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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7686 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-02-03 20:03:29 +00:00
parent 301e696b5e
commit 7fb5f449e4
7 changed files with 257 additions and 131 deletions
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123
src/domain.cpp
View File

@ -31,10 +31,12 @@
#include "region.h"
#include "lattice.h"
#include "comm.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define BIG 1.0e20
#define SMALL 1.0e-4
@ -132,16 +134,11 @@ void Domain::set_initial_box()
if (boxlo[0] >= boxhi[0] || boxlo[1] >= boxhi[1] || boxlo[2] >= boxhi[2])
error->one(FLERR,"Box bounds are invalid");
// error check on triclinic tilt factors
if (triclinic) {
if (domain->dimension == 2 && (xz != 0.0 || yz != 0.0))
error->all(FLERR,"Cannot skew triclinic box in z for 2d simulation");
if (xy != 0.0 && (!xperiodic || !yperiodic))
error->all(FLERR,"Triclinic box must be periodic in skewed dimensions");
if (xz != 0.0 && (!xperiodic || !zperiodic))
error->all(FLERR,"Triclinic box must be periodic in skewed dimensions");
if (yz != 0.0 && (!yperiodic || !zperiodic))
error->all(FLERR,"Triclinic box must be periodic in skewed dimensions");
if (fabs(xy/(boxhi[0]-boxlo[0])) > 0.5)
error->all(FLERR,"Triclinic box skew is too large");
if (fabs(xz/(boxhi[0]-boxlo[0])) > 0.5)
@ -150,21 +147,28 @@ void Domain::set_initial_box()
error->all(FLERR,"Triclinic box skew is too large");
}
// set small based on box size and SMALL
// this works for any unit system
small[0] = SMALL * (boxhi[0] - boxlo[0]);
small[1] = SMALL * (boxhi[1] - boxlo[1]);
small[2] = SMALL * (boxhi[2] - boxlo[2]);
// adjust box lo/hi for shrink-wrapped dims
if (boundary[0][0] == 2) boxlo[0] -= SMALL;
if (boundary[0][0] == 2) boxlo[0] -= small[0];
else if (boundary[0][0] == 3) minxlo = boxlo[0];
if (boundary[0][1] == 2) boxhi[0] += SMALL;
if (boundary[0][1] == 2) boxhi[0] += small[0];
else if (boundary[0][1] == 3) minxhi = boxhi[0];
if (boundary[1][0] == 2) boxlo[1] -= SMALL;
if (boundary[1][0] == 2) boxlo[1] -= small[1];
else if (boundary[1][0] == 3) minylo = boxlo[1];
if (boundary[1][1] == 2) boxhi[1] += SMALL;
if (boundary[1][1] == 2) boxhi[1] += small[1];
else if (boundary[1][1] == 3) minyhi = boxhi[1];
if (boundary[2][0] == 2) boxlo[2] -= SMALL;
if (boundary[2][0] == 2) boxlo[2] -= small[2];
else if (boundary[2][0] == 3) minzlo = boxlo[2];
if (boundary[2][1] == 2) boxhi[2] += SMALL;
if (boundary[2][1] == 2) boxhi[2] += small[2];
else if (boundary[2][1] == 3) minzhi = boxhi[2];
}
@ -270,19 +274,16 @@ void Domain::set_local_box()
/* ----------------------------------------------------------------------
reset global & local boxes due to global box boundary changes
if shrink-wrapped, determine atom extent and reset boxlo/hi
if shrink-wrapped and triclinic, perform shrink-wrap in box coords
if triclinic, perform any shrink-wrap in lamda space
------------------------------------------------------------------------- */
void Domain::reset_box()
{
if (nonperiodic == 2) {
// convert back to box coords for shrink-wrap operation
if (triclinic) lamda2x(atom->nlocal);
// perform shrink-wrapping
// compute extent of atoms on this proc
// for triclinic, this is done in lamda space
if (nonperiodic == 2) {
double extent[3][2],all[3][2];
extent[2][0] = extent[1][0] = extent[0][0] = BIG;
@ -309,37 +310,91 @@ void Domain::reset_box()
MPI_Allreduce(extent,all,6,MPI_DOUBLE,MPI_MAX,world);
// for triclinic, convert back to box coords before changing box
if (triclinic) lamda2x(atom->nlocal);
// in shrink-wrapped dims, set box by atom extent
// if minimum set, enforce min box size settings
// for triclinic, convert lamda extent to box coords, then set box lo/hi
// decided NOT to do the next comment - don't want to sneakily change tilt
// for triclinic, adjust tilt factors if 2nd dim is shrink-wrapped,
// so that displacement in 1st dim stays the same
if (triclinic == 0) {
if (xperiodic == 0) {
if (boundary[0][0] == 2) boxlo[0] = -all[0][0] - SMALL;
else if (boundary[0][0] == 3) boxlo[0] = MIN(-all[0][0]-SMALL,minxlo);
if (boundary[0][1] == 2) boxhi[0] = all[0][1] + SMALL;
else if (boundary[0][1] == 3) boxhi[0] = MAX(all[0][1]+SMALL,minxhi);
if (boundary[0][0] == 2) boxlo[0] = -all[0][0] - small[0];
else if (boundary[0][0] == 3)
boxlo[0] = MIN(-all[0][0]-small[0],minxlo);
if (boundary[0][1] == 2) boxhi[0] = all[0][1] + small[0];
else if (boundary[0][1] == 3) boxhi[0] = MAX(all[0][1]+small[0],minxhi);
if (boxlo[0] > boxhi[0]) error->all(FLERR,"Illegal simulation box");
}
if (yperiodic == 0) {
if (boundary[1][0] == 2) boxlo[1] = -all[1][0] - SMALL;
else if (boundary[1][0] == 3) boxlo[1] = MIN(-all[1][0]-SMALL,minylo);
if (boundary[1][1] == 2) boxhi[1] = all[1][1] + SMALL;
else if (boundary[1][1] == 3) boxhi[1] = MAX(all[1][1]+SMALL,minyhi);
if (boundary[1][0] == 2) boxlo[1] = -all[1][0] - small[1];
else if (boundary[1][0] == 3)
boxlo[1] = MIN(-all[1][0]-small[1],minylo);
if (boundary[1][1] == 2) boxhi[1] = all[1][1] + small[1];
else if (boundary[1][1] == 3) boxhi[1] = MAX(all[1][1]+small[1],minyhi);
if (boxlo[1] > boxhi[1]) error->all(FLERR,"Illegal simulation box");
}
if (zperiodic == 0) {
if (boundary[2][0] == 2) boxlo[2] = -all[2][0] - SMALL;
else if (boundary[2][0] == 3) boxlo[2] = MIN(-all[2][0]-SMALL,minzlo);
if (boundary[2][1] == 2) boxhi[2] = all[2][1] + SMALL;
else if (boundary[2][1] == 3) boxhi[2] = MAX(all[2][1]+SMALL,minzhi);
if (boundary[2][0] == 2) boxlo[2] = -all[2][0] - small[2];
else if (boundary[2][0] == 3)
boxlo[2] = MIN(-all[2][0]-small[2],minzlo);
if (boundary[2][1] == 2) boxhi[2] = all[2][1] + small[2];
else if (boundary[2][1] == 3) boxhi[2] = MAX(all[2][1]+small[2],minzhi);
if (boxlo[2] > boxhi[2]) error->all(FLERR,"Illegal simulation box");
}
} else {
double lo[3],hi[3];
if (xperiodic == 0) {
lo[0] = -all[0][0]; lo[1] = 0.0; lo[2] = 0.0;
lamda2x(lo,lo);
hi[0] = all[0][1]; hi[1] = 0.0; hi[2] = 0.0;
lamda2x(hi,hi);
if (boundary[0][0] == 2) boxlo[0] = lo[0] - small[0];
else if (boundary[0][0] == 3) boxlo[0] = MIN(lo[0]-small[0],minxlo);
if (boundary[0][1] == 2) boxhi[0] = hi[0] + small[0];
else if (boundary[0][1] == 3) boxhi[0] = MAX(hi[0]+small[0],minxhi);
if (boxlo[0] > boxhi[0]) error->all(FLERR,"Illegal simulation box");
}
if (yperiodic == 0) {
lo[0] = 0.0; lo[1] = -all[1][0]; lo[2] = 0.0;
lamda2x(lo,lo);
hi[0] = 0.0; hi[1] = all[1][1]; hi[2] = 0.0;
lamda2x(hi,hi);
if (boundary[1][0] == 2) boxlo[1] = lo[1] - small[1];
else if (boundary[1][0] == 3) boxlo[1] = MIN(lo[1]-small[1],minylo);
if (boundary[1][1] == 2) boxhi[1] = hi[1] + small[1];
else if (boundary[1][1] == 3) boxhi[1] = MAX(hi[1]+small[1],minyhi);
if (boxlo[1] > boxhi[1]) error->all(FLERR,"Illegal simulation box");
//xy *= (boxhi[1]-boxlo[1]) / yprd;
}
if (zperiodic == 0) {
lo[0] = 0.0; lo[1] = 0.0; lo[2] = -all[2][0];
lamda2x(lo,lo);
hi[0] = 0.0; hi[1] = 0.0; hi[2] = all[2][1];
lamda2x(hi,hi);
if (boundary[2][0] == 2) boxlo[2] = lo[2] - small[2];
else if (boundary[2][0] == 3) boxlo[2] = MIN(lo[2]-small[2],minzlo);
if (boundary[2][1] == 2) boxhi[2] = hi[2] + small[2];
else if (boundary[2][1] == 3) boxhi[2] = MAX(hi[2]+small[2],minzhi);
if (boxlo[2] > boxhi[2]) error->all(FLERR,"Illegal simulation box");
//xz *= (boxhi[2]-boxlo[2]) / xprd;
//yz *= (boxhi[2]-boxlo[2]) / yprd;
}
}
}
// reset box whether shrink-wrapping or not
set_global_box();
set_local_box();
// if shrink-wrapped, convert to lamda coords for new box
// must re-invoke pbc() b/c x2lamda result can be outside 0,1 due to roundoff
// if shrink-wrapped & triclinic, re-convert to lamda coords for new box
// re-invoke pbc() b/c x2lamda result can be outside [0,1] due to roundoff
if (nonperiodic == 2 && triclinic) {
x2lamda(atom->nlocal);

6
src/domain.h
View File

@ -101,7 +101,8 @@ class Domain : protected Pointers {
int minimum_image_check(double, double, double);
void minimum_image(double &, double &, double &);
void minimum_image(double *);
void closest_image(const double * const, const double * const, double * const);
void closest_image(const double * const, const double * const,
double * const);
void set_lattice(int, char **);
void add_region(int, char **);
void delete_region(int, char **);
@ -115,6 +116,9 @@ class Domain : protected Pointers {
void x2lamda(double *, double *);
void bbox(double *, double *, double *, double *);
void box_corners();
private:
double small[3]; // fractions of box lengths
};
}

8
src/finish.cpp
View File

@ -50,6 +50,11 @@ void Finish::end(int flag)
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// recompute natoms in case atoms have been lost
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->nlocal,1,MPI_LMP_BIGINT,MPI_SUM,world);
// choose flavors of statistical output
// flag determines caller
// flag = 0 = just loop summary
@ -591,7 +596,8 @@ void Finish::end(int flag)
double nspec_all;
if (atom->molecular) {
nspec = 0;
for (i = 0; i < atom->nlocal; i++) nspec += atom->nspecial[i][2];
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) nspec += atom->nspecial[i][2];
tmp = nspec;
MPI_Allreduce(&tmp,&nspec_all,1,MPI_DOUBLE,MPI_SUM,world);
}

23
src/fix_box_relax.cpp
View File

@ -198,18 +198,26 @@ FixBoxRelax::FixBoxRelax(LAMMPS *lmp, int narg, char **arg) :
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all(FLERR,"Invalid fix box/relax command pressure settings");
// require periodicity in tensile dimension
if (p_flag[0] && domain->xperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a non-periodic dimension");
// require periodicity in 2nd dim of off-diagonal tilt component
if (p_flag[3] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a 2nd non-periodic dimension");
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a 2nd non-periodic dimension");
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix box/relax on a 2nd non-periodic dimension");
error->all(FLERR,
"Cannot use fix box/relax on a 2nd non-periodic dimension");
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
@ -689,18 +697,21 @@ int FixBoxRelax::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID");
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,"Fix_modify temperature ID does not compute temperature");
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning(FLERR,"Temperature for fix modify is not for group all");
// reset id_temp of pressure to new temperature ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all(FLERR,"Pressure ID for fix modify does not exist");
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix modify does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
return 2;

118
src/fix_deform.cpp
View File

@ -223,19 +223,31 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (dimflag[0] || dimflag[1] || dimflag[2]) box_change_size = 1;
if (dimflag[3] || dimflag[4] || dimflag[5]) box_change_shape = 1;
// check periodicity
// no tensile deformation on shrink-wrapped dims
// b/c shrink wrap will change box-length
if ((set[0].style && domain->xperiodic == 0) ||
(set[1].style && domain->yperiodic == 0) ||
(set[2].style && domain->zperiodic == 0))
error->all(FLERR,"Cannot use fix deform on a non-periodic boundary");
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");
if (set[3].style && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix deform on a 2nd non-periodic boundary");
if (set[4].style && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix deform on a 2nd non-periodic boundary");
if (set[5].style && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix deform on a 2nd non-periodic 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[4].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
@ -563,11 +575,11 @@ void FixDeform::init()
lo = set[3].tilt_min;
hi = set[3].tilt_max;
} else lo = hi = set[3].tilt_stop;
if (lo < -0.5*(set[1].hi_start-set[1].lo_start) ||
hi > 0.5*(set[1].hi_start-set[1].lo_start)) flag = 1;
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 < -0.5*(set[1].hi_stop-set[1].lo_stop) ||
hi > 0.5*(set[1].hi_stop-set[1].lo_stop)) flag = 1;
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");
}
@ -623,6 +635,8 @@ void FixDeform::init()
/* ----------------------------------------------------------------------
box flipped on previous step
do not allow box flip in a non-periodic dimension (can tilt but not flip)
this is b/c the box length will be changed (dramatically) by flip
perform irregular comm to migrate atoms to new procs
reset box tilts for flipped config and create new box in domain
remap to put far-away atoms back into new box
@ -666,14 +680,17 @@ void FixDeform::end_of_step()
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 NONE, target is current box size
// for others except VOLUME, target is linear value between start and stop
for (i = 0; i < 3; i++) {
if (set[i].style == TRATE) {
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));
@ -696,9 +713,6 @@ void FixDeform::end_of_step()
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 == NONE) {
set[i].lo_target = domain->boxlo[i];
set[i].hi_target = domain->boxhi[i];
} else if (set[i].style != VOLUME) {
set[i].lo_target = set[i].lo_start +
delta*(set[i].lo_stop - set[i].lo_start);
@ -758,17 +772,21 @@ void FixDeform::end_of_step()
}
// 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 NONE, target is current tilt
// 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 == TRATE) {
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];
@ -782,10 +800,6 @@ void FixDeform::end_of_step()
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 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 {
set[i].tilt_target = set[i].tilt_start +
delta*(set[i].tilt_stop - set[i].tilt_start);
@ -801,6 +815,7 @@ void FixDeform::end_of_step()
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)
@ -813,36 +828,59 @@ void FixDeform::end_of_step()
if (varflag) modify->addstep_compute(update->ntimestep + nevery);
// if any tilt targets exceed bounds, set flip flag and new tilt_flip values
// flip will be performed on next timestep before reneighboring
// if any tilt ratios exceed 0.5, set flip = 1 & compute new tilt_flip values
// do not flip in x or y if non-periodic
// when yz flips and xy is non-zero, xz must also change
// this is to keep the edge vectors of the flipped shape matrix
// an integer combination of the edge vectors of the unflipped shape matrix
// flip is performed on next timestep before reneighboring
if (triclinic) {
double xprd = set[0].hi_target - set[0].lo_target;
double yprd = set[1].hi_target - set[1].lo_target;
if (set[3].tilt_target < -0.5*yprd || set[3].tilt_target > 0.5*yprd ||
set[4].tilt_target < -0.5*xprd || set[4].tilt_target > 0.5*xprd ||
set[5].tilt_target < -0.5*xprd || set[5].tilt_target > 0.5*xprd) {
flip = 1;
next_reneighbor = update->ntimestep + 1;
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;
if (set[3].tilt_flip < -0.5*yprd) {
if (domain->yperiodic) {
if (set[3].tilt_flip*yprdinv < -0.5) {
set[3].tilt_flip += yprd;
set[4].tilt_flip += set[5].tilt_flip;
} else if (set[3].tilt_flip >= 0.5*yprd) {
flip = 1;
} else if (set[3].tilt_flip*yprdinv > 0.5) {
set[3].tilt_flip -= yprd;
set[4].tilt_flip -= set[5].tilt_flip;
flipy = 1;
}
if (set[4].tilt_flip < -0.5*xprd) set[4].tilt_flip += xprd;
if (set[4].tilt_flip > 0.5*xprd) set[4].tilt_flip -= xprd;
if (set[5].tilt_flip < -0.5*xprd) set[5].tilt_flip += xprd;
if (set[5].tilt_flip > 0.5*xprd) set[5].tilt_flip -= xprd;
}
if (domain->xperiodic) {
if (set[4].tilt_flip*xprdinv < -0.5) {
set[4].tilt_flip += xprd;
flip = 1;
}
if (set[4].tilt_flip*xprdinv > 0.5) {
set[4].tilt_flip -= xprd;
flip = 1;
}
if (set[5].tilt_flip*xprdinv < -0.5) {
set[5].tilt_flip += xprd;
flip = 1;
}
if (set[5].tilt_flip*xprdinv > 0.5) {
set[5].tilt_flip -= xprd;
flip = 1;
}
}
if (flip) next_reneighbor = update->ntimestep + 1;
}
}

3
src/fix_deform.h
View File

@ -37,7 +37,8 @@ class FixDeform : public Fix {
void end_of_step();
private:
int triclinic,scaleflag,flip;
int triclinic,scaleflag;
int flip,flipx,flipy;
double *h_rate,*h_ratelo;
int varflag; // 1 if VARIABLE option is used, 0 if not
int kspace_flag; // 1 if KSpace invoked, 0 if not

33
src/fix_nh.cpp
View File

@ -312,18 +312,26 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
// require periodicity in tensile dimension
if (p_flag[0] && domain->xperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
// require periodicity in 2nd dim of off-diagonal tilt component
if (p_flag[3] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
error->all(FLERR,
"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
error->all(FLERR,
"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
error->all(FLERR,
"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (scaleyz == 1 && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix nvt/npt/nph "
@ -2120,11 +2128,12 @@ void FixNH::nh_omega_dot()
}
/* ----------------------------------------------------------------------
if box tilt exceeds limits,
create new box in domain
remap to put far-away atoms back into new box
if any tilt ratios exceed 0.5, set flip = 1 & compute new tilt_flip values
do not flip in x or y if non-periodic
when yz flips and xy is non-zero, xz must also change
this is to keep the edge vectors of the flipped shape matrix
an integer combination of the edge vectors of the unflipped shape matrix
perform irregular on atoms in lamda coords to get atoms to new procs
force reneighboring on next timestep
------------------------------------------------------------------------- */
void FixNH::pre_exchange()
@ -2132,14 +2141,15 @@ void FixNH::pre_exchange()
double xprd = domain->xprd;
double yprd = domain->yprd;
// flip is triggered when tilt exceeds 0.5 by
// an amount DELTAFLIP that is somewhat arbitrary
// flip is triggered when tilt exceeds 0.5 by an amount DELTAFLIP
// this avoids immediate re-flipping due to tilt oscillations
double xtiltmax = (0.5+DELTAFLIP)*xprd;
double ytiltmax = (0.5+DELTAFLIP)*yprd;
int flip = 0;
if (domain->yperiodic) {
if (domain->yz < -ytiltmax) {
flip = 1;
domain->yz += yprd;
@ -2149,7 +2159,9 @@ void FixNH::pre_exchange()
domain->yz -= yprd;
domain->xz -= domain->xy;
}
}
if (domain->xperiodic) {
if (domain->xz < -xtiltmax) {
flip = 1;
domain->xz += xprd;
@ -2157,7 +2169,6 @@ void FixNH::pre_exchange()
flip = 1;
domain->xz -= xprd;
}
if (domain->xy < -xtiltmax) {
flip = 1;
domain->xy += xprd;
@ -2165,6 +2176,7 @@ void FixNH::pre_exchange()
flip = 1;
domain->xy -= xprd;
}
}
if (flip) {
domain->set_global_box();
@ -2180,4 +2192,3 @@ void FixNH::pre_exchange()
domain->lamda2x(atom->nlocal);
}
}