--- /dev/null
- bool bFlex;
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "domdec.h"
+#include "gmx_wallcycle.h"
+#include "trnio.h"
+#include "smalloc.h"
+#include "network.h"
+#include "pbc.h"
+#include "futil.h"
+#include "mdrun.h"
+#include "txtdump.h"
+#include "names.h"
+#include "mtop_util.h"
+#include "names.h"
+#include "nrjac.h"
+#include "vec.h"
+#include "gmx_ga2la.h"
+#include "xvgr.h"
+#include "gmxfio.h"
+#include "mpelogging.h"
+#include "groupcoord.h"
+
+
+/* Set the minimum weight for the determination of the slab centers */
+#define WEIGHT_MIN (10*GMX_FLOAT_MIN)
+
+/* Helper structure for sorting positions along rotation vector */
+typedef struct {
+ real xcproj; /* Projection of xc on the rotation vector */
+ int ind; /* Index of xc */
+ real m; /* Mass */
+ rvec x; /* Position */
+ rvec x_ref; /* Reference position */
+} sort_along_vec_t;
+
+
+/* Enforced rotation / flexible: determine the angle of each slab */
+typedef struct gmx_slabdata
+{
+ int nat; /* Number of atoms belonging to this slab */
+ rvec *x; /* The positions belonging to this slab. In
+ general, this should be all positions of the
+ whole rotation group, but we leave those away
+ that have a small enough weight */
+ rvec *ref; /* Same for reference */
+ real *weight; /* The weight for each atom */
+} t_gmx_slabdata;
+
+
+/* Enforced rotation data for all groups */
+typedef struct gmx_enfrot
+{
+ FILE *out_rot; /* Output file for rotation data */
+ FILE *out_torque; /* Output file for torque data */
+ FILE *out_angles; /* Output file for slab angles for flexible type */
+ FILE *out_slabs; /* Output file for slab centers */
+ int bufsize; /* Allocation size of buf */
+ rvec *xbuf; /* Coordinate buffer variable for sorting */
+ real *mbuf; /* Masses buffer variable for sorting */
+ sort_along_vec_t *data; /* Buffer variable needed for position sorting */
+ real *mpi_inbuf; /* MPI buffer */
+ real *mpi_outbuf; /* MPI buffer */
+ int mpi_bufsize; /* Allocation size of in & outbuf */
+ real Vrot; /* (Local) part of the enf. rotation potential */
+} t_gmx_enfrot;
+
+
+/* Global enforced rotation data for a single rotation group */
+typedef struct gmx_enfrotgrp
+{
+ real degangle; /* Rotation angle in degree */
+ matrix rotmat; /* Rotation matrix */
+ atom_id *ind_loc; /* Local rotation indices */
+ int nat_loc; /* Number of local group atoms */
+ int nalloc_loc; /* Allocation size for ind_loc and weight_loc */
+
+ real V; /* Rotation potential for this rotation group */
+ rvec *f_rot_loc; /* Array to store the forces on the local atoms
+ resulting from enforced rotation potential */
+
+ /* Collective coordinates for the whole rotation group */
+ real *xc_ref_length; /* Length of each x_rotref vector after x_rotref
+ has been put into origin */
+ int *xc_ref_ind; /* Position of each local atom in the collective
+ array */
+ rvec xc_center; /* Center of the rotation group positions, may
+ be mass weighted */
+ rvec xc_ref_center; /* dito, for the reference positions */
+ rvec *xc; /* Current (collective) positions */
+ ivec *xc_shifts; /* Current (collective) shifts */
+ ivec *xc_eshifts; /* Extra shifts since last DD step */
+ rvec *xc_old; /* Old (collective) positions */
+ rvec *xc_norm; /* Normalized form of the current positions */
+ rvec *xc_ref_sorted; /* Reference positions (sorted in the same order
+ as xc when sorted) */
+ int *xc_sortind; /* Where is a position found after sorting? */
+ real *mc; /* Collective masses */
+ real *mc_sorted;
+ real invmass; /* one over the total mass of the rotation group */
+ /* Fixed rotation only */
+ rvec *xr_loc; /* Local reference coords, correctly rotated */
+ rvec *x_loc_pbc; /* Local current coords, correct PBC image */
+ real *m_loc; /* Masses of the current local atoms */
+ real fix_torque_v; /* Torque in the direction of rotation vector */
+ real fix_angles_v;
+ real fix_weight_v;
+ /* Flexible rotation only */
+ int nslabs_alloc; /* For this many slabs memory is allocated */
+ int slab_first; /* Lowermost slab for that the calculation needs
+ to be performed at a given time step */
+ int slab_last; /* Uppermost slab ... */
+ int slab_first_ref; /* First slab for which reference COG is stored */
+ int slab_last_ref; /* Last ... */
+ int slab_buffer; /* Slab buffer region around reference slabs */
+ int *firstatom; /* First relevant atom for a slab */
+ int *lastatom; /* Last relevant atom for a slab */
+ rvec *slab_center; /* Gaussian-weighted slab center (COG) */
+ rvec *slab_center_ref; /* Gaussian-weighted slab COG for the
+ reference positions */
+ real *slab_weights; /* Sum of gaussian weights in a slab */
+ real *slab_torque_v; /* Torque T = r x f for each slab. */
+ /* torque_v = m.v = angular momentum in the
+ direction of v */
+ real max_beta; /* min_gaussian from inputrec->rotgrp is the
+ minimum value the gaussian must have so that
+ the force is actually evaluated max_beta is
+ just another way to put it */
+ real *gn_atom; /* Precalculated gaussians for a single atom */
+ int *gn_slabind; /* Tells to which slab each precalculated gaussian
+ belongs */
+ rvec *slab_innersumvec;/* Inner sum of the flexible2 potential per slab;
+ this is precalculated for optimization reasons */
+ t_gmx_slabdata *slab_data; /* Holds atom positions and gaussian weights
+ of atoms belonging to a slab */
+} t_gmx_enfrotgrp;
+
+
+static double** allocate_square_matrix(int dim)
+{
+ int i;
+ double** mat = NULL;
+
+
+ snew(mat, dim);
+ for(i=0; i<dim; i++)
+ snew(mat[i], dim);
+
+ return mat;
+}
+
+
+static void free_square_matrix(double** mat, int dim)
+{
+ int i;
+
+
+ for (i=0; i<dim; i++)
+ sfree(mat[i]);
+ sfree(mat);
+}
+
+
+/* Output rotation energy and torque for each rotation group */
+static void reduce_output(t_commrec *cr, t_rot *rot, real t)
+{
+ int g,i,islab,nslabs=0;
+ int count; /* MPI element counter */
+ t_rotgrp *rotg;
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
- bool bOutStep, /* Is this an output step? */
- bool bReference) /* If this routine is called from
++ gmx_bool bFlex;
+
+
+ er=rot->enfrot;
+
+ /* Fill the MPI buffer with stuff to reduce: */
+ if (PAR(cr))
+ {
+ count=0;
+ for (g=0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+ nslabs = erg->slab_last - erg->slab_first + 1;
+ er->mpi_inbuf[count++] = erg->V;
+ switch (rotg->eType)
+ {
+ case erotgISO:
+ case erotgISOPF:
+ case erotgPM:
+ case erotgPMPF:
+ case erotgRM:
+ case erotgRMPF:
+ case erotgRM2:
+ case erotgRM2PF:
+ er->mpi_inbuf[count++] = erg->fix_torque_v;
+ er->mpi_inbuf[count++] = erg->fix_angles_v;
+ er->mpi_inbuf[count++] = erg->fix_weight_v;
+ break;
+ case erotgFLEX:
+ case erotgFLEX2:
+ /* (Re-)allocate memory for MPI buffer: */
+ if (er->mpi_bufsize < count+nslabs)
+ {
+ er->mpi_bufsize = count+nslabs;
+ srenew(er->mpi_inbuf , er->mpi_bufsize);
+ srenew(er->mpi_outbuf, er->mpi_bufsize);
+ }
+ for (i=0; i<nslabs; i++)
+ er->mpi_inbuf[count++] = erg->slab_torque_v[i];
+ break;
+ default:
+ break;
+ }
+ }
+#ifdef GMX_MPI
+ MPI_Reduce(er->mpi_inbuf, er->mpi_outbuf, count, GMX_MPI_REAL, MPI_SUM, MASTERRANK(cr), cr->mpi_comm_mygroup);
+#endif
+ /* Copy back the reduced data from the buffer on the master */
+ if (MASTER(cr))
+ {
+ count=0;
+ for (g=0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+ nslabs = erg->slab_last - erg->slab_first + 1;
+ erg->V = er->mpi_outbuf[count++];
+ switch (rotg->eType)
+ {
+ case erotgISO:
+ case erotgISOPF:
+ case erotgPM:
+ case erotgPMPF:
+ case erotgRM:
+ case erotgRMPF:
+ case erotgRM2:
+ case erotgRM2PF:
+ erg->fix_torque_v = er->mpi_outbuf[count++];
+ erg->fix_angles_v = er->mpi_outbuf[count++];
+ erg->fix_weight_v = er->mpi_outbuf[count++];
+ break;
+ case erotgFLEX:
+ case erotgFLEX2:
+ for (i=0; i<nslabs; i++)
+ erg->slab_torque_v[i] = er->mpi_outbuf[count++];
+ break;
+ default:
+ break;
+ }
+ }
+ }
+ }
+
+ /* Output */
+ if (MASTER(cr))
+ {
+ /* Av. angle and total torque for each rotation group */
+ for (g=0; g < rot->ngrp; g++)
+ {
+ rotg=&rot->grp[g];
+ bFlex = (rotg->eType==erotgFLEX) || (rotg->eType==erotgFLEX2);
+
+ erg=rotg->enfrotgrp;
+
+ /* Output to main rotation log file: */
+ if (!bFlex)
+ {
+ fprintf(er->out_rot, "%12.4f%12.3e",
+ (erg->fix_angles_v/erg->fix_weight_v)*180.0*M_1_PI,
+ erg->fix_torque_v);
+ }
+ fprintf(er->out_rot, "%12.3e", erg->V);
+
+ /* Output to torque log file: */
+ if (bFlex)
+ {
+ fprintf(er->out_torque, "%12.3e%6d", t, g);
+ for (i=erg->slab_first; i<=erg->slab_last; i++)
+ {
+ islab = i - erg->slab_first; /* slab index */
+ /* Only output if enough weight is in slab */
+ if (erg->slab_weights[islab] > rotg->min_gaussian)
+ fprintf(er->out_torque, "%6d%12.3e", i, erg->slab_torque_v[islab]);
+ }
+ fprintf(er->out_torque , "\n");
+ }
+ }
+ fprintf(er->out_rot, "\n");
+ }
+}
+
+
+/* Add the forces from enforced rotation potential to the local forces.
+ * Should be called after the SR forces have been evaluated */
+extern real add_rot_forces(t_rot *rot, rvec f[], t_commrec *cr, int step, real t)
+{
+ int g,l,ii;
+ t_rotgrp *rotg;
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ er=rot->enfrot;
+
+ GMX_MPE_LOG(ev_add_rot_forces_start);
+
+ /* Reduce energy,torque, angles etc. to get the sum values (per rotation group)
+ * on the master and output these values to file. */
+ if (do_per_step(step, rot->nsttout))
+ reduce_output(cr, rot, t);
+
+ /* Total rotation potential is the sum over all rotation groups */
+ er->Vrot = 0.0;
+
+ /* Loop over enforced rotation groups (usually 1, though)
+ * Apply the forces from rotation potentials */
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+ er->Vrot += erg->V;
+ for (l=0; l<erg->nat_loc; l++)
+ {
+ /* Get the right index of the local force */
+ ii = erg->ind_loc[l];
+ /* Add */
+ rvec_inc(f[ii],erg->f_rot_loc[l]);
+ }
+ }
+
+ GMX_MPE_LOG(ev_add_rot_forces_finish);
+
+ return (MASTER(cr)? er->Vrot : 0.0);
+}
+
+
+/* Calculate the maximum beta that leads to a gaussian larger min_gaussian,
+ * also does some checks
+ */
+static double calc_beta_max(real min_gaussian, real slab_dist)
+{
+ const double norm = 0.5698457353514458216; /* = 1/1.7548609 */
+ double sigma;
+ double arg;
+
+
+ /* Actually the next two checks are already made in grompp */
+ if (slab_dist <= 0)
+ gmx_fatal(FARGS, "Slab distance of flexible rotation groups must be >=0 !");
+ if (min_gaussian <= 0)
+ gmx_fatal(FARGS, "Cutoff value for Gaussian must be > 0. (You requested %f)");
+
+ /* Define the sigma value */
+ sigma = 0.7*slab_dist;
+
+ /* Calculate the argument for the logarithm and check that the log() result is negative or 0 */
+ arg = min_gaussian/norm;
+ if (arg > 1.0)
+ gmx_fatal(FARGS, "min_gaussian of flexible rotation groups must be <%g", norm);
+
+ return sqrt(-2.0*sigma*sigma*log(min_gaussian/norm));
+}
+
+
+static inline real calc_beta(rvec curr_x, t_rotgrp *rotg, int n)
+{
+ return iprod(curr_x, rotg->vec) - rotg->slab_dist * n;
+}
+
+
+static inline real gaussian_weight(rvec curr_x, t_rotgrp *rotg, int n)
+{
+ /* norm is chosen such that the sum of the gaussians
+ * over the slabs is approximately 1.0 everywhere */
+ const real norm = 0.5698457353514458216; /* = 1/1.7548609 */
+ real sigma;
+
+
+ /* Define the sigma value */
+ sigma = 0.7*rotg->slab_dist;
+ /* Calculate the Gaussian value of slab n for position curr_x */
+ return norm * exp( -0.5 * sqr( calc_beta(curr_x, rotg, n)/sigma ) );
+}
+
+
+/* Returns the weight in a single slab, also calculates the Gaussian- and mass-
+ * weighted sum of positions for that slab */
+static real get_slab_weight(int j, t_rotgrp *rotg, rvec xc[], real mc[], rvec *x_weighted_sum)
+{
+ rvec curr_x; /* The position of an atom */
+ rvec curr_x_weighted; /* The gaussian-weighted position */
+ real gaussian; /* A single gaussian weight */
+ real wgauss; /* gaussian times current mass */
+ real slabweight = 0.0; /* The sum of weights in the slab */
+ int i,islab;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+ clear_rvec(*x_weighted_sum);
+
+ /* Slab index */
+ islab = j - erg->slab_first;
+
+ /* Loop over all atoms in the rotation group */
+ for (i=0; i<rotg->nat; i++)
+ {
+ copy_rvec(xc[i], curr_x);
+ gaussian = gaussian_weight(curr_x, rotg, j);
+ wgauss = gaussian * mc[i];
+ svmul(wgauss, curr_x, curr_x_weighted);
+ rvec_add(*x_weighted_sum, curr_x_weighted, *x_weighted_sum);
+ slabweight += wgauss;
+ } /* END of loop over rotation group atoms */
+
+ return slabweight;
+}
+
+
+static void get_slab_centers(
+ t_rotgrp *rotg, /* The rotation group information */
+ rvec *xc, /* The rotation group positions; will
+ typically be enfrotgrp->xc, but at first call
+ it is enfrotgrp->xc_ref */
+ real *mc, /* The masses of the rotation group atoms */
+ t_commrec *cr, /* Communication record */
+ int g, /* The number of the rotation group */
+ real time, /* Used for output only */
+ FILE *out_slabs, /* For outputting center per slab information */
- bool bCalcTorque,
++ gmx_bool bOutStep, /* Is this an output step? */
++ gmx_bool bReference) /* If this routine is called from
+ init_rot_group we need to store
+ the reference slab centers */
+{
+ int j,islab;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Loop over slabs */
+ for (j = erg->slab_first; j <= erg->slab_last; j++)
+ {
+ islab = j - erg->slab_first;
+ erg->slab_weights[islab] = get_slab_weight(j, rotg, xc, mc, &erg->slab_center[islab]);
+
+ /* We can do the calculations ONLY if there is weight in the slab! */
+ if (erg->slab_weights[islab] > WEIGHT_MIN)
+ {
+ svmul(1.0/erg->slab_weights[islab], erg->slab_center[islab], erg->slab_center[islab]);
+ }
+ else
+ {
+ /* We need to check this here, since we divide through slab_weights
+ * in the flexible low-level routines! */
+ gmx_fatal(FARGS, "Not enough weight in slab %d. Slab center cannot be determined!", j);
+ }
+
+ /* At first time step: save the centers of the reference structure */
+ if (bReference)
+ copy_rvec(erg->slab_center[islab], erg->slab_center_ref[islab]);
+ } /* END of loop over slabs */
+
+ /* Output on the master */
+ if (MASTER(cr) && bOutStep)
+ {
+ fprintf(out_slabs, "%12.3e%6d", time, g);
+ for (j = erg->slab_first; j <= erg->slab_last; j++)
+ {
+ islab = j - erg->slab_first;
+ fprintf(out_slabs, "%6d%12.3e%12.3e%12.3e",
+ j,erg->slab_center[islab][XX],erg->slab_center[islab][YY],erg->slab_center[islab][ZZ]);
+ }
+ fprintf(out_slabs, "\n");
+ }
+}
+
+
+static void calc_rotmat(
+ rvec vec,
+ real degangle, /* Angle alpha of rotation at time t in degrees */
+ matrix rotmat) /* Rotation matrix */
+{
+ real radangle; /* Rotation angle in radians */
+ real cosa; /* cosine alpha */
+ real sina; /* sine alpha */
+ real OMcosa; /* 1 - cos(alpha) */
+ real dumxy, dumxz, dumyz; /* save computations */
+ rvec rot_vec; /* Rotate around rot_vec ... */
+
+
+ radangle = degangle * M_PI/180.0;
+ copy_rvec(vec , rot_vec );
+
+ /* Precompute some variables: */
+ cosa = cos(radangle);
+ sina = sin(radangle);
+ OMcosa = 1.0 - cosa;
+ dumxy = rot_vec[XX]*rot_vec[YY]*OMcosa;
+ dumxz = rot_vec[XX]*rot_vec[ZZ]*OMcosa;
+ dumyz = rot_vec[YY]*rot_vec[ZZ]*OMcosa;
+
+ /* Construct the rotation matrix for this rotation group: */
+ /* 1st column: */
+ rotmat[XX][XX] = cosa + rot_vec[XX]*rot_vec[XX]*OMcosa;
+ rotmat[YY][XX] = dumxy + rot_vec[ZZ]*sina;
+ rotmat[ZZ][XX] = dumxz - rot_vec[YY]*sina;
+ /* 2nd column: */
+ rotmat[XX][YY] = dumxy - rot_vec[ZZ]*sina;
+ rotmat[YY][YY] = cosa + rot_vec[YY]*rot_vec[YY]*OMcosa;
+ rotmat[ZZ][YY] = dumyz + rot_vec[XX]*sina;
+ /* 3rd column: */
+ rotmat[XX][ZZ] = dumxz + rot_vec[YY]*sina;
+ rotmat[YY][ZZ] = dumyz - rot_vec[XX]*sina;
+ rotmat[ZZ][ZZ] = cosa + rot_vec[ZZ]*rot_vec[ZZ]*OMcosa;
+
+#ifdef PRINTMATRIX
+ int iii,jjj;
+
+ for (iii=0; iii<3; iii++) {
+ for (jjj=0; jjj<3; jjj++)
+ fprintf(stderr, " %10.8f ", rotmat[iii][jjj]);
+ fprintf(stderr, "\n");
+ }
+#endif
+}
+
+
+/* Calculates torque on the rotation axis tau = position x force */
+static inline real torque(
+ rvec rotvec, /* rotation vector; MUST be normalized! */
+ rvec force, /* force */
+ rvec x, /* position of atom on which the force acts */
+ rvec pivot) /* pivot point of rotation axis */
+{
+ rvec vectmp, tau;
+
+
+ /* Subtract offset */
+ rvec_sub(x,pivot,vectmp);
+
+ /* position x force */
+ cprod(vectmp, force, tau);
+
+ /* Return the part of the torque which is parallel to the rotation vector */
+ return iprod(tau, rotvec);
+}
+
+
+/* Right-aligned output of value with standard width */
+static void print_aligned(FILE *fp, char *str)
+{
+ fprintf(fp, "%12s", str);
+}
+
+
+/* Right-aligned output of value with standard short width */
+static void print_aligned_short(FILE *fp, char *str)
+{
+ fprintf(fp, "%6s", str);
+}
+
+
+/* Right-aligned output of value with standard width */
+static void print_aligned_group(FILE *fp, char *str, int g)
+{
+ char sbuf[STRLEN];
+
+
+ sprintf(sbuf, "%s%d", str, g);
+ fprintf(fp, "%12s", sbuf);
+}
+
+
+static FILE *open_output_file(const char *fn, int steps)
+{
+ FILE *fp;
+
+
+ fp = ffopen(fn, "w");
+
+ fprintf(fp, "# Output is written every %d time steps.\n\n", steps);
+
+ return fp;
+}
+
+
+/* Open output file for slab COG data. Call on master only */
+static FILE *open_slab_out(t_rot *rot, const char *fn)
+{
+ FILE *fp=NULL;
+ int g;
+ t_rotgrp *rotg;
+
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (rotg->eType == erotgFLEX || rotg->eType == erotgFLEX2)
+ {
+ if (NULL == fp)
+ fp = open_output_file(fn, rot->nsttout);
+ fprintf(fp, "# Rotation group %d (%s), slab distance %f nm\n", g, erotg_names[rotg->eType], rotg->slab_dist);
+ }
+ }
+
+ if (fp != NULL)
+ {
+ fprintf(fp, "# The following columns will have the syntax: (COG = center of geometry, gaussian weighted)\n");
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "t");
+ print_aligned_short(fp, "grp");
+ print_aligned_short(fp, "slab");
+ print_aligned(fp, "COG-X");
+ print_aligned(fp, "COG-Y");
+ print_aligned(fp, "COG-Z");
+ print_aligned_short(fp, "slab");
+ print_aligned(fp, "COG-X");
+ print_aligned(fp, "COG-Y");
+ print_aligned(fp, "COG-Z");
+ print_aligned_short(fp, "slab");
+ fprintf(fp, " ...\n");
+ fflush(fp);
+ }
+
+ return fp;
+}
+
+
+/* Open output file and print some general information about the rotation groups.
+ * Call on master only */
+static FILE *open_rot_out(const char *fn, t_rot *rot, const output_env_t oenv,
+ unsigned long Flags)
+{
+ FILE *fp;
+ int g,nsets;
+ t_rotgrp *rotg;
+ const char **setname;
+ char buf[50];
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ if (Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn,"a");
+ }
+ else
+ {
+ fp = xvgropen(fn, "Rotation angles and energy", "Time [ps]", "angles [degree] and energies [kJ/mol]", oenv);
+ fprintf(fp, "# The scalar tau is the torque [kJ/mol] in the direction of the rotation vector v.\n");
+ fprintf(fp, "# To obtain the vectorial torque, multiply tau with the group's rot_vec.\n#\n");
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+
+ fprintf(fp, "# Rotation group %d, potential type '%s':\n" , g, erotg_names[rotg->eType]);
+ fprintf(fp, "# rot_massw%d %s\n" , g, yesno_names[rotg->bMassW]);
+ fprintf(fp, "# rot_vec%d %12.5e %12.5e %12.5e\n" , g, rotg->vec[XX], rotg->vec[YY], rotg->vec[ZZ]);
+ fprintf(fp, "# rot_rate%d %12.5e degree/ps\n" , g, rotg->rate);
+ fprintf(fp, "# rot_k%d %12.5e kJ/(mol*nm^2)\n" , g, rotg->k);
+ if ( rotg->eType==erotgISO || rotg->eType==erotgPM || rotg->eType==erotgRM || rotg->eType==erotgRM2)
+ fprintf(fp, "# rot_pivot%d %12.5e %12.5e %12.5e nm\n", g, rotg->pivot[XX], rotg->pivot[YY], rotg->pivot[ZZ]);
+
+ if ( (rotg->eType==erotgFLEX) || (rotg->eType==erotgFLEX2) )
+ {
+ fprintf(fp, "# rot_slab_distance%d %f nm\n", g, rotg->slab_dist);
+ fprintf(fp, "# rot_min_gaussian%d %12.5e\n", g, rotg->min_gaussian);
+ }
+
+ /* Output the centers of the rotation groups for the pivot-free potentials */
+ if ((rotg->eType==erotgISOPF) || (rotg->eType==erotgPMPF) || (rotg->eType==erotgRMPF) || (rotg->eType==erotgRM2PF
+ || (rotg->eType==erotgFLEX) || (rotg->eType==erotgFLEX2)) )
+ {
+ fprintf(fp, "# %s of ref. grp. %d %12.5e %12.5e %12.5e\n",
+ rotg->bMassW? "COM":"COG", g,
+ erg->xc_ref_center[XX], erg->xc_ref_center[YY], erg->xc_ref_center[ZZ]);
+
+ fprintf(fp, "# initial %s grp. %d %12.5e %12.5e %12.5e\n",
+ rotg->bMassW? "COM":"COG", g,
+ erg->xc_center[XX], erg->xc_center[YY], erg->xc_center[ZZ]);
+ }
+
+ if ( (rotg->eType == erotgRM2) || (rotg->eType==erotgFLEX2) )
+ {
+ fprintf(fp, "# rot_eps%d %12.5e nm^2\n", g, rotg->eps);
+ }
+ }
+
+ fprintf(fp, "#\n# Legend for the following data columns:\n");
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "t");
+ nsets = 0;
+ snew(setname, 4*rot->ngrp);
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ sprintf(buf, "theta_ref%d [degree]", g);
+ print_aligned_group(fp, "theta_ref", g);
+ setname[nsets] = strdup(buf);
+ nsets++;
+ }
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ /* For flexible axis rotation we use RMSD fitting to determine the
+ * actual angle of the rotation group */
+ if ( (rotg->eType!=erotgFLEX) && (rotg->eType!=erotgFLEX2) )
+ {
+ sprintf(buf, "theta-av%d [degree]", g);
+ print_aligned_group(fp, "theta_av", g);
+ setname[nsets] = strdup(buf);
+ nsets++;
+ sprintf(buf, "tau%d [kJ/mol]", g);
+ print_aligned_group(fp, "tau", g);
+ setname[nsets] = strdup(buf);
+ nsets++;
+ }
+ sprintf(buf, "energy%d [kJ/mol]", g);
+ print_aligned_group(fp, "energy", g);
+ setname[nsets] = strdup(buf);
+ nsets++;
+ }
+ fprintf(fp, "\n#\n");
+
+ if (nsets > 1)
+ xvgr_legend(fp, nsets, setname, oenv);
+ sfree(setname);
+
+ fflush(fp);
+ }
+
+ return fp;
+}
+
+
+/* Call on master only */
+static FILE *open_angles_out(t_rot *rot, const char *fn)
+{
+ int g;
+ FILE *fp=NULL;
+ t_rotgrp *rotg;
+
+
+ /* Open output file and write some information about it's structure: */
+ fp = open_output_file(fn, rot->nstrout);
+ fprintf(fp, "# All angles given in degrees, time in ps\n");
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (rotg->eType == erotgFLEX || rotg->eType == erotgFLEX2)
+ fprintf(fp, "# Rotation group %d (%s), slab distance %f nm, fit type %s\n",
+ g, erotg_names[rotg->eType], rotg->slab_dist, erotg_fitnames[rotg->eFittype]);
+ }
+ fprintf(fp, "# The following columns will have the syntax:\n");
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "t");
+ print_aligned_short(fp, "grp");
+ print_aligned(fp, "theta_ref");
+ print_aligned(fp, "theta_fit");
+ print_aligned_short(fp, "slab");
+ print_aligned_short(fp, "atoms");
+ print_aligned(fp, "theta_fit");
+ print_aligned_short(fp, "slab");
+ print_aligned_short(fp, "atoms");
+ print_aligned(fp, "theta_fit");
+ fprintf(fp, " ...\n");
+ fflush(fp);
+ return fp;
+}
+
+
+/* Open torque output file and write some information about it's structure.
+ * Call on master only */
+static FILE *open_torque_out(t_rot *rot, const char *fn)
+{
+ FILE *fp;
+ int g;
+ t_rotgrp *rotg;
+
+
+ fp = open_output_file(fn, rot->nsttout);
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (rotg->eType == erotgFLEX || rotg->eType == erotgFLEX2)
+ {
+ fprintf(fp, "# Rotation group %d (%s), slab distance %f nm\n", g, erotg_names[rotg->eType], rotg->slab_dist);
+ fprintf(fp, "# The scalar tau is the torque [kJ/mol] in the direction of the rotation vector.\n");
+ fprintf(fp, "# To obtain the vectorial torque, multiply tau with\n");
+ fprintf(fp, "# rot_vec%d %10.3e %10.3e %10.3e\n", g, rotg->vec[XX], rotg->vec[YY], rotg->vec[ZZ]);
+ fprintf(fp, "#\n");
+ }
+ }
+ fprintf(fp, "# The following columns will have the syntax (tau=torque for that slab):\n");
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "t");
+ print_aligned_short(fp, "grp");
+ print_aligned_short(fp, "slab");
+ print_aligned(fp, "tau");
+ print_aligned_short(fp, "slab");
+ print_aligned(fp, "tau");
+ fprintf(fp, " ...\n");
+ fflush(fp);
+
+ return fp;
+}
+
+
+static void swap_val(double* vec, int i, int j)
+{
+ double tmp = vec[j];
+
+
+ vec[j]=vec[i];
+ vec[i]=tmp;
+}
+
+
+static void swap_col(double **mat, int i, int j)
+{
+ double tmp[3] = {mat[0][j], mat[1][j], mat[2][j]};
+
+
+ mat[0][j]=mat[0][i];
+ mat[1][j]=mat[1][i];
+ mat[2][j]=mat[2][i];
+
+ mat[0][i]=tmp[0];
+ mat[1][i]=tmp[1];
+ mat[2][i]=tmp[2];
+}
+
+
+/* Eigenvectors are stored in columns of eigen_vec */
+static void diagonalize_symmetric(
+ double **matrix,
+ double **eigen_vec,
+ double eigenval[3])
+{
+ int n_rot;
+
+
+ jacobi(matrix,3,eigenval,eigen_vec,&n_rot);
+
+ /* sort in ascending order */
+ if (eigenval[0] > eigenval[1])
+ {
+ swap_val(eigenval, 0, 1);
+ swap_col(eigen_vec, 0, 1);
+ }
+ if (eigenval[1] > eigenval[2])
+ {
+ swap_val(eigenval, 1, 2);
+ swap_col(eigen_vec, 1, 2);
+ }
+ if (eigenval[0] > eigenval[1])
+ {
+ swap_val(eigenval, 0, 1);
+ swap_col(eigen_vec, 0, 1);
+ }
+}
+
+
+static void align_with_z(
+ rvec* s, /* Structure to align */
+ int natoms,
+ rvec axis)
+{
+ int i, j, k;
+ rvec zet = {0.0, 0.0, 1.0};
+ rvec rot_axis={0.0, 0.0, 0.0};
+ rvec *rotated_str=NULL;
+ real ooanorm;
+ real angle;
+ matrix rotmat;
+
+
+ snew(rotated_str, natoms);
+
+ /* Normalize the axis */
+ ooanorm = 1.0/norm(axis);
+ svmul(ooanorm, axis, axis);
+
+ /* Calculate the angle for the fitting procedure */
+ cprod(axis, zet, rot_axis);
+ angle = acos(axis[2]);
+ if (angle < 0.0)
+ angle += M_PI;
+
+ /* Calculate the rotation matrix */
+ calc_rotmat(rot_axis, angle*180.0/M_PI, rotmat);
+
+ /* Apply the rotation matrix to s */
+ for (i=0; i<natoms; i++)
+ {
+ for(j=0; j<3; j++)
+ {
+ for(k=0; k<3; k++)
+ {
+ rotated_str[i][j] += rotmat[j][k]*s[i][k];
+ }
+ }
+ }
+
+ /* Rewrite the rotated structure to s */
+ for(i=0; i<natoms; i++)
+ {
+ for(j=0; j<3; j++)
+ {
+ s[i][j]=rotated_str[i][j];
+ }
+ }
+
+ sfree(rotated_str);
+}
+
+
+static void calc_correl_matrix(rvec* Xstr, rvec* Ystr, double** Rmat, int natoms)
+{
+ int i, j, k;
+
+
+ for (i=0; i<3; i++)
+ for (j=0; j<3; j++)
+ Rmat[i][j] = 0.0;
+
+ for (i=0; i<3; i++)
+ for (j=0; j<3; j++)
+ for (k=0; k<natoms; k++)
+ Rmat[i][j] += Ystr[k][i] * Xstr[k][j];
+}
+
+
+static void weigh_coords(rvec* str, real* weight, int natoms)
+{
+ int i, j;
+
+
+ for(i=0; i<natoms; i++)
+ {
+ for(j=0; j<3; j++)
+ str[i][j] *= sqrt(weight[i]);
+ }
+}
+
+
+static double opt_angle_analytic(
+ rvec* ref_s,
+ rvec* act_s,
+ real* weight,
+ int natoms,
+ rvec ref_com,
+ rvec act_com,
+ rvec axis)
+{
+ int i, j, k;
+ rvec *ref_s_1=NULL;
+ rvec *act_s_1=NULL;
+ rvec shift;
+ double **Rmat, **RtR, **eigvec;
+ double eigval[3];
+ double V[3][3], WS[3][3];
+ double rot_matrix[3][3];
+ double opt_angle;
+
+
+ /* Do not change the original coordinates */
+ snew(ref_s_1, natoms);
+ snew(act_s_1, natoms);
+ for(i=0; i<natoms; i++)
+ {
+ copy_rvec(ref_s[i], ref_s_1[i]);
+ copy_rvec(act_s[i], act_s_1[i]);
+ }
+
+ /* Translate the structures to the origin */
+ shift[XX] = -ref_com[XX];
+ shift[YY] = -ref_com[YY];
+ shift[ZZ] = -ref_com[ZZ];
+ translate_x(ref_s_1, natoms, shift);
+
+ shift[XX] = -act_com[XX];
+ shift[YY] = -act_com[YY];
+ shift[ZZ] = -act_com[ZZ];
+ translate_x(act_s_1, natoms, shift);
+
+ /* Align rotation axis with z */
+ align_with_z(ref_s_1, natoms, axis);
+ align_with_z(act_s_1, natoms, axis);
+
+ /* Correlation matrix */
+ Rmat = allocate_square_matrix(3);
+
+ for (i=0; i<natoms; i++)
+ {
+ ref_s_1[i][2]=0.0;
+ act_s_1[i][2]=0.0;
+ }
+
+ /* Weight positions with sqrt(weight) */
+ if (weight)
+ {
+ weigh_coords(ref_s_1, weight, natoms);
+ weigh_coords(act_s_1, weight, natoms);
+ }
+
+ /* Calculate correlation matrices R=YXt (X=ref_s; Y=act_s) */
+ calc_correl_matrix(ref_s_1, act_s_1, Rmat, natoms);
+
+ /* Calculate RtR */
+ RtR = allocate_square_matrix(3);
+ for (i=0; i<3; i++)
+ {
+ for (j=0; j<3; j++)
+ {
+ for (k=0; k<3; k++)
+ {
+ RtR[i][j] += Rmat[k][i] * Rmat[k][j];
+ }
+ }
+ }
+ /* Diagonalize RtR */
+ snew(eigvec,3);
+ for (i=0; i<3; i++)
+ snew(eigvec[i],3);
+
+ diagonalize_symmetric(RtR, eigvec, eigval);
+ swap_col(eigvec,0,1);
+ swap_col(eigvec,1,2);
+ swap_val(eigval,0,1);
+ swap_val(eigval,1,2);
+
+ /* Calculate V */
+ for(i=0; i<3; i++)
+ {
+ for(j=0; j<3; j++)
+ {
+ V[i][j] = 0.0;
+ WS[i][j] = 0.0;
+ }
+ }
+
+ for (i=0; i<2; i++)
+ for (j=0; j<2; j++)
+ WS[i][j] = eigvec[i][j] / sqrt(eigval[j]);
+
+ for (i=0; i<3; i++)
+ {
+ for (j=0; j<3; j++)
+ {
+ for (k=0; k<3; k++)
+ {
+ V[i][j] += Rmat[i][k]*WS[k][j];
+ }
+ }
+ }
+ free_square_matrix(Rmat, 3);
+
+ /* Calculate optimal rotation matrix */
+ for (i=0; i<3; i++)
+ for (j=0; j<3; j++)
+ rot_matrix[i][j] = 0.0;
+
+ for (i=0; i<3; i++)
+ {
+ for(j=0; j<3; j++)
+ {
+ for(k=0; k<3; k++){
+ rot_matrix[i][j] += eigvec[i][k]*V[j][k];
+ }
+ }
+ }
+ rot_matrix[2][2] = 1.0;
+
+ /* Determine the optimal rotation angle: */
+ opt_angle = (-1.0)*acos(rot_matrix[0][0])*180.0/M_PI;
+ if (rot_matrix[0][1] < 0.0)
+ opt_angle = (-1.0)*opt_angle;
+
+ /* Give back some memory */
+ free_square_matrix(RtR, 3);
+ sfree(ref_s_1);
+ sfree(act_s_1);
+ for (i=0; i<3; i++)
+ sfree(eigvec[i]);
+ sfree(eigvec);
+
+ return opt_angle;
+}
+
+
+/* Determine actual angle of this slab by RMSD fit */
+/* Not parallelized, call this routine only on the master */
+/* TODO: make this routine mass-weighted */
+static void flex_fit_angle(
+ int g,
+ t_rotgrp *rotg,
+ double t,
+ real degangle,
+ FILE *fp)
+{
+ int i,l,n,islab,ind;
+ rvec curr_x, ref_x;
+ rvec *fitcoords=NULL;
+ rvec act_center; /* Center of actual positions that are passed to the fit routine */
+ rvec ref_center; /* Same for the reference positions */
+ double fitangle; /* This will be the actual angle of the rotation group derived
+ * from an RMSD fit to the reference structure at t=0 */
+ t_gmx_slabdata *sd;
+ rvec coord;
+ real scal;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ /**********************************/
+ /* First collect the data we need */
+ /**********************************/
+
+ /* Loop over slabs */
+ for (n = erg->slab_first; n <= erg->slab_last; n++)
+ {
+ islab = n - erg->slab_first; /* slab index */
+ sd = &(rotg->enfrotgrp->slab_data[islab]);
+ sd->nat = erg->lastatom[islab]-erg->firstatom[islab]+1;
+ ind = 0;
+
+ /* Loop over the relevant atoms in the slab */
+ for (l=erg->firstatom[islab]; l<=erg->lastatom[islab]; l++)
+ {
+ /* Current position of this atom: x[ii][XX/YY/ZZ] */
+ copy_rvec(erg->xc[l], curr_x);
+
+ /* The (unrotated) reference position of this atom is copied to ref_x.
+ * Beware, the xc coords have been sorted in do_flex! */
+ copy_rvec(erg->xc_ref_sorted[l], ref_x);
+
+ /* Save data for doing angular RMSD fit later */
+ /* Save the current atom position */
+ copy_rvec(curr_x, sd->x[ind]);
+ /* Save the corresponding reference position */
+ copy_rvec(ref_x , sd->ref[ind]);
+ /* Save the weight for this atom in this slab */
+ sd->weight[ind] = gaussian_weight(curr_x, rotg, n);
+
+ /* Next atom in this slab */
+ ind++;
+ }
+ }
+
+ /* Get the geometrical center of the whole rotation group: */
+ get_center(erg->xc, NULL, rotg->nat, act_center);
+
+
+ /******************************/
+ /* Now do the fit calculation */
+ /******************************/
+
+ /* === Determine the optimal fit angle for the whole rotation group === */
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ /* Normalize every position to it's reference length
+ * prior to performing the fit */
+ for (i=0; i<rotg->nat; i++)
+ {
+ /* First put geometrical center of positions into origin */
+ rvec_sub(erg->xc[i], act_center, coord);
+ /* Determine the scaling factor for the length: */
+ scal = erg->xc_ref_length[erg->xc_sortind[i]] / norm(coord);
+ /* Get position, multiply with the scaling factor and save in buf[i] */
+ svmul(scal, coord, erg->xc_norm[i]);
+ }
+ fitcoords = erg->xc_norm;
+ }
+ else
+ {
+ fitcoords = erg->xc;
+ }
+ /* Note that from the point of view of the current positions, the reference has rotated backwards,
+ * but we want to output the angle relative to the fixed reference, therefore the minus sign. */
+ fitangle = -opt_angle_analytic(erg->xc_ref_sorted, fitcoords, NULL, rotg->nat, erg->xc_ref_center, act_center, rotg->vec);
+ fprintf(fp, "%12.3e%6d%12.3f%12.3lf", t, g, degangle, fitangle);
+
+
+ /* === Now do RMSD fitting for each slab === */
+ /* We require at least SLAB_MIN_ATOMS in a slab, such that the fit makes sense. */
+#define SLAB_MIN_ATOMS 4
+
+ for (n = erg->slab_first; n <= erg->slab_last; n++)
+ {
+ islab = n - erg->slab_first; /* slab index */
+ sd = &(rotg->enfrotgrp->slab_data[islab]);
+ if (sd->nat >= SLAB_MIN_ATOMS)
+ {
+ /* Get the center of the slabs reference and current positions */
+ get_center(sd->ref, sd->weight, sd->nat, ref_center);
+ get_center(sd->x , sd->weight, sd->nat, act_center);
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ /* Normalize every position to it's reference length
+ * prior to performing the fit */
+ for (i=0; i<sd->nat;i++) /* Center */
+ {
+ rvec_dec(sd->ref[i], ref_center);
+ rvec_dec(sd->x[i] , act_center);
+ /* Normalize x_i such that it gets the same length as ref_i */
+ svmul( norm(sd->ref[i])/norm(sd->x[i]), sd->x[i], sd->x[i] );
+ }
+ /* We already subtracted the centers */
+ clear_rvec(ref_center);
+ clear_rvec(act_center);
+ }
+ fitangle = -opt_angle_analytic(sd->ref, sd->x, sd->weight, sd->nat, ref_center, act_center, rotg->vec);
+ fprintf(fp, "%6d%6d%12.3f", n, sd->nat, fitangle);
+ }
+ }
+ fprintf(fp , "\n");
+
+#undef SLAB_MIN_ATOMS
+}
+
+
+/* Shift x with is */
+static inline void shift_single_coord(matrix box, rvec x, const ivec is)
+{
+ int tx,ty,tz;
+
+
+ tx=is[XX];
+ ty=is[YY];
+ tz=is[ZZ];
+
+ if(TRICLINIC(box))
+ {
+ x[XX] += tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
+ x[YY] += ty*box[YY][YY]+tz*box[ZZ][YY];
+ x[ZZ] += tz*box[ZZ][ZZ];
+ } else
+ {
+ x[XX] += tx*box[XX][XX];
+ x[YY] += ty*box[YY][YY];
+ x[ZZ] += tz*box[ZZ][ZZ];
+ }
+}
+
+
+/* Determine the 'home' slab of this atom which is the
+ * slab with the highest Gaussian weight of all */
+#define round(a) (int)(a+0.5)
+static inline int get_homeslab(
+ rvec curr_x, /* The position for which the home slab shall be determined */
+ rvec rotvec, /* The rotation vector */
+ real slabdist) /* The slab distance */
+{
+ real dist;
+
+
+ /* The distance of the atom to the coordinate center (where the
+ * slab with index 0) is */
+ dist = iprod(rotvec, curr_x);
+
+ return round(dist / slabdist);
+}
+
+
+/* For a local atom determine the relevant slabs, i.e. slabs in
+ * which the gaussian is larger than min_gaussian
+ */
+static int get_single_atom_gaussians(
+ rvec curr_x,
+ t_commrec *cr,
+ t_rotgrp *rotg)
+{
+ int slab, homeslab;
+ real g;
+ int count = 0;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Determine the 'home' slab of this atom: */
+ homeslab = get_homeslab(curr_x, rotg->vec, rotg->slab_dist);
+
+ /* First determine the weight in the atoms home slab: */
+ g = gaussian_weight(curr_x, rotg, homeslab);
+
+ erg->gn_atom[count] = g;
+ erg->gn_slabind[count] = homeslab;
+ count++;
+
+
+ /* Determine the max slab */
+ slab = homeslab;
+ while (g > rotg->min_gaussian)
+ {
+ slab++;
+ g = gaussian_weight(curr_x, rotg, slab);
+ erg->gn_slabind[count]=slab;
+ erg->gn_atom[count]=g;
+ count++;
+ }
+ count--;
+
+ /* Determine the max slab */
+ slab = homeslab;
+ do
+ {
+ slab--;
+ g = gaussian_weight(curr_x, rotg, slab);
+ erg->gn_slabind[count]=slab;
+ erg->gn_atom[count]=g;
+ count++;
+ }
+ while (g > rotg->min_gaussian);
+ count--;
+
+ return count;
+}
+
+
+static void flex2_precalc_inner_sum(t_rotgrp *rotg, t_commrec *cr)
+{
+ int i,n,islab;
+ rvec xi; /* positions in the i-sum */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ real gaussian_xi;
+ rvec yi0;
+ rvec rin; /* Helper variables */
+ real fac,fac2;
+ rvec innersumvec;
+ real OOpsii,OOpsiistar;
+ real sin_rin; /* s_ii.r_ii */
+ rvec s_in,tmpvec,tmpvec2;
+ real mi,wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+ N_M = rotg->nat * erg->invmass;
+
+ /* Loop over all slabs that contain something */
+ for (n=erg->slab_first; n <= erg->slab_last; n++)
+ {
+ islab = n - erg->slab_first; /* slab index */
+
+ /* The current center of this slab is saved in xcn: */
+ copy_rvec(erg->slab_center[islab], xcn);
+ /* ... and the reference center in ycn: */
+ copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
+
+ /*** D. Calculate the whole inner sum used for second and third sum */
+ /* For slab n, we need to loop over all atoms i again. Since we sorted
+ * the atoms with respect to the rotation vector, we know that it is sufficient
+ * to calculate from firstatom to lastatom only. All other contributions will
+ * be very small. */
+ clear_rvec(innersumvec);
+ for (i = erg->firstatom[islab]; i <= erg->lastatom[islab]; i++)
+ {
+ /* Coordinate xi of this atom */
+ copy_rvec(erg->xc[i],xi);
+
+ /* The i-weights */
+ gaussian_xi = gaussian_weight(xi,rotg,n);
+ mi = erg->mc_sorted[i]; /* need the sorted mass here */
+ wi = N_M*mi;
+
+ /* Calculate rin */
+ copy_rvec(erg->xc_ref_sorted[i],yi0); /* Reference position yi0 */
+ rvec_sub(yi0, ycn, tmpvec2); /* tmpvec2 = yi0 - ycn */
+ mvmul(erg->rotmat, tmpvec2, rin); /* rin = Omega.(yi0 - ycn) */
+
+ /* Calculate psi_i* and sin */
+ rvec_sub(xi, xcn, tmpvec2); /* tmpvec2 = xi - xcn */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xi - xcn) */
+ OOpsiistar = norm2(tmpvec)+rotg->eps; /* OOpsii* = 1/psii* = |v x (xi-xcn)|^2 + eps */
+ OOpsii = norm(tmpvec); /* OOpsii = 1 / psii = |v x (xi - xcn)| */
+
+ /* v x (xi - xcn) */
+ unitv(tmpvec, s_in); /* sin = ---------------- */
+ /* |v x (xi - xcn)| */
+
+ sin_rin=iprod(s_in,rin); /* sin_rin = sin . rin */
+
+ /* Now the whole sum */
+ fac = OOpsii/OOpsiistar;
+ svmul(fac, rin, tmpvec);
+ fac2 = fac*fac*OOpsii;
+ svmul(fac2*sin_rin, s_in, tmpvec2);
+ rvec_dec(tmpvec, tmpvec2);
+
+ svmul(wi*gaussian_xi*sin_rin, tmpvec, tmpvec2);
+
+ rvec_inc(innersumvec,tmpvec2);
+ } /* now we have the inner sum, used both for sum2 and sum3 */
+
+ /* Save it to be used in do_flex2_lowlevel */
+ copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
+ } /* END of loop over slabs */
+}
+
+
+static void flex_precalc_inner_sum(t_rotgrp *rotg, t_commrec *cr)
+{
+ int i,n,islab;
+ rvec xi; /* position */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ rvec qin,rin; /* q_i^n and r_i^n */
+ real bin;
+ rvec tmpvec;
+ rvec innersumvec; /* Inner part of sum_n2 */
+ real gaussian_xi; /* Gaussian weight gn(xi) */
+ real mi,wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+ N_M = rotg->nat * erg->invmass;
+
+ /* Loop over all slabs that contain something */
+ for (n=erg->slab_first; n <= erg->slab_last; n++)
+ {
+ islab = n - erg->slab_first; /* slab index */
+
+ /* The current center of this slab is saved in xcn: */
+ copy_rvec(erg->slab_center[islab], xcn);
+ /* ... and the reference center in ycn: */
+ copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
+
+ /* For slab n, we need to loop over all atoms i again. Since we sorted
+ * the atoms with respect to the rotation vector, we know that it is sufficient
+ * to calculate from firstatom to lastatom only. All other contributions will
+ * be very small. */
+ clear_rvec(innersumvec);
+ for (i=erg->firstatom[islab]; i<=erg->lastatom[islab]; i++)
+ {
+ /* Coordinate xi of this atom */
+ copy_rvec(erg->xc[i],xi);
+
+ /* The i-weights */
+ gaussian_xi = gaussian_weight(xi,rotg,n);
+ mi = erg->mc_sorted[i]; /* need the sorted mass here */
+ wi = N_M*mi;
+
+ /* Calculate rin and qin */
+ rvec_sub(erg->xc_ref_sorted[i], ycn, tmpvec); /* tmpvec = yi0-ycn */
+ mvmul(erg->rotmat, tmpvec, rin); /* rin = Omega.(yi0 - ycn) */
+ cprod(rotg->vec, rin, tmpvec); /* tmpvec = v x Omega*(yi0-ycn) */
+
+ /* v x Omega*(yi0-ycn) */
+ unitv(tmpvec, qin); /* qin = --------------------- */
+ /* |v x Omega*(yi0-ycn)| */
+
+ /* Calculate bin */
+ rvec_sub(xi, xcn, tmpvec); /* tmpvec = xi-xcn */
+ bin = iprod(qin, tmpvec); /* bin = qin*(xi-xcn) */
+
+ svmul(wi*gaussian_xi*bin, qin, tmpvec);
+
+ /* Add this contribution to the inner sum: */
+ rvec_add(innersumvec, tmpvec, innersumvec);
+ } /* now we have the inner sum vector S^n for this slab */
+ /* Save it to be used in do_flex_lowlevel */
+ copy_rvec(innersumvec, erg->slab_innersumvec[islab]);
+ }
+}
+
+
+static real do_flex2_lowlevel(
+ t_rotgrp *rotg,
+ real sigma, /* The Gaussian width sigma */
+ rvec x[],
- bool bCalcTorque,
++ gmx_bool bCalcTorque,
+ matrix box,
+ t_commrec *cr)
+{
+ int count,ic,ii,j,m,n,islab,iigrp;
+ rvec xj; /* position in the i-sum */
+ rvec yj0; /* the reference position in the j-sum */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ real V; /* This node's part of the rotation pot. energy */
+ real gaussian_xj; /* Gaussian weight */
+ real beta;
+
+ real numerator;
+ rvec rjn; /* Helper variables */
+ real fac,fac2;
+
+ real OOpsij,OOpsijstar;
+ real OOsigma2; /* 1/(sigma^2) */
+ real sjn_rjn;
+ real betasigpsi;
+ rvec sjn,tmpvec,tmpvec2;
+ rvec sum1vec_part,sum1vec,sum2vec_part,sum2vec,sum3vec,sum4vec,innersumvec;
+ real sum3,sum4;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ real mj,wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ real Wjn; /* g_n(x_j) m_j / Mjn */
+
+ /* To calculate the torque per slab */
+ rvec slab_force; /* Single force from slab n on one atom */
+ rvec slab_sum1vec_part;
+ real slab_sum3part,slab_sum4part;
+ rvec slab_sum1vec, slab_sum2vec, slab_sum3vec, slab_sum4vec;
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Pre-calculate the inner sums, so that we do not have to calculate
+ * them again for every atom */
+ flex2_precalc_inner_sum(rotg, cr);
+
+ /********************************************************/
+ /* Main loop over all local atoms of the rotation group */
+ /********************************************************/
+ N_M = rotg->nat * erg->invmass;
+ V = 0.0;
+ OOsigma2 = 1.0 / (sigma*sigma);
+ for (j=0; j<erg->nat_loc; j++)
+ {
+ /* Local index of a rotation group atom */
+ ii = erg->ind_loc[j];
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Mass-weighting */
+ mj = erg->mc[iigrp]; /* need the unsorted mass here */
+ wj = N_M*mj;
+
+ /* Current position of this atom: x[ii][XX/YY/ZZ] */
+ copy_rvec(x[ii], xj);
+
+ /* Shift this atom such that it is near its reference */
+ shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
+
+ /* Determine the slabs to loop over, i.e. the ones with contributions
+ * larger than min_gaussian */
+ count = get_single_atom_gaussians(xj, cr, rotg);
+
+ clear_rvec(sum1vec_part);
+ clear_rvec(sum2vec_part);
+ sum3 = 0.0;
+ sum4 = 0.0;
+ /* Loop over the relevant slabs for this atom */
+ for (ic=0; ic < count; ic++)
+ {
+ n = erg->gn_slabind[ic];
+
+ /* Get the precomputed Gaussian value of curr_slab for curr_x */
+ gaussian_xj = erg->gn_atom[ic];
+
+ islab = n - erg->slab_first; /* slab index */
+
+ /* The (unrotated) reference position of this atom is copied to yj0: */
+ copy_rvec(rotg->x_ref[iigrp], yj0);
+
+ beta = calc_beta(xj, rotg,n);
+
+ /* The current center of this slab is saved in xcn: */
+ copy_rvec(erg->slab_center[islab], xcn);
+ /* ... and the reference center in ycn: */
+ copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
+
+ rvec_sub(yj0, ycn, tmpvec2); /* tmpvec2 = yj0 - ycn */
+
+ /* Rotate: */
+ mvmul(erg->rotmat, tmpvec2, rjn); /* rjn = Omega.(yj0 - ycn) */
+
+ /* Subtract the slab center from xj */
+ rvec_sub(xj, xcn, tmpvec2); /* tmpvec2 = xj - xcn */
+
+ /* Calculate sjn */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x (xj - xcn) */
+
+ OOpsijstar = norm2(tmpvec)+rotg->eps; /* OOpsij* = 1/psij* = |v x (xj-xcn)|^2 + eps */
+
+ numerator = sqr(iprod(tmpvec, rjn));
+
+ /*********************************/
+ /* Add to the rotation potential */
+ /*********************************/
+ V += 0.5*rotg->k*wj*gaussian_xj*numerator/OOpsijstar;
+
+
+ /*************************************/
+ /* Now calculate the force on atom j */
+ /*************************************/
+
+ OOpsij = norm(tmpvec); /* OOpsij = 1 / psij = |v x (xj - xcn)| */
+
+ /* v x (xj - xcn) */
+ unitv(tmpvec, sjn); /* sjn = ---------------- */
+ /* |v x (xj - xcn)| */
+
+ sjn_rjn=iprod(sjn,rjn); /* sjn_rjn = sjn . rjn */
+
+
+ /*** A. Calculate the first of the four sum terms: ****************/
+ fac = OOpsij/OOpsijstar;
+ svmul(fac, rjn, tmpvec);
+ fac2 = fac*fac*OOpsij;
+ svmul(fac2*sjn_rjn, sjn, tmpvec2);
+ rvec_dec(tmpvec, tmpvec2);
+ fac2 = wj*gaussian_xj; /* also needed for sum4 */
+ svmul(fac2*sjn_rjn, tmpvec, slab_sum1vec_part);
+ /********************/
+ /*** Add to sum1: ***/
+ /********************/
+ rvec_inc(sum1vec_part, slab_sum1vec_part); /* sum1 still needs to vector multiplied with v */
+
+ /*** B. Calculate the forth of the four sum terms: ****************/
+ betasigpsi = beta*OOsigma2*OOpsij; /* this is also needed for sum3 */
+ /********************/
+ /*** Add to sum4: ***/
+ /********************/
+ slab_sum4part = fac2*betasigpsi*fac*sjn_rjn*sjn_rjn; /* Note that fac is still valid from above */
+ sum4 += slab_sum4part;
+
+ /*** C. Calculate Wjn for second and third sum */
+ /* Note that we can safely divide by slab_weights since we check in
+ * get_slab_centers that it is non-zero. */
+ Wjn = gaussian_xj*mj/erg->slab_weights[islab];
+
+ /* We already have precalculated the inner sum for slab n */
+ copy_rvec(erg->slab_innersumvec[islab], innersumvec);
+
+ /* Weigh the inner sum vector with Wjn */
+ svmul(Wjn, innersumvec, innersumvec);
+
+ /*** E. Calculate the second of the four sum terms: */
+ /********************/
+ /*** Add to sum2: ***/
+ /********************/
+ rvec_inc(sum2vec_part, innersumvec); /* sum2 still needs to be vector crossproduct'ed with v */
+
+ /*** F. Calculate the third of the four sum terms: */
+ slab_sum3part = betasigpsi * iprod(sjn, innersumvec);
+ sum3 += slab_sum3part; /* still needs to be multiplied with v */
+
+ /*** G. Calculate the torque on the local slab's axis: */
+ if (bCalcTorque)
+ {
+ /* Sum1 */
+ cprod(slab_sum1vec_part, rotg->vec, slab_sum1vec);
+ /* Sum2 */
+ cprod(innersumvec, rotg->vec, slab_sum2vec);
+ /* Sum3 */
+ svmul(slab_sum3part, rotg->vec, slab_sum3vec);
+ /* Sum4 */
+ svmul(slab_sum4part, rotg->vec, slab_sum4vec);
+
+ /* The force on atom ii from slab n only: */
+ for (m=0; m<DIM; m++)
+ slab_force[m] = rotg->k * (-slab_sum1vec[m] + slab_sum2vec[m] - slab_sum3vec[m] + 0.5*slab_sum4vec[m]);
+
+ erg->slab_torque_v[islab] += torque(rotg->vec, slab_force, xj, xcn);
+ }
+ } /* END of loop over slabs */
+
+ /* Construct the four individual parts of the vector sum: */
+ cprod(sum1vec_part, rotg->vec, sum1vec); /* sum1vec = { } x v */
+ cprod(sum2vec_part, rotg->vec, sum2vec); /* sum2vec = { } x v */
+ svmul(sum3, rotg->vec, sum3vec); /* sum3vec = { } . v */
+ svmul(sum4, rotg->vec, sum4vec); /* sum4vec = { } . v */
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ for (m=0; m<DIM; m++)
+ erg->f_rot_loc[j][m] = rotg->k * (-sum1vec[m] + sum2vec[m] - sum3vec[m] + 0.5*sum4vec[m]);
+
+#ifdef INFOF
+ fprintf(stderr," FORCE on ATOM %d/%d = (%15.8f %15.8f %15.8f) \n",
+ j,ii,erg->f_rot_loc[j][XX], erg->f_rot_loc[j][YY], erg->f_rot_loc[j][ZZ]);
+#endif
+
+#ifdef SUM_PARTS
+ fprintf(stderr, "sum1: %15.8f %15.8f %15.8f\n", -rotg->k*sum1vec[XX], -rotg->k*sum1vec[YY], -rotg->k*sum1vec[ZZ]);
+ fprintf(stderr, "sum2: %15.8f %15.8f %15.8f\n", rotg->k*sum2vec[XX], rotg->k*sum2vec[YY], rotg->k*sum2vec[ZZ]);
+ fprintf(stderr, "sum3: %15.8f %15.8f %15.8f\n", -rotg->k*sum3vec[XX], -rotg->k*sum3vec[YY], -rotg->k*sum3vec[ZZ]);
+ fprintf(stderr, "sum4: %15.8f %15.8f %15.8f\n", 0.5*rotg->k*sum4vec[XX], 0.5*rotg->k*sum4vec[YY], 0.5*rotg->k*sum4vec[ZZ]);
+#endif
+ } /* END of loop over local atoms */
+
+#ifdef INFOF
+ fprintf(stderr, "THE POTENTIAL IS V=%f\n", V);
+#endif
+
+ return V;
+}
+
+
+static real do_flex_lowlevel(
+ t_rotgrp *rotg,
+ real sigma, /* The Gaussian width sigma */
+ rvec x[],
- static bool bFirst=1;
++ gmx_bool bCalcTorque,
+ matrix box,
+ t_commrec *cr)
+{
+ int count,ic,ii,j,m,n,islab,iigrp;
+ rvec xj,yj0; /* current and reference position */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ rvec xj_xcn; /* xj - xcn */
+ rvec qjn; /* q_i^n */
+ rvec sum_n1,sum_n2; /* Two contributions to the rotation force */
+ rvec innersumvec; /* Inner part of sum_n2 */
+ rvec s_n;
+ rvec force_n; /* Single force from slab n on one atom */
+ rvec tmpvec,tmpvec2,tmp_f; /* Helper variables */
+ real V; /* The rotation potential energy */
+ real OOsigma2; /* 1/(sigma^2) */
+ real beta; /* beta_n(xj) */
+ real bjn; /* b_j^n */
+ real gaussian_xj; /* Gaussian weight gn(xj) */
+ real betan_xj_sigma2;
+ real mj,wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Pre-calculate the inner sums, so that we do not have to calculate
+ * them again for every atom */
+ flex_precalc_inner_sum(rotg, cr);
+
+ /********************************************************/
+ /* Main loop over all local atoms of the rotation group */
+ /********************************************************/
+ OOsigma2 = 1.0/(sigma*sigma);
+ N_M = rotg->nat * erg->invmass;
+ V = 0.0;
+ for (j=0; j<erg->nat_loc; j++)
+ {
+ /* Local index of a rotation group atom */
+ ii = erg->ind_loc[j];
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Mass-weighting */
+ mj = erg->mc[iigrp]; /* need the unsorted mass here */
+ wj = N_M*mj;
+
+ /* Current position of this atom: x[ii][XX/YY/ZZ] */
+ copy_rvec(x[ii], xj);
+
+ /* Shift this atom such that it is near its reference */
+ shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
+
+ /* Determine the slabs to loop over, i.e. the ones with contributions
+ * larger than min_gaussian */
+ count = get_single_atom_gaussians(xj, cr, rotg);
+
+ clear_rvec(sum_n1);
+ clear_rvec(sum_n2);
+
+ /* Loop over the relevant slabs for this atom */
+ for (ic=0; ic < count; ic++)
+ {
+ n = erg->gn_slabind[ic];
+
+ /* Get the precomputed Gaussian for xj in slab n */
+ gaussian_xj = erg->gn_atom[ic];
+
+ islab = n - erg->slab_first; /* slab index */
+
+ /* The (unrotated) reference position of this atom is saved in yj0: */
+ copy_rvec(rotg->x_ref[iigrp], yj0);
+
+ beta = calc_beta(xj, rotg, n);
+
+ /* The current center of this slab is saved in xcn: */
+ copy_rvec(erg->slab_center[islab], xcn);
+ /* ... and the reference center in ycn: */
+ copy_rvec(erg->slab_center_ref[islab+erg->slab_buffer], ycn);
+
+ rvec_sub(yj0, ycn, tmpvec); /* tmpvec = yj0 - ycn */
+
+ /* Rotate: */
+ mvmul(erg->rotmat, tmpvec, tmpvec2); /* tmpvec2 = Omega.(yj0-ycn) */
+
+ /* Subtract the slab center from xj */
+ rvec_sub(xj, xcn, xj_xcn); /* xj_xcn = xj - xcn */
+
+ /* Calculate qjn */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(xj-xcn) */
+
+ /* v x Omega.(xj-xcn) */
+ unitv(tmpvec,qjn); /* qjn = -------------------- */
+ /* |v x Omega.(xj-xcn)| */
+
+ bjn = iprod(qjn, xj_xcn); /* bjn = qjn * (xj - xcn) */
+
+ /*********************************/
+ /* Add to the rotation potential */
+ /*********************************/
+ V += 0.5*rotg->k*wj*gaussian_xj*sqr(bjn);
+
+ /****************************************************************/
+ /* sum_n1 will typically be the main contribution to the force: */
+ /****************************************************************/
+ betan_xj_sigma2 = beta*OOsigma2; /* beta_n(xj)/sigma^2 */
+
+ /* The next lines calculate
+ * qjn - (bjn*beta(xj)/(2sigma^2))v */
+ svmul(bjn*0.5*betan_xj_sigma2, rotg->vec, tmpvec2);
+ rvec_sub(qjn,tmpvec2,tmpvec);
+
+ /* Multiply with gn(xj)*bjn: */
+ svmul(gaussian_xj*bjn,tmpvec,tmpvec2);
+
+ /* Sum over n: */
+ rvec_inc(sum_n1,tmpvec2);
+
+ /* We already have precalculated the Sn term for slab n */
+ copy_rvec(erg->slab_innersumvec[islab], s_n);
+ /* beta_n(xj) */
+ svmul(betan_xj_sigma2*iprod(s_n, xj_xcn), rotg->vec, tmpvec); /* tmpvec = ---------- s_n (xj-xcn) */
+ /* sigma^2 */
+
+ rvec_sub(s_n, tmpvec, innersumvec);
+
+ /* We can safely divide by slab_weights since we check in get_slab_centers
+ * that it is non-zero. */
+ svmul(gaussian_xj/erg->slab_weights[islab], innersumvec, innersumvec);
+
+ rvec_add(sum_n2, innersumvec, sum_n2);
+
+ GMX_MPE_LOG(ev_inner_loop_finish);
+
+ /* Calculate the torque: */
+ if (bCalcTorque)
+ {
+ /* The force on atom ii from slab n only: */
+ rvec_sub(innersumvec, tmpvec2, force_n);
+ svmul(rotg->k, force_n, force_n);
+ erg->slab_torque_v[islab] += torque(rotg->vec, force_n, xj, xcn);
+ }
+ } /* END of loop over slabs */
+
+ /* Put both contributions together: */
+ svmul(wj, sum_n1, sum_n1);
+ svmul(mj, sum_n2, sum_n2);
+ rvec_sub(sum_n2,sum_n1,tmp_f); /* F = -grad V */
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ for(m=0; m<DIM; m++)
+ erg->f_rot_loc[j][m] = rotg->k*tmp_f[m];
+#ifdef INFOF
+ fprintf(stderr," FORCE on atom %d = %15.8f %15.8f %15.8f 1: %15.8f %15.8f %15.8f 2: %15.8f %15.8f %15.8f\n", iigrp,
+ rotg->k*tmp_f[XX] , rotg->k*tmp_f[YY] , rotg->k*tmp_f[ZZ] ,
+ -rotg->k*sum_n1[XX], -rotg->k*sum_n1[YY], -rotg->k*sum_n1[ZZ],
+ rotg->k*sum_n2[XX], rotg->k*sum_n2[YY], rotg->k*sum_n2[ZZ]);
+#endif
+ } /* END of loop over local atoms */
+
+ return V;
+}
+
+#ifdef PRINT_COORDS
+static void print_coordinates(t_commrec *cr, t_rotgrp *rotg, rvec x[], matrix box, int step)
+{
+ int i;
+ static FILE *fp;
+ static char buf[STRLEN];
- bool bOutstep)
++ static gmx_bool bFirst=1;
+
+
+ if (bFirst)
+ {
+ sprintf(buf, "coords%d.txt", cr->nodeid);
+ fp = fopen(buf, "w");
+ bFirst = 0;
+ }
+
+ fprintf(fp, "\nStep %d\n", step);
+ fprintf(fp, "box: %f %f %f %f %f %f %f %f %f\n",
+ box[XX][XX], box[XX][YY], box[XX][ZZ],
+ box[YY][XX], box[YY][YY], box[YY][ZZ],
+ box[ZZ][XX], box[ZZ][ZZ], box[ZZ][ZZ]);
+ for (i=0; i<rotg->nat; i++)
+ {
+ fprintf(fp, "%4d %f %f %f\n", i,
+ erg->xc[i][XX], erg->xc[i][YY], erg->xc[i][ZZ]);
+ }
+ fflush(fp);
+
+}
+#endif
+
+
+static int projection_compare(const void *a, const void *b)
+{
+ sort_along_vec_t *xca, *xcb;
+
+
+ xca = (sort_along_vec_t *)a;
+ xcb = (sort_along_vec_t *)b;
+
+ if (xca->xcproj < xcb->xcproj)
+ return -1;
+ else if (xca->xcproj > xcb->xcproj)
+ return 1;
+ else
+ return 0;
+}
+
+
+static void sort_collective_coordinates(
+ t_rotgrp *rotg, /* Rotation group */
+ sort_along_vec_t *data) /* Buffer for sorting the positions */
+{
+ int i;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* The projection of the position vector on the rotation vector is
+ * the relevant value for sorting. Fill the 'data' structure */
+ for (i=0; i<rotg->nat; i++)
+ {
+ data[i].xcproj = iprod(erg->xc[i], rotg->vec); /* sort criterium */
+ data[i].m = erg->mc[i];
+ data[i].ind = i;
+ copy_rvec(erg->xc[i] , data[i].x );
+ copy_rvec(rotg->x_ref[i], data[i].x_ref);
+ }
+ /* Sort the 'data' structure */
+ qsort(data, rotg->nat, sizeof(sort_along_vec_t), projection_compare);
+
+ /* Copy back the sorted values */
+ for (i=0; i<rotg->nat; i++)
+ {
+ copy_rvec(data[i].x , erg->xc[i] );
+ copy_rvec(data[i].x_ref, erg->xc_ref_sorted[i]);
+ erg->mc_sorted[i] = data[i].m;
+ erg->xc_sortind[i] = data[i].ind;
+ }
+}
+
+
+/* For each slab, get the first and the last index of the sorted atom
+ * indices */
+static void get_firstlast_atom_per_slab(t_rotgrp *rotg, t_commrec *cr)
+{
+ int i,islab,n;
+ real beta;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ GMX_MPE_LOG(ev_get_firstlast_start);
+
+ /* Find the first atom that needs to enter the calculation for each slab */
+ n = erg->slab_first; /* slab */
+ i = 0; /* start with the first atom */
+ do
+ {
+ /* Find the first atom that significantly contributes to this slab */
+ do /* move forward in position until a large enough beta is found */
+ {
+ beta = calc_beta(erg->xc[i], rotg, n);
+ i++;
+ } while ((beta < -erg->max_beta) && (i < rotg->nat));
+ i--;
+ islab = n - erg->slab_first; /* slab index */
+ erg->firstatom[islab] = i;
+ /* Proceed to the next slab */
+ n++;
+ } while (n <= erg->slab_last);
+
+ /* Find the last atom for each slab */
+ n = erg->slab_last; /* start with last slab */
+ i = rotg->nat-1; /* start with the last atom */
+ do
+ {
+ do /* move backward in position until a large enough beta is found */
+ {
+ beta = calc_beta(erg->xc[i], rotg, n);
+ i--;
+ } while ((beta > erg->max_beta) && (i > -1));
+ i++;
+ islab = n - erg->slab_first; /* slab index */
+ erg->lastatom[islab] = i;
+ /* Proceed to the next slab */
+ n--;
+ } while (n >= erg->slab_first);
+
+ GMX_MPE_LOG(ev_get_firstlast_finish);
+}
+
+
+/* Determine the very first and very last slab that needs to be considered
+ * For the first slab that needs to be considered, we have to find the smallest
+ * n that obeys:
+ *
+ * x_first * v - n*Delta_x <= beta_max
+ *
+ * slab index n, slab distance Delta_x, rotation vector v. For the last slab we
+ * have to find the largest n that obeys
+ *
+ * x_last * v - n*Delta_x >= -beta_max
+ *
+ */
+static inline int get_first_slab(
+ t_rotgrp *rotg, /* The rotation group (inputrec data) */
+ real max_beta, /* The max_beta value, instead of min_gaussian */
+ rvec firstatom) /* First atom after sorting along the rotation vector v */
+{
+ /* Find the first slab for the first atom */
+ return ceil((iprod(firstatom, rotg->vec) - max_beta)/rotg->slab_dist);
+}
+
+
+static inline int get_last_slab(
+ t_rotgrp *rotg, /* The rotation group (inputrec data) */
+ real max_beta, /* The max_beta value, instead of min_gaussian */
+ rvec lastatom) /* Last atom along v */
+{
+ /* Find the last slab for the last atom */
+ return floor((iprod(lastatom, rotg->vec) + max_beta)/rotg->slab_dist);
+}
+
+
+static void get_firstlast_slab_check(
+ t_rotgrp *rotg, /* The rotation group (inputrec data) */
+ t_gmx_enfrotgrp *erg, /* The rotation group (data only accessible in this file) */
+ rvec firstatom, /* First atom after sorting along the rotation vector v */
+ rvec lastatom, /* Last atom along v */
+ int g, /* The rotation group number */
+ t_commrec *cr)
+{
+ erg->slab_first = get_first_slab(rotg, erg->max_beta, firstatom);
+ erg->slab_last = get_last_slab(rotg, erg->max_beta, lastatom);
+
+ /* Check whether we have reference data to compare against */
+ if (erg->slab_first < erg->slab_first_ref)
+ gmx_fatal(FARGS, "Enforced rotation: No reference data for first slab (n=%d), unable to proceed.",
+ erg->slab_first);
+
+ /* Check whether we have reference data to compare against */
+ if (erg->slab_last > erg->slab_last_ref)
+ gmx_fatal(FARGS, "Enforced rotation: No reference data for last slab (n=%d), unable to proceed.",
+ erg->slab_last);
+}
+
+
+/* Enforced rotation with a flexible axis */
+static void do_flexible(
+ t_commrec *cr,
+ gmx_enfrot_t enfrot, /* Other rotation data */
+ t_rotgrp *rotg, /* The rotation group */
+ int g, /* Group number */
+ rvec x[], /* The local positions */
+ matrix box,
+ double t, /* Time in picoseconds */
+ int step, /* The time step */
- bool bTorque)
++ gmx_bool bOutstep)
+{
+ int l,nslabs;
+ real sigma; /* The Gaussian width sigma */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Define the sigma value */
+ sigma = 0.7*rotg->slab_dist;
+
+ /* Sort the collective coordinates erg->xc along the rotation vector. This is
+ * an optimization for the inner loop.
+ */
+ sort_collective_coordinates(rotg, enfrot->data);
+
+ /* Determine the first relevant slab for the first atom and the last
+ * relevant slab for the last atom */
+ get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1], g, cr);
+
+ /* Determine for each slab depending on the min_gaussian cutoff criterium,
+ * a first and a last atom index inbetween stuff needs to be calculated */
+ get_firstlast_atom_per_slab(rotg, cr);
+
+ /* Determine the gaussian-weighted center of positions for all slabs */
+ get_slab_centers(rotg,erg->xc,erg->mc_sorted,cr,g,t,enfrot->out_slabs,bOutstep,FALSE);
+
+ /* Clear the torque per slab from last time step: */
+ nslabs = erg->slab_last - erg->slab_first + 1;
+ for (l=0; l<nslabs; l++)
+ erg->slab_torque_v[l] = 0.0;
+
+ /* Call the rotational forces kernel */
+ GMX_MPE_LOG(ev_flexll_start);
+ if (rotg->eType == erotgFLEX)
+ erg->V = do_flex_lowlevel(rotg, sigma, x, bOutstep, box, cr);
+ else if (rotg->eType == erotgFLEX2)
+ erg->V = do_flex2_lowlevel(rotg, sigma, x, bOutstep, box, cr);
+ else
+ gmx_fatal(FARGS, "Unknown flexible rotation type");
+ GMX_MPE_LOG(ev_flexll_finish);
+
+ /* Determine actual angle of this slab by RMSD fit and output to file - Let's hope */
+ /* this only happens once in a while, since this is not parallelized! */
+ if (bOutstep && MASTER(cr))
+ flex_fit_angle(g, rotg, t, erg->degangle, enfrot->out_angles);
+}
+
+
+/* Calculate the angle between reference and actual rotation group atom,
+ * both projected into a plane perpendicular to the rotation vector: */
+static void angle(t_rotgrp *rotg,
+ rvec x_act,
+ rvec x_ref,
+ real *alpha,
+ real *weight) /* atoms near the rotation axis should count less than atoms far away */
+{
+ rvec xp, xrp; /* current and reference positions projected on a plane perpendicular to pg->vec */
+ rvec dum;
+
+
+ /* Project x_ref and x into a plane through the origin perpendicular to rot_vec: */
+ /* Project x_ref: xrp = x_ref - (vec * x_ref) * vec */
+ svmul(iprod(rotg->vec, x_ref), rotg->vec, dum);
+ rvec_sub(x_ref, dum, xrp);
+ /* Project x_act: */
+ svmul(iprod(rotg->vec, x_act), rotg->vec, dum);
+ rvec_sub(x_act, dum, xp);
+
+ /* Retrieve information about which vector precedes. gmx_angle always
+ * returns a positive angle. */
+ cprod(xp, xrp, dum); /* if reference precedes, this is pointing into the same direction as vec */
+
+ if (iprod(rotg->vec, dum) >= 0)
+ *alpha = -gmx_angle(xrp, xp);
+ else
+ *alpha = +gmx_angle(xrp, xp);
+
+ /* Also return the weight */
+ *weight = norm(xp);
+}
+
+
+/* Project first vector onto a plane perpendicular to the second vector
+ * dr = dr - (dr.v)v
+ * Note that v must be of unit length.
+ */
+static inline void project_onto_plane(rvec dr, const rvec v)
+{
+ rvec tmp;
+
+
+ svmul(iprod(dr,v),v,tmp); /* tmp = (dr.v)v */
+ rvec_dec(dr, tmp); /* dr = dr - (dr.v)v */
+}
+
+
+/* Fixed rotation: The rotation reference group rotates around an axis */
+/* The atoms of the actual rotation group are attached with imaginary */
+/* springs to the reference atoms. */
+static void do_fixed(
+ t_commrec *cr,
+ t_rotgrp *rotg, /* The rotation group */
+ rvec x[], /* The positions */
+ matrix box, /* The simulation box */
+ double t, /* Time in picoseconds */
+ int step, /* The time step */
- bool bProject;
++ gmx_bool bTorque)
+{
+ int i,m;
+ rvec dr;
+ rvec tmp_f; /* Force */
+ real alpha; /* a single angle between an actual and a reference position */
+ real weight; /* single weight for a single angle */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec tmpvec;
+
+ /* for mass weighting: */
+ real wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ real k_wi; /* k times wi */
+
- bool bTorque)
++ gmx_bool bProject;
+
+
+ erg=rotg->enfrotgrp;
+ bProject = (rotg->eType==erotgPM) || (rotg->eType==erotgPMPF);
+
+ /* Clear values from last time step */
+ erg->V = 0.0;
+ erg->fix_torque_v = 0.0;
+ erg->fix_angles_v = 0.0;
+ erg->fix_weight_v = 0.0;
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Each process calculates the forces on its local atoms */
+ for (i=0; i<erg->nat_loc; i++)
+ {
+ /* Calculate (x_i-x_c) resp. (x_i-u) */
+ rvec_sub(erg->x_loc_pbc[i], erg->xc_center, tmpvec);
+
+ /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
+ rvec_sub(erg->xr_loc[i], tmpvec, dr);
+
+ if (bProject)
+ project_onto_plane(dr, rotg->vec);
+
+ /* Mass-weighting */
+ wi = N_M*erg->m_loc[i];
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ k_wi = rotg->k*wi;
+ for (m=0; m<DIM; m++)
+ {
+ tmp_f[m] = k_wi*dr[m];
+ erg->f_rot_loc[i][m] = tmp_f[m];
+ erg->V += 0.5*k_wi*sqr(dr[m]);
+ }
+
+ if (bTorque)
+ {
+ /* Add to the torque of this rotation group */
+ erg->fix_torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[i], erg->xc_center);
+
+ /* Calculate the angle between reference and actual rotation group atom. */
+ angle(rotg, tmpvec, erg->xr_loc[i], &alpha, &weight); /* angle in rad, weighted */
+ erg->fix_angles_v += alpha * weight;
+ erg->fix_weight_v += weight;
+ }
+ /* If you want enforced rotation to contribute to the virial,
+ * activate the following lines:
+ if (MASTER(cr))
+ {
+ Add the rotation contribution to the virial
+ for(j=0; j<DIM; j++)
+ for(m=0;m<DIM;m++)
+ vir[j][m] += 0.5*f[ii][j]*dr[m];
+ }
+ */
+#ifdef INFOF
+ fprintf(stderr,"step %d node%d FORCE on ATOM %d = (%15.8f %15.8f %15.8f) torque=%15.8f\n", step, cr->nodeid,
+ erg->xc_ref_ind[i],erg->f_rot_loc[i][XX], erg->f_rot_loc[i][YY], erg->f_rot_loc[i][ZZ],erg->fix_torque_v);
+#endif
+ } /* end of loop over local rotation group atoms */
+}
+
+
+/* Calculate the radial motion potential and forces */
+static void do_radial_motion(
+ t_commrec *cr,
+ t_rotgrp *rotg, /* The rotation group */
+ rvec x[], /* The positions */
+ matrix box, /* The simulation box */
+ double t, /* Time in picoseconds */
+ int step, /* The time step */
- bool bTorque)
++ gmx_bool bTorque)
+{
+ int j;
+ rvec tmp_f; /* Force */
+ real alpha; /* a single angle between an actual and a reference position */
+ real weight; /* single weight for a single angle */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xj_u; /* xj - u */
+ rvec tmpvec;
+ real fac,fac2,sum;
+ rvec pj;
+
+ /* For mass weighting: */
+ real wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Clear values from last time step */
+ erg->V = 0.0;
+ sum = 0.0;
+ erg->fix_torque_v = 0.0;
+ erg->fix_angles_v = 0.0;
+ erg->fix_weight_v = 0.0;
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Each process calculates the forces on its local atoms */
+ for (j=0; j<erg->nat_loc; j++)
+ {
+ /* Calculate (xj-u) */
+ rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xj_u); /* xj_u = xj-u */
+
+ /* Calculate Omega.(yj-u) */
+ cprod(rotg->vec, erg->xr_loc[j], tmpvec); /* tmpvec = v x Omega.(yj-u) */
+
+ /* v x Omega.(yj-u) */
+ unitv(tmpvec, pj); /* pj = -------------------- */
+ /* | v x Omega.(yj-u) | */
+
+ fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
+ fac2 = fac*fac;
+
+ /* Mass-weighting */
+ wj = N_M*erg->m_loc[j];
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ svmul(-rotg->k*wj*fac, pj, tmp_f);
+ copy_rvec(tmp_f, erg->f_rot_loc[j]);
+ sum += wj*fac2;
+ if (bTorque)
+ {
+ /* Add to the torque of this rotation group */
+ erg->fix_torque_v += torque(rotg->vec, tmp_f, erg->x_loc_pbc[j], erg->xc_center);
+
+ /* Calculate the angle between reference and actual rotation group atom. */
+ angle(rotg, xj_u, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
+ erg->fix_angles_v += alpha * weight;
+ erg->fix_weight_v += weight;
+ }
+#ifdef INFOF
+ fprintf(stderr,"RM: step %d node%d FORCE on ATOM %d = (%15.8f %15.8f %15.8f) torque=%15.8f\n", step, cr->nodeid,
+ erg->xc_ref_ind[j],erg->f_rot_loc[j][XX], erg->f_rot_loc[j][YY], erg->f_rot_loc[j][ZZ],erg->fix_torque_v);
+#endif
+ } /* end of loop over local rotation group atoms */
+ erg->V = 0.5*rotg->k*sum;
+}
+
+
+/* Calculate the radial motion pivot-free potential and forces */
+static void do_radial_motion_pf(
+ t_commrec *cr,
+ t_rotgrp *rotg, /* The rotation group */
+ rvec x[], /* The positions */
+ matrix box, /* The simulation box */
+ double t, /* Time in picoseconds */
+ int step, /* The time step */
- bool bTorque)
++ gmx_bool bTorque)
+{
+ int i,ii,iigrp,j;
+ rvec xj; /* Current position */
+ rvec xj_xc; /* xj - xc */
+ rvec yj0_yc0; /* yj0 - yc0 */
+ rvec tmp_f; /* Force */
+ real alpha; /* a single angle between an actual and a reference position */
+ real weight; /* single weight for a single angle */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec tmpvec, tmpvec2;
+ rvec innersumvec; /* Precalculation of the inner sum */
+ rvec innersumveckM;
+ real fac,fac2,V;
+ rvec qi,qj;
+
+ /* For mass weighting: */
+ real mj,wi,wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Clear values from last time step */
+ erg->V = 0.0;
+ V = 0.0;
+ erg->fix_torque_v = 0.0;
+ erg->fix_angles_v = 0.0;
+ erg->fix_weight_v = 0.0;
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Get the current center of the rotation group: */
+ get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
+
+ /* Precalculate Sum_i [ wi qi.(xi-xc) qi ] which is needed for every single j */
+ clear_rvec(innersumvec);
+ for (i=0; i < rotg->nat; i++)
+ {
+ /* Mass-weighting */
+ wi = N_M*erg->mc[i];
+
+ /* Calculate qi. Note that xc_ref_center has already been subtracted from
+ * x_ref in init_rot_group.*/
+ mvmul(erg->rotmat, rotg->x_ref[i], tmpvec); /* tmpvec = Omega.(yi0-yc0) */
+
+ cprod(rotg->vec, tmpvec, tmpvec2); /* tmpvec2 = v x Omega.(yi0-yc0) */
+
+ /* v x Omega.(yi0-yc0) */
+ unitv(tmpvec2, qi); /* qi = ----------------------- */
+ /* | v x Omega.(yi0-yc0) | */
+
+ rvec_sub(erg->xc[i], erg->xc_center, tmpvec); /* tmpvec = xi-xc */
+
+ svmul(wi*iprod(qi, tmpvec), qi, tmpvec2);
+
+ rvec_inc(innersumvec, tmpvec2);
+ }
+ svmul(rotg->k*erg->invmass, innersumvec, innersumveckM);
+
+ /* Each process calculates the forces on its local atoms */
+ for (j=0; j<erg->nat_loc; j++)
+ {
+ /* Local index of a rotation group atom */
+ ii = erg->ind_loc[j];
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Mass-weighting */
+ mj = erg->mc[iigrp]; /* need the unsorted mass here */
+ wj = N_M*mj;
+
+ /* Current position of this atom: x[ii][XX/YY/ZZ] */
+ copy_rvec(x[ii], xj);
+
+ /* Shift this atom such that it is near its reference */
+ shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
+
+ /* The (unrotated) reference position is yj0. yc0 has already
+ * been subtracted in init_rot_group */
+ copy_rvec(rotg->x_ref[iigrp], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
+
+ /* Calculate Omega.(yj0-yc0) */
+ mvmul(erg->rotmat, yj0_yc0, tmpvec2); /* tmpvec2 = Omega.(yj0 - yc0) */
+
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec = v x Omega.(yj0-yc0) */
+
+ /* v x Omega.(yj0-yc0) */
+ unitv(tmpvec, qj); /* qj = ----------------------- */
+ /* | v x Omega.(yj0-yc0) | */
+
+ /* Calculate (xj-xc) */
+ rvec_sub(xj, erg->xc_center, xj_xc); /* xj_xc = xj-xc */
+
+ fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
+ fac2 = fac*fac;
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ svmul(-rotg->k*wj*fac, qj, tmp_f); /* part 1 of force */
+ svmul(mj, innersumveckM, tmpvec); /* part 2 of force */
+ rvec_inc(tmp_f, tmpvec);
+ copy_rvec(tmp_f, erg->f_rot_loc[j]);
+ V += wj*fac2;
+ if (bTorque)
+ {
+ /* Add to the torque of this rotation group */
+ erg->fix_torque_v += torque(rotg->vec, tmp_f, xj, erg->xc_center);
+
+ /* Calculate the angle between reference and actual rotation group atom. */
+ angle(rotg, xj_xc, yj0_yc0, &alpha, &weight); /* angle in rad, weighted */
+ erg->fix_angles_v += alpha * weight;
+ erg->fix_weight_v += weight;
+ }
+#ifdef INFOF
+ fprintf(stderr,"RM-PF: step %d node%d FORCE on ATOM %d = (%15.8f %15.8f %15.8f) torque=%15.8f\n", step, cr->nodeid,
+ erg->xc_ref_ind[j],erg->f_rot_loc[j][XX], erg->f_rot_loc[j][YY], erg->f_rot_loc[j][ZZ],erg->fix_torque_v);
+#endif
+ } /* end of loop over local rotation group atoms */
+ erg->V = 0.5*rotg->k*V;
+}
+
+
+/* Precalculate the inner sum for the radial motion 2 forces */
+static void radial_motion2_precalc_inner_sum(t_rotgrp *rotg, rvec innersumvec)
+{
+ int i;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xi_xc; /* xj - xc */
+ rvec tmpvec,tmpvec2;
+ real fac,fac2;
+ rvec ri,si;
+ real siri;
+ rvec v_xi_xc; /* v x (xj - u) */
+ real psii,psiistar;
+ real wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ rvec sumvec;
+
+ erg=rotg->enfrotgrp;
+ N_M = rotg->nat * erg->invmass;
+
+ /* Loop over the collective set of positions */
+ clear_rvec(sumvec);
+ for (i=0; i<rotg->nat; i++)
+ {
+ /* Mass-weighting */
+ wi = N_M*erg->mc[i];
+
+ rvec_sub(erg->xc[i], erg->xc_center, xi_xc); /* xi_xc = xi-xc */
+
+ /* Calculate ri. Note that xc_ref_center has already been subtracted from
+ * x_ref in init_rot_group.*/
+ mvmul(erg->rotmat, rotg->x_ref[i], ri); /* ri = Omega.(yi0-yc0) */
+
+ cprod(rotg->vec, xi_xc, v_xi_xc); /* v_xi_xc = v x (xi-u) */
+
+ fac = norm2(v_xi_xc);
+ /* 1 */
+ psiistar = 1.0/(fac + rotg->eps); /* psiistar = --------------------- */
+ /* |v x (xi-xc)|^2 + eps */
+
+ psii = gmx_invsqrt(fac); /* 1 */
+ /* psii = ------------- */
+ /* |v x (xi-xc)| */
+
+ svmul(psii, v_xi_xc, si); /* si = psii * (v x (xi-xc) ) */
+
+ fac = iprod(v_xi_xc, ri); /* fac = (v x (xi-xc)).ri */
+ fac2 = fac*fac;
+
+ siri = iprod(si, ri); /* siri = si.ri */
+
+ svmul(psiistar/psii, ri, tmpvec);
+ svmul(psiistar*psiistar/(psii*psii*psii) * siri, si, tmpvec2);
+ rvec_dec(tmpvec, tmpvec2);
+ cprod(tmpvec, rotg->vec, tmpvec2);
+
+ svmul(wi*siri, tmpvec2, tmpvec);
+
+ rvec_inc(sumvec, tmpvec);
+ }
+ svmul(rotg->k*erg->invmass, sumvec, innersumvec);
+}
+
+
+/* Calculate the radial motion 2 potential and forces */
+static void do_radial_motion2(
+ t_commrec *cr,
+ t_rotgrp *rotg, /* The rotation group */
+ rvec x[], /* The positions */
+ matrix box, /* The simulation box */
+ double t, /* Time in picoseconds */
+ int step, /* The time step */
- bool bPF;
++ gmx_bool bTorque)
+{
+ int ii,iigrp,j;
+ rvec xj; /* Position */
+ real alpha; /* a single angle between an actual and a reference position */
+ real weight; /* single weight for a single angle */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xj_u; /* xj - u */
+ rvec tmpvec,tmpvec2;
+ real fac,fac2,Vpart;
+ rvec rj,sj;
+ real sjrj;
+ rvec v_xj_u; /* v x (xj - u) */
+ real psij,psijstar;
+ real mj,wj; /* For mass-weighting of the positions */
+ real N_M; /* N/M */
- bool bFlex,bColl;
++ gmx_bool bPF;
+ rvec innersumvec;
+
+
+ erg=rotg->enfrotgrp;
+
+ bPF = rotg->eType==erotgRM2PF;
+ clear_rvec(innersumvec);
+ if (bPF)
+ {
+ /* For the pivot-free variant we have to use the current center of
+ * mass of the rotation group instead of the pivot u */
+ get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
+
+ /* Also, we precalculate the second term of the forces that is identical
+ * (up to the weight factor mj) for all forces */
+ radial_motion2_precalc_inner_sum(rotg,innersumvec);
+ }
+
+ /* Clear values from last time step */
+ erg->V = 0.0;
+ Vpart = 0.0;
+ erg->fix_torque_v = 0.0;
+ erg->fix_angles_v = 0.0;
+ erg->fix_weight_v = 0.0;
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Each process calculates the forces on its local atoms */
+ for (j=0; j<erg->nat_loc; j++)
+ {
+ if (bPF)
+ {
+ /* Local index of a rotation group atom */
+ ii = erg->ind_loc[j];
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Mass-weighting */
+ mj = erg->mc[iigrp];
+
+ /* Current position of this atom: x[ii] */
+ copy_rvec(x[ii], xj);
+
+ /* Shift this atom such that it is near its reference */
+ shift_single_coord(box, xj, erg->xc_shifts[iigrp]);
+
+ /* The (unrotated) reference position is yj0. yc0 has already
+ * been subtracted in init_rot_group */
+ copy_rvec(rotg->x_ref[iigrp], tmpvec); /* tmpvec = yj0 - yc0 */
+
+ /* Calculate Omega.(yj0-yc0) */
+ mvmul(erg->rotmat, tmpvec, rj); /* rj = Omega.(yj0-yc0) */
+ }
+ else
+ {
+ mj = erg->m_loc[j];
+ copy_rvec(erg->x_loc_pbc[j], xj);
+ copy_rvec(erg->xr_loc[j], rj); /* rj = Omega.(yj0-u) */
+ }
+ /* Mass-weighting */
+ wj = N_M*mj;
+
+ /* Calculate (xj-u) resp. (xj-xc) */
+ rvec_sub(xj, erg->xc_center, xj_u); /* xj_u = xj-u */
+
+ cprod(rotg->vec, xj_u, v_xj_u); /* v_xj_u = v x (xj-u) */
+
+ fac = norm2(v_xj_u);
+ /* 1 */
+ psijstar = 1.0/(fac + rotg->eps); /* psistar = -------------------- */
+ /* |v x (xj-u)|^2 + eps */
+
+ psij = gmx_invsqrt(fac); /* 1 */
+ /* psij = ------------ */
+ /* |v x (xj-u)| */
+
+ svmul(psij, v_xj_u, sj); /* sj = psij * (v x (xj-u) ) */
+
+ fac = iprod(v_xj_u, rj); /* fac = (v x (xj-u)).rj */
+ fac2 = fac*fac;
+
+ sjrj = iprod(sj, rj); /* sjrj = sj.rj */
+
+ svmul(psijstar/psij, rj, tmpvec);
+ svmul(psijstar*psijstar/(psij*psij*psij) * sjrj, sj, tmpvec2);
+ rvec_dec(tmpvec, tmpvec2);
+ cprod(tmpvec, rotg->vec, tmpvec2);
+
+ /* Store the additional force so that it can be added to the force
+ * array after the normal forces have been evaluated */
+ svmul(-rotg->k*wj*sjrj, tmpvec2, tmpvec);
+ svmul(mj, innersumvec, tmpvec2); /* This is != 0 only for the pivot-free variant */
+
+ rvec_add(tmpvec2, tmpvec, erg->f_rot_loc[j]);
+ Vpart += wj*psijstar*fac2;
+ if (bTorque)
+ {
+ /* Add to the torque of this rotation group */
+ erg->fix_torque_v += torque(rotg->vec, erg->f_rot_loc[j], xj, erg->xc_center);
+
+ /* Calculate the angle between reference and actual rotation group atom. */
+ angle(rotg, xj_u, rj, &alpha, &weight); /* angle in rad, weighted */
+ erg->fix_angles_v += alpha * weight;
+ erg->fix_weight_v += weight;
+ }
+#ifdef INFOF
+ fprintf(stderr,"RM2: step %d node%d FORCE on ATOM %d = (%15.8f %15.8f %15.8f) torque=%15.8f\n", step, cr->nodeid,
+ erg->xc_ref_ind[j],erg->f_rot_loc[j][XX], erg->f_rot_loc[j][YY], erg->f_rot_loc[j][ZZ],erg->fix_torque_v);
+#endif
+ } /* end of loop over local rotation group atoms */
+ erg->V = 0.5*rotg->k*Vpart;
+}
+
+
+/* Determine the smallest and largest position vector (with respect to the
+ * rotation vector) for the reference group */
+static void get_firstlast_atom_ref(
+ t_rotgrp *rotg,
+ int *firstindex,
+ int *lastindex)
+{
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ int i;
+ real xcproj; /* The projection of a reference position on the
+ rotation vector */
+ real minproj, maxproj; /* Smallest and largest projection on v */
+
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Start with some value */
+ minproj = iprod(rotg->x_ref[0], rotg->vec);
+ maxproj = minproj;
+
+ /* This is just to ensure that it still works if all the atoms of the
+ * reference structure are situated in a plane perpendicular to the rotation
+ * vector */
+ *firstindex = 0;
+ *lastindex = rotg->nat-1;
+
+ /* Loop over all atoms of the reference group,
+ * project them on the rotation vector to find the extremes */
+ for (i=0; i<rotg->nat; i++)
+ {
+ xcproj = iprod(rotg->x_ref[i], rotg->vec);
+ if (xcproj < minproj)
+ {
+ minproj = xcproj;
+ *firstindex = i;
+ }
+ if (xcproj > maxproj)
+ {
+ maxproj = xcproj;
+ *lastindex = i;
+ }
+ }
+}
+
+
+/* Allocate memory for the slabs */
+static void allocate_slabs(
+ t_rotgrp *rotg,
+ FILE *fplog,
+ int g,
+ t_commrec *cr)
+{
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ int i, nslabs;
+
+
+ erg=rotg->enfrotgrp;
+
+ /* More slabs than are defined for the reference are never needed */
+ nslabs = erg->slab_last_ref - erg->slab_first_ref + 1;
+
+ /* Remember how many we allocated */
+ erg->nslabs_alloc = nslabs;
+
+ if (MASTER(cr))
+ fprintf(fplog, "Enforced rotation: allocating memory to store data for %d slabs (rotation group %d).\n",nslabs,g);
+ snew(erg->slab_center , nslabs);
+ snew(erg->slab_center_ref , nslabs);
+ snew(erg->slab_weights , nslabs);
+ snew(erg->slab_torque_v , nslabs);
+ snew(erg->slab_data , nslabs);
+ snew(erg->gn_atom , nslabs);
+ snew(erg->gn_slabind , nslabs);
+ snew(erg->slab_innersumvec, nslabs);
+ for (i=0; i<nslabs; i++)
+ {
+ snew(erg->slab_data[i].x , rotg->nat);
+ snew(erg->slab_data[i].ref , rotg->nat);
+ snew(erg->slab_data[i].weight, rotg->nat);
+ }
+ snew(erg->xc_ref_sorted, rotg->nat);
+ snew(erg->xc_sortind , rotg->nat);
+ snew(erg->firstatom , nslabs);
+ snew(erg->lastatom , nslabs);
+}
+
+
+/* From the extreme coordinates of the reference group, determine the first
+ * and last slab of the reference. We can never have more slabs in the real
+ * simulation than calculated here for the reference.
+ */
+static void get_firstlast_slab_ref(t_rotgrp *rotg, real mc[], int ref_firstindex, int ref_lastindex)
+{
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ int first,last,firststart;
+ rvec dummy;
+
+
+ erg=rotg->enfrotgrp;
+ first = get_first_slab(rotg, erg->max_beta, rotg->x_ref[ref_firstindex]);
+ last = get_last_slab( rotg, erg->max_beta, rotg->x_ref[ref_lastindex ]);
+ firststart = first;
+
+ while (get_slab_weight(first, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
+ {
+ first--;
+ }
+ erg->slab_first_ref = first+1;
+ while (get_slab_weight(last, rotg, rotg->x_ref, mc, &dummy) > WEIGHT_MIN)
+ {
+ last++;
+ }
+ erg->slab_last_ref = last-1;
+
+ erg->slab_buffer = firststart - erg->slab_first_ref;
+}
+
+
+
+extern void init_rot_group(FILE *fplog,t_commrec *cr,int g,t_rotgrp *rotg,
+ rvec *x,gmx_mtop_t *mtop,FILE *out_slabs)
+{
+ int i,ii;
+ rvec coord,*xdum;
- bool bNS)
++ gmx_bool bFlex,bColl;
+ t_atom *atom;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ int ref_firstindex, ref_lastindex;
+ real mass,totalmass;
+
+
+ /* Do we have a flexible axis? */
+ bFlex = (rotg->eType==erotgFLEX) || (rotg->eType==erotgFLEX2);
+ /* Do we use a global set of coordinates? */
+ bColl = bFlex || (rotg->eType==erotgRMPF) || (rotg->eType==erotgRM2PF);
+
+ erg=rotg->enfrotgrp;
+
+ /* Allocate space for collective coordinates if needed */
+ if (bColl)
+ {
+ snew(erg->xc , rotg->nat);
+ snew(erg->xc_shifts , rotg->nat);
+ snew(erg->xc_eshifts, rotg->nat);
+
+ /* Save the original (whole) set of positions such that later the
+ * molecule can always be made whole again */
+ snew(erg->xc_old , rotg->nat);
+ if (MASTER(cr))
+ {
+ for (i=0; i<rotg->nat; i++)
+ {
+ ii = rotg->ind[i];
+ copy_rvec(x[ii], erg->xc_old[i]);
+ }
+ }
+#ifdef GMX_MPI
+ if (PAR(cr))
+ gmx_bcast(rotg->nat*sizeof(erg->xc_old[0]),erg->xc_old, cr);
+#endif
+
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ snew(erg->xc_ref_length, rotg->nat); /* in case fit type NORM is chosen */
+ snew(erg->xc_norm , rotg->nat);
+ }
+ }
+ else
+ {
+ snew(erg->xr_loc , rotg->nat);
+ snew(erg->x_loc_pbc, rotg->nat);
+ }
+
+ snew(erg->f_rot_loc , rotg->nat);
+ snew(erg->xc_ref_ind, rotg->nat);
+
+ /* xc_ref_ind needs to be set to identity in the serial case */
+ if (!PAR(cr))
+ for (i=0; i<rotg->nat; i++)
+ erg->xc_ref_ind[i] = i;
+
+ /* Copy the masses so that the COM can be determined. For all types of
+ * enforced rotation, we store the masses in the erg->mc array. */
+ snew(erg->mc, rotg->nat);
+ if (bFlex)
+ snew(erg->mc_sorted, rotg->nat);
+ if (!bColl)
+ snew(erg->m_loc, rotg->nat);
+ totalmass=0.0;
+ for (i=0; i<rotg->nat; i++)
+ {
+ if (rotg->bMassW)
+ {
+ gmx_mtop_atomnr_to_atom(mtop,rotg->ind[i],&atom);
+ mass=atom->m;
+ }
+ else
+ {
+ mass=1.0;
+ }
+ erg->mc[i] = mass;
+ totalmass += mass;
+ }
+ erg->invmass = 1.0/totalmass;
+
+ /* Set xc_ref_center for any rotation potential */
+ if ((rotg->eType==erotgISO) || (rotg->eType==erotgPM) || (rotg->eType==erotgRM) || (rotg->eType==erotgRM2))
+ {
+ /* Set the pivot point for the fixed, stationary-axis potentials. This
+ * won't change during the simulation */
+ copy_rvec(rotg->pivot, erg->xc_ref_center);
+ copy_rvec(rotg->pivot, erg->xc_center );
+ }
+ else
+ {
+ /* Center of the reference positions */
+ get_center(rotg->x_ref, erg->mc, rotg->nat, erg->xc_ref_center);
+
+ /* Center of the actual positions */
+ if (MASTER(cr))
+ {
+ snew(xdum, rotg->nat);
+ for (i=0; i<rotg->nat; i++)
+ {
+ ii = rotg->ind[i];
+ copy_rvec(x[ii], xdum[i]);
+ }
+ get_center(xdum, erg->mc, rotg->nat, erg->xc_center);
+ sfree(xdum);
+ }
+#ifdef GMX_MPI
+ if (PAR(cr))
+ gmx_bcast(sizeof(erg->xc_center), erg->xc_center, cr);
+#endif
+ }
+
+ if (!bFlex)
+ {
+ /* Put the reference positions into origin: */
+ for (i=0; i<rotg->nat; i++)
+ rvec_dec(rotg->x_ref[i], erg->xc_ref_center);
+ }
+
+ /* Enforced rotation with flexible axis */
+ if (bFlex)
+ {
+ /* Calculate maximum beta value from minimum gaussian (performance opt.) */
+ erg->max_beta = calc_beta_max(rotg->min_gaussian, rotg->slab_dist);
+
+ /* Determine the smallest and largest coordinate with respect to the rotation vector */
+ get_firstlast_atom_ref(rotg, &ref_firstindex, &ref_lastindex);
+
+ /* From the extreme coordinates of the reference group, determine the first
+ * and last slab of the reference. */
+ get_firstlast_slab_ref(rotg, erg->mc, ref_firstindex, ref_lastindex);
+
+ /* Allocate memory for the slabs */
+ allocate_slabs(rotg, fplog, g, cr);
+
+ /* Flexible rotation: determine the reference centers for the rest of the simulation */
+ erg->slab_first = erg->slab_first_ref;
+ erg->slab_last = erg->slab_last_ref;
+ get_slab_centers(rotg,rotg->x_ref,erg->mc,cr,g,-1,out_slabs,TRUE,TRUE);
+
+ /* Length of each x_rotref vector from center (needed if fit routine NORM is chosen): */
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ for (i=0; i<rotg->nat; i++)
+ {
+ rvec_sub(rotg->x_ref[i], erg->xc_ref_center, coord);
+ erg->xc_ref_length[i] = norm(coord);
+ }
+ }
+ }
+}
+
+
+void dd_make_local_rotation_groups(gmx_domdec_t *dd,t_rot *rot,t_mdatoms *md)
+{
+ gmx_ga2la_t ga2la;
+ int g;
+ t_rotgrp *rotg;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+ ga2la = dd->ga2la;
+
+ for(g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+
+
+ dd_make_local_group_indices(ga2la,rotg->nat,rotg->ind,
+ &erg->nat_loc,&erg->ind_loc,&erg->nalloc_loc,erg->xc_ref_ind);
+ }
+}
+
+
+void init_rot(FILE *fplog,t_inputrec *ir,int nfile,const t_filenm fnm[],
+ t_commrec *cr, rvec *x, gmx_mtop_t *mtop, const output_env_t oenv,
+ unsigned long Flags)
+{
+ t_rot *rot;
+ t_rotgrp *rotg;
+ int g;
+ int nat_max=0; /* Size of biggest rotation group */
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ if ( (PAR(cr)) && !DOMAINDECOMP(cr) )
+ gmx_fatal(FARGS, "Enforced rotation is only implemented for domain decomposition!");
+
+ rot = ir->rot;
+ snew(rot->enfrot, 1);
+ er=rot->enfrot;
+
+ /* Output every step for reruns */
+ if (Flags & MD_RERUN)
+ {
+ if (fplog)
+ fprintf(fplog, "Enforced rotation: rerun - will write rotation output every available step.\n");
+ rot->nstrout = 1;
+ rot->nsttout = 1;
+ }
+
+ er->out_slabs = NULL;
+ if (MASTER(cr))
+ er->out_slabs = open_slab_out(rot, opt2fn("-rs",nfile,fnm));
+
+ for(g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+
+ if (fplog)
+ fprintf(fplog,"Enforced rotation: group %d type '%s'\n", g, erotg_names[rotg->eType]);
+
+ if (rotg->nat > 0)
+ {
+ /* Allocate space for the rotation group's data: */
+ snew(rotg->enfrotgrp, 1);
+ erg = rotg->enfrotgrp;
+
+ nat_max=max(nat_max, rotg->nat);
+
+ if (PAR(cr))
+ {
+ erg->nat_loc = 0;
+ erg->nalloc_loc = 0;
+ erg->ind_loc = NULL;
+ }
+ else
+ {
+ erg->nat_loc = rotg->nat;
+ erg->ind_loc = rotg->ind;
+ }
+ init_rot_group(fplog,cr,g,rotg,x,mtop,er->out_slabs);
+ }
+ }
+
+ /* Allocate space for enforced rotation buffer variables */
+ er->bufsize = nat_max;
+ snew(er->data, nat_max);
+ snew(er->xbuf, nat_max);
+ snew(er->mbuf, nat_max);
+
+ /* Buffers for MPI reducing torques, angles, weights (for each group), and V */
+ er->mpi_bufsize = 4*rot->ngrp; /* To start with */
+ snew(er->mpi_inbuf , er->mpi_bufsize);
+ snew(er->mpi_outbuf, er->mpi_bufsize);
+
+ /* Only do I/O on the MASTER */
+ er->out_angles = NULL;
+ er->out_rot = NULL;
+ er->out_torque = NULL;
+ if (MASTER(cr))
+ {
+ er->out_rot = open_rot_out(opt2fn("-ro",nfile,fnm), rot, oenv, Flags);
+ if ( (rotg->eType == erotgFLEX) || (rotg->eType == erotgFLEX2) )
+ {
+ if (rot->nstrout > 0)
+ er->out_angles = open_angles_out(rot, opt2fn("-ra",nfile,fnm));
+ if (rot->nsttout > 0)
+ er->out_torque = open_torque_out(rot, opt2fn("-rt",nfile,fnm));
+ }
+ }
+}
+
+
+void finish_rot(FILE *fplog,t_rot *rot)
+{
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+
+
+ er=rot->enfrot;
+ if (er->out_rot)
+ gmx_fio_fclose(er->out_rot);
+ if (er->out_slabs)
+ gmx_fio_fclose(er->out_slabs);
+ if (er->out_angles)
+ gmx_fio_fclose(er->out_angles);
+ if (er->out_torque)
+ gmx_fio_fclose(er->out_torque);
+}
+
+
+/* Rotate the local reference positions and store them in
+ * erg->xr_loc[0...(nat_loc-1)]
+ *
+ * Note that we already subtracted u or y_c from the reference positions
+ * in init_rot_group().
+ */
+static void rotate_local_reference(t_rotgrp *rotg)
+{
+ gmx_enfrotgrp_t erg;
+ int i,ii;
+
+
+ erg=rotg->enfrotgrp;
+
+ for (i=0; i<erg->nat_loc; i++)
+ {
+ /* Index of this rotation group atom with respect to the whole rotation group */
+ ii = erg->xc_ref_ind[i];
+ /* Rotate */
+ mvmul(erg->rotmat, rotg->x_ref[ii], erg->xr_loc[i]);
+ }
+}
+
+
+/* Select the PBC representation for each local x position and store that
+ * for later usage. The right PBC image of an x is the one nearest to its
+ * rotated reference */
+static void choose_pbc_image(rvec x[], t_rotgrp *rotg, matrix box, int npbcdim)
+{
+ int d,i,ii,m;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec xref,xcurr,dx;
+ ivec shift;
+
+
+ erg=rotg->enfrotgrp;
+
+ for (i=0; i<erg->nat_loc; i++)
+ {
+ clear_ivec(shift);
+
+ /* Index of a rotation group atom */
+ ii = erg->ind_loc[i];
+
+ /* Get the already rotated reference position */
+ copy_rvec(erg->xr_loc[i], xref);
+
+ /* Subtract the (old) center from the current positions
+ * (just to determine the shifts!) */
+ rvec_sub(x[ii], erg->xc_center, xcurr);
+
+ /* Shortest PBC distance between the atom and its reference */
+ rvec_sub(xref, xcurr, dx);
+
+ /* Determine the shift for this atom */
+ for(m=npbcdim-1; m>=0; m--)
+ {
+ while (dx[m] < -0.5*box[m][m])
+ {
+ for(d=0; d<DIM; d++)
+ dx[d] += box[m][d];
+ shift[m]++;
+ }
+ while (dx[m] >= 0.5*box[m][m])
+ {
+ for(d=0; d<DIM; d++)
+ dx[d] -= box[m][d];
+ shift[m]--;
+ }
+ }
+
+ /* Apply the shift to the current atom */
+ copy_rvec(x[ii], erg->x_loc_pbc[i]);
+ shift_single_coord(box, erg->x_loc_pbc[i], shift);
+ }
+}
+
+
+extern void do_rotation(
+ t_commrec *cr,
+ t_inputrec *ir,
+ matrix box,
+ rvec x[],
+ real t,
+ int step,
+ gmx_wallcycle_t wcycle,
- bool outstep_torque;
- bool bFlex,bColl;
++ gmx_bool bNS)
+{
+ int g,i,ii;
+ t_rot *rot;
+ t_rotgrp *rotg;
++ gmx_bool outstep_torque;
++ gmx_bool bFlex,bColl;
+ float cycles_rot;
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+#ifdef TAKETIME
+ double t0;
+#endif
+
+
+ rot=ir->rot;
+ er=rot->enfrot;
+
+ /* At which time steps do we want to output the torque */
+ outstep_torque = do_per_step(step, rot->nsttout);
+
+ /* Output time into rotation output file */
+ if (outstep_torque && MASTER(cr))
+ fprintf(er->out_rot, "%12.3e",t);
+
+ /**************************************************************************/
+ /* First do ALL the communication! */
+ for(g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+
+ /* Do we have a flexible axis? */
+ bFlex = (rotg->eType==erotgFLEX) || (rotg->eType==erotgFLEX2);
+ /* Do we use a collective (global) set of coordinates? */
+ bColl = bFlex || (rotg->eType==erotgRMPF) || (rotg->eType==erotgRM2PF);
+
+ /* Calculate the rotation matrix for this angle: */
+ erg->degangle = rotg->rate * t;
+ calc_rotmat(rotg->vec,erg->degangle,erg->rotmat);
+
+ if (bColl)
+ {
+ /* Transfer the rotation group's positions such that every node has
+ * all of them. Every node contributes its local positions x and stores
+ * it in the collective erg->xc array. */
+ communicate_group_positions(cr,erg->xc, erg->xc_shifts, erg->xc_eshifts, bNS,
+ x, rotg->nat, erg->nat_loc, erg->ind_loc, erg->xc_ref_ind, erg->xc_old, box);
+ }
+ else
+ {
+ /* Fill the local masses array;
+ * this array changes in DD/neighborsearching steps */
+ if (bNS)
+ {
+ for (i=0; i<erg->nat_loc; i++)
+ {
+ /* Index of local atom w.r.t. the collective rotation group */
+ ii = erg->xc_ref_ind[i];
+ erg->m_loc[i] = erg->mc[ii];
+ }
+ }
+
+ /* Calculate Omega*(y_i-y_c) for the local positions */
+ rotate_local_reference(rotg);
+
+ /* Choose the nearest PBC images of the group atoms with respect
+ * to the rotated reference positions */
+ choose_pbc_image(x, rotg, box, 3);
+
+ /* Get the center of the rotation group */
+ if ( (rotg->eType==erotgISOPF) || (rotg->eType==erotgPMPF) )
+ get_center_comm(cr, erg->x_loc_pbc, erg->m_loc, erg->nat_loc, rotg->nat, erg->xc_center);
+ }
+
+ } /* End of loop over rotation groups */
+
+ /**************************************************************************/
+ /* Done communicating, we can start to count cycles now ... */
+ wallcycle_start(wcycle, ewcROT);
+ GMX_MPE_LOG(ev_rotcycles_start);
+
+#ifdef TAKETIME
+ t0 = MPI_Wtime();
+#endif
+
+ for(g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+
+ bFlex = (rotg->eType==erotgFLEX) || (rotg->eType==erotgFLEX2);
+ bColl = bFlex || (rotg->eType==erotgRMPF) || (rotg->eType==erotgRM2PF);
+
+ if (outstep_torque && MASTER(cr))
+ fprintf(er->out_rot, "%12.4f", erg->degangle);
+
+ switch(rotg->eType)
+ {
+ case erotgISO:
+ case erotgISOPF:
+ case erotgPM:
+ case erotgPMPF:
+ do_fixed(cr,rotg,x,box,t,step,outstep_torque);
+ break;
+ case erotgRM:
+ do_radial_motion(cr,rotg,x,box,t,step,outstep_torque);
+ break;
+ case erotgRMPF:
+ do_radial_motion_pf(cr,rotg,x,box,t,step,outstep_torque);
+ break;
+ case erotgRM2:
+ case erotgRM2PF:
+ do_radial_motion2(cr,rotg,x,box,t,step,outstep_torque);
+ break;
+ case erotgFLEX:
+ case erotgFLEX2:
+ /* Subtract the center of the rotation group */
+ /* get_center(erg->xc, erg->mc, rotg->nat, center); */
+ /* svmul(-1.0, center, transvec); */
+ /* translate_x(erg->xc, rotg->nat, transvec); */
+ do_flexible(cr,er,rotg,g,x,box,t,step,outstep_torque);
+ break;
+ default:
+ gmx_fatal(FARGS, "No such rotation potential.");
+ break;
+ }
+ }
+
+#ifdef TAKETIME
+ if (MASTER(cr))
+ fprintf(stderr, "Enforced rotation calculation (step %d) took %g seconds.\n", step, MPI_Wtime()-t0);
+#endif
+
+ /* Stop the cycle counter and add to the force cycles for load balancing */
+ cycles_rot = wallcycle_stop(wcycle,ewcROT);
+ if (DOMAINDECOMP(cr) && wcycle)
+ dd_cycles_add(cr->dd,cycles_rot,ddCyclF);
+ GMX_MPE_LOG(ev_rotcycles_finish);
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff