forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1607 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
c939c91289
commit
62590294d6
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@ -5,13 +5,9 @@ if ($1 == 1) then
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cp style_dipole.h ..
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cp atom_vec_dipole.cpp ..
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cp compute_temp_dipole.cpp ..
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cp fix_nve_dipole.cpp ..
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cp pair_dipole_cut.cpp ..
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cp atom_vec_dipole.h ..
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cp compute_temp_dipole.h ..
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cp fix_nve_dipole.h ..
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cp pair_dipole_cut.h ..
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else if ($1 == 0) then
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@ -20,13 +16,9 @@ else if ($1 == 0) then
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touch ../style_dipole.h
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rm ../atom_vec_dipole.cpp
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rm ../compute_temp_dipole.cpp
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rm ../fix_nve_dipole.cpp
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rm ../pair_dipole_cut.cpp
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rm ../atom_vec_dipole.h
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rm ../compute_temp_dipole.h
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rm ../fix_nve_dipole.h
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rm ../pair_dipole_cut.h
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endif
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@ -1,150 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, 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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#include "mpi.h"
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#include "compute_temp_dipole.h"
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#include "atom.h"
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#include "force.h"
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#include "domain.h"
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#include "group.h"
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#include "modify.h"
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#include "fix.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define INVOKED_SCALAR 1
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#define INVOKED_VECTOR 2
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#define INERTIA 0.4 // moment of inertia for a sphere
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/* ---------------------------------------------------------------------- */
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ComputeTempDipole::ComputeTempDipole(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all("Illegal compute temp/dipole command");
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if (!atom->omega_flag || atom->shape == NULL)
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error->all("Compute temp/dipole requires atom attributes omega, shape");
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scalar_flag = vector_flag = 1;
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size_vector = 6;
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extscalar = 0;
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extvector = 1;
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tempflag = 1;
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vector = new double[6];
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inertia = new double[atom->ntypes + 1];
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}
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/* ---------------------------------------------------------------------- */
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ComputeTempDipole::~ComputeTempDipole()
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{
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delete [] vector;
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delete [] inertia;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempDipole::init()
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{
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fix_dof = 0;
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for (int i = 0; i < modify->nfix; i++)
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fix_dof += modify->fix[i]->dof(igroup);
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recount();
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// moment of inertia for each particle type
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double *mass = atom->mass;
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double **shape = atom->shape;
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for (int i = 1; i <= atom->ntypes; i++)
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inertia[i] = INERTIA * mass[i] * 0.25*shape[i][0]*shape[i][0];
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempDipole::recount()
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{
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double natoms = group->count(igroup);
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dof = 2.0 * domain->dimension * natoms;
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dof -= extra_dof + fix_dof;
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if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
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else tfactor = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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double ComputeTempDipole::compute_scalar()
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{
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invoked |= INVOKED_SCALAR;
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double **v = atom->v;
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double *mass = atom->mass;
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double **omega = atom->omega;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// rotational and translational kinetic energy
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double t = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
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mass[type[i]]
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+ (omega[i][0] * omega[i][0] + omega[i][1] * omega[i][1] +
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omega[i][2] * omega[i][2]) * inertia[type[i]];
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MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
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if (dynamic) recount();
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scalar *= tfactor;
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return scalar;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeTempDipole::compute_vector()
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{
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int i;
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invoked |= INVOKED_VECTOR;
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double **v = atom->v;
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double *mass = atom->mass;
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double **omega = atom->omega;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double rmass,imass,t[6];
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for (i = 0; i < 6; i++) t[i] = 0.0;
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// rotational and translational kinetic energy
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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rmass = mass[type[i]];
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imass = inertia[type[i]];
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t[0] += rmass*v[i][0]*v[i][0] + imass*omega[i][0]*omega[i][0];
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t[1] += rmass*v[i][1]*v[i][1] + imass*omega[i][1]*omega[i][1];
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t[2] += rmass*v[i][2]*v[i][2] + imass*omega[i][2]*omega[i][2];
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t[3] += rmass*v[i][0]*v[i][1] + imass*omega[i][0]*omega[i][1];
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t[4] += rmass*v[i][0]*v[i][2] + imass*omega[i][0]*omega[i][2];
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t[5] += rmass*v[i][1]*v[i][2] + imass*omega[i][1]*omega[i][2];
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}
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MPI_Allreduce(&t,&vector,6,MPI_DOUBLE,MPI_SUM,world);
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for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
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}
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@ -1,39 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, 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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#ifndef COMPUTE_TEMP_DIPOLE_H
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#define COMPUTE_TEMP_DIPOLE_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeTempDipole : public Compute {
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public:
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ComputeTempDipole(class LAMMPS *, int, char **);
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~ComputeTempDipole();
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void init();
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double compute_scalar();
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void compute_vector();
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private:
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int fix_dof;
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double tfactor;
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double *inertia;
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void recount();
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};
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}
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#endif
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@ -1,201 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, 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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#include "math.h"
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#include "string.h"
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#include "fix_nve_dipole.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "force.h"
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#include "update.h"
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#include "respa.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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// moment of inertia for a sphere
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#define INERTIA 0.4
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/* ---------------------------------------------------------------------- */
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FixNVEDipole::FixNVEDipole(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 3) error->all("Illegal fix nve/dipole command");
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if (!atom->mu_flag || !atom->omega_flag ||
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!atom->torque_flag || !atom->avec->shape_type)
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error->all("Fix nve/dipole requires atom attributes "
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"mu, omega, torque, shape");
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inertia = new double[atom->ntypes+1];
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}
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/* ---------------------------------------------------------------------- */
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FixNVEDipole::~FixNVEDipole()
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{
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delete [] inertia;
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}
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/* ---------------------------------------------------------------------- */
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int FixNVEDipole::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= INITIAL_INTEGRATE_RESPA;
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mask |= FINAL_INTEGRATE_RESPA;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEDipole::init()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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if (strcmp(update->integrate_style,"respa") == 0)
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step_respa = ((Respa *) update->integrate)->step;
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// moment of inertia for each particle type
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double *mass = atom->mass;
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double **shape = atom->shape;
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for (int i = 1; i <= atom->ntypes; i++)
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inertia[i] = INERTIA * mass[i] * 0.25*shape[i][0]*shape[i][0];
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEDipole::initial_integrate(int vflag)
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{
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double dtfm,msq,scale;
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double **mu = atom->mu;
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double **omega = atom->omega;
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double **torque = atom->torque;
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double *mass = atom->mass;
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double *dipole = atom->dipole;
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int *type = atom->type;
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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 g[3];
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// update v,x for all particles
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// update omega,mu for all dipoles
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// d_omega/dt = torque / inertia
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// d_mu/dt = omega cross mu
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// renormalize mu to dipole length
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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if (dipole[type[i]] > 0.0) {
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dtfm = dtf / inertia[type[i]];
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omega[i][0] += dtfm * torque[i][0];
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omega[i][1] += dtfm * torque[i][1];
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omega[i][2] += dtfm * torque[i][2];
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g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2] - omega[i][2]*mu[i][1]);
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g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0] - omega[i][0]*mu[i][2]);
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g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1] - omega[i][1]*mu[i][0]);
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msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
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scale = dipole[type[i]]/sqrt(msq);
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mu[i][0] = g[0]*scale;
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mu[i][1] = g[1]*scale;
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mu[i][2] = g[2]*scale;
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEDipole::final_integrate()
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{
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double dtfm;
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double **v = atom->v;
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double **f = atom->f;
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double **omega = atom->omega;
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double **torque = atom->torque;
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double *mass = atom->mass;
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double *dipole = atom->dipole;
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int *type = atom->type;
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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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// update v for all particles
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// update omega for all dipoles
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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if (dipole[type[i]] > 0.0) {
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dtfm = dtf / inertia[type[i]];
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omega[i][0] += dtfm * torque[i][0];
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omega[i][1] += dtfm * torque[i][1];
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omega[i][2] += dtfm * torque[i][2];
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEDipole::initial_integrate_respa(int vflag, int ilevel, int flag)
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{
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if (flag) return; // only used by NPT,NPH
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dtv = step_respa[ilevel];
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dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
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if (ilevel == 0) initial_integrate(vflag);
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else final_integrate();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEDipole::final_integrate_respa(int ilevel)
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{
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dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
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final_integrate();
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}
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/* ---------------------------------------------------------------------- */
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void FixNVEDipole::reset_dt()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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}
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@ -1,41 +0,0 @@
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/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
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.
|
||||
------------------------------------------------------------------------- */
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#ifndef FIX_NVE_DIPOLE_H
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#define FIX_NVE_DIPOLE_H
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixNVEDipole : public Fix {
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public:
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FixNVEDipole(class LAMMPS *, int, char **);
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~FixNVEDipole();
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int setmask();
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void init();
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void initial_integrate(int);
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void final_integrate();
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void initial_integrate_respa(int, int, int);
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void final_integrate_respa(int);
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void reset_dt();
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private:
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double dtv,dtf;
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double *step_respa;
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double *inertia;
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};
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}
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#endif
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@ -19,22 +19,6 @@
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AtomStyle(dipole,AtomVecDipole)
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#endif
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#ifdef ComputeInclude
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#include "compute_temp_dipole.h"
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#endif
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#ifdef ComputeClass
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ComputeStyle(temp/dipole,ComputeTempDipole)
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#endif
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#ifdef FixInclude
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#include "fix_nve_dipole.h"
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#endif
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#ifdef FixClass
|
||||
FixStyle(nve/dipole,FixNVEDipole)
|
||||
#endif
|
||||
|
||||
#ifdef PairInclude
|
||||
#include "pair_dipole_cut.h"
|
||||
#endif
|
||||
|
|
|
|||
Loading…
Reference in New Issue