refactor command to be more flexible and capable
This commit is contained in:
Axel Kohlmeyer
@ -8,17 +8,27 @@ Syntax
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.. code-block:: LAMMPS
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region2vmd file args
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region2vmd file keyword arg ...
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* file = name of VMD script file to write
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* args = one or more region IDs may be appended
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* filename = name of file to write VMD script commands to
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* zero or more keyword/arg pairs may be appended
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* keyword = *region* or *color* or *material* or *command*
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.. parsed-literal::
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*region* region-ID = name of region to translate to VMD graphics
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*color* color-name = set color for following visualized objects
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*material* material-name = set material for following visualized objects
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*command* string = string with custom VMD script command (in quotes)
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Examples
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""""""""
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.. code-block:: LAMMPS
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region2vmd regions.vmd box c1 c2
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region2vmd regions.vmd material Opaque color red region c1 color green region c2
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region2vmd vizbox.vmd command "mol new system.lammpstrj waitfor all" region box
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region2vmd regdefs.vmd region upper region lower region hole
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Description
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"""""""""""
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@ -28,17 +38,106 @@ Description
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Write a `VMD <https:://ks.uiuc.edu/Research/vmd/>`_ Tcl script file with
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commands that aim to create a visualization of :doc:`LAMMPS regions
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<region>`. There may be multiple region visualizations stored in a
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single file. Only a limited amount of region styles and settings are
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currently supported. See **Restrictions** below.
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single file.
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The visualization is implemented by creating a new (and empty) "VMD
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molecule" and then using VMD graphics primitives to represent the region
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in VMD. Each region will be stored in a separate "VMD molecule" with
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the name "LAMMPS region <region ID>".
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molecule" and then assigning a sequence of VMD graphics primitives to
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represent the region in VMD. Each region will be stored in a separate
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"VMD molecule" with the name "LAMMPS region <region ID>".
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The *region2vmd* command is following by the filename for the resulting
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VMD script and an arbitrary number of keyword argument pairs to either
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write out a new *region* visualization, change the *color* or *material*
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setting, or to insert arbitrary VMD script *command*s. The keywords
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and arguments are processed in sequence.
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The *region* keyword must be followed by a previously defined LAMMPS
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:doc:`region <region>`. Only a limited set region styles and region
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settings are currently supported. See **Restrictions** below.
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Unsupported region styles or regions with unsupported settings will be
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skipped and a corresponding message is printed.
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The *color* keyword must be followed by a color name that is defined in
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VMD. This color will be used by all following region visualizations.
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The default setting is 'silver'. VMD has the following colors
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pre-defined:
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.. table_from_list::
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:columns: 11
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* blue
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* red
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* gray
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* orange
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* yellow
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* tan
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* silver
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* green
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* white
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* pink
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* cyan
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* purple
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* lime
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* mauve
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* ochre
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* iceblue
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* black
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* yellow2
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* yellow3
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* green2
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* green3
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* cyan2
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* cyan3
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* blue2
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* blue3
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* violet
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* violet2
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* magenta
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* magenta2
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* red2
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* red3
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* orange2
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* orange3
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The *material* keyword must be followed by a material name that is defined in
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VMD. This material will be used by all following visualizations. The
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default setting is 'Transparent'. VMD has the following materials
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pre-defined:
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.. table_from_list::
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:columns: 7
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* Opaque
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* Transparent
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* BrushedMetal
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* Diffuse
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* Ghost
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* Glass1
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* Glass2
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* Glass3
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* Glossy
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* HardPlastic
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* MetallicPastel
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* Steel
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* Translucent
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* Edgy
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* EdgyShiny
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* EdgyGlass
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* Goodsell
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* AOShiny
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* AOChalky
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* AOEdgy
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* BlownGlass
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* GlassBubble
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* RTChrome
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The *command* keyword must be followed by a VMD script command as a
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single string in quotes. This command will be directly inserted into
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the created VMD script.
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The created file can be loaded into VMD either from the command line
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with the -e flag, or from the command prompt with play <script file>, or
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from the File menu via "Load VMD visualization state".
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with the '-e' flag, or from the command prompt with 'play <script
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file>', or from the File menu via "Load VMD visualization state".
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----------
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@ -62,7 +161,7 @@ Related commands
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:doc:`region <region>`
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Default
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"""""""
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Defaults
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""""""""
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none
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*color* = silver, *material* = Transparent
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