296 lines
8.9 KiB
C++
296 lines
8.9 KiB
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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#include <math.h>
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#include <stdio.h>
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#include <string.h>
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#include "fix_nve_sphere.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "respa.h"
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#include "force.h"
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#include "error.h"
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#include "domain.h" //NP modified GM
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#include "fix_property_atom.h"
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#include "fix_cfd_coupling_force_implicit.h"
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#include "modify.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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#define INERTIA 0.4 // moment of inertia prefactor for sphere
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enum{NONE,DIPOLE};
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/* ---------------------------------------------------------------------- */
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FixNVESphere::FixNVESphere(LAMMPS *lmp, int narg, char **arg) :
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FixNVE(lmp, narg, arg),
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implicitIntegration_(false),
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fix_Ksl_(0),
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fix_cfd_coupling_force_implicit_(0)
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{
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if (narg < 3) error->all(FLERR,"Illegal fix nve/sphere command");
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time_integrate = 1;
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// process extra keywords
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extra = NONE;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"update") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix nve/sphere command");
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if (strcmp(arg[iarg+1],"dipole") == 0) extra = DIPOLE;
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else error->all(FLERR,"Illegal fix nve/sphere command");
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iarg += 2;
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}
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else if(strcmp(arg[iarg],"implicit_integration") == 0)
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{
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if(narg < iarg+2)
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error->fix_error(FLERR,this,"not enough arguments for 'transfer_reactant'");
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iarg++;
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if(strcmp(arg[iarg],"yes") == 0)
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implicitIntegration_ = true;
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else if(strcmp(arg[iarg],"no") == 0)
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implicitIntegration_ = false;
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else
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error->fix_error(FLERR,this,"expecting 'yes' or 'no' after 'implicit_integration'");
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iarg++;
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}
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else error->all(FLERR,"Illegal fix nve/sphere command");
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}
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// error checks
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if (!atom->sphere_flag)
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error->all(FLERR,"Fix nve/sphere requires atom style sphere");
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if (extra == DIPOLE && !atom->mu_flag)
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error->all(FLERR,"Fix nve/sphere requires atom attribute mu");
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESphere::post_create()
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{
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if (implicitIntegration_)
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{
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fix_Ksl_ = static_cast<FixPropertyAtom*>(modify->find_fix_property("Ksl","property/atom","scalar",0,0,style,false));
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if (!fix_Ksl_)
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{
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error->fix_error(FLERR,this,"Fix NVE/sphere could not find fix 'Ksl' for the drag coefficient");
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}
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fix_cfd_coupling_force_implicit_ = static_cast<FixCfdCouplingForceImplicit*>(modify->find_fix_style_strict("couple/cfd/force/implicit",0));
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if (!fix_cfd_coupling_force_implicit_)
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{
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error->fix_error(FLERR,this,"Could not find fix ID 'couple/cfd/force/implicit'");
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}
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if (!fix_cfd_coupling_force_implicit_->implicitIntegration())
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{
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error->fix_error(FLERR,this,"Fix 'couple/cfd/force/implicit' is not in mode for implicit integration.");
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}
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}
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}
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void FixNVESphere::init()
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{
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FixNVE::init();
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// check that all particles are finite-size spheres
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// no point particles allowed
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double *radius = atom->radius;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (radius[i] == 0.0)
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error->one(FLERR,"Fix nve/sphere requires extended particles");
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}
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/* ---------------------------------------------------------------------- */
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void FixNVESphere::initial_integrate(int vflag)
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{
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double dtfm,dtirotate,msq,scale;
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double g[3];
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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 **omega = atom->omega;
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double **torque = atom->torque;
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double *radius = atom->radius;
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double *rmass = atom->rmass;
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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 invImpDenom;
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double *Ksl;
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if (implicitIntegration_) Ksl = fix_Ksl_->vector_atom;
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// set timestep here since dt may have changed or come via rRESPA
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double dtfrotate; //NP modified GM
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if (domain->dimension == 2) dtfrotate = dtf / 0.5; // for discs the formula is I=0.5*Mass*Radius^2
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else dtfrotate = dtf / INERTIA;
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// update v,x,omega for all particles
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// d_omega/dt = torque / inertia
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if (implicitIntegration_)
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{
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for (int i = 0; i < nlocal; i++)
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{
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if (mask[i] & groupbit)
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{
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dtfm = dtf / rmass[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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invImpDenom = 1.0/(1.0 + dtfm * Ksl[i]);
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v[i][0] *= invImpDenom;
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v[i][1] *= invImpDenom;
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v[i][2] *= invImpDenom;
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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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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] += dtirotate * torque[i][0];
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omega[i][1] += dtirotate * torque[i][1];
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omega[i][2] += dtirotate * torque[i][2];
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}
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}
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}
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else
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{
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for (int i = 0; i < nlocal; i++)
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{
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if (mask[i] & groupbit)
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{
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dtfm = dtf / rmass[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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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] += dtirotate * torque[i][0];
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omega[i][1] += dtirotate * torque[i][1];
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omega[i][2] += dtirotate * torque[i][2];
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}
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}
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}
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// update mu for dipoles
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// d_mu/dt = omega cross mu
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// renormalize mu to dipole length
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if (extra == DIPOLE) {
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double **mu = atom->mu;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (mu[i][3] > 0.0) {
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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 = mu[i][3]/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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void FixNVESphere::final_integrate()
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{
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double dtfm,dtirotate;
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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 *rmass = atom->rmass;
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double *radius = atom->radius;
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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 invImpDenom;
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double *Ksl;
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if (implicitIntegration_) Ksl = fix_Ksl_->vector_atom;
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// set timestep here since dt may have changed or come via rRESPA
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double dtfrotate; //NP modified GM
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if (domain->dimension == 2) dtfrotate = dtf / 0.5; // for discs the formula is I=0.5*Mass*Radius^2
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else dtfrotate = dtf / INERTIA;
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// update v,omega for all particles
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// d_omega/dt = torque / inertia
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if (implicitIntegration_)
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{
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for (int i = 0; i < nlocal; i++)
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{
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if (mask[i] & groupbit)
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{
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dtfm = dtf / rmass[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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invImpDenom = 1.0/(1.0 + dtfm * Ksl[i]);
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v[i][0] *= invImpDenom;
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v[i][1] *= invImpDenom;
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v[i][2] *= invImpDenom;
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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] += dtirotate * torque[i][0];
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omega[i][1] += dtirotate * torque[i][1];
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omega[i][2] += dtirotate * torque[i][2];
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}
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}
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}
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else
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{
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for (int i = 0; i < nlocal; i++)
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{
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if (mask[i] & groupbit)
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{
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dtfm = dtf / rmass[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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dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
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omega[i][0] += dtirotate * torque[i][0];
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omega[i][1] += dtirotate * torque[i][1];
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omega[i][2] += dtirotate * torque[i][2];
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}
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}
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}
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}
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