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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@785 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-08-08 14:55:11 +00:00
parent e78440db6f
commit d0a7e5db4c
2 changed files with 92 additions and 79 deletions
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162
src/fix_deform.cpp
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@ -205,48 +205,10 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
else if (set[i].style == VEL) set[i].vel *= map[i]; else if (set[i].style == VEL) set[i].vel *= map[i];
} }
// set initial/final values for box size and shape for FINAL,DELTA,SCALE
// final not possible for VEL,ERATE,TRATE since don't know length of run yet
// final = initial if no setting
for (int i = 0; i < 3; i++) {
set[i].lo_target = set[i].lo_stop = set[i].lo_start = domain->boxlo[i];
set[i].hi_target = set[i].hi_stop = set[i].hi_start = domain->boxhi[i];
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);
}
}
for (int i = 3; i < 6; i++) {
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;
set[i].tilt_flip = set[i].tilt_target =
set[i].tilt_stop = set[i].tilt_start;
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;
}
}
// for VOLUME, setup links to other dims // for VOLUME, setup links to other dims
// fixed, dynamic1,2, vol_start // fixed, dynamic1, dynamic2
for (int i = 0; i < 3; i++) { for (int i = 0; i < 3; i++) {
set[i].vol_start = domain->xprd * domain->yprd * domain->zprd;
if (set[i].style != VOLUME) continue; if (set[i].style != VOLUME) continue;
int other1 = (i+1) % 3; int other1 = (i+1) % 3;
int other2 = (i+2) % 3; int other2 = (i+2) % 3;
@ -282,6 +244,19 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
} }
} }
// 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];
}
for (int i = 3; i < 6; i++) {
if (i == 5) set[i].tilt_initial = domain->xy;
else if (i == 4) set[i].tilt_initial = domain->xz;
else if (i == 3) set[i].tilt_initial = domain->yz;
set[i].vol_initial = domain->xprd * domain->yprd * domain->zprd;
}
// initial settings // initial settings
// reneighboring only forced if flips will occur due to shape changes // reneighboring only forced if flips will occur due to shape changes
@ -329,15 +304,36 @@ void FixDeform::init()
else kspace_flag = 0; else kspace_flag = 0;
// elapsed time for entire simulation, including multiple runs if defined // elapsed time for entire simulation, including multiple runs if defined
// cannot be 0.0 since can't deform a finite distance in 0 time
double delt = (update->endstep - update->beginstep) * update->dt; double delt = (update->endstep - update->beginstep) * update->dt;
// set final values for box size and shape for VEL,ERATE,TRATE // set start/stop values for box size and shape
// now possible since length of run is known // 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 NONE, no need to set
for (int i = 0; i < 3; i++) { for (int i = 0; i < 3; i++) {
if (set[i].style == VEL) { if (update->firststep == update->beginstep) {
set[i].lo_start = domain->boxlo[i];
set[i].hi_start = domain->boxhi[i];
} else {
set[i].lo_start = set[i].lo_initial;
set[i].hi_start = set[i].hi_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].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; set[i].hi_stop = set[i].hi_start + 0.5*delt*set[i].vel;
} else if (set[i].style == ERATE) { } else if (set[i].style == ERATE) {
@ -356,7 +352,21 @@ void FixDeform::init()
} }
for (int i = 3; i < 6; i++) { for (int i = 3; i < 6; i++) {
if (set[i].style == VEL) { 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;
set[i].vol_start = domain->xprd * domain->yprd * domain->zprd;
} else {
set[i].tilt_start = set[i].tilt_initial;
set[i].vol_start = set[i].vol_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; set[i].tilt_stop = set[i].tilt_start + delt*set[i].vel;
} else if (set[i].style == ERATE) { } else if (set[i].style == ERATE) {
if (i == 3) set[i].tilt_stop = set[i].tilt_start + if (i == 3) set[i].tilt_stop = set[i].tilt_start +
@ -373,27 +383,29 @@ void FixDeform::init()
// if using tilt TRATE, then initial tilt must be non-zero // if using tilt TRATE, then initial tilt must be non-zero
for (int i = 3; i < 6; i++) for (int i = 3; i < 6; i++)
if (set[i].style == TRATE) if (set[i].style == TRATE && set[i].tilt_start == 0.0)
if ((i == 5 && domain->xy == 0.0) || error->all("Cannot use fix deform trate on a box with zero tilt");
(i == 4 && domain->xz == 0.0) ||
(i == 3 && domain->yz == 0.0))
error->all("Cannot use fix deform trate on a box with zero tilt");
// if yz changes and will cause box flip, then xy cannot be changing // if yz changes and will cause box flip, then xy cannot be changing
// this is b/c the flips would induce continuous changes in xz // this is b/c the flips would induce continuous changes in xz
// in order to keep the edge vectors of the flipped shape matrix // in order to keep the edge vectors of the flipped shape matrix
// a linear combination of the edge vectors of the unflipped shape matrix // a linear combination of the edge vectors of the unflipped shape matrix
if (set[3].style && set[5].style) if (set[3].style && set[5].style) {
int flag = 0;
if (set[3].tilt_stop < -0.5*(set[1].hi_start-set[1].lo_start) || if (set[3].tilt_stop < -0.5*(set[1].hi_start-set[1].lo_start) ||
set[3].tilt_stop > 0.5*(set[1].hi_start-set[1].lo_start) || set[3].tilt_stop > 0.5*(set[1].hi_start-set[1].lo_start)) flag = 1;
set[3].tilt_stop < -0.5*(set[1].hi_stop-set[1].lo_stop) || if (set[1].style) {
set[3].tilt_stop > 0.5*(set[1].hi_stop-set[1].lo_stop)) if (set[3].tilt_stop < -0.5*(set[1].hi_stop-set[1].lo_stop) ||
set[3].tilt_stop > 0.5*(set[1].hi_stop-set[1].lo_stop)) flag = 1;
}
if (flag)
error->all("Fix deform is changing yz by too much with changing xy"); error->all("Fix deform is changing yz by too much with changing xy");
}
// set domain->h_rate values for use by domain and other fixes/computes // set domain->h_rate values for use by domain and other fixes/computes
// initialize all rates to 0.0 // initialize all rates to 0.0
// cannot set h_rate now for TRATE,VOLUME styles since not constant // cannot set h_rate for TRATE,VOLUME styles since not constant
h_rate = domain->h_rate; h_rate = domain->h_rate;
h_ratelo = domain->h_ratelo; h_ratelo = domain->h_ratelo;
@ -483,11 +495,10 @@ void FixDeform::end_of_step()
// set new box size // set new box size
// for TRATE, set target directly based on current time and set h_rate // for TRATE, set target directly based on current time and set h_rate
// for NONE, target is current box size
// for others except VOLUME, target is linear value between start and stop // for others except VOLUME, target is linear value between start and stop
for (i = 0; i < 3; i++) { for (i = 0; i < 3; i++) {
if (set[i].style == NONE) continue;
if (set[i].style == TRATE) { if (set[i].style == TRATE) {
double delt = (update->ntimestep - update->beginstep) * update->dt; double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) - set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
@ -496,7 +507,9 @@ void FixDeform::end_of_step()
0.5*((set[i].hi_start-set[i].lo_start)*pow(1.0+set[i].rate,delt)); 0.5*((set[i].hi_start-set[i].lo_start)*pow(1.0+set[i].rate,delt));
h_rate[i] = set[i].rate * domain->h[i]; h_rate[i] = set[i].rate * domain->h[i];
h_ratelo[i] = -0.5*h_rate[i]; 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) { } else if (set[i].style != VOLUME) {
set[i].lo_target = set[i].lo_start + set[i].lo_target = set[i].lo_start +
delta*(set[i].lo_stop - set[i].lo_start); delta*(set[i].lo_stop - set[i].lo_start);
@ -556,20 +569,23 @@ void FixDeform::end_of_step()
} }
// for triclinic, set new box shape // for triclinic, set new box shape
// for TRATE, set target directly based on current time and set h_rate // for TRATE, set target directly based on current time. also set h_rate
// for NONE, target is current tilt
// for other styles, target is linear value between start and stop values // for other styles, target is linear value between start and stop values
if (triclinic) { if (triclinic) {
double *h = domain->h; double *h = domain->h;
for (i = 3; i < 6; i++) { for (i = 3; i < 6; i++) {
if (set[i].style == NONE) continue;
if (set[i].style == TRATE) { if (set[i].style == TRATE) {
double delt = (update->ntimestep - update->beginstep) * update->dt; double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].tilt_target = set[i].tilt_start * pow(1.0+set[i].rate,delt); set[i].tilt_target = set[i].tilt_start * pow(1.0+set[i].rate,delt);
h_rate[i] = set[i].rate * domain->h[i]; h_rate[i] = set[i].rate * domain->h[i];
} else if (set[i].style) { } 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 + set[i].tilt_target = set[i].tilt_start +
delta*(set[i].tilt_stop - set[i].tilt_start); delta*(set[i].tilt_stop - set[i].tilt_start);
} }
@ -627,7 +643,7 @@ void FixDeform::end_of_step()
} }
} }
// convert atoms to lamda coords // convert atoms and rigid bodies to lamda coords
if (remapflag == X_REMAP) { if (remapflag == X_REMAP) {
double **x = atom->x; double **x = atom->x;
@ -637,7 +653,11 @@ void FixDeform::end_of_step()
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) if (mask[i] & groupbit)
domain->x2lamda(x[i],x[i]); 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 // reset global and local box to new size/shape
// only if deform fix is controlling the dimension // only if deform fix is controlling the dimension
@ -663,7 +683,7 @@ void FixDeform::end_of_step()
domain->set_global_box(); domain->set_global_box();
domain->set_local_box(); domain->set_local_box();
// convert atoms back to box coords // convert atoms and rigid bodies back to box coords
if (remapflag == X_REMAP) { if (remapflag == X_REMAP) {
double **x = atom->x; double **x = atom->x;
@ -673,18 +693,12 @@ void FixDeform::end_of_step()
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) if (mask[i] & groupbit)
domain->lamda2x(x[i],x[i]); domain->lamda2x(x[i],x[i]);
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
} }
// remap centers-of-mass of rigid bodies
// needs to be new call, not dilate
// check where else fix dilate is called from
/*
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->dilate(2,oldlo,oldhi,newlo,newhi);
*/
// redo KSpace coeffs since box has changed // redo KSpace coeffs since box has changed
if (kspace_flag) force->kspace->setup(); if (kspace_flag) force->kspace->setup();

9
src/fix_deform.h
View File

@ -41,11 +41,10 @@ class FixDeform : public Fix {
double flo,fhi,ftilt; double flo,fhi,ftilt;
double dlo,dhi,dtilt; double dlo,dhi,dtilt;
double scale,vel,rate; double scale,vel,rate;
double lo_start,hi_start; double lo_initial,hi_initial;
double lo_stop,hi_stop; double lo_start,hi_start,lo_stop,hi_stop,lo_target,hi_target;
double lo_target,hi_target; double tilt_initial,tilt_start,tilt_stop,tilt_target,tilt_flip;
double tilt_start,tilt_stop,tilt_target; double vol_initial,vol_start;
double vol_start,tilt_flip;
int fixed,dynamic1,dynamic2; int fixed,dynamic1,dynamic2;
}; };
Set *set; Set *set;