Homec4science
Diffusion lammps (master) Browse

lammps/src/fix_uniaxial.cpp
9e1f8bcd6ad4master

Last Change
Raw File

fix_uniaxial.cpp
View Options

/* ----------------------------------------------------------------------
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: Carsten Svaneborg
(Max Planck Institute for Complex Systems, Dresden, Germany)
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_uniaxial.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "comm.h"
#include "kspace.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixUniaxial::FixUniaxial(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 6) error->all("Illegal fix uniaxial command");
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix uniaxial command");
if (strcmp(arg[4],"x") == 0) dir = 0;
else if (strcmp(arg[4],"y") == 0) dir = 1;
else if (strcmp(arg[4],"z") == 0) dir = 2;
else error->all("Illegal fix uniaxial command");
lambda_final = atof(arg[5]);
if (lambda_final <= 0) error->all("Illegal fix uniaxial command");
if (domain->nonperiodic)
error->all("Cannot use fix uniaxial on non-periodic system");
if (domain->triclinic)
error->all("Cannot use fix uniaxial with triclinic box");
nrigid = 0;
rfix = NULL;
}
/* ---------------------------------------------------------------------- */
FixUniaxial::~FixUniaxial()
{
delete [] rfix;
}
/* ---------------------------------------------------------------------- */
int FixUniaxial::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixUniaxial::init()
{
// store pointers to domain variable so can loop over dimensions
domainlo[0] = &domain->boxxlo;
domainlo[1] = &domain->boxylo;
domainlo[2] = &domain->boxzlo;
domainhi[0] = &domain->boxxhi;
domainhi[1] = &domain->boxyhi;
domainhi[2] = &domain->boxzhi;
domainprd[0] = &domain->xprd;
domainprd[1] = &domain->yprd;
domainprd[2] = &domain->zprd;
double L = pow((domain->boxxhi-domain->boxxlo)*
(domain->boxyhi-domain->boxylo)*
(domain->boxzhi-domain->boxzlo) ,1.0/3.0);
// save box sizes for coordinate rescaling
// calculate strains and asymmetry parameter
// alpha=lampdai[first]/lampbdai[second] for the two perp directions
alpha0 = 1.0;
for (int m = 0; m < 3; m++) {
domainloi[m] = *domainlo[m];
domainhii[m] = *domainhi[m];
lambdai[m] = (*domainhi[m] - *domainlo[m])/L;
lambdaf[m] = ( m==dir ? lambda_final : 1.0/sqrt(lambda_final) ) ;
if (m != dir) {
alpha0*= lambdai[m];
alpha0=1.0/alpha0;
}
}
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Initial strain = %g %g %g\n",
lambdai[0],lambdai[1],lambdai[2]);
fprintf(screen,"Target strain = %g %g %g\n",
lambdaf[0],lambdaf[1],lambdaf[2]);
}
if (logfile) {
fprintf(logfile,"Initial strain = %g %g %g\n",
lambdai[0],lambdai[1],lambdai[2]);
fprintf(logfile,"Target strain = %g %g %g\n",
lambdaf[0],lambdaf[1],lambdaf[2]);
}
}
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
// detect if any fix rigid exist so rigid bodies can be re-scaled
// rfix[] = indices to each fix rigid
delete [] rfix;
nrigid = 0;
rfix = NULL;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0 ||
strcmp(modify->fix[i]->style,"poems") == 0) nrigid++;
if (nrigid) {
rfix = new int[nrigid];
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0 ||
strcmp(modify->fix[i]->style,"poems") == 0) rfix[nrigid++] = i;
}
}
/* ---------------------------------------------------------------------- */
void FixUniaxial::end_of_step()
{
int i,m;
double oldlo,oldhi,newlo,newhi,ratio;
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
double lvalue[3];
// linear interpolation of strain in specified direction
lvalue[dir] = lambdai[dir]*(1.0-delta) + lambdaf[dir]*delta;
// linear interpolation of asymmetry parameter in the perp direction
double alpha = alpha0*(1-delta) + delta;
// calculate strains perpendicular to dir
for (m = 0; m < 3; m++)
if (m != dir) {
lvalue[m] = sqrt(alpha/lvalue[dir]);
alpha=1.0/alpha;
}
// apply appropriate rescaling in each dimension
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (m = 0; m < 3; m++) {
oldlo = *domainlo[m];
oldhi = *domainhi[m];
newlo = domainloi[m] * lvalue[m]/lambdai[m];
newhi = domainhii[m] * lvalue[m]/lambdai[m];
ratio = (newhi - newlo) / *domainprd[m];
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
x[i][m] = newlo + (x[i][m] - oldlo) * ratio;
*domainlo[m] = newlo;
*domainhi[m] = newhi;
*domainprd[m] = newhi - newlo;
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->dilate(m,oldlo,oldhi,newlo,newhi);
}
// redo KSpace coeffs since volume has changed
if (kspace_flag) force->kspace->setup();
}
c4science · Help