doc adjust and code comments
This commit is contained in:
Steve Plimpton
@ -4,6 +4,9 @@
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fix deform command
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==================
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:doc:`fix deform/pressure <fix_deform_pressure>` command
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==================
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Accelerator Variants: *deform/kk*
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Syntax
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@ -11,18 +14,18 @@ Syntax
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.. code-block:: LAMMPS
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fix ID group-ID deform N parameter args ... keyword value ...
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fix ID group-ID fixstyle N parameter style args ... keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* deform = style name of this fix command
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* fixstyle = *deform* or *deform/pressure*
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* N = perform box deformation every this many timesteps
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* one or more parameter/arg pairs may be appended
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* one or more parameter/style/args sequences of arguments may be appended
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.. parsed-literal::
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parameter = *x* or *y* or *z* or *xy* or *xz* or *yz*
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*x*, *y*, *z* args = style value(s)
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style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable*
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style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean*
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*final* values = lo hi
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lo hi = box boundaries at end of run (distance units)
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*delta* values = dlo dhi
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@ -43,6 +46,13 @@ Syntax
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*variable* values = v_name1 v_name2
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v_name1 = variable with name1 for box length change as function of time
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v_name2 = variable with name2 for change rate as function of time
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*pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
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target = target pressure (pressure units)
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gain = proportional gain constant (1/(time * pressure) or 1/time units)
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*pressure/mean* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
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target = target pressure (pressure units)
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gain = proportional gain constant (1/(time * pressure) or 1/time units)
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*xy*, *xz*, *yz* args = style value
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style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable*
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*final* value = tilt
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@ -62,9 +72,12 @@ Syntax
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*variable* values = v_name1 v_name2
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v_name1 = variable with name1 for tilt change as function of time
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v_name2 = variable with name2 for change rate as function of time
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*pressure* values = target gain (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
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target = target pressure (pressure units)
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gain = proportional gain constant (1/(time * pressure) or 1/time units)
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* zero or more keyword/value pairs may be appended
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* keyword = *remap* or *flip* or *units*
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* keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure*
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.. parsed-literal::
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@ -77,6 +90,15 @@ Syntax
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*units* value = *lattice* or *box*
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lattice = distances are defined in lattice units
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box = distances are defined in simulation box units
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*couple* value = *none* or *xyz* or *xy* or *yz* or *xz* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
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couple pressure values of various dimensions
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*vol/balance/p* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
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Modifies the behavior of the *volume* option to try and balance pressures
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*max/rate* value = *rate* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
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rate = maximum strain rate for pressure control
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*normalize/pressure* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
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Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
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Examples
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""""""""
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@ -88,6 +110,8 @@ Examples
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fix 1 all deform 1 xy erate 0.001 remap v
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fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0
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See examples for :doc:`fix deform/pressure <fix_deform_pressure>` on its doc page
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Description
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"""""""""""
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@ -95,31 +119,46 @@ Change the volume and/or shape of the simulation box during a dynamics
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run. Orthogonal simulation boxes have 3 adjustable parameters
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(x,y,z). Triclinic (non-orthogonal) simulation boxes have 6
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adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be
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adjusted independently and simultaneously by this command. For
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additional pressure-based controls, see
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:doc:`fix deform/pressure <fix_deform_pressure>`.
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adjusted independently and simultaneously.
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This fix can be used to perform non-equilibrium MD (NEMD) simulations
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of a continuously strained system. See the :doc:`fix nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform <compute_temp_deform>` commands for more details. Note
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that simulation of a continuously extended system (extensional flow)
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can be modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix commands <fix_nh_uef>`.
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The fix deform command allows use of all the arguments listed above,
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except those flagged as available ONLY for the :doc:`fix
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deform/pressure <fix_deform_pressure>` command, which are
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pressure-based controls. The fix deform/pressure command allows use
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of all the arguments listed above.
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The rest of this doc page explains the options common to both
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commands. The :doc:`fix deform/pressure <fix_deform_pressure>` doc
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page explains the options available ONLY with the fix deform/pressure
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command. Note that a simulation can define only a single deformation
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command: fix deform or fix deform/pressure.
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Both these fixes can be used to perform non-equilibrium MD (NEMD)
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simulations of a continuously strained system. See the :doc:`fix
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nvt/sllod <fix_nvt_sllod>` and :doc:`compute temp/deform
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<compute_temp_deform>` commands for more details. Note that
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simulation of a continuously extended system (extensional flow) can be
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modeled using the :ref:`UEF package <PKG-UEF>` and its :doc:`fix
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commands <fix_nh_uef>`.
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For the *x*, *y*, *z* parameters, the associated dimension cannot be
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shrink-wrapped. For the *xy*, *yz*, *xz* parameters, the associated
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second dimension cannot be shrink-wrapped. Dimensions not varied by this
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command can be periodic or non-periodic. Dimensions corresponding to
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unspecified parameters can also be controlled by a :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
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second dimension cannot be shrink-wrapped. Dimensions not varied by
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this command can be periodic or non-periodic. Dimensions
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corresponding to unspecified parameters can also be controlled by a
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:doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>` command.
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The size and shape of the simulation box at the beginning of the
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simulation run were either specified by the
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:doc:`create_box <create_box>` or :doc:`read_data <read_data>` or
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:doc:`read_restart <read_restart>` command used to setup the simulation
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initially if it is the first run, or they are the values from the end
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of the previous run. The :doc:`create_box <create_box>`, :doc:`read data <read_data>`, and :doc:`read_restart <read_restart>` commands
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specify whether the simulation box is orthogonal or non-orthogonal
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(triclinic) and explain the meaning of the xy,xz,yz tilt factors. If
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fix deform changes the xy,xz,yz tilt factors, then the simulation box
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must be triclinic, even if its initial tilt factors are 0.0.
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simulation run were either specified by the :doc:`create_box
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<create_box>` or :doc:`read_data <read_data>` or :doc:`read_restart
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<read_restart>` command used to setup the simulation initially if it
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is the first run, or they are the values from the end of the previous
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run. The :doc:`create_box <create_box>`, :doc:`read data
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<read_data>`, and :doc:`read_restart <read_restart>` commands specify
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whether the simulation box is orthogonal or non-orthogonal (triclinic)
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and explain the meaning of the xy,xz,yz tilt factors. If fix deform
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changes the xy,xz,yz tilt factors, then the simulation box must be
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triclinic, even if its initial tilt factors are 0.0.
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As described below, the desired simulation box size and shape at the
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end of the run are determined by the parameters of the fix deform
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@ -260,21 +299,22 @@ of the units keyword below.
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The *variable* style changes the specified box length dimension by
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evaluating a variable, which presumably is a function of time. The
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variable with *name1* must be an :doc:`equal-style variable <variable>`
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and should calculate a change in box length in units of distance.
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Note that this distance is in box units, not lattice units; see the
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discussion of the *units* keyword below. The formula associated with
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variable *name1* can reference the current timestep. Note that it
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should return the "change" in box length, not the absolute box length.
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This means it should evaluate to 0.0 when invoked on the initial
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timestep of the run following the definition of fix deform. It should
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evaluate to a value > 0.0 to dilate the box at future times, or a
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value < 0.0 to compress the box.
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variable with *name1* must be an :doc:`equal-style variable
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<variable>` and should calculate a change in box length in units of
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distance. Note that this distance is in box units, not lattice units;
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see the discussion of the *units* keyword below. The formula
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associated with variable *name1* can reference the current timestep.
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Note that it should return the "change" in box length, not the
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absolute box length. This means it should evaluate to 0.0 when
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invoked on the initial timestep of the run following the definition of
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fix deform. It should evaluate to a value > 0.0 to dilate the box at
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future times, or a value < 0.0 to compress the box.
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The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of box length
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change, in units of distance/time, i.e. the time-derivative of the
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*name1* variable. This quantity is used internally by LAMMPS to reset
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atom velocities when they cross periodic boundaries. It is computed
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The variable *name2* must also be an :doc:`equal-style variable
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<variable>` and should calculate the rate of box length change, in
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units of distance/time, i.e. the time-derivative of the *name1*
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variable. This quantity is used internally by LAMMPS to reset atom
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velocities when they cross periodic boundaries. It is computed
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internally for the other styles, but you must provide it when using an
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arbitrary variable.
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@ -416,12 +456,13 @@ can reference the current timestep. Note that it should return the
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should evaluate to 0.0 when invoked on the initial timestep of the run
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following the definition of fix deform.
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The variable *name2* must also be an :doc:`equal-style variable <variable>` and should calculate the rate of tilt change,
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in units of distance/time, i.e. the time-derivative of the *name1*
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variable. This quantity is used internally by LAMMPS to reset atom
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velocities when they cross periodic boundaries. It is computed
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internally for the other styles, but you must provide it when using an
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arbitrary variable.
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The variable *name2* must also be an :doc:`equal-style variable
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<variable>` and should calculate the rate of tilt change, in units of
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distance/time, i.e. the time-derivative of the *name1* variable. This
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quantity is used internally by LAMMPS to reset atom velocities when
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they cross periodic boundaries. It is computed internally for the
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other styles, but you must provide it when using an arbitrary
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variable.
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Here is an example of using the *variable* style to perform the same
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box deformation as the *wiggle* style formula listed above, where we
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@ -512,33 +553,40 @@ box without explicit remapping of their coordinates.
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.. note::
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For non-equilibrium MD (NEMD) simulations using "remap v" it is
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usually desirable that the fluid (or flowing material, e.g. granular
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particles) stream with a velocity profile consistent with the
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deforming box. As mentioned above, using a thermostat such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin <fix_langevin>`
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(with a bias provided by :doc:`compute temp/deform <compute_temp_deform>`), will typically accomplish
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that. If you do not use a thermostat, then there is no driving force
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pushing the atoms to flow in a manner consistent with the deforming
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box. E.g. for a shearing system the box deformation velocity may vary
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usually desirable that the fluid (or flowing material,
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e.g. granular particles) stream with a velocity profile consistent
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with the deforming box. As mentioned above, using a thermostat
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such as :doc:`fix nvt/sllod <fix_nvt_sllod>` or :doc:`fix lavgevin
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<fix_langevin>` (with a bias provided by :doc:`compute temp/deform
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<compute_temp_deform>`), will typically accomplish that. If you do
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not use a thermostat, then there is no driving force pushing the
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atoms to flow in a manner consistent with the deforming box.
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E.g. for a shearing system the box deformation velocity may vary
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from 0 at the bottom to 10 at the top of the box. But the stream
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velocity profile of the atoms may vary from -5 at the bottom to +5 at
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the top. You can monitor these effects using the :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform <compute_temp_deform>`, and :doc:`compute temp/profile <compute_temp_profile>` commands. One way to induce
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atoms to stream consistent with the box deformation is to give them an
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velocity profile of the atoms may vary from -5 at the bottom to +5
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at the top. You can monitor these effects using the :doc:`fix
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ave/chunk <fix_ave_chunk>`, :doc:`compute temp/deform
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<compute_temp_deform>`, and :doc:`compute temp/profile
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<compute_temp_profile>` commands. One way to induce atoms to
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stream consistent with the box deformation is to give them an
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initial velocity profile, via the :doc:`velocity ramp <velocity>`
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command, that matches the box deformation rate. This also typically
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helps the system come to equilibrium more quickly, even if a
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thermostat is used.
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command, that matches the box deformation rate. This also
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typically helps the system come to equilibrium more quickly, even
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if a thermostat is used.
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.. note::
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If a :doc:`fix rigid <fix_rigid>` is defined for rigid bodies, and
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*remap* is set to *x*, then the center-of-mass coordinates of rigid
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bodies will be remapped to the changing simulation box. This will be
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done regardless of whether atoms in the rigid bodies are in the fix
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deform group or not. The velocity of the centers of mass are not
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remapped even if *remap* is set to *v*, since :doc:`fix nvt/sllod <fix_nvt_sllod>` does not currently do anything special
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bodies will be remapped to the changing simulation box. This will
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be done regardless of whether atoms in the rigid bodies are in the
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fix deform group or not. The velocity of the centers of mass are
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not remapped even if *remap* is set to *v*, since :doc:`fix
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nvt/sllod <fix_nvt_sllod>` does not currently do anything special
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for rigid particles. If you wish to perform a NEMD simulation of
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rigid particles, you can either thermostat them independently or
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include a background fluid and thermostat the fluid via :doc:`fix nvt/sllod <fix_nvt_sllod>`.
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include a background fluid and thermostat the fluid via :doc:`fix
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nvt/sllod <fix_nvt_sllod>`.
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The *flip* keyword allows the tilt factors for a triclinic box to
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exceed half the distance of the parallel box length, as discussed
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@ -570,7 +618,8 @@ command if you want to include lattice spacings in a variable formula.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix will restore the initial box settings from :doc:`binary restart files <restart>`, which allows the fix to be properly continue
|
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This fix will restore the initial box settings from :doc:`binary
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restart files <restart>`, which allows the fix to be properly continue
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deformation, when using the start/stop options of the :doc:`run <run>`
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command. None of the :doc:`fix_modify <fix_modify>` options are
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relevant to this fix. No global or per-atom quantities are stored by
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@ -588,13 +637,15 @@ Restrictions
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You cannot apply x, y, or z deformations to a dimension that is
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shrink-wrapped via the :doc:`boundary <boundary>` command.
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You cannot apply xy, yz, or xz deformations to a second dimension (y in
|
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xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.
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You cannot apply xy, yz, or xz deformations to a second dimension (y
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in xy) that is shrink-wrapped via the :doc:`boundary <boundary>`
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command.
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Related commands
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""""""""""""""""
|
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:doc:`fix deform/pressure <fix_deform_pressure>`, :doc:`change_box <change_box>`
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:doc:`fix deform/pressure <fix_deform_pressure>`, :doc:`change_box
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<change_box>`
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Default
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"""""""
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@ -8,12 +8,12 @@ Syntax
|
||||
|
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.. parsed-literal::
|
||||
|
||||
fix ID group-ID deform N parameter args ... keyword value ...
|
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fix ID group-ID deform/pressure N parameter style args ... keyword value ...
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
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* deform = style name of this fix command
|
||||
* deform/pressure = style name of this fix command
|
||||
* N = perform box deformation every this many timesteps
|
||||
* one or more parameter/arg pairs may be appended
|
||||
* one or more parameter/arg sequences may be appended
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
@ -26,13 +26,15 @@ Syntax
|
||||
*pressure/mean* values = target gain
|
||||
target = target pressure (pressure units)
|
||||
gain = proportional gain constant (1/(time * pressure) or 1/time units)
|
||||
All other styles operate identically to those in :doc:`fix deform <fix_deform>`
|
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NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
|
||||
|
||||
*xy*, *xz*, *yz* args = style value
|
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style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure*
|
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*pressure* values = target gain
|
||||
target = target pressure (pressure units)
|
||||
gain = proportional gain constant (1/(time * pressure) or 1/time units)
|
||||
All other styles operate identically to those in :doc:`fix deform <fix_deform>`
|
||||
NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
|
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|
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*box* = style value
|
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style = *volume* or *pressure*
|
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*volume* value = none = isotropically adjust system to preserve volume of system
|
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@ -53,7 +55,7 @@ Syntax
|
||||
rate = maximum strain rate for pressure control
|
||||
*normalize/pressure* value = *yes* or *no*
|
||||
Modifies pressure controls such that the deviation in pressure is normalized by the target pressure
|
||||
All other options operate identically to those in :doc:`fix deform <fix_deform>`
|
||||
NOTE: All other keywords are documented by the :doc:`fix deform <fix_deform>` command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
@ -67,19 +69,20 @@ Examples
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This fix is an extension of :doc:`fix deform <fix_deform>`, inheriting
|
||||
all of its features and adding new pressure-based controls to allow for
|
||||
new deformation protocols. All details in :doc:`fix deform <fix_deform>`
|
||||
apply to this fix unless otherwise noted.
|
||||
This fix is an extension of the :doc:`fix deform <fix_deform>`
|
||||
command, which allows all of its options to be used as well as new
|
||||
pressure-based controls implemented by this command.
|
||||
|
||||
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
|
||||
doc page explains the arguments specific to this fix. Note that a
|
||||
simulation can define only a single deformation command: fix deform or
|
||||
fix deform/pressure.
|
||||
|
||||
----------
|
||||
|
||||
For the *x*, *y*, and *z* parameters, this is the meaning of their
|
||||
styles and values.
|
||||
|
||||
The *final*, *delta*, *scale*, *vel*, *erate*, *trate*, *volume*,
|
||||
*wiggle*, and *variable* styles all behave identically to those in
|
||||
:doc:`fix deform <fix_deform>`. Additional styles are described below.
|
||||
For the *x*, *y*, and *z* parameters, this is the meaning of the
|
||||
styles and values provided by this fix.
|
||||
|
||||
The *pressure* style adjusts a dimension's box length to control the
|
||||
corresponding component of the pressure tensor. This option attempts to
|
||||
@ -127,13 +130,9 @@ along one dimension.
|
||||
|
||||
----------
|
||||
|
||||
For the *xy*, *xz*, and *yz* parameters, this is the meaning of their
|
||||
styles and values. Note that changing the tilt factors of a triclinic
|
||||
box does not change its volume.
|
||||
|
||||
The *final*, *delta*, *vel*, *erate*, *trate*, *wiggle*, and *variable*
|
||||
styles all behave identically to those in :doc:`fix deform <fix_deform>`.
|
||||
Additional styles are described below.
|
||||
For the *xy*, *xz*, and *yz* parameters, this is the meaning of the
|
||||
styles and values provided by this fix. Note that changing the
|
||||
tilt factors of a triclinic box does not change its volume.
|
||||
|
||||
The *pressure* style adjusts a tilt factor to control the corresponding
|
||||
off-diagonal component of the pressure tensor. This option attempts to
|
||||
@ -144,29 +143,32 @@ tilt factor T evolves according to the equation
|
||||
|
||||
\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 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.
|
||||
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 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.
|
||||
|
||||
----------
|
||||
|
||||
The *box* parameter provides an additonal control over the *x*, *y*,
|
||||
and *z* box lengths by isotropically dilating or contracting the box to
|
||||
either maintain a fixed mean pressure or volume. This isotropic scaling
|
||||
is applied after the box is deformed by the above *x*, *y*, *z*, *xy*,
|
||||
*xz*, and *yz* styles, acting as a second deformation step. This parameter
|
||||
will change the overall strain rate in the *x*, *y*, or *z* dimensions.
|
||||
This parameter can only be used in combination with the *x*, *y*, or *z*
|
||||
commands: *vel*, *erate*, *trate*, *pressure*, or *wiggle*. This is the meaning
|
||||
of its styles and values.
|
||||
The *box* parameter provides an additional control over the *x*, *y*,
|
||||
and *z* box lengths by isotropically dilating or contracting the box
|
||||
to either maintain a fixed mean pressure or volume. This isotropic
|
||||
scaling is applied after the box is deformed by the above *x*, *y*,
|
||||
*z*, *xy*, *xz*, and *yz* styles, acting as a second deformation
|
||||
step. This parameter will change the overall strain rate in the *x*,
|
||||
*y*, or *z* dimensions. This parameter can only be used in
|
||||
combination with the *x*, *y*, or *z* commands: *vel*, *erate*,
|
||||
*trate*, *pressure*, or *wiggle*. 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. This style
|
||||
@ -186,9 +188,7 @@ dimensions (deforming the shape of the box), while maintaining a mean pressure.
|
||||
|
||||
----------
|
||||
|
||||
The *flip*, *remap*, and *units* keywords all behave identically
|
||||
to those in :doc:`fix deform <fix_deform>`. Additional optional
|
||||
keywords are described below.
|
||||
The optional keywords provided by this fix are described below.
|
||||
|
||||
.. _deform_normalize:
|
||||
|
||||
@ -240,44 +240,47 @@ 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:
|
||||
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
|
||||
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.
|
||||
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.
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
This fix will restore the initial box settings from :doc:`binary restart files <restart>`, which allows the fix to be properly continue
|
||||
This fix will restore the initial box settings from :doc:`binary
|
||||
restart files <restart>`, which allows the fix to be properly continue
|
||||
deformation, when using the start/stop options of the :doc:`run <run>`
|
||||
command. No global or per-atom quantities are stored by this fix for access
|
||||
by various :doc:`output commands <Howto_output>`.
|
||||
command. 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, unklike in :doc:`fix deform <fix_deform>`.
|
||||
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
|
||||
If any pressure controls are used, the :doc:`fix_modify <fix_modify>`
|
||||
*temp* and *press* options are supported by this fix, unlike in
|
||||
:doc:`fix deform <fix_deform>`. 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*
|
||||
@ -292,8 +295,9 @@ Restrictions
|
||||
You cannot apply x, y, or z deformations to a dimension that is
|
||||
shrink-wrapped via the :doc:`boundary <boundary>` command.
|
||||
|
||||
You cannot apply xy, yz, or xz deformations to a second dimension (y in
|
||||
xy) that is shrink-wrapped via the :doc:`boundary <boundary>` command.
|
||||
You cannot apply xy, yz, or xz deformations to a second dimension (y
|
||||
in xy) that is shrink-wrapped via the :doc:`boundary <boundary>`
|
||||
command.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
@ -303,8 +307,7 @@ Related commands
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The option defaults are remap = x, flip = yes, units = lattice, and
|
||||
normalize/pressure = no.
|
||||
The option defaults are normalize/pressure = no.
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -55,7 +55,7 @@ FixDeformPressure::FixDeformPressure(LAMMPS *lmp, int narg, char **arg) :
|
||||
memset(set_extra, 0, 7 * sizeof(SetExtra));
|
||||
memset(&set_box, 0, sizeof(Set));
|
||||
|
||||
// parse child-specific arguments
|
||||
// parse only parameter/style arguments specific to this child class
|
||||
|
||||
int index, iarg;
|
||||
int i = 0;
|
||||
@ -115,6 +115,7 @@ FixDeformPressure::FixDeformPressure(LAMMPS *lmp, int narg, char **arg) :
|
||||
set_extra[index].pgain = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
|
||||
i += 4;
|
||||
} else error->all(FLERR, "Illegal fix deform/pressure command: {}", arg[iarg + 1]);
|
||||
|
||||
} else if (strcmp(arg[iarg], "box") == 0) {
|
||||
if (strcmp(arg[iarg + 1], "volume") == 0) {
|
||||
set_box.style = VOLUME;
|
||||
@ -850,7 +851,6 @@ void FixDeformPressure::restart(char *buf)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixDeformPressure::options(int i, int narg, char **arg)
|
||||
@ -860,6 +860,8 @@ void FixDeformPressure::options(int i, int narg, char **arg)
|
||||
vol_balance_flag = 0;
|
||||
normalize_pressure_flag = 0;
|
||||
|
||||
// parse only options not handled by parent class
|
||||
|
||||
int iarg, nskip;
|
||||
while (i < leftover_iarg.size()) {
|
||||
iarg = leftover_iarg[i];
|
||||
|
||||
@ -72,7 +72,8 @@ irregular(nullptr), set(nullptr)
|
||||
set = new Set[6];
|
||||
memset(set, 0, 6 * sizeof(Set));
|
||||
|
||||
// parse arguments
|
||||
// parse all parameter/style arguments for this parent and also child classes
|
||||
// for child classes, simply store them in leftover_iarg and skip over them
|
||||
|
||||
triclinic = domain->triclinic;
|
||||
|
||||
@ -1009,6 +1010,9 @@ void FixDeform::options(int narg, char **arg)
|
||||
{"vol/balance/p", 2}});
|
||||
}
|
||||
|
||||
// parse all optional arguments for this parent and also child classes
|
||||
// for child classes, simply store them in leftover_iarg and skip over them
|
||||
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg], "remap") == 0) {
|
||||
|
||||
Reference in New Issue
Block a user