be added to the force
2700	* array after the normal forces have been evaluated */
2701	k_wi = rotg->k*wi;
2702	for (m = 0; m < DIM3; m++)
2703	{
2704	tmp_f[m] = k_wi*dr[m];
2705	erg->f_rot_loc[j][m] = tmp_f[m];
2706	erg->V += 0.5k_wisqr(dr[m]);
2707	}
2708
2709	/* If requested, also calculate the potential for a set of angles
2710	* near the current reference angle */
2711	if (bCalcPotFit)
2712	{
2713	for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2714	{
2715	/* Index of this rotation group atom with respect to the whole rotation group */
2716	jj = erg->xc_ref_ind[j];
2717
2718	/* Rotate with the alternative angle. Like rotate_local_reference(),
2719	* just for a single local atom */
2720	mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_xr_loc); /* fit_xr_loc = Omega(y_i-y_c) /
2721
2722	/* Calculate Omega(y_i-y_c)-(x_i-x_c) /
2723	rvec_sub(fit_xr_loc, xi_xc, dr);
2724
2725	if (bProject)
2726	{
2727	project_onto_plane(dr, rotg->vec);
2728	}
2729
2730	/* Add to the rotation potential for this angle: */
2731	erg->PotAngleFit->V[ifit] += 0.5k_winorm2(dr);
2732	}
2733	}
2734
2735	if (bOutstepRot)
2736	{
2737	/* Add to the torque of this rotation group */
2738	erg->torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2739
2740	/* Calculate the angle between reference and actual rotation group atom. */
2741	angle(rotg, xi_xc, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2742	erg->angle_v += alpha * weight;
2743	erg->weight_v += weight;
2744	}
2745	/* If you want enforced rotation to contribute to the virial,
2746	* activate the following lines:
2747	if (MASTER(cr))
2748	{
2749	Add the rotation contribution to the virial
2750	for(j=0; j<DIM; j++)
2751	for(m=0;m<DIM;m++)
2752	vir[j][m] += 0.5f[ii][j]dr[m];
2753	}
2754	*/
2755
2756	PRINT_FORCE_J
2757
2758	} /* end of loop over local rotation group atoms */
2759	}
2760
2761
2762	/* Calculate the radial motion potential and forces */
2763	static void do_radial_motion(
2764	t_rotgrp rotg, / The rotation group */
2765	gmx_bool bOutstepRot, /* Output to main rotation output file */
2766	gmx_bool bOutstepSlab) /* Output per-slab data */
2767	{
2768	int j, jj, ifit;
2769	rvec tmp_f; /* Force */
2770	real alpha; /* a single angle between an actual and a reference position */
2771	real weight; /* single weight for a single angle */
2772	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2773	rvec xj_u; /* xj - u */
2774	rvec tmpvec, fit_tmpvec;
2775	real fac, fac2, sum = 0.0;
2776	rvec pj;
2777	gmx_bool bCalcPotFit;
2778
2779	/* For mass weighting: */
2780	real wj; /* Mass-weighting of the positions */
2781	real N_M; /* N/M */
2782
2783
2784	erg = rotg->enfrotgrp;
2785	bCalcPotFit = (bOutstepRot \|\| bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2786
2787	N_M = rotg->nat * erg->invmass;
2788
2789	/* Each process calculates the forces on its local atoms */
2790	for (j = 0; j < erg->nat_loc; j++)
2791	{
2792	/* Calculate (xj-u) */
2793	rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xj_u); /* xj_u = xj-u */
2794
2795	/* Calculate Omega.(yj0-u) */
2796	cprod(rotg->vec, erg->xr_loc[j], tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2797
2798	/* * v x Omega.(yj0-u) */
2799	unitv(tmpvec, pj); /* pj = --------------------- */
2800	/* \| v x Omega.(yj0-u) \| */
2801
2802	fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2803	fac2 = fac*fac;
2804
2805	/* Mass-weighting */
2806	wj = N_M*erg->m_loc[j];
2807
2808	/* Store the additional force so that it can be added to the force
2809	* array after the normal forces have been evaluated */
2810	svmul(-rotg->kwjfac, pj, tmp_f);
2811	copy_rvec(tmp_f, erg->f_rot_loc[j]);
2812	sum += wj*fac2;
2813
2814	/* If requested, also calculate the potential for a set of angles
2815	* near the current reference angle */
2816	if (bCalcPotFit)
2817	{
2818	for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2819	{
2820	/* Index of this rotation group atom with respect to the whole rotation group */
2821	jj = erg->xc_ref_ind[j];
2822
2823	/* Rotate with the alternative angle. Like rotate_local_reference(),
2824	* just for a single local atom */
2825	mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_tmpvec); /* fit_tmpvec = Omega(yj0-u) /
2826
2827	/* Calculate Omega.(yj0-u) */
2828	cprod(rotg->vec, fit_tmpvec, tmpvec); /* tmpvec = v x Omega.(yj0-u) */
2829	/* * v x Omega.(yj0-u) */
2830	unitv(tmpvec, pj); /* pj = --------------------- */
2831	/* \| v x Omega.(yj0-u) \| */
2832
2833	fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
2834	fac2 = fac*fac;
2835
2836	/* Add to the rotation potential for this angle: */
2837	erg->PotAngleFit->V[ifit] += 0.5rotg->kwj*fac2;
2838	}
2839	}
2840
2841	if (bOutstepRot)
2842	{
2843	/* Add to the torque of this rotation group */
2844	erg->torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
2845
2846	/* Calculate the angle between reference and actual rotation group atom. */
2847	angle(rotg, xj_u, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
2848	erg->angle_v += alpha * weight;
2849	erg->weight_v += weight;
2850	}
2851
2852	PRINT_FORCE_J
2853
2854	} /* end of loop over local rotation group atoms */
2855	erg->V = 0.5rotg->ksum;
2856	}
2857
2858
2859	/* Calculate the radial motion pivot-free potential and forces */
2860	static void do_radial_motion_pf(
2861	t_rotgrp rotg, / The rotation group */
2862	rvec x[], /* The positions */
2863	matrix box, /* The simulation box */
2864	gmx_bool bOutstepRot, /* Output to main rotation output file */
2865	gmx_bool bOutstepSlab) /* Output per-slab data */
2866	{
2867	int i, ii, iigrp, ifit, j;
2868	rvec xj; /* Current position */
2869	rvec xj_xc; /* xj - xc */
2870	rvec yj0_yc0; /* yj0 - yc0 */
2871	rvec tmp_f; /* Force */
2872	real alpha; /* a single angle between an actual and a reference position */
2873	real weight; /* single weight for a single angle */
2874	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
2875	rvec tmpvec, tmpvec2;
2876	rvec innersumvec; /* Precalculation of the inner sum */
2877	rvec innersumveckM;
2878	real fac, fac2, V = 0.0;
2879	rvec qi, qj;
2880	gmx_bool bCalcPotFit;
2881
2882	/* For mass weighting: */
2883	real mj, wi, wj; /* Mass-weighting of the positions */
2884	real N_M; /* N/M */
2885
2886
2887	erg = rotg->enfrotgrp;
2888	bCalcPotFit = (bOutstepRot \|\| bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
2889
2890	N_M = rotg->nat * erg->invmass;
2891
2892	/* Get the current center of the rotation group: */
2893	get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
2894
2895	/* Precalculate Sum_i [ wi qi.(xi-xc) qi ] which is needed for every single j */
2896	clear_rvec(innersumvec);
2897	for (i = 0; i < rotg->nat; i++)
2898	{
2899	/* Mass-weighting */
2900	wi = N_M*erg->mc[i];
2901
2902	/* Calculate qi. Note that xc_ref_center has already been subtracted from
2903	* x_ref in init_rot_group.*/
2904	mvmul(erg->rotmat, rotg->x_ref[i], tmpvec); /* tmpvec = Omega.(yi0-yc0) */
2905
2906	cprod(rotg->vec, tmpvec, tmpvec2); /* tmpvec2 = v x Omega.(yi0-yc0) */
2907
2908	/* * v x Omega.(yi0-yc0) */
2909	unitv(tmpvec2, qi); /* qi = ----------------------- */
2910	/* \| v x Omega.(yi0-yc0) \| */
2911
2912	rvec_sub(erg->xc[i], erg->xc_center, tmpvec); /* tmpvec = xi-xc */
2913
2914	svmul(wi*iprod(qi, tmpvec), qi, tmpvec2);
2915
2916	rvec_inc(innersumvec, tmpvec2);
2917	}
2918	svmul(rotg->k*erg->invmass, innersumvec, innersumveckM);
2919
2920	/* Each process calculates the forces on its local atoms */
2921	for (j = 0; j < erg->nat_loc; j++)
2922	{
2923	/* Local index of a rotation group atom */
2924	ii = erg->ind_loc[j];
2925	/* Position of this atom in the collective array */
2926	iigrp = erg->xc_ref_ind[j];
2927	/* Mass-weighting */
2928	mj = erg->mc[iigrp]; /* need the unsorted mass here */
2929	wj = N_M*mj;
2930
2931	/* Current position of this atom: x[ii][XX/YY/ZZ] */
2932	copy_rvec(x[ii], xj);
2933
2934	/* Shift this atom such that it is near its reference */
2935	shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
2936
2937	/* The (unrotated) reference position is yj0. yc0 has already
2938	* been subtracted in init_rot_group */
2939	copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
2940
2941	/* Calculate Omega.(yj0-yc0) */
2942	mvmul(erg->rotmat, yj0_yc0, tmpvec2); /* tmpvec2 = Omega.(yj0 - yc0) */
2943
2944	cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
2945
2946	/* * v x Omega.(yj0-yc0) */
2947	unitv(tmpvec, qj); /* qj = ----------------------- */
2948	/* \| v x Omega.(yj0-yc0) \| */
2949
2950	/* Calculate (xj-xc) */
2951	rvec_sub(xj, erg->xc_center, xj_xc); /* xj_xc = xj-xc */
2952
2953	fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
2954	fac2 = fac*fac;
2955
2956	/* Store the additional force so that it can be added to the force
2957	* array after the normal forces have been evaluated */
2958	svmul(-rotg->kwjfac, qj, tmp_f); /* part 1 of force */
2959	svmul(mj, innersumveckM, tmpvec); /* part 2 of force */
2960	rvec_inc(tmp_f, tmpvec);
2961	copy_rvec(tmp_f, erg->f_rot_loc[j]);
2962	V += wj*fac2;
2963
2964	/* If requested, also calculate the potential for a set of angles
2965	* near the current reference angle */
2966	if (bCalcPotFit)
2967	{
2968	for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
2969	{
2970	/* Rotate with the alternative angle. Like rotate_local_reference(),
2971	* just for a single local atom */
2972	mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, tmpvec2); /* tmpvec2 = Omega(yj0-yc0) /
2973
2974	/* Calculate Omega.(yj0-u) */
2975	cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
2976	/* * v x Omega.(yj0-yc0) */
2977	unitv(tmpvec, qj); /* qj = ----------------------- */
2978	/* \| v x Omega.(yj0-yc0) \| */
2979
2980	fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
2981	fac2 = fac*fac;
2982
2983	/* Add to the rotation potential for this angle: */
2984	erg->PotAngleFit->V[ifit] += 0.5rotg->kwj*fac2;
2985	}
2986	}
2987
2988	if (bOutstepRot)
2989	{
2990	/* Add to the torque of this rotation group */
2991	erg->torque_v += torque(rotg->vec, tmp_f, xj, erg->xc_center);
2992
2993	/* Calculate the angle between reference and actual rotation group atom. */
2994	angle(rotg, xj_xc, yj0_yc0, &alpha, &weight); /* angle in rad, weighted */
2995	erg->angle_v += alpha * weight;
2996	erg->weight_v += weight;
2997	}
2998
2999	PRINT_FORCE_J
3000
3001	} /* end of loop over local rotation group atoms */
3002	erg->V = 0.5rotg->kV;
3003	}
3004
3005
3006	/* Precalculate the inner sum for the radial motion 2 forces */
3007	static void radial_motion2_precalc_inner_sum(t_rotgrp *rotg, rvec innersumvec)
3008	{
3009	int i;
3010	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3011	rvec xi_xc; /* xj - xc */
3012	rvec tmpvec, tmpvec2;
3013	real fac, fac2;
3014	rvec ri, si;
3015	real siri;
3016	rvec v_xi_xc; /* v x (xj - u) */
3017	real psii, psiistar;
3018	real wi; /* Mass-weighting of the positions */
3019	real N_M; /* N/M */
3020	rvec sumvec;
3021
3022	erg = rotg->enfrotgrp;
3023	N_M = rotg->nat * erg->invmass;
3024
3025	/* Loop over the collective set of positions */
3026	clear_rvec(sumvec);
3027	for (i = 0; i < rotg->nat; i++)
3028	{
3029	/* Mass-weighting */
3030	wi = N_M*erg->mc[i];
3031
3032	rvec_sub(erg->xc[i], erg->xc_center, xi_xc); /* xi_xc = xi-xc */
3033
3034	/* Calculate ri. Note that xc_ref_center has already been subtracted from
3035	* x_ref in init_rot_group.*/
3036	mvmul(erg->rotmat, rotg->x_ref[i], ri); /* ri = Omega.(yi0-yc0) */
3037
3038	cprod(rotg->vec, xi_xc, v_xi_xc); /* v_xi_xc = v x (xi-u) */
3039
3040	fac = norm2(v_xi_xc);
3041	/* * 1 */
3042	psiistar = 1.0/(fac + rotg->eps); /* psiistar = --------------------- */
3043	/* \|v x (xi-xc)\|^2 + eps */
3044
3045	psii = gmx_invsqrt(fac)gmx_software_invsqrt(fac); /* 1 */
3046	/* psii = ------------- */
3047	/* \|v x (xi-xc)\| */
3048
3049	svmul(psii, v_xi_xc, si); /* si = psii * (v x (xi-xc) ) */
3050
3051	fac = iprod(v_xi_xc, ri); /* fac = (v x (xi-xc)).ri */
3052	fac2 = fac*fac;
	Value stored to 'fac2' is never read
3053
3054	siri = iprod(si, ri); /* siri = si.ri */
3055
3056	svmul(psiistar/psii, ri, tmpvec);
3057	svmul(psiistarpsiistar/(psiipsiipsii) siri, si, tmpvec2);
3058	rvec_dec(tmpvec, tmpvec2);
3059	cprod(tmpvec, rotg->vec, tmpvec2);
3060
3061	svmul(wi*siri, tmpvec2, tmpvec);
3062
3063	rvec_inc(sumvec, tmpvec);
3064	}
3065	svmul(rotg->k*erg->invmass, sumvec, innersumvec);
3066	}
3067
3068
3069	/* Calculate the radial motion 2 potential and forces */
3070	static void do_radial_motion2(
3071	t_rotgrp rotg, / The rotation group */
3072	rvec x[], /* The positions */
3073	matrix box, /* The simulation box */
3074	gmx_bool bOutstepRot, /* Output to main rotation output file */
3075	gmx_bool bOutstepSlab) /* Output per-slab data */
3076	{
3077	int ii, iigrp, ifit, j;
3078	rvec xj; /* Position */
3079	real alpha; /* a single angle between an actual and a reference position */
3080	real weight; /* single weight for a single angle */
3081	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3082	rvec xj_u; /* xj - u */
3083	rvec yj0_yc0; /* yj0 -yc0 */
3084	rvec tmpvec, tmpvec2;
3085	real fac, fit_fac, fac2, Vpart = 0.0;
3086	rvec rj, fit_rj, sj;
3087	real sjrj;
3088	rvec v_xj_u; /* v x (xj - u) */
3089	real psij, psijstar;
3090	real mj, wj; /* For mass-weighting of the positions */
3091	real N_M; /* N/M */
3092	gmx_bool bPF;
3093	rvec innersumvec;
3094	gmx_bool bCalcPotFit;
3095
3096
3097	erg = rotg->enfrotgrp;
3098
3099	bPF = rotg->eType == erotgRM2PF;
3100	bCalcPotFit = (bOutstepRot \|\| bOutstepSlab) && (erotgFitPOT == rotg->eFittype);
3101
3102
3103	clear_rvec(yj0_yc0); /* Make the compiler happy */
3104
3105	clear_rvec(innersumvec);
3106	if (bPF)
3107	{
3108	/* For the pivot-free variant we have to use the current center of
3109	* mass of the rotation group instead of the pivot u */
3110	get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
3111
3112	/* Also, we precalculate the second term of the forces that is identical
3113	* (up to the weight factor mj) for all forces */
3114	radial_motion2_precalc_inner_sum(rotg, innersumvec);
3115	}
3116
3117	N_M = rotg->nat * erg->invmass;
3118
3119	/* Each process calculates the forces on its local atoms */
3120	for (j = 0; j < erg->nat_loc; j++)
3121	{
3122	if (bPF)
3123	{
3124	/* Local index of a rotation group atom */
3125	ii = erg->ind_loc[j];
3126	/* Position of this atom in the collective array */
3127	iigrp = erg->xc_ref_ind[j];
3128	/* Mass-weighting */
3129	mj = erg->mc[iigrp];
3130
3131	/* Current position of this atom: x[ii] */
3132	copy_rvec(x[ii], xj);
3133
3134	/* Shift this atom such that it is near its reference */
3135	shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
3136
3137	/* The (unrotated) reference position is yj0. yc0 has already
3138	* been subtracted in init_rot_group */
3139	copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
3140
3141	/* Calculate Omega.(yj0-yc0) */
3142	mvmul(erg->rotmat, yj0_yc0, rj); /* rj = Omega.(yj0-yc0) */
3143	}
3144	else
3145	{
3146	mj = erg->m_loc[j];
3147	copy_rvec(erg->x_loc_pbc[j], xj);
3148	copy_rvec(erg->xr_loc[j], rj); /* rj = Omega.(yj0-u) */
3149	}
3150	/* Mass-weighting */
3151	wj = N_M*mj;
3152
3153	/* Calculate (xj-u) resp. (xj-xc) */
3154	rvec_sub(xj, erg->xc_center, xj_u); /* xj_u = xj-u */
3155
3156	cprod(rotg->vec, xj_u, v_xj_u); /* v_xj_u = v x (xj-u) */
3157
3158	fac = norm2(v_xj_u);
3159	/* * 1 */
3160	psijstar = 1.0/(fac + rotg->eps); /* psistar = -------------------- */
3161	/* \|v x (xj-u)\|^2 + eps */
3162
3163	psij = gmx_invsqrt(fac)gmx_software_invsqrt(fac); /* 1 */
3164	/* psij = ------------ */
3165	/* \|v x (xj-u)\| */
3166
3167	svmul(psij, v_xj_u, sj); /* sj = psij * (v x (xj-u) ) */
3168
3169	fac = iprod(v_xj_u, rj); /* fac = (v x (xj-u)).rj */
3170	fac2 = fac*fac;
3171
3172	sjrj = iprod(sj, rj); /* sjrj = sj.rj */
3173
3174	svmul(psijstar/psij, rj, tmpvec);
3175	svmul(psijstarpsijstar/(psijpsijpsij) sjrj, sj, tmpvec2);
3176	rvec_dec(tmpvec, tmpvec2);
3177	cprod(tmpvec, rotg->vec, tmpvec2);
3178
3179	/* Store the additional force so that it can be added to the force
3180	* array after the normal forces have been evaluated */
3181	svmul(-rotg->kwjsjrj, tmpvec2, tmpvec);
3182	svmul(mj, innersumvec, tmpvec2); /* This is != 0 only for the pivot-free variant */
3183
3184	rvec_add(tmpvec2, tmpvec, erg->f_rot_loc[j]);
3185	Vpart += wjpsijstarfac2;
3186
3187	/* If requested, also calculate the potential for a set of angles
3188	* near the current reference angle */
3189	if (bCalcPotFit)
3190	{
3191	for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
3192	{
3193	if (bPF)
3194	{
3195	mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, fit_rj); /* fit_rj = Omega.(yj0-yc0) */
3196	}
3197	else
3198	{
3199	/* Position of this atom in the collective array */
3200	iigrp = erg->xc_ref_ind[j];
3201	/* Rotate with the alternative angle. Like rotate_local_reference(),
3202	* just for a single local atom */
3203	mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[iigrp], fit_rj); /* fit_rj = Omega(yj0-u) /
3204	}
3205	fit_fac = iprod(v_xj_u, fit_rj); /* fac = (v x (xj-u)).fit_rj */
3206	/* Add to the rotation potential for this angle: */
3207	erg->PotAngleFit->V[ifit] += 0.5rotg->kwjpsijstarfit_fac*fit_fac;
3208	}
3209	}
3210
3211	if (bOutstepRot)
3212	{
3213	/* Add to the torque of this rotation group */
3214	erg->torque_v += torque(rotg->vec, erg->f_rot_loc[j], xj, erg->xc_center);
3215
3216	/* Calculate the angle between reference and actual rotation group atom. */
3217	angle(rotg, xj_u, rj, &alpha, &weight); /* angle in rad, weighted */
3218	erg->angle_v += alpha * weight;
3219	erg->weight_v += weight;
3220	}
3221
3222	PRINT_FORCE_J
3223
3224	} /* end of loop over local rotation group atoms */
3225	erg->V = 0.5rotg->kVpart;
3226	}
3227
3228
3229	/* Determine the smallest and largest position vector (with respect to the
3230	* rotation vector) for the reference group */
3231	static void get_firstlast_atom_ref(
3232	t_rotgrp *rotg,
3233	int *firstindex,
3234	int *lastindex)
3235	{
3236	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3237	int i;
3238	real xcproj; /* The projection of a reference position on the
3239	rotation vector */
3240	real minproj, maxproj; /* Smallest and largest projection on v */
3241
3242
3243
3244	erg = rotg->enfrotgrp;
3245
3246	/* Start with some value */
3247	minproj = iprod(rotg->x_ref[0], rotg->vec);
3248	maxproj = minproj;
3249
3250	/* This is just to ensure that it still works if all the atoms of the
3251	* reference structure are situated in a plane perpendicular to the rotation
3252	* vector */
3253	*firstindex = 0;
3254	*lastindex = rotg->nat-1;
3255
3256	/* Loop over all atoms of the reference group,
3257	* project them on the rotation vector to find the extremes */
3258	for (i = 0; i < rotg->nat; i++)
3259	{
3260	xcproj = iprod(rotg->x_ref[i], rotg->vec);
3261	if (xcproj < minproj)
3262	{
3263	minproj = xcproj;
3264	*firstindex = i;
3265	}
3266	if (xcproj > maxproj)
3267	{
3268	maxproj = xcproj;
3269	*lastindex = i;
3270	}
3271	}
3272	}
3273
3274
3275	/* Allocate memory for the slabs */
3276	static void allocate_slabs(
3277	t_rotgrp *rotg,
3278	FILE *fplog,
3279	int g,
3280	gmx_bool bVerbose)
3281	{
3282	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3283	int i, nslabs;
3284
3285
3286	erg = rotg->enfrotgrp;
3287
3288	/* More slabs than are defined for the reference are never needed */
3289	nslabs = erg->slab_last_ref - erg->slab_first_ref + 1;
3290
3291	/* Remember how many we allocated */
3292	erg->nslabs_alloc = nslabs;
3293
3294	if ( (NULL((void*)0) != fplog) && bVerbose)
3295	{
3296	fprintf(fplog, "%s allocating memory to store data for %d slabs (rotation group %d).\n",
3297	RotStr, nslabs, g);
3298	}
3299	snew(erg->slab_center, nslabs)(erg->slab_center) = save_calloc("erg->slab_center", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3299, (nslabs), sizeof(*(erg->slab_center)));
3300	snew(erg->slab_center_ref, nslabs)(erg->slab_center_ref) = save_calloc("erg->slab_center_ref" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3300, (nslabs), sizeof(*(erg->slab_center_ref)));
3301	snew(erg->slab_weights, nslabs)(erg->slab_weights) = save_calloc("erg->slab_weights", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3301, (nslabs), sizeof(*(erg->slab_weights)));
3302	snew(erg->slab_torque_v, nslabs)(erg->slab_torque_v) = save_calloc("erg->slab_torque_v" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3302, (nslabs), sizeof(*(erg->slab_torque_v)));
3303	snew(erg->slab_data, nslabs)(erg->slab_data) = save_calloc("erg->slab_data", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3303, (nslabs), sizeof(*(erg->slab_data)));
3304	snew(erg->gn_atom, nslabs)(erg->gn_atom) = save_calloc("erg->gn_atom", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3304, (nslabs), sizeof(*(erg->gn_atom)));
3305	snew(erg->gn_slabind, nslabs)(erg->gn_slabind) = save_calloc("erg->gn_slabind", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3305, (nslabs), sizeof(*(erg->gn_slabind)));
3306	snew(erg->slab_innersumvec, nslabs)(erg->slab_innersumvec) = save_calloc("erg->slab_innersumvec" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3306, (nslabs), sizeof(*(erg->slab_innersumvec)));
3307	for (i = 0; i < nslabs; i++)
3308	{
3309	snew(erg->slab_data[i].x, rotg->nat)(erg->slab_data[i].x) = save_calloc("erg->slab_data[i].x" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3309, (rotg->nat), sizeof(*(erg->slab_data[i].x)));
3310	snew(erg->slab_data[i].ref, rotg->nat)(erg->slab_data[i].ref) = save_calloc("erg->slab_data[i].ref" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3310, (rotg->nat), sizeof(*(erg->slab_data[i].ref)));
3311	snew(erg->slab_data[i].weight, rotg->nat)(erg->slab_data[i].weight) = save_calloc("erg->slab_data[i].weight" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3311, (rotg->nat), sizeof(*(erg->slab_data[i].weight) ));
3312	}
3313	snew(erg->xc_ref_sorted, rotg->nat)(erg->xc_ref_sorted) = save_calloc("erg->xc_ref_sorted" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3313, (rotg->nat), sizeof(*(erg->xc_ref_sorted)));
3314	snew(erg->xc_sortind, rotg->nat)(erg->xc_sortind) = save_calloc("erg->xc_sortind", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3314, (rotg->nat), sizeof(*(erg->xc_sortind)));
3315	snew(erg->firstatom, nslabs)(erg->firstatom) = save_calloc("erg->firstatom", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3315, (nslabs), sizeof(*(erg->firstatom)));
3316	snew(erg->lastatom, nslabs)(erg->lastatom) = save_calloc("erg->lastatom", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3316, (nslabs), sizeof(*(erg->lastatom)));
3317	}
3318
3319
3320	/* From the extreme positions of the reference group, determine the first
3321	* and last slab of the reference. We can never have more slabs in the real
3322	* simulation than calculated here for the reference.
3323	*/
3324	static void get_firstlast_slab_ref(t_rotgrp *rotg, real mc[], int ref_firstindex, int ref_lastindex)
3325	{
3326	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3327	int first, last;
3328	rvec dummy;
3329
3330
3331	erg = rotg->enfrotgrp;
3332	first = get_first_slab(rotg, erg->max_beta, rotg->x_ref[ref_firstindex]);
3333	last = get_last_slab( rotg, erg->max_beta, rotg->x_ref[ref_lastindex ]);
3334
3335	while (get_slab_weight(first, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN(10*1.17549435E-38))
3336	{
3337	first--;
3338	}
3339	erg->slab_first_ref = first+1;
3340	while (get_slab_weight(last, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN(10*1.17549435E-38))
3341	{
3342	last++;
3343	}
3344	erg->slab_last_ref = last-1;
3345	}
3346
3347
3348	/* Special version of copy_rvec:
3349	* During the copy procedure of xcurr to b, the correct PBC image is chosen
3350	* such that the copied vector ends up near its reference position xref */
3351	static gmx_inlineinline void copy_correct_pbc_image(
3352	const rvec xcurr, /* copy vector xcurr ... */
3353	rvec b, /* ... to b ... */
3354	const rvec xref, /* choosing the PBC image such that b ends up near xref */
3355	matrix box,
3356	int npbcdim)
3357	{
3358	rvec dx;
3359	int d, m;
3360	ivec shift;
3361
3362
3363	/* Shortest PBC distance between the atom and its reference */
3364	rvec_sub(xcurr, xref, dx);
3365
3366	/* Determine the shift for this atom */
3367	clear_ivec(shift);
3368	for (m = npbcdim-1; m >= 0; m--)
3369	{
3370	while (dx[m] < -0.5*box[m][m])
3371	{
3372	for (d = 0; d < DIM3; d++)
3373	{
3374	dx[d] += box[m][d];
3375	}
3376	shift[m]++;
3377	}
3378	while (dx[m] >= 0.5*box[m][m])
3379	{
3380	for (d = 0; d < DIM3; d++)
3381	{
3382	dx[d] -= box[m][d];
3383	}
3384	shift[m]--;
3385	}
3386	}
3387
3388	/* Apply the shift to the position */
3389	copy_rvec(xcurr, b);
3390	shift_single_coord(box, b, shift);
3391	}
3392
3393
3394	static void init_rot_group(FILE fplog, t_commrec cr, int g, t_rotgrp *rotg,
3395	rvec x, gmx_mtop_t mtop, gmx_bool bVerbose, FILE *out_slabs, matrix box,
3396	t_inputrec *ir, gmx_bool bOutputCenters)
3397	{
3398	int i, ii;
3399	rvec coord, xref, *xdum;
3400	gmx_bool bFlex, bColl;
3401	t_atom *atom;
3402	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3403	int ref_firstindex, ref_lastindex;
3404	gmx_mtop_atomlookup_t alook = NULL((void*)0);
3405	real mass, totalmass;
3406	real start = 0.0;
3407	double t_start;
3408
3409
3410	/* Do we have a flexible axis? */
3411	bFlex = ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) );
3412	/* Do we use a global set of coordinates? */
3413	bColl = ISCOLL(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) \|\| (rotg->eType == erotgRMPF) \|\| (rotg->eType == erotgRM2PF ) );
3414
3415	erg = rotg->enfrotgrp;
3416
3417	/* Allocate space for collective coordinates if needed */
3418	if (bColl)
3419	{
3420	snew(erg->xc, rotg->nat)(erg->xc) = save_calloc("erg->xc", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3420, (rotg->nat), sizeof(*(erg->xc)));
3421	snew(erg->xc_shifts, rotg->nat)(erg->xc_shifts) = save_calloc("erg->xc_shifts", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3421, (rotg->nat), sizeof(*(erg->xc_shifts)));
3422	snew(erg->xc_eshifts, rotg->nat)(erg->xc_eshifts) = save_calloc("erg->xc_eshifts", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3422, (rotg->nat), sizeof(*(erg->xc_eshifts)));
3423	snew(erg->xc_old, rotg->nat)(erg->xc_old) = save_calloc("erg->xc_old", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3423, (rotg->nat), sizeof(*(erg->xc_old)));
3424
3425	if (rotg->eFittype == erotgFitNORM)
3426	{
3427	snew(erg->xc_ref_length, rotg->nat)(erg->xc_ref_length) = save_calloc("erg->xc_ref_length" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3427, (rotg->nat), sizeof((erg->xc_ref_length))); / in case fit type NORM is chosen */
3428	snew(erg->xc_norm, rotg->nat)(erg->xc_norm) = save_calloc("erg->xc_norm", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3428, (rotg->nat), sizeof(*(erg->xc_norm)));
3429	}
3430	}
3431	else
3432	{
3433	snew(erg->xr_loc, rotg->nat)(erg->xr_loc) = save_calloc("erg->xr_loc", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3433, (rotg->nat), sizeof(*(erg->xr_loc)));
3434	snew(erg->x_loc_pbc, rotg->nat)(erg->x_loc_pbc) = save_calloc("erg->x_loc_pbc", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3434, (rotg->nat), sizeof(*(erg->x_loc_pbc)));
3435	}
3436
3437	snew(erg->f_rot_loc, rotg->nat)(erg->f_rot_loc) = save_calloc("erg->f_rot_loc", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3437, (rotg->nat), sizeof(*(erg->f_rot_loc)));
3438	snew(erg->xc_ref_ind, rotg->nat)(erg->xc_ref_ind) = save_calloc("erg->xc_ref_ind", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3438, (rotg->nat), sizeof(*(erg->xc_ref_ind)));
3439
3440	/* Make space for the calculation of the potential at other angles (used
3441	* for fitting only) */
3442	if (erotgFitPOT == rotg->eFittype)
3443	{
3444	snew(erg->PotAngleFit, 1)(erg->PotAngleFit) = save_calloc("erg->PotAngleFit", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3444, (1), sizeof(*(erg->PotAngleFit)));
3445	snew(erg->PotAngleFit->degangle, rotg->PotAngle_nstep)(erg->PotAngleFit->degangle) = save_calloc("erg->PotAngleFit->degangle" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3445, (rotg->PotAngle_nstep), sizeof(*(erg->PotAngleFit ->degangle)));
3446	snew(erg->PotAngleFit->V, rotg->PotAngle_nstep)(erg->PotAngleFit->V) = save_calloc("erg->PotAngleFit->V" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3446, (rotg->PotAngle_nstep), sizeof(*(erg->PotAngleFit ->V)));
3447	snew(erg->PotAngleFit->rotmat, rotg->PotAngle_nstep)(erg->PotAngleFit->rotmat) = save_calloc("erg->PotAngleFit->rotmat" , "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3447, (rotg->PotAngle_nstep), sizeof(*(erg->PotAngleFit ->rotmat)));
3448
3449	/* Get the set of angles around the reference angle */
3450	start = -0.5 * (rotg->PotAngle_nstep - 1)*rotg->PotAngle_step;
3451	for (i = 0; i < rotg->PotAngle_nstep; i++)
3452	{
3453	erg->PotAngleFit->degangle[i] = start + i*rotg->PotAngle_step;
3454	}
3455	}
3456	else
3457	{
3458	erg->PotAngleFit = NULL((void*)0);
3459	}
3460
3461	/* xc_ref_ind needs to be set to identity in the serial case */
3462	if (!PAR(cr)((cr)->nnodes > 1))
3463	{
3464	for (i = 0; i < rotg->nat; i++)
3465	{
3466	erg->xc_ref_ind[i] = i;
3467	}
3468	}
3469
3470	/* Copy the masses so that the center can be determined. For all types of
3471	* enforced rotation, we store the masses in the erg->mc array. */
3472	if (rotg->bMassW)
3473	{
3474	alook = gmx_mtop_atomlookup_init(mtop);
3475	}
3476	snew(erg->mc, rotg->nat)(erg->mc) = save_calloc("erg->mc", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3476, (rotg->nat), sizeof(*(erg->mc)));
3477	if (bFlex)
3478	{
3479	snew(erg->mc_sorted, rotg->nat)(erg->mc_sorted) = save_calloc("erg->mc_sorted", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3479, (rotg->nat), sizeof(*(erg->mc_sorted)));
3480	}
3481	if (!bColl)
3482	{
3483	snew(erg->m_loc, rotg->nat)(erg->m_loc) = save_calloc("erg->m_loc", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3483, (rotg->nat), sizeof(*(erg->m_loc)));
3484	}
3485	totalmass = 0.0;
3486	for (i = 0; i < rotg->nat; i++)
3487	{
3488	if (rotg->bMassW)
3489	{
3490	gmx_mtop_atomnr_to_atom(alook, rotg->ind[i], &atom);
3491	mass = atom->m;
3492	}
3493	else
3494	{
3495	mass = 1.0;
3496	}
3497	erg->mc[i] = mass;
3498	totalmass += mass;
3499	}
3500	erg->invmass = 1.0/totalmass;
3501
3502	if (rotg->bMassW)
3503	{
3504	gmx_mtop_atomlookup_destroy(alook);
3505	}
3506
3507	/* Set xc_ref_center for any rotation potential */
3508	if ((rotg->eType == erotgISO) \|\| (rotg->eType == erotgPM) \|\| (rotg->eType == erotgRM) \|\| (rotg->eType == erotgRM2))
3509	{
3510	/* Set the pivot point for the fixed, stationary-axis potentials. This
3511	* won't change during the simulation */
3512	copy_rvec(rotg->pivot, erg->xc_ref_center);
3513	copy_rvec(rotg->pivot, erg->xc_center );
3514	}
3515	else
3516	{
3517	/* Center of the reference positions */
3518	get_center(rotg->x_ref, erg->mc, rotg->nat, erg->xc_ref_center);
3519
3520	/* Center of the actual positions */
3521	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
3522	{
3523	snew(xdum, rotg->nat)(xdum) = save_calloc("xdum", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3523, (rotg->nat), sizeof(*(xdum)));
3524	for (i = 0; i < rotg->nat; i++)
3525	{
3526	ii = rotg->ind[i];
3527	copy_rvec(x[ii], xdum[i]);
3528	}
3529	get_center(xdum, erg->mc, rotg->nat, erg->xc_center);
3530	sfree(xdum)save_free("xdum", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3530, (xdum));
3531	}
3532	#ifdef GMX_MPI
3533	if (PAR(cr)((cr)->nnodes > 1))
3534	{
3535	gmx_bcast(sizeof(erg->xc_center), erg->xc_center, cr);
3536	}
3537	#endif
3538	}
3539
3540	if (bColl)
3541	{
3542	/* Save the original (whole) set of positions in xc_old such that at later
3543	* steps the rotation group can always be made whole again. If the simulation is
3544	* restarted, we compute the starting reference positions (given the time)
3545	* and assume that the correct PBC image of each position is the one nearest
3546	* to the current reference */
3547	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
3548	{
3549	/* Calculate the rotation matrix for this angle: */
3550	t_start = ir->init_t + ir->init_step*ir->delta_t;
3551	erg->degangle = rotg->rate * t_start;
3552	calc_rotmat(rotg->vec, erg->degangle, erg->rotmat);
3553
3554	for (i = 0; i < rotg->nat; i++)
3555	{
3556	ii = rotg->ind[i];
3557
3558	/* Subtract pivot, rotate, and add pivot again. This will yield the
3559	* reference position for time t */
3560	rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
3561	mvmul(erg->rotmat, coord, xref);
3562	rvec_inc(xref, erg->xc_ref_center);
3563
3564	copy_correct_pbc_image(x[ii], erg->xc_old[i], xref, box, 3);
3565	}
3566	}
3567	#ifdef GMX_MPI
3568	if (PAR(cr)((cr)->nnodes > 1))
3569	{
3570	gmx_bcast(rotg->nat*sizeof(erg->xc_old[0]), erg->xc_old, cr);
3571	}
3572	#endif
3573	}
3574
3575	if ( (rotg->eType != erotgFLEX) && (rotg->eType != erotgFLEX2) )
3576	{
3577	/* Put the reference positions into origin: */
3578	for (i = 0; i < rotg->nat; i++)
3579	{
3580	rvec_dec(rotg->x_ref[i], erg->xc_ref_center);
3581	}
3582	}
3583
3584	/* Enforced rotation with flexible axis */
3585	if (bFlex)
3586	{
3587	/* Calculate maximum beta value from minimum gaussian (performance opt.) */
3588	erg->max_beta = calc_beta_max(rotg->min_gaussian, rotg->slab_dist);
3589
3590	/* Determine the smallest and largest coordinate with respect to the rotation vector */
3591	get_firstlast_atom_ref(rotg, &ref_firstindex, &ref_lastindex);
3592
3593	/* From the extreme positions of the reference group, determine the first
3594	* and last slab of the reference. */
3595	get_firstlast_slab_ref(rotg, erg->mc, ref_firstindex, ref_lastindex);
3596
3597	/* Allocate memory for the slabs */
3598	allocate_slabs(rotg, fplog, g, bVerbose);
3599
3600	/* Flexible rotation: determine the reference centers for the rest of the simulation */
3601	erg->slab_first = erg->slab_first_ref;
3602	erg->slab_last = erg->slab_last_ref;
3603	get_slab_centers(rotg, rotg->x_ref, erg->mc, g, -1, out_slabs, bOutputCenters, TRUE1);
3604
3605	/* Length of each x_rotref vector from center (needed if fit routine NORM is chosen): */
3606	if (rotg->eFittype == erotgFitNORM)
3607	{
3608	for (i = 0; i < rotg->nat; i++)
3609	{
3610	rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
3611	erg->xc_ref_length[i] = norm(coord);
3612	}
3613	}
3614	}
3615	}
3616
3617
3618	extern void dd_make_local_rotation_groups(gmx_domdec_t dd, t_rot rot)
3619	{
3620	gmx_ga2la_t ga2la;
3621	int g;
3622	t_rotgrp *rotg;
3623	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3624
3625	ga2la = dd->ga2la;
3626
3627	for (g = 0; g < rot->ngrp; g++)
3628	{
3629	rotg = &rot->grp[g];
3630	erg = rotg->enfrotgrp;
3631
3632
3633	dd_make_local_group_indices(ga2la, rotg->nat, rotg->ind,
3634	&erg->nat_loc, &erg->ind_loc, &erg->nalloc_loc, erg->xc_ref_ind);
3635	}
3636	}
3637
3638
3639	/* Calculate the size of the MPI buffer needed in reduce_output() */
3640	static int calc_mpi_bufsize(t_rot *rot)
3641	{
3642	int g;
3643	int count_group, count_total;
3644	t_rotgrp *rotg;
3645	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3646
3647
3648	count_total = 0;
3649	for (g = 0; g < rot->ngrp; g++)
3650	{
3651	rotg = &rot->grp[g];
3652	erg = rotg->enfrotgrp;
3653
3654	/* Count the items that are transferred for this group: */
3655	count_group = 4; /* V, torque, angle, weight */
3656
3657	/* Add the maximum number of slabs for flexible groups */
3658	if (ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) ))
3659	{
3660	count_group += erg->slab_last_ref - erg->slab_first_ref + 1;
3661	}
3662
3663	/* Add space for the potentials at different angles: */
3664	if (erotgFitPOT == rotg->eFittype)
3665	{
3666	count_group += rotg->PotAngle_nstep;
3667	}
3668
3669	/* Add to the total number: */
3670	count_total += count_group;
3671	}
3672
3673	return count_total;
3674	}
3675
3676
3677	extern void init_rot(FILE fplog, t_inputrec ir, int nfile, const t_filenm fnm[],
3678	t_commrec cr, rvec x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
3679	gmx_bool bVerbose, unsigned long Flags)
3680	{
3681	t_rot *rot;
3682	t_rotgrp *rotg;
3683	int g;
3684	int nat_max = 0; /* Size of biggest rotation group */
3685	gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3686	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3687	rvec x_pbc = NULL((void)0); /* Space for the pbc-correct atom positions */
3688
3689
3690	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)) && bVerbose)
3691	{
3692	fprintf(stdoutstdout, "%s Initializing ...\n", RotStr);
3693	}
3694
3695	rot = ir->rot;
3696	snew(rot->enfrot, 1)(rot->enfrot) = save_calloc("rot->enfrot", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3696, (1), sizeof(*(rot->enfrot)));
3697	er = rot->enfrot;
3698	er->Flags = Flags;
3699
3700	/* When appending, skip first output to avoid duplicate entries in the data files */
3701	if (er->Flags & MD_APPENDFILES(1<<15))
3702	{
3703	er->bOut = FALSE0;
3704	}
3705	else
3706	{
3707	er->bOut = TRUE1;
3708	}
3709
3710	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)) && er->bOut)
3711	{
3712	please_cite(fplog, "Kutzner2011");
3713	}
3714
3715	/* Output every step for reruns */
3716	if (er->Flags & MD_RERUN(1<<4))
3717	{
3718	if (NULL((void*)0) != fplog)
3719	{
3720	fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
3721	}
3722	rot->nstrout = 1;
3723	rot->nstsout = 1;
3724	}
3725
3726	er->out_slabs = NULL((void*)0);
3727	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)) && HaveFlexibleGroups(rot) )
3728	{
3729	er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), rot);
3730	}
3731
3732	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
3733	{
3734	/* Remove pbc, make molecule whole.
3735	* When ir->bContinuation=TRUE this has already been done, but ok. */
3736	snew(x_pbc, mtop->natoms)(x_pbc) = save_calloc("x_pbc", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3736, (mtop->natoms), sizeof(*(x_pbc)));
3737	m_rveccopy(mtop->natoms, x, x_pbc);
3738	do_pbc_first_mtop(NULL((void*)0), ir->ePBC, box, mtop, x_pbc);
3739	/* All molecules will be whole now, but not necessarily in the home box.
3740	* Additionally, if a rotation group consists of more than one molecule
3741	* (e.g. two strands of DNA), each one of them can end up in a different
3742	* periodic box. This is taken care of in init_rot_group. */
3743	}
3744
3745	for (g = 0; g < rot->ngrp; g++)
3746	{
3747	rotg = &rot->grp[g];
3748
3749	if (NULL((void*)0) != fplog)
3750	{
3751	fprintf(fplog, "%s group %d type '%s'\n", RotStr, g, erotg_names[rotg->eType]);
3752	}
3753
3754	if (rotg->nat > 0)
3755	{
3756	/* Allocate space for the rotation group's data: */
3757	snew(rotg->enfrotgrp, 1)(rotg->enfrotgrp) = save_calloc("rotg->enfrotgrp", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3757, (1), sizeof(*(rotg->enfrotgrp)));
3758	erg = rotg->enfrotgrp;
3759
3760	nat_max = max(nat_max, rotg->nat)(((nat_max) > (rotg->nat)) ? (nat_max) : (rotg->nat) );
3761
3762	if (PAR(cr)((cr)->nnodes > 1))
3763	{
3764	erg->nat_loc = 0;
3765	erg->nalloc_loc = 0;
3766	erg->ind_loc = NULL((void*)0);
3767	}
3768	else
3769	{
3770	erg->nat_loc = rotg->nat;
3771	erg->ind_loc = rotg->ind;
3772	}
3773	init_rot_group(fplog, cr, g, rotg, x_pbc, mtop, bVerbose, er->out_slabs, box, ir,
3774	!(er->Flags & MD_APPENDFILES(1<<15)) ); /* Do not output the reference centers
3775	* again if we are appending */
3776	}
3777	}
3778
3779	/* Allocate space for enforced rotation buffer variables */
3780	er->bufsize = nat_max;
3781	snew(er->data, nat_max)(er->data) = save_calloc("er->data", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3781, (nat_max), sizeof(*(er->data)));
3782	snew(er->xbuf, nat_max)(er->xbuf) = save_calloc("er->xbuf", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3782, (nat_max), sizeof(*(er->xbuf)));
3783	snew(er->mbuf, nat_max)(er->mbuf) = save_calloc("er->mbuf", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3783, (nat_max), sizeof(*(er->mbuf)));
3784
3785	/* Buffers for MPI reducing torques, angles, weights (for each group), and V */
3786	if (PAR(cr)((cr)->nnodes > 1))
3787	{
3788	er->mpi_bufsize = calc_mpi_bufsize(rot) + 100; /* larger to catch errors */
3789	snew(er->mpi_inbuf, er->mpi_bufsize)(er->mpi_inbuf) = save_calloc("er->mpi_inbuf", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3789, (er->mpi_bufsize), sizeof(*(er->mpi_inbuf)));
3790	snew(er->mpi_outbuf, er->mpi_bufsize)(er->mpi_outbuf) = save_calloc("er->mpi_outbuf", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3790, (er->mpi_bufsize), sizeof(*(er->mpi_outbuf)));
3791	}
3792	else
3793	{
3794	er->mpi_bufsize = 0;
3795	er->mpi_inbuf = NULL((void*)0);
3796	er->mpi_outbuf = NULL((void*)0);
3797	}
3798
3799	/* Only do I/O on the MASTER */
3800	er->out_angles = NULL((void*)0);
3801	er->out_rot = NULL((void*)0);
3802	er->out_torque = NULL((void*)0);
3803	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
3804	{
3805	er->out_rot = open_rot_out(opt2fn("-ro", nfile, fnm), rot, oenv);
3806
3807	if (rot->nstsout > 0)
3808	{
3809	if (HaveFlexibleGroups(rot) \|\| HavePotFitGroups(rot) )
3810	{
3811	er->out_angles = open_angles_out(opt2fn("-ra", nfile, fnm), rot);
3812	}
3813	if (HaveFlexibleGroups(rot) )
3814	{
3815	er->out_torque = open_torque_out(opt2fn("-rt", nfile, fnm), rot);
3816	}
3817	}
3818
3819	sfree(x_pbc)save_free("x_pbc", "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 3819, (x_pbc));
3820	}
3821	}
3822
3823
3824	extern void finish_rot(t_rot *rot)
3825	{
3826	gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3827
3828
3829	er = rot->enfrot;
3830	if (er->out_rot)
3831	{
3832	gmx_fio_fclose(er->out_rot);
3833	}
3834	if (er->out_slabs)
3835	{
3836	gmx_fio_fclose(er->out_slabs);
3837	}
3838	if (er->out_angles)
3839	{
3840	gmx_fio_fclose(er->out_angles);
3841	}
3842	if (er->out_torque)
3843	{
3844	gmx_fio_fclose(er->out_torque);
3845	}
3846	}
3847
3848
3849	/* Rotate the local reference positions and store them in
3850	* erg->xr_loc[0...(nat_loc-1)]
3851	*
3852	* Note that we already subtracted u or y_c from the reference positions
3853	* in init_rot_group().
3854	*/
3855	static void rotate_local_reference(t_rotgrp *rotg)
3856	{
3857	gmx_enfrotgrp_t erg;
3858	int i, ii;
3859
3860
3861	erg = rotg->enfrotgrp;
3862
3863	for (i = 0; i < erg->nat_loc; i++)
3864	{
3865	/* Index of this rotation group atom with respect to the whole rotation group */
3866	ii = erg->xc_ref_ind[i];
3867	/* Rotate */
3868	mvmul(erg->rotmat, rotg->x_ref[ii], erg->xr_loc[i]);
3869	}
3870	}
3871
3872
3873	/* Select the PBC representation for each local x position and store that
3874	* for later usage. We assume the right PBC image of an x is the one nearest to
3875	* its rotated reference */
3876	static void choose_pbc_image(rvec x[], t_rotgrp *rotg, matrix box, int npbcdim)
3877	{
3878	int i, ii;
3879	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3880	rvec xref;
3881
3882
3883	erg = rotg->enfrotgrp;
3884
3885	for (i = 0; i < erg->nat_loc; i++)
3886	{
3887	/* Index of a rotation group atom */
3888	ii = erg->ind_loc[i];
3889
3890	/* Get the correctly rotated reference position. The pivot was already
3891	* subtracted in init_rot_group() from the reference positions. Also,
3892	* the reference positions have already been rotated in
3893	* rotate_local_reference(). For the current reference position we thus
3894	* only need to add the pivot again. */
3895	copy_rvec(erg->xr_loc[i], xref);
3896	rvec_inc(xref, erg->xc_ref_center);
3897
3898	copy_correct_pbc_image(x[ii], erg->x_loc_pbc[i], xref, box, npbcdim);
3899	}
3900	}
3901
3902
3903	extern void do_rotation(
3904	t_commrec *cr,
3905	t_inputrec *ir,
3906	matrix box,
3907	rvec x[],
3908	real t,
3909	gmx_int64_t step,
3910	gmx_wallcycle_t wcycle,
3911	gmx_bool bNS)
3912	{
3913	int g, i, ii;
3914	t_rot *rot;
3915	t_rotgrp *rotg;
3916	gmx_bool outstep_slab, outstep_rot;
3917	gmx_bool bFlex, bColl;
3918	gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
3919	gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
3920	rvec transvec;
3921	t_gmx_potfit fit = NULL((void)0); /* For fit type 'potential' determine the fit
3922	angle via the potential minimum */
3923
3924	/* Enforced rotation cycle counting: */
3925	gmx_cycles_t cycles_comp; /* Cycles for the enf. rotation computation
3926	only, does not count communication. This
3927	counter is used for load-balancing */
3928
3929	#ifdef TAKETIME
3930	double t0;
3931	#endif
3932
3933	rot = ir->rot;
3934	er = rot->enfrot;
3935
3936	/* When to output in main rotation output file */
3937	outstep_rot = do_per_step(step, rot->nstrout) && er->bOut;
3938	/* When to output per-slab data */
3939	outstep_slab = do_per_step(step, rot->nstsout) && er->bOut;
3940
3941	/* Output time into rotation output file */
3942	if (outstep_rot && MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
3943	{
3944	fprintf(er->out_rot, "%12.3e", t);
3945	}
3946
3947	/**************************************************************************/
3948	/* First do ALL the communication! */
3949	for (g = 0; g < rot->ngrp; g++)
3950	{
3951	rotg = &rot->grp[g];
3952	erg = rotg->enfrotgrp;
3953
3954	/* Do we have a flexible axis? */
3955	bFlex = ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) );
3956	/* Do we use a collective (global) set of coordinates? */
3957	bColl = ISCOLL(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) \|\| (rotg->eType == erotgRMPF) \|\| (rotg->eType == erotgRM2PF ) );
3958
3959	/* Calculate the rotation matrix for this angle: */
3960	erg->degangle = rotg->rate * t;
3961	calc_rotmat(rotg->vec, erg->degangle, erg->rotmat);
3962
3963	if (bColl)
3964	{
3965	/* Transfer the rotation group's positions such that every node has
3966	* all of them. Every node contributes its local positions x and stores
3967	* it in the collective erg->xc array. */
3968	communicate_group_positions(cr, erg->xc, erg->xc_shifts, erg->xc_eshifts, bNS,
3969	x, rotg->nat, erg->nat_loc, erg->ind_loc, erg->xc_ref_ind, erg->xc_old, box);
3970	}
3971	else
3972	{
3973	/* Fill the local masses array;
3974	* this array changes in DD/neighborsearching steps */
3975	if (bNS)
3976	{
3977	for (i = 0; i < erg->nat_loc; i++)
3978	{
3979	/* Index of local atom w.r.t. the collective rotation group */
3980	ii = erg->xc_ref_ind[i];
3981	erg->m_loc[i] = erg->mc[ii];
3982	}
3983	}
3984
3985	/* Calculate Omega(y_i-y_c) for the local positions /
3986	rotate_local_reference(rotg);
3987
3988	/* Choose the nearest PBC images of the group atoms with respect
3989	* to the rotated reference positions */
3990	choose_pbc_image(x, rotg, box, 3);
3991
3992	/* Get the center of the rotation group */
3993	if ( (rotg->eType == erotgISOPF) \|\| (rotg->eType == erotgPMPF) )
3994	{
3995	get_center_comm(cr, erg->x_loc_pbc, erg->m_loc, erg->nat_loc, rotg->nat, erg->xc_center);
3996	}
3997	}
3998
3999	} /* End of loop over rotation groups */
4000
4001	/**************************************************************************/
4002	/* Done communicating, we can start to count cycles for the load balancing now ... */
4003	cycles_comp = gmx_cycles_read();
4004
4005
4006	#ifdef TAKETIME
4007	t0 = MPI_WtimetMPI_Wtime();
4008	#endif
4009
4010	for (g = 0; g < rot->ngrp; g++)
4011	{
4012	rotg = &rot->grp[g];
4013	erg = rotg->enfrotgrp;
4014
4015	bFlex = ISFLEX(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) );
4016	bColl = ISCOLL(rotg)( (rotg->eType == erotgFLEX) \|\| (rotg->eType == erotgFLEXT ) \|\| (rotg->eType == erotgFLEX2) \|\| (rotg->eType == erotgFLEX2T ) \|\| (rotg->eType == erotgRMPF) \|\| (rotg->eType == erotgRM2PF ) );
4017
4018	if (outstep_rot && MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
4019	{
4020	fprintf(er->out_rot, "%12.4f", erg->degangle);
4021	}
4022
4023	/* Calculate angles and rotation matrices for potential fitting: */
4024	if ( (outstep_rot \|\| outstep_slab) && (erotgFitPOT == rotg->eFittype) )
4025	{
4026	fit = erg->PotAngleFit;
4027	for (i = 0; i < rotg->PotAngle_nstep; i++)
4028	{
4029	calc_rotmat(rotg->vec, erg->degangle + fit->degangle[i], fit->rotmat[i]);
4030
4031	/* Clear value from last step */
4032	erg->PotAngleFit->V[i] = 0.0;
4033	}
4034	}
4035
4036	/* Clear values from last time step */
4037	erg->V = 0.0;
4038	erg->torque_v = 0.0;
4039	erg->angle_v = 0.0;
4040	erg->weight_v = 0.0;
4041
4042	switch (rotg->eType)
4043	{
4044	case erotgISO:
4045	case erotgISOPF:
4046	case erotgPM:
4047	case erotgPMPF:
4048	do_fixed(rotg, outstep_rot, outstep_slab);
4049	break;
4050	case erotgRM:
4051	do_radial_motion(rotg, outstep_rot, outstep_slab);
4052	break;
4053	case erotgRMPF:
4054	do_radial_motion_pf(rotg, x, box, outstep_rot, outstep_slab);
4055	break;
4056	case erotgRM2:
4057	case erotgRM2PF:
4058	do_radial_motion2(rotg, x, box, outstep_rot, outstep_slab);
4059	break;
4060	case erotgFLEXT:
4061	case erotgFLEX2T:
4062	/* Subtract the center of the rotation group from the collective positions array
4063	* Also store the center in erg->xc_center since it needs to be subtracted
4064	* in the low level routines from the local coordinates as well */
4065	get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
4066	svmul(-1.0, erg->xc_center, transvec);
4067	translate_x(erg->xc, rotg->nat, transvec);
4068	do_flexible(MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)), er, rotg, g, x, box, t, outstep_rot, outstep_slab);
4069	break;
4070	case erotgFLEX:
4071	case erotgFLEX2:
4072	/* Do NOT subtract the center of mass in the low level routines! */
4073	clear_rvec(erg->xc_center);
4074	do_flexible(MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)), er, rotg, g, x, box, t, outstep_rot, outstep_slab);
4075	break;
4076	default:
4077	gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/pulling/pull_rotation.c" , 4077, "No such rotation potential.");
4078	break;
4079	}
4080	}
4081
4082	#ifdef TAKETIME
4083	if (MASTER(cr)(((cr)->nodeid == 0) \|\| !((cr)->nnodes > 1)))
4084	{
4085	fprintf(stderrstderr, "%s calculation (step %d) took %g seconds.\n", RotStr, step, MPI_WtimetMPI_Wtime()-t0);
4086	}
4087	#endif
4088
4089	/* Stop the enforced rotation cycle counter and add the computation-only
4090	* cycles to the force cycles for load balancing */
4091	cycles_comp = gmx_cycles_read() - cycles_comp;
4092
4093	if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes > 1)) && wcycle)
4094	{
4095	dd_cycles_add(cr->dd, cycles_comp, ddCyclF);
4096	}
4097	}