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fix_deform.cpp
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Sun, Nov 10, 21:13

fix_deform.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: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "fix_deform.h"
#include "atom.h"
#include "update.h"
#include "comm.h"
#include "irregular.h"
#include "domain.h"
#include "lattice.h"
#include "force.h"
#include "modify.h"
#include "math_const.h"
#include "kspace.h"
#include "input.h"
#include "variable.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE};
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
// same as domain.cpp, fix_nvt_sllod.cpp, compute_temp_deform.cpp
enum{NO_REMAP,X_REMAP,V_REMAP};
/* ---------------------------------------------------------------------- */
FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
rfix(NULL), irregular(NULL), set(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix deform command");
no_change_box = 1;
restart_global = 1;
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix deform command");
// set defaults
set = new Set[6];
memset(set,0,6*sizeof(Set));
// parse arguments
triclinic = domain->triclinic;
int index;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 ||
strcmp(arg[iarg],"y") == 0 ||
strcmp(arg[iarg],"z") == 0) {
if (strcmp(arg[iarg],"x") == 0) index = 0;
else if (strcmp(arg[iarg],"y") == 0) index = 1;
else if (strcmp(arg[iarg],"z") == 0) index = 2;
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
if (strcmp(arg[iarg+1],"final") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = FINAL;
set[index].flo = force->numeric(FLERR,arg[iarg+2]);
set[index].fhi = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = DELTA;
set[index].dlo = force->numeric(FLERR,arg[iarg+2]);
set[index].dhi = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg+1],"scale") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = SCALE;
set[index].scale = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"vel") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = VEL;
set[index].vel = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"erate") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = ERATE;
set[index].rate = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"trate") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = TRATE;
set[index].rate = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"volume") == 0) {
set[index].style = VOLUME;
iarg += 2;
} else if (strcmp(arg[iarg+1],"wiggle") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = WIGGLE;
set[index].amplitude = force->numeric(FLERR,arg[iarg+2]);
set[index].tperiod = force->numeric(FLERR,arg[iarg+3]);
if (set[index].tperiod <= 0.0)
error->all(FLERR,"Illegal fix deform command");
iarg += 4;
} else if (strcmp(arg[iarg+1],"variable") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = VARIABLE;
if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
error->all(FLERR,"Illegal fix deform command");
if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
error->all(FLERR,"Illegal fix deform command");
delete [] set[index].hstr;
delete [] set[index].hratestr;
int n = strlen(&arg[iarg+2][2]) + 1;
set[index].hstr = new char[n];
strcpy(set[index].hstr,&arg[iarg+2][2]);
n = strlen(&arg[iarg+3][2]) + 1;
set[index].hratestr = new char[n];
strcpy(set[index].hratestr,&arg[iarg+3][2]);
iarg += 4;
} else error->all(FLERR,"Illegal fix deform command");
} else if (strcmp(arg[iarg],"xy") == 0 ||
strcmp(arg[iarg],"xz") == 0 ||
strcmp(arg[iarg],"yz") == 0) {
if (triclinic == 0)
error->all(FLERR,"Fix deform tilt factors require triclinic box");
if (strcmp(arg[iarg],"xy") == 0) index = 5;
else if (strcmp(arg[iarg],"xz") == 0) index = 4;
else if (strcmp(arg[iarg],"yz") == 0) index = 3;
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
if (strcmp(arg[iarg+1],"final") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = FINAL;
set[index].ftilt = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = DELTA;
set[index].dtilt = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"vel") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = VEL;
set[index].vel = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"erate") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = ERATE;
set[index].rate = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"trate") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = TRATE;
set[index].rate = force->numeric(FLERR,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"wiggle") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = WIGGLE;
set[index].amplitude = force->numeric(FLERR,arg[iarg+2]);
set[index].tperiod = force->numeric(FLERR,arg[iarg+3]);
if (set[index].tperiod <= 0.0)
error->all(FLERR,"Illegal fix deform command");
iarg += 4;
} else if (strcmp(arg[iarg+1],"variable") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deform command");
set[index].style = VARIABLE;
if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
error->all(FLERR,"Illegal fix deform command");
if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
error->all(FLERR,"Illegal fix deform command");
delete [] set[index].hstr;
delete [] set[index].hratestr;
int n = strlen(&arg[iarg+2][2]) + 1;
set[index].hstr = new char[n];
strcpy(set[index].hstr,&arg[iarg+2][2]);
n = strlen(&arg[iarg+3][2]) + 1;
set[index].hratestr = new char[n];
strcpy(set[index].hratestr,&arg[iarg+3][2]);
iarg += 4;
} else error->all(FLERR,"Illegal fix deform command");
} else break;
}
// read options from end of input line
// no x remap effectively moves atoms within box, so set restart_pbc
options(narg-iarg,&arg[iarg]);
if (remapflag != X_REMAP) restart_pbc = 1;
// setup dimflags used by other classes to check for volume-change conflicts
for (int i = 0; i < 6; i++)
if (set[i].style == NONE) dimflag[i] = 0;
else dimflag[i] = 1;
if (dimflag[0] || dimflag[1] || dimflag[2]) box_change_size = 1;
if (dimflag[3] || dimflag[4] || dimflag[5]) box_change_shape = 1;
// no tensile deformation on shrink-wrapped dims
// b/c shrink wrap will change box-length
if (set[0].style &&
(domain->boundary[0][0] >= 2 || domain->boundary[0][1] >= 2))
error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary");
if (set[1].style &&
(domain->boundary[1][0] >= 2 || domain->boundary[1][1] >= 2))
error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary");
if (set[2].style &&
(domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2))
error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary");
// no tilt deformation on shrink-wrapped 2nd dim
// b/c shrink wrap will change tilt factor in domain::reset_box()
if (set[3].style &&
(domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2))
error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim");
if (set[4].style &&
(domain->boundary[2][0] >= 2 || domain->boundary[2][1] >= 2))
error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim");
if (set[5].style &&
(domain->boundary[1][0] >= 2 || domain->boundary[1][1] >= 2))
error->all(FLERR,"Cannot use fix deform tilt on a shrink-wrapped 2nd dim");
// apply scaling to FINAL,DELTA,VEL,WIGGLE since they have dist/vel units
int flag = 0;
for (int i = 0; i < 6; i++)
if (set[i].style == FINAL || set[i].style == DELTA ||
set[i].style == VEL || set[i].style == WIGGLE) flag = 1;
double xscale,yscale,zscale;
if (flag && scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// for 3,4,5: scaling is in 1st dimension, e.g. x for xz
double map[6];
map[0] = xscale; map[1] = yscale; map[2] = zscale;
map[3] = yscale; map[4] = xscale; map[5] = xscale;
for (int i = 0; i < 3; i++) {
if (set[i].style == FINAL) {
set[i].flo *= map[i];
set[i].fhi *= map[i];
} else if (set[i].style == DELTA) {
set[i].dlo *= map[i];
set[i].dhi *= map[i];
} else if (set[i].style == VEL) {
set[i].vel *= map[i];
} else if (set[i].style == WIGGLE) {
set[i].amplitude *= map[i];
}
}
for (int i = 3; i < 6; i++) {
if (set[i].style == FINAL) set[i].ftilt *= map[i];
else if (set[i].style == DELTA) set[i].dtilt *= map[i];
else if (set[i].style == VEL) set[i].vel *= map[i];
else if (set[i].style == WIGGLE) set[i].amplitude *= map[i];
}
// for VOLUME, setup links to other dims
// fixed, dynamic1, dynamic2
for (int i = 0; i < 3; i++) {
if (set[i].style != VOLUME) continue;
int other1 = (i+1) % 3;
int other2 = (i+2) % 3;
if (set[other1].style == NONE) {
if (set[other2].style == NONE || set[other2].style == VOLUME)
error->all(FLERR,"Fix deform volume setting is invalid");
set[i].substyle = ONE_FROM_ONE;
set[i].fixed = other1;
set[i].dynamic1 = other2;
} else if (set[other2].style == NONE) {
if (set[other1].style == NONE || set[other1].style == VOLUME)
error->all(FLERR,"Fix deform volume setting is invalid");
set[i].substyle = ONE_FROM_ONE;
set[i].fixed = other2;
set[i].dynamic1 = other1;
} else if (set[other1].style == VOLUME) {
if (set[other2].style == NONE || set[other2].style == VOLUME)
error->all(FLERR,"Fix deform volume setting is invalid");
set[i].substyle = TWO_FROM_ONE;
set[i].fixed = other1;
set[i].dynamic1 = other2;
} else if (set[other2].style == VOLUME) {
if (set[other1].style == NONE || set[other1].style == VOLUME)
error->all(FLERR,"Fix deform volume setting is invalid");
set[i].substyle = TWO_FROM_ONE;
set[i].fixed = other2;
set[i].dynamic1 = other1;
} else {
set[i].substyle = ONE_FROM_TWO;
set[i].dynamic1 = other1;
set[i].dynamic2 = other2;
}
}
// set varflag
varflag = 0;
for (int i = 0; i < 6; i++)
if (set[i].style == VARIABLE) varflag = 1;
// set initial values at time fix deform is issued
for (int i = 0; i < 3; i++) {
set[i].lo_initial = domain->boxlo[i];
set[i].hi_initial = domain->boxhi[i];
set[i].vol_initial = domain->xprd * domain->yprd * domain->zprd;
}
set[3].tilt_initial = domain->yz;
set[4].tilt_initial = domain->xz;
set[5].tilt_initial = domain->xy;
// reneighboring only forced if flips can occur due to shape changes
if (flipflag && (set[3].style || set[4].style || set[5].style))
force_reneighbor = 1;
next_reneighbor = -1;
nrigid = 0;
flip = 0;
if (force_reneighbor) irregular = new Irregular(lmp);
else irregular = NULL;
TWOPI = 2.0*MY_PI;
}
/* ---------------------------------------------------------------------- */
FixDeform::~FixDeform()
{
if(set) {
for (int i = 0; i < 6; i++) {
delete [] set[i].hstr;
delete [] set[i].hratestr;
}
}
delete [] set;
delete [] rfix;
delete irregular;
// reset domain's h_rate = 0.0, since this fix may have made it non-zero
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
h_rate[0] = h_rate[1] = h_rate[2] =
h_rate[3] = h_rate[4] = h_rate[5] = 0.0;
h_ratelo[0] = h_ratelo[1] = h_ratelo[2] = 0.0;
}
/* ---------------------------------------------------------------------- */
int FixDeform::setmask()
{
int mask = 0;
if (force_reneighbor) mask |= PRE_EXCHANGE;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixDeform::init()
{
// error if more than one fix deform
// domain, fix nvt/sllod, compute temp/deform only work on single h_rate
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) count++;
if (count > 1) error->all(FLERR,"More than one fix deform");
// Kspace setting
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
// elapsed time for entire simulation, including multiple runs if defined
double delt = (update->endstep - update->beginstep) * update->dt;
// check variables for VARIABLE style
for (int i = 0; i < 6; i++) {
if (set[i].style != VARIABLE) continue;
set[i].hvar = input->variable->find(set[i].hstr);
if (set[i].hvar < 0)
error->all(FLERR,"Variable name for fix deform does not exist");
if (!input->variable->equalstyle(set[i].hvar))
error->all(FLERR,"Variable for fix deform is invalid style");
set[i].hratevar = input->variable->find(set[i].hratestr);
if (set[i].hratevar < 0)
error->all(FLERR,"Variable name for fix deform does not exist");
if (!input->variable->equalstyle(set[i].hratevar))
error->all(FLERR,"Variable for fix deform is invalid style");
}
// set start/stop values for box size and shape
// if single run, start is current values
// if multiple runs enabled via run start/stop settings,
// start is value when fix deform was issued
// if VARIABLE or NONE, no need to set
for (int i = 0; i < 3; i++) {
if (update->firststep == update->beginstep) {
set[i].lo_start = domain->boxlo[i];
set[i].hi_start = domain->boxhi[i];
set[i].vol_start = domain->xprd * domain->yprd * domain->zprd;
} else {
set[i].lo_start = set[i].lo_initial;
set[i].hi_start = set[i].hi_initial;
set[i].vol_start = set[i].vol_initial;
}
if (set[i].style == FINAL) {
set[i].lo_stop = set[i].flo;
set[i].hi_stop = set[i].fhi;
} else if (set[i].style == DELTA) {
set[i].lo_stop = set[i].lo_start + set[i].dlo;
set[i].hi_stop = set[i].hi_start + set[i].dhi;
} else if (set[i].style == SCALE) {
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*set[i].scale*(set[i].hi_start-set[i].lo_start);
} else if (set[i].style == VEL) {
set[i].lo_stop = set[i].lo_start - 0.5*delt*set[i].vel;
set[i].hi_stop = set[i].hi_start + 0.5*delt*set[i].vel;
} else if (set[i].style == ERATE) {
set[i].lo_stop = set[i].lo_start -
0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start);
set[i].hi_stop = set[i].hi_start +
0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start);
if (set[i].hi_stop <= set[i].lo_stop)
error->all(FLERR,"Final box dimension due to fix deform is < 0.0");
} else if (set[i].style == TRATE) {
set[i].lo_stop = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
set[i].hi_stop = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
} else if (set[i].style == WIGGLE) {
set[i].lo_stop = set[i].lo_start -
0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
set[i].hi_stop = set[i].hi_start +
0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
}
}
for (int i = 3; i < 6; i++) {
if (update->firststep == update->beginstep) {
if (i == 5) set[i].tilt_start = domain->xy;
else if (i == 4) set[i].tilt_start = domain->xz;
else if (i == 3) set[i].tilt_start = domain->yz;
} else set[i].tilt_start = set[i].tilt_initial;
if (set[i].style == FINAL) {
set[i].tilt_stop = set[i].ftilt;
} else if (set[i].style == DELTA) {
set[i].tilt_stop = set[i].tilt_start + set[i].dtilt;
} else if (set[i].style == VEL) {
set[i].tilt_stop = set[i].tilt_start + delt*set[i].vel;
} else if (set[i].style == ERATE) {
if (i == 3) set[i].tilt_stop = set[i].tilt_start +
delt*set[i].rate * (set[2].hi_start-set[2].lo_start);
if (i == 4) set[i].tilt_stop = set[i].tilt_start +
delt*set[i].rate * (set[2].hi_start-set[2].lo_start);
if (i == 5) set[i].tilt_stop = set[i].tilt_start +
delt*set[i].rate * (set[1].hi_start-set[1].lo_start);
} else if (set[i].style == TRATE) {
set[i].tilt_stop = set[i].tilt_start * exp(set[i].rate*delt);
} else if (set[i].style == WIGGLE) {
set[i].tilt_stop = set[i].tilt_start +
set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
// compute min/max for WIGGLE = extrema tilt factor will ever reach
if (set[i].amplitude >= 0.0) {
if (delt < 0.25*set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start;
set[i].tilt_max = set[i].tilt_start +
set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
} else if (delt < 0.5*set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start;
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
} else if (delt < 0.75*set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start -
set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
} else {
set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
}
} else {
if (delt < 0.25*set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start -
set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
set[i].tilt_max = set[i].tilt_start;
} else if (delt < 0.5*set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
set[i].tilt_max = set[i].tilt_start;
} else if (delt < 0.75*set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
set[i].tilt_max = set[i].tilt_start +
set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
} else {
set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
}
}
}
}
// if using tilt TRATE, then initial tilt must be non-zero
for (int i = 3; i < 6; i++)
if (set[i].style == TRATE && set[i].tilt_start == 0.0)
error->all(FLERR,"Cannot use fix deform trate on a box with zero tilt");
// if yz changes and will cause box flip, then xy cannot be changing
// yz = [3], xy = [5]
// this is b/c the flips would induce continuous changes in xz
// in order to keep the edge vectors of the flipped shape matrix
// an integer combination of the edge vectors of the unflipped shape matrix
// VARIABLE for yz is error, since no way to calculate if box flip occurs
// WIGGLE lo/hi flip test is on min/max oscillation limit, not tilt_stop
// only trigger actual errors if flipflag is set
if (set[3].style && set[5].style) {
int flag = 0;
double lo,hi;
if (flipflag && set[3].style == VARIABLE)
error->all(FLERR,"Fix deform cannot use yz variable with xy");
if (set[3].style == WIGGLE) {
lo = set[3].tilt_min;
hi = set[3].tilt_max;
} else lo = hi = set[3].tilt_stop;
if (flipflag) {
if (lo/(set[1].hi_start-set[1].lo_start) < -0.5 ||
hi/(set[1].hi_start-set[1].lo_start) > 0.5) flag = 1;
if (set[1].style) {
if (lo/(set[1].hi_stop-set[1].lo_stop) < -0.5 ||
hi/(set[1].hi_stop-set[1].lo_stop) > 0.5) flag = 1;
}
if (flag)
error->all(FLERR,"Fix deform is changing yz too much with xy");
}
}
// set domain->h_rate values for use by domain and other fixes/computes
// initialize all rates to 0.0
// cannot set here for TRATE,VOLUME,WIGGLE,VARIABLE since not constant
h_rate = domain->h_rate;
h_ratelo = domain->h_ratelo;
for (int i = 0; i < 3; i++) {
h_rate[i] = h_ratelo[i] = 0.0;
if (set[i].style == FINAL || set[i].style == DELTA ||
set[i].style == SCALE || set[i].style == VEL ||
set[i].style == ERATE) {
double dlo_dt,dhi_dt;
if (delt != 0.0) {
dlo_dt = (set[i].lo_stop - set[i].lo_start) / delt;
dhi_dt = (set[i].hi_stop - set[i].hi_start) / delt;
} else dlo_dt = dhi_dt = 0.0;
h_rate[i] = dhi_dt - dlo_dt;
h_ratelo[i] = dlo_dt;
}
}
for (int i = 3; i < 6; i++) {
h_rate[i] = 0.0;
if (set[i].style == FINAL || set[i].style == DELTA ||
set[i].style == VEL || set[i].style == ERATE) {
if (delt != 0.0)
h_rate[i] = (set[i].tilt_stop - set[i].tilt_start) / delt;
else h_rate[i] = 0.0;
}
}
// detect if any rigid fixes exist so rigid bodies can be rescaled
// rfix[] = indices to each fix rigid
delete [] rfix;
nrigid = 0;
rfix = NULL;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) nrigid++;
if (nrigid) {
rfix = new int[nrigid];
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i;
}
}
/* ----------------------------------------------------------------------
box flipped on previous step
reset box tilts for flipped config and create new box in domain
image_flip() adjusts image flags due to box shape change induced by flip
remap() puts atoms outside the new box back into the new box
perform irregular on atoms in lamda coords to migrate atoms to new procs
important that image_flip comes before remap, since remap may change
image flags to new values, making eqs in doc of Domain:image_flip incorrect
------------------------------------------------------------------------- */
void FixDeform::pre_exchange()
{
if (flip == 0) return;
domain->yz = set[3].tilt_target = set[3].tilt_flip;
domain->xz = set[4].tilt_target = set[4].tilt_flip;
domain->xy = set[5].tilt_target = set[5].tilt_flip;
domain->set_global_box();
domain->set_local_box();
domain->image_flip(flipxy,flipxz,flipyz);
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
domain->x2lamda(atom->nlocal);
irregular->migrate_atoms();
domain->lamda2x(atom->nlocal);
flip = 0;
}
/* ---------------------------------------------------------------------- */
void FixDeform::end_of_step()
{
int i;
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
// wrap variable evaluations with clear/add
if (varflag) modify->clearstep_compute();
// set new box size
// for NONE, target is current box size
// for TRATE, set target directly based on current time, also set h_rate
// for WIGGLE, set target directly based on current time, also set h_rate
// for VARIABLE, set target directly via variable eval, also set h_rate
// for others except VOLUME, target is linear value between start and stop
for (i = 0; i < 3; i++) {
if (set[i].style == NONE) {
set[i].lo_target = domain->boxlo[i];
set[i].hi_target = domain->boxhi[i];
} else if (set[i].style == TRATE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
h_rate[i] = set[i].rate * domain->h[i];
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == WIGGLE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].lo_target = set[i].lo_start -
0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
set[i].hi_target = set[i].hi_start +
0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
cos(TWOPI*delt/set[i].tperiod);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == VARIABLE) {
double del = input->variable->compute_equal(set[i].hvar);
set[i].lo_target = set[i].lo_start - 0.5*del;
set[i].hi_target = set[i].hi_start + 0.5*del;
h_rate[i] = input->variable->compute_equal(set[i].hratevar);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style != VOLUME) {
set[i].lo_target = set[i].lo_start +
delta*(set[i].lo_stop - set[i].lo_start);
set[i].hi_target = set[i].hi_start +
delta*(set[i].hi_stop - set[i].hi_start);
}
}
// set new box size for VOLUME dims that are linked to other dims
// NOTE: still need to set h_rate for these dims
for (int i = 0; i < 3; i++) {
if (set[i].style != VOLUME) continue;
if (set[i].substyle == ONE_FROM_ONE) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
} else if (set[i].substyle == ONE_FROM_TWO) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].dynamic2].hi_target -
set[set[i].dynamic2].lo_target));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].dynamic2].hi_target -
set[set[i].dynamic2].lo_target));
} else if (set[i].substyle == TWO_FROM_ONE) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*sqrt(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start -
set[set[i].fixed].lo_start) *
(set[i].hi_start - set[i].lo_start));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*sqrt(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start -
set[set[i].fixed].lo_start) *
(set[i].hi_start - set[i].lo_start));
}
}
// for triclinic, set new box shape
// for NONE, target is current tilt
// for TRATE, set target directly based on current time. also set h_rate
// for WIGGLE, set target directly based on current time. also set h_rate
// for VARIABLE, set target directly via variable eval. also set h_rate
// for other styles, target is linear value between start and stop values
if (triclinic) {
double *h = domain->h;
for (i = 3; i < 6; i++) {
if (set[i].style == NONE) {
if (i == 5) set[i].tilt_target = domain->xy;
else if (i == 4) set[i].tilt_target = domain->xz;
else if (i == 3) set[i].tilt_target = domain->yz;
} else if (set[i].style == TRATE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].tilt_target = set[i].tilt_start * exp(set[i].rate*delt);
h_rate[i] = set[i].rate * domain->h[i];
} else if (set[i].style == WIGGLE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].tilt_target = set[i].tilt_start +
set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
cos(TWOPI*delt/set[i].tperiod);
} else if (set[i].style == VARIABLE) {
double delta_tilt = input->variable->compute_equal(set[i].hvar);
set[i].tilt_target = set[i].tilt_start + delta_tilt;
h_rate[i] = input->variable->compute_equal(set[i].hratevar);
} else {
set[i].tilt_target = set[i].tilt_start +
delta*(set[i].tilt_stop - set[i].tilt_start);
}
// tilt_target can be large positive or large negative value
// add/subtract box lengths until tilt_target is closest to current value
int idenom;
if (i == 5) idenom = 0;
else if (i == 4) idenom = 0;
else if (i == 3) idenom = 1;
double denom = set[idenom].hi_target - set[idenom].lo_target;
double current = h[i]/h[idenom];
while (set[i].tilt_target/denom - current > 0.0)
set[i].tilt_target -= denom;
while (set[i].tilt_target/denom - current < 0.0)
set[i].tilt_target += denom;
if (fabs(set[i].tilt_target/denom - 1.0 - current) <
fabs(set[i].tilt_target/denom - current))
set[i].tilt_target -= denom;
}
}
if (varflag) modify->addstep_compute(update->ntimestep + nevery);
// if any tilt ratios exceed 0.5, set flip = 1 and compute new tilt values
// do not flip in x or y if non-periodic (can tilt but not flip)
// this is b/c the box length would be changed (dramatically) by flip
// if yz tilt exceeded, adjust C vector by one B vector
// if xz tilt exceeded, adjust C vector by one A vector
// if xy tilt exceeded, adjust B vector by one A vector
// check yz first since it may change xz, then xz check comes after
// flip is performed on next timestep, before reneighboring in pre-exchange()
if (triclinic && flipflag) {
double xprd = set[0].hi_target - set[0].lo_target;
double yprd = set[1].hi_target - set[1].lo_target;
double xprdinv = 1.0 / xprd;
double yprdinv = 1.0 / yprd;
if (set[3].tilt_target*yprdinv < -0.5 ||
set[3].tilt_target*yprdinv > 0.5 ||
set[4].tilt_target*xprdinv < -0.5 ||
set[4].tilt_target*xprdinv > 0.5 ||
set[5].tilt_target*xprdinv < -0.5 ||
set[5].tilt_target*xprdinv > 0.5) {
set[3].tilt_flip = set[3].tilt_target;
set[4].tilt_flip = set[4].tilt_target;
set[5].tilt_flip = set[5].tilt_target;
flipxy = flipxz = flipyz = 0;
if (domain->yperiodic) {
if (set[3].tilt_flip*yprdinv < -0.5) {
set[3].tilt_flip += yprd;
set[4].tilt_flip += set[5].tilt_flip;
flipyz = 1;
} else if (set[3].tilt_flip*yprdinv > 0.5) {
set[3].tilt_flip -= yprd;
set[4].tilt_flip -= set[5].tilt_flip;
flipyz = -1;
}
}
if (domain->xperiodic) {
if (set[4].tilt_flip*xprdinv < -0.5) {
set[4].tilt_flip += xprd;
flipxz = 1;
}
if (set[4].tilt_flip*xprdinv > 0.5) {
set[4].tilt_flip -= xprd;
flipxz = -1;
}
if (set[5].tilt_flip*xprdinv < -0.5) {
set[5].tilt_flip += xprd;
flipxy = 1;
}
if (set[5].tilt_flip*xprdinv > 0.5) {
set[5].tilt_flip -= xprd;
flipxy = -1;
}
}
flip = 0;
if (flipxy || flipxz || flipyz) flip = 1;
if (flip) next_reneighbor = update->ntimestep + 1;
}
}
// convert atoms and rigid bodies to lamda coords
if (remapflag == X_REMAP) {
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->x2lamda(x[i],x[i]);
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(0);
}
// reset global and local box to new size/shape
// only if deform fix is controlling the dimension
if (set[0].style) {
domain->boxlo[0] = set[0].lo_target;
domain->boxhi[0] = set[0].hi_target;
}
if (set[1].style) {
domain->boxlo[1] = set[1].lo_target;
domain->boxhi[1] = set[1].hi_target;
}
if (set[2].style) {
domain->boxlo[2] = set[2].lo_target;
domain->boxhi[2] = set[2].hi_target;
}
if (triclinic) {
if (set[3].style) domain->yz = set[3].tilt_target;
if (set[4].style) domain->xz = set[4].tilt_target;
if (set[5].style) domain->xy = set[5].tilt_target;
}
domain->set_global_box();
domain->set_local_box();
// convert atoms and rigid bodies back to box coords
if (remapflag == X_REMAP) {
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]);
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
}
// redo KSpace coeffs since box has changed
if (kspace_flag) force->kspace->setup();
}
/* ----------------------------------------------------------------------
write Set data to restart file
------------------------------------------------------------------------- */
void FixDeform::write_restart(FILE *fp)
{
if (comm->me == 0) {
int size = 6*sizeof(Set);
fwrite(&size,sizeof(int),1,fp);
fwrite(set,sizeof(Set),6,fp);
}
}
/* ----------------------------------------------------------------------
use selected state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixDeform::restart(char *buf)
{
int samestyle = 1;
Set *set_restart = (Set *) buf;
for (int i=0; i<6; ++i) {
// restore data from initial state
set[i].lo_initial = set_restart[i].lo_initial;
set[i].hi_initial = set_restart[i].hi_initial;
set[i].vol_initial = set_restart[i].vol_initial;
set[i].tilt_initial = set_restart[i].tilt_initial;
// check if style settings are consitent (should do the whole set?)
if (set[i].style != set_restart[i].style)
samestyle = 0;
if (set[i].substyle != set_restart[i].substyle)
samestyle = 0;
}
if (!samestyle)
error->all(FLERR,"Fix deform settings not consistent with restart");
}
/* ---------------------------------------------------------------------- */
void FixDeform::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal fix deform command");
remapflag = X_REMAP;
scaleflag = 1;
flipflag = 1;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"remap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
if (strcmp(arg[iarg+1],"x") == 0) remapflag = X_REMAP;
else if (strcmp(arg[iarg+1],"v") == 0) remapflag = V_REMAP;
else if (strcmp(arg[iarg+1],"none") == 0) remapflag = NO_REMAP;
else error->all(FLERR,"Illegal fix deform command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal fix deform command");
iarg += 2;
} else if (strcmp(arg[iarg],"flip") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
if (strcmp(arg[iarg+1],"yes") == 0) flipflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) flipflag = 0;
else error->all(FLERR,"Illegal fix deform command");
iarg += 2;
} else error->all(FLERR,"Illegal fix deform command");
}
}
/* ----------------------------------------------------------------------
memory usage of Irregular
------------------------------------------------------------------------- */
double FixDeform::memory_usage()
{
double bytes = 0.0;
if (irregular) bytes += irregular->memory_usage();
return bytes;
}

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