git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/fix_indent.cpp
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339
src/fix_indent.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Ravi Agrawal (Northwestern U)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "stdlib.h"
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#include "fix_indent.h"
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#include "atom.h"
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#include "domain.h"
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#include "update.h"
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#include "output.h"
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#include "respa.h"
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#include "error.h"
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#define NONE 0
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#define SPHERE 1
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#define CYLINDER 2
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/* ---------------------------------------------------------------------- */
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FixIndent::FixIndent(int narg, char **arg) : Fix(narg, arg)
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{
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if (narg < 4) error->all("Illegal fix indent command");
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k = atof(arg[3]);
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// set input line defaults
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istyle = NONE;
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vx = vy = vz = 0.0;
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scaleflag = 1;
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radflag = 0;
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r0_start = 0.0;
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// read options from end of input line
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options(narg-4,&arg[4]);
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// setup scaling
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if (scaleflag && strcmp(domain->lattice_style,"none") == 0)
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error->all("Use of fix indent with undefined lattice");
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double xscale,yscale,zscale;
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if (scaleflag) {
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xscale = domain->xlattice;
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yscale = domain->ylattice;
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zscale = domain->zlattice;
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}
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else xscale = yscale = zscale = 1.0;
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// apply scaling to indenter force constant, geometry, and velocity
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k /= xscale;
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k3 = k/3.0;
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vx *= xscale;
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vy *= yscale;
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vz *= zscale;
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if (istyle == SPHERE) {
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x0 *= xscale;
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y0 *= yscale;
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z0 *= zscale;
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r0_stop *= xscale;
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r0_start *= xscale;
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} else if (istyle == CYLINDER) {
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if (cdim == 0) {
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c1 *= yscale;
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c2 *= zscale;
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r0_stop *= xscale;
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r0_start *= xscale;
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} else if (cdim == 1) {
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c1 *= xscale;
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c2 *= zscale;
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r0_stop *= yscale;
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r0_start *= yscale;
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} else if (cdim == 2) {
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c1 *= xscale;
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c2 *= yscale;
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r0_stop *= zscale;
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r0_start *= zscale;
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}
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} else error->all("Illegal fix indent command");
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// time 0 for the indenter movement
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ntimestep_initial = update->ntimestep;
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}
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/* ---------------------------------------------------------------------- */
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int FixIndent::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= THERMO;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixIndent::init()
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{
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if (strcmp(update->integrate_style,"respa") == 0)
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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if (thermo_print || thermo_energy) thermo_flag = 1;
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else thermo_flag = 0;
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}
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/* ---------------------------------------------------------------------- */
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void FixIndent::setup()
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{
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eflag_on = 1;
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if (strcmp(update->integrate_style,"verlet") == 0)
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post_force(1);
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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(1,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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eflag_on = 0;
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}
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/* ---------------------------------------------------------------------- */
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void FixIndent::min_setup()
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{
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eflag_on = 1;
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post_force(1);
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}
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/* ---------------------------------------------------------------------- */
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void FixIndent::post_force(int vflag)
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{
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bool eflag = false;
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if (thermo_flag) {
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if (eflag_on) eflag = true;
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else if (output->next_thermo == update->ntimestep) eflag = true;
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}
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if (eflag) eng = 0.0;
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// set current r0
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// for minimization, always set to r0_stop
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double r0;
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if (!radflag || update->whichflag) r0 = r0_stop;
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else {
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double delta = update->ntimestep - update->beginstep;
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delta /= update->endstep - update->beginstep;
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r0 = r0_start + delta * (r0_stop-r0_start);
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}
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// spherical indenter
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if (istyle == SPHERE) {
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// x1,y1,z1 = current position of indenter from original x0,y0,z0
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double delta = (update->ntimestep - ntimestep_initial) * update->dt;
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double x1 = x0 + delta*vx;
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double y1 = y0 + delta*vy;
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double z1 = z0 + delta*vz;
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double **x = atom->x;
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double **f = atom->f;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double delx,dely,delz,r,dr,fmag;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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delx = x[i][0] - x1;
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dely = x[i][1] - y1;
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delz = x[i][2] - z1;
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r = sqrt(delx*delx + dely*dely + delz*delz);
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dr = r - r0;
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if (dr >= 0.0) continue;
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fmag = k*dr*dr;
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f[i][0] += delx*fmag/r;
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f[i][1] += dely*fmag/r;
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f[i][2] += delz*fmag/r;
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if (eflag) eng -= k3 * dr*dr*dr;
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}
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// cylindrical indenter
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} else {
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// c1new,c2new = current coords of indenter axis from original c1,c2
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double delta = (update->ntimestep - ntimestep_initial) * update->dt;
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double c1new,c2new;
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if (cdim == 0) {
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c1new = c1 + delta*vy;
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c2new = c2 + delta*vz;
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} else if (cdim == 1) {
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c1new = c1 + delta*vx;
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c2new = c2 + delta*vz;
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} else {
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c1new = c1 + delta*vx;
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c2new = c2 + delta*vy;
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}
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double **x = atom->x;
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double **f = atom->f;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double delx,dely,delz,r,dr,fmag;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (cdim == 0) {
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delx = 0;
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dely = x[i][1] - c1new;
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delz = x[i][2] - c2new;
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} else if (cdim == 1) {
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delx = x[i][0] - c1new;
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dely = 0;
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delz = x[i][2] - c2new;
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} else {
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delx = x[i][0] - c1new;
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dely = x[i][1] - c2new;
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delz = 0;
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}
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r = sqrt(delx*delx + dely*dely + delz*delz);
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dr = r - r0;
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if (dr >= 0.0) continue;
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fmag = k*dr*dr;
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f[i][0] += delx*fmag/r;
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f[i][1] += dely*fmag/r;
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f[i][2] += delz*fmag/r;
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if (eflag) eng -= k3 * dr*dr*dr;
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}
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}
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if (eflag) MPI_Allreduce(&eng,&etotal,1,MPI_DOUBLE,MPI_SUM,world);
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}
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/* ---------------------------------------------------------------------- */
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void FixIndent::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 FixIndent::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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int FixIndent::thermo_fields(int n, int *flags, char **keywords)
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{
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if (n == 0) return 1;
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flags[0] = 3;
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strcpy(keywords[0],"Indent");
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return 1;
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}
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/* ---------------------------------------------------------------------- */
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int FixIndent::thermo_compute(double *values)
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{
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values[0] = etotal;
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return 1;
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}
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/* ----------------------------------------------------------------------
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parse optional parameters at end of fix indent input line
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------------------------------------------------------------------------- */
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void FixIndent::options(int narg, char **arg)
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{
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if (narg < 0) error->all("Illegal fix indent command");
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int iarg = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"sphere") == 0) {
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if (iarg+5 > narg) error->all("Illegal fix indent command");
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x0 = atof(arg[iarg+1]);
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y0 = atof(arg[iarg+2]);
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z0 = atof(arg[iarg+3]);
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r0_stop = atof(arg[iarg+4]);
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istyle = SPHERE;
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iarg += 5;
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} else if (strcmp(arg[iarg],"cylinder") == 0) {
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if (iarg+5 > narg) error->all("Illegal fix indent command");
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if (strcmp(arg[iarg+1],"x") == 0) cdim = 0;
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else if (strcmp(arg[iarg+1],"y") == 0) cdim = 1;
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else if (strcmp(arg[iarg+1],"z") == 0) cdim = 2;
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else error->all("Illegal fix indent command");
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c1 = atof(arg[iarg+2]);
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c2 = atof(arg[iarg+3]);
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r0_stop = atof(arg[iarg+4]);
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istyle = CYLINDER;
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iarg += 5;
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} else if (strcmp(arg[iarg],"vel") == 0) {
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if (iarg+4 > narg) error->all("Illegal fix indent command");
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vx = atof(arg[iarg+1]);
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vy = atof(arg[iarg+2]);
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vz = atof(arg[iarg+3]);
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iarg += 4;
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} else if (strcmp(arg[iarg],"rstart") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix indent command");
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radflag = 1;
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r0_start = atof(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"units") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix indent command");
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if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
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else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
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else error->all("Illegal fix indent command");
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iarg += 2;
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} else error->all("Illegal fix indent command");
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}
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}
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