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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10957 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-11-04 20:55:25 +00:00
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2
src/USER-MISC/README
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@ -37,6 +37,8 @@ dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009 fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009
fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008 fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
fix ti/rs, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
improper_style cossq, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12 improper_style cossq, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
improper_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 improper_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12 improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12

197
src/USER-MISC/fix_ti_rs.cpp Executable file
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@ -0,0 +1,197 @@
/* -------------------------------------------------------------------------
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 "math.h"
#include "fix_ti_rs.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
// Class constructor initialize all variables.
FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
// Checking the input information.
if (narg < 7 || narg > 9) error->all(FLERR,"Illegal fix ti/rs command");
// Fix flags.
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 1;
// Time variables.
t_switch = atof(arg[5]);
t_equil = atof(arg[6]);
t0 = update->ntimestep;
if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/rs command");
if (t_equil < 0.0) error->all(FLERR,"Illegal fix ti/rs command");
// Coupling parameter limits and initialization.
l_initial = atof(arg[3]);
l_final = atof(arg[4]);
sf = 1;
if (narg > 7) {
if (strcmp(arg[7], "function") == 0) sf = atoi(arg[8]);
else error->all(FLERR,"Illegal fix ti/rs switching function");
if ((sf<1) || (sf>3))
error->all(FLERR,"Illegal fix ti/rs switching function");
}
lambda = switch_func(0);
dlambda = dswitch_func(0);
}
/* ---------------------------------------------------------------------- */
FixTIRS::~FixTIRS()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
}
/* ---------------------------------------------------------------------- */
int FixTIRS::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTIRS::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixTIRS::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 FixTIRS::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTIRS::post_force(int vflag)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
double **f = atom->f;
// Scaling forces.
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
f[i][0] = lambda * f[i][0];
f[i][1] = lambda * f[i][1];
f[i][2] = lambda * f[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixTIRS::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTIRS::min_post_force(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTIRS::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);
}
}
/* ---------------------------------------------------------------------- */
double FixTIRS::compute_vector(int n)
{
linfo[0] = lambda;
linfo[1] = dlambda;
return linfo[n];
}
/* ---------------------------------------------------------------------- */
double FixTIRS::switch_func(double t)
{
if (sf == 2) return l_initial / (1 + t * (l_initial/l_final - 1));
if (sf == 3) return l_initial / (1 + log2(1+t) * (l_initial/l_final - 1));
// Default option is sf = 1.
return l_initial + (l_final - l_initial) * t;
}
/* ---------------------------------------------------------------------- */
double FixTIRS::dswitch_func(double t)
{
double aux = (1.0/l_initial - 1.0/l_final);
if (sf == 2) return lambda * lambda * aux / t_switch;
if (sf == 3) return lambda * lambda * aux / (t_switch * log(2) * (1 + t));
// Default option is sf = 1.
return (l_final-l_initial)/t_switch;
}

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src/USER-MISC/fix_ti_rs.h Executable file
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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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(ti/rs,FixTIRS)
#else
#ifndef LMP_FIX_TI_RS_H
#define LMP_FIX_TI_RS_H
#include "fix.h"
namespace LAMMPS_NS {
class FixTIRS : public Fix {
public:
FixTIRS(class LAMMPS *, int, char **);
~FixTIRS();
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);
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

359
src/USER-MISC/fix_ti_spring.cpp Executable file
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@ -0,0 +1,359 @@
/* -------------------------------------------------------------------------
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"
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;
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extscalar = 1;
extvector = 1;
// Spring constant.
k = atof(arg[3]);
espring = 0.0;
if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
// Initial position.
xoriginal = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
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 = atof(arg[4]); // Switching time.
t_equil = atof(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);
}
/* ---------------------------------------------------------------------- */
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;
espring = 0.0;
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];
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)
{
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;
}

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src/USER-MISC/fix_ti_spring.h Executable file
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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.
------------------------------------------------------------------------- */
#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 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.
*/