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disentangle the fix deform and fix deform/pressure pages somewhere for easier reading

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This commit is contained in:
Axel Kohlmeyer
2024-07-12 23:42:42 -04:00
parent 0e6ff7d70a
commit a0fb12c265
2 changed files with 59 additions and 44 deletions
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48
doc/src/fix_deform.rst
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@ -4,9 +4,6 @@
fix deform command fix deform command
================== ==================
:doc:`fix deform/pressure <fix_deform_pressure>` command
========================================================
Accelerator Variants: *deform/kk* Accelerator Variants: *deform/kk*
Syntax Syntax
@ -14,12 +11,11 @@ Syntax
.. code-block:: LAMMPS .. code-block:: LAMMPS
fix ID group-ID fix_style N parameter style args ... keyword value ... fix ID group-ID deform N parameter style args ... keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* fix_style = *deform* or *deform/pressure*
* N = perform box deformation every this many timesteps * N = perform box deformation every this many timesteps
* one or more parameter/style/args sequences of arguments may be appended * one or more parameter/args sequences may be appended
.. parsed-literal:: .. parsed-literal::
@ -46,12 +42,6 @@ Syntax
*variable* values = v_name1 v_name2 *variable* values = v_name1 v_name2
v_name1 = variable with name1 for box length change as function of time v_name1 = variable with name1 for box length change as function of time
v_name2 = variable with name2 for change rate as function of time v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*pressure/mean* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
*xy*, *xz*, *yz* args = style value *xy*, *xz*, *yz* args = style value
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable*
@ -64,8 +54,6 @@ Syntax
effectively an engineering shear strain rate effectively an engineering shear strain rate
*erate* value = R *erate* value = R
R = engineering shear strain rate (1/time units) R = engineering shear strain rate (1/time units)
*erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
R = engineering shear strain rate (1/time units)
*trate* value = R *trate* value = R
R = true shear strain rate (1/time units) R = true shear strain rate (1/time units)
*wiggle* values = A Tp *wiggle* values = A Tp
@ -74,9 +62,6 @@ Syntax
*variable* values = v_name1 v_name2 *variable* values = v_name1 v_name2
v_name1 = variable with name1 for tilt change as function of time v_name1 = variable with name1 for tilt change as function of time
v_name2 = variable with name2 for change rate as function of time v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units)
* zero or more keyword/value pairs may be appended * 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* * keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
@ -92,15 +77,6 @@ Syntax
*units* value = *lattice* or *box* *units* value = *lattice* or *box*
lattice = distances are defined in lattice units lattice = distances are defined in lattice units
box = distances are defined in simulation box units box = distances are defined in simulation box units
*couple* value = *none* or *xyz* or *xy* or *yz* or *xz* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
couple pressure values of various dimensions
*vol/balance/p* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
Modifies the behavior of the *volume* option to try and balance pressures
*max/rate* value = *rate* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
rate = maximum strain rate for pressure control
*normalize/pressure* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
Examples Examples
"""""""" """"""""
@ -112,8 +88,6 @@ Examples
fix 1 all deform 1 xy erate 0.001 remap v 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 10 y delta -0.5 0.5 xz vel 1.0
See examples for :doc:`fix deform/pressure <fix_deform_pressure>` on its doc page
Description Description
""""""""""" """""""""""
@ -123,17 +97,13 @@ run. Orthogonal simulation boxes have 3 adjustable parameters
adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
adjusted independently and simultaneously. adjusted independently and simultaneously.
The fix deform command allows use of all the arguments listed above, The :doc:`fix deform/pressure <fix_deform_pressure>` command extends
except those flagged as available ONLY for the :doc:`fix this command with additional keywords and arguments. The rest of this
deform/pressure <fix_deform_pressure>` command, which are page explains the options common to both commands. The :doc:`fix
pressure-based controls. The fix deform/pressure command allows use deform/pressure <fix_deform_pressure>` page explains the options
of all the arguments listed above. available ONLY with the fix deform/pressure command. Note that a
simulation can define only a single deformation command: fix deform or
The rest of this doc page explains the options common to both fix deform/pressure.
commands. The :doc:`fix deform/pressure <fix_deform_pressure>` doc
page explains the options available ONLY with the fix deform/pressure
command. Note that a simulation can define only a single deformation
command: fix deform or fix deform/pressure.
Both these fixes can be used to perform non-equilibrium MD (NEMD) Both these fixes can be used to perform non-equilibrium MD (NEMD)
simulations of a continuously strained system. See the :doc:`fix simulations of a continuously strained system. See the :doc:`fix

55
doc/src/fix_deform_pressure.rst
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@ -13,29 +13,66 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* deform/pressure = style name of this fix command * deform/pressure = style name of this fix command
* N = perform box deformation every this many timesteps * N = perform box deformation every this many timesteps
* one or more parameter/arg sequences may be appended * one or more parameter/args sequences may be appended
.. parsed-literal:: .. parsed-literal::
parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *box* parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *box*
*x*, *y*, *z* args = style value(s) *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* or *pressure* or *pressure/mean* style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
*final* values = lo hi
lo hi = box boundaries at end of run (distance units)
*delta* values = dlo dhi
dlo dhi = change in box boundaries at end of run (distance units)
*scale* values = factor
factor = multiplicative factor for change in box length at end of run
*vel* value = V
V = change box length at this velocity (distance/time units),
effectively an engineering strain rate
*erate* value = R
R = engineering strain rate (1/time units)
*trate* value = R
R = true strain rate (1/time units)
*volume* value = none = adjust this dim to preserve volume of system
*wiggle* values = A Tp
A = amplitude of oscillation (distance units)
Tp = period of oscillation (time units)
*variable* values = v_name1 v_name2
v_name1 = variable with name1 for box length change as function of time
v_name2 = variable with name2 for change rate as function of time
*pressure* values = target gain *pressure* values = target gain
target = target pressure (pressure units) target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units) gain = proportional gain constant (1/(time * pressure) or 1/time units)
*pressure/mean* values = target gain *pressure/mean* values = target gain
target = target pressure (pressure units) target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units) gain = proportional gain constant (1/(time * pressure) or 1/time units)
NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
*xy*, *xz*, *yz* args = style value *xy*, *xz*, *yz* args = style value
style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale* style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale*
*final* value = tilt
tilt = tilt factor at end of run (distance units)
*delta* value = dtilt
dtilt = change in tilt factor at end of run (distance units)
*vel* value = V
V = change tilt factor at this velocity (distance/time units),
effectively an engineering shear strain rate
*erate* value = R
R = engineering shear strain rate (1/time units)
*erate/rescale* value = R
R = engineering shear strain rate (1/time units)
*trate* value = R
R = true shear strain rate (1/time units)
*wiggle* values = A Tp
A = amplitude of oscillation (distance units)
Tp = period of oscillation (time units)
*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
*pressure* values = target gain *pressure* values = target gain
target = target pressure (pressure units) target = target pressure (pressure units)
gain = proportional gain constant (1/(time * pressure) or 1/time units) gain = proportional gain constant (1/(time * pressure) or 1/time units)
*erate/rescale* value = R *erate/rescale* value = R
R = engineering shear strain rate (1/time units) 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 *box* = style value
style = *volume* or *pressure* style = *volume* or *pressure*
@ -49,6 +86,15 @@ Syntax
.. parsed-literal:: .. parsed-literal::
*remap* value = *x* or *v* or *none*
x = remap coords of atoms in group into deforming box
v = remap velocities of atoms in group when they cross periodic boundaries
none = no remapping of x or v
*flip* value = *yes* or *no*
allow or disallow box flips when it becomes highly skewed
*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* value = *none* or *xyz* or *xy* or *yz* or *xz*
couple pressure values of various dimensions couple pressure values of various dimensions
*vol/balance/p* value = *yes* or *no* *vol/balance/p* value = *yes* or *no*
@ -57,7 +103,6 @@ Syntax
rate = maximum strain rate for pressure control rate = maximum strain rate for pressure control
*normalize/pressure* value = *yes* or *no* *normalize/pressure* value = *yes* or *no*
Modifies pressure controls such that the deviation in pressure is normalized by the target pressure Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
NOTE: All other keywords are documented by the :doc:`fix deform <fix_deform>` command
Examples Examples
"""""""" """"""""
@ -79,7 +124,7 @@ pressure-based controls implemented by this command.
All arguments described on the :doc:`fix deform <fix_deform>` doc page All arguments described on the :doc:`fix deform <fix_deform>` doc page
also apply to this fix unless otherwise noted below. The rest of this also apply to this fix unless otherwise noted below. The rest of this
doc page explains the arguments specific to this fix. Note that a page explains the arguments specific to this fix only. Note that a
simulation can define only a single deformation command: fix deform or simulation can define only a single deformation command: fix deform or
fix deform/pressure. fix deform/pressure.