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fix_indent.cpp
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Sat, Aug 10, 07:16
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rLAMMPS lammps
fix_indent.cpp
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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 author: Ravi Agrawal (Northwestern U)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_indent.h"
#include "atom.h"
#include "domain.h"
#include "lattice.h"
#include "update.h"
#include "output.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{NONE,SPHERE,CYLINDER,PLANE};
enum{INSIDE,OUTSIDE};
/* ---------------------------------------------------------------------- */
FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4) error->all("Illegal fix indent command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
global_freq = 1;
extscalar = 1;
extvector = 1;
k = atof(arg[3]);
// read options from end of input line
options(narg-4,&arg[4]);
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all("Use of fix indent with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// apply scaling factors to force constant, velocity, and geometry
k /= xscale;
k3 = k/3.0;
vx *= xscale;
vy *= yscale;
vz *= zscale;
if (istyle == SPHERE) {
x0 *= xscale;
y0 *= yscale;
z0 *= zscale;
r0_stop *= xscale;
r0_start *= xscale;
} else if (istyle == CYLINDER) {
if (cdim == 0) {
c1 *= yscale;
c2 *= zscale;
r0_stop *= xscale;
r0_start *= xscale;
} else if (cdim == 1) {
c1 *= xscale;
c2 *= zscale;
r0_stop *= yscale;
r0_start *= yscale;
} else if (cdim == 2) {
c1 *= xscale;
c2 *= yscale;
r0_stop *= zscale;
r0_start *= zscale;
}
} else if (istyle == PLANE) {
if (cdim == 0) planepos *= xscale;
else if (cdim == 1) planepos *= yscale;
else if (cdim == 2) planepos *= zscale;
} else error->all("Illegal fix indent command");
indenter_flag = 0;
indenter[0] = indenter[1] = indenter[2] = indenter[3] = 0.0;
}
/* ---------------------------------------------------------------------- */
int FixIndent::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixIndent::init()
{
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixIndent::setup(int vflag)
{
if (strcmp(update->integrate_style,"verlet") == 0)
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 FixIndent::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixIndent::post_force(int vflag)
{
// set current r0
// for minimization, always set to r0_stop
double r0;
if (!radflag || update->whichflag == 2) r0 = r0_stop;
else {
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
r0 = r0_start + delta * (r0_stop-r0_start);
}
// indenter values, 0 = energy, 1-3 = force components
indenter_flag = 0;
indenter[0] = indenter[1] = indenter[2] = indenter[3] = 0.0;
// spherical indenter
if (istyle == SPHERE) {
// ctr = current indenter center from original x0,y0,z0
// remap into periodic box
double ctr[3];
double delta = (update->ntimestep - update->beginstep) * update->dt;
ctr[0] = x0 + delta*vx;
ctr[1] = y0 + delta*vy;
ctr[2] = z0 + delta*vz;
domain->remap(ctr);
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double delx,dely,delz,r,dr,fmag,fx,fy,fz;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
delx = x[i][0] - ctr[0];
dely = x[i][1] - ctr[1];
delz = x[i][2] - ctr[2];
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
if (side == OUTSIDE) {
dr = r - r0;
fmag = k*dr*dr;
} else {
dr = r0 - r;
fmag = -k*dr*dr;
}
if (dr >= 0.0) continue;
fx = delx*fmag/r;
fy = dely*fmag/r;
fz = delz*fmag/r;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
indenter[0] -= k3 * dr*dr*dr;
indenter[1] -= fx;
indenter[2] -= fy;
indenter[3] -= fz;
}
// cylindrical indenter
} else if (istyle == CYLINDER) {
// ctr = current indenter axis from original c1,c2
// remap into periodic box
// 3rd coord is just near box for remap(), since isn't used
double ctr[3];
double delta = (update->ntimestep - update->beginstep) * update->dt;
if (cdim == 0) {
ctr[0] = domain->boxlo[0];
ctr[1] = c1 + delta*vy;
ctr[2] = c2 + delta*vz;
} else if (cdim == 1) {
ctr[0] = c1 + delta*vx;
ctr[1] = domain->boxlo[1];
ctr[2] = c2 + delta*vz;
} else {
ctr[0] = c1 + delta*vx;
ctr[1] = c2 + delta*vy;
ctr[2] = domain->boxlo[2];
}
domain->remap(ctr);
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double delx,dely,delz,r,dr,fmag,fx,fy,fz;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (cdim == 0) {
delx = 0;
dely = x[i][1] - ctr[1];
delz = x[i][2] - ctr[2];
} else if (cdim == 1) {
delx = x[i][0] - ctr[0];
dely = 0;
delz = x[i][2] - ctr[2];
} else {
delx = x[i][0] - ctr[0];
dely = x[i][1] - ctr[1];
delz = 0;
}
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
if (side == OUTSIDE) {
dr = r - r0;
fmag = k*dr*dr;
} else {
dr = r0 - r;
fmag = -k*dr*dr;
}
if (dr >= 0.0) continue;
fx = delx*fmag/r;
fy = dely*fmag/r;
fz = delz*fmag/r;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
indenter[0] -= k3 * dr*dr*dr;
indenter[1] -= fx;
indenter[2] -= fy;
indenter[3] -= fz;
}
// planar indenter
} else {
// posnew = current coord of plane from original planepos
double delta = (update->ntimestep - update->beginstep) * update->dt;
double posnew;
if (cdim == 0) posnew = planepos + delta*vx;
else if (cdim == 1) posnew = planepos + delta*vy;
else if (cdim == 2) posnew = planepos + delta*vz;
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double dr,fatom;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dr = planeside * (posnew - x[i][cdim]);
if (dr >= 0.0) continue;
fatom = -planeside * k*dr*dr;
f[i][cdim] += fatom;
indenter[0] -= k3 * dr*dr*dr;
indenter[cdim+1] -= fatom;
}
}
}
/* ---------------------------------------------------------------------- */
void FixIndent::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixIndent::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
energy of indenter interaction
------------------------------------------------------------------------- */
double FixIndent::compute_scalar()
{
// only sum across procs one time
if (indenter_flag == 0) {
MPI_Allreduce(indenter,indenter_all,4,MPI_DOUBLE,MPI_SUM,world);
indenter_flag = 1;
}
return indenter_all[0];
}
/* ----------------------------------------------------------------------
components of force on indenter
------------------------------------------------------------------------- */
double FixIndent::compute_vector(int n)
{
// only sum across procs one time
if (indenter_flag == 0) {
MPI_Allreduce(indenter,indenter_all,4,MPI_DOUBLE,MPI_SUM,world);
indenter_flag = 1;
}
return indenter_all[n+1];
}
/* ----------------------------------------------------------------------
parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixIndent::options(int narg, char **arg)
{
if (narg < 0) error->all("Illegal fix indent command");
istyle = NONE;
vx = vy = vz = 0.0;
radflag = 0;
r0_start = 0.0;
scaleflag = 1;
side = OUTSIDE;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"sphere") == 0) {
if (iarg+5 > narg) error->all("Illegal fix indent command");
x0 = atof(arg[iarg+1]);
y0 = atof(arg[iarg+2]);
z0 = atof(arg[iarg+3]);
r0_stop = atof(arg[iarg+4]);
istyle = SPHERE;
iarg += 5;
} else if (strcmp(arg[iarg],"cylinder") == 0) {
if (iarg+5 > narg) error->all("Illegal fix indent command");
if (strcmp(arg[iarg+1],"x") == 0) cdim = 0;
else if (strcmp(arg[iarg+1],"y") == 0) cdim = 1;
else if (strcmp(arg[iarg+1],"z") == 0) cdim = 2;
else error->all("Illegal fix indent command");
c1 = atof(arg[iarg+2]);
c2 = atof(arg[iarg+3]);
r0_stop = atof(arg[iarg+4]);
istyle = CYLINDER;
iarg += 5;
} else if (strcmp(arg[iarg],"plane") == 0) {
if (iarg+4 > narg) error->all("Illegal fix indent command");
if (strcmp(arg[iarg+1],"x") == 0) cdim = 0;
else if (strcmp(arg[iarg+1],"y") == 0) cdim = 1;
else if (strcmp(arg[iarg+1],"z") == 0) cdim = 2;
else error->all("Illegal fix indent command");
planepos = atof(arg[iarg+2]);
if (strcmp(arg[iarg+3],"lo") == 0) planeside = -1;
else if (strcmp(arg[iarg+3],"hi") == 0) planeside = 1;
else error->all("Illegal fix indent command");
istyle = PLANE;
iarg += 4;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+4 > narg) error->all("Illegal fix indent command");
vx = atof(arg[iarg+1]);
vy = atof(arg[iarg+2]);
vz = atof(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"rstart") == 0) {
if (iarg+2 > narg) error->all("Illegal fix indent command");
radflag = 1;
r0_start = atof(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal fix indent command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all("Illegal fix indent command");
iarg += 2;
} else if (strcmp(arg[iarg],"side") == 0) {
if (iarg+2 > narg) error->all("Illegal fix indent command");
if (strcmp(arg[iarg+1],"in") == 0) side = INSIDE;
else if (strcmp(arg[iarg+1],"out") == 0) side = OUTSIDE;
else error->all("Illegal fix indent command");
iarg += 2;
} else error->all("Illegal fix indent command");
}
}
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