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change_box.cpp
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Sat, Jun 29, 10:28

change_box.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.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "change_box.h"
#include "atom.h"
#include "modify.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "comm.h"
#include "irregular.h"
#include "output.h"
#include "group.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
enum{XYZ=0,TILT,BOUNDARY,ORTHO,TRICLINIC,SET,REMAP};
enum{FINAL=0,DELTA,SCALE};
enum{X=0,Y,Z,YZ,XZ,XY};
/* ---------------------------------------------------------------------- */
ChangeBox::ChangeBox(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void ChangeBox::command(int narg, char **arg)
{
int i;
if (domain->box_exist == 0)
error->all(FLERR,"Change_box command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal change_box command");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot change_box after "
"reading restart file with per-atom info");
if (comm->me == 0 && screen) fprintf(screen,"Changing box ...\n");
// group
int igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find change_box group ID");
int groupbit = group->bitmask[igroup];
// parse operation arguments
// allocate ops to max possible length
// volume option does not increment nops
int dimension = domain->dimension;
ops = new Operation[narg-1];
memset(ops,0,(narg-1)*sizeof(Operation));
nops = 0;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 ||
strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].style = XYZ;
if (strcmp(arg[iarg],"x") == 0) ops[nops].dim = X;
else if (strcmp(arg[iarg],"y") == 0) ops[nops].dim = Y;
else if (strcmp(arg[iarg],"z") == 0) ops[nops].dim = Z;
if (dimension == 2 && ops[nops].dim == Z)
error->all(FLERR,"Cannot change_box in z dimension for 2d simulation");
if (strcmp(arg[iarg+1],"final") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = FINAL;
ops[nops].flo = force->numeric(FLERR,arg[iarg+2]);
ops[nops].fhi = force->numeric(FLERR,arg[iarg+3]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 4;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = DELTA;
ops[nops].dlo = force->numeric(FLERR,arg[iarg+2]);
ops[nops].dhi = force->numeric(FLERR,arg[iarg+3]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 4;
} else if (strcmp(arg[iarg+1],"scale") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = SCALE;
ops[nops].scale = force->numeric(FLERR,arg[iarg+2]);
ops[nops].vdim1 = ops[nops].vdim2 = -1;
nops++;
iarg += 3;
} else if (strcmp(arg[iarg+1],"volume") == 0) {
if (nops == 0 || ops[nops-1].style != XYZ ||
ops[nops].dim == ops[nops-1].dim)
error->all(FLERR,"Change_box volume used incorrectly");
if (ops[nops-1].vdim2 >= 0)
error->all(FLERR,"Change_box volume used incorrectly");
else if (ops[nops-1].vdim1 >= 0) ops[nops-1].vdim2 = ops[nops].dim;
else ops[nops-1].vdim1 = ops[nops].dim;
iarg += 2;
} else error->all(FLERR,"Illegal change_box command");
} else if (strcmp(arg[iarg],"xy") == 0 || strcmp(arg[iarg],"xz") == 0 ||
strcmp(arg[iarg],"yz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].style = TILT;
if (strcmp(arg[iarg],"xy") == 0) ops[nops].dim = XY;
else if (strcmp(arg[iarg],"xz") == 0) ops[nops].dim = XZ;
else if (strcmp(arg[iarg],"yz") == 0) ops[nops].dim = YZ;
if (dimension == 2 && (ops[nops].dim == XZ || ops[nops].dim == YZ))
error->all(FLERR,"Cannot change_box in xz or yz for 2d simulation");
if (strcmp(arg[iarg+1],"final") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = FINAL;
ops[nops].ftilt = force->numeric(FLERR,arg[iarg+2]);
nops++;
iarg += 3;
} else if (strcmp(arg[iarg+1],"delta") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].flavor = DELTA;
ops[nops].dtilt = force->numeric(FLERR,arg[iarg+2]);
nops++;
iarg += 3;
} else error->all(FLERR,"Illegal change_box command");
} else if (strcmp(arg[iarg],"boundary") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].style = BOUNDARY;
ops[nops].boundindex = iarg+1;
nops++;
iarg += 4;
} else if (strcmp(arg[iarg],"ortho") == 0) {
ops[nops].style = ORTHO;
nops++;
iarg += 1;
} else if (strcmp(arg[iarg],"triclinic") == 0) {
ops[nops].style = TRICLINIC;
nops++;
iarg += 1;
} else if (strcmp(arg[iarg],"set") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal change_box command");
ops[nops].style = SET;
nops++;
iarg += 1;
} else if (strcmp(arg[iarg],"remap") == 0) {
ops[nops].style = REMAP;
nops++;
iarg += 1;
} else break;
}
if (nops == 0) error->all(FLERR,"Illegal change_box command");
// read options from end of input line
options(narg-iarg,&arg[iarg]);
// compute scale factors if FINAL,DELTA used since they have distance units
int flag = 0;
for (int i = 0; i < nops; i++)
if (ops[i].style == FINAL || ops[i].style == DELTA) flag = 1;
if (flag && scaleflag) {
scale[0] = domain->lattice->xlattice;
scale[1] = domain->lattice->ylattice;
scale[2] = domain->lattice->zlattice;
}
else scale[0] = scale[1] = scale[2] = 1.0;
// perform sequence of operations
// first insure atoms are in current box & update box via shrink-wrap
// no exchange() since doesn't matter if atoms are assigned to correct procs
// save current box state so can remap atoms from it, if requested
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
save_box_state();
for (int m = 0; m < nops; m++) {
if (ops[m].style == XYZ) {
double volume;
if (domain->dimension == 2) volume = domain->xprd * domain->yprd;
else volume = domain->xprd * domain->yprd * domain->zprd;
if (ops[m].flavor == FINAL) {
domain->boxlo[ops[m].dim] = scale[ops[m].dim]*ops[m].flo;
domain->boxhi[ops[m].dim] = scale[ops[m].dim]*ops[m].fhi;
if (ops[m].vdim1 >= 0)
volume_preserve(ops[m].vdim1,ops[m].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[m].flavor == DELTA) {
domain->boxlo[ops[m].dim] += scale[ops[m].dim]*ops[m].dlo;
domain->boxhi[ops[m].dim] += scale[ops[m].dim]*ops[m].dhi;
if (ops[m].vdim1 >= 0)
volume_preserve(ops[m].vdim1,ops[m].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[m].flavor == SCALE) {
double mid = 0.5 *
(domain->boxlo[ops[m].dim] + domain->boxhi[ops[m].dim]);
double delta = domain->boxlo[ops[m].dim] - mid;
domain->boxlo[ops[m].dim] = mid + ops[m].scale*delta;
delta = domain->boxhi[ops[m].dim] - mid;
domain->boxhi[ops[m].dim] = mid + ops[m].scale*delta;
if (ops[m].vdim1 >= 0)
volume_preserve(ops[m].vdim1,ops[m].vdim2,volume);
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
}
} else if (ops[m].style == TILT) {
if (domain->triclinic == 0)
error->all(FLERR,"Cannot change box tilt factors for orthogonal box");
if (ops[m].flavor == FINAL) {
if (ops[m].dim == XY) domain->xy = scale[X]*ops[m].ftilt;
else if (ops[m].dim == XZ) domain->xz = scale[X]*ops[m].ftilt;
else if (ops[m].dim == YZ) domain->yz = scale[Y]*ops[m].ftilt;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[m].flavor == DELTA) {
if (ops[m].dim == XY) domain->xy += scale[X]*ops[m].dtilt;
else if (ops[m].dim == XZ) domain->xz += scale[X]*ops[m].dtilt;
else if (ops[m].dim == YZ) domain->yz += scale[Y]*ops[m].dtilt;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
}
} else if (ops[m].style == BOUNDARY) {
domain->set_boundary(3,&arg[ops[m].boundindex],1);
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,
"Cannot change box z boundary to "
"nonperiodic for a 2d simulation");
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
} else if (ops[m].style == ORTHO) {
if (domain->xy != 0.0 || domain->yz != 0.0 || domain->xz != 0.0)
error->all(FLERR,
"Cannot change box to orthogonal when tilt is non-zero");
if (output->ndump)
error->all(FLERR,
"Cannot change box ortho/triclinic with dumps defined");
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->no_change_box)
error->all(FLERR,
"Cannot change box ortho/triclinic with "
"certain fixes defined");
domain->triclinic = 0;
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[m].style == TRICLINIC) {
if (output->ndump)
error->all(FLERR,
"Cannot change box ortho/triclinic with dumps defined");
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->no_change_box)
error->all(FLERR,
"Cannot change box ortho/triclinic with "
"certain fixes defined");
domain->triclinic = 1;
domain->set_lamda_box();
domain->set_initial_box();
domain->set_global_box();
domain->set_local_box();
domain->print_box(" ");
} else if (ops[m].style == SET) {
save_box_state();
} else if (ops[m].style == REMAP) {
// convert atoms to lamda coords, using last box state
// convert atoms back to box coords, using current box state
// save current box state
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],boxlo,h_inv);
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]);
save_box_state();
}
}
// clean up
delete [] ops;
// apply shrink-wrap boundary conditions
if (domain->nonperiodic == 2) {
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
// move atoms back inside simulation box and to new processors
// use remap() instead of pbc()
// in case box moved a long distance relative to atoms
// use irregular() in case box moved a long distance relative to atoms
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->reset_box();
Irregular *irregular = new Irregular(lmp);
irregular->migrate_atoms(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// check if any atoms were lost
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms && comm->me == 0) {
char str[128];
sprintf(str,"Lost atoms via change_box: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->warning(FLERR,str);
}
}
/* ----------------------------------------------------------------------
parse optional parameters
------------------------------------------------------------------------- */
void ChangeBox::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal change_box command");
scaleflag = 1;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal change_box 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 change_box command");
iarg += 2;
} else error->all(FLERR,"Illegal change_box command");
}
}
/* ----------------------------------------------------------------------
save current box state for converting atoms to lamda coords
------------------------------------------------------------------------- */
void ChangeBox::save_box_state()
{
boxlo[0] = domain->boxlo[0];
boxlo[1] = domain->boxlo[1];
boxlo[2] = domain->boxlo[2];
for (int i = 0; i < 6; i++)
h_inv[i] = domain->h_inv[i];
}
/* ----------------------------------------------------------------------
oldvol = box volume before dim3 changed
newvol = box volume after dim3 changed
reset box lengths of dim1/2 to preserve old volume
------------------------------------------------------------------------- */
void ChangeBox::volume_preserve(int dim1, int dim2, double oldvol)
{
// invoke set_initial_box()
// in case change by caller to dim3 was invalid or on shrink-wrapped dim
domain->set_initial_box();
// calculate newvol using boxlo/hi since xyz prd are not yet reset
double newvol;
if (domain->dimension == 2) {
newvol = domain->boxhi[0] - domain->boxlo[0];
newvol *= domain->boxhi[1] - domain->boxlo[1];
} else {
newvol = domain->boxhi[0] - domain->boxlo[0];
newvol *= domain->boxhi[1] - domain->boxlo[1];
newvol *= domain->boxhi[2] - domain->boxlo[2];
}
double scale = oldvol/newvol;
double mid,delta;
// change dim1 only
if (dim2 < 0) {
mid = 0.5 * (domain->boxlo[dim1] + domain->boxhi[dim1]);
delta = domain->boxlo[dim1] - mid;
domain->boxlo[dim1] = mid + scale*delta;
delta = domain->boxhi[dim1] - mid;
domain->boxhi[dim1] = mid + scale*delta;
// change dim1 and dim2, keeping their relative aspect ratio constant
// both are scaled by sqrt(scale)
} else {
mid = 0.5 * (domain->boxlo[dim1] + domain->boxhi[dim1]);
delta = domain->boxlo[dim1] - mid;
domain->boxlo[dim1] = mid + sqrt(scale)*delta;
delta = domain->boxhi[dim1] - mid;
domain->boxhi[dim1] = mid + sqrt(scale)*delta;
mid = 0.5 * (domain->boxlo[dim2] + domain->boxhi[dim2]);
delta = domain->boxlo[dim2] - mid;
domain->boxlo[dim2] = mid + sqrt(scale)*delta;
delta = domain->boxhi[dim2] - mid;
domain->boxhi[dim2] = mid + sqrt(scale)*delta;
}
}

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