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Adding documentation, various updates

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This commit is contained in:
jtclemm
2022-10-22 19:03:52 -06:00
parent 66471c1465
commit 173e2382b3
3 changed files with 425 additions and 233 deletions
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169
doc/src/fix_deform.rst
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@ -34,6 +34,12 @@ Syntax
effectively an engineering strain rate
*erate* value = R
R = engineering strain rate (1/time units)
*pressure* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*pressure/mean* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*trate* value = R
R = true strain rate (1/time units)
*volume* value = none = adjust this dim to preserve volume of system
@ -54,6 +60,9 @@ Syntax
effectively an engineering shear strain rate
*erate* value = R
R = engineering shear strain rate (1/time units)
*pressure* values = target gain
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*trate* value = R
R = true shear strain rate (1/time units)
*wiggle* values = A Tp
@ -64,7 +73,7 @@ Syntax
v_name2 = variable with name2 for change rate as function of time
* zero or more keyword/value pairs may be appended
* keyword = *remap* or *flip* or *units*
* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
.. parsed-literal::
@ -77,6 +86,14 @@ Syntax
*units* value = *lattice* or *box*
lattice = distances are defined in lattice units
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*
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
""""""""
@ -87,6 +104,9 @@ Examples
fix 1 all deform 1 x trate 0.1 y volume z volume
fix 1 all deform 1 xy erate 0.001 remap v
fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
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
Description
"""""""""""
@ -230,7 +250,11 @@ the product of x,z lengths constant. If "x scale 1.1 y volume z
volume" is specified, then both the y,z box lengths will shrink as x
increases to keep the volume constant (product of x,y,z lengths). In
this case, the y,z box lengths shrink so as to keep their relative
aspect ratio constant.
aspect ratio constant. When maintaining a constant volume using two
separate dimensions, one can alternatively allow the two dimensions
to adjust their aspect ratio to attempt to maintain equivalent
pressures along the two dimensions. See the
:ref:`vol/balance/p <deform_balance>` option for more details.
For solids or liquids, note that when one dimension of the box is
expanded via fix deform (i.e. tensile strain), it may be physically
@ -292,6 +316,38 @@ For the *scale*, *vel*, *erate*, *trate*, *volume*, *wiggle*, and
*variable* styles, the box length is expanded or compressed around its
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
.. parsed-literal::
\frac{d L(t)}{dt} = L(t) k (P_t - P)
where :math:`k` is a proportional gain constant, :math:`P_t` is the target
pressure, and :math:`P` is the current pressure along that dimension. This
approach is similar to the method used to control the pressure by
:doc:`fix press/berendsen <fix_press_berendsen>`. The target pressure
accepts either a constant numeric value or a LAMMPS :ref:`variable <variable>`.
Notably, this variable can be a function of time or other components of
the pressure tensor. By default, :math:`k` has units of 1/(time * pressure)
although this will change if the *normalize/pessure* option is set as
:ref:`discussed below <deform_normalize>`. There is no proven method
to choosing an appropriate value of :math:`k` as it will depend on the
specific 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 and couple
pressures in different dimensions using the :ref:`couple <deform_couple>`
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
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.
----------
For the *xy*, *xz*, and *yz* parameters, this is the meaning of their
@ -433,6 +489,27 @@ assume that the current timestep = 0.
variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
fix 2 all deform 1 xy variable v_displace v_rate remap v
The *pressure* style adjusts a tilt factor to control the corresponding
off-diagonal component of the pressure tensor. This option attempts to
maintain a specified target value using a linear controller where the
tilt factor T evolves according to the equation
.. parsed-literal::
\frac{d T(t)}{dt} = L(t) k (P - P_t)
where :math:`k` is a proportional gain constant, :math:`P_t` is the target
pressure, :math:`P` is the current pressure, and :math:`L` is the perpendicular
box length. The target pressure accepts either a constant numeric value or a
LAMMPS :ref:`variable <variable>`. Notably, this variable can be a function
of time or other components of the pressure tensor. By default, :math:`k`
has units of 1/(time * pressure) although this will change if the
*normalize/pessure* option is set as :ref:`discussed below <deform_normalize>`.
There is no proven method to choosing an appropriate value of :math:`k` as it
will depend on thespecific details of a simulation and testing different
values isrecommended. One can also apply a maximum limit to the magnitude
of the applied strain using the :ref:`max/rate <deform_max_rate>` option.
----------
All of the tilt styles change the xy, xz, yz tilt factors during a
@ -561,6 +638,73 @@ does not affect the *variable* style. You should use the *xlat*,
*ylat*, *zlat* keywords of the :doc:`thermo_style <thermo_style>`
command if you want to include lattice spacings in a variable formula.
.. _deform_normalize:
The *normalize/pressure* keyword changes how box dimensions evolve when
using the *pressure* or *pressure/mean* deformation options. If the
*deform/normalize* value is set to *yes*, then the deviation from the
target pressure is normalized by the absolute value of the target
pressure such that the proportional gain constant scales a percentage
error and has units of 1/time. If the target pressure is ever zero, this
will produce an error unless the *max/rate* keyword is defined,
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.
.. _deform_couple:
The *couple* keyword allows two or three of the diagonal components of
the pressure tensor to be "coupled" together for the *pressure* option.
The value specified with the keyword determines which are coupled. For
example, *xz* means the *Pxx* and *Pzz* components of the stress tensor
are coupled. *Xyz* means all 3 diagonal components are coupled. Coupling
means two things: the instantaneous stress will be computed as an average
of the corresponding diagonal components, and the coupled box dimensions
will be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The target
pressures and gain constants for any coupled dimensions must be identical.
*Couple xyz* can be used for a 2d simulation; the *z* dimension is simply
ignored.
.. _deform_balance:
The *vol/balance/p* keyword modifies the behavior of *volume* when two
dimensions are used to maintain a fixed volume. Instead of straining
the two dimensions in lockstep, the two dimensions are allowed to
separately dilate or contract in a manner to maintain a constant
volume while simultaneously trying to keep the pressure along each
dimension equal using a method described in :ref:`(Huang2014) <Huang2014>`.
----------
If any pressure controls are used, this fix computes a temperature and
pressure each timestep. To do this, the fix creates its own computes of
style "temp" and "pressure", as if these commands had been issued:
.. code-block:: LAMMPS
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>` commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
+ underscore + "press", and the group for the new computes is the same
as the fix group.
Note that these are NOT the computes used by thermodynamic output (see
the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*
and *thermo_press*. This means you can change the attributes of this
fix's temperature or pressure via the
:doc:`compute_modify <compute_modify>` command or print this temperature
or pressure during thermodynamic output via the
:doc:`thermo_style custom <thermo_style>` command using the appropriate
compute-ID. It also means that changing attributes of *thermo_temp* or
*thermo_press* will have no effect on this fix.
----------
.. include:: accel_styles.rst
@ -574,6 +718,15 @@ command. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
this fix for access by various :doc:`output commands <Howto_output>`.
If any pressure controls are used, the :doc:`fix_modify <fix_modify>` *temp*
and *press* options are supported by this fix. You can use them to assign a
:doc:`compute <compute>` you have defined to this fix which will be used
in its temperature and pressure calculations. If you do this, note
that the kinetic energy derived from the compute temperature should be
consistent with the virial term computed using all atoms for the
pressure. LAMMPS will warn you if you choose to compute temperature
on a subset of atoms.
This fix can perform deformation over multiple runs, using the *start*
and *stop* keywords of the :doc:`run <run>` command. See the
:doc:`run <run>` command for details of how to do this.
@ -597,4 +750,14 @@ Related commands
Default
"""""""
The option defaults are remap = x, flip = yes, and units = lattice.
The option defaults are remap = x, flip = yes, units = lattice, and
normalize/pressure = no.
----------
.. _Li2014b:
**(Huang2014)** X. Huang,
"Exploring critical-state behavior using DEM",
Doctoral dissertation, Imperial College.
(2014). https://doi.org/10.25560/25316

392
src/fix_deform.cpp
View File

@ -13,13 +13,9 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Pieter in 't Veld (SNL)
Contributing author: Pieter in 't Veld (SNL), Joel Clemmer (SNL)
------------------------------------------------------------------------- */
// Save previous state to restart file for derivatives
// define hrate_lo/hi for volume/pressure
// add logic for hi_stop and flip flag
#include "fix_deform.h"
#include "atom.h"
@ -44,7 +40,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE,PISOTROPIC};
enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE,PRESSURE,PMEAN};
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
enum{NOCOUPLE=0,XYZ,XY,YZ,XZ};
@ -60,6 +56,9 @@ irregular(nullptr), set(nullptr)
pre_exchange_migrate = 1;
pcouple = NOCOUPLE;
dimension = domain->dimension;
max_h_rate = 0.0;
vol_balance_flag = 0;
normalize_pressure_flag = 0;
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix deform command");
@ -153,9 +152,9 @@ irregular(nullptr), set(nullptr)
if (set[index].pgain <= 0.0)
error->all(FLERR,"Illegal fix deform pressure gain, must be positive");
iarg += 4;
} else if (strcmp(arg[iarg+1],"pressure/isotropic") == 0) {
if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure/isotropic", error);
set[index].style = PISOTROPIC;
} else if (strcmp(arg[iarg+1],"pressure/mean") == 0) {
if (iarg+4 > narg) utils::missing_cmd_args(FLERR, "fix deform pressure/mean", error);
set[index].style = PMEAN;
if (strstr(arg[iarg+2],"v_") != arg[iarg+2]) {
set[index].ptarget = utils::numeric(FLERR,arg[iarg+2],false,lmp);
} else {
@ -266,21 +265,21 @@ irregular(nullptr), set(nullptr)
for (int i = 0; i < 3; i++) {
if (coupled_indices[i]) {
set[i].coupled_flag = 1;
if (set[i].style != VOLUME && set[i].style != PRESSURE && set[i].style != NONE)
error->all(FLERR, "Cannot couple dimensions unless they are controlled using the pressure or volume option in fix deform");
if (set[i].style == PRESSURE || set[i].style == VOLUME)
if (set[i].style != PRESSURE && set[i].style != NONE)
error->all(FLERR, "Cannot couple non-pressure-controlled dimensions");
if (set[i].style == PRESSURE)
j = i;
}
}
if (j == -1)
error->all(FLERR, "Must specify pressure style for a coupled dimension in fix deform");
error->all(FLERR, "Must specify deformation style for at least one coupled dimension");
// Copy or compare data for each coupled dimension
for (int i = 0; i < 3; i++) {
if (coupled_indices[i]) {
// Copy coupling information if dimension style is undefined
if (set[j].style == PRESSURE && set[i].style == NONE) {
if (set[i].style == NONE) {
set[i].style = PRESSURE;
set[i].pgain = set[j].pgain;
if (set[j].pvar_flag) {
@ -289,32 +288,21 @@ irregular(nullptr), set(nullptr)
} else {
set[i].ptarget = set[j].ptarget;
}
} else if (set[j].style == VOLUME && set[i].style == NONE) {
set[i].style = VOLUME;
if (domain->dimension == 2)
error->all(FLERR, "Cannot couple pressure with constant volume in two dimensions");
}
} else {
// Check for incompatibilities in style
if (set[j].style != set[i].style && set[i].style != NONE)
error->all(FLERR, "Cannot couple dimensions with different control options");
if (set[j].style != PRESSURE) continue;
// If pressure controlled, check for incompatibilities in parameters
if (set[i].pgain != set[j].pgain)
error->all(FLERR, "Coupled dimensions must have identical gain parameters\n");
if (set[i].pgain != set[j].pgain || set[i].pvar_flag != set[j].pvar_flag ||
set[i].ptarget != set[j].ptarget)
error->all(FLERR, "Coupled dimensions must have identical gain parameters");
if (set[i].pvar_flag != set[j].pvar_flag)
error->all(FLERR, "Coupled dimensions must have the same target pressure\n");
if (set[j].pvar_flag)
if (strcmp(set[i].pstr, set[j].pstr) != 0)
error->all(FLERR, "Coupled dimensions must have the same target pressure\n");
if (set[i].ptarget != set[j].ptarget)
error->all(FLERR, "Coupled dimensions must have the same target pressure\n");
} else {
if (set[i].style == VOLUME && set[j].style == VOLUME)
error->all(FLERR, "Dimensions used to maintain constant volume must either all be coupled or uncoupled");
error->all(FLERR, "Coupled dimensions must have the same target pressure");
}
}
}
}
@ -335,27 +323,18 @@ irregular(nullptr), set(nullptr)
// no tensile deformation on shrink-wrapped dims
// b/c shrink wrap will change box-length
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))
for (int i = 0; i < 3; i++)
if (set[i].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
// 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))
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))
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[5].style &&
(domain->boundary[1][0] >= 2 || domain->boundary[1][1] >= 2))
if (set[5].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
@ -436,6 +415,9 @@ irregular(nullptr), set(nullptr)
set[i].dynamic1 = other1;
set[i].dynamic2 = other2;
}
if (vol_balance_flag && set[i].substyle != TWO_FROM_ONE)
error->all(FLERR, "Two dimensions must maintain constant volume to use the vol/balance/p option");
}
// set strain_flag
@ -443,30 +425,41 @@ irregular(nullptr), set(nullptr)
strain_flag = 0;
for (int i = 0; i < 6; i++)
if (set[i].style != NONE && set[i].style != VOLUME &&
set[i].style != PRESSURE && set[i].style != PISOTROPIC)
set[i].style != PRESSURE && set[i].style != PMEAN)
strain_flag = 1;
// set varflag
varflag = 0;
for (int i = 0; i < 6; i++)
for (int i = 0; i < 6; i++) {
if (set[i].style == VARIABLE) varflag = 1;
if (set[i].pvar_flag) varflag = 1;
}
// set pressure_flag
pressure_flag = 0;
for (int i = 0; i < 6; i++) {
if (set[i].style == PRESSURE || set[i].style == PISOTROPIC) pressure_flag = 1;
if (set[i].style == PRESSURE || set[i].style == PMEAN) pressure_flag = 1;
if (set[i].coupled_flag) pressure_flag = 1;
}
if (vol_balance_flag) pressure_flag = 1;
// check conflict between constant volume/pressure
if (volume_flag)
for (int i = 0; i < 6; i++)
if (set[i].style == PISOTROPIC)
if (set[i].style == PMEAN)
error->all(FLERR, "Cannot use fix deform to assign constant volume and pressure");
// check pressure used for max rate and normalize error flag
if (!pressure_flag && max_h_rate != 0)
error->all(FLERR, "Can only assign a maximum strain rate using pressure-controlled dimensions");
if (!pressure_flag && normalize_pressure_flag)
error->all(FLERR, "Can only normalize error using pressure-controlled dimensions");
// set initial values at time fix deform is issued
for (int i = 0; i < 3; i++) {
@ -489,8 +482,6 @@ irregular(nullptr), set(nullptr)
if (force_reneighbor) irregular = new Irregular(lmp);
else irregular = nullptr;
TWOPI = 2.0*MY_PI;
// Create pressure compute, if needed
pflag = 0;
@ -592,7 +583,7 @@ void FixDeform::init()
error->all(FLERR,"Variable {} for fix deform is invalid style", set[i].hratestr);
}
// check optional variables for PRESSURE or PISOTROPIC style
// check optional variables for PRESSURE or PMEAN style
for (int i = 0; i < 6; i++) {
if (!set[i].pvar_flag) continue;
@ -627,30 +618,26 @@ void FixDeform::init()
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);
double shift = 0.5 * set[i].scale * (set[i].hi_start - set[i].lo_start);
set[i].lo_stop = 0.5 * (set[i].lo_start + set[i].hi_start) - shift;
set[i].hi_stop = 0.5 * (set[i].lo_start + set[i].hi_start) + shift;
} else if (set[i].style == 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;
} else if (set[i].style == ERATE) {
set[i].lo_stop = set[i].lo_start -
0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start);
set[i].hi_stop = set[i].hi_start +
0.5*delt*set[i].rate * (set[i].hi_start-set[i].lo_start);
double shift = 0.5 * delt * set[i].rate * (set[i].hi_start - set[i].lo_start);
set[i].lo_stop = set[i].lo_start - shift;
set[i].hi_stop = set[i].hi_start + shift;
if (set[i].hi_stop <= set[i].lo_stop)
error->all(FLERR,"Final box dimension due to fix deform is < 0.0");
} else if (set[i].style == TRATE) {
set[i].lo_stop = 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));
set[i].hi_stop = 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));
double shift = 0.5 * ((set[i].hi_start - set[i].lo_start) * exp(set[i].rate * delt));
set[i].lo_stop = 0.5 * (set[i].lo_start + set[i].hi_start) - shift;
set[i].hi_stop = 0.5 * (set[i].lo_start + set[i].hi_start) + shift;
} else if (set[i].style == WIGGLE) {
set[i].lo_stop = set[i].lo_start -
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);
double shift = 0.5 * set[i].amplitude * sin(MY_2PI * delt / set[i].tperiod);
set[i].lo_stop = set[i].lo_start - shift;
set[i].hi_stop = set[i].hi_start + shift;
}
}
@ -677,22 +664,20 @@ void FixDeform::init()
} else if (set[i].style == TRATE) {
set[i].tilt_stop = set[i].tilt_start * exp(set[i].rate * delt);
} else if (set[i].style == WIGGLE) {
set[i].tilt_stop = set[i].tilt_start +
set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
double shift = set[i].amplitude * sin(MY_2PI * delt / set[i].tperiod);
set[i].tilt_stop = set[i].tilt_start + shift;
// compute min/max for WIGGLE = extrema tilt factor will ever reach
if (set[i].amplitude >= 0.0) {
if (delt < 0.25 * set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start;
set[i].tilt_max = set[i].tilt_start +
set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
set[i].tilt_max = set[i].tilt_start + shift;
} else if (delt < 0.5 * set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start;
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
} else if (delt < 0.75 * set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start -
set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
set[i].tilt_min = set[i].tilt_start - shift;
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
} else {
set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
@ -700,16 +685,14 @@ void FixDeform::init()
}
} else {
if (delt < 0.25 * set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start -
set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
set[i].tilt_min = set[i].tilt_start - shift;
set[i].tilt_max = set[i].tilt_start;
} else if (delt < 0.5 * set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
set[i].tilt_max = set[i].tilt_start;
} else if (delt < 0.75 * set[i].tperiod) {
set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
set[i].tilt_max = set[i].tilt_start +
set[i].amplitude*sin(TWOPI*delt/set[i].tperiod);
set[i].tilt_max = set[i].tilt_start + shift;
} else {
set[i].tilt_min = set[i].tilt_start - set[i].amplitude;
set[i].tilt_max = set[i].tilt_start + set[i].amplitude;
@ -729,15 +712,15 @@ void FixDeform::init()
// 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
// VARIABLE or PRESSURE 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
// only trigger actual errors if flipflag is set
if (set[3].style && set[5].style) {
int flag = 0;
double lo,hi;
if (flipflag && set[3].style == VARIABLE)
error->all(FLERR,"Fix deform cannot use yz variable with xy");
if (flipflag && (set[3].style == VARIABLE || set[3].style == PRESSURE))
error->all(FLERR,"Fix deform cannot use yz variable or pressure with xy");
if (set[3].style == WIGGLE) {
lo = set[3].tilt_min;
hi = set[3].tilt_max;
@ -798,13 +781,11 @@ void FixDeform::init()
if (pressure_flag) {
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix deform does not exist");
if (icompute < 0) error->all(FLERR,"Temperature ID for fix deform does not exist");
temperature = modify->compute[icompute];
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all(FLERR,"Pressure ID for fix deform does not exist");
if (icompute < 0) error->all(FLERR,"Pressure ID for fix deform does not exist");
pressure = modify->compute[icompute];
}
}
@ -816,7 +797,6 @@ void FixDeform::init()
void FixDeform::setup(int /*vflag*/)
{
// trigger virial computation on next timestep
if (pressure_flag) pressure->addstep(update->ntimestep+1);
}
@ -876,9 +856,6 @@ void FixDeform::end_of_step()
set[i].saved = 1;
set[i].prior_rate = 0.0;
set[i].prior_pressure = pressure->vector[i];
if (i == 0) set[i].box_length = domain->xprd;
else if (i == 1) set[i].box_length = domain->yprd;
else set[i].box_length = domain->zprd;
}
}
set_pressure();
@ -892,15 +869,39 @@ void FixDeform::end_of_step()
// Save pressure/strain rate if required
if (pressure_flag) {
double dt_inv = 1.0 / update->dt;
for (int i = 0; i < 3; i++) {
set[i].prior_pressure = pressure->vector[i];
set[i].prior_rate = ((set[i].hi_target - set[i].lo_target) / set[i].box_length - 1.0) * dt_inv;
set[i].prior_rate = ((set[i].hi_target - set[i].lo_target) /
(domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt;
}
}
if (varflag) modify->addstep_compute(update->ntimestep + nevery);
// tilt_target can be large positive or large negative value
// add/subtract box lengths until tilt_target is closest to current value
if (triclinic) {
double *h = domain->h;
for (int i = 3; i < 6; i++) {
int idenom = 0;
if (i == 5) idenom = 0;
else if (i == 4) idenom = 0;
else if (i == 3) idenom = 1;
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)
set[i].tilt_target += denom;
if (fabs(set[i].tilt_target / denom - 1.0 - current) <
fabs(set[i].tilt_target / denom - current))
set[i].tilt_target -= denom;
}
}
// if any tilt ratios exceed 0.5, set flip = 1 and compute new tilt values
// do not flip in x or y if non-periodic (can tilt but not flip)
// this is b/c the box length would be changed (dramatically) by flip
@ -1023,12 +1024,8 @@ void FixDeform::end_of_step()
// trigger virial computation, if needed, on next timestep
if (pressure_flag) {
if (pressure_flag)
pressure->addstep(update->ntimestep+1);
set[0].box_length = domain->xprd;
set[1].box_length = domain->yprd;
set[2].box_length = domain->zprd;
}
}
/* ----------------------------------------------------------------------
@ -1052,20 +1049,18 @@ void FixDeform::set_strain()
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));
set[i].hi_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));
double shift = 0.5 * ((set[i].hi_start - set[i].lo_start) * exp(set[i].rate * delt));
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;
h_rate[i] = set[i].rate * domain->h[i];
h_ratelo[i] = -0.5 * h_rate[i];
} else if (set[i].style == WIGGLE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].lo_target = set[i].lo_start -
0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
set[i].hi_target = set[i].hi_start +
0.5*set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
cos(TWOPI*delt/set[i].tperiod);
double shift = 0.5 * set[i].amplitude * sin(MY_2PI * delt / set[i].tperiod);
set[i].lo_target = set[i].lo_start - shift;
set[i].hi_target = set[i].hi_start + shift;
h_rate[i] = MY_2PI / set[i].tperiod * set[i].amplitude *
cos(MY_2PI * delt / set[i].tperiod);
h_ratelo[i] = -0.5 * h_rate[i];
} else if (set[i].style == VARIABLE) {
double del = input->variable->compute_equal(set[i].hvar);
@ -1074,14 +1069,11 @@ void FixDeform::set_strain()
h_rate[i] = input->variable->compute_equal(set[i].hratevar);
h_ratelo[i] = -0.5 * h_rate[i];
} else if (set[i].style != VOLUME) {
set[i].lo_target = set[i].lo_start +
delta*(set[i].lo_stop - set[i].lo_start);
set[i].hi_target = set[i].hi_start +
delta*(set[i].hi_stop - set[i].hi_start);
set[i].lo_target = set[i].lo_start + delta * (set[i].lo_stop - set[i].lo_start);
set[i].hi_target = set[i].hi_start + delta * (set[i].hi_stop - set[i].hi_start);
}
}
// 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
@ -1104,36 +1096,16 @@ void FixDeform::set_strain()
} else if (set[i].style == WIGGLE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].tilt_target = set[i].tilt_start +
set[i].amplitude * sin(TWOPI*delt/set[i].tperiod);
h_rate[i] = TWOPI/set[i].tperiod * set[i].amplitude *
cos(TWOPI*delt/set[i].tperiod);
set[i].amplitude * sin(MY_2PI * delt / set[i].tperiod);
h_rate[i] = MY_2PI / set[i].tperiod * set[i].amplitude *
cos(MY_2PI * delt / set[i].tperiod);
} else if (set[i].style == VARIABLE) {
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 {
set[i].tilt_target = set[i].tilt_start +
delta*(set[i].tilt_stop - set[i].tilt_start);
set[i].tilt_target = set[i].tilt_start + delta * (set[i].tilt_stop - set[i].tilt_start);
}
// tilt_target can be large positive or large negative value
// add/subtract box lengths until tilt_target is closest to current value
int idenom = 0;
if (i == 5) idenom = 0;
else if (i == 4) idenom = 0;
else if (i == 3) idenom = 1;
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)
set[i].tilt_target += denom;
if (fabs(set[i].tilt_target/denom - 1.0 - current) <
fabs(set[i].tilt_target/denom - current))
set[i].tilt_target -= denom;
}
}
}
@ -1156,7 +1128,7 @@ void FixDeform::set_pressure()
double p_current[3];
if (pcouple == XYZ) {
double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
double ave = THIRD * (tensor[0] + tensor[1] + tensor[2]);
p_current[0] = p_current[1] = p_current[2] = ave;
} else if (pcouple == XY) {
double ave = 0.5 * (tensor[0] + tensor[1]);
@ -1172,30 +1144,68 @@ void FixDeform::set_pressure()
p_current[1] = tensor[1];
} else {
if (set[0].style == PRESSURE) p_current[0] = tensor[0];
else if (set[0].style == PISOTROPIC) p_current[0] = scalar;
else if (set[0].style == PMEAN) p_current[0] = scalar;
if (set[1].style == PRESSURE) p_current[1] = tensor[1];
else if (set[1].style == PISOTROPIC) p_current[1] = scalar;
else if (set[1].style == PMEAN) p_current[1] = scalar;
if (set[2].style == PRESSURE) p_current[2] = tensor[2];
else if (set[2].style == PISOTROPIC) p_current[2] = scalar;
else if (set[2].style == PMEAN) p_current[2] = scalar;
}
for (int i = 0; i < 3; i++) {
if (set[i].style != PRESSURE && set[i].style != PISOTROPIC) continue;
double dilation = 1.0 - update->dt * set[i].pgain * (set[i].ptarget - p_current[i]);
double center_start = 0.5 * (set[i].lo_start + set[i].hi_start);
double offset = 0.5 * set[i].box_length * dilation;
//printf("ptarget %g vs %g, dilation %g cs %g ofset %g box %g\n", set[i].ptarget, p_current[i], dilation, center_start, offset, set[i].box_length);
set[i].lo_target = center_start - offset;
set[i].hi_target = center_start + offset;
if (set[i].style != PRESSURE && set[i].style != PMEAN) continue;
h_rate[i] = set[i].pgain * (p_current[i] - set[i].ptarget);
if (normalize_pressure_flag) {
if (set[i].ptarget == 0) {
if (max_h_rate == 0) {
error->all(FLERR, "Cannot normalize error for zero pressure without defining a max rate");
} else h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]);
} else h_rate[i] /= fabs(set[i].ptarget);
}
if (max_h_rate != 0)
if (fabs(set[i].ptarget) > max_h_rate)
h_rate[i] = max_h_rate * h_rate[i] / fabs(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;
}
for (int i = 3; i < 6; i++) {
double shift = update->dt * set[i].pgain * (set[i].ptarget - tensor[i]);
if (i == 3) set[i].tilt_target = domain->xy + shift * domain->xprd;
else if (i == 4) set[i].tilt_target = domain->xz + shift * domain->xprd;
else set[i].tilt_target = domain->yz + shift * domain->yprd;
if (set[i].style != PRESSURE) continue;
double L, tilt, 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];
}
h_rate[i] = L * set[i].pgain * (pcurrent - set[i].ptarget);
if (normalize_pressure_flag) {
if (set[i].ptarget == 0) {
if (max_h_rate == 0) {
error->all(FLERR, "Cannot normalize error for zero pressure without defining a max rate");
} else h_rate[i] = max_h_rate * h_rate[i] / fabs(h_rate[i]);
} else h_rate[i] /= fabs(set[i].ptarget);
}
if (max_h_rate != 0)
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];
}
}
@ -1211,61 +1221,65 @@ void FixDeform::set_volume()
for (int i = 0; i < 3; i++) {
if (set[i].style != VOLUME) continue;
int dynamic1 = set[i].dynamic1;
int dynamic2 = set[i].dynamic2;
int fixed = set[i].fixed;
double v0 = set[i].vol_start;
double center_start = 0.5 * (set[i].lo_start + set[i].hi_start);
double offset;
double shift;
if (set[i].substyle == ONE_FROM_ONE) {
offset = 0.5 * (v0 /
(set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
shift = 0.5 * (v0 / (set[dynamic1].hi_target - set[dynamic1].lo_target) /
(set[fixed].hi_start-set[fixed].lo_start));
} else if (set[i].substyle == ONE_FROM_TWO) {
offset = 0.5 * (v0 /
(set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) /
(set[set[i].dynamic2].hi_target - set[set[i].dynamic2].lo_target));
shift = 0.5 * (v0 / (set[dynamic1].hi_target - set[dynamic1].lo_target) /
(set[dynamic2].hi_target - set[dynamic2].lo_target));
} else if (set[i].substyle == TWO_FROM_ONE) {
if (!set[i].coupled_flag) {
offset = 0.5 * sqrt(v0 * (set[i].hi_start - set[i].lo_start) /
(set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start - set[set[i].fixed].lo_start));
if (!vol_balance_flag) {
shift = 0.5 * sqrt(v0 * (set[i].hi_start - set[i].lo_start) /
(set[dynamic1].hi_target - set[dynamic1].lo_target) /
(set[fixed].hi_start - set[fixed].lo_start));
} else {
double dt = update->dt;
double e1i = set[i].prior_rate;
double e2i = set[set[i].fixed].prior_rate;
double L3 = (set[set[i].dynamic1].hi_target - set[set[i].dynamic1].lo_target);
double e3 = (L3 / set[set[i].dynamic1].box_length - 1.0) / dt;
double e2i = set[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 L3 = (set[dynamic1].hi_target - set[dynamic1].lo_target);
double e3 = (L3 / L3i - 1.0) / dt;
double p1 = pressure->vector[i];
double p2 = pressure->vector[set[i].fixed];
double p2 = pressure->vector[fixed];
double p1i = set[i].prior_pressure;
double p2i = set[set[i].fixed].prior_pressure;
double p2i = set[fixed].prior_pressure;
if (e3 == 0) {
e1 = 0.0;
e2 = 0.0;
offset = 0.5 * set[i].box_length;
shift = 0.5 * L1i;
} else if (e1i == 0 || e2i == 0 || (p2 == p2i && p1 == p1i)) {
// If no prior strain or no change in pressure (initial step) just scale offset by relative box lengths
offset = 0.5 * sqrt(v0 * set[i].box_length / L3 / set[set[i].fixed].box_length);
// If no prior strain or no change in pressure (initial step) just scale shift by relative box lengths
shift = 0.5 * sqrt(v0 * L1i / L3 / L2i);
} else {
if (!linked_pressure) {
// Calculate first strain rate by expanding stress to linear order in strain to achieve p1(t+dt) = p2(t+dt)
e1 = -e3 / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2);
e1 /= (p2 - p2i + (p1 - p1i) / e1i * e2i);
// Calculate first strain rate by expanding stress to linear order, p1(t+dt) = p2(t+dt)
// Calculate second strain rate to preserve volume
e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt));
e2 /= (1 + e3 * dt) * (1 + e1 * dt) * dt;
e1 = -e3 / (1 + e3 * dt) * (p2 - p2i) - e2i * (p1 - p2) / (p2 - p2i + (p1 - p1i) / e1i * e2i);
e2 = (1.0 - (1 + e3 * dt) * (1 + e1 * dt)) / ((1 + e3 * dt) * (1 + e1 * dt) * dt);
offset = 0.5 * set[i].box_length * (1.0 + e1 * dt);
shift = 0.5 * L1i * (1.0 + e1 * dt);
linked_pressure = 1;
} else {
offset = 0.5 * set[i].box_length * (1.0 + e2 * dt);
// Already calculated value of e2
shift = 0.5 * L1i * (1.0 + e2 * dt);
}
}
}
}
set[i].lo_target = center_start - offset;
set[i].hi_target = center_start + offset;
h_rate[i] = (2.0 * shift / (domain->boxhi[i] - domain->boxlo[i]) - 1.0) / update->dt;
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;
}
}
@ -1296,6 +1310,9 @@ void FixDeform::restart(char *buf)
set[i].hi_initial = set_restart[i].hi_initial;
set[i].vol_initial = set_restart[i].vol_initial;
set[i].tilt_initial = set_restart[i].tilt_initial;
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;
// check if style settings are consistent (should do the whole set?)
if (set[i].style != set_restart[i].style)
samestyle = 0;
@ -1344,6 +1361,20 @@ void FixDeform::options(int narg, char **arg)
else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NOCOUPLE;
else error->all(FLERR,"Illegal fix fix deform couple command: {}", arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"max/rate") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform max/rate", error);
max_h_rate = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (max_h_rate <= 0.0)
error->all(FLERR,"Maximum strain rate must be a positive, non-zero value");
iarg += 2;
} else if (strcmp(arg[iarg],"normalize/pressure") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform normalize/pressure", error);
normalize_pressure_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"vol/balance/p") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "fix deform vol/balance/p", error);
vol_balance_flag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else error->all(FLERR,"Illegal fix deform command: {}", arg[iarg]);
}
@ -1363,7 +1394,6 @@ double FixDeform::memory_usage()
return bytes;
}
/* ---------------------------------------------------------------------- */
int FixDeform::modify_param(int narg, char **arg)

7
src/fix_deform.h
View File

@ -44,17 +44,17 @@ class FixDeform : public Fix {
protected:
int dimension, triclinic, scaleflag, flipflag, pcouple;
int flip, flipxy, flipxz, flipyz;
double *h_rate, *h_ratelo;
double *h_rate, *h_ratelo, max_h_rate;
int varflag; // 1 if VARIABLE option is used, 0 if not
int strain_flag; // 1 if strain-based option is used, 0 if not
int volume_flag; // 1 if VOLUME option is used, 0 if not
int pressure_flag; // 1 if pressure tensor used, 0 if not
int kspace_flag; // 1 if KSpace invoked, 0 if not
int normalize_pressure_flag; // 1 if normalize pressure deviation by target
int vol_balance_flag; // 1 if pressures balanced when maintaining const vol
std::vector<Fix *> rfix; // pointers to rigid fixes
class Irregular *irregular; // for migrating atoms after box flips
double TWOPI;
char *id_temp, *id_press;
class Compute *temperature, *pressure;
int tflag, pflag;
@ -72,7 +72,6 @@ class FixDeform : public Fix {
double vol_initial, vol_start;
double ptarget, pgain;
double prior_pressure, prior_rate;
double box_length;
int saved;
int fixed, dynamic1, dynamic2;
char *hstr, *hratestr, *pstr;