132 lines
4.1 KiB
C++
132 lines
4.1 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/
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LAMMPS development team: developers@lammps.org, Sandia National Laboratories
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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: Pieter in 't Veld (SNL)
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------------------------------------------------------------------------- */
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#include "fix_nvt_sllod.h"
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#include "atom.h"
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#include "compute.h"
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#include "domain.h"
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#include "error.h"
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#include "fix_deform.h"
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#include "group.h"
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#include "math_extra.h"
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#include "modify.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) :
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FixNH(lmp, narg, arg)
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{
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if (!tstat_flag)
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error->all(FLERR,"Temperature control must be used with fix nvt/sllod");
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if (pstat_flag)
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error->all(FLERR,"Pressure control can not be used with fix nvt/sllod");
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// default values
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psllod_flag = 0;
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if (mtchain_default_flag) mtchain = 1;
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// select SLLOD/p-SLLOD/g-SLLOD variant
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"psllod") == 0) {
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if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix nvt/sllod psllod", error);
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psllod_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
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iarg += 2;
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} else iarg++;
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}
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// create a new compute temp style
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// id = fix-ID + temp
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id_temp = utils::strdup(std::string(id) + "_temp");
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modify->add_compute(fmt::format("{} {} temp/deform",id_temp,group->names[igroup]));
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tcomputeflag = 1;
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nondeformbias = 0;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVTSllod::init()
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{
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FixNH::init();
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if (!temperature->tempbias)
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error->all(FLERR,"Temperature for fix {} does not have a bias", style);
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nondeformbias = 0;
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if (strcmp(temperature->style,"temp/deform") != 0) nondeformbias = 1;
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// check fix deform remap settings
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auto deform = modify->get_fix_by_style("^deform");
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if (deform.size() < 1) error->all(FLERR,"Using fix {} with no fix deform defined", style);
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for (auto &ifix : deform) {
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auto f = dynamic_cast<FixDeform *>(ifix);
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if (f && (f->remapflag != Domain::V_REMAP))
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error->all(FLERR,"Using fix {} with inconsistent fix deform remap option", style);
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}
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}
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/* ----------------------------------------------------------------------
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perform half-step scaling of velocities
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-----------------------------------------------------------------------*/
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void FixNVTSllod::nh_v_temp()
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{
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// remove and restore bias = streaming velocity = Hrate*lamda + Hratelo
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// thermostat thermal velocity only
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// vdelu = SLLOD correction = Hrate*Hinv*vthermal
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// for non temp/deform BIAS:
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// calculate temperature since some computes require temp
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// computed on current nlocal atoms to remove bias
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if (nondeformbias) temperature->compute_scalar();
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double **v = atom->v;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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double h_two[6],vdelu[3];
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MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two);
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (!psllod_flag) temperature->remove_bias(i,v[i]);
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vdelu[0] = h_two[0]*v[i][0] + h_two[5]*v[i][1] + h_two[4]*v[i][2];
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vdelu[1] = h_two[1]*v[i][1] + h_two[3]*v[i][2];
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vdelu[2] = h_two[2]*v[i][2];
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if (psllod_flag) temperature->remove_bias(i,v[i]);
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v[i][0] = v[i][0]*factor_eta - dthalf*vdelu[0];
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v[i][1] = v[i][1]*factor_eta - dthalf*vdelu[1];
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v[i][2] = v[i][2]*factor_eta - dthalf*vdelu[2];
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temperature->restore_bias(i,v[i]);
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}
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}
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}
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