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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15019 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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commit
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Peter Wirnsberger (University of Cambridge)
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This source file implements the asymmetric version of the enhanced heat
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exchange (eHEX/a) algorithm. The paper is available for download on
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arXiv: http://arxiv.org/pdf/1507.07081.pdf.
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This file is based on fix_heat.cpp written by Paul Crozier (SNL)
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which implements the heat exchange (HEX) algorithm.
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------------------------------------------------------------------------- */
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#include <math.h>
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#include <stdlib.h>
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#include <string.h>
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#include "fix_ehex.h"
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#include "atom.h"
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#include "domain.h"
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#include "region.h"
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#include "group.h"
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#include "force.h"
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#include "update.h"
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#include "modify.h"
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#include "input.h"
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#include "variable.h"
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#include "memory.h"
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#include "error.h"
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#include "fix_shake.h"
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#include "neighbor.h"
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#include "comm.h"
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#include "timer.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{CONSTANT,EQUAL,ATOM};
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/* ---------------------------------------------------------------------- */
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FixEHEX::FixEHEX(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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{
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MPI_Comm_rank(world, &me);
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// check
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if (narg < 4) error->all(FLERR,"Illegal fix ehex command: wrong number of parameters ");
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scalar_flag = 1;
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global_freq = 1;
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extscalar = 0;
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// apply fix every nevery timesteps
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nevery = force->inumeric(FLERR,arg[3]);
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if (nevery <= 0) error->all(FLERR,"Illegal fix ehex command");
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// heat flux into the reservoir
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heat_input = force->numeric(FLERR,arg[4]);
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// optional args
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iregion = -1;
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idregion = NULL;
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// NOTE: constraints are deactivated by default
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constraints = 0;
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// NOTE: cluster rescaling is deactivated by default
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cluster = 0;
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// NOTE: hex = 1 means that no coordinate correction is applied in which case eHEX reduces to HEX
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hex = 0;
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int iarg = 5;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"region") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix ehex command: wrong number of parameters ");
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iregion = domain->find_region(arg[iarg+1]);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix ehex does not exist");
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int n = strlen(arg[iarg+1]) + 1;
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idregion = new char[n];
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strcpy(idregion,arg[iarg+1]);
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iarg += 2;
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}
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// apply constraints (shake/rattle) at the end of the timestep
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else if (strcmp(arg[iarg], "constrain") == 0) {
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constraints = 1;
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iarg += 1;
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}
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// rescale only if the entire molecule is contained within the region
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else if (strcmp(arg[iarg], "com") == 0) {
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cluster = 1;
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iarg += 1;
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}
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// don't apply a coordinate correction if this keyword is specified
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else if (strcmp(arg[iarg], "hex") == 0) {
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hex = 1;
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iarg+= 1;
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}
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else
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error->all(FLERR, "Illegal fix ehex keyword ");
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}
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// check options
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if (cluster && !constraints)
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error->all(FLERR, "You can only use the keyword 'com' together with the keyword 'constrain' ");
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scale = 1.0;
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scalingmask = NULL;
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grow_arrays(atom->nmax);
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atom->add_callback(0);
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}
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/* ---------------------------------------------------------------------- */
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void FixEHEX::grow_arrays(int nmax) {
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memory->grow(scalingmask, nmax,"ehex:scalingmask");
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}
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/* ---------------------------------------------------------------------- */
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FixEHEX::~FixEHEX()
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{
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atom->delete_callback(id,0);
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delete [] idregion;
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memory->destroy(scalingmask);
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}
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/* ---------------------------------------------------------------------- */
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int FixEHEX::setmask()
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{
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int mask = 0;
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mask |= END_OF_STEP;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixEHEX::init()
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{
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// set index and check validity of region
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if (iregion >= 0) {
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix ehex does not exist");
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}
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// cannot have 0 atoms in group
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if (group->count(igroup) == 0)
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error->all(FLERR,"Fix ehex group has no atoms");
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fshake = NULL;
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if (constraints) {
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// check if constraining algorithm is used (FixRattle inherits from FixShake)
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int cnt_shake = 0;
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int id_shake;
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for (int i = 0; i < modify->nfix; i++) {
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if (strcmp("rattle", modify->fix[i]->style) == 0 ||
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strcmp("shake", modify->fix[i]->style) == 0) {
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cnt_shake++;
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id_shake = i;
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}
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}
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if (cnt_shake > 1)
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error->all(FLERR,"Multiple instances of fix shake/rattle detected (not supported yet)");
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else if (cnt_shake == 1) {
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fshake = ((FixShake*) modify->fix[id_shake]);
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}
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else if (cnt_shake == 0)
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error->all(FLERR, "Fix ehex was configured with keyword constrain, but shake/rattle was not defined");
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixEHEX::end_of_step() {
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// store local pointers
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x = atom->x;
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f = atom->f;
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v = atom->v;
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mass = atom->mass;
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rmass = atom->rmass;
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type = atom->type;
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nlocal = atom->nlocal;
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// determine which sites are to be rescaled
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update_scalingmask();
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// rescale velocities
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rescale();
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// if required use shake/rattle to correct coordinates and velocities
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if (constraints && fshake)
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fshake->shake_end_of_step(0);
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}
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/* ----------------------------------------------------------------------
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Iterate over all atoms, rescale the velocities and apply coordinate
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corrections.
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------------------------------------------------------------------------- */
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void FixEHEX::rescale() {
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double heat,ke,massone;
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double Kr, Ke, escale;
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double vsub[3],vcm[3], sfr[3];
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double dvcmdt[3];
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double mi;
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double dt;
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double F, mr, Fo2Kr, epsr_ik, sfvr, eta_ik;
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dt = update->dt;
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// calculate centre of mass properties
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com_properties(vcm, sfr, &sfvr, &Ke, &Kr, &masstotal);
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// heat flux into the reservoir
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F = heat_input * force->ftm2v * nevery;
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// total mass
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mr = masstotal;
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Fo2Kr = F / (2.*Kr);
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// energy scaling factor
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escale = 1. + (F*dt)/Kr;
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// safety check for kinetic energy
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if (escale < 0.0) error->all(FLERR,"Fix ehex kinetic energy went negative");
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scale = sqrt(escale);
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vsub[0] = (scale-1.0) * vcm[0];
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vsub[1] = (scale-1.0) * vcm[1];
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vsub[2] = (scale-1.0) * vcm[2];
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for (int i = 0; i < nlocal; i++){
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if (scalingmask[i]) {
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mi = (rmass) ? rmass[i] : mass[type[i]];
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for (int k=0; k<3; k++) {
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// apply coordinate correction unless running in hex mode
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if (!hex) {
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// epsr_ik implements Eq. (20) in the paper
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eta_ik = mi * F/(2.*Kr) * (v[i][k] - vcm[k]);
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epsr_ik = eta_ik / (mi*Kr) * (F/48. + sfvr/6.*force->ftm2v) - F/(12.*Kr) * (f[i][k]/mi - sfr[k]/mr)*force->ftm2v;
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x[i][k] -= dt*dt*dt * epsr_ik;
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}
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// rescale the velocity
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v[i][k] = scale*v[i][k] - vsub[k];
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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double FixEHEX::compute_scalar()
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{
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return scale;
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based arrays
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------------------------------------------------------------------------- */
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double FixEHEX::memory_usage()
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{
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double bytes = 0.0;
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bytes += atom->nmax * sizeof(double);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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Update the array scalingmask depending on which individual atoms
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will be rescaled or not.
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------------------------------------------------------------------------- */
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void FixEHEX::update_scalingmask() {
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int m;
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int lid;
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bool stat;
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int nsites;
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// prematch region
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Region *region = NULL;
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if (iregion >= 0) {
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region = domain->regions[iregion];
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region->prematch();
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}
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// only rescale molecules whose center of mass if fully contained in the region
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if (cluster) {
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// loop over all clusters
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for (int i=0; i < fshake->nlist; i++) {
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// cluster id
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m = fshake->list[i];
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// check if the centre of mass of the cluster is inside the region
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// if region == NULL, just check the group information of all sites
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if (fshake->shake_flag[m] == 1) nsites = 3;
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else if (fshake->shake_flag[m] == 2) nsites = 2;
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else if (fshake->shake_flag[m] == 3) nsites = 3;
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else if (fshake->shake_flag[m] == 4) nsites = 4;
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else nsites = 0;
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if (nsites == 0) {
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error->all(FLERR,"Internal error: shake_flag[m] has to be between 1 and 4 for m in nlist");
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}
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stat = check_cluster(fshake->shake_atom[m], nsites, region);
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for (int l=0; l < nsites; l++) {
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lid = atom->map(fshake->shake_atom[m][l]);
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scalingmask[lid] = stat;
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}
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}
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// check atoms that do not belong to any cluster
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for (int i=0; i<atom->nlocal; i++) {
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if (fshake->shake_flag[i] == 0)
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scalingmask[i] = rescale_atom(i,region);
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}
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}
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// no clusters, just individual sites (e.g. monatomic system or flexible molecules)
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else {
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for (int i=0; i<atom->nlocal; i++)
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scalingmask[i] = rescale_atom(i,region);
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}
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}
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/* ----------------------------------------------------------------------
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Check if the centre of mass of the cluster to be constrained is
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inside the region.
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------------------------------------------------------------------------- */
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bool FixEHEX::check_cluster(int *shake_atom, int n, Region * region) {
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// IMPORTANT NOTE: If any site of the cluster belongs to a group
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// which should not be rescaled than all of the sites
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// will be ignored!
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double **x = atom->x;
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double * rmass = atom->rmass;
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double * mass = atom->mass;
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int * type = atom->type;
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int * mask = atom->mask;
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double xcom[3], xtemp[3];
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double mcluster, mi;
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bool stat;
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int lid[4];
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// accumulate mass and centre of mass position
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stat = true;
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xcom[0] = 0.;
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xcom[1] = 0.;
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xcom[2] = 0.;
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mcluster = 0;
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for (int i = 0; i < n; i++) {
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// get local id
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lid[i] = atom->map(shake_atom[i]);
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// check if all sites of the cluster belong to the correct group
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stat = stat && (mask[lid[i]] & groupbit);
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if (region && stat) {
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// check if reduced mass is used
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mi = (rmass) ? rmass[lid[i]] : mass[type[lid[i]]];
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mcluster += mi;
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// accumulate centre of mass
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// NOTE: you can either use unwrapped coordinates or take site x[lid[0]] as reference,
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// i.e. reconstruct the molecule around this site and calculate the com.
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for (int k=0; k<3; k++)
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xtemp[k] = x[lid[i]][k] - x[lid[0]][k];
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// take into account pbc
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domain->minimum_image(xtemp);
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for (int k=0; k<3; k++)
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xcom[k] += mi * (x[lid[0]][k] + xtemp[k]) ;
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}
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}
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// check if centre of mass is inside the region (if specified)
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if (region && stat) {
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// check mass
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if (mcluster < 1.e-14) {
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error->all(FLERR, "Fix ehex shake cluster has almost zero mass.");
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}
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// divide by total mass
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for (int k=0; k<3; k++)
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xcom[k] = xcom[k]/mcluster;
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// apply periodic boundary conditions (centre of mass could be outside the box)
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// and check if molecule is inside the region
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domain->remap(xcom);
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stat = stat && region->match(xcom[0], xcom[1], xcom[2]);
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}
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return stat;
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}
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/* ----------------------------------------------------------------------
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Check if atom i has the correct group and is inside the region.
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------------------------------------------------------------------------- */
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bool FixEHEX::rescale_atom(int i, Region*region) {
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bool stat;
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double x_r[3];
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// check mask and group
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stat = (atom->mask[i] & groupbit);
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if (region) {
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x_r[0] = atom->x[i][0];
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x_r[1] = atom->x[i][1];
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x_r[2] = atom->x[i][2];
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// apply periodic boundary conditions
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domain->remap(x_r);
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// check if the atom is in the group/region
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stat = stat && region->match(x_r[0],x_r[1],x_r[2]);
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}
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return stat;
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}
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/* ----------------------------------------------------------------------
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Calculate global properties of the atoms inside the reservoir.
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(e.g. com velocity, kinetic energy, total mass,...)
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------------------------------------------------------------------------- */
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void FixEHEX::com_properties(double * vr, double * sfr, double *sfvr, double *K, double *Kr, double *mr) {
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double ** f = atom->f;
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double ** v = atom->v;
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int nlocal = atom->nlocal;
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double *rmass= atom->rmass;
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double *mass = atom->mass;
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int *type = atom->type;
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double l_vr[3];
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double l_mr;
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double l_sfr[3];
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double l_sfvr;
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double l_K;
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double mi;
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double l_buf[9];
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double buf[9];
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// calculate partial sums
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|
||||
l_vr[0] = l_vr[1] = l_vr[2] = 0;
|
||||
l_sfr[0] = l_sfr[1] = l_sfr[2] = 0;
|
||||
l_sfvr = 0;
|
||||
l_mr = 0;
|
||||
l_K = 0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (scalingmask[i]) {
|
||||
|
||||
// check if reduced mass is used
|
||||
|
||||
mi = (rmass) ? rmass[i] : mass[type[i]];
|
||||
|
||||
// accumulate total mass
|
||||
|
||||
l_mr += mi;
|
||||
|
||||
// accumulate kinetic energy
|
||||
|
||||
l_K += mi/2. * (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
|
||||
|
||||
// sum_j f_j * v_j
|
||||
|
||||
l_sfvr += f[i][0]*v[i][0] + f[i][1]*v[i][1] + f[i][2]*v[i][2];
|
||||
|
||||
// accumulate com velocity and sum of forces
|
||||
|
||||
for (int k=0; k<3; k++) {
|
||||
l_vr[k] += mi * v[i][k];
|
||||
l_sfr[k]+= f[i][k];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// reduce sums
|
||||
|
||||
l_buf[0] = l_vr[0];
|
||||
l_buf[1] = l_vr[1];
|
||||
l_buf[2] = l_vr[2];
|
||||
l_buf[3] = l_K;
|
||||
l_buf[4] = l_mr;
|
||||
l_buf[5] = l_sfr[0];
|
||||
l_buf[6] = l_sfr[1];
|
||||
l_buf[7] = l_sfr[2];
|
||||
l_buf[8] = l_sfvr;
|
||||
|
||||
MPI_Allreduce(l_buf, buf, 9, MPI_DOUBLE, MPI_SUM, world);
|
||||
|
||||
// total mass of region
|
||||
|
||||
*mr = buf[4];
|
||||
|
||||
if (*mr < 1.e-14) {
|
||||
error->all(FLERR, "Fix ehex error mass of region is close to zero");
|
||||
}
|
||||
|
||||
// total kinetic energy of region
|
||||
|
||||
*K = buf[3];
|
||||
|
||||
// centre of mass velocity of region
|
||||
|
||||
vr[0] = buf[0]/(*mr);
|
||||
vr[1] = buf[1]/(*mr);
|
||||
vr[2] = buf[2]/(*mr);
|
||||
|
||||
// sum of forces
|
||||
|
||||
sfr[0] = buf[5];
|
||||
sfr[1] = buf[6];
|
||||
sfr[2] = buf[7];
|
||||
|
||||
// calculate non-translational kinetic energy
|
||||
|
||||
*Kr = *K - 0.5* (*mr) * (vr[0]*vr[0]+vr[1]*vr[1]+vr[2]*vr[2]);
|
||||
|
||||
// calculate sum_j f_j * (v_j - v_r) = sum_j f_j * v_j - v_r * sum_j f_j
|
||||
|
||||
*sfvr = buf[8] - (vr[0]*sfr[0] + vr[1]*sfr[1] + vr[2]*sfr[2]);
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,130 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(ehex,FixEHEX)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_EHEX_H
|
||||
#define LMP_FIX_EHEX_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "fix_shake.h"
|
||||
#include "region.h"
|
||||
#define EHEX_DEBUG 0
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixEHEX : public Fix {
|
||||
|
||||
public:
|
||||
FixEHEX(class LAMMPS *, int, char **);
|
||||
~FixEHEX();
|
||||
int setmask();
|
||||
void init();
|
||||
void end_of_step();
|
||||
void rescale();
|
||||
double compute_scalar();
|
||||
double memory_usage();
|
||||
void update_scalingmask();
|
||||
void com_properties(double *, double *, double *, double*, double *, double*);
|
||||
bool rescale_atom(int i, Region*region);
|
||||
virtual void grow_arrays(int nmax);
|
||||
bool check_cluster(int *shake_atom, int n, Region * region);
|
||||
|
||||
private:
|
||||
int iregion;
|
||||
double heat_input;
|
||||
double masstotal;
|
||||
double scale;
|
||||
char *idregion;
|
||||
int me;
|
||||
|
||||
double ** x; // coordinates
|
||||
double ** f; // forces
|
||||
double ** v; // velocities
|
||||
double * mass; // masses
|
||||
double * rmass; // reduced masses
|
||||
int * type; // atom types
|
||||
int nlocal; // number of local atoms
|
||||
FixShake * fshake; // pointer to fix_shake/fix_rattle
|
||||
int constraints; // constraints (0/1)
|
||||
int cluster; // rescaling entire clusters (0/1)
|
||||
int hex; // HEX mode (0/1)
|
||||
bool * scalingmask; // scalingmask[i] determines whether
|
||||
// the velocity of atom i is to be rescaled
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal fix ehex command: wrong number of parameters
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Illegal fix ehex command: integer value expected
|
||||
|
||||
Self-explanatory. Check the value for nevery.
|
||||
|
||||
E: Region ID for fix ehex does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: You can only use the keyword 'com' together with the keyword 'constrain' .
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Illegal fix ehex keyword
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix ehex group has no atoms
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Multiple instances of fix shake/rattle detected (not supported yet)
|
||||
|
||||
You can only have one instance of fix rattle/shake at the moment.
|
||||
|
||||
E: Fix ehex was configured with keyword constrain, but shake/rattle was not defined
|
||||
|
||||
The option constrain requires either fix shake or fix rattle which is missing in the input script.
|
||||
|
||||
E: Fix heat kinetic energy went negative
|
||||
|
||||
This will cause the velocity rescaling about to be performed by fix
|
||||
heat to be invalid.
|
||||
|
||||
E: Fix heat kinetic energy of an atom went negative
|
||||
|
||||
This will cause the velocity rescaling about to be performed by fix
|
||||
heat to be invalid.
|
||||
|
||||
E: Internal error: shake_flag[m] has to be between 1 and 4 for m in nlist
|
||||
|
||||
Contact developers.
|
||||
|
||||
E: Fix ehex error mass of region is close to zero
|
||||
|
||||
Check your configuration.
|
||||
|
||||
*/
|
||||
|
|
@ -44,13 +44,22 @@ using namespace FixConst;
|
|||
using namespace MathConst;
|
||||
using namespace MathExtra;
|
||||
|
||||
// set RATTLE_DEBUG = 1 to check constraints at end of timestep
|
||||
// set RATTLE_DEBUG 1 to check constraints at end of timestep
|
||||
|
||||
#define RATTLE_DEBUG 0
|
||||
#define RATTLE_TEST_VEL true
|
||||
#define RATTLE_TEST_POS true
|
||||
|
||||
enum{V,VP,XSHAKE,X};
|
||||
// set RATTLE_RAISE_ERROR 1 if you want this fix to raise
|
||||
// an error if the constraints cannot be satisfied
|
||||
|
||||
#define RATTLE_RAISE_ERROR 0
|
||||
|
||||
// You can enable velocity and coordinate checks separately
|
||||
// by setting RATTLE_TEST_VEL/POS true
|
||||
|
||||
#define RATTLE_TEST_VEL false
|
||||
#define RATTLE_TEST_POS false
|
||||
|
||||
enum{V,VP,XSHAKE};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
|
@ -59,10 +68,6 @@ FixRattle::FixRattle(LAMMPS *lmp, int narg, char **arg) :
|
|||
{
|
||||
rattle = 1;
|
||||
|
||||
// define timestep for velocity integration
|
||||
|
||||
dtfv = 0.5 * update->dt * force->ftm2v;
|
||||
|
||||
// allocate memory for unconstrained velocity update
|
||||
|
||||
vp = NULL;
|
||||
|
|
@ -74,6 +79,9 @@ FixRattle::FixRattle(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
comm_mode = XSHAKE;
|
||||
vflag_post_force = 0;
|
||||
|
||||
verr_max = 0;
|
||||
derr_max = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -81,6 +89,25 @@ FixRattle::FixRattle(LAMMPS *lmp, int narg, char **arg) :
|
|||
FixRattle::~FixRattle()
|
||||
{
|
||||
memory->destroy(vp);
|
||||
|
||||
|
||||
if (RATTLE_DEBUG) {
|
||||
|
||||
// communicate maximum distance error
|
||||
|
||||
double global_derr_max, global_verr_max;
|
||||
int npid;
|
||||
|
||||
MPI_Reduce(&derr_max, &global_derr_max, 1 , MPI_DOUBLE, MPI_MAX, 0, world);
|
||||
MPI_Reduce(&verr_max, &global_verr_max, 1 , MPI_DOUBLE, MPI_MAX, 0, world);
|
||||
|
||||
MPI_Comm_rank (world, &npid); // Find out process rank
|
||||
|
||||
if (npid == 0 && screen) {
|
||||
fprintf(screen, "RATTLE: Maximum overall relative position error ( (r_ij-d_ij)/d_ij ): %.10g\n", global_derr_max);
|
||||
fprintf(screen, "RATTLE: Maximum overall absolute velocity error (r_ij * v_ij): %.10g\n", global_verr_max);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
@ -118,7 +145,7 @@ void FixRattle::init() {
|
|||
|
||||
if (flag && comm->me == 0)
|
||||
error->warning(FLERR,
|
||||
"Fix rattle should come after all other integration fixes");
|
||||
"Fix rattle should come after all other integration fixes ");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -213,30 +240,36 @@ void FixRattle::final_integrate_respa(int ilevel, int iloop)
|
|||
void FixRattle::vrattle3angle(int m)
|
||||
{
|
||||
tagint i0,i1,i2;
|
||||
int nlist,list[3];
|
||||
double c[3], l[3], a[3][3], r01[3], imass[3],
|
||||
r02[3], r12[3], vp01[3], vp02[3], vp12[3];
|
||||
|
||||
// local atom IDs and constraint distances
|
||||
|
||||
i0 = atom->map(shake_atom[m][0]);
|
||||
i1 = atom->map(shake_atom[m][1]);
|
||||
i2 = atom->map(shake_atom[m][2]);
|
||||
|
||||
// r01,r02,r12 = distance vec between atoms
|
||||
|
||||
MathExtra::sub3(x[i1],x[i0],r01);
|
||||
MathExtra::sub3(x[i2],x[i0],r02);
|
||||
MathExtra::sub3(x[i2],x[i1],r12);
|
||||
|
||||
// take into account periodicity
|
||||
|
||||
domain->minimum_image(r01);
|
||||
domain->minimum_image(r02);
|
||||
domain->minimum_image(r12);
|
||||
|
||||
// v01,v02,v12 = velocity differences
|
||||
|
||||
MathExtra::sub3(vp[i1],vp[i0],vp01);
|
||||
MathExtra::sub3(vp[i2],vp[i0],vp02);
|
||||
MathExtra::sub3(vp[i2],vp[i1],vp12);
|
||||
|
||||
// matrix coeffs and rhs for lamda equations
|
||||
|
||||
if (rmass) {
|
||||
imass[0] = 1.0/rmass[i0];
|
||||
imass[1] = 1.0/rmass[i1];
|
||||
|
|
@ -248,6 +281,7 @@ void FixRattle::vrattle3angle(int m)
|
|||
}
|
||||
|
||||
// setup matrix
|
||||
|
||||
a[0][0] = (imass[1] + imass[0]) * MathExtra::dot3(r01,r01);
|
||||
a[0][1] = (imass[0] ) * MathExtra::dot3(r01,r02);
|
||||
a[0][2] = (-imass[1] ) * MathExtra::dot3(r01,r12);
|
||||
|
|
@ -259,14 +293,17 @@ void FixRattle::vrattle3angle(int m)
|
|||
a[2][2] = (imass[2] + imass[1]) * MathExtra::dot3(r12,r12);
|
||||
|
||||
// sestup RHS
|
||||
|
||||
c[0] = -MathExtra::dot3(vp01,r01);
|
||||
c[1] = -MathExtra::dot3(vp02,r02);
|
||||
c[2] = -MathExtra::dot3(vp12,r12);
|
||||
|
||||
// calculate the inverse matrix exactly
|
||||
|
||||
solve3x3exactly(a,c,l);
|
||||
|
||||
// add corrections to the velocities if processor owns atom
|
||||
|
||||
if (i0 < nlocal) {
|
||||
for (int k=0; k<3; k++)
|
||||
v[i0][k] -= imass[0]* ( l[0] * r01[k] + l[1] * r02[k] );
|
||||
|
|
@ -286,20 +323,25 @@ void FixRattle::vrattle3angle(int m)
|
|||
void FixRattle::vrattle2(int m)
|
||||
{
|
||||
tagint i0, i1;
|
||||
int nlist,list[2];
|
||||
double imass[2], r01[3], vp01[3];
|
||||
|
||||
// local atom IDs and constraint distances
|
||||
|
||||
i0 = atom->map(shake_atom[m][0]);
|
||||
i1 = atom->map(shake_atom[m][1]);
|
||||
|
||||
// r01 = distance vec between atoms, with PBC
|
||||
|
||||
MathExtra::sub3(x[i1],x[i0],r01);
|
||||
domain->minimum_image(r01);
|
||||
|
||||
// v01 = distance vectors for velocities
|
||||
|
||||
MathExtra::sub3(vp[i1],vp[i0],vp01);
|
||||
|
||||
// matrix coeffs and rhs for lamda equations
|
||||
|
||||
if (rmass) {
|
||||
imass[0] = 1.0/rmass[i0];
|
||||
imass[1] = 1.0/rmass[i1];
|
||||
|
|
@ -309,10 +351,12 @@ void FixRattle::vrattle2(int m)
|
|||
}
|
||||
|
||||
// Lagrange multiplier: exact solution
|
||||
|
||||
double l01 = - MathExtra::dot3(r01,vp01) /
|
||||
(MathExtra::dot3(r01,r01) * (imass[0] + imass[1]));
|
||||
|
||||
// add corrections to the velocities if the process owns this atom
|
||||
|
||||
if (i0 < nlocal) {
|
||||
for (int k=0; k<3; k++)
|
||||
v[i0][k] -= imass[0] * l01 * r01[k];
|
||||
|
|
@ -328,15 +372,18 @@ void FixRattle::vrattle2(int m)
|
|||
void FixRattle::vrattle3(int m)
|
||||
{
|
||||
tagint i0,i1,i2;
|
||||
int nlist,list[3];
|
||||
double imass[3], r01[3], r02[3], vp01[3], vp02[3],
|
||||
a[2][2],c[2],l[2];
|
||||
|
||||
// local atom IDs and constraint distances
|
||||
|
||||
i0 = atom->map(shake_atom[m][0]);
|
||||
i1 = atom->map(shake_atom[m][1]);
|
||||
i2 = atom->map(shake_atom[m][2]);
|
||||
|
||||
// r01,r02 = distance vec between atoms, with PBC
|
||||
|
||||
MathExtra::sub3(x[i1],x[i0],r01);
|
||||
MathExtra::sub3(x[i2],x[i0],r02);
|
||||
|
||||
|
|
@ -344,6 +391,7 @@ void FixRattle::vrattle3(int m)
|
|||
domain->minimum_image(r02);
|
||||
|
||||
// vp01,vp02 = distance vectors between velocities
|
||||
|
||||
MathExtra::sub3(vp[i1],vp[i0],vp01);
|
||||
MathExtra::sub3(vp[i2],vp[i0],vp02);
|
||||
|
||||
|
|
@ -358,19 +406,23 @@ void FixRattle::vrattle3(int m)
|
|||
}
|
||||
|
||||
// setup matrix
|
||||
|
||||
a[0][0] = (imass[1] + imass[0]) * MathExtra::dot3(r01,r01);
|
||||
a[0][1] = (imass[0] ) * MathExtra::dot3(r01,r02);
|
||||
a[1][0] = a[0][1];
|
||||
a[1][1] = (imass[0] + imass[2]) * MathExtra::dot3(r02,r02);
|
||||
|
||||
// setup RHS
|
||||
|
||||
c[0] = - MathExtra::dot3(vp01,r01);
|
||||
c[1] = - MathExtra::dot3(vp02,r02);
|
||||
|
||||
// calculate the inverse 2x2 matrix exactly
|
||||
|
||||
solve2x2exactly(a,c,l);
|
||||
|
||||
// add corrections to the velocities if the process owns this atom
|
||||
|
||||
if (i0 < nlocal) {
|
||||
for (int k=0; k<3; k++)
|
||||
v[i0][k] -= imass[0] * ( l[0] * r01[k] + l[1] * r02[k] );
|
||||
|
|
@ -390,16 +442,19 @@ void FixRattle::vrattle3(int m)
|
|||
void FixRattle::vrattle4(int m)
|
||||
{
|
||||
tagint i0,i1,i2,i3;
|
||||
int nlist,list[4];
|
||||
double imass[4], c[3], l[3], a[3][3],
|
||||
r01[3], r02[3], r03[3], vp01[3], vp02[3], vp03[3];
|
||||
|
||||
// local atom IDs and constraint distances
|
||||
|
||||
i0 = atom->map(shake_atom[m][0]);
|
||||
i1 = atom->map(shake_atom[m][1]);
|
||||
i2 = atom->map(shake_atom[m][2]);
|
||||
i3 = atom->map(shake_atom[m][3]);
|
||||
|
||||
// r01,r02,r12 = distance vec between atoms, with PBC
|
||||
|
||||
MathExtra::sub3(x[i1],x[i0],r01);
|
||||
MathExtra::sub3(x[i2],x[i0],r02);
|
||||
MathExtra::sub3(x[i3],x[i0],r03);
|
||||
|
|
@ -409,11 +464,13 @@ void FixRattle::vrattle4(int m)
|
|||
domain->minimum_image(r03);
|
||||
|
||||
// vp01,vp02,vp03 = distance vectors between velocities
|
||||
|
||||
MathExtra::sub3(vp[i1],vp[i0],vp01);
|
||||
MathExtra::sub3(vp[i2],vp[i0],vp02);
|
||||
MathExtra::sub3(vp[i3],vp[i0],vp03);
|
||||
|
||||
// matrix coeffs and rhs for lamda equations
|
||||
|
||||
if (rmass) {
|
||||
imass[0] = 1.0/rmass[i0];
|
||||
imass[1] = 1.0/rmass[i1];
|
||||
|
|
@ -427,6 +484,7 @@ void FixRattle::vrattle4(int m)
|
|||
}
|
||||
|
||||
// setup matrix
|
||||
|
||||
a[0][0] = (imass[0] + imass[1]) * MathExtra::dot3(r01,r01);
|
||||
a[0][1] = (imass[0] ) * MathExtra::dot3(r01,r02);
|
||||
a[0][2] = (imass[0] ) * MathExtra::dot3(r01,r03);
|
||||
|
|
@ -438,14 +496,17 @@ void FixRattle::vrattle4(int m)
|
|||
a[2][2] = (imass[0] + imass[3]) * MathExtra::dot3(r03,r03);
|
||||
|
||||
// setup RHS
|
||||
|
||||
c[0] = - MathExtra::dot3(vp01,r01);
|
||||
c[1] = - MathExtra::dot3(vp02,r02);
|
||||
c[2] = - MathExtra::dot3(vp03,r03);
|
||||
|
||||
// calculate the inverse 3x3 matrix exactly
|
||||
|
||||
solve3x3exactly(a,c,l);
|
||||
|
||||
// add corrections to the velocities if the process owns this atom
|
||||
|
||||
if (i0 < nlocal) {
|
||||
for (int k=0; k<3; k++)
|
||||
v[i0][k] -= imass[0] * ( l[0] * r01[k] + l[1] * r02[k] + l[2] * r03[k]);
|
||||
|
|
@ -472,13 +533,16 @@ void FixRattle::solve2x2exactly(const double a[][2],
|
|||
double determ, determinv;
|
||||
|
||||
// calculate the determinant of the matrix
|
||||
|
||||
determ = a[0][0] * a[1][1] - a[0][1] * a[1][0];
|
||||
|
||||
// check if matrix is actually invertible
|
||||
if (determ == 0.0) error->one(FLERR,"RATTLE determinant = 0.0");
|
||||
|
||||
if (determ == 0.0) error->one(FLERR,"Rattle determinant = 0.0");
|
||||
determinv = 1.0/determ;
|
||||
|
||||
// Calcualte the solution: (l01, l02)^T = A^(-1) * c
|
||||
// Calculate the solution: (l01, l02)^T = A^(-1) * c
|
||||
|
||||
l[0] = determinv * ( a[1][1] * c[0] - a[0][1] * c[1]);
|
||||
l[1] = determinv * (-a[1][0] * c[0] + a[0][0] * c[1]);
|
||||
}
|
||||
|
|
@ -492,14 +556,17 @@ void FixRattle::solve3x3exactly(const double a[][3],
|
|||
double determ, determinv;
|
||||
|
||||
// calculate the determinant of the matrix
|
||||
|
||||
determ = a[0][0]*a[1][1]*a[2][2] + a[0][1]*a[1][2]*a[2][0] +
|
||||
a[0][2]*a[1][0]*a[2][1] - a[0][0]*a[1][2]*a[2][1] -
|
||||
a[0][1]*a[1][0]*a[2][2] - a[0][2]*a[1][1]*a[2][0];
|
||||
|
||||
// check if matrix is actually invertible
|
||||
if (determ == 0.0) error->one(FLERR,"RATTLE determinant = 0.0");
|
||||
|
||||
if (determ == 0.0) error->one(FLERR,"Rattle determinant = 0.0");
|
||||
|
||||
// calculate the inverse 3x3 matrix: A^(-1) = (ai_jk)
|
||||
|
||||
determinv = 1.0/determ;
|
||||
ai[0][0] = determinv * (a[1][1]*a[2][2] - a[1][2]*a[2][1]);
|
||||
ai[0][1] = -determinv * (a[0][1]*a[2][2] - a[0][2]*a[2][1]);
|
||||
|
|
@ -512,6 +579,7 @@ void FixRattle::solve3x3exactly(const double a[][3],
|
|||
ai[2][2] = determinv * (a[0][0]*a[1][1] - a[0][1]*a[1][0]);
|
||||
|
||||
// calculate the solution: (l01, l02, l12)^T = A^(-1) * c
|
||||
|
||||
for (int i=0; i<3; i++) {
|
||||
l[i] = 0;
|
||||
for (int j=0; j<3; j++)
|
||||
|
|
@ -534,6 +602,8 @@ void FixRattle::reset_dt()
|
|||
void FixRattle::update_v_half_nocons()
|
||||
{
|
||||
double dtfvinvm;
|
||||
dtfv = 0.5 * update->dt * force->ftm2v;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (shake_flag[i]) {
|
||||
|
|
@ -563,9 +633,11 @@ void FixRattle::update_v_half_nocons()
|
|||
void FixRattle::update_v_half_nocons_respa(int ilevel)
|
||||
{
|
||||
// select timestep for current level
|
||||
|
||||
dtfv = 0.5 * step_respa[ilevel] * force->ftm2v;
|
||||
|
||||
// carry out unconstrained velocity update
|
||||
|
||||
update_v_half_nocons();
|
||||
}
|
||||
|
||||
|
|
@ -621,15 +693,6 @@ int FixRattle::pack_forward_comm(int n, int *list, double *buf,
|
|||
buf[m++] = v[j][2];
|
||||
}
|
||||
break;
|
||||
|
||||
case X:
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = x[j][0];
|
||||
buf[m++] = x[j][1];
|
||||
buf[m++] = x[j][2];
|
||||
}
|
||||
break;
|
||||
}
|
||||
return m;
|
||||
}
|
||||
|
|
@ -662,25 +725,74 @@ void FixRattle::unpack_forward_comm(int n, int first, double *buf)
|
|||
v[i][2] = buf[m++];
|
||||
}
|
||||
break;
|
||||
|
||||
case X:
|
||||
for (i = first; i < last; i++) {
|
||||
x[i][0] = buf[m++];
|
||||
x[i][1] = buf[m++];
|
||||
x[i][2] = buf[m++];
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
wrapper method for end_of_step fixes which modify the coordinates
|
||||
Let shake calculate new constraining forces for the coordinates;
|
||||
As opposed to the regular shake call, this method is usually called from
|
||||
end_of_step fixes after the second velocity integration has happened.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRattle::coordinate_constraints_end_of_step() {
|
||||
void FixRattle::shake_end_of_step(int vflag) {
|
||||
|
||||
if (nprocs > 1) {
|
||||
comm_mode = V;
|
||||
comm->forward_comm_fix(this);
|
||||
}
|
||||
|
||||
comm_mode = XSHAKE;
|
||||
FixShake::coordinate_constraints_end_of_step();
|
||||
FixShake::shake_end_of_step(vflag);
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Let shake calculate new constraining forces and correct the
|
||||
coordinates. Nothing to do for rattle here.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRattle::correct_coordinates(int vflag) {
|
||||
comm_mode = XSHAKE;
|
||||
FixShake::correct_coordinates(vflag);
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Remove the velocity component along any bond.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRattle::correct_velocities() {
|
||||
|
||||
// Copy current velocities instead of unconstrained_update, because the correction
|
||||
// should happen instantaneously and not after the next half step.
|
||||
|
||||
for (int i = 0; i < atom->nlocal; i++) {
|
||||
if (shake_flag[i]) {
|
||||
for (int k=0; k<3; k++)
|
||||
vp[i][k] = v[i][k];
|
||||
}
|
||||
else
|
||||
vp[i][0] = vp[i][1] = vp[i][2] = 0;
|
||||
}
|
||||
|
||||
// communicate the unconstrained velocities
|
||||
|
||||
if (nprocs > 1) {
|
||||
comm_mode = VP;
|
||||
comm->forward_comm_fix(this);
|
||||
}
|
||||
|
||||
// correct the velocity for each molecule accordingly
|
||||
|
||||
int m;
|
||||
for (int i = 0; i < nlist; i++) {
|
||||
m = list[i];
|
||||
if (shake_flag[m] == 2) vrattle2(m);
|
||||
else if (shake_flag[m] == 3) vrattle3(m);
|
||||
else if (shake_flag[m] == 4) vrattle4(m);
|
||||
else vrattle3angle(m);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -695,18 +807,16 @@ void FixRattle::coordinate_constraints_end_of_step() {
|
|||
|
||||
void FixRattle::end_of_step()
|
||||
{
|
||||
// communicate velocities and coordinates (x and v)
|
||||
if (nprocs > 1) {
|
||||
comm_mode = V;
|
||||
comm->forward_comm_fix(this);
|
||||
comm_mode = X;
|
||||
comm->forward_comm_fix(this);
|
||||
}
|
||||
if (!check_constraints(v, RATTLE_TEST_POS, RATTLE_TEST_VEL)) {
|
||||
error->one(FLERR, "RATTLE failed");
|
||||
if (!check_constraints(v, RATTLE_TEST_POS, RATTLE_TEST_VEL) && RATTLE_RAISE_ERROR) {
|
||||
error->one(FLERR, "Rattle failed ");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
bool FixRattle::check_constraints(double **v, bool checkr, bool checkv)
|
||||
|
|
@ -721,6 +831,7 @@ bool FixRattle::check_constraints(double **v, bool checkr, bool checkv)
|
|||
else if (shake_flag[m] == 4) ret = check4(v,m,checkr,checkv);
|
||||
else ret = check3angle(v,m,checkr,checkv);
|
||||
i++;
|
||||
if (!RATTLE_RAISE_ERROR) ret = true;
|
||||
}
|
||||
return ret;
|
||||
}
|
||||
|
|
@ -743,13 +854,13 @@ bool FixRattle::check2(double **v, int m, bool checkr, bool checkv)
|
|||
|
||||
stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol));
|
||||
if (!stat)
|
||||
error->one(FLERR,"RATTLE coordinate constraints are not satisfied "
|
||||
"up to desired tolerance");
|
||||
error->one(FLERR,"Coordinate constraints are not satisfied "
|
||||
"up to desired tolerance ");
|
||||
|
||||
stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol));
|
||||
if (!stat)
|
||||
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
|
||||
"up to desired tolerance");
|
||||
error->one(FLERR,"Velocity constraints are not satisfied "
|
||||
"up to desired tolerance ");
|
||||
return stat;
|
||||
}
|
||||
|
||||
|
|
@ -780,14 +891,14 @@ bool FixRattle::check3(double **v, int m, bool checkr, bool checkv)
|
|||
stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
|
||||
fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol));
|
||||
if (!stat)
|
||||
error->one(FLERR,"RATTLE coordinate constraints are not satisfied "
|
||||
"up to desired tolerance");
|
||||
error->one(FLERR,"Coordinate constraints are not satisfied "
|
||||
"up to desired tolerance ");
|
||||
|
||||
stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
|
||||
fabs(MathExtra::dot3(r02,v02)) > tol));
|
||||
if (!stat)
|
||||
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
|
||||
"up to desired tolerance");
|
||||
error->one(FLERR,"Velocity constraints are not satisfied "
|
||||
"up to desired tolerance ");
|
||||
return stat;
|
||||
}
|
||||
|
||||
|
|
@ -823,15 +934,15 @@ bool FixRattle::check4(double **v, int m, bool checkr, bool checkv)
|
|||
fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol ||
|
||||
fabs(sqrt(MathExtra::dot3(r03,r03))-bond3) > tol));
|
||||
if (!stat)
|
||||
error->one(FLERR,"RATTLE coordinate constraints are not satisfied "
|
||||
"up to desired tolerance");
|
||||
error->one(FLERR,"Coordinate constraints are not satisfied "
|
||||
"up to desired tolerance ");
|
||||
|
||||
stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
|
||||
fabs(MathExtra::dot3(r02,v02)) > tol ||
|
||||
fabs(MathExtra::dot3(r03,v03)) > tol));
|
||||
if (!stat)
|
||||
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
|
||||
"up to desired tolerance");
|
||||
error->one(FLERR,"Velocity constraints are not satisfied "
|
||||
"up to desired tolerance ");
|
||||
return stat;
|
||||
}
|
||||
|
||||
|
|
@ -862,18 +973,44 @@ bool FixRattle::check3angle(double **v, int m, bool checkr, bool checkv)
|
|||
MathExtra::sub3(v[i2],v[i0],v02);
|
||||
MathExtra::sub3(v[i2],v[i1],v12);
|
||||
|
||||
stat = !(checkr && (fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1) > tol ||
|
||||
fabs(sqrt(MathExtra::dot3(r02,r02))-bond2) > tol ||
|
||||
fabs(sqrt(MathExtra::dot3(r12,r12))-bond12) > tol));
|
||||
if (!stat)
|
||||
error->one(FLERR,"RATTLE coordinate constraints are not satisfied "
|
||||
"up to desired tolerance");
|
||||
|
||||
stat = !(checkv && (fabs(MathExtra::dot3(r01,v01)) > tol ||
|
||||
fabs(MathExtra::dot3(r02,v02)) > tol ||
|
||||
fabs(MathExtra::dot3(r12,v12)) > tol));
|
||||
if (!stat)
|
||||
error->one(FLERR,"RATTLE velocity constraints are not satisfied "
|
||||
"up to desired tolerance");
|
||||
|
||||
double db1 = fabs(sqrt(MathExtra::dot3(r01,r01)) - bond1);
|
||||
double db2 = fabs(sqrt(MathExtra::dot3(r02,r02))-bond2);
|
||||
double db12 = fabs(sqrt(MathExtra::dot3(r12,r12))-bond12);
|
||||
|
||||
|
||||
stat = !(checkr && (db1 > tol ||
|
||||
db2 > tol ||
|
||||
db12 > tol));
|
||||
|
||||
if (derr_max < db1/bond1) derr_max = db1/bond1;
|
||||
if (derr_max < db2/bond2) derr_max = db2/bond2;
|
||||
if (derr_max < db12/bond12) derr_max = db12/bond12;
|
||||
|
||||
|
||||
if (!stat && RATTLE_RAISE_ERROR)
|
||||
error->one(FLERR,"Coordinate constraints are not satisfied "
|
||||
"up to desired tolerance ");
|
||||
|
||||
double dv1 = fabs(MathExtra::dot3(r01,v01));
|
||||
double dv2 = fabs(MathExtra::dot3(r02,v02));
|
||||
double dv12 = fabs(MathExtra::dot3(r12,v12));
|
||||
|
||||
if (verr_max < dv1) verr_max = dv1;
|
||||
if (verr_max < dv2) verr_max = dv2;
|
||||
if (verr_max < dv12) verr_max = dv12;
|
||||
|
||||
|
||||
stat = !(checkv && (dv1 > tol ||
|
||||
dv2 > tol ||
|
||||
dv12> tol));
|
||||
|
||||
|
||||
if (!stat && RATTLE_RAISE_ERROR)
|
||||
error->one(FLERR,"Velocity constraints are not satisfied "
|
||||
"up to desired tolerance!");
|
||||
|
||||
|
||||
return stat;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -30,22 +30,27 @@ class FixRattle : public FixShake {
|
|||
double **vp; // array for unconstrained velocities
|
||||
double dtfv; // timestep for velocity update
|
||||
int comm_mode; // mode for communication pack/unpack
|
||||
double derr_max; // distance error
|
||||
double verr_max; // velocity error
|
||||
|
||||
FixRattle(class LAMMPS *, int, char **);
|
||||
~FixRattle();
|
||||
int setmask();
|
||||
void init();
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void final_integrate();
|
||||
void final_integrate_respa(int,int);
|
||||
void coordinate_constraints_end_of_step();
|
||||
virtual void init();
|
||||
virtual void post_force(int);
|
||||
virtual void post_force_respa(int, int, int);
|
||||
virtual void final_integrate();
|
||||
virtual void final_integrate_respa(int,int);
|
||||
|
||||
double memory_usage();
|
||||
void grow_arrays(int);
|
||||
int pack_forward_comm(int, int *, double *, int, int *);
|
||||
void unpack_forward_comm(int, int, double *);
|
||||
void reset_dt();
|
||||
virtual void correct_coordinates(int vflag);
|
||||
virtual void correct_velocities();
|
||||
virtual void shake_end_of_step(int vflag);
|
||||
|
||||
virtual double memory_usage();
|
||||
virtual void grow_arrays(int);
|
||||
virtual int pack_forward_comm(int, int *, double *, int, int *);
|
||||
virtual void unpack_forward_comm(int, int, double *);
|
||||
virtual void reset_dt();
|
||||
|
||||
private:
|
||||
void update_v_half_nocons();
|
||||
|
|
@ -58,7 +63,7 @@ class FixRattle : public FixShake {
|
|||
void solve3x3exactly(const double a[][3], const double c[], double l[]);
|
||||
void solve2x2exactly(const double a[][2], const double c[], double l[]);
|
||||
|
||||
// debugging methosd
|
||||
// debugging methods
|
||||
|
||||
bool check3angle(double ** v, int m, bool checkr, bool checkv);
|
||||
bool check2(double **v, int m, bool checkr, bool checkv);
|
||||
|
|
@ -73,6 +78,7 @@ class FixRattle : public FixShake {
|
|||
#endif
|
||||
#endif
|
||||
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
W: Fix rattle should come after all other integration fixes
|
||||
|
|
@ -82,20 +88,20 @@ atom positions. Thus it should be the last integration fix specified.
|
|||
If not, it will not satisfy the desired constraints as well as it
|
||||
otherwise would.
|
||||
|
||||
E: RATTLE determinant = 0.0
|
||||
E: Rattle determinant = 0.0
|
||||
|
||||
The determinant of the matrix being solved for a single cluster
|
||||
specified by the fix rattle command is numerically invalid.
|
||||
|
||||
E: RATTLE failed
|
||||
E: Rattle failed
|
||||
|
||||
Certain constraints were not satisfied.
|
||||
|
||||
E: RATTLE coordinate constraints are not satisfied up to desired tolerance
|
||||
E: Coordinate constraints are not satisfied up to desired tolerance
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: RATTLE velocity constraints are not satisfied up to desired tolerance
|
||||
E: Rattle velocity constraints are not satisfied up to desired tolerance
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
|
|
|
|||
|
|
@ -17,6 +17,7 @@
|
|||
#include <string.h>
|
||||
#include <stdio.h>
|
||||
#include "fix_shake.h"
|
||||
#include "fix_rattle.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec.h"
|
||||
#include "molecule.h"
|
||||
|
|
@ -56,7 +57,6 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
|
|||
virial_flag = 1;
|
||||
create_attribute = 1;
|
||||
dof_flag = 1;
|
||||
|
||||
// error check
|
||||
|
||||
molecular = atom->molecular;
|
||||
|
|
@ -71,6 +71,9 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
|
|||
shake_type = NULL;
|
||||
xshake = NULL;
|
||||
|
||||
ftmp = NULL;
|
||||
vtmp = NULL;
|
||||
|
||||
grow_arrays(atom->nmax);
|
||||
atom->add_callback(0);
|
||||
|
||||
|
|
@ -206,7 +209,6 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
|
|||
// SHAKE vs RATTLE
|
||||
|
||||
rattle = 0;
|
||||
vflag_post_force = 0;
|
||||
|
||||
// identify all SHAKE clusters
|
||||
|
||||
|
|
@ -255,6 +257,9 @@ FixShake::~FixShake()
|
|||
memory->destroy(shake_atom);
|
||||
memory->destroy(shake_type);
|
||||
memory->destroy(xshake);
|
||||
memory->destroy(ftmp);
|
||||
memory->destroy(vtmp);
|
||||
|
||||
|
||||
delete [] bond_flag;
|
||||
delete [] angle_flag;
|
||||
|
|
@ -433,30 +438,27 @@ void FixShake::setup(int vflag)
|
|||
next_output = (ntimestep/output_every)*output_every + output_every;
|
||||
} else next_output = -1;
|
||||
|
||||
// half timestep constraint on pre-step, full timestep thereafter
|
||||
|
||||
if (strstr(update->integrate_style,"verlet")) {
|
||||
// set respa to 0 if verlet is used and to 1 otherwise
|
||||
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
respa = 0;
|
||||
dtv = update->dt;
|
||||
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
|
||||
FixShake::post_force(vflag);
|
||||
if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v;
|
||||
|
||||
} else {
|
||||
else
|
||||
respa = 1;
|
||||
dtv = step_respa[0];
|
||||
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
|
||||
dtf_inner = dtf_innerhalf;
|
||||
|
||||
// apply correction to all rRESPA levels
|
||||
|
||||
for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) {
|
||||
((Respa *) update->integrate)->copy_flevel_f(ilevel);
|
||||
FixShake::post_force_respa(vflag,ilevel,loop_respa[ilevel]-1);
|
||||
((Respa *) update->integrate)->copy_f_flevel(ilevel);
|
||||
}
|
||||
if (!rattle) dtf_inner = step_respa[0] * force->ftm2v;
|
||||
}
|
||||
// correct geometry of cluster if necessary
|
||||
|
||||
correct_coordinates(vflag);
|
||||
|
||||
// remove velocities along any bonds
|
||||
|
||||
correct_velocities();
|
||||
|
||||
// precalculate constraining forces for first integration step
|
||||
|
||||
shake_end_of_step(vflag);
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -572,7 +574,6 @@ void FixShake::post_force(int vflag)
|
|||
}
|
||||
|
||||
// store vflag for coordinate_constraints_end_of_step()
|
||||
|
||||
vflag_post_force = vflag;
|
||||
}
|
||||
|
||||
|
|
@ -620,7 +621,6 @@ void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
|
|||
}
|
||||
|
||||
// store vflag for coordinate_constraints_end_of_step()
|
||||
|
||||
vflag_post_force = vflag;
|
||||
}
|
||||
|
||||
|
|
@ -2397,6 +2397,11 @@ void FixShake::grow_arrays(int nmax)
|
|||
memory->grow(shake_type,nmax,3,"shake:shake_type");
|
||||
memory->destroy(xshake);
|
||||
memory->create(xshake,nmax,3,"shake:xshake");
|
||||
memory->destroy(ftmp);
|
||||
memory->create(ftmp,nmax,3,"shake:ftmp");
|
||||
memory->destroy(vtmp);
|
||||
memory->create(vtmp,nmax,3,"shake:vtmp");
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -2683,25 +2688,116 @@ void *FixShake::extract(const char *str, int &dim)
|
|||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
wrapper method for end_of_step fixes which modify the coordinates
|
||||
Add coordinate constraining forces; this method is called
|
||||
at the end of a timestep.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixShake::coordinate_constraints_end_of_step() {
|
||||
void FixShake::shake_end_of_step(int vflag) {
|
||||
|
||||
if (!respa) {
|
||||
dtv = update->dt;
|
||||
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
|
||||
FixShake::post_force(vflag_post_force);
|
||||
FixShake::post_force(vflag);
|
||||
if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v;
|
||||
}
|
||||
else {
|
||||
|
||||
} else {
|
||||
dtv = step_respa[0];
|
||||
dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
|
||||
dtf_inner = dtf_innerhalf;
|
||||
|
||||
// apply correction to all rRESPA levels
|
||||
|
||||
for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) {
|
||||
((Respa *) update->integrate)->copy_flevel_f(ilevel);
|
||||
FixShake::post_force_respa(vflag_post_force,ilevel,loop_respa[ilevel]-1);
|
||||
FixShake::post_force_respa(vflag,ilevel,loop_respa[ilevel]-1);
|
||||
((Respa *) update->integrate)->copy_f_flevel(ilevel);
|
||||
}
|
||||
if (!rattle) dtf_inner = step_respa[0] * force->ftm2v;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
wrapper method for end_of_step fixes which modify velocities
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixShake::correct_velocities() {
|
||||
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Calculate constraining forces based on the current configuration
|
||||
and change coordinates.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixShake::correct_coordinates(int vflag) {
|
||||
|
||||
// save current forces and velocities so that you
|
||||
// initialise them to zero such that FixShake::unconstrained_coordinate_update has no effect
|
||||
|
||||
for (int j=0; j<nlocal; j++) {
|
||||
for (int k=0; k<3; k++) {
|
||||
|
||||
// store current value of forces and velocities
|
||||
|
||||
ftmp[j][k] = f[j][k];
|
||||
vtmp[j][k] = v[j][k];
|
||||
|
||||
// set f and v to zero for SHAKE
|
||||
|
||||
v[j][k] = 0;
|
||||
f[j][k] = 0;
|
||||
}
|
||||
}
|
||||
|
||||
// call SHAKE to correct the coordinates which were updated without constraints
|
||||
// IMPORTANT: use 1 as argument and thereby enforce velocity Verlet
|
||||
|
||||
dtfsq = 0.5 * update->dt * update->dt * force->ftm2v;
|
||||
FixShake::post_force(vflag);
|
||||
|
||||
// integrate coordiantes: x' = xnp1 + dt^2/2m_i * f, where f is the constraining force
|
||||
// NOTE: After this command, the coordinates geometry of the molecules will be correct!
|
||||
|
||||
double dtfmsq;
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfmsq = dtfsq/ rmass[i];
|
||||
x[i][0] = x[i][0] + dtfmsq*f[i][0];
|
||||
x[i][1] = x[i][1] + dtfmsq*f[i][1];
|
||||
x[i][2] = x[i][2] + dtfmsq*f[i][2];
|
||||
}
|
||||
}
|
||||
else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
dtfmsq = dtfsq / mass[type[i]];
|
||||
x[i][0] = x[i][0] + dtfmsq*f[i][0];
|
||||
x[i][1] = x[i][1] + dtfmsq*f[i][1];
|
||||
x[i][2] = x[i][2] + dtfmsq*f[i][2];
|
||||
}
|
||||
}
|
||||
|
||||
// copy forces and velocities back
|
||||
|
||||
for (int j=0; j<nlocal; j++) {
|
||||
for (int k=0; k<3; k++) {
|
||||
f[j][k] = ftmp[j][k];
|
||||
v[j][k] = vtmp[j][k];
|
||||
}
|
||||
}
|
||||
|
||||
if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v;
|
||||
|
||||
// communicate changes
|
||||
// NOTE: for compatibility xshake is temporarily set to x, such that pack/unpack_forward
|
||||
// can be used for communicating the coordinates.
|
||||
|
||||
double **xtmp = xshake;
|
||||
xshake = x;
|
||||
if (nprocs > 1) {
|
||||
comm->forward_comm_fix(this);
|
||||
}
|
||||
xshake = xtmp;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -25,6 +25,9 @@ FixStyle(shake,FixShake)
|
|||
namespace LAMMPS_NS {
|
||||
|
||||
class FixShake : public Fix {
|
||||
|
||||
friend class FixEHEX;
|
||||
|
||||
public:
|
||||
FixShake(class LAMMPS *, int, char **);
|
||||
virtual ~FixShake();
|
||||
|
|
@ -46,7 +49,13 @@ class FixShake : public Fix {
|
|||
virtual int unpack_exchange(int, double *);
|
||||
virtual int pack_forward_comm(int, int *, double *, int, int *);
|
||||
virtual void unpack_forward_comm(int, int, double *);
|
||||
virtual void coordinate_constraints_end_of_step();
|
||||
|
||||
|
||||
|
||||
virtual void shake_end_of_step(int vflag);
|
||||
virtual void correct_coordinates(int vflag);
|
||||
virtual void correct_velocities();
|
||||
|
||||
|
||||
int dof(int);
|
||||
virtual void reset_dt();
|
||||
|
|
@ -77,6 +86,8 @@ class FixShake : public Fix {
|
|||
double *step_respa;
|
||||
|
||||
double **x,**v,**f; // local ptrs to atom class quantities
|
||||
double **ftmp, **vtmp; // pointers to temporary arrays for forces and velocities
|
||||
|
||||
double *mass,*rmass;
|
||||
int *type;
|
||||
int nlocal;
|
||||
|
|
|
|||
Loading…
Reference in New Issue