forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10987 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
6c76b65621
commit
05649f1189
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@ -1,197 +1,197 @@
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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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||||
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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 authors:
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Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
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Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "string.h"
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#include "math.h"
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#include "fix_ti_rs.h"
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#include "atom.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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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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// Class constructor initialize all variables.
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FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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{
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// Checking the input information.
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if (narg < 7 || narg > 9) error->all(FLERR,"Illegal fix ti/rs command");
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// Fix flags.
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vector_flag = 1;
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size_vector = 2;
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global_freq = 1;
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extvector = 1;
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// Time variables.
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t_switch = atoi(arg[5]);
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t_equil = atoi(arg[6]);
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t0 = update->ntimestep;
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if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/rs command");
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if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/rs command");
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// Coupling parameter limits and initialization.
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l_initial = atof(arg[3]);
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l_final = atof(arg[4]);
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sf = 1;
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if (narg > 7) {
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if (strcmp(arg[7], "function") == 0) sf = atoi(arg[8]);
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else error->all(FLERR,"Illegal fix ti/rs switching function");
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if ((sf<1) || (sf>3))
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error->all(FLERR,"Illegal fix ti/rs switching function");
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}
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lambda = switch_func(0);
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dlambda = dswitch_func(0);
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}
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/* ---------------------------------------------------------------------- */
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FixTIRS::~FixTIRS()
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{
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// unregister callbacks to this fix from Atom class
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atom->delete_callback(id,0);
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atom->delete_callback(id,1);
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}
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/* ---------------------------------------------------------------------- */
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int FixTIRS::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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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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void FixTIRS::init()
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{
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if (strstr(update->integrate_style,"respa"))
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixTIRS::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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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(vflag,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixTIRS::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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void FixTIRS::post_force(int vflag)
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{
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double **f = atom->f;
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// Scaling forces.
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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f[i][0] = lambda * f[i][0];
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f[i][1] = lambda * f[i][1];
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f[i][2] = lambda * f[i][2];
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixTIRS::post_force_respa(int vflag, int ilevel, int iloop)
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{
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if (ilevel == nlevels_respa-1) post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixTIRS::min_post_force(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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void FixTIRS::initial_integrate(int vflag)
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{
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// Update the coupling parameter value.
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double t = update->ntimestep - (t0+t_equil);
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if( (t >= 0) && (t <= t_switch) ) {
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lambda = switch_func(t/t_switch);
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dlambda = dswitch_func(t/t_switch);
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}
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if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
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lambda = switch_func(1.0 - (t - t_switch - t_equil)/t_switch);
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dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch);
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}
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}
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/* ---------------------------------------------------------------------- */
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double FixTIRS::compute_vector(int n)
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{
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linfo[0] = lambda;
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linfo[1] = dlambda;
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return linfo[n];
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}
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/* ---------------------------------------------------------------------- */
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double FixTIRS::switch_func(double t)
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{
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if (sf == 2) return l_initial / (1 + t * (l_initial/l_final - 1));
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if (sf == 3) return l_initial / (1 + log2(1+t) * (l_initial/l_final - 1));
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// Default option is sf = 1.
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return l_initial + (l_final - l_initial) * t;
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}
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/* ---------------------------------------------------------------------- */
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double FixTIRS::dswitch_func(double t)
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{
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double aux = (1.0/l_initial - 1.0/l_final);
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if (sf == 2) return lambda * lambda * aux / t_switch;
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if (sf == 3) return lambda * lambda * aux / (t_switch * log(2) * (1 + t));
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// Default option is sf = 1.
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return (l_final-l_initial)/t_switch;
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}
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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
|
||||
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 authors:
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Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
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Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "string.h"
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#include "math.h"
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#include "fix_ti_rs.h"
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#include "atom.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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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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// Class constructor initialize all variables.
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FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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{
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// Checking the input information.
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if (narg < 7 || narg > 9) error->all(FLERR,"Illegal fix ti/rs command");
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// Fix flags.
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vector_flag = 1;
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size_vector = 2;
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global_freq = 1;
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extvector = 1;
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// Time variables.
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t_switch = atoi(arg[5]);
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t_equil = atoi(arg[6]);
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t0 = update->ntimestep;
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if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/rs command");
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if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/rs command");
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// Coupling parameter limits and initialization.
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l_initial = atof(arg[3]);
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l_final = atof(arg[4]);
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sf = 1;
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if (narg > 7) {
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if (strcmp(arg[7], "function") == 0) sf = atoi(arg[8]);
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else error->all(FLERR,"Illegal fix ti/rs switching function");
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if ((sf<1) || (sf>3))
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error->all(FLERR,"Illegal fix ti/rs switching function");
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}
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lambda = switch_func(0);
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dlambda = dswitch_func(0);
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}
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/* ---------------------------------------------------------------------- */
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FixTIRS::~FixTIRS()
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{
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// unregister callbacks to this fix from Atom class
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atom->delete_callback(id,0);
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atom->delete_callback(id,1);
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}
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/* ---------------------------------------------------------------------- */
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int FixTIRS::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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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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void FixTIRS::init()
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{
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if (strstr(update->integrate_style,"respa"))
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixTIRS::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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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(vflag,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixTIRS::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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void FixTIRS::post_force(int vflag)
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{
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double **f = atom->f;
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// Scaling forces.
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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f[i][0] = lambda * f[i][0];
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f[i][1] = lambda * f[i][1];
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f[i][2] = lambda * f[i][2];
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixTIRS::post_force_respa(int vflag, int ilevel, int iloop)
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{
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if (ilevel == nlevels_respa-1) post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixTIRS::min_post_force(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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void FixTIRS::initial_integrate(int vflag)
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{
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// Update the coupling parameter value.
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double t = update->ntimestep - (t0+t_equil);
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if( (t >= 0) && (t <= t_switch) ) {
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lambda = switch_func(t/t_switch);
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dlambda = dswitch_func(t/t_switch);
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}
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if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
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lambda = switch_func(1.0 - (t - t_switch - t_equil)/t_switch);
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dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch);
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}
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}
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/* ---------------------------------------------------------------------- */
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double FixTIRS::compute_vector(int n)
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{
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linfo[0] = lambda;
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linfo[1] = dlambda;
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return linfo[n];
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}
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/* ---------------------------------------------------------------------- */
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double FixTIRS::switch_func(double t)
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{
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if (sf == 2) return l_initial / (1 + t * (l_initial/l_final - 1));
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if (sf == 3) return l_initial / (1 + log2(1+t) * (l_initial/l_final - 1));
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// Default option is sf = 1.
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return l_initial + (l_final - l_initial) * t;
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}
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/* ---------------------------------------------------------------------- */
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double FixTIRS::dswitch_func(double t)
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{
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double aux = (1.0/l_initial - 1.0/l_final);
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if (sf == 2) return lambda * lambda * aux / t_switch;
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if (sf == 3) return lambda * lambda * aux / (t_switch * log(2) * (1 + t));
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// Default option is sf = 1.
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return (l_final-l_initial)/t_switch;
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}
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|
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@ -1,66 +1,66 @@
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|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors:
|
||||
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
|
||||
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
|
||||
------------------------------------------------------------------------- */
|
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#ifdef FIX_CLASS
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FixStyle(ti/rs,FixTIRS)
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#else
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#ifndef LMP_FIX_TI_RS_H
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#define LMP_FIX_TI_RS_H
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixTIRS : public Fix {
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public:
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FixTIRS(class LAMMPS *, int, char **);
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~FixTIRS();
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int setmask();
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void init();
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void setup(int);
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void min_setup(int);
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void post_force(int);
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void post_force_respa(int, int, int);
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void min_post_force(int);
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virtual void initial_integrate(int);
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double compute_vector(int);
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private:
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double switch_func(double);
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double dswitch_func(double);
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double lambda; // Coupling parameter.
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double dlambda; // Lambda variation with t.
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double l_initial; // Lambda initial value.
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double l_final; // Lambda final value.
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double linfo[2]; // Current lambda status.
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int t_switch; // Total switching steps.
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int t_equil; // Equilibration time.
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int t0; // Initial time.
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int sf; // Switching function option.
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int nlevels_respa;
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};
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}
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#endif
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#endif
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||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors:
|
||||
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
|
||||
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
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FixStyle(ti/rs,FixTIRS)
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#else
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#ifndef LMP_FIX_TI_RS_H
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#define LMP_FIX_TI_RS_H
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|
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#include "fix.h"
|
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|
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namespace LAMMPS_NS {
|
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|
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class FixTIRS : public Fix {
|
||||
public:
|
||||
FixTIRS(class LAMMPS *, int, char **);
|
||||
~FixTIRS();
|
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int setmask();
|
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void init();
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void min_post_force(int);
|
||||
virtual void initial_integrate(int);
|
||||
double compute_vector(int);
|
||||
|
||||
private:
|
||||
double switch_func(double);
|
||||
double dswitch_func(double);
|
||||
|
||||
double lambda; // Coupling parameter.
|
||||
double dlambda; // Lambda variation with t.
|
||||
double l_initial; // Lambda initial value.
|
||||
double l_final; // Lambda final value.
|
||||
double linfo[2]; // Current lambda status.
|
||||
int t_switch; // Total switching steps.
|
||||
int t_equil; // Equilibration time.
|
||||
int t0; // Initial time.
|
||||
int sf; // Switching function option.
|
||||
int nlevels_respa;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -1,365 +1,365 @@
|
|||
/* -------------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* -------------------------------------------------------------------------
|
||||
Contributing authors:
|
||||
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
|
||||
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "fix_ti_spring.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "respa.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 6 || narg > 8)
|
||||
error->all(FLERR,"Illegal fix ti/spring command");
|
||||
|
||||
// Flags.
|
||||
restart_peratom = 1;
|
||||
scalar_flag = 1;
|
||||
global_freq = 1;
|
||||
vector_flag = 1;
|
||||
size_vector = 2;
|
||||
global_freq = 1;
|
||||
extscalar = 1;
|
||||
extvector = 1;
|
||||
|
||||
// Spring constant.
|
||||
k = force->numeric(FLERR,arg[3]);
|
||||
if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
|
||||
|
||||
// Perform initial allocation of atom-based array.
|
||||
// Registar with Atom class.
|
||||
xoriginal = NULL;
|
||||
grow_arrays(atom->nmax);
|
||||
atom->add_callback(0);
|
||||
atom->add_callback(1);
|
||||
|
||||
// xoriginal = initial unwrapped positions of atom.
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
tagint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
|
||||
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
|
||||
}
|
||||
|
||||
// Time variables.
|
||||
t_switch = atoi(arg[4]); // Switching time.
|
||||
t_equil = atoi(arg[5]); // Equilibration time.
|
||||
t0 = update->ntimestep; // Initial time.
|
||||
if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
|
||||
if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
|
||||
|
||||
// Coupling parameter initialization.
|
||||
sf = 1;
|
||||
if (narg > 6) {
|
||||
if (strcmp(arg[6], "function") == 0) sf = atoi(arg[7]);
|
||||
else error->all(FLERR,"Illegal fix ti/spring switching function");
|
||||
if ((sf!=1) && (sf!=2))
|
||||
error->all(FLERR,"Illegal fix ti/spring switching function");
|
||||
}
|
||||
lambda = switch_func(0);
|
||||
dlambda = dswitch_func(0);
|
||||
|
||||
espring = 0.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixTISpring::~FixTISpring()
|
||||
{
|
||||
// unregister callbacks to this fix from Atom class
|
||||
atom->delete_callback(id,0);
|
||||
atom->delete_callback(id,1);
|
||||
|
||||
// delete locally stored array
|
||||
memory->destroy(xoriginal);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= POST_FORCE;
|
||||
mask |= POST_FORCE_RESPA;
|
||||
mask |= MIN_POST_FORCE;
|
||||
mask |= THERMO_ENERGY;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::init()
|
||||
{
|
||||
if (strstr(update->integrate_style,"respa"))
|
||||
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::setup(int vflag)
|
||||
{
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
post_force(vflag);
|
||||
else {
|
||||
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
|
||||
post_force_respa(vflag,nlevels_respa-1,0);
|
||||
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::min_setup(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::post_force(int vflag)
|
||||
{
|
||||
// If on the first equilibration do not calculate forces.
|
||||
int t = update->ntimestep - t0;
|
||||
if(t < t_equil) return;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
tagint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double dx, dy, dz;
|
||||
double unwrap[3];
|
||||
|
||||
espring = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - xoriginal[i][0];
|
||||
dy = unwrap[1] - xoriginal[i][1];
|
||||
dz = unwrap[2] - xoriginal[i][2];
|
||||
f[i][0] = (1-lambda) * f[i][0] + lambda * (-k*dx);
|
||||
f[i][1] = (1-lambda) * f[i][1] + lambda * (-k*dy);
|
||||
f[i][2] = (1-lambda) * f[i][2] + lambda * (-k*dz);
|
||||
espring += k * (dx*dx + dy*dy + dz*dz);
|
||||
}
|
||||
|
||||
espring *= 0.5;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::post_force_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
if (ilevel == nlevels_respa-1) post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::min_post_force(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::initial_integrate(int vflag)
|
||||
{
|
||||
// Update the coupling parameter value.
|
||||
double t = update->ntimestep - (t0+t_equil);
|
||||
|
||||
if( (t >= 0) && (t <= t_switch) ) {
|
||||
lambda = switch_func(t/t_switch);
|
||||
dlambda = dswitch_func(t/t_switch);
|
||||
}
|
||||
|
||||
if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
|
||||
lambda = switch_func(1.0 - (t - t_switch - t_equil)/t_switch );
|
||||
dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch );
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
energy of stretched springs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::compute_scalar()
|
||||
{
|
||||
double all;
|
||||
MPI_Allreduce(&espring,&all,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
return all;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
information about coupling parameter
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::compute_vector(int n)
|
||||
{
|
||||
linfo[0] = lambda;
|
||||
linfo[1] = dlambda;
|
||||
return linfo[n];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::memory_usage()
|
||||
{
|
||||
double bytes = atom->nmax*3 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::grow_arrays(int nmax)
|
||||
{
|
||||
memory->grow(xoriginal,nmax,3,"fix_ti/spring:xoriginal");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
copy values within local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::copy_arrays(int i, int j, int delflag)
|
||||
{
|
||||
xoriginal[j][0] = xoriginal[i][0];
|
||||
xoriginal[j][1] = xoriginal[i][1];
|
||||
xoriginal[j][2] = xoriginal[i][2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack values in local atom-based array for exchange with another proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::pack_exchange(int i, double *buf)
|
||||
{
|
||||
buf[0] = xoriginal[i][0];
|
||||
buf[1] = xoriginal[i][1];
|
||||
buf[2] = xoriginal[i][2];
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack values in local atom-based array from exchange with another proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
xoriginal[nlocal][0] = buf[0];
|
||||
xoriginal[nlocal][1] = buf[1];
|
||||
xoriginal[nlocal][2] = buf[2];
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack values in local atom-based arrays for restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::pack_restart(int i, double *buf)
|
||||
{
|
||||
buf[0] = 4;
|
||||
buf[1] = xoriginal[i][0];
|
||||
buf[2] = xoriginal[i][1];
|
||||
buf[3] = xoriginal[i][2];
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack values from atom->extra array to restart the fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::unpack_restart(int nlocal, int nth)
|
||||
{
|
||||
double **extra = atom->extra;
|
||||
|
||||
// skip to Nth set of extra values
|
||||
|
||||
int m = 0;
|
||||
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
|
||||
m++;
|
||||
|
||||
xoriginal[nlocal][0] = extra[nlocal][m++];
|
||||
xoriginal[nlocal][1] = extra[nlocal][m++];
|
||||
xoriginal[nlocal][2] = extra[nlocal][m++];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
maxsize of any atom's restart data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::maxsize_restart()
|
||||
{
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
size of atom nlocal's restart data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::size_restart(int nlocal)
|
||||
{
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Switching function.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::switch_func(double t)
|
||||
{
|
||||
if (sf == 1) return t;
|
||||
|
||||
double t2 = t*t;
|
||||
double t5 = t2*t2*t;
|
||||
return ((70.0*t2*t2 - 315.0*t2*t + 540.0*t2 - 420.0*t + 126.0)*t5);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Switching function derivative.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::dswitch_func(double t)
|
||||
{
|
||||
if(sf == 1) return 1.0/t_switch;
|
||||
|
||||
double t2 = t*t;
|
||||
double t4 = t2*t2;
|
||||
return ((630*t2*t2 - 2520*t2*t + 3780*t2 - 2520*t + 630)*t4) / t_switch;
|
||||
}
|
||||
/* -------------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* -------------------------------------------------------------------------
|
||||
Contributing authors:
|
||||
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
|
||||
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "fix_ti_spring.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "domain.h"
|
||||
#include "respa.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 6 || narg > 8)
|
||||
error->all(FLERR,"Illegal fix ti/spring command");
|
||||
|
||||
// Flags.
|
||||
restart_peratom = 1;
|
||||
scalar_flag = 1;
|
||||
global_freq = 1;
|
||||
vector_flag = 1;
|
||||
size_vector = 2;
|
||||
global_freq = 1;
|
||||
extscalar = 1;
|
||||
extvector = 1;
|
||||
|
||||
// Spring constant.
|
||||
k = force->numeric(FLERR,arg[3]);
|
||||
if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
|
||||
|
||||
// Perform initial allocation of atom-based array.
|
||||
// Registar with Atom class.
|
||||
xoriginal = NULL;
|
||||
grow_arrays(atom->nmax);
|
||||
atom->add_callback(0);
|
||||
atom->add_callback(1);
|
||||
|
||||
// xoriginal = initial unwrapped positions of atom.
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
tagint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
|
||||
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
|
||||
}
|
||||
|
||||
// Time variables.
|
||||
t_switch = atoi(arg[4]); // Switching time.
|
||||
t_equil = atoi(arg[5]); // Equilibration time.
|
||||
t0 = update->ntimestep; // Initial time.
|
||||
if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
|
||||
if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
|
||||
|
||||
// Coupling parameter initialization.
|
||||
sf = 1;
|
||||
if (narg > 6) {
|
||||
if (strcmp(arg[6], "function") == 0) sf = atoi(arg[7]);
|
||||
else error->all(FLERR,"Illegal fix ti/spring switching function");
|
||||
if ((sf!=1) && (sf!=2))
|
||||
error->all(FLERR,"Illegal fix ti/spring switching function");
|
||||
}
|
||||
lambda = switch_func(0);
|
||||
dlambda = dswitch_func(0);
|
||||
|
||||
espring = 0.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixTISpring::~FixTISpring()
|
||||
{
|
||||
// unregister callbacks to this fix from Atom class
|
||||
atom->delete_callback(id,0);
|
||||
atom->delete_callback(id,1);
|
||||
|
||||
// delete locally stored array
|
||||
memory->destroy(xoriginal);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= POST_FORCE;
|
||||
mask |= POST_FORCE_RESPA;
|
||||
mask |= MIN_POST_FORCE;
|
||||
mask |= THERMO_ENERGY;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::init()
|
||||
{
|
||||
if (strstr(update->integrate_style,"respa"))
|
||||
nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::setup(int vflag)
|
||||
{
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
post_force(vflag);
|
||||
else {
|
||||
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
|
||||
post_force_respa(vflag,nlevels_respa-1,0);
|
||||
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::min_setup(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::post_force(int vflag)
|
||||
{
|
||||
// If on the first equilibration do not calculate forces.
|
||||
int t = update->ntimestep - t0;
|
||||
if(t < t_equil) return;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
tagint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double dx, dy, dz;
|
||||
double unwrap[3];
|
||||
|
||||
espring = 0.0;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
dx = unwrap[0] - xoriginal[i][0];
|
||||
dy = unwrap[1] - xoriginal[i][1];
|
||||
dz = unwrap[2] - xoriginal[i][2];
|
||||
f[i][0] = (1-lambda) * f[i][0] + lambda * (-k*dx);
|
||||
f[i][1] = (1-lambda) * f[i][1] + lambda * (-k*dy);
|
||||
f[i][2] = (1-lambda) * f[i][2] + lambda * (-k*dz);
|
||||
espring += k * (dx*dx + dy*dy + dz*dz);
|
||||
}
|
||||
|
||||
espring *= 0.5;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::post_force_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
if (ilevel == nlevels_respa-1) post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::min_post_force(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::initial_integrate(int vflag)
|
||||
{
|
||||
// Update the coupling parameter value.
|
||||
double t = update->ntimestep - (t0+t_equil);
|
||||
|
||||
if( (t >= 0) && (t <= t_switch) ) {
|
||||
lambda = switch_func(t/t_switch);
|
||||
dlambda = dswitch_func(t/t_switch);
|
||||
}
|
||||
|
||||
if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
|
||||
lambda = switch_func(1.0 - (t - t_switch - t_equil)/t_switch );
|
||||
dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch );
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
energy of stretched springs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::compute_scalar()
|
||||
{
|
||||
double all;
|
||||
MPI_Allreduce(&espring,&all,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
return all;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
information about coupling parameter
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::compute_vector(int n)
|
||||
{
|
||||
linfo[0] = lambda;
|
||||
linfo[1] = dlambda;
|
||||
return linfo[n];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::memory_usage()
|
||||
{
|
||||
double bytes = atom->nmax*3 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::grow_arrays(int nmax)
|
||||
{
|
||||
memory->grow(xoriginal,nmax,3,"fix_ti/spring:xoriginal");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
copy values within local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::copy_arrays(int i, int j, int delflag)
|
||||
{
|
||||
xoriginal[j][0] = xoriginal[i][0];
|
||||
xoriginal[j][1] = xoriginal[i][1];
|
||||
xoriginal[j][2] = xoriginal[i][2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack values in local atom-based array for exchange with another proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::pack_exchange(int i, double *buf)
|
||||
{
|
||||
buf[0] = xoriginal[i][0];
|
||||
buf[1] = xoriginal[i][1];
|
||||
buf[2] = xoriginal[i][2];
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack values in local atom-based array from exchange with another proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
xoriginal[nlocal][0] = buf[0];
|
||||
xoriginal[nlocal][1] = buf[1];
|
||||
xoriginal[nlocal][2] = buf[2];
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack values in local atom-based arrays for restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::pack_restart(int i, double *buf)
|
||||
{
|
||||
buf[0] = 4;
|
||||
buf[1] = xoriginal[i][0];
|
||||
buf[2] = xoriginal[i][1];
|
||||
buf[3] = xoriginal[i][2];
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack values from atom->extra array to restart the fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixTISpring::unpack_restart(int nlocal, int nth)
|
||||
{
|
||||
double **extra = atom->extra;
|
||||
|
||||
// skip to Nth set of extra values
|
||||
|
||||
int m = 0;
|
||||
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
|
||||
m++;
|
||||
|
||||
xoriginal[nlocal][0] = extra[nlocal][m++];
|
||||
xoriginal[nlocal][1] = extra[nlocal][m++];
|
||||
xoriginal[nlocal][2] = extra[nlocal][m++];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
maxsize of any atom's restart data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::maxsize_restart()
|
||||
{
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
size of atom nlocal's restart data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixTISpring::size_restart(int nlocal)
|
||||
{
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Switching function.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::switch_func(double t)
|
||||
{
|
||||
if (sf == 1) return t;
|
||||
|
||||
double t2 = t*t;
|
||||
double t5 = t2*t2*t;
|
||||
return ((70.0*t2*t2 - 315.0*t2*t + 540.0*t2 - 420.0*t + 126.0)*t5);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Switching function derivative.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixTISpring::dswitch_func(double t)
|
||||
{
|
||||
if(sf == 1) return 1.0/t_switch;
|
||||
|
||||
double t2 = t*t;
|
||||
double t4 = t2*t2;
|
||||
return ((630*t2*t2 - 2520*t2*t + 3780*t2 - 2520*t + 630)*t4) / t_switch;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,94 +1,94 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors:
|
||||
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
|
||||
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(ti/spring,FixTISpring)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_TI_SPRING_H
|
||||
#define LMP_FIX_TI_SPRING_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixTISpring : public Fix {
|
||||
public:
|
||||
FixTISpring(class LAMMPS *, int, char **);
|
||||
~FixTISpring();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void min_post_force(int);
|
||||
void initial_integrate(int);
|
||||
double compute_scalar();
|
||||
double compute_vector(int);
|
||||
|
||||
double memory_usage();
|
||||
void grow_arrays(int);
|
||||
void copy_arrays(int, int, int);
|
||||
int pack_exchange(int, double *);
|
||||
int unpack_exchange(int, double *);
|
||||
int pack_restart(int, double *);
|
||||
void unpack_restart(int, int);
|
||||
int size_restart(int);
|
||||
int maxsize_restart();
|
||||
|
||||
private:
|
||||
double switch_func(double); // Switching function.
|
||||
double dswitch_func(double); // Switching function derivative.
|
||||
|
||||
double k; // Spring constant.
|
||||
double espring; // Springs energies.
|
||||
double **xoriginal; // Original coords of atoms.
|
||||
double lambda; // Coupling parameter.
|
||||
double dlambda; // Lambda variation with t.
|
||||
double linfo[2]; // Current lambda status.
|
||||
int t_switch; // Total switching steps.
|
||||
int t_equil; // Equilibration time.
|
||||
int t0; // Initial time.
|
||||
int sf; // Switching function option.
|
||||
int nlevels_respa;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#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: Illegal fix ti/spring switching function
|
||||
|
||||
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.
|
||||
|
||||
*/
|
||||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors:
|
||||
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
|
||||
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(ti/spring,FixTISpring)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_TI_SPRING_H
|
||||
#define LMP_FIX_TI_SPRING_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixTISpring : public Fix {
|
||||
public:
|
||||
FixTISpring(class LAMMPS *, int, char **);
|
||||
~FixTISpring();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void min_post_force(int);
|
||||
void initial_integrate(int);
|
||||
double compute_scalar();
|
||||
double compute_vector(int);
|
||||
|
||||
double memory_usage();
|
||||
void grow_arrays(int);
|
||||
void copy_arrays(int, int, int);
|
||||
int pack_exchange(int, double *);
|
||||
int unpack_exchange(int, double *);
|
||||
int pack_restart(int, double *);
|
||||
void unpack_restart(int, int);
|
||||
int size_restart(int);
|
||||
int maxsize_restart();
|
||||
|
||||
private:
|
||||
double switch_func(double); // Switching function.
|
||||
double dswitch_func(double); // Switching function derivative.
|
||||
|
||||
double k; // Spring constant.
|
||||
double espring; // Springs energies.
|
||||
double **xoriginal; // Original coords of atoms.
|
||||
double lambda; // Coupling parameter.
|
||||
double dlambda; // Lambda variation with t.
|
||||
double linfo[2]; // Current lambda status.
|
||||
int t_switch; // Total switching steps.
|
||||
int t_equil; // Equilibration time.
|
||||
int t0; // Initial time.
|
||||
int sf; // Switching function option.
|
||||
int nlevels_respa;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#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: Illegal fix ti/spring switching function
|
||||
|
||||
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.
|
||||
|
||||
*/
|
||||
|
|
|
|||
Loading…
Reference in New Issue