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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7632 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-02-01 01:19:23 +00:00
parent 915cd9188e
commit 74ad43e245
4 changed files with 55 additions and 41 deletions
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60
src/fix_deform.cpp
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@ -236,7 +236,7 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
if (set[5].style && domain->yperiodic == 0)
error->all(FLERR,"Cannot use fix deform on a 2nd non-periodic boundary");
// apply scaling to FINAL,DELTA,VEL,WIGGLE since they have distance/vel units
// apply scaling to FINAL,DELTA,VEL,WIGGLE since they have dist/vel units
int flag = 0;
for (int i = 0; i < 6; i++)
@ -320,6 +320,12 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
}
}
// 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++) {
@ -333,7 +339,7 @@ FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
else if (i == 3) set[i].tilt_initial = domain->yz;
}
// reneighboring only forced if flips will occur due to shape changes
// reneighboring only forced if flips can occur due to shape changes
if (set[3].style || set[4].style || set[5].style) force_reneighbor = 1;
next_reneighbor = -1;
@ -422,7 +428,7 @@ void FixDeform::init()
// 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
// if VARIABLE or NONE, no need to set
for (int i = 0; i < 3; i++) {
if (update->firststep == update->beginstep) {
@ -466,13 +472,6 @@ void FixDeform::init()
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);
} else if (set[i].style == VARIABLE) {
bigint holdstep = update->ntimestep;
update->ntimestep = update->endstep;
double delta = input->variable->compute_equal(set[i].hvar);
update->ntimestep = holdstep;
set[i].lo_stop = set[i].lo_start - 0.5*delta;
set[i].hi_stop = set[i].hi_start + 0.5*delta;
}
}
@ -537,13 +536,6 @@ void FixDeform::init()
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
}
}
} else if (set[i].style == VARIABLE) {
bigint holdstep = update->ntimestep;
update->ntimestep = update->endstep;
double delta_tilt = input->variable->compute_equal(set[i].hvar);
update->ntimestep = holdstep;
set[i].tilt_stop = set[i].tilt_start + delta_tilt;
}
}
@ -554,33 +546,29 @@ void FixDeform::init()
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
// NOTE: is this comment correct, not what is tested below?
// test for WIGGLE is on min/max oscillation limit, not tilt_stop
// test for VARIABLE is error, since no way to calculate min/max limits
// 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
if (set[3].style && set[5].style) {
int flag = 0;
double lo,hi;
if (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 (set[3].style == VARIABLE)
error->all(FLERR,"Fix deform is changing yz with xy variable");
// NOTE is this preceding error test and message correct?
// NOTE is this test on set[1] correct? which is y dim?
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 (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 (flag)
error->all(FLERR,
"Fix deform is changing yz by too much with changing xy");
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
@ -672,10 +660,14 @@ void FixDeform::end_of_step()
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
// wrap variable evaluations with clear/add
if (varflag) modify->clearstep_compute();
// set new 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 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
@ -698,11 +690,9 @@ void FixDeform::end_of_step()
cos(TWOPI*delt/set[i].tperiod);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == VARIABLE) {
// NOTE: worry about clearstep, addstep, maybe set on
// outside of loop with global varflag
double delta = input->variable->compute_equal(set[i].hvar);
set[i].lo_target = set[i].lo_start - 0.5*delta;
set[i].hi_target = set[i].hi_start + 0.5*delta;
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 == NONE) {
@ -769,7 +759,7 @@ void FixDeform::end_of_step()
// for triclinic, set new box shape
// 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 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
@ -820,6 +810,8 @@ 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
// when yz flips and xy is non-zero, xz must also change