mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15023 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
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@ -1,625 +0,0 @@
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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]);
|
||||
}
|
||||
|
||||
|
|
@ -1,130 +0,0 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue