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Adding iso options to fix deform

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This commit is contained in:
jtclemm
2023-06-14 13:39:24 -06:00
parent 63618d2490
commit 6de50fbd33
3 changed files with 155 additions and 22 deletions
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46
doc/src/fix_deform.rst
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@ -20,7 +20,7 @@ Syntax
.. parsed-literal::
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz*
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *iso*
*x*, *y*, *z* args = style value(s)
style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable*
*final* values = lo hi
@ -71,6 +71,12 @@ Syntax
*variable* values = v_name1 v_name2
v_name1 = variable with name1 for tilt change as function of time
v_name2 = variable with name2 for change rate as function of time
*iso* = style value
style = *volume* or *pressure*
*volume* value = none = isotropically adjust system to preserve volume of system
*pressure* values = target gain
target = target mean pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
* zero or more keyword/value pairs may be appended
* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
@ -88,12 +94,10 @@ Syntax
box = distances are defined in simulation box units
*couple* value = *none* or *xyz* or *xy* or *yz* or *xz*
couple pressure values of various dimensions
*vol/balance/p* = *yes* or *no*
*vol/balance/p* value = *yes* or *no*
Modifies the behavior of the *volume* option to try and balance pressures
*max/rate* value = *rate*
rate = maximum strain rate for pressure control
*normalize/pressure* value = *yes* or *no*
determine whether pressure deviation is normalized by target pressure
Examples
""""""""
@ -107,6 +111,7 @@ Examples
fix 1 all deform 1 x pressure 2.0 0.1 normalize/pressure yes max/rate 0.001
fix 1 all deform 1 x trate 0.1 y volume z volume vol/balance/p yes
fix 1 all deform 1 x trate 0.1 y pressure/mean 0.0 1.0 z pressure/mean 0.0 1.0
fix 1 all deform 1 x trate 0.1 y trate -0.1 overlay/pressure/mean 1.0 0.1
Description
"""""""""""
@ -318,8 +323,8 @@ mid point.
The *pressure* style adjusts a dimensions's box length to control that
component of the pressure tensor. This option attempts to maintain a
specified target value using a linear controller where the box length L
evolves according to the equation
specified target value using a linear controller where the box length
:math:`L` evolves according to the equation
.. parsed-literal::
@ -343,7 +348,7 @@ option.
The *pressure/mean* style is changes a dimension in order to maintain
a constant mean pressure defined as the trace of the pressure tensor.
This option is therefore very similar to the *presssure* style with
This option is therefore very similar to the *pressure* style with
identical arguments except the current and target pressures refer to the
mean trace of the pressure tensor. The same options also apply except
for the :ref:`couple <deform_couple>` option.
@ -512,6 +517,25 @@ of the applied strain using the :ref:`max/rate <deform_max_rate>` option.
----------
The *iso* parameter provides an additonal control over the x, y,
and z box lengths. This parameter can only be used in combination with
the *x*, *y*, or *z* comamnds: *vel*, *erate*, *trate*, *pressure*, or
*wiggle*. Note that this parameter will change the overall strain rate in
the *x*, *y*, or *z* dimensions. This is the meaning of its styles and values.
The *volume* style isotropically scales box lengths to maintain a constant
box volume in response to deformation from other parameters.
The *pressure* style controls the box volume to maintain the mean pressure
of the system. This is accomplished by isotropically scaling all box
lengths :math:`L` by an additional factor of :math:`k (P_t - P_m)` where
:math:`k` is the proportional gain constant, :math:`P_t` is the target
pressure, and :math:`P_m` is the current mean pressure (the trace of the
pressure tensor). This style allows one to control the deviatoric strain
tensor while maintaining a fixed mean pressure.
----------
All of the tilt styles change the xy, xz, yz tilt factors during a
simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
are normally bounded by half the distance of the parallel box length.
@ -652,8 +676,12 @@ described below, which will cap the divergence.
.. _deform_max_rate:
The *max/rate* keyword sets an upper threshold, *rate*, that limits the
maximum magnitude of the strain rate applied in any dimension. This keyword
only applies to the *pressure* and *pressure/mean* options.
maximum magnitude of the instantaneous strain rate applied in any dimension.
This keyword only applies to the *pressure* and *pressure/mean* options. If
a pressure-controlled rate is used for both *iso* and either *x*, *y*, or
*z*, then this threshold will apply separately to each individual controller
such that the cumulative strain rate on a box dimension may be up to twice
the value of *rate*.
.. _deform_couple:

129
src/fix_deform.cpp
View File

@ -65,8 +65,8 @@ irregular(nullptr), set(nullptr)
// set defaults
set = new Set[6];
memset(set,0,6*sizeof(Set));
set = new Set[7];
memset(set,0,7*sizeof(Set));
// parse arguments
@ -237,6 +237,25 @@ irregular(nullptr), set(nullptr)
error->all(FLERR,"Illegal fix deform pressure gain, must be positive");
iarg += 4;
} else error->all(FLERR,"Illegal fix deform command: {}", arg[iarg+1]);
} else if (strcmp(arg[iarg],"iso") == 0) {
index = 6;
if (strcmp(arg[iarg+1],"volume") == 0) {
set[index].style = VOLUME;
iarg += 2;
} else if (strcmp(arg[iarg+1],"pressure") == 0) {
if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure", error);
set[index].style = PRESSURE;
if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) {
set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp);
} else {
set[index].pstr = utils::strdup(&arg[iarg+2][2]);
set[index].pvar_flag = 1;
}
set[index].pgain = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (set[index].pgain <= 0.0)
error->all(FLERR,"Illegal fix deform pressure gain, must be positive");
iarg += 4;
}
} else break;
}
@ -313,6 +332,12 @@ irregular(nullptr), set(nullptr)
if (set[i].style == NONE) dimflag[i] = 0;
else dimflag[i] = 1;
if (set[6].style != NONE) {
dimflag[0] = 1;
dimflag[1] = 1;
dimflag[2] = 1;
}
if (dimflag[0]) box_change |= BOX_CHANGE_X;
if (dimflag[1]) box_change |= BOX_CHANGE_Y;
if (dimflag[2]) box_change |= BOX_CHANGE_Z;
@ -324,7 +349,7 @@ irregular(nullptr), set(nullptr)
// b/c shrink wrap will change box-length
for (int i = 0; i < 3; i++)
if (set[i].style && (domain->boundary[i][0] >= 2 || domain->boundary[i][1] >= 2))
if ((set[i].style || set[6].style) && (domain->boundary[i][0] >= 2 || domain->boundary[i][1] >= 2))
error->all(FLERR,"Cannot use fix deform on a shrink-wrapped boundary");
// no tilt deformation on shrink-wrapped 2nd dim
@ -431,7 +456,7 @@ irregular(nullptr), set(nullptr)
// set varflag
varflag = 0;
for (int i = 0; i < 6; i++) {
for (int i = 0; i < 7; i++) {
if (set[i].style == VARIABLE) varflag = 1;
if (set[i].pvar_flag) varflag = 1;
}
@ -439,7 +464,7 @@ irregular(nullptr), set(nullptr)
// set pressure_flag
pressure_flag = 0;
for (int i = 0; i < 6; i++) {
for (int i = 0; i < 7; i++) {
if (set[i].style == PRESSURE || set[i].style == PMEAN) pressure_flag = 1;
if (set[i].coupled_flag) pressure_flag = 1;
}
@ -452,6 +477,14 @@ irregular(nullptr), set(nullptr)
if (set[i].style == PMEAN)
error->all(FLERR, "Cannot use fix deform to assign constant volume and pressure");
// check conflicts between x,y,z styles and iso
if (set[6].style)
for (int i = 0; i < 3; i++) {
if (set[i].style == FINAL || set[i].style == DELTA || set[i].style == SCALE || set[i].style == PMEAN || set[i].style == VARIABLE)
error->all(FLERR, "Cannot use fix deform iso parameter with x, y, or z styles other than vel, erate, trate, pressure, and wiggle");
}
// check pressure used for max rate and normalize error flag
if (!pressure_flag && max_h_rate != 0)
@ -470,6 +503,7 @@ irregular(nullptr), set(nullptr)
set[3].tilt_initial = domain->yz;
set[4].tilt_initial = domain->xz;
set[5].tilt_initial = domain->xy;
set[6].vol_initial = domain->xprd * domain->yprd * domain->zprd;
// reneighboring only forced if flips can occur due to shape changes
@ -511,7 +545,7 @@ irregular(nullptr), set(nullptr)
FixDeform::~FixDeform()
{
if (set) {
for (int i = 0; i < 6; i++) {
for (int i = 0; i < 7; i++) {
delete[] set[i].hstr;
delete[] set[i].hratestr;
delete[] set[i].pstr;
@ -569,7 +603,7 @@ void FixDeform::init()
// check variables for VARIABLE style
for (int i = 0; i < 6; i++) {
for (int i = 0; i < 7; i++) {
if (set[i].style != VARIABLE) continue;
set[i].hvar = input->variable->find(set[i].hstr);
if (set[i].hvar < 0)
@ -585,7 +619,7 @@ void FixDeform::init()
// check optional variables for PRESSURE or PMEAN style
for (int i = 0; i < 6; i++) {
for (int i = 0; i < 7; i++) {
if (!set[i].pvar_flag) continue;
set[i].pvar = input->variable->find(set[i].pstr);
if (set[i].pvar < 0)
@ -701,6 +735,8 @@ void FixDeform::init()
}
}
set[6].vol_start = domain->xprd * domain->yprd * domain->zprd;
// if using tilt TRATE, then initial tilt must be non-zero
for (int i = 3; i < 6; i++)
@ -740,6 +776,7 @@ void FixDeform::init()
// set domain->h_rate values for use by domain and other fixes/computes
// initialize all rates to 0.0
// cannot set here for TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE since not constant
// if iso style is used, these will also not be constant
h_rate = domain->h_rate;
h_ratelo = domain->h_ratelo;
@ -867,6 +904,10 @@ void FixDeform::end_of_step()
if (volume_flag) set_volume();
// apply any final isotropic scalings
if (set[6].style) set_iso();
// Save pressure/strain rate if required
if (pressure_flag) {
@ -983,15 +1024,15 @@ void FixDeform::end_of_step()
// reset global and local box to new size/shape
// only if deform fix is controlling the dimension
if (set[0].style) {
if (set[0].style || set[6].style) {
domain->boxlo[0] = set[0].lo_target;
domain->boxhi[0] = set[0].hi_target;
}
if (set[1].style) {
if (set[1].style || set[6].style) {
domain->boxlo[1] = set[1].lo_target;
domain->boxhi[1] = set[1].hi_target;
}
if (set[2].style) {
if (set[2].style || set[6].style) {
domain->boxlo[2] = set[2].lo_target;
domain->boxhi[2] = set[2].hi_target;
}
@ -1285,6 +1326,67 @@ void FixDeform::set_volume()
}
}
/* ----------------------------------------------------------------------
apply isotropic controls
------------------------------------------------------------------------- */
void FixDeform::set_iso()
{
int i;
double scale, shift;
double v_rate;
if (set[6].style == VOLUME) {
double v0 = set[6].vol_start;
double v = 1.0;
for (i = 0; i < 3; i++)
v *= (set[i].hi_target - set[i].lo_target);
scale = std::pow(v0 / v, THIRD);
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;
// 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] /= update->dt;
}
} else if (set[6].style == PRESSURE) {
// If variable pressure, calculate current target
if (set[6].pvar_flag)
set[6].ptarget = input->variable->compute_equal(set[6].pvar);
v_rate = set[6].pgain * (pressure->scalar- set[6].ptarget);
if (normalize_pressure_flag) {
if (set[6].ptarget == 0) {
if (max_h_rate == 0) {
error->all(FLERR, "Cannot normalize error for zero pressure without defining a max rate");
} else v_rate = max_h_rate * v_rate / fabs(v_rate);
} else v_rate /= fabs(set[6].ptarget);
}
if (max_h_rate != 0)
if (fabs(set[6].ptarget) > max_h_rate)
v_rate = max_h_rate * v_rate / fabs(v_rate);
set[6].cumulative_strain += update->dt * v_rate;
scale = (1.0 + set[6].cumulative_strain);
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;
// 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] /= update->dt;
}
}
}
/* ----------------------------------------------------------------------
write Set data to restart file
------------------------------------------------------------------------- */
@ -1294,7 +1396,7 @@ void FixDeform::write_restart(FILE *fp)
if (comm->me == 0) {
int size = 6 * sizeof(Set);
fwrite(&size,sizeof(int),1,fp);
fwrite(set,sizeof(Set),6,fp);
fwrite(set,sizeof(Set),7,fp);
}
}
@ -1306,7 +1408,7 @@ void FixDeform::restart(char *buf)
{
int samestyle = 1;
Set *set_restart = (Set *) buf;
for (int i=0; i<6; ++i) {
for (int i=0; i<7; ++i) {
// restore data from initial state
set[i].lo_initial = set_restart[i].lo_initial;
set[i].hi_initial = set_restart[i].hi_initial;
@ -1315,6 +1417,7 @@ void FixDeform::restart(char *buf)
set[i].saved = set_restart[i].saved;
set[i].prior_rate = set_restart[i].prior_rate;
set[i].prior_pressure = set_restart[i].prior_pressure;
set[i].cumulative_strain = set_restart[i].cumulative_strain;
// check if style settings are consistent (should do the whole set?)
if (set[i].style != set_restart[i].style)
samestyle = 0;

2
src/fix_deform.h
View File

@ -72,6 +72,7 @@ class FixDeform : public Fix {
double vol_initial, vol_start;
double ptarget, pgain;
double prior_pressure, prior_rate;
double cumulative_strain;
int saved;
int fixed, dynamic1, dynamic2;
char *hstr, *hratestr, *pstr;
@ -85,6 +86,7 @@ class FixDeform : public Fix {
void set_strain();
void set_pressure();
void set_volume();
void set_iso();
void couple();
};