forked from lijiext/lammps
initial import of adapted gREM code by David Stelter and Edyta Malolepsza
The following changes were made: - the modifications to compute pressure were transferred to a derived class compute pressure/grem - fix scaleforce was renamed to fix grem - identifying the grem fix was simplified as fix grem passes an additional argument to compute pressure/grem - dead code was removed in both files - checking of arguments was tightened
This commit is contained in:
Axel Kohlmeyer
parent
9806da69f3
commit
20daf82463
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@ -205,6 +205,8 @@
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/compute_pe_tally.h
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/compute_plasticity_atom.cpp
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/compute_plasticity_atom.h
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/compute_pressure_grem.cpp
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/compute_pressure_grem.h
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/compute_rigid_local.cpp
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/compute_rigid_local.h
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/compute_spec_atom.cpp
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@ -343,6 +345,8 @@
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/fix_gle.h
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/fix_gpu.cpp
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/fix_gpu.h
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/fix_grem.cpp
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/fix_grem.h
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/fix_imd.cpp
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/fix_imd.h
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/fix_ipi.cpp
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@ -0,0 +1,149 @@
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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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#include <mpi.h>
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#include <string.h>
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#include <stdlib.h>
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#include "compute_pressure_grem.h"
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#include "atom.h"
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#include "update.h"
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#include "domain.h"
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#include "modify.h"
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#include "fix.h"
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#include "force.h"
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#include "pair.h"
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#include "kspace.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ----------------------------------------------------------------------
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Last argument is the id of the gREM fix
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------------------------------------------------------------------------- */
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ComputePressureGrem::ComputePressureGrem(LAMMPS *lmp, int narg, char **arg) :
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ComputePressure(lmp, narg-1, arg)
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{
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fix_grem = arg[narg-1];
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}
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/* ---------------------------------------------------------------------- */
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void ComputePressureGrem::init()
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{
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ComputePressure::init();
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// Initialize hook to gREM fix
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int ifix = modify->find_fix(fix_grem);
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if (ifix < 0)
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error->all(FLERR,"Fix grem ID for compute pressure/grem does not exist");
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int dim;
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scale_grem = (double *)modify->fix[ifix]->extract("scale_grem",dim);
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if (scale_grem == NULL || dim != 0)
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error->all(FLERR,"Cannot extract gREM scale factor from fix grem");
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}
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/* ----------------------------------------------------------------------
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compute total pressure, averaged over Pxx, Pyy, Pzz
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------------------------------------------------------------------------- */
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double ComputePressureGrem::compute_scalar()
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{
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invoked_scalar = update->ntimestep;
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if (update->vflag_global != invoked_scalar)
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error->all(FLERR,"Virial was not tallied on needed timestep");
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// invoke temperature if it hasn't been already
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double t;
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if (keflag) {
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if (temperature->invoked_scalar != update->ntimestep)
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t = temperature->compute_scalar() * (*scale_grem);
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else t = temperature->scalar * (*scale_grem);
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}
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if (dimension == 3) {
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inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
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virial_compute(3,3);
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if (keflag)
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scalar = (temperature->dof * boltz * t +
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virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
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else
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scalar = (virial[0] + virial[1] + virial[2]) / 3.0 * inv_volume * nktv2p;
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} else {
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inv_volume = 1.0 / (domain->xprd * domain->yprd);
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virial_compute(2,2);
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if (keflag)
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scalar = (temperature->dof * boltz * t +
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virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
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else
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scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
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}
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return scalar;
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}
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/* ----------------------------------------------------------------------
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compute pressure tensor
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assume KE tensor has already been computed
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------------------------------------------------------------------------- */
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void ComputePressureGrem::compute_vector()
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{
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invoked_vector = update->ntimestep;
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if (update->vflag_global != invoked_vector)
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error->all(FLERR,"Virial was not tallied on needed timestep");
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if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
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error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
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"tensor components with kspace_style msm");
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// invoke temperature if it hasn't been already
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double *ke_tensor;
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if (keflag) {
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if (temperature->invoked_vector != update->ntimestep)
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temperature->compute_vector();
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ke_tensor = temperature->vector;
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}
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for (int i = 0; i < 6; i++)
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ke_tensor[i] *= *scale_grem;
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if (dimension == 3) {
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inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
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virial_compute(6,3);
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if (keflag) {
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for (int i = 0; i < 6; i++)
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vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
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} else
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for (int i = 0; i < 6; i++)
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vector[i] = virial[i] * inv_volume * nktv2p;
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} else {
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inv_volume = 1.0 / (domain->xprd * domain->yprd);
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virial_compute(4,2);
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if (keflag) {
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vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
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vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
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vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
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vector[2] = vector[4] = vector[5] = 0.0;
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} else {
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vector[0] = virial[0] * inv_volume * nktv2p;
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vector[1] = virial[1] * inv_volume * nktv2p;
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vector[3] = virial[3] * inv_volume * nktv2p;
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vector[2] = vector[4] = vector[5] = 0.0;
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}
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}
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}
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@ -0,0 +1,91 @@
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/* -*- c++ -*- ----------------------------------------------------------
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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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#ifdef COMPUTE_CLASS
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ComputeStyle(pressure/grem,ComputePressureGrem)
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#else
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#ifndef LMP_COMPUTE_PRESSURE_GREM_H
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#define LMP_COMPUTE_PRESSURE_GREM_H
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#include "compute_pressure.h"
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namespace LAMMPS_NS {
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class ComputePressureGrem : public ComputePressure {
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public:
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ComputePressureGrem(class LAMMPS *, int, char **);
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virtual ~ComputePressureGrem() {};
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virtual void init();
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virtual double compute_scalar();
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virtual void compute_vector();
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protected:
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// Access to gREM fix scale factor
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char *fix_grem;
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double *scale_grem;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Compute pressure must use group all
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Virial contributions computed by potentials (pair, bond, etc) are
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computed on all atoms.
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E: Could not find compute pressure temperature ID
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The compute ID for calculating temperature does not exist.
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E: Compute pressure temperature ID does not compute temperature
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The compute ID assigned to a pressure computation must compute
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temperature.
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E: Compute pressure requires temperature ID to include kinetic energy
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The keflag cannot be used unless a temperature compute is provided.
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E: Virial was not tallied on needed timestep
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You are using a thermo keyword that requires potentials to
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have tallied the virial, but they didn't on this timestep. See the
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variable doc page for ideas on how to make this work.
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E: Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm
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Otherwise MSM will compute only a scalar pressure. See the kspace_modify
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command for details on this setting.
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E: Fix grem ID for compute pressure/grem does not exist
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Compute pressure/grem was passed an invalid fix id
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E: Cannot extract gREM scale factor from fix grem
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The fix id passed to compute pressure/grem refers to an incompatible fix
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*/
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@ -0,0 +1,239 @@
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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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Force scaling fix for gREM.
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Cite: http://dx.doi.org/10.1063/1.3432176
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Cite: http://dx.doi.org/10.1021/acs.jpcb.5b07614
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Edyta Malolepsza (Broad Institute)
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Contributing author: David Stelter (Boston University)
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Contributing author: Tom Keyes (Boston University)
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------------------------------------------------------------------------- */
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#include <string.h>
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#include <stdlib.h>
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#include <math.h>
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#include "comm.h"
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#include "fix_grem.h"
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#include "atom.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 "domain.h"
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#include "input.h"
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#include "compute.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{NONE,CONSTANT,EQUAL,ATOM};
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/* ---------------------------------------------------------------------- */
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FixGrem::FixGrem(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 8) error->all(FLERR,"Illegal fix grem command");
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scalar_flag = 1;
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vector_flag = 1;
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size_vector = 3;
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global_freq = 1;
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extscalar = 1;
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extvector = 1;
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// tbath - temp of bath, the same as defined in thermostat
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lambda = force->numeric(FLERR,arg[3]);
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eta = force->numeric(FLERR,arg[4]);
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h0 = force->numeric(FLERR,arg[5]);
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tbath = force->numeric(FLERR,arg[6]);
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pressref = force->numeric(FLERR,arg[7]);
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// create a new compute temp style
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// id = fix-ID + temp
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// compute group = all since pressure is always global (group all)
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// and thus its KE/temperature contribution should use group all
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int n = strlen(id) + 6;
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id_temp = new char[n];
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strcpy(id_temp,id);
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strcat(id_temp,"_temp");
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char **newarg = new char*[3];
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newarg[0] = id_temp;
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newarg[1] = (char *) "all";
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newarg[2] = (char *) "temp";
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modify->add_compute(3,newarg);
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delete [] newarg;
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tflag = 1;
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// create a new compute pressure style
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// id = fix-ID + press, compute group = all
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// pass id_temp as 4th arg to pressure constructor
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n = strlen(id) + 7;
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id_press = new char[n];
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strcpy(id_press,id);
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strcat(id_press,"_press");
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newarg = new char*[5];
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newarg[0] = id_press;
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newarg[1] = (char *) "all";
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newarg[2] = (char *) "pressure/grem";
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newarg[3] = id_temp;
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newarg[4] = id;
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modify->add_compute(5,newarg);
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delete [] newarg;
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// create a new compute ke style
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// id = fix-ID + ke
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n = strlen(id) + 8;
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id_ke = new char[n];
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strcpy(id_ke,id);
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strcat(id_ke,"_ke");
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newarg = new char*[3];
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newarg[0] = id_ke;
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newarg[1] = (char *) "all";
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newarg[2] = (char *) "ke";
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modify->add_compute(3,newarg);
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delete [] newarg;
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keflag = 1;
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// create a new compute pe style
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// id = fix-ID + pe
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n = strlen(id) + 9;
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id_pe = new char[n];
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strcpy(id_pe,id);
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strcat(id_pe,"_pe");
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newarg = new char*[3];
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newarg[0] = id_pe;
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newarg[1] = (char *) "all";
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newarg[2] = (char *) "pe";
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modify->add_compute(3,newarg);
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delete [] newarg;
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peflag = 1;
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}
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/* ---------------------------------------------------------------------- */
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FixGrem::~FixGrem()
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{
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// delete temperature, pressure and energies if fix created them
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|
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if (tflag) modify->delete_compute(id_temp);
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if (pflag) modify->delete_compute(id_press);
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if (keflag) modify->delete_compute(id_ke);
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if (peflag) modify->delete_compute(id_pe);
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delete [] id_temp;
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delete [] id_press;
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delete [] id_ke;
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delete [] id_pe;
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}
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/* ---------------------------------------------------------------------- */
|
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int FixGrem::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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return mask;
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}
|
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|
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/* ---------------------------------------------------------------------- */
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void FixGrem::init()
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{
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// add check of sign of eta
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// set temperature and pressure ptrs
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|
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int icompute = modify->find_compute(id_temp);
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if (icompute < 0)
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error->all(FLERR,"Temperature ID for fix scaledforce does not exist");
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temperature = modify->compute[icompute];
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|
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icompute = modify->find_compute(id_ke);
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if (icompute < 0)
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error->all(FLERR,"Ke ID for fix scaledforce does not exist");
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ke = modify->compute[icompute];
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icompute = modify->find_compute(id_pe);
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if (icompute < 0)
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error->all(FLERR,"Pe ID for fix scaledforce does not exist");
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pe = modify->compute[icompute];
|
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}
|
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|
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/* ---------------------------------------------------------------------- */
|
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void FixGrem::setup(int vflag)
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{
|
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if (strstr(update->integrate_style,"verlet"))
|
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post_force(vflag);
|
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}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
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|
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void FixGrem::min_setup(int vflag)
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{
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post_force(vflag);
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}
|
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|
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/* ---------------------------------------------------------------------- */
|
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|
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void FixGrem::post_force(int vflag)
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{
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double **f = atom->f;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
|
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|
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double tmpvolume = domain->xprd * domain->yprd * domain->zprd;
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double tmppe = pe->compute_scalar();
|
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// potential energy
|
||||
double tmpenthalpy = tmppe+pressref*tmpvolume/(force->nktv2p);
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|
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double teffective = lambda+eta*(tmpenthalpy-h0);
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scale_grem = tbath/teffective;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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f[i][0] *= scale_grem;
|
||||
f[i][1] *= scale_grem;
|
||||
f[i][2] *= scale_grem;
|
||||
}
|
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pe->addstep(update->ntimestep+1);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
extract scale factor
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void *FixGrem::extract(const char *str, int &dim)
|
||||
{
|
||||
dim=0;
|
||||
if (strcmp(str,"scale_grem") == 0) {
|
||||
return &scale_grem;
|
||||
}
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,84 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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(grem,FixGrem)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_GREM_H
|
||||
#define LMP_FIX_GREM_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixGrem : public Fix {
|
||||
public:
|
||||
FixGrem(class LAMMPS *, int, char **);
|
||||
~FixGrem();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void *extract(const char *, int &);
|
||||
double scale_grem;
|
||||
|
||||
private:
|
||||
double lambda,eta,h0,tbath,pressref;
|
||||
|
||||
protected:
|
||||
char *id_temp,*id_press,*id_ke,*id_pe;
|
||||
class Compute *temperature,*pressure,*ke,*pe;
|
||||
int pflag,tflag,keflag,peflag;
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
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: Region ID for fix grem does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Variable name for fix grem does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Variable for fix grem is invalid style
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot use variable energy with constant force in fix grem
|
||||
|
||||
This is because for constant force, LAMMPS can compute the change
|
||||
in energy directly.
|
||||
|
||||
E: Must use variable energy with fix grem
|
||||
|
||||
Must define an energy vartiable when applyting a dynamic
|
||||
force during minimization.
|
||||
|
||||
*/
|
||||
|
|
@ -28,9 +28,9 @@ class ComputePressure : public Compute {
|
|||
public:
|
||||
ComputePressure(class LAMMPS *, int, char **);
|
||||
virtual ~ComputePressure();
|
||||
void init();
|
||||
double compute_scalar();
|
||||
void compute_vector();
|
||||
virtual void init();
|
||||
virtual double compute_scalar();
|
||||
virtual void compute_vector();
|
||||
void reset_extra_compute_fix(const char *);
|
||||
|
||||
protected:
|
||||
|
|
|
|||
Loading…
Reference in New Issue