--- /dev/null
- t_commrec *cr, /* Communication record */
+/*
+ *
+ * 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 "groupcoord.h"
+#include "pull_rotation.h"
+#include "gmx_sort.h"
++#include "copyrite.h"
++#include "gmx_cyclecounter.h"
+#include "macros.h"
+
+
+static char *RotStr = {"Enforced rotation:"};
+
+
+/* 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;
+
+
+/* Helper structure for potential fitting */
+typedef struct gmx_potfit
+{
+ real *degangle; /* Set of angles for which the potential is
+ calculated. The optimum fit is determined as
+ the angle for with the potential is minimal */
+ real *V; /* Potential for the different angles */
+ matrix *rotmat; /* Rotation matrix corresponding to the angles */
+} t_gmx_potfit;
+
+
+/* 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 */
+ unsigned long Flags; /* mdrun flags */
+ gmx_bool bOut; /* Used to skip first output when appending to
+ * avoid duplicate entries in rotation outfiles */
+} t_gmx_enfrot;
+
+
+/* Global enforced rotation data for a single rotation group */
+typedef struct gmx_enfrotgrp
+{
+ real degangle; /* Rotation angle in degrees */
+ 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 */
+
+ real torque_v; /* Torque in the direction of rotation vector */
+ real angle_v; /* Actual angle of the whole rotation group */
+ /* Fixed rotation only */
+ real weight_v; /* Weights for angle determination */
+ 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 */
+
+ /* 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 ref. center 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 */
+ rvec *slab_center_ref; /* Gaussian-weighted slab center 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 */
+
+ /* For potential fits with varying angle: */
+ t_gmx_potfit *PotAngleFit; /* Used for fit type 'potential' */
+} t_gmx_enfrotgrp;
+
+
+/* Activate output of forces for correctness checks */
+/* #define PRINT_FORCES */
+#ifdef PRINT_FORCES
+#define PRINT_FORCE_J fprintf(stderr,"f%d = %15.8f %15.8f %15.8f\n",erg->xc_ref_ind[j],erg->f_rot_loc[j][XX], erg->f_rot_loc[j][YY], erg->f_rot_loc[j][ZZ]);
+#define PRINT_POT_TAU if (MASTER(cr)) { \
+ fprintf(stderr,"potential = %15.8f\n" "torque = %15.8f\n", erg->V, erg->torque_v); \
+ }
+#else
+#define PRINT_FORCE_J
+#define PRINT_POT_TAU
+#endif
+
+/* Shortcuts for often used queries */
+#define ISFLEX(rg) ( (rg->eType==erotgFLEX) || (rg->eType==erotgFLEXT) || (rg->eType==erotgFLEX2) || (rg->eType==erotgFLEX2T) )
+#define ISCOLL(rg) ( (rg->eType==erotgFLEX) || (rg->eType==erotgFLEXT) || (rg->eType==erotgFLEX2) || (rg->eType==erotgFLEX2T) || (rg->eType==erotgRMPF) || (rg->eType==erotgRM2PF) )
+
+
+/* Does any of the rotation groups use slab decomposition? */
+static gmx_bool HaveFlexibleGroups(t_rot *rot)
+{
+ int g;
+ t_rotgrp *rotg;
+
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (ISFLEX(rotg))
+ return TRUE;
+ }
+
+ return FALSE;
+}
+
+
+/* Is for any group the fit angle determined by finding the minimum of the
+ * rotation potential? */
+static gmx_bool HavePotFitGroups(t_rot *rot)
+{
+ int g;
+ t_rotgrp *rotg;
+
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (erotgFitPOT == rotg->eFittype)
+ return TRUE;
+ }
+
+ return FALSE;
+}
+
+
+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);
+}
+
+
+/* Return the angle for which the potential is minimal */
+static real get_fitangle(t_rotgrp *rotg, gmx_enfrotgrp_t erg)
+{
+ int i;
+ real fitangle = -999.9;
+ real pot_min = GMX_FLOAT_MAX;
+ t_gmx_potfit *fit;
+
+
+ fit = erg->PotAngleFit;
+
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ if (fit->V[i] < pot_min)
+ {
+ pot_min = fit->V[i];
+ fitangle = fit->degangle[i];
+ }
+ }
+
+ return fitangle;
+}
+
+
+/* Reduce potential angle fit data for this group at this time step? */
+static gmx_inline gmx_bool bPotAngle(t_rot *rot, t_rotgrp *rotg, gmx_large_int_t step)
+{
+ return ( (erotgFitPOT==rotg->eFittype) && (do_per_step(step, rot->nstsout) || do_per_step(step, rot->nstrout)) );
+}
+
+/* Reduce slab torqe data for this group at this time step? */
+static gmx_inline gmx_bool bSlabTau(t_rot *rot, t_rotgrp *rotg, gmx_large_int_t step)
+{
+ return ( (ISFLEX(rotg)) && do_per_step(step, rot->nstsout) );
+}
+
+/* Output rotation energy, torques, etc. for each rotation group */
+static void reduce_output(t_commrec *cr, t_rot *rot, real t, gmx_large_int_t step)
+{
+ 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 */
+ real fitangle;
+ gmx_bool bFlex;
+
+
+ er=rot->enfrot;
+
+ /* Fill the MPI buffer with stuff to reduce. If items are added for reduction
+ * here, the MPI buffer size has to be enlarged also in calc_mpi_bufsize() */
+ 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;
+ er->mpi_inbuf[count++] = erg->torque_v;
+ er->mpi_inbuf[count++] = erg->angle_v;
+ er->mpi_inbuf[count++] = erg->weight_v; /* weights are not needed for flex types, but this is just a single value */
+
+ if (bPotAngle(rot, rotg, step))
+ {
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ er->mpi_inbuf[count++] = erg->PotAngleFit->V[i];
+ }
+ if (bSlabTau(rot, rotg, step))
+ {
+ for (i=0; i<nslabs; i++)
+ er->mpi_inbuf[count++] = erg->slab_torque_v[i];
+ }
+ }
+ if (count > er->mpi_bufsize)
+ gmx_fatal(FARGS, "%s MPI buffer overflow, please report this error.", RotStr);
+
+#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++];
+ erg->torque_v = er->mpi_outbuf[count++];
+ erg->angle_v = er->mpi_outbuf[count++];
+ erg->weight_v = er->mpi_outbuf[count++];
+
+ if (bPotAngle(rot, rotg, step))
+ {
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ erg->PotAngleFit->V[i] = er->mpi_outbuf[count++];
+ }
+ if (bSlabTau(rot, rotg, step))
+ {
+ for (i=0; i<nslabs; i++)
+ erg->slab_torque_v[i] = er->mpi_outbuf[count++];
+ }
+ }
+ }
+ }
+
+ /* Output */
+ if (MASTER(cr))
+ {
+ /* Angle and torque for each rotation group */
+ for (g=0; g < rot->ngrp; g++)
+ {
+ rotg=&rot->grp[g];
+ bFlex = ISFLEX(rotg);
+
+ erg=rotg->enfrotgrp;
+
+ /* Output to main rotation output file: */
+ if ( do_per_step(step, rot->nstrout) )
+ {
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ fitangle = get_fitangle(rotg, erg);
+ }
+ else
+ {
+ if (bFlex)
+ fitangle = erg->angle_v; /* RMSD fit angle */
+ else
+ fitangle = (erg->angle_v/erg->weight_v)*180.0*M_1_PI;
+ }
+ fprintf(er->out_rot, "%12.4f", fitangle);
+ fprintf(er->out_rot, "%12.3e", erg->torque_v);
+ fprintf(er->out_rot, "%12.3e", erg->V);
+ }
+
+ if ( do_per_step(step, rot->nstsout) )
+ {
+ /* 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");
+ }
+
+ /* Output to angles log file: */
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ fprintf(er->out_angles, "%12.3e%6d%12.4f", t, g, erg->degangle);
+ /* Output energies at a set of angles around the reference angle */
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ fprintf(er->out_angles, "%12.3e", erg->PotAngleFit->V[i]);
+ fprintf(er->out_angles, "\n");
+ }
+ }
+ }
+ if ( do_per_step(step, rot->nstrout) )
+ 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, gmx_large_int_t 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 */
+ real Vrot = 0.0; /* If more than one rotation group is present, Vrot
+ assembles the local parts from all groups */
+
+
+ er=rot->enfrot;
+
+ /* 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;
+ Vrot += erg->V; /* add the local parts from the nodes */
+ 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]);
+ }
+ }
+
+ /* 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->nstrout) || do_per_step(step, rot->nstsout)) && er->bOut)
+ reduce_output(cr, rot, t, step);
+
+ /* When appending, er->bOut is FALSE the first time to avoid duplicate entries */
+ er->bOut = TRUE;
+
+ PRINT_POT_TAU
+
+ return Vrot;
+}
+
+
+/* The Gaussian norm is chosen such that the sum of the gaussian functions
+ * over the slabs is approximately 1.0 everywhere */
+#define GAUSS_NORM 0.569917543430618
+
+
+/* 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)
+{
+ 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/GAUSS_NORM;
+ if (arg > 1.0)
+ gmx_fatal(FARGS, "min_gaussian of flexible rotation groups must be <%g", GAUSS_NORM);
+
+ return sqrt(-2.0*sigma*sigma*log(min_gaussian/GAUSS_NORM));
+}
+
+
+static gmx_inline real calc_beta(rvec curr_x, t_rotgrp *rotg, int n)
+{
+ return iprod(curr_x, rotg->vec) - rotg->slab_dist * n;
+}
+
+
+static gmx_inline real gaussian_weight(rvec curr_x, t_rotgrp *rotg, int n)
+{
+ const real norm = GAUSS_NORM;
+ 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 */
- if (MASTER(cr) && bOutStep)
+ int g, /* The number of the rotation group */
+ real time, /* Used for output only */
+ FILE *out_slabs, /* For outputting center per slab information */
+ 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 */
- fp = xvgropen(fn, "Rotation angles and energy", "Time [ps]", "angles [degrees] and energies [kJ/mol]", oenv);
++ if ( (NULL != out_slabs) && 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 gmx_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);
+}
+
+
+static FILE *open_output_file(const char *fn, int steps, const char what[])
+{
+ FILE *fp;
+
+
+ fp = ffopen(fn, "w");
+
+ fprintf(fp, "# Output of %s is written in intervals of %d time step%s.\n#\n",
+ what,steps, steps>1 ? "s":"");
+
+ return fp;
+}
+
+
+/* Open output file for slab center data. Call on master only */
+static FILE *open_slab_out(const char *fn, t_rot *rot, const output_env_t oenv)
+{
+ FILE *fp;
+ int g,i;
+ t_rotgrp *rotg;
+
+
+ if (rot->enfrot->Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn,"a");
+ }
+ else
+ {
+ fp = open_output_file(fn, rot->nstsout, "gaussian weighted slab centers");
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (ISFLEX(rotg))
+ {
+ fprintf(fp, "# Rotation group %d (%s), slab distance %f nm, %s.\n",
+ g, erotg_names[rotg->eType], rotg->slab_dist,
+ rotg->bMassW? "centers of mass":"geometrical centers");
+ }
+ }
+
+ fprintf(fp, "# Reference centers are listed first (t=-1).\n");
+ fprintf(fp, "# The following columns have the syntax:\n");
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "t");
+ print_aligned_short(fp, "grp");
+ /* Print legend for the first two entries only ... */
+ for (i=0; i<2; i++)
+ {
+ print_aligned_short(fp, "slab");
+ print_aligned(fp, "X center");
+ print_aligned(fp, "Y center");
+ print_aligned(fp, "Z center");
+ }
+ fprintf(fp, " ...\n");
+ fflush(fp);
+ }
+
+ return fp;
+}
+
+
+/* Adds 'buf' to 'str' */
+static void add_to_string(char **str, char *buf)
+{
+ int len;
+
+
+ len = strlen(*str) + strlen(buf) + 1;
+ srenew(*str, len);
+ strcat(*str, buf);
+}
+
+
+static void add_to_string_aligned(char **str, char *buf)
+{
+ char buf_aligned[STRLEN];
+
+ sprintf(buf_aligned, "%12s", buf);
+ add_to_string(str, buf_aligned);
+}
+
+
+/* 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)
+{
+ FILE *fp;
+ int g,nsets;
+ t_rotgrp *rotg;
+ const char **setname;
+ char buf[50], buf2[75];
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ gmx_bool bFlex;
+ char *LegendStr=NULL;
+
+
+ if (rot->enfrot->Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn,"a");
+ }
+ else
+ {
- fprintf(fp, "# The scalar tau is the torque [kJ/mol] in the direction of the rotation vector v.\n");
++ fp = xvgropen(fn, "Rotation angles and energy", "Time (ps)", "angles (degrees) and energies (kJ/mol)", oenv);
+ fprintf(fp, "# Output of enforced rotation data is written in intervals of %d time step%s.\n#\n", rot->nstrout, rot->nstrout > 1 ? "s":"");
- sprintf(buf2, "%s [degrees]", buf);
++ 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");
+ fprintf(fp, "# For flexible groups, tau(t,n) from all slabs n have been summed in a single value tau(t) here.\n");
+ fprintf(fp, "# The torques tau(t,n) are found in the rottorque.log (-rt) output file\n");
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+ bFlex = ISFLEX(rotg);
+
+ fprintf(fp, "#\n");
+ 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 degrees/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 (bFlex)
+ {
+ 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==erotgFLEXT) || (rotg->eType==erotgFLEX2T)) )
+ {
+ fprintf(fp, "# ref. grp. %d center %12.5e %12.5e %12.5e\n", g,
+ erg->xc_ref_center[XX], erg->xc_ref_center[YY], erg->xc_ref_center[ZZ]);
+
+ fprintf(fp, "# grp. %d init.center %12.5e %12.5e %12.5e\n", g,
+ erg->xc_center[XX], erg->xc_center[YY], erg->xc_center[ZZ]);
+ }
+
+ if ( (rotg->eType == erotgRM2) || (rotg->eType==erotgFLEX2) || (rotg->eType==erotgFLEX2T) )
+ {
+ fprintf(fp, "# rot_eps%d %12.5e nm^2\n", g, rotg->eps);
+ }
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ fprintf(fp, "#\n");
+ fprintf(fp, "# theta_fit%d is determined by first evaluating the potential for %d angles around theta_ref%d.\n",
+ g, rotg->PotAngle_nstep, g);
+ fprintf(fp, "# The fit angle is the one with the smallest potential. It is given as the deviation\n");
+ fprintf(fp, "# from the reference angle, i.e. if theta_ref=X and theta_fit=Y, then the angle with\n");
+ fprintf(fp, "# minimal value of the potential is X+Y. Angular resolution is %g degrees.\n", rotg->PotAngle_step);
+ }
+ }
+
+ /* Print a nice legend */
+ snew(LegendStr, 1);
+ LegendStr[0] = '\0';
+ sprintf(buf, "# %6s", "time");
+ add_to_string_aligned(&LegendStr, buf);
+
+ nsets = 0;
+ snew(setname, 4*rot->ngrp);
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ sprintf(buf, "theta_ref%d", g);
+ add_to_string_aligned(&LegendStr, buf);
+
- sprintf(buf2, "%s [degrees]", buf);
++ sprintf(buf2, "%s (degrees)", buf);
+ setname[nsets] = strdup(buf2);
+ nsets++;
+ }
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ bFlex = ISFLEX(rotg);
+
+ /* For flexible axis rotation we use RMSD fitting to determine the
+ * actual angle of the rotation group */
+ if (bFlex || erotgFitPOT == rotg->eFittype)
+ sprintf(buf, "theta_fit%d", g);
+ else
+ sprintf(buf, "theta_av%d", g);
+ add_to_string_aligned(&LegendStr, buf);
- sprintf(buf2, "%s [kJ/mol]", buf);
++ sprintf(buf2, "%s (degrees)", buf);
+ setname[nsets] = strdup(buf2);
+ nsets++;
+
+ sprintf(buf, "tau%d", g);
+ add_to_string_aligned(&LegendStr, buf);
- sprintf(buf2, "%s [kJ/mol]", buf);
++ sprintf(buf2, "%s (kJ/mol)", buf);
+ setname[nsets] = strdup(buf2);
+ nsets++;
+
+ sprintf(buf, "energy%d", g);
+ add_to_string_aligned(&LegendStr, buf);
- fprintf(fp, "# The scalar tau is the torque [kJ/mol] in the direction of the rotation vector.\n");
++ sprintf(buf2, "%s (kJ/mol)", buf);
+ setname[nsets] = strdup(buf2);
+ nsets++;
+ }
+ fprintf(fp, "#\n");
+
+ if (nsets > 1)
+ xvgr_legend(fp, nsets, setname, oenv);
+ sfree(setname);
+
+ fprintf(fp, "#\n# Legend for the following data columns:\n");
+ fprintf(fp, "%s\n", LegendStr);
+ sfree(LegendStr);
+
+ fflush(fp);
+ }
+
+ return fp;
+}
+
+
+/* Call on master only */
+static FILE *open_angles_out(const char *fn, t_rot *rot, const output_env_t oenv)
+{
+ int g,i;
+ FILE *fp;
+ t_rotgrp *rotg;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ char buf[100];
+
+
+ if (rot->enfrot->Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn,"a");
+ }
+ else
+ {
+ /* Open output file and write some information about it's structure: */
+ fp = open_output_file(fn, rot->nstsout, "rotation group angles");
+ fprintf(fp, "# All angles given in degrees, time in ps.\n");
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+
+ /* Output for this group happens only if potential type is flexible or
+ * if fit type is potential! */
+ if ( ISFLEX(rotg) || (erotgFitPOT == rotg->eFittype) )
+ {
+ if (ISFLEX(rotg))
+ sprintf(buf, " slab distance %f nm, ", rotg->slab_dist);
+ else
+ buf[0] = '\0';
+
+ fprintf(fp, "#\n# ROTATION GROUP %d '%s',%s fit type '%s'.\n",
+ g, erotg_names[rotg->eType], buf, erotg_fitnames[rotg->eFittype]);
+
+ /* Special type of fitting using the potential minimum. This is
+ * done for the whole group only, not for the individual slabs. */
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ fprintf(fp, "# To obtain theta_fit%d, the potential is evaluated for %d angles around theta_ref%d\n", g, rotg->PotAngle_nstep, g);
+ fprintf(fp, "# The fit angle in the rotation standard outfile is the one with minimal energy E(theta_fit) [kJ/mol].\n");
+ fprintf(fp, "#\n");
+ }
+
+ fprintf(fp, "# Legend for the group %d data columns:\n", g);
+ fprintf(fp, "# ");
+ print_aligned_short(fp, "time");
+ print_aligned_short(fp, "grp");
+ print_aligned(fp, "theta_ref");
+
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ /* Output the set of angles around the reference angle */
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ sprintf(buf, "E(%g)", erg->PotAngleFit->degangle[i]);
+ print_aligned(fp, buf);
+ }
+ }
+ else
+ {
+ /* Output fit angle for each slab */
+ 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, " ...");
+ }
+ 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(const char *fn, t_rot *rot, const output_env_t oenv)
+{
+ FILE *fp;
+ int g;
+ t_rotgrp *rotg;
+
+
+ if (rot->enfrot->Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn,"a");
+ }
+ else
+ {
+ fp = open_output_file(fn, rot->nstsout,"torques");
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ if (ISFLEX(rotg))
+ {
+ fprintf(fp, "# Rotation group %d (%s), slab distance %f nm.\n", g, erotg_names[rotg->eType], rotg->slab_dist);
- t_commrec *cr,
++ 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, "# Legend for the following data columns: (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 real 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 (NULL != 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;
+
+ /* In some cases abs(rot_matrix[0][0]) can be slighly larger
+ * than unity due to numerical inacurracies. To be able to calculate
+ * the acos function, we put these values back in range. */
+ if (rot_matrix[0][0] > 1.0)
+ {
+ rot_matrix[0][0] = 1.0;
+ }
+ else if (rot_matrix[0][0] < -1.0)
+ {
+ rot_matrix[0][0] = -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 (real) opt_angle;
+}
+
+
+/* Determine angle of the group by RMSD fit to the reference */
+/* Not parallelized, call this routine only on the master */
+static real flex_fit_angle(t_rotgrp *rotg)
+{
+ int i;
+ rvec *fitcoords=NULL;
+ rvec center; /* Center of positions passed to the fit routine */
+ real fitangle; /* Angle of the rotation group derived by fitting */
+ rvec coord;
+ real scal;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Get the center of the rotation group.
+ * Note, again, erg->xc has been sorted in do_flexible */
+ get_center(erg->xc, erg->mc_sorted, rotg->nat, center);
+
+ /* === Determine the optimal fit angle for the rotation group === */
+ if (rotg->eFittype == erotgFitNORM)
+ {
+ /* Normalize every position to it's reference length */
+ for (i=0; i<rotg->nat; i++)
+ {
+ /* Put the center of the positions into the origin */
+ rvec_sub(erg->xc[i], 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 */
+ svmul(scal, coord, erg->xc_norm[i]);
+ }
+ fitcoords = erg->xc_norm;
+ }
+ else
+ {
+ fitcoords = erg->xc;
+ }
+ /* From the point of view of the current positions, the reference has rotated
+ * backwards. Since we output the angle relative to the fixed reference,
+ * we need the minus sign. */
+ fitangle = -opt_angle_analytic(erg->xc_ref_sorted, fitcoords, erg->mc_sorted,
+ rotg->nat, erg->xc_ref_center, center, rotg->vec);
+
+ return fitangle;
+}
+
+
+/* Determine actual angle of each slab by RMSD fit to the reference */
+/* Not parallelized, call this routine only on the master */
+static void flex_fit_angle_perslab(
+ int g,
+ t_rotgrp *rotg,
+ double t,
+ real degangle,
+ FILE *fp)
+{
+ int i,l,n,islab,ind;
+ rvec curr_x, ref_x;
+ rvec act_center; /* Center of actual positions that are passed to the fit routine */
+ rvec ref_center; /* Same for the reference positions */
+ real fitangle; /* Angle of a slab derived from an RMSD fit to
+ * the reference structure at t=0 */
+ t_gmx_slabdata *sd;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ real OOm_av; /* 1/average_mass of a rotation group atom */
+ real m_rel; /* Relative mass of a rotation group atom */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Average mass of a rotation group atom: */
+ OOm_av = erg->invmass*rotg->nat;
+
+ /**********************************/
+ /* First collect the data we need */
+ /**********************************/
+
+ /* Collect the data for the individual 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_flexible */
+ 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]);
+
+ /* Maybe also mass-weighting was requested. If yes, additionally
+ * multiply the weights with the relative mass of the atom. If not,
+ * multiply with unity. */
+ m_rel = erg->mc_sorted[l]*OOm_av;
+
+ /* Save the weight for this atom in this slab */
+ sd->weight[ind] = gaussian_weight(curr_x, rotg, n) * m_rel;
+
+ /* Next atom in this slab */
+ ind++;
+ }
+ }
+
+ /******************************/
+ /* Now do the fit calculation */
+ /******************************/
+
+ fprintf(fp, "%12.3e%6d%12.3f", t, g, degangle);
+
+ /* === 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 gmx_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 gmx_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,
- static void flex2_precalc_inner_sum(t_rotgrp *rotg, 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 flex_precalc_inner_sum(t_rotgrp *rotg, t_commrec *cr)
++static void flex2_precalc_inner_sum(t_rotgrp *rotg)
+{
+ 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 */
+}
+
+
- matrix box,
- t_commrec *cr)
++static void flex_precalc_inner_sum(t_rotgrp *rotg)
+{
+ 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[],
+ gmx_bool bOutstepRot,
+ gmx_bool bOutstepSlab,
- flex2_precalc_inner_sum(rotg, cr);
++ matrix box)
+{
+ int count,ic,ii,j,m,n,islab,iigrp,ifit;
+ 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,fit_numerator;
+ rvec rjn,fit_rjn; /* Helper variables */
+ real fac,fac2;
+
+ real OOpsij,OOpsijstar;
+ real OOsigma2; /* 1/(sigma^2) */
+ real sjn_rjn;
+ real betasigpsi;
+ rvec sjn,tmpvec,tmpvec2,yj0_ycn;
+ 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 */
+ gmx_bool bCalcPotFit;
+
+ /* 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 */
- count = get_single_atom_gaussians(xj, cr, rotg);
++ flex2_precalc_inner_sum(rotg);
+
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT==rotg->eFittype);
+
+ /********************************************************/
+ /* 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]
+ * Note that erg->xc_center contains the center of mass in case the flex2-t
+ * potential was chosen. For the flex2 potential erg->xc_center must be
+ * zero. */
+ rvec_sub(x[ii], erg->xc_center, 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 */
- matrix box,
- t_commrec *cr)
++ count = get_single_atom_gaussians(xj, 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, yj0_ycn); /* yj0_ycn = yj0 - ycn */
+
+ /* Rotate: */
+ mvmul(erg->rotmat, yj0_ycn, 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;
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, fit_rjn);
+ fit_numerator = sqr(iprod(tmpvec, fit_rjn));
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*gaussian_xj*fit_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 (bOutstepRot)
+ {
+ /* 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 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
+
+ PRINT_FORCE_J
+
+ } /* END of loop over local atoms */
+
+ return V;
+}
+
+
+static real do_flex_lowlevel(
+ t_rotgrp *rotg,
+ real sigma, /* The Gaussian width sigma */
+ rvec x[],
+ gmx_bool bOutstepRot,
+ gmx_bool bOutstepSlab,
- flex_precalc_inner_sum(rotg, cr);
++ matrix box)
+{
+ int count,ic,ifit,ii,j,m,n,islab,iigrp;
+ rvec xj,yj0; /* current and reference position */
+ rvec xcn, ycn; /* the current and the reference slab centers */
+ rvec yj0_ycn; /* yj0 - ycn */
+ rvec xj_xcn; /* xj - xcn */
+ rvec qjn,fit_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 force_n1,force_n2; /* First and second part of force_n */
+ 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, fit_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 */
+ gmx_bool bCalcPotFit;
+
+
+ erg=rotg->enfrotgrp;
+
+ /* Pre-calculate the inner sums, so that we do not have to calculate
+ * them again for every atom */
- count = get_single_atom_gaussians(xj, cr, rotg);
++ flex_precalc_inner_sum(rotg);
+
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT==rotg->eFittype);
+
+ /********************************************************/
+ /* 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]
+ * Note that erg->xc_center contains the center of mass in case the flex-t
+ * potential was chosen. For the flex potential erg->xc_center must be
+ * zero. */
+ rvec_sub(x[ii], erg->xc_center, 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 */
- static void print_coordinates(t_commrec *cr, t_rotgrp *rotg, rvec x[], matrix box, int step)
++ count = get_single_atom_gaussians(xj, 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, yj0_ycn); /* yj0_ycn = yj0 - ycn */
+
+ /* Rotate: */
+ mvmul(erg->rotmat, yj0_ycn, 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.(yj0-ycn) */
+
+ /* v x Omega.(yj0-ycn) */
+ unitv(tmpvec,qjn); /* qjn = --------------------- */
+ /* |v x Omega.(yj0-ycn)| */
+
+ bjn = iprod(qjn, xj_xcn); /* bjn = qjn * (xj - xcn) */
+
+ /*********************************/
+ /* Add to the rotation potential */
+ /*********************************/
+ V += 0.5*rotg->k*wj*gaussian_xj*sqr(bjn);
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ /* As above calculate Omega.(yj0-ycn), now for the other angles */
+ mvmul(erg->PotAngleFit->rotmat[ifit], yj0_ycn, tmpvec2); /* tmpvec2= Omega.(yj0-ycn) */
+ /* As above calculate qjn */
+ cprod(rotg->vec, tmpvec2, tmpvec); /* tmpvec= v x Omega.(yj0-ycn) */
+ /* v x Omega.(yj0-ycn) */
+ unitv(tmpvec,fit_qjn); /* fit_qjn = --------------------- */
+ /* |v x Omega.(yj0-ycn)| */
+ fit_bjn = iprod(fit_qjn, xj_xcn); /* fit_bjn = fit_qjn * (xj - xcn) */
+ /* Add to the rotation potential for this angle */
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*gaussian_xj*sqr(fit_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);
+
+ /* Calculate the torque: */
+ if (bOutstepRot)
+ {
+ /* The force on atom ii from slab n only: */
+ svmul(-rotg->k*wj, tmpvec2 , force_n1); /* part 1 */
+ svmul( rotg->k*mj, innersumvec, force_n2); /* part 2 */
+ rvec_add(force_n1, force_n2, 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];
+
+ PRINT_FORCE_J
+
+ } /* END of loop over local atoms */
+
+ return V;
+}
+
+#ifdef PRINT_COORDS
- static void get_firstlast_atom_per_slab(t_rotgrp *rotg, t_commrec *cr)
++static void print_coordinates(t_rotgrp *rotg, rvec x[], matrix box, int step)
+{
+ int i;
+ static FILE *fp;
+ static char buf[STRLEN];
+ 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 */
+ gmx_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 */
- int g, /* The rotation group number */
- t_commrec *cr)
++static void get_firstlast_atom_per_slab(t_rotgrp *rotg)
+{
+ int i,islab,n;
+ real beta;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ erg=rotg->enfrotgrp;
+
+ /* 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);
+}
+
+
+/* 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 gmx_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 gmx_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 */
- t_commrec *cr,
++ int g) /* The rotation group number */
+{
+ 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, "%s No reference data for first slab (n=%d), unable to proceed.",
+ RotStr, erg->slab_first);
+
+ /* Check whether we have reference data to compare against */
+ if (erg->slab_last > erg->slab_last_ref)
+ gmx_fatal(FARGS, "%s No reference data for last slab (n=%d), unable to proceed.",
+ RotStr, erg->slab_last);
+}
+
+
+/* Enforced rotation with a flexible axis */
+static void do_flexible(
- get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1], g, cr);
++ gmx_bool bMaster,
+ 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 */
+ gmx_large_int_t step, /* The time step */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ 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_atom_per_slab(rotg, cr);
++ get_firstlast_slab_check(rotg, erg, erg->xc[0], erg->xc[rotg->nat-1], g);
+
+ /* 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_slab_centers(rotg,erg->xc,erg->mc_sorted,cr,g,t,enfrot->out_slabs,bOutstepSlab,FALSE);
++ get_firstlast_atom_per_slab(rotg);
+
+ /* Determine the gaussian-weighted center of positions for all slabs */
- erg->V = do_flex_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box, cr);
++ get_slab_centers(rotg,erg->xc,erg->mc_sorted,g,t,enfrot->out_slabs,bOutstepSlab,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 */
+ if (rotg->eType == erotgFLEX || rotg->eType == erotgFLEXT)
- erg->V = do_flex2_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box, cr);
++ erg->V = do_flex_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
+ else if (rotg->eType == erotgFLEX2 || rotg->eType == erotgFLEX2T)
- if (MASTER(cr) && (erotgFitPOT != rotg->eFittype) )
++ erg->V = do_flex2_lowlevel(rotg, sigma, x, bOutstepRot, bOutstepSlab, box);
+ else
+ gmx_fatal(FARGS, "Unknown flexible rotation type");
+
+ /* Determine angle by RMSD fit to the reference - Let's hope this */
+ /* only happens once in a while, since this is not parallelized! */
- t_commrec *cr,
++ if ( bMaster && (erotgFitPOT != rotg->eFittype) )
+ {
+ if (bOutstepRot)
+ {
+ /* Fit angle of the whole rotation group */
+ erg->angle_v = flex_fit_angle(rotg);
+ }
+ if (bOutstepSlab)
+ {
+ /* Fit angle of each slab */
+ flex_fit_angle_perslab(g, rotg, t, erg->degangle, enfrot->out_angles);
+ }
+ }
+
+ /* Lump together the torques from all slabs: */
+ erg->torque_v = 0.0;
+ for (l=0; l<nslabs; l++)
+ erg->torque_v += erg->slab_torque_v[l];
+}
+
+
+/* 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 gmx_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 the v 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 */
+ gmx_large_int_t step, /* The time step */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int ifit,j,jj,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 xi_xc; /* xi - xc */
+ gmx_bool bCalcPotFit;
+ rvec fit_xr_loc;
+
+ /* for mass weighting: */
+ real wi; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+ real k_wi; /* k times wi */
+
+ gmx_bool bProject;
+
+
+ erg=rotg->enfrotgrp;
+ bProject = (rotg->eType==erotgPM) || (rotg->eType==erotgPMPF);
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT==rotg->eFittype);
+
+ N_M = rotg->nat * erg->invmass;
+
+ /* Each process calculates the forces on its local atoms */
+ for (j=0; j<erg->nat_loc; j++)
+ {
+ /* Calculate (x_i-x_c) resp. (x_i-u) */
+ rvec_sub(erg->x_loc_pbc[j], erg->xc_center, xi_xc);
+
+ /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
+ rvec_sub(erg->xr_loc[j], xi_xc, dr);
+
+ if (bProject)
+ project_onto_plane(dr, rotg->vec);
+
+ /* Mass-weighting */
+ wi = 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 */
+ k_wi = rotg->k*wi;
+ for (m=0; m<DIM; m++)
+ {
+ tmp_f[m] = k_wi*dr[m];
+ erg->f_rot_loc[j][m] = tmp_f[m];
+ erg->V += 0.5*k_wi*sqr(dr[m]);
+ }
+
+ /* If requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ /* Index of this rotation group atom with respect to the whole rotation group */
+ jj = erg->xc_ref_ind[j];
+
+ /* Rotate with the alternative angle. Like rotate_local_reference(),
+ * just for a single local atom */
+ mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_xr_loc); /* fit_xr_loc = Omega*(y_i-y_c) */
+
+ /* Calculate Omega*(y_i-y_c)-(x_i-x_c) */
+ rvec_sub(fit_xr_loc, xi_xc, dr);
+
+ if (bProject)
+ project_onto_plane(dr, rotg->vec);
+
+ /* Add to the rotation potential for this angle: */
+ erg->PotAngleFit->V[ifit] += 0.5*k_wi*norm2(dr);
+ }
+ }
+
+ if (bOutstepRot)
+ {
+ /* Add to the torque of this rotation group */
+ erg->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, xi_xc, erg->xr_loc[j], &alpha, &weight); /* angle in rad, weighted */
+ erg->angle_v += alpha * weight;
+ erg->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];
+ }
+ */
+
+ PRINT_FORCE_J
+
+ } /* 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 */
+ gmx_large_int_t step, /* The time step */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int j,jj,ifit;
+ 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,fit_tmpvec;
+ real fac,fac2,sum=0.0;
+ rvec pj;
+ gmx_bool bCalcPotFit;
+
+ /* For mass weighting: */
+ real wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+
+
+ erg=rotg->enfrotgrp;
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT==rotg->eFittype);
+
+ 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.(yj0-u) */
+ cprod(rotg->vec, erg->xr_loc[j], tmpvec); /* tmpvec = v x Omega.(yj0-u) */
+
+ /* v x Omega.(yj0-u) */
+ unitv(tmpvec, pj); /* pj = --------------------- */
+ /* | v x Omega.(yj0-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 requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ /* Index of this rotation group atom with respect to the whole rotation group */
+ jj = erg->xc_ref_ind[j];
+
+ /* Rotate with the alternative angle. Like rotate_local_reference(),
+ * just for a single local atom */
+ mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[jj], fit_tmpvec); /* fit_tmpvec = Omega*(yj0-u) */
+
+ /* Calculate Omega.(yj0-u) */
+ cprod(rotg->vec, fit_tmpvec, tmpvec); /* tmpvec = v x Omega.(yj0-u) */
+ /* v x Omega.(yj0-u) */
+ unitv(tmpvec, pj); /* pj = --------------------- */
+ /* | v x Omega.(yj0-u) | */
+
+ fac = iprod(pj, xj_u); /* fac = pj.(xj-u) */
+ fac2 = fac*fac;
+
+ /* Add to the rotation potential for this angle: */
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*fac2;
+ }
+ }
+
+ if (bOutstepRot)
+ {
+ /* Add to the torque of this rotation group */
+ erg->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->angle_v += alpha * weight;
+ erg->weight_v += weight;
+ }
+
+ PRINT_FORCE_J
+
+ } /* 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 */
+ gmx_large_int_t step, /* The time step */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int i,ii,iigrp,ifit,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=0.0;
+ rvec qi,qj;
+ gmx_bool bCalcPotFit;
+
+ /* For mass weighting: */
+ real mj,wi,wj; /* Mass-weighting of the positions */
+ real N_M; /* N/M */
+
+
+ erg=rotg->enfrotgrp;
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT==rotg->eFittype);
+
+ 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 requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ /* Rotate with the alternative angle. Like rotate_local_reference(),
+ * just for a single local atom */
+ mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, tmpvec2); /* tmpvec2 = Omega*(yj0-yc0) */
+
+ /* Calculate Omega.(yj0-u) */
+ 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) | */
+
+ fac = iprod(qj, xj_xc); /* fac = qj.(xj-xc) */
+ fac2 = fac*fac;
+
+ /* Add to the rotation potential for this angle: */
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*fac2;
+ }
+ }
+
+ if (bOutstepRot)
+ {
+ /* Add to the torque of this rotation group */
+ erg->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->angle_v += alpha * weight;
+ erg->weight_v += weight;
+ }
+
+ PRINT_FORCE_J
+
+ } /* 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(
- gmx_bool bVerbose,
- t_commrec *cr)
+ t_rotgrp *rotg, /* The rotation group */
+ rvec x[], /* The positions */
+ matrix box, /* The simulation box */
+ double t, /* Time in picoseconds */
+ gmx_large_int_t step, /* The time step */
+ gmx_bool bOutstepRot, /* Output to main rotation output file */
+ gmx_bool bOutstepSlab) /* Output per-slab data */
+{
+ int ii,iigrp,ifit,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 yj0_yc0; /* yj0 -yc0 */
+ rvec tmpvec,tmpvec2;
+ real fac,fit_fac,fac2,Vpart=0.0;
+ rvec rj,fit_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 */
+ gmx_bool bPF;
+ rvec innersumvec;
+ gmx_bool bCalcPotFit;
+
+
+ erg=rotg->enfrotgrp;
+
+ bPF = rotg->eType==erotgRM2PF;
+ bCalcPotFit = (bOutstepRot || bOutstepSlab) && (erotgFitPOT==rotg->eFittype);
+
+
+ clear_rvec(yj0_yc0); /* Make the compiler happy */
+
+ 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);
+ }
+
+ 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], yj0_yc0); /* yj0_yc0 = yj0 - yc0 */
+
+ /* Calculate Omega.(yj0-yc0) */
+ mvmul(erg->rotmat, yj0_yc0, 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 requested, also calculate the potential for a set of angles
+ * near the current reference angle */
+ if (bCalcPotFit)
+ {
+ for (ifit = 0; ifit < rotg->PotAngle_nstep; ifit++)
+ {
+ if (bPF)
+ {
+ mvmul(erg->PotAngleFit->rotmat[ifit], yj0_yc0, fit_rj); /* fit_rj = Omega.(yj0-yc0) */
+ }
+ else
+ {
+ /* Position of this atom in the collective array */
+ iigrp = erg->xc_ref_ind[j];
+ /* Rotate with the alternative angle. Like rotate_local_reference(),
+ * just for a single local atom */
+ mvmul(erg->PotAngleFit->rotmat[ifit], rotg->x_ref[iigrp], fit_rj); /* fit_rj = Omega*(yj0-u) */
+ }
+ fit_fac = iprod(v_xj_u, fit_rj); /* fac = (v x (xj-u)).fit_rj */
+ /* Add to the rotation potential for this angle: */
+ erg->PotAngleFit->V[ifit] += 0.5*rotg->k*wj*psijstar*fit_fac*fit_fac;
+ }
+ }
+
+ if (bOutstepRot)
+ {
+ /* Add to the torque of this rotation group */
+ erg->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->angle_v += alpha * weight;
+ erg->weight_v += weight;
+ }
+
+ PRINT_FORCE_J
+
+ } /* 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,
- if (MASTER(cr) && bVerbose)
++ gmx_bool bVerbose)
+{
+ 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;
+
- allocate_slabs(rotg, fplog, g, bVerbose, cr);
++ if ( (NULL != fplog) && bVerbose )
+ fprintf(fplog, "%s allocating memory to store data for %d slabs (rotation group %d).\n",
+ RotStr, 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;
+}
+
+
+
+static void init_rot_group(FILE *fplog,t_commrec *cr,int g,t_rotgrp *rotg,
+ rvec *x,gmx_mtop_t *mtop,gmx_bool bVerbose,FILE *out_slabs, gmx_bool bOutputCenters)
+{
+ int i,ii;
+ rvec coord,*xdum;
+ 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;
+ real start=0.0;
+
+
+ /* Do we have a flexible axis? */
+ bFlex = ISFLEX(rotg);
+ /* Do we use a global set of coordinates? */
+ bColl = ISCOLL(rotg);
+
+ 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);
+
+ /* Make space for the calculation of the potential at other angles (used
+ * for fitting only) */
+ if (erotgFitPOT == rotg->eFittype)
+ {
+ snew(erg->PotAngleFit, 1);
+ snew(erg->PotAngleFit->degangle, rotg->PotAngle_nstep);
+ snew(erg->PotAngleFit->V , rotg->PotAngle_nstep);
+ snew(erg->PotAngleFit->rotmat , rotg->PotAngle_nstep);
+
+ /* Get the set of angles around the reference angle */
+ start = -0.5 * (rotg->PotAngle_nstep - 1)*rotg->PotAngle_step;
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ erg->PotAngleFit->degangle[i] = start + i*rotg->PotAngle_step;
+ }
+ else
+ {
+ erg->PotAngleFit = NULL;
+ }
+
+ /* 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 center 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 ( (rotg->eType != erotgFLEX) && (rotg->eType != erotgFLEX2) )
+ {
+ /* 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 */
- get_slab_centers(rotg,rotg->x_ref,erg->mc,cr,g,-1,out_slabs,bOutputCenters,TRUE);
++ allocate_slabs(rotg, fplog, g, bVerbose);
+
+ /* 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,g,-1,out_slabs,bOutputCenters,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);
+ }
+ }
+ }
+}
+
+
+extern void dd_make_local_rotation_groups(gmx_domdec_t *dd,t_rot *rot)
+{
+ 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);
+ }
+}
+
+
+/* Calculate the size of the MPI buffer needed in reduce_output() */
+static int calc_mpi_bufsize(t_rot *rot)
+{
+ int g;
+ int count_group, count_total;
+ t_rotgrp *rotg;
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+
+
+ count_total = 0;
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg = rotg->enfrotgrp;
+
+ /* Count the items that are transferred for this group: */
+ count_group = 4; /* V, torque, angle, weight */
+
+ /* Add the maximum number of slabs for flexible groups */
+ if (ISFLEX(rotg))
+ count_group += erg->slab_last_ref - erg->slab_first_ref + 1;
+
+ /* Add space for the potentials at different angles: */
+ if (erotgFitPOT == rotg->eFittype)
+ count_group += rotg->PotAngle_nstep;
+
+ /* Add to the total number: */
+ count_total += count_group;
+ }
+
+ return count_total;
+}
+
+
+extern void init_rot(FILE *fplog,t_inputrec *ir,int nfile,const t_filenm fnm[],
+ t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const output_env_t oenv,
+ gmx_bool bVerbose, 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 */
+ rvec *x_pbc=NULL; /* Space for the pbc-correct atom positions */
+
+
+ if ( (PAR(cr)) && !DOMAINDECOMP(cr) )
+ gmx_fatal(FARGS, "Enforced rotation is only implemented for domain decomposition!");
+
+ if ( MASTER(cr) && bVerbose)
+ fprintf(stdout, "%s Initializing ...\n", RotStr);
+
-
+ rot = ir->rot;
+ snew(rot->enfrot, 1);
+ er = rot->enfrot;
+ er->Flags = Flags;
+
+ /* When appending, skip first output to avoid duplicate entries in the data files */
+ if (er->Flags & MD_APPENDFILES)
+ er->bOut = FALSE;
+ else
+ er->bOut = TRUE;
- if (fplog)
++
++ if ( MASTER(cr) && er->bOut )
++ please_cite(fplog, "Kutzner2011");
++
+ /* Output every step for reruns */
+ if (er->Flags & MD_RERUN)
+ {
- if (fplog)
++ if (NULL != fplog)
+ fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
+ rot->nstrout = 1;
+ rot->nstsout = 1;
+ }
+
+ er->out_slabs = NULL;
+ if ( MASTER(cr) && HaveFlexibleGroups(rot) )
+ er->out_slabs = open_slab_out(opt2fn("-rs",nfile,fnm), rot, oenv);
+
+ if (MASTER(cr))
+ {
+ /* Remove pbc, make molecule whole.
+ * When ir->bContinuation=TRUE this has already been done, but ok. */
+ snew(x_pbc,mtop->natoms);
+ m_rveccopy(mtop->natoms,x,x_pbc);
+ do_pbc_first_mtop(NULL,ir->ePBC,box,mtop,x_pbc);
+ }
+
+ for (g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+
- double cycles_rot;
++ if (NULL != fplog)
+ fprintf(fplog,"%s group %d type '%s'\n", RotStr, 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_pbc,mtop,bVerbose,er->out_slabs,
+ !(er->Flags & MD_APPENDFILES) ); /* Do not output the reference centers
+ * again if we are appending */
+ }
+ }
+
+ /* 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 */
+ if (PAR(cr))
+ {
+ er->mpi_bufsize = calc_mpi_bufsize(rot) + 100; /* larger to catch errors */
+ snew(er->mpi_inbuf , er->mpi_bufsize);
+ snew(er->mpi_outbuf, er->mpi_bufsize);
+ }
+ else
+ {
+ er->mpi_bufsize = 0;
+ er->mpi_inbuf = NULL;
+ er->mpi_outbuf = NULL;
+ }
+
+ /* 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);
+
+ if (rot->nstsout > 0)
+ {
+ if ( HaveFlexibleGroups(rot) || HavePotFitGroups(rot) )
+ er->out_angles = open_angles_out(opt2fn("-ra",nfile,fnm), rot, oenv);
+ if ( HaveFlexibleGroups(rot) )
+ er->out_torque = open_torque_out(opt2fn("-rt",nfile,fnm), rot, oenv);
+ }
+
+ sfree(x_pbc);
+ }
+}
+
+
+extern 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. We assume 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 reference position. The pivot was already
+ * subtracted in init_rot_group() from the reference positions. Also,
+ * the reference positions have already been rotated in
+ * rotate_local_reference() */
+ 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(xcurr, xref, 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,
+ gmx_large_int_t step,
+ gmx_wallcycle_t wcycle,
+ gmx_bool bNS)
+{
+ int g,i,ii;
+ t_rot *rot;
+ t_rotgrp *rotg;
+ gmx_bool outstep_slab, outstep_rot;
+ gmx_bool bFlex,bColl;
-
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec transvec;
+ t_gmx_potfit *fit=NULL; /* For fit type 'potential' determine the fit
+ angle via the potential minimum */
++
++ /* Enforced rotation cycle counting: */
++ gmx_cycles_t cycles_comp; /* Cycles for the enf. rotation computation
++ only, does not count communication. This
++ counter is used for load-balancing */
++
+#ifdef TAKETIME
+ double t0;
+#endif
+
- /* Done communicating, we can start to count cycles now ... */
- wallcycle_start(wcycle, ewcROT);
+ rot=ir->rot;
+ er=rot->enfrot;
+
+ /* When to output in main rotation output file */
+ outstep_rot = do_per_step(step, rot->nstrout) && er->bOut;
+ /* When to output per-slab data */
+ outstep_slab = do_per_step(step, rot->nstsout) && er->bOut;
+
+ /* Output time into rotation output file */
+ if (outstep_rot && 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 = ISFLEX(rotg);
+ /* Do we use a collective (global) set of coordinates? */
+ bColl = ISCOLL(rotg);
+
+ /* 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 */
+
+ /**************************************************************************/
- do_fixed(cr,rotg,x,box,t,step,outstep_rot,outstep_slab);
++ /* Done communicating, we can start to count cycles for the load balancing now ... */
++ cycles_comp = gmx_cycles_read();
++
+
+#ifdef TAKETIME
+ t0 = MPI_Wtime();
+#endif
+
+ for(g=0; g<rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ erg=rotg->enfrotgrp;
+
+ bFlex = ISFLEX(rotg);
+ bColl = ISCOLL(rotg);
+
+ if (outstep_rot && MASTER(cr))
+ fprintf(er->out_rot, "%12.4f", erg->degangle);
+
+ /* Calculate angles and rotation matrices for potential fitting: */
+ if ( (outstep_rot || outstep_slab) && (erotgFitPOT == rotg->eFittype) )
+ {
+ fit = erg->PotAngleFit;
+ for (i = 0; i < rotg->PotAngle_nstep; i++)
+ {
+ calc_rotmat(rotg->vec, erg->degangle + fit->degangle[i], fit->rotmat[i]);
+
+ /* Clear value from last step */
+ erg->PotAngleFit->V[i] = 0.0;
+ }
+ }
+
+ /* Clear values from last time step */
+ erg->V = 0.0;
+ erg->torque_v = 0.0;
+ erg->angle_v = 0.0;
+ erg->weight_v = 0.0;
+
+ switch(rotg->eType)
+ {
+ case erotgISO:
+ case erotgISOPF:
+ case erotgPM:
+ case erotgPMPF:
- do_radial_motion(cr,rotg,x,box,t,step,outstep_rot,outstep_slab);
++ do_fixed(rotg,x,box,t,step,outstep_rot,outstep_slab);
+ break;
+ case erotgRM:
- do_radial_motion_pf(cr,rotg,x,box,t,step,outstep_rot,outstep_slab);
++ do_radial_motion(rotg,x,box,t,step,outstep_rot,outstep_slab);
+ break;
+ case erotgRMPF:
- do_radial_motion2(cr,rotg,x,box,t,step,outstep_rot,outstep_slab);
++ do_radial_motion_pf(rotg,x,box,t,step,outstep_rot,outstep_slab);
+ break;
+ case erotgRM2:
+ case erotgRM2PF:
- do_flexible(cr,er,rotg,g,x,box,t,step,outstep_rot,outstep_slab);
++ do_radial_motion2(rotg,x,box,t,step,outstep_rot,outstep_slab);
+ break;
+ case erotgFLEXT:
+ case erotgFLEX2T:
+ /* Subtract the center of the rotation group from the collective positions array
+ * Also store the center in erg->xc_center since it needs to be subtracted
+ * in the low level routines from the local coordinates as well */
+ get_center(erg->xc, erg->mc, rotg->nat, erg->xc_center);
+ svmul(-1.0, erg->xc_center, transvec);
+ translate_x(erg->xc, rotg->nat, transvec);
- do_flexible(cr,er,rotg,g,x,box,t,step,outstep_rot,outstep_slab);
++ do_flexible(MASTER(cr),er,rotg,g,x,box,t,step,outstep_rot,outstep_slab);
+ break;
+ case erotgFLEX:
+ case erotgFLEX2:
+ /* Do NOT subtract the center of mass in the low level routines! */
+ clear_rvec(erg->xc_center);
- /* Stop the cycle counter and add to the force cycles for load balancing */
- cycles_rot = wallcycle_stop(wcycle,ewcROT);
++ do_flexible(MASTER(cr),er,rotg,g,x,box,t,step,outstep_rot,outstep_slab);
+ break;
+ default:
+ gmx_fatal(FARGS, "No such rotation potential.");
+ break;
+ }
+ }
+
+#ifdef TAKETIME
+ if (MASTER(cr))
+ fprintf(stderr, "%s calculation (step %d) took %g seconds.\n", RotStr, step, MPI_Wtime()-t0);
+#endif
+
- dd_cycles_add(cr->dd,cycles_rot,ddCyclF);
++ /* Stop the enforced rotation cycle counter and add the computation-only
++ * cycles to the force cycles for load balancing */
++ cycles_comp = gmx_cycles_read() - cycles_comp;
++
+ if (DOMAINDECOMP(cr) && wcycle)
++ dd_cycles_add(cr->dd,cycles_comp,ddCyclF);
+}
--- /dev/null
- * coordinates have been communicated. It is added to ddCyclF */
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, 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:
+ * GROwing Monsters And Cloning Shrimps
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifdef GMX_CRAY_XT3
+#include<catamount/dclock.h>
+#endif
+
+
+#include <stdio.h>
+#include <time.h>
+#ifdef HAVE_SYS_TIME_H
+#include <sys/time.h>
+#endif
+#include <math.h>
+#include "typedefs.h"
+#include "string2.h"
+#include "gmxfio.h"
+#include "smalloc.h"
+#include "names.h"
+#include "confio.h"
+#include "mvdata.h"
+#include "txtdump.h"
+#include "pbc.h"
+#include "chargegroup.h"
+#include "vec.h"
+#include "time.h"
+#include "nrnb.h"
+#include "mshift.h"
+#include "mdrun.h"
+#include "update.h"
+#include "physics.h"
+#include "main.h"
+#include "mdatoms.h"
+#include "force.h"
+#include "bondf.h"
+#include "pme.h"
+#include "pppm.h"
+#include "disre.h"
+#include "orires.h"
+#include "network.h"
+#include "calcmu.h"
+#include "constr.h"
+#include "xvgr.h"
+#include "trnio.h"
+#include "xtcio.h"
+#include "copyrite.h"
+#include "pull_rotation.h"
+#include "domdec.h"
+#include "partdec.h"
+#include "gmx_wallcycle.h"
+#include "genborn.h"
+
+#ifdef GMX_LIB_MPI
+#include <mpi.h>
+#endif
+#ifdef GMX_THREADS
+#include "tmpi.h"
+#endif
+
+#include "qmmm.h"
+
+#if 0
+typedef struct gmx_timeprint {
+
+} t_gmx_timeprint;
+#endif
+
+/* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
+char *
+gmx_ctime_r(const time_t *clock,char *buf, int n);
+
+
+double
+gmx_gettime()
+{
+#ifdef HAVE_GETTIMEOFDAY
+ struct timeval t;
+ double seconds;
+
+ gettimeofday(&t,NULL);
+
+ seconds = (double) t.tv_sec + 1e-6*(double)t.tv_usec;
+
+ return seconds;
+#else
+ double seconds;
+
+ seconds = time(NULL);
+
+ return seconds;
+#endif
+}
+
+
+#define difftime(end,start) ((double)(end)-(double)(start))
+
+void print_time(FILE *out,gmx_runtime_t *runtime,gmx_large_int_t step,
+ t_inputrec *ir, t_commrec *cr)
+{
+ time_t finish;
+ char timebuf[STRLEN];
+ double dt;
+ char buf[48];
+
+#ifndef GMX_THREADS
+ if (!PAR(cr))
+#endif
+ {
+ fprintf(out,"\r");
+ }
+ fprintf(out,"step %s",gmx_step_str(step,buf));
+ if ((step >= ir->nstlist))
+ {
+ if ((ir->nstlist == 0) || ((step % ir->nstlist) == 0))
+ {
+ /* We have done a full cycle let's update time_per_step */
+ runtime->last = gmx_gettime();
+ dt = difftime(runtime->last,runtime->real);
+ runtime->time_per_step = dt/(step - ir->init_step + 1);
+ }
+ dt = (ir->nsteps + ir->init_step - step)*runtime->time_per_step;
+
+ if (ir->nsteps >= 0)
+ {
+ if (dt >= 300)
+ {
+ finish = (time_t) (runtime->last + dt);
+ gmx_ctime_r(&finish,timebuf,STRLEN);
+ sprintf(buf,"%s",timebuf);
+ buf[strlen(buf)-1]='\0';
+ fprintf(out,", will finish %s",buf);
+ }
+ else
+ fprintf(out,", remaining runtime: %5d s ",(int)dt);
+ }
+ else
+ {
+ fprintf(out," performance: %.1f ns/day ",
+ ir->delta_t/1000*24*60*60/runtime->time_per_step);
+ }
+ }
+#ifndef GMX_THREADS
+ if (PAR(cr))
+ {
+ fprintf(out,"\n");
+ }
+#endif
+
+ fflush(out);
+}
+
+#ifdef NO_CLOCK
+#define clock() -1
+#endif
+
+static double set_proctime(gmx_runtime_t *runtime)
+{
+ double diff;
+#ifdef GMX_CRAY_XT3
+ double prev;
+
+ prev = runtime->proc;
+ runtime->proc = dclock();
+
+ diff = runtime->proc - prev;
+#else
+ clock_t prev;
+
+ prev = runtime->proc;
+ runtime->proc = clock();
+
+ diff = (double)(runtime->proc - prev)/(double)CLOCKS_PER_SEC;
+#endif
+ if (diff < 0)
+ {
+ /* The counter has probably looped, ignore this data */
+ diff = 0;
+ }
+
+ return diff;
+}
+
+void runtime_start(gmx_runtime_t *runtime)
+{
+ runtime->real = gmx_gettime();
+ runtime->proc = 0;
+ set_proctime(runtime);
+ runtime->realtime = 0;
+ runtime->proctime = 0;
+ runtime->last = 0;
+ runtime->time_per_step = 0;
+}
+
+void runtime_end(gmx_runtime_t *runtime)
+{
+ double now;
+
+ now = gmx_gettime();
+
+ runtime->proctime += set_proctime(runtime);
+ runtime->realtime = now - runtime->real;
+ runtime->real = now;
+}
+
+void runtime_upd_proc(gmx_runtime_t *runtime)
+{
+ runtime->proctime += set_proctime(runtime);
+}
+
+void print_date_and_time(FILE *fplog,int nodeid,const char *title,
+ const gmx_runtime_t *runtime)
+{
+ int i;
+ char timebuf[STRLEN];
+ char time_string[STRLEN];
+ time_t tmptime;
+
+ if (fplog)
+ {
+ if (runtime != NULL)
+ {
+ tmptime = (time_t) runtime->real;
+ gmx_ctime_r(&tmptime,timebuf,STRLEN);
+ }
+ else
+ {
+ tmptime = (time_t) gmx_gettime();
+ gmx_ctime_r(&tmptime,timebuf,STRLEN);
+ }
+ for(i=0; timebuf[i]>=' '; i++)
+ {
+ time_string[i]=timebuf[i];
+ }
+ time_string[i]='\0';
+
+ fprintf(fplog,"%s on node %d %s\n",title,nodeid,time_string);
+ }
+}
+
+static void sum_forces(int start,int end,rvec f[],rvec flr[])
+{
+ int i;
+
+ if (gmx_debug_at) {
+ pr_rvecs(debug,0,"fsr",f+start,end-start);
+ pr_rvecs(debug,0,"flr",flr+start,end-start);
+ }
+ for(i=start; (i<end); i++)
+ rvec_inc(f[i],flr[i]);
+}
+
+/*
+ * calc_f_el calculates forces due to an electric field.
+ *
+ * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
+ *
+ * Et[] contains the parameters for the time dependent
+ * part of the field (not yet used).
+ * Ex[] contains the parameters for
+ * the spatial dependent part of the field. You can have cool periodic
+ * fields in principle, but only a constant field is supported
+ * now.
+ * The function should return the energy due to the electric field
+ * (if any) but for now returns 0.
+ *
+ * WARNING:
+ * There can be problems with the virial.
+ * Since the field is not self-consistent this is unavoidable.
+ * For neutral molecules the virial is correct within this approximation.
+ * For neutral systems with many charged molecules the error is small.
+ * But for systems with a net charge or a few charged molecules
+ * the error can be significant when the field is high.
+ * Solution: implement a self-consitent electric field into PME.
+ */
+static void calc_f_el(FILE *fp,int start,int homenr,
+ real charge[],rvec x[],rvec f[],
+ t_cosines Ex[],t_cosines Et[],double t)
+{
+ rvec Ext;
+ real t0;
+ int i,m;
+
+ for(m=0; (m<DIM); m++)
+ {
+ if (Et[m].n > 0)
+ {
+ if (Et[m].n == 3)
+ {
+ t0 = Et[m].a[1];
+ Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2])));
+ }
+ else
+ {
+ Ext[m] = cos(Et[m].a[0]*t);
+ }
+ }
+ else
+ {
+ Ext[m] = 1.0;
+ }
+ if (Ex[m].n > 0)
+ {
+ /* Convert the field strength from V/nm to MD-units */
+ Ext[m] *= Ex[m].a[0]*FIELDFAC;
+ for(i=start; (i<start+homenr); i++)
+ f[i][m] += charge[i]*Ext[m];
+ }
+ else
+ {
+ Ext[m] = 0;
+ }
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp,"%10g %10g %10g %10g #FIELD\n",t,
+ Ext[XX]/FIELDFAC,Ext[YY]/FIELDFAC,Ext[ZZ]/FIELDFAC);
+ }
+}
+
+static void calc_virial(FILE *fplog,int start,int homenr,rvec x[],rvec f[],
+ tensor vir_part,t_graph *graph,matrix box,
+ t_nrnb *nrnb,const t_forcerec *fr,int ePBC)
+{
+ int i,j;
+ tensor virtest;
+
+ /* The short-range virial from surrounding boxes */
+ clear_mat(vir_part);
+ calc_vir(fplog,SHIFTS,fr->shift_vec,fr->fshift,vir_part,ePBC==epbcSCREW,box);
+ inc_nrnb(nrnb,eNR_VIRIAL,SHIFTS);
+
+ /* Calculate partial virial, for local atoms only, based on short range.
+ * Total virial is computed in global_stat, called from do_md
+ */
+ f_calc_vir(fplog,start,start+homenr,x,f,vir_part,graph,box);
+ inc_nrnb(nrnb,eNR_VIRIAL,homenr);
+
+ /* Add position restraint contribution */
+ for(i=0; i<DIM; i++) {
+ vir_part[i][i] += fr->vir_diag_posres[i];
+ }
+
+ /* Add wall contribution */
+ for(i=0; i<DIM; i++) {
+ vir_part[i][ZZ] += fr->vir_wall_z[i];
+ }
+
+ if (debug)
+ pr_rvecs(debug,0,"vir_part",vir_part,DIM);
+}
+
+static void print_large_forces(FILE *fp,t_mdatoms *md,t_commrec *cr,
+ gmx_large_int_t step,real pforce,rvec *x,rvec *f)
+{
+ int i;
+ real pf2,fn2;
+ char buf[STEPSTRSIZE];
+
+ pf2 = sqr(pforce);
+ for(i=md->start; i<md->start+md->homenr; i++) {
+ fn2 = norm2(f[i]);
+ /* We also catch NAN, if the compiler does not optimize this away. */
+ if (fn2 >= pf2 || fn2 != fn2) {
+ fprintf(fp,"step %s atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
+ gmx_step_str(step,buf),
+ ddglatnr(cr->dd,i),x[i][XX],x[i][YY],x[i][ZZ],sqrt(fn2));
+ }
+ }
+}
+
+void do_force(FILE *fplog,t_commrec *cr,
+ t_inputrec *inputrec,
+ gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
+ gmx_localtop_t *top,
+ gmx_mtop_t *mtop,
+ gmx_groups_t *groups,
+ matrix box,rvec x[],history_t *hist,
+ rvec f[],
+ tensor vir_force,
+ t_mdatoms *mdatoms,
+ gmx_enerdata_t *enerd,t_fcdata *fcd,
+ real lambda,t_graph *graph,
+ t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot,
+ double t,FILE *field,gmx_edsam_t ed,
+ gmx_bool bBornRadii,
+ int flags)
+{
+ int cg0,cg1,i,j;
+ int start,homenr;
+ double mu[2*DIM];
+ gmx_bool bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS;
+ gmx_bool bDoLongRange,bDoForces,bSepLRF;
+ matrix boxs;
+ real e,v,dvdl;
+ t_pbc pbc;
+ float cycles_ppdpme,cycles_pme,cycles_seppme,cycles_force;
+
+ start = mdatoms->start;
+ homenr = mdatoms->homenr;
+
+ bSepDVDL = (fr->bSepDVDL && do_per_step(step,inputrec->nstlog));
+
+ clear_mat(vir_force);
+
+ if (PARTDECOMP(cr))
+ {
+ pd_cg_range(cr,&cg0,&cg1);
+ }
+ else
+ {
+ cg0 = 0;
+ if (DOMAINDECOMP(cr))
+ {
+ cg1 = cr->dd->ncg_tot;
+ }
+ else
+ {
+ cg1 = top->cgs.nr;
+ }
+ if (fr->n_tpi > 0)
+ {
+ cg1--;
+ }
+ }
+
+ bStateChanged = (flags & GMX_FORCE_STATECHANGED);
+ bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE);
+ bFillGrid = (bNS && bStateChanged);
+ bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
+ bDoLongRange = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DOLR));
+ bDoForces = (flags & GMX_FORCE_FORCES);
+ bSepLRF = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
+
+ if (bStateChanged)
+ {
+ update_forcerec(fplog,fr,box);
+
+ /* Calculate total (local) dipole moment in a temporary common array.
+ * This makes it possible to sum them over nodes faster.
+ */
+ calc_mu(start,homenr,
+ x,mdatoms->chargeA,mdatoms->chargeB,mdatoms->nChargePerturbed,
+ mu,mu+DIM);
+ }
+
+ if (fr->ePBC != epbcNONE) {
+ /* Compute shift vectors every step,
+ * because of pressure coupling or box deformation!
+ */
+ if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
+ calc_shifts(box,fr->shift_vec);
+
+ if (bCalcCGCM) {
+ put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,box,
+ &(top->cgs),x,fr->cg_cm);
+ inc_nrnb(nrnb,eNR_CGCM,homenr);
+ inc_nrnb(nrnb,eNR_RESETX,cg1-cg0);
+ }
+ else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph) {
+ unshift_self(graph,box,x);
+ }
+ }
+ else if (bCalcCGCM) {
+ calc_cgcm(fplog,cg0,cg1,&(top->cgs),x,fr->cg_cm);
+ inc_nrnb(nrnb,eNR_CGCM,homenr);
+ }
+
+ if (bCalcCGCM) {
+ if (PAR(cr)) {
+ move_cgcm(fplog,cr,fr->cg_cm);
+ }
+ if (gmx_debug_at)
+ pr_rvecs(debug,0,"cgcm",fr->cg_cm,top->cgs.nr);
+ }
+
+#ifdef GMX_MPI
+ if (!(cr->duty & DUTY_PME)) {
+ /* Send particle coordinates to the pme nodes.
+ * Since this is only implemented for domain decomposition
+ * and domain decomposition does not use the graph,
+ * we do not need to worry about shifting.
+ */
+
+ wallcycle_start(wcycle,ewcPP_PMESENDX);
+
+ bBS = (inputrec->nwall == 2);
+ if (bBS) {
+ copy_mat(box,boxs);
+ svmul(inputrec->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
+ }
+
+ gmx_pme_send_x(cr,bBS ? boxs : box,x,
+ mdatoms->nChargePerturbed,lambda,
+ ( flags & GMX_FORCE_VIRIAL),step);
+
+ wallcycle_stop(wcycle,ewcPP_PMESENDX);
+ }
+#endif /* GMX_MPI */
+
+ /* Communicate coordinates and sum dipole if necessary */
+ if (PAR(cr))
+ {
+ wallcycle_start(wcycle,ewcMOVEX);
+ if (DOMAINDECOMP(cr))
+ {
+ dd_move_x(cr->dd,box,x);
+ }
+ else
+ {
+ move_x(fplog,cr,GMX_LEFT,GMX_RIGHT,x,nrnb);
+ }
+ /* When we don't need the total dipole we sum it in global_stat */
+ if (bStateChanged && NEED_MUTOT(*inputrec))
+ {
+ gmx_sumd(2*DIM,mu,cr);
+ }
+ wallcycle_stop(wcycle,ewcMOVEX);
+ }
+ if (bStateChanged)
+ {
+ for(i=0; i<2; i++)
+ {
+ for(j=0;j<DIM;j++)
+ {
+ fr->mu_tot[i][j] = mu[i*DIM + j];
+ }
+ }
+ }
+ if (fr->efep == efepNO)
+ {
+ copy_rvec(fr->mu_tot[0],mu_tot);
+ }
+ else
+ {
+ for(j=0; j<DIM; j++)
+ {
+ mu_tot[j] =
+ (1.0 - lambda)*fr->mu_tot[0][j] + lambda*fr->mu_tot[1][j];
+ }
+ }
+
+ /* Reset energies */
+ reset_enerdata(&(inputrec->opts),fr,bNS,enerd,MASTER(cr));
+ clear_rvecs(SHIFTS,fr->fshift);
+
+ if (bNS)
+ {
+ wallcycle_start(wcycle,ewcNS);
+
+ if (graph && bStateChanged)
+ {
+ /* Calculate intramolecular shift vectors to make molecules whole */
+ mk_mshift(fplog,graph,fr->ePBC,box,x);
+ }
+
+ /* Reset long range forces if necessary */
+ if (fr->bTwinRange)
+ {
+ /* Reset the (long-range) forces if necessary */
+ clear_rvecs(fr->natoms_force_constr,bSepLRF ? fr->f_twin : f);
+ }
+
+ /* Do the actual neighbour searching and if twin range electrostatics
+ * also do the calculation of long range forces and energies.
+ */
+ dvdl = 0;
+ ns(fplog,fr,x,box,
+ groups,&(inputrec->opts),top,mdatoms,
+ cr,nrnb,lambda,&dvdl,&enerd->grpp,bFillGrid,
+ bDoLongRange,bDoForces,bSepLRF ? fr->f_twin : f);
+ if (bSepDVDL)
+ {
+ fprintf(fplog,sepdvdlformat,"LR non-bonded",0.0,dvdl);
+ }
+ enerd->dvdl_lin += dvdl;
+
+ wallcycle_stop(wcycle,ewcNS);
+ }
+
+ if (inputrec->implicit_solvent && bNS)
+ {
+ make_gb_nblist(cr,inputrec->gb_algorithm,inputrec->rlist,
+ x,box,fr,&top->idef,graph,fr->born);
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ if (!(cr->duty & DUTY_PME))
+ {
+ wallcycle_start(wcycle,ewcPPDURINGPME);
+ dd_force_flop_start(cr->dd,nrnb);
+ }
+ }
+
+ if (inputrec->bRot)
+ {
+ /* Enforced rotation has its own cycle counter that starts after the collective
- enerd->term[F_COM_PULL] =
++ * coordinates have been communicated. It is added to ddCyclF to allow
++ * for proper load-balancing */
++ wallcycle_start(wcycle,ewcROT);
+ do_rotation(cr,inputrec,box,x,t,step,wcycle,bNS);
++ wallcycle_stop(wcycle,ewcROT);
+ }
+
+ /* Start the force cycle counter.
+ * This counter is stopped in do_forcelow_level.
+ * No parallel communication should occur while this counter is running,
+ * since that will interfere with the dynamic load balancing.
+ */
+ wallcycle_start(wcycle,ewcFORCE);
+
+ if (bDoForces)
+ {
+ /* Reset forces for which the virial is calculated separately:
+ * PME/Ewald forces if necessary */
+ if (fr->bF_NoVirSum)
+ {
+ if (flags & GMX_FORCE_VIRIAL)
+ {
+ fr->f_novirsum = fr->f_novirsum_alloc;
+ if (fr->bDomDec)
+ {
+ clear_rvecs(fr->f_novirsum_n,fr->f_novirsum);
+ }
+ else
+ {
+ clear_rvecs(homenr,fr->f_novirsum+start);
+ }
+ }
+ else
+ {
+ /* We are not calculating the pressure so we do not need
+ * a separate array for forces that do not contribute
+ * to the pressure.
+ */
+ fr->f_novirsum = f;
+ }
+ }
+
+ if (bSepLRF)
+ {
+ /* Add the long range forces to the short range forces */
+ for(i=0; i<fr->natoms_force_constr; i++)
+ {
+ copy_rvec(fr->f_twin[i],f[i]);
+ }
+ }
+ else if (!(fr->bTwinRange && bNS))
+ {
+ /* Clear the short-range forces */
+ clear_rvecs(fr->natoms_force_constr,f);
+ }
+
+ clear_rvec(fr->vir_diag_posres);
+ }
+ if (inputrec->ePull == epullCONSTRAINT)
+ {
+ clear_pull_forces(inputrec->pull);
+ }
+
+ /* update QMMMrec, if necessary */
+ if(fr->bQMMM)
+ {
+ update_QMMMrec(cr,fr,x,mdatoms,box,top);
+ }
+
+ if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
+ {
+ /* Position restraints always require full pbc */
+ set_pbc(&pbc,inputrec->ePBC,box);
+ v = posres(top->idef.il[F_POSRES].nr,top->idef.il[F_POSRES].iatoms,
+ top->idef.iparams_posres,
+ (const rvec*)x,fr->f_novirsum,fr->vir_diag_posres,
+ inputrec->ePBC==epbcNONE ? NULL : &pbc,lambda,&dvdl,
+ fr->rc_scaling,fr->ePBC,fr->posres_com,fr->posres_comB);
+ if (bSepDVDL)
+ {
+ fprintf(fplog,sepdvdlformat,
+ interaction_function[F_POSRES].longname,v,dvdl);
+ }
+ enerd->term[F_POSRES] += v;
+ /* This linear lambda dependence assumption is only correct
+ * when only k depends on lambda,
+ * not when the reference position depends on lambda.
+ * grompp checks for this.
+ */
+ enerd->dvdl_lin += dvdl;
+ inc_nrnb(nrnb,eNR_POSRES,top->idef.il[F_POSRES].nr/2);
+ }
+
+ /* Compute the bonded and non-bonded energies and optionally forces */
+ do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
+ cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
+ x,hist,f,enerd,fcd,mtop,top,fr->born,
+ &(top->atomtypes),bBornRadii,box,
+ lambda,graph,&(top->excls),fr->mu_tot,
+ flags,&cycles_pme);
+
+ cycles_force = wallcycle_stop(wcycle,ewcFORCE);
+
+ if (ed)
+ {
+ do_flood(fplog,cr,x,f,ed,box,step);
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ dd_force_flop_stop(cr->dd,nrnb);
+ if (wcycle)
+ {
+ dd_cycles_add(cr->dd,cycles_force-cycles_pme,ddCyclF);
+ }
+ }
+
+ if (bDoForces)
+ {
+ if (IR_ELEC_FIELD(*inputrec))
+ {
+ /* Compute forces due to electric field */
+ calc_f_el(MASTER(cr) ? field : NULL,
+ start,homenr,mdatoms->chargeA,x,fr->f_novirsum,
+ inputrec->ex,inputrec->et,t);
+ }
+
+ /* Communicate the forces */
+ if (PAR(cr))
+ {
+ wallcycle_start(wcycle,ewcMOVEF);
+ if (DOMAINDECOMP(cr))
+ {
+ dd_move_f(cr->dd,f,fr->fshift);
+ /* Do we need to communicate the separate force array
+ * for terms that do not contribute to the single sum virial?
+ * Position restraints and electric fields do not introduce
+ * inter-cg forces, only full electrostatics methods do.
+ * When we do not calculate the virial, fr->f_novirsum = f,
+ * so we have already communicated these forces.
+ */
+ if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
+ (flags & GMX_FORCE_VIRIAL))
+ {
+ dd_move_f(cr->dd,fr->f_novirsum,NULL);
+ }
+ if (bSepLRF)
+ {
+ /* We should not update the shift forces here,
+ * since f_twin is already included in f.
+ */
+ dd_move_f(cr->dd,fr->f_twin,NULL);
+ }
+ }
+ else
+ {
+ pd_move_f(cr,f,nrnb);
+ if (bSepLRF)
+ {
+ pd_move_f(cr,fr->f_twin,nrnb);
+ }
+ }
+ wallcycle_stop(wcycle,ewcMOVEF);
+ }
+
+ /* If we have NoVirSum forces, but we do not calculate the virial,
+ * we sum fr->f_novirum=f later.
+ */
+ if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
+ {
+ wallcycle_start(wcycle,ewcVSITESPREAD);
+ spread_vsite_f(fplog,vsite,x,f,fr->fshift,nrnb,
+ &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
+ wallcycle_stop(wcycle,ewcVSITESPREAD);
+
+ if (bSepLRF)
+ {
+ wallcycle_start(wcycle,ewcVSITESPREAD);
+ spread_vsite_f(fplog,vsite,x,fr->f_twin,NULL,
+ nrnb,
+ &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
+ wallcycle_stop(wcycle,ewcVSITESPREAD);
+ }
+ }
+
+ if (flags & GMX_FORCE_VIRIAL)
+ {
+ /* Calculation of the virial must be done after vsites! */
+ calc_virial(fplog,mdatoms->start,mdatoms->homenr,x,f,
+ vir_force,graph,box,nrnb,fr,inputrec->ePBC);
+ }
+ }
+
++ enerd->term[F_COM_PULL] = 0;
+ if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
+ {
+ /* Calculate the center of mass forces, this requires communication,
+ * which is why pull_potential is called close to other communication.
+ * The virial contribution is calculated directly,
+ * which is why we call pull_potential after calc_virial.
+ */
+ set_pbc(&pbc,inputrec->ePBC,box);
+ dvdl = 0;
- else
- enerd->term[F_COM_PULL] = 0.0;
++ enerd->term[F_COM_PULL] +=
+ pull_potential(inputrec->ePull,inputrec->pull,mdatoms,&pbc,
+ cr,t,lambda,x,f,vir_force,&dvdl);
+ if (bSepDVDL)
+ {
+ fprintf(fplog,sepdvdlformat,"Com pull",enerd->term[F_COM_PULL],dvdl);
+ }
+ enerd->dvdl_lin += dvdl;
+ }
- enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr, step, t);
-
+
+ /* Add the forces from enforced rotation potentials (if any) */
+ if (inputrec->bRot)
++ {
++ wallcycle_start(wcycle,ewcROTadd);
++ enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr,step,t);
++ wallcycle_stop(wcycle,ewcROTadd);
++ }
+
+ if (PAR(cr) && !(cr->duty & DUTY_PME))
+ {
+ cycles_ppdpme = wallcycle_stop(wcycle,ewcPPDURINGPME);
+ dd_cycles_add(cr->dd,cycles_ppdpme,ddCyclPPduringPME);
+
+ /* In case of node-splitting, the PP nodes receive the long-range
+ * forces, virial and energy from the PME nodes here.
+ */
+ wallcycle_start(wcycle,ewcPP_PMEWAITRECVF);
+ dvdl = 0;
+ gmx_pme_receive_f(cr,fr->f_novirsum,fr->vir_el_recip,&e,&dvdl,
+ &cycles_seppme);
+ if (bSepDVDL)
+ {
+ fprintf(fplog,sepdvdlformat,"PME mesh",e,dvdl);
+ }
+ enerd->term[F_COUL_RECIP] += e;
+ enerd->dvdl_lin += dvdl;
+ if (wcycle)
+ {
+ dd_cycles_add(cr->dd,cycles_seppme,ddCyclPME);
+ }
+ wallcycle_stop(wcycle,ewcPP_PMEWAITRECVF);
+ }
+
+ if (bDoForces && fr->bF_NoVirSum)
+ {
+ if (vsite)
+ {
+ /* Spread the mesh force on virtual sites to the other particles...
+ * This is parallellized. MPI communication is performed
+ * if the constructing atoms aren't local.
+ */
+ wallcycle_start(wcycle,ewcVSITESPREAD);
+ spread_vsite_f(fplog,vsite,x,fr->f_novirsum,NULL,nrnb,
+ &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
+ wallcycle_stop(wcycle,ewcVSITESPREAD);
+ }
+ if (flags & GMX_FORCE_VIRIAL)
+ {
+ /* Now add the forces, this is local */
+ if (fr->bDomDec)
+ {
+ sum_forces(0,fr->f_novirsum_n,f,fr->f_novirsum);
+ }
+ else
+ {
+ sum_forces(start,start+homenr,f,fr->f_novirsum);
+ }
+ if (EEL_FULL(fr->eeltype))
+ {
+ /* Add the mesh contribution to the virial */
+ m_add(vir_force,fr->vir_el_recip,vir_force);
+ }
+ if (debug)
+ {
+ pr_rvecs(debug,0,"vir_force",vir_force,DIM);
+ }
+ }
+ }
+
+ /* Sum the potential energy terms from group contributions */
+ sum_epot(&(inputrec->opts),enerd);
+
+ if (fr->print_force >= 0 && bDoForces)
+ {
+ print_large_forces(stderr,mdatoms,cr,step,fr->print_force,x,f);
+ }
+}
+
+void do_constrain_first(FILE *fplog,gmx_constr_t constr,
+ t_inputrec *ir,t_mdatoms *md,
+ t_state *state,rvec *f,
+ t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
+ t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir)
+{
+ int i,m,start,end;
+ gmx_large_int_t step;
+ double mass,tmass,vcm[4];
+ real dt=ir->delta_t;
+ real dvdlambda;
+ rvec *savex;
+
+ snew(savex,state->natoms);
+
+ start = md->start;
+ end = md->homenr + start;
+
+ if (debug)
+ fprintf(debug,"vcm: start=%d, homenr=%d, end=%d\n",
+ start,md->homenr,end);
+ /* Do a first constrain to reset particles... */
+ step = ir->init_step;
+ if (fplog)
+ {
+ char buf[STEPSTRSIZE];
+ fprintf(fplog,"\nConstraining the starting coordinates (step %s)\n",
+ gmx_step_str(step,buf));
+ }
+ dvdlambda = 0;
+
+ /* constrain the current position */
+ constrain(NULL,TRUE,FALSE,constr,&(top->idef),
+ ir,NULL,cr,step,0,md,
+ state->x,state->x,NULL,
+ state->box,state->lambda,&dvdlambda,
+ NULL,NULL,nrnb,econqCoord,ir->epc==epcMTTK,state->veta,state->veta);
+ if (EI_VV(ir->eI))
+ {
+ /* constrain the inital velocity, and save it */
+ /* also may be useful if we need the ekin from the halfstep for velocity verlet */
+ /* might not yet treat veta correctly */
+ constrain(NULL,TRUE,FALSE,constr,&(top->idef),
+ ir,NULL,cr,step,0,md,
+ state->x,state->v,state->v,
+ state->box,state->lambda,&dvdlambda,
+ NULL,NULL,nrnb,econqVeloc,ir->epc==epcMTTK,state->veta,state->veta);
+ }
+ /* constrain the inital velocities at t-dt/2 */
+ if (EI_STATE_VELOCITY(ir->eI) && ir->eI!=eiVV)
+ {
+ for(i=start; (i<end); i++)
+ {
+ for(m=0; (m<DIM); m++)
+ {
+ /* Reverse the velocity */
+ state->v[i][m] = -state->v[i][m];
+ /* Store the position at t-dt in buf */
+ savex[i][m] = state->x[i][m] + dt*state->v[i][m];
+ }
+ }
+ /* Shake the positions at t=-dt with the positions at t=0
+ * as reference coordinates.
+ */
+ if (fplog)
+ {
+ char buf[STEPSTRSIZE];
+ fprintf(fplog,"\nConstraining the coordinates at t0-dt (step %s)\n",
+ gmx_step_str(step,buf));
+ }
+ dvdlambda = 0;
+ constrain(NULL,TRUE,FALSE,constr,&(top->idef),
+ ir,NULL,cr,step,-1,md,
+ state->x,savex,NULL,
+ state->box,state->lambda,&dvdlambda,
+ state->v,NULL,nrnb,econqCoord,ir->epc==epcMTTK,state->veta,state->veta);
+
+ for(i=start; i<end; i++) {
+ for(m=0; m<DIM; m++) {
+ /* Re-reverse the velocities */
+ state->v[i][m] = -state->v[i][m];
+ }
+ }
+ }
+
+ for(m=0; (m<4); m++)
+ vcm[m] = 0;
+ for(i=start; i<end; i++) {
+ mass = md->massT[i];
+ for(m=0; m<DIM; m++) {
+ vcm[m] += state->v[i][m]*mass;
+ }
+ vcm[3] += mass;
+ }
+
+ if (ir->nstcomm != 0 || debug) {
+ /* Compute the global sum of vcm */
+ if (debug)
+ fprintf(debug,"vcm: %8.3f %8.3f %8.3f,"
+ " total mass = %12.5e\n",vcm[XX],vcm[YY],vcm[ZZ],vcm[3]);
+ if (PAR(cr))
+ gmx_sumd(4,vcm,cr);
+ tmass = vcm[3];
+ for(m=0; (m<DIM); m++)
+ vcm[m] /= tmass;
+ if (debug)
+ fprintf(debug,"vcm: %8.3f %8.3f %8.3f,"
+ " total mass = %12.5e\n",vcm[XX],vcm[YY],vcm[ZZ],tmass);
+ if (ir->nstcomm != 0) {
+ /* Now we have the velocity of center of mass, let's remove it */
+ for(i=start; (i<end); i++) {
+ for(m=0; (m<DIM); m++)
+ state->v[i][m] -= vcm[m];
+ }
+
+ }
+ }
+ sfree(savex);
+}
+
+void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr)
+{
+ double eners[2],virs[2],enersum,virsum,y0,f,g,h;
+ double r0,r1,r,rc3,rc9,ea,eb,ec,pa,pb,pc,pd;
+ double invscale,invscale2,invscale3;
+ int ri0,ri1,ri,i,offstart,offset;
+ real scale,*vdwtab;
+
+ fr->enershiftsix = 0;
+ fr->enershifttwelve = 0;
+ fr->enerdiffsix = 0;
+ fr->enerdifftwelve = 0;
+ fr->virdiffsix = 0;
+ fr->virdifftwelve = 0;
+
+ if (eDispCorr != edispcNO) {
+ for(i=0; i<2; i++) {
+ eners[i] = 0;
+ virs[i] = 0;
+ }
+ if ((fr->vdwtype == evdwSWITCH) || (fr->vdwtype == evdwSHIFT)) {
+ if (fr->rvdw_switch == 0)
+ gmx_fatal(FARGS,
+ "With dispersion correction rvdw-switch can not be zero "
+ "for vdw-type = %s",evdw_names[fr->vdwtype]);
+
+ scale = fr->nblists[0].tab.scale;
+ vdwtab = fr->nblists[0].vdwtab;
+
+ /* Round the cut-offs to exact table values for precision */
+ ri0 = floor(fr->rvdw_switch*scale);
+ ri1 = ceil(fr->rvdw*scale);
+ r0 = ri0/scale;
+ r1 = ri1/scale;
+ rc3 = r0*r0*r0;
+ rc9 = rc3*rc3*rc3;
+
+ if (fr->vdwtype == evdwSHIFT) {
+ /* Determine the constant energy shift below rvdw_switch */
+ fr->enershiftsix = (real)(-1.0/(rc3*rc3)) - vdwtab[8*ri0];
+ fr->enershifttwelve = (real)( 1.0/(rc9*rc3)) - vdwtab[8*ri0 + 4];
+ }
+ /* Add the constant part from 0 to rvdw_switch.
+ * This integration from 0 to rvdw_switch overcounts the number
+ * of interactions by 1, as it also counts the self interaction.
+ * We will correct for this later.
+ */
+ eners[0] += 4.0*M_PI*fr->enershiftsix*rc3/3.0;
+ eners[1] += 4.0*M_PI*fr->enershifttwelve*rc3/3.0;
+
+ invscale = 1.0/(scale);
+ invscale2 = invscale*invscale;
+ invscale3 = invscale*invscale2;
+
+ /* following summation derived from cubic spline definition,
+ Numerical Recipies in C, second edition, p. 113-116. Exact
+ for the cubic spline. We first calculate the negative of
+ the energy from rvdw to rvdw_switch, assuming that g(r)=1,
+ and then add the more standard, abrupt cutoff correction to
+ that result, yielding the long-range correction for a
+ switched function. We perform both the pressure and energy
+ loops at the same time for simplicity, as the computational
+ cost is low. */
+
+ for (i=0;i<2;i++) {
+ enersum = 0.0; virsum = 0.0;
+ if (i==0)
+ offstart = 0;
+ else
+ offstart = 4;
+ for (ri=ri0; ri<ri1; ri++) {
+ r = ri*invscale;
+ ea = invscale3;
+ eb = 2.0*invscale2*r;
+ ec = invscale*r*r;
+
+ pa = invscale3;
+ pb = 3.0*invscale2*r;
+ pc = 3.0*invscale*r*r;
+ pd = r*r*r;
+
+ /* this "8" is from the packing in the vdwtab array - perhaps
+ should be #define'ed? */
+ offset = 8*ri + offstart;
+ y0 = vdwtab[offset];
+ f = vdwtab[offset+1];
+ g = vdwtab[offset+2];
+ h = vdwtab[offset+3];
+
+ enersum += y0*(ea/3 + eb/2 + ec) + f*(ea/4 + eb/3 + ec/2)+
+ g*(ea/5 + eb/4 + ec/3) + h*(ea/6 + eb/5 + ec/4);
+ virsum += f*(pa/4 + pb/3 + pc/2 + pd) +
+ 2*g*(pa/5 + pb/4 + pc/3 + pd/2) + 3*h*(pa/6 + pb/5 + pc/4 + pd/3);
+
+ }
+ enersum *= 4.0*M_PI;
+ virsum *= 4.0*M_PI;
+ eners[i] -= enersum;
+ virs[i] -= virsum;
+ }
+
+ /* now add the correction for rvdw_switch to infinity */
+ eners[0] += -4.0*M_PI/(3.0*rc3);
+ eners[1] += 4.0*M_PI/(9.0*rc9);
+ virs[0] += 8.0*M_PI/rc3;
+ virs[1] += -16.0*M_PI/(3.0*rc9);
+ }
+ else if ((fr->vdwtype == evdwCUT) || (fr->vdwtype == evdwUSER)) {
+ if (fr->vdwtype == evdwUSER && fplog)
+ fprintf(fplog,
+ "WARNING: using dispersion correction with user tables\n");
+ rc3 = fr->rvdw*fr->rvdw*fr->rvdw;
+ rc9 = rc3*rc3*rc3;
+ eners[0] += -4.0*M_PI/(3.0*rc3);
+ eners[1] += 4.0*M_PI/(9.0*rc9);
+ virs[0] += 8.0*M_PI/rc3;
+ virs[1] += -16.0*M_PI/(3.0*rc9);
+ } else {
+ gmx_fatal(FARGS,
+ "Dispersion correction is not implemented for vdw-type = %s",
+ evdw_names[fr->vdwtype]);
+ }
+ fr->enerdiffsix = eners[0];
+ fr->enerdifftwelve = eners[1];
+ /* The 0.5 is due to the Gromacs definition of the virial */
+ fr->virdiffsix = 0.5*virs[0];
+ fr->virdifftwelve = 0.5*virs[1];
+ }
+}
+
+void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
+ gmx_large_int_t step,int natoms,
+ matrix box,real lambda,tensor pres,tensor virial,
+ real *prescorr, real *enercorr, real *dvdlcorr)
+{
+ gmx_bool bCorrAll,bCorrPres;
+ real dvdlambda,invvol,dens,ninter,avcsix,avctwelve,enerdiff,svir=0,spres=0;
+ int m;
+
+ *prescorr = 0;
+ *enercorr = 0;
+ *dvdlcorr = 0;
+
+ clear_mat(virial);
+ clear_mat(pres);
+
+ if (ir->eDispCorr != edispcNO) {
+ bCorrAll = (ir->eDispCorr == edispcAllEner ||
+ ir->eDispCorr == edispcAllEnerPres);
+ bCorrPres = (ir->eDispCorr == edispcEnerPres ||
+ ir->eDispCorr == edispcAllEnerPres);
+
+ invvol = 1/det(box);
+ if (fr->n_tpi)
+ {
+ /* Only correct for the interactions with the inserted molecule */
+ dens = (natoms - fr->n_tpi)*invvol;
+ ninter = fr->n_tpi;
+ }
+ else
+ {
+ dens = natoms*invvol;
+ ninter = 0.5*natoms;
+ }
+
+ if (ir->efep == efepNO)
+ {
+ avcsix = fr->avcsix[0];
+ avctwelve = fr->avctwelve[0];
+ }
+ else
+ {
+ avcsix = (1 - lambda)*fr->avcsix[0] + lambda*fr->avcsix[1];
+ avctwelve = (1 - lambda)*fr->avctwelve[0] + lambda*fr->avctwelve[1];
+ }
+
+ enerdiff = ninter*(dens*fr->enerdiffsix - fr->enershiftsix);
+ *enercorr += avcsix*enerdiff;
+ dvdlambda = 0.0;
+ if (ir->efep != efepNO)
+ {
+ dvdlambda += (fr->avcsix[1] - fr->avcsix[0])*enerdiff;
+ }
+ if (bCorrAll)
+ {
+ enerdiff = ninter*(dens*fr->enerdifftwelve - fr->enershifttwelve);
+ *enercorr += avctwelve*enerdiff;
+ if (fr->efep != efepNO)
+ {
+ dvdlambda += (fr->avctwelve[1] - fr->avctwelve[0])*enerdiff;
+ }
+ }
+
+ if (bCorrPres)
+ {
+ svir = ninter*dens*avcsix*fr->virdiffsix/3.0;
+ if (ir->eDispCorr == edispcAllEnerPres)
+ {
+ svir += ninter*dens*avctwelve*fr->virdifftwelve/3.0;
+ }
+ /* The factor 2 is because of the Gromacs virial definition */
+ spres = -2.0*invvol*svir*PRESFAC;
+
+ for(m=0; m<DIM; m++) {
+ virial[m][m] += svir;
+ pres[m][m] += spres;
+ }
+ *prescorr += spres;
+ }
+
+ /* Can't currently control when it prints, for now, just print when degugging */
+ if (debug)
+ {
+ if (bCorrAll) {
+ fprintf(debug,"Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
+ avcsix,avctwelve);
+ }
+ if (bCorrPres)
+ {
+ fprintf(debug,
+ "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
+ *enercorr,spres,svir);
+ }
+ else
+ {
+ fprintf(debug,"Long Range LJ corr.: Epot %10g\n",*enercorr);
+ }
+ }
+
+ if (fr->bSepDVDL && do_per_step(step,ir->nstlog))
+ {
+ fprintf(fplog,sepdvdlformat,"Dispersion correction",
+ *enercorr,dvdlambda);
+ }
+ if (fr->efep != efepNO)
+ {
+ *dvdlcorr += dvdlambda;
+ }
+ }
+}
+
+void do_pbc_first(FILE *fplog,matrix box,t_forcerec *fr,
+ t_graph *graph,rvec x[])
+{
+ if (fplog)
+ fprintf(fplog,"Removing pbc first time\n");
+ calc_shifts(box,fr->shift_vec);
+ if (graph) {
+ mk_mshift(fplog,graph,fr->ePBC,box,x);
+ if (gmx_debug_at)
+ p_graph(debug,"do_pbc_first 1",graph);
+ shift_self(graph,box,x);
+ /* By doing an extra mk_mshift the molecules that are broken
+ * because they were e.g. imported from another software
+ * will be made whole again. Such are the healing powers
+ * of GROMACS.
+ */
+ mk_mshift(fplog,graph,fr->ePBC,box,x);
+ if (gmx_debug_at)
+ p_graph(debug,"do_pbc_first 2",graph);
+ }
+ if (fplog)
+ fprintf(fplog,"Done rmpbc\n");
+}
+
+static void low_do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
+ gmx_mtop_t *mtop,rvec x[],
+ gmx_bool bFirst)
+{
+ t_graph *graph;
+ int mb,as,mol;
+ gmx_molblock_t *molb;
+
+ if (bFirst && fplog)
+ fprintf(fplog,"Removing pbc first time\n");
+
+ snew(graph,1);
+ as = 0;
+ for(mb=0; mb<mtop->nmolblock; mb++) {
+ molb = &mtop->molblock[mb];
+ if (molb->natoms_mol == 1 ||
+ (!bFirst && mtop->moltype[molb->type].cgs.nr == 1)) {
+ /* Just one atom or charge group in the molecule, no PBC required */
+ as += molb->nmol*molb->natoms_mol;
+ } else {
+ /* Pass NULL iso fplog to avoid graph prints for each molecule type */
+ mk_graph_ilist(NULL,mtop->moltype[molb->type].ilist,
+ 0,molb->natoms_mol,FALSE,FALSE,graph);
+
+ for(mol=0; mol<molb->nmol; mol++) {
+ mk_mshift(fplog,graph,ePBC,box,x+as);
+
+ shift_self(graph,box,x+as);
+ /* The molecule is whole now.
+ * We don't need the second mk_mshift call as in do_pbc_first,
+ * since we no longer need this graph.
+ */
+
+ as += molb->natoms_mol;
+ }
+ done_graph(graph);
+ }
+ }
+ sfree(graph);
+}
+
+void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
+ gmx_mtop_t *mtop,rvec x[])
+{
+ low_do_pbc_mtop(fplog,ePBC,box,mtop,x,TRUE);
+}
+
+void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
+ gmx_mtop_t *mtop,rvec x[])
+{
+ low_do_pbc_mtop(fplog,ePBC,box,mtop,x,FALSE);
+}
+
+void finish_run(FILE *fplog,t_commrec *cr,const char *confout,
+ t_inputrec *inputrec,
+ t_nrnb nrnb[],gmx_wallcycle_t wcycle,
+ gmx_runtime_t *runtime,
+ gmx_bool bWriteStat)
+{
+ int i,j;
+ t_nrnb *nrnb_tot=NULL;
+ real delta_t;
+ double nbfs,mflop;
+ double cycles[ewcNR];
+
+ wallcycle_sum(cr,wcycle,cycles);
+
+ if (cr->nnodes > 1) {
+ if (SIMMASTER(cr))
+ snew(nrnb_tot,1);
+#ifdef GMX_MPI
+ MPI_Reduce(nrnb->n,nrnb_tot->n,eNRNB,MPI_DOUBLE,MPI_SUM,
+ MASTERRANK(cr),cr->mpi_comm_mysim);
+#endif
+ } else {
+ nrnb_tot = nrnb;
+ }
+
+ if (SIMMASTER(cr)) {
+ print_flop(fplog,nrnb_tot,&nbfs,&mflop);
+ if (cr->nnodes > 1) {
+ sfree(nrnb_tot);
+ }
+ }
+
+ if ((cr->duty & DUTY_PP) && DOMAINDECOMP(cr)) {
+ print_dd_statistics(cr,inputrec,fplog);
+ }
+
+#ifdef GMX_MPI
+ if (PARTDECOMP(cr))
+ {
+ if (MASTER(cr))
+ {
+ t_nrnb *nrnb_all;
+ int s;
+ MPI_Status stat;
+
+ snew(nrnb_all,cr->nnodes);
+ nrnb_all[0] = *nrnb;
+ for(s=1; s<cr->nnodes; s++)
+ {
+ MPI_Recv(nrnb_all[s].n,eNRNB,MPI_DOUBLE,s,0,
+ cr->mpi_comm_mysim,&stat);
+ }
+ pr_load(fplog,cr,nrnb_all);
+ sfree(nrnb_all);
+ }
+ else
+ {
+ MPI_Send(nrnb->n,eNRNB,MPI_DOUBLE,MASTERRANK(cr),0,
+ cr->mpi_comm_mysim);
+ }
+ }
+#endif
+
+ if (SIMMASTER(cr)) {
+ wallcycle_print(fplog,cr->nnodes,cr->npmenodes,runtime->realtime,
+ wcycle,cycles);
+
+ if (EI_DYNAMICS(inputrec->eI)) {
+ delta_t = inputrec->delta_t;
+ } else {
+ delta_t = 0;
+ }
+
+ if (fplog) {
+ print_perf(fplog,runtime->proctime,runtime->realtime,
+ cr->nnodes-cr->npmenodes,
+ runtime->nsteps_done,delta_t,nbfs,mflop);
+ }
+ if (bWriteStat) {
+ print_perf(stderr,runtime->proctime,runtime->realtime,
+ cr->nnodes-cr->npmenodes,
+ runtime->nsteps_done,delta_t,nbfs,mflop);
+ }
+
+ /*
+ runtime=inputrec->nsteps*inputrec->delta_t;
+ if (bWriteStat) {
+ if (cr->nnodes == 1)
+ fprintf(stderr,"\n\n");
+ print_perf(stderr,nodetime,realtime,runtime,&ntot,
+ cr->nnodes-cr->npmenodes,FALSE);
+ }
+ wallcycle_print(fplog,cr->nnodes,cr->npmenodes,realtime,wcycle,cycles);
+ print_perf(fplog,nodetime,realtime,runtime,&ntot,cr->nnodes-cr->npmenodes,
+ TRUE);
+ if (PARTDECOMP(cr))
+ pr_load(fplog,cr,nrnb_all);
+ if (cr->nnodes > 1)
+ sfree(nrnb_all);
+ */
+ }
+}
+
+void init_md(FILE *fplog,
+ t_commrec *cr,t_inputrec *ir,const output_env_t oenv,
+ double *t,double *t0,
+ real *lambda,double *lam0,
+ t_nrnb *nrnb,gmx_mtop_t *mtop,
+ gmx_update_t *upd,
+ int nfile,const t_filenm fnm[],
+ gmx_mdoutf_t **outf,t_mdebin **mdebin,
+ tensor force_vir,tensor shake_vir,rvec mu_tot,
+ gmx_bool *bSimAnn,t_vcm **vcm, t_state *state, unsigned long Flags)
+{
+ int i,j,n;
+ real tmpt,mod;
+
+ /* Initial values */
+ *t = *t0 = ir->init_t;
+ if (ir->efep != efepNO)
+ {
+ *lam0 = ir->init_lambda;
+ *lambda = *lam0 + ir->init_step*ir->delta_lambda;
+ }
+ else
+ {
+ *lambda = *lam0 = 0.0;
+ }
+
+ *bSimAnn=FALSE;
+ for(i=0;i<ir->opts.ngtc;i++)
+ {
+ /* set bSimAnn if any group is being annealed */
+ if(ir->opts.annealing[i]!=eannNO)
+ {
+ *bSimAnn = TRUE;
+ }
+ }
+ if (*bSimAnn)
+ {
+ update_annealing_target_temp(&(ir->opts),ir->init_t);
+ }
+
+ if (upd)
+ {
+ *upd = init_update(fplog,ir);
+ }
+
+ if (vcm != NULL)
+ {
+ *vcm = init_vcm(fplog,&mtop->groups,ir);
+ }
+
+ if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES))
+ {
+ if (ir->etc == etcBERENDSEN)
+ {
+ please_cite(fplog,"Berendsen84a");
+ }
+ if (ir->etc == etcVRESCALE)
+ {
+ please_cite(fplog,"Bussi2007a");
+ }
+ }
+
+ init_nrnb(nrnb);
+
+ if (nfile != -1)
+ {
+ *outf = init_mdoutf(nfile,fnm,Flags,cr,ir,oenv);
+
+ *mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : (*outf)->fp_ene,
+ mtop,ir, (*outf)->fp_dhdl);
+ }
+
+ /* Initiate variables */
+ clear_mat(force_vir);
+ clear_mat(shake_vir);
+ clear_rvec(mu_tot);
+
+ debug_gmx();
+}
+
--- /dev/null
- #include "md_openmm.h"
-
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, 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 <signal.h>
+#include <stdlib.h>
+
+#if ((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
+/* _isnan() */
+#include <float.h>
+#endif
+
+#include "typedefs.h"
+#include "smalloc.h"
+#include "sysstuff.h"
+#include "statutil.h"
+#include "mdrun.h"
+#include "network.h"
+#include "pull.h"
+#include "pull_rotation.h"
+#include "names.h"
+#include "disre.h"
+#include "orires.h"
+#include "dihre.h"
+#include "pppm.h"
+#include "pme.h"
+#include "mdatoms.h"
+#include "repl_ex.h"
+#include "qmmm.h"
+#include "domdec.h"
+#include "partdec.h"
+#include "coulomb.h"
+#include "constr.h"
+#include "mvdata.h"
+#include "checkpoint.h"
+#include "mtop_util.h"
+#include "sighandler.h"
+#include "tpxio.h"
+#include "txtdump.h"
++#include "pull_rotation.h"
+#include "membed.h"
+#include "macros.h"
+
+#ifdef GMX_LIB_MPI
+#include <mpi.h>
+#endif
+#ifdef GMX_THREADS
+#include "tmpi.h"
+#endif
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+#ifdef GMX_OPENMM
+#include "md_openmm.h"
+#endif
+
+
+typedef struct {
+ gmx_integrator_t *func;
+} gmx_intp_t;
+
+/* The array should match the eI array in include/types/enums.h */
+#ifdef GMX_OPENMM /* FIXME do_md_openmm needs fixing */
+const gmx_intp_t integrator[eiNR] = { {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm}, {do_md_openmm},{do_md_openmm}};
+#else
+const gmx_intp_t integrator[eiNR] = { {do_md}, {do_steep}, {do_cg}, {do_md}, {do_md}, {do_nm}, {do_lbfgs}, {do_tpi}, {do_tpi}, {do_md}, {do_md},{do_md}};
+#endif
+
+gmx_large_int_t deform_init_init_step_tpx;
+matrix deform_init_box_tpx;
+#ifdef GMX_THREADS
+tMPI_Thread_mutex_t deform_init_box_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
+#endif
+
+
+#ifdef GMX_THREADS
+struct mdrunner_arglist
+{
+ FILE *fplog;
+ t_commrec *cr;
+ int nfile;
+ const t_filenm *fnm;
+ output_env_t oenv;
+ gmx_bool bVerbose;
+ gmx_bool bCompact;
+ int nstglobalcomm;
+ ivec ddxyz;
+ int dd_node_order;
+ real rdd;
+ real rconstr;
+ const char *dddlb_opt;
+ real dlb_scale;
+ const char *ddcsx;
+ const char *ddcsy;
+ const char *ddcsz;
+ int nstepout;
+ int resetstep;
+ int nmultisim;
+ int repl_ex_nst;
+ int repl_ex_seed;
+ real pforce;
+ real cpt_period;
+ real max_hours;
+ const char *deviceOptions;
+ unsigned long Flags;
+ int ret; /* return value */
+};
+
+
+/* The function used for spawning threads. Extracts the mdrunner()
+ arguments from its one argument and calls mdrunner(), after making
+ a commrec. */
+static void mdrunner_start_fn(void *arg)
+{
+ struct mdrunner_arglist *mda=(struct mdrunner_arglist*)arg;
+ struct mdrunner_arglist mc=*mda; /* copy the arg list to make sure
+ that it's thread-local. This doesn't
+ copy pointed-to items, of course,
+ but those are all const. */
+ t_commrec *cr; /* we need a local version of this */
+ FILE *fplog=NULL;
+ t_filenm *fnm;
+
+ fnm = dup_tfn(mc.nfile, mc.fnm);
+
+ cr = init_par_threads(mc.cr);
+
+ if (MASTER(cr))
+ {
+ fplog=mc.fplog;
+ }
+
+ mda->ret=mdrunner(cr->nnodes, fplog, cr, mc.nfile, fnm, mc.oenv,
+ mc.bVerbose, mc.bCompact, mc.nstglobalcomm,
+ mc.ddxyz, mc.dd_node_order, mc.rdd,
+ mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
+ mc.ddcsx, mc.ddcsy, mc.ddcsz, mc.nstepout, mc.resetstep,
+ mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_seed, mc.pforce,
+ mc.cpt_period, mc.max_hours, mc.deviceOptions, mc.Flags);
+}
+
+/* called by mdrunner() to start a specific number of threads (including
+ the main thread) for thread-parallel runs. This in turn calls mdrunner()
+ for each thread.
+ All options besides nthreads are the same as for mdrunner(). */
+static t_commrec *mdrunner_start_threads(int nthreads,
+ FILE *fplog,t_commrec *cr,int nfile,
+ const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
+ gmx_bool bCompact, int nstglobalcomm,
+ ivec ddxyz,int dd_node_order,real rdd,real rconstr,
+ const char *dddlb_opt,real dlb_scale,
+ const char *ddcsx,const char *ddcsy,const char *ddcsz,
+ int nstepout,int resetstep,int nmultisim,int repl_ex_nst,
+ int repl_ex_seed, real pforce,real cpt_period, real max_hours,
+ const char *deviceOptions, unsigned long Flags)
+{
+ int ret;
+ struct mdrunner_arglist *mda;
+ t_commrec *crn; /* the new commrec */
+ t_filenm *fnmn;
+
+ /* first check whether we even need to start tMPI */
+ if (nthreads<2)
+ return cr;
+
+ /* a few small, one-time, almost unavoidable memory leaks: */
+ snew(mda,1);
+ fnmn=dup_tfn(nfile, fnm);
+
+ /* fill the data structure to pass as void pointer to thread start fn */
+ mda->fplog=fplog;
+ mda->cr=cr;
+ mda->nfile=nfile;
+ mda->fnm=fnmn;
+ mda->oenv=oenv;
+ mda->bVerbose=bVerbose;
+ mda->bCompact=bCompact;
+ mda->nstglobalcomm=nstglobalcomm;
+ mda->ddxyz[XX]=ddxyz[XX];
+ mda->ddxyz[YY]=ddxyz[YY];
+ mda->ddxyz[ZZ]=ddxyz[ZZ];
+ mda->dd_node_order=dd_node_order;
+ mda->rdd=rdd;
+ mda->rconstr=rconstr;
+ mda->dddlb_opt=dddlb_opt;
+ mda->dlb_scale=dlb_scale;
+ mda->ddcsx=ddcsx;
+ mda->ddcsy=ddcsy;
+ mda->ddcsz=ddcsz;
+ mda->nstepout=nstepout;
+ mda->resetstep=resetstep;
+ mda->nmultisim=nmultisim;
+ mda->repl_ex_nst=repl_ex_nst;
+ mda->repl_ex_seed=repl_ex_seed;
+ mda->pforce=pforce;
+ mda->cpt_period=cpt_period;
+ mda->max_hours=max_hours;
+ mda->deviceOptions=deviceOptions;
+ mda->Flags=Flags;
+
+ fprintf(stderr, "Starting %d threads\n",nthreads);
+ fflush(stderr);
+ /* now spawn new threads that start mdrunner_start_fn(), while
+ the main thread returns */
+ ret=tMPI_Init_fn(TRUE, nthreads, mdrunner_start_fn, (void*)(mda) );
+ if (ret!=TMPI_SUCCESS)
+ return NULL;
+
+ /* make a new comm_rec to reflect the new situation */
+ crn=init_par_threads(cr);
+ return crn;
+}
+
+
+/* get the number of threads based on how many there were requested,
+ which algorithms we're using, and how many particles there are. */
+static int get_nthreads(int nthreads_requested, t_inputrec *inputrec,
+ gmx_mtop_t *mtop)
+{
+ int nthreads,nthreads_new;
+ int min_atoms_per_thread;
+ char *env;
+
+ nthreads = nthreads_requested;
+
+ /* determine # of hardware threads. */
+ if (nthreads_requested < 1)
+ {
+ if ((env = getenv("GMX_MAX_THREADS")) != NULL)
+ {
+ nthreads = 0;
+ sscanf(env,"%d",&nthreads);
+ if (nthreads < 1)
+ {
+ gmx_fatal(FARGS,"GMX_MAX_THREADS (%d) should be larger than 0",
+ nthreads);
+ }
+ }
+ else
+ {
+ nthreads = tMPI_Thread_get_hw_number();
+ }
+ }
+
+ if (inputrec->eI == eiNM || EI_TPI(inputrec->eI))
+ {
+ /* Steps are divided over the nodes iso splitting the atoms */
+ min_atoms_per_thread = 0;
+ }
+ else
+ {
+ min_atoms_per_thread = MIN_ATOMS_PER_THREAD;
+ }
+
+ /* Check if an algorithm does not support parallel simulation. */
+ if (nthreads != 1 &&
+ ( inputrec->eI == eiLBFGS ||
+ inputrec->coulombtype == eelEWALD ) )
+ {
+ fprintf(stderr,"\nThe integration or electrostatics algorithm doesn't support parallel runs. Not starting any threads.\n");
+ nthreads = 1;
+ }
+ else if (nthreads_requested < 1 &&
+ mtop->natoms/nthreads < min_atoms_per_thread)
+ {
+ /* the thread number was chosen automatically, but there are too many
+ threads (too few atoms per thread) */
+ nthreads_new = max(1,mtop->natoms/min_atoms_per_thread);
+
+ if (nthreads_new > 8 || (nthreads == 8 && nthreads_new > 4))
+ {
+ /* Use only multiples of 4 above 8 threads
+ * or with an 8-core processor
+ * (to avoid 6 threads on 8 core processors with 4 real cores).
+ */
+ nthreads_new = (nthreads_new/4)*4;
+ }
+ else if (nthreads_new > 4)
+ {
+ /* Avoid 5 or 7 threads */
+ nthreads_new = (nthreads_new/2)*2;
+ }
+
+ nthreads = nthreads_new;
+
+ fprintf(stderr,"\n");
+ fprintf(stderr,"NOTE: Parallelization is limited by the small number of atoms,\n");
+ fprintf(stderr," only starting %d threads.\n",nthreads);
+ fprintf(stderr," You can use the -nt option to optimize the number of threads.\n\n");
+ }
+ return nthreads;
+}
+#endif
+
+
+int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
+ const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
+ gmx_bool bCompact, int nstglobalcomm,
+ ivec ddxyz,int dd_node_order,real rdd,real rconstr,
+ const char *dddlb_opt,real dlb_scale,
+ const char *ddcsx,const char *ddcsy,const char *ddcsz,
+ int nstepout,int resetstep,int nmultisim,int repl_ex_nst,
+ int repl_ex_seed, real pforce,real cpt_period,real max_hours,
+ const char *deviceOptions, unsigned long Flags)
+{
+ double nodetime=0,realtime;
+ t_inputrec *inputrec;
+ t_state *state=NULL;
+ matrix box;
+ gmx_ddbox_t ddbox={0};
+ int npme_major,npme_minor;
+ real tmpr1,tmpr2;
+ t_nrnb *nrnb;
+ gmx_mtop_t *mtop=NULL;
+ t_mdatoms *mdatoms=NULL;
+ t_forcerec *fr=NULL;
+ t_fcdata *fcd=NULL;
+ real ewaldcoeff=0;
+ gmx_pme_t *pmedata=NULL;
+ gmx_vsite_t *vsite=NULL;
+ gmx_constr_t constr;
+ int i,m,nChargePerturbed=-1,status,nalloc;
+ char *gro;
+ gmx_wallcycle_t wcycle;
+ gmx_bool bReadRNG,bReadEkin;
+ int list;
+ gmx_runtime_t runtime;
+ int rc;
+ gmx_large_int_t reset_counters;
+ gmx_edsam_t ed=NULL;
+ t_commrec *cr_old=cr;
+ int nthreads=1;
+ gmx_membed_t *membed=NULL;
+
+ /* CAUTION: threads may be started later on in this function, so
+ cr doesn't reflect the final parallel state right now */
+ snew(inputrec,1);
+ snew(mtop,1);
+
+ if (bVerbose && SIMMASTER(cr))
+ {
+ fprintf(stderr,"Getting Loaded...\n");
+ }
+
+ if (Flags & MD_APPENDFILES)
+ {
+ fplog = NULL;
+ }
+
+ snew(state,1);
+ if (MASTER(cr))
+ {
+ /* Read (nearly) all data required for the simulation */
+ read_tpx_state(ftp2fn(efTPX,nfile,fnm),inputrec,state,NULL,mtop);
+
+ /* NOW the threads will be started: */
+#ifdef GMX_THREADS
+ nthreads = get_nthreads(nthreads_requested, inputrec, mtop);
+
+ if (nthreads > 1)
+ {
+ /* now start the threads. */
+ cr=mdrunner_start_threads(nthreads, fplog, cr_old, nfile, fnm,
+ oenv, bVerbose, bCompact, nstglobalcomm,
+ ddxyz, dd_node_order, rdd, rconstr,
+ dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
+ nstepout, resetstep, nmultisim,
+ repl_ex_nst, repl_ex_seed, pforce,
+ cpt_period, max_hours, deviceOptions,
+ Flags);
+ /* the main thread continues here with a new cr. We don't deallocate
+ the old cr because other threads may still be reading it. */
+ if (cr == NULL)
+ {
+ gmx_comm("Failed to spawn threads");
+ }
+ }
+#endif
+ }
+ /* END OF CAUTION: cr is now reliable */
+
+ /* g_membed initialisation *
+ * Because we change the mtop, init_membed is called before the init_parallel *
+ * (in case we ever want to make it run in parallel) */
+ if (opt2bSet("-membed",nfile,fnm))
+ {
+ fprintf(stderr,"Entering membed code");
+ snew(membed,1);
+ init_membed(fplog,membed,nfile,fnm,mtop,inputrec,state,cr,&cpt_period);
+ }
+
+ if (PAR(cr))
+ {
+ /* now broadcast everything to the non-master nodes/threads: */
+ init_parallel(fplog, cr, inputrec, mtop);
+ }
+ if (fplog != NULL)
+ {
+ pr_inputrec(fplog,0,"Input Parameters",inputrec,FALSE);
+ }
+
+ /* now make sure the state is initialized and propagated */
+ set_state_entries(state,inputrec,cr->nnodes);
+
+ /* A parallel command line option consistency check that we can
+ only do after any threads have started. */
+ if (!PAR(cr) &&
+ (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || cr->npmenodes > 0))
+ {
+ gmx_fatal(FARGS,
+ "The -dd or -npme option request a parallel simulation, "
+#ifndef GMX_MPI
+ "but mdrun was compiled without threads or MPI enabled"
+#else
+#ifdef GMX_THREADS
+ "but the number of threads (option -nt) is 1"
+#else
+ "but mdrun was not started through mpirun/mpiexec or only one process was requested through mpirun/mpiexec"
+#endif
+#endif
+ );
+ }
+
+ if ((Flags & MD_RERUN) &&
+ (EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
+ {
+ gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
+ }
+
+ if (can_use_allvsall(inputrec,mtop,TRUE,cr,fplog))
+ {
+ /* All-vs-all loops do not work with domain decomposition */
+ Flags |= MD_PARTDEC;
+ }
+
+ if (!EEL_PME(inputrec->coulombtype) || (Flags & MD_PARTDEC))
+ {
+ cr->npmenodes = 0;
+ }
+
+#ifdef GMX_FAHCORE
+ fcRegisterSteps(inputrec->nsteps,inputrec->init_step);
+#endif
+
+ /* NMR restraints must be initialized before load_checkpoint,
+ * since with time averaging the history is added to t_state.
+ * For proper consistency check we therefore need to extend
+ * t_state here.
+ * So the PME-only nodes (if present) will also initialize
+ * the distance restraints.
+ */
+ snew(fcd,1);
+
+ /* This needs to be called before read_checkpoint to extend the state */
+ init_disres(fplog,mtop,inputrec,cr,Flags & MD_PARTDEC,fcd,state);
+
+ if (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0)
+ {
+ if (PAR(cr) && !(Flags & MD_PARTDEC))
+ {
+ gmx_fatal(FARGS,"Orientation restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
+ }
+ /* Orientation restraints */
+ if (MASTER(cr))
+ {
+ init_orires(fplog,mtop,state->x,inputrec,cr->ms,&(fcd->orires),
+ state);
+ }
+ }
+
+ if (DEFORM(*inputrec))
+ {
+ /* Store the deform reference box before reading the checkpoint */
+ if (SIMMASTER(cr))
+ {
+ copy_mat(state->box,box);
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box),box,cr);
+ }
+ /* Because we do not have the update struct available yet
+ * in which the reference values should be stored,
+ * we store them temporarily in static variables.
+ * This should be thread safe, since they are only written once
+ * and with identical values.
+ */
+#ifdef GMX_THREADS
+ tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+#endif
+ deform_init_init_step_tpx = inputrec->init_step;
+ copy_mat(box,deform_init_box_tpx);
+#ifdef GMX_THREADS
+ tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+#endif
+ }
+
+ if (opt2bSet("-cpi",nfile,fnm))
+ {
+ /* Check if checkpoint file exists before doing continuation.
+ * This way we can use identical input options for the first and subsequent runs...
+ */
+ if( gmx_fexist_master(opt2fn_master("-cpi",nfile,fnm,cr),cr) )
+ {
+ load_checkpoint(opt2fn_master("-cpi",nfile,fnm,cr),&fplog,
+ cr,Flags & MD_PARTDEC,ddxyz,
+ inputrec,state,&bReadRNG,&bReadEkin,
+ (Flags & MD_APPENDFILES));
+
+ if (bReadRNG)
+ {
+ Flags |= MD_READ_RNG;
+ }
+ if (bReadEkin)
+ {
+ Flags |= MD_READ_EKIN;
+ }
+ }
+ }
+
+ if (((MASTER(cr) || (Flags & MD_SEPPOT)) && (Flags & MD_APPENDFILES))
+#ifdef GMX_THREADS
+ /* With thread MPI only the master node/thread exists in mdrun.c,
+ * therefore non-master nodes need to open the "seppot" log file here.
+ */
+ || (!MASTER(cr) && (Flags & MD_SEPPOT))
+#endif
+ )
+ {
+ gmx_log_open(ftp2fn(efLOG,nfile,fnm),cr,!(Flags & MD_SEPPOT),
+ Flags,&fplog);
+ }
+
+ if (SIMMASTER(cr))
+ {
+ copy_mat(state->box,box);
+ }
+
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(box),box,cr);
+ }
+
+ /* Essential dynamics */
+ if (opt2bSet("-ei",nfile,fnm))
+ {
+ /* Open input and output files, allocate space for ED data structure */
+ ed = ed_open(nfile,fnm,Flags,cr);
+ }
+
+ if (bVerbose && SIMMASTER(cr))
+ {
+ fprintf(stderr,"Loaded with Money\n\n");
+ }
+
+ if (PAR(cr) && !((Flags & MD_PARTDEC) ||
+ EI_TPI(inputrec->eI) ||
+ inputrec->eI == eiNM))
+ {
+ cr->dd = init_domain_decomposition(fplog,cr,Flags,ddxyz,rdd,rconstr,
+ dddlb_opt,dlb_scale,
+ ddcsx,ddcsy,ddcsz,
+ mtop,inputrec,
+ box,state->x,
+ &ddbox,&npme_major,&npme_minor);
+
+ make_dd_communicators(fplog,cr,dd_node_order);
+
+ /* Set overallocation to avoid frequent reallocation of arrays */
+ set_over_alloc_dd(TRUE);
+ }
+ else
+ {
+ /* PME, if used, is done on all nodes with 1D decomposition */
+ cr->npmenodes = 0;
+ cr->duty = (DUTY_PP | DUTY_PME);
+ npme_major = 1;
+ npme_minor = 1;
+ if (!EI_TPI(inputrec->eI))
+ {
+ npme_major = cr->nnodes;
+ }
+
+ if (inputrec->ePBC == epbcSCREW)
+ {
+ gmx_fatal(FARGS,
+ "pbc=%s is only implemented with domain decomposition",
+ epbc_names[inputrec->ePBC]);
+ }
+ }
+
+ if (PAR(cr))
+ {
+ /* After possible communicator splitting in make_dd_communicators.
+ * we can set up the intra/inter node communication.
+ */
+ gmx_setup_nodecomm(fplog,cr);
+ }
+
+ wcycle = wallcycle_init(fplog,resetstep,cr);
+ if (PAR(cr))
+ {
+ /* Master synchronizes its value of reset_counters with all nodes
+ * including PME only nodes */
+ reset_counters = wcycle_get_reset_counters(wcycle);
+ gmx_bcast_sim(sizeof(reset_counters),&reset_counters,cr);
+ wcycle_set_reset_counters(wcycle, reset_counters);
+ }
+
+
+ snew(nrnb,1);
+ if (cr->duty & DUTY_PP)
+ {
+ /* For domain decomposition we allocate dynamically
+ * in dd_partition_system.
+ */
+ if (DOMAINDECOMP(cr))
+ {
+ bcast_state_setup(cr,state);
+ }
+ else
+ {
+ if (PAR(cr))
+ {
+ bcast_state(cr,state,TRUE);
+ }
+ }
+
+ /* Dihedral Restraints */
+ if (gmx_mtop_ftype_count(mtop,F_DIHRES) > 0)
+ {
+ init_dihres(fplog,mtop,inputrec,fcd);
+ }
+
+ /* Initiate forcerecord */
+ fr = mk_forcerec();
+ init_forcerec(fplog,oenv,fr,fcd,inputrec,mtop,cr,box,FALSE,
+ opt2fn("-table",nfile,fnm),
+ opt2fn("-tablep",nfile,fnm),
+ opt2fn("-tableb",nfile,fnm),FALSE,pforce);
+
+ /* version for PCA_NOT_READ_NODE (see md.c) */
+ /*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
+ "nofile","nofile","nofile",FALSE,pforce);
+ */
+ fr->bSepDVDL = ((Flags & MD_SEPPOT) == MD_SEPPOT);
+
+ /* Initialize QM-MM */
+ if(fr->bQMMM)
+ {
+ init_QMMMrec(cr,box,mtop,inputrec,fr);
+ }
+
+ /* Initialize the mdatoms structure.
+ * mdatoms is not filled with atom data,
+ * as this can not be done now with domain decomposition.
+ */
+ mdatoms = init_mdatoms(fplog,mtop,inputrec->efep!=efepNO);
+
+ /* Initialize the virtual site communication */
+ vsite = init_vsite(mtop,cr);
+
+ calc_shifts(box,fr->shift_vec);
+
+ /* With periodic molecules the charge groups should be whole at start up
+ * and the virtual sites should not be far from their proper positions.
+ */
+ if (!inputrec->bContinuation && MASTER(cr) &&
+ !(inputrec->ePBC != epbcNONE && inputrec->bPeriodicMols))
+ {
+ /* Make molecules whole at start of run */
+ if (fr->ePBC != epbcNONE)
+ {
+ do_pbc_first_mtop(fplog,inputrec->ePBC,box,mtop,state->x);
+ }
+ if (vsite)
+ {
+ /* Correct initial vsite positions are required
+ * for the initial distribution in the domain decomposition
+ * and for the initial shell prediction.
+ */
+ construct_vsites_mtop(fplog,vsite,mtop,state->x);
+ }
+ }
+
+ /* Initiate PPPM if necessary */
+ if (fr->eeltype == eelPPPM)
+ {
+ if (mdatoms->nChargePerturbed)
+ {
+ gmx_fatal(FARGS,"Free energy with %s is not implemented",
+ eel_names[fr->eeltype]);
+ }
+ status = gmx_pppm_init(fplog,cr,oenv,FALSE,TRUE,box,
+ getenv("GMXGHAT"),inputrec, (Flags & MD_REPRODUCIBLE));
+ if (status != 0)
+ {
+ gmx_fatal(FARGS,"Error %d initializing PPPM",status);
+ }
+ }
+
+ if (EEL_PME(fr->eeltype))
+ {
+ ewaldcoeff = fr->ewaldcoeff;
+ pmedata = &fr->pmedata;
+ }
+ else
+ {
+ pmedata = NULL;
+ }
+ }
+ else
+ {
+ /* This is a PME only node */
+
+ /* We don't need the state */
+ done_state(state);
+
+ ewaldcoeff = calc_ewaldcoeff(inputrec->rcoulomb, inputrec->ewald_rtol);
+ snew(pmedata,1);
+ }
+
+ /* Initiate PME if necessary,
+ * either on all nodes or on dedicated PME nodes only. */
+ if (EEL_PME(inputrec->coulombtype))
+ {
+ if (mdatoms)
+ {
+ nChargePerturbed = mdatoms->nChargePerturbed;
+ }
+ if (cr->npmenodes > 0)
+ {
+ /* The PME only nodes need to know nChargePerturbed */
+ gmx_bcast_sim(sizeof(nChargePerturbed),&nChargePerturbed,cr);
+ }
+ if (cr->duty & DUTY_PME)
+ {
+ status = gmx_pme_init(pmedata,cr,npme_major,npme_minor,inputrec,
+ mtop ? mtop->natoms : 0,nChargePerturbed,
+ (Flags & MD_REPRODUCIBLE));
+ if (status != 0)
+ {
+ gmx_fatal(FARGS,"Error %d initializing PME",status);
+ }
+ }
+ }
+
+
+ if (integrator[inputrec->eI].func == do_md
+#ifdef GMX_OPENMM
+ ||
+ integrator[inputrec->eI].func == do_md_openmm
+#endif
+ )
+ {
+ /* Turn on signal handling on all nodes */
+ /*
+ * (A user signal from the PME nodes (if any)
+ * is communicated to the PP nodes.
+ */
+ signal_handler_install();
+ }
+
+ if (cr->duty & DUTY_PP)
+ {
+ if (inputrec->ePull != epullNO)
+ {
+ /* Initialize pull code */
+ init_pull(fplog,inputrec,nfile,fnm,mtop,cr,oenv,
+ EI_DYNAMICS(inputrec->eI) && MASTER(cr),Flags);
+ }
+
+ if (inputrec->bRot)
+ {
+ /* Initialize enforced rotation code */
+ init_rot(fplog,inputrec,nfile,fnm,cr,state->x,state->box,mtop,oenv,
+ bVerbose,Flags);
+ }
+
+ constr = init_constraints(fplog,mtop,inputrec,ed,state,cr);
+
+ if (DOMAINDECOMP(cr))
+ {
+ dd_init_bondeds(fplog,cr->dd,mtop,vsite,constr,inputrec,
+ Flags & MD_DDBONDCHECK,fr->cginfo_mb);
+
+ set_dd_parameters(fplog,cr->dd,dlb_scale,inputrec,fr,&ddbox);
+
+ setup_dd_grid(fplog,cr->dd);
+ }
+
+ /* Now do whatever the user wants us to do (how flexible...) */
+ integrator[inputrec->eI].func(fplog,cr,nfile,fnm,
+ oenv,bVerbose,bCompact,
+ nstglobalcomm,
+ vsite,constr,
+ nstepout,inputrec,mtop,
+ fcd,state,
+ mdatoms,nrnb,wcycle,ed,fr,
+ repl_ex_nst,repl_ex_seed,
+ membed,
+ cpt_period,max_hours,
+ deviceOptions,
+ Flags,
+ &runtime);
+
+ if (inputrec->ePull != epullNO)
+ {
+ finish_pull(fplog,inputrec->pull);
+ }
+
+ if (inputrec->bRot)
+ {
+ finish_rot(fplog,inputrec->rot);
+ }
+
+ }
+ else
+ {
+ /* do PME only */
+ gmx_pmeonly(*pmedata,cr,nrnb,wcycle,ewaldcoeff,FALSE,inputrec);
+ }
+
+ if (EI_DYNAMICS(inputrec->eI) || EI_TPI(inputrec->eI))
+ {
+ /* Some timing stats */
+ if (SIMMASTER(cr))
+ {
+ if (runtime.proc == 0)
+ {
+ runtime.proc = runtime.real;
+ }
+ }
+ else
+ {
+ runtime.real = 0;
+ }
+ }
+
+ wallcycle_stop(wcycle,ewcRUN);
+
+ /* Finish up, write some stuff
+ * if rerunMD, don't write last frame again
+ */
+ finish_run(fplog,cr,ftp2fn(efSTO,nfile,fnm),
+ inputrec,nrnb,wcycle,&runtime,
+ EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
+
+ if (opt2bSet("-membed",nfile,fnm))
+ {
+ sfree(membed);
+ }
+
+ /* Does what it says */
+ print_date_and_time(fplog,cr->nodeid,"Finished mdrun",&runtime);
+
+ /* Close logfile already here if we were appending to it */
+ if (MASTER(cr) && (Flags & MD_APPENDFILES))
+ {
+ gmx_log_close(fplog);
+ }
+
+ rc=(int)gmx_get_stop_condition();
+
+#ifdef GMX_THREADS
+ /* we need to join all threads. The sub-threads join when they
+ exit this function, but the master thread needs to be told to
+ wait for that. */
+ if (PAR(cr) && MASTER(cr))
+ {
+ tMPI_Finalize();
+ }
+#endif
+
+ return rc;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff