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Improvements & bug fixes to fix def/press

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This commit is contained in:
jtclemm
2024-04-19 15:14:42 -06:00
parent c5ecef82c1
commit 97d8ecbac1
5 changed files with 100 additions and 26 deletions
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19
doc/src/fix_deform_pressure.rst
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@ -29,10 +29,12 @@ Syntax
NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
*xy*, *xz*, *yz* args = style value
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure*
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale*
*pressure* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*erate/rescale* value = R
R = engineering shear strain rate (1/time units)
NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
*box* = style value
@ -159,6 +161,21 @@ details of a simulation and testing different values is
recommended. One can also apply a maximum limit to the magnitude of
the applied strain using the :ref:`max/rate <deform_max_rate>` option.
The *erate/rescale* style operates similarly to the *erate* style with
a specified strain rate in units of 1/time. The difference is that
the change in the tilt factor will depend on the current length of
the box perpendicular to the shear direction, L, instead of the
original length, L0. The tilt factor T as a function of time will
change as
.. parsed-literal::
T(t) = T(t-1) + L\*erate\* \Delta t
where T(t-1) is the tilt factor on the previous timestep and :math:`\Delta t`
is the timestep size. This option may be useful in scenarios where
L changes in time.
----------
The *box* parameter provides an additional control over the *x*, *y*,

100
src/EXTRA-FIX/fix_deform_pressure.cpp
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@ -110,6 +110,12 @@ FixDeformPressure::FixDeformPressure(LAMMPS *lmp, int narg, char **arg) :
}
set_extra[index].pgain = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
i += 4;
} else if (strcmp(arg[iarg + 1], "erate/rescale") == 0) {
if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix deform/pressure erate/rescale", error);
set[index].style = ERATERS;
set[index].rate = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
iarg += 3;
i += 3;
} else error->all(FLERR, "Illegal fix deform/pressure command: {}", arg[iarg + 1]);
} else if (strcmp(arg[iarg], "box") == 0) {
@ -424,16 +430,31 @@ void FixDeformPressure::init()
if (!pressure)
error->all(FLERR, "Pressure ID {} for fix deform/pressure does not exist", id_press);
}
// if yz [3] changes and will cause box flip, then xy [5] cannot be changing
// 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
// error if style PRESSURE/ERATEER for yz, can't calculate if box flip occurs
if (set[3].style && set[5].style) {
int flag = 0;
double lo,hi;
if (flipflag && set[3].style == PRESSURE)
error->all(FLERR, "Fix {} cannot use yz pressure with xy", style);
if (flipflag && set[3].style == ERATERS)
error->all(FLERR, "Fix {} cannot use yz erate/rescale with xy", style);
}
}
/* ----------------------------------------------------------------------
compute T,P if needed before integrator starts
compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixDeformPressure::setup(int /*vflag*/)
{
// trigger virial computation on next timestep
if (pressure_flag) pressure->addstep(update->ntimestep+1);
// trigger virial computation, if needed, on next timestep
if (pressure_flag) pressure->addstep(update->ntimestep + 1);
}
/* ---------------------------------------------------------------------- */
@ -446,7 +467,20 @@ void FixDeformPressure::end_of_step()
// set new box size for strain-based dims
if (strain_flag) FixDeform::apply_strain();
if (strain_flag) {
FixDeform::apply_strain();
for (int i = 3; i < 6; i++) {
if (set[i].style == ERATERS) {
double L = domain->zprd;
if (i == 5) L = domain->yprd;
h_rate[i] = set[i].rate * L;
set_extra[i].cumulative_shift += update->dt * h_rate[i];
set[i].tilt_target = set[i].tilt_start + set_extra[i].cumulative_shift;
}
}
}
// set new box size for pressure-based dims
@ -479,12 +513,33 @@ void FixDeformPressure::end_of_step()
for (int i = 0; i < 3; i++) {
set_extra[i].prior_pressure = pressure->vector[i];
set_extra[i].prior_rate = ((set[i].hi_target - set[i].lo_target) /
(domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt;
domain->prd[i] - 1.0) / update->dt;
}
}
if (varflag) modify->addstep_compute(update->ntimestep + nevery);
// If tilting while evolving linear dimension, sum remapping effects
// otherwise, update_domain() will inaccurately use the current
// linear dimension to apply prior remappings
for (int i = 3; i < 6; i++) {
int idenom = 0;
if (i == 3) idenom = 1;
if (set[i].style && (set_box.style || set[idenom].style)) {
// Add prior remappings. If the box remaps this timestep, don't
// add it yet so update_domain() will first detect the remapping
set[i].tilt_target += set_extra[i].cumulative_remap;
// Update remapping for next timestep
double prd = set[idenom].hi_target - set[idenom].lo_target;
double prdinv = 1.0 / prd;
if (set[i].tilt_target * prdinv < -0.5)
set_extra[i].cumulative_remap += prd;
if (set[i].tilt_target * prdinv > 0.5)
set_extra[i].cumulative_remap -= prd;
}
}
FixDeform::update_domain();
@ -556,26 +611,24 @@ void FixDeformPressure::apply_pressure()
h_ratelo[i] = -0.5 * h_rate[i];
double offset = 0.5 * (domain->boxhi[i] - domain->boxlo[i]) * (1.0 + update->dt * h_rate[i]);
set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - offset;
set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + offset;
double shift = domain->prd[i] * update->dt * h_rate[i];
set_extra[i].cumulative_shift += shift;
set[i].lo_target = set[i].lo_start - 0.5 * set_extra[i].cumulative_shift;
set[i].hi_target = set[i].hi_start + 0.5 * set_extra[i].cumulative_shift;
}
for (int i = 3; i < 6; i++) {
if (set[i].style != PRESSURE) continue;
double L, tilt, pcurrent;
double L, pcurrent;
if (i == 3) {
L = domain->zprd;
tilt = domain->yz;
pcurrent = tensor[5];
} else if (i == 4) {
L = domain->zprd;
tilt = domain->xz + update->dt;
pcurrent = tensor[4];
} else {
L = domain->yprd;
tilt = domain->xy;
pcurrent = tensor[3];
}
@ -592,7 +645,8 @@ void FixDeformPressure::apply_pressure()
if (fabs(h_rate[i]) > max_h_rate)
h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]);
set[i].tilt_target = tilt + update->dt * h_rate[i];
set_extra[i].cumulative_shift += update->dt * h_rate[i];
set[i].tilt_target = set[i].tilt_start + set_extra[i].cumulative_shift;
}
}
@ -629,9 +683,9 @@ void FixDeformPressure::apply_volume()
double dt = update->dt;
double e1i = set_extra[i].prior_rate;
double e2i = set_extra[fixed].prior_rate;
double L1i = domain->boxhi[i] - domain->boxlo[i];
double L2i = domain->boxhi[fixed] - domain->boxlo[fixed];
double L3i = domain->boxhi[dynamic1] - domain->boxlo[dynamic1];
double L1i = domain->prd[i];
double L2i = domain->prd[fixed];
double L3i = domain->prd[dynamic1];
double L3 = (set[dynamic1].hi_target - set[dynamic1].lo_target);
double Vi = L1i * L2i * L3i;
double V = L3 * L1i * L2i;
@ -680,7 +734,7 @@ void FixDeformPressure::apply_volume()
}
}
h_rate[i] = (2.0 * shift / (domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt;
h_rate[i] = (2.0 * shift / domain->prd[i] - 1.0) / update->dt;
h_ratelo[i] = -0.5 * h_rate[i];
set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift;
@ -742,7 +796,7 @@ void FixDeformPressure::apply_box()
set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift;
// Recalculate h_rate
h_rate[i] = (set[i].hi_target - set[i].lo_target) / (domain->boxhi[i] - domain->boxlo[i]) - 1.0;
h_rate[i] = (set[i].hi_target - set[i].lo_target) / domain->prd[i] - 1.0;
h_rate[i] /= update->dt;
h_ratelo[i] = -0.5 * h_rate[i];
}
@ -767,14 +821,14 @@ void FixDeformPressure::apply_box()
if (fabs(v_rate) > max_h_rate)
v_rate = max_h_rate * v_rate / fabs(v_rate);
scale = (1.0 + update->dt * v_rate);
for (i = 0; i < 3; i++) {
shift = 0.5 * (set[i].hi_target - set[i].lo_target) * scale;
set[i].lo_target = 0.5 * (set[i].lo_start + set[i].hi_start) - shift;
set[i].hi_target = 0.5 * (set[i].lo_start + set[i].hi_start) + shift;
shift = (set[i].hi_target - set[i].lo_target) * update->dt * v_rate;
set_extra[6].cumulative_vshift[i] += shift;
set[i].lo_target -= 0.5 * set_extra[6].cumulative_vshift[i];
set[i].hi_target += 0.5 * set_extra[6].cumulative_vshift[i];
// Recalculate h_rate
h_rate[i] = (set[i].hi_target - set[i].lo_target) / (domain->boxhi[i] - domain->boxlo[i]) - 1.0;
h_rate[i] = (set[i].hi_target - set[i].lo_target) / domain->prd[i] - 1.0;
h_rate[i] /= update->dt;
h_ratelo[i] = -0.5 * h_rate[i];
}

3
src/EXTRA-FIX/fix_deform_pressure.h
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@ -51,6 +51,9 @@ class FixDeformPressure : public FixDeform {
struct SetExtra {
double ptarget, pgain;
double prior_pressure, prior_rate;
double cumulative_shift;
double cumulative_vshift[3];
double cumulative_remap;
int saved;
char *pstr;
int pvar, pvar_flag;

2
src/fix_deform.cpp
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@ -63,7 +63,7 @@ irregular(nullptr), set(nullptr)
int nskip;
if (utils::strmatch(style, "^deform/pressure")) {
child_parameters.insert("box");
child_styles.insert({{"pressure", 4}, {"pressure/mean", 4}, {"volume", 2}});
child_styles.insert({{"pressure", 4}, {"pressure/mean", 4}, {"erate/rescale", 3}, {"volume", 2}});
}
// set defaults

2
src/fix_deform.h
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@ -29,7 +29,7 @@ class FixDeform : public Fix {
int remapflag; // whether x,v are remapped across PBC
int dimflag[6]; // which dims are deformed
enum { NONE, FINAL, DELTA, SCALE, VEL, ERATE, TRATE, VOLUME, WIGGLE, VARIABLE, PRESSURE, PMEAN };
enum { NONE, FINAL, DELTA, SCALE, VEL, ERATE, TRATE, VOLUME, WIGGLE, VARIABLE, PRESSURE, PMEAN, ERATERS };
enum { ONE_FROM_ONE, ONE_FROM_TWO, TWO_FROM_ONE };
FixDeform(class LAMMPS *, int, char **);