Merge pull request #4468 from akohlmey/add-region2vmd-command
Add a new region2vmd command for visualizing regions with VMD
This commit is contained in:
Axel Kohlmeyer
@ -140,6 +140,7 @@ additional letter in parenthesis: k = KOKKOS.
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* :doc:`plugin <plugin>`
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* :doc:`prd <prd>`
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* :doc:`python <python>`
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* :doc:`region2vmd <region2vmd>`
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* :doc:`tad <tad>`
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* :doc:`temper <temper>`
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* :doc:`temper/grem <temper_grem>`
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@ -82,6 +82,7 @@ Commands
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read_dump
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read_restart
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region
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region2vmd
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replicate
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rerun
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reset_atoms
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183
doc/src/region2vmd.rst
Normal file
183
doc/src/region2vmd.rst
Normal file
@ -0,0 +1,183 @@
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.. index:: region2vmd
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region2vmd command
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==================
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Syntax
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""""""
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.. code-block:: LAMMPS
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region2vmd file keyword arg ...
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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 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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.. versionadded:: TBD
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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:`regions <region>`.
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There may be multiple region visualizations stored in a single file.
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The visualization is implemented by creating a new (and empty) "VMD
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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: 8
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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 VMD command will be directly inserted
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into 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
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file>', or from the File menu via "Load VMD visualization state".
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.. admonition:: Setting the "top" molecule in VMD
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:class: note
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It is usually desirable to have the "molecule" with the LAMMPS
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trajectory set at "top" molecule in VMD and not one of the "region
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molecules". The VMD script generated by this region2vmd assumes that
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this molecule is already loaded and set as the current "top"
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molecule. Thus at the beginning of the script the index of the top
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molecule is stored in the VMD variable 'oldtop' and at the end of the
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script, that "top" molecule is restored. If no molecule is loaded,
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this can be inserted into the script with a custom command. The
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molecule index to this new molecules should be assigned to the oldtop
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variable. This can be done with e.g. ``set oldtop [mol new
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{regions.vmd} waitfor all]``
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----------
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Restrictions
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""""""""""""
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This command is part of the EXTRA-COMMAND package. It is only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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Only the following region styles are currently supported: *block*,
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*cone*, *cylinder*, *ellipsoid*, *prism*, and *sphere*. Regions formed
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from unions or intersections of other regions are not supported.
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For region style *cone* one of the two radii must be zero, since the
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equivalent VMD graphics primitive does not support truncated cones.
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Also the VMD graphics primitive does not support open cones.
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Rotating regions are not supported.
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Related commands
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""""""""""""""""
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:doc:`region <region>`
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Defaults
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""""""""
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*color* = silver, *material* = Transparent
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@ -1353,6 +1353,7 @@ Goga
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Goldfarb
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Gompper
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Gonzalez-Melchor
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Goodsell
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googlemail
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googletest
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Gordan
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@ -1544,6 +1545,7 @@ Ibanez
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ibar
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ibm
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icc
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iceblue
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ico
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icosahedral
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idealgas
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@ -2724,6 +2726,7 @@ nylo
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nz
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Nz
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nzlo
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ochre
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ocl
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octahedral
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octants
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@ -2738,6 +2741,7 @@ Okazaki
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O'Keefe
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OKeefe
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oldlace
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oldtop
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olecular
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Oleinik
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Olfason
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2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -1549,6 +1549,8 @@
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/reaxff_inline.h
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/reaxff_omp.h
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/reaxff_types.h
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/region2vmd.cpp
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/region2vmd.h
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/remap.cpp
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/remap.h
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/remap_wrap.cpp
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517
src/EXTRA-COMMAND/region2vmd.cpp
Normal file
517
src/EXTRA-COMMAND/region2vmd.cpp
Normal file
@ -0,0 +1,517 @@
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/* -*- c++ -*--------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "region2vmd.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "error.h"
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#include "region.h"
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#include "region_block.h"
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#include "region_cone.h"
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#include "region_cylinder.h"
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#include "region_ellipsoid.h"
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#include "region_prism.h"
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#include "region_sphere.h"
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#include <cstring>
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#include <unordered_set>
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using namespace LAMMPS_NS;
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static constexpr double SMALL = 1.0e-10;
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static constexpr double DELTA = 1.0e-5;
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static const std::unordered_set<std::string> vmdcolors{
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"blue", "red", "gray", "orange", "yellow", "tan", "silver", "green", "white",
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"pink", "cyan", "purple", "lime", "mauve", "ochre", "iceblue", "black", "yellow2",
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"yellow3", "green2", "green3", "cyan2", "cyan3", "blue2", "blue3", "violet", "violet2",
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"magenta", "magenta2", "red2", "red3", "orange2", "orange3"};
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static const std::unordered_set<std::string> vmdmaterials{
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"Opaque", "Transparent", "BrushedMetal", "Diffuse", "Ghost", "Glass1",
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"Glass2", "Glass3", "Glossy", "HardPlastic", "MetallicPastel", "Steel",
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"Translucent", "Edgy", "EdgyShiny", "EdgyGlass", "Goodsell", "AOShiny",
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"AOChalky", "AOEdgy", "BlownGlass", "GlassBubble", "RTChrome"};
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static constexpr char draw_ellipsoid_function[] =
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"\n# VMD script code to emulate ellipsoids with trinorm graphics objects\n"
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"proc vmd_draw_ellipsoid {mol level {center {0.0 0.0 0.0}} {radius {1.0 1.0 1.0}}} {\n"
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" set orient {1.0 0.0 0.0 0.0}\n"
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" set gid {}\n\n"
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" # vertices of an octahedron inscribed\n"
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" # in a sphere with radius 1.0.\n"
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" set vec1 {-1.0 0.0 0.0}\n"
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" set vec2 { 1.0 0.0 0.0}\n"
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" set vec3 { 0.0 -1.0 0.0}\n"
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" set vec4 { 0.0 1.0 0.0}\n"
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" set vec5 { 0.0 0.0 -1.0}\n"
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" set vec6 { 0.0 0.0 1.0}\n\n"
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" # build list of triangles representing\n"
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" # the octahedron. the points of the \n"
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" # triangles have to be given clockwise from\n"
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" # looking at the surface from the outside.\n"
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" set trilist [list \\\n"
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" [list $vec1 $vec4 $vec5] \\\n"
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" [list $vec5 $vec4 $vec2] \\\n"
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" [list $vec2 $vec4 $vec6] \\\n"
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" [list $vec6 $vec4 $vec1] \\\n"
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" [list $vec5 $vec3 $vec1] \\\n"
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" [list $vec2 $vec3 $vec5] \\\n"
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" [list $vec6 $vec3 $vec2] \\\n"
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" [list $vec1 $vec3 $vec6] ]\n\n"
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" # refinement iterations to approximate a sphere:\n"
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" # each triangle is split into 4 subtriangles\n"
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" # p2\n"
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" # /\\\n"
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" # / \\\n"
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" # pb/____\\pc\n"
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" # /\\ /\\\n"
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" # / \\ / \\\n"
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" # /____\\/____\\\n"
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" # p1 pa p3\n\n"
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" # we construct vectors to the three midpoints and rescale\n"
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" # them to unit length. then build new triangles enumerating\n"
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" # the points in clockwise order again.\n"
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" for {set i 0} {$i < $level} {incr i} {\n"
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" set newlist {}\n"
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" foreach tri $trilist {\n"
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" foreach {p1 p2 p3} $tri {}\n"
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" set pa [vecnorm [vecadd $p1 $p3]]\n"
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" set pb [vecnorm [vecadd $p1 $p2]]\n"
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" set pc [vecnorm [vecadd $p2 $p3]]\n"
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" lappend newlist [list $p1 $pb $pa]\n"
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" lappend newlist [list $pb $p2 $pc]\n"
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" lappend newlist [list $pa $pb $pc]\n"
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" lappend newlist [list $pa $pc $p3]\n"
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" }\n"
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" set trilist $newlist\n"
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" }\n\n"
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" # compute vertex scaling factor to deform a sphere to an ellipsoid\n"
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" proc radscale {radius vector} {\n"
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" foreach {a b c} $radius {}\n"
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" foreach {x y z} $vector {}\n"
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" return [expr {sqrt(1.0/($x/$a*$x/$a+$y/$b*$y/$b+$z/$c*$z/$c))}]\n"
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" }\n\n"
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" # convert quaternion to rotation matrix\n"
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" proc quattorot {quat} {\n"
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" foreach {w x y z} $quat {}\n"
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" set norm [expr {$w*$w + $x*$x + $y*$y +$z*$z}]\n"
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" set sc 0.0\n"
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" if {$norm > 0.0} { set s [expr {2.0/$norm}] }\n"
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" set X [expr {$x*$s}]\n"
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" set Y [expr {$y*$s}]\n"
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" set Z [expr {$z*$s}]\n"
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" return [list \\\n"
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" [list [expr {1.0-($y*$y*$s + $z*$z*$s)}] \\\n"
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" [expr {$x*$y*$s - $w*$z*$s}] \\\n"
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" [expr {$x*$z*$s + $w*$y*$s}] ] \\\n"
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" [list [expr {$x*$y*$s + $w*$z*$s}] \\\n"
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" [expr {1.0-($x*$x*$s + $z*$z*$s)}] \\\n"
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" [expr {$y*$z*$s - $w*$x*$s}] ] \\\n"
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" [list [expr {$x*$z*$s - $w*$y*$s}] \\\n"
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" [expr {$y*$z*$s + $w*$x*$s}] \\\n"
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" [expr {1.0-($x*$x*$s + $y*$y*$s)}] ] ]\n"
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" }\n\n"
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" # apply rotation matrix to vector\n"
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" proc rotvec {mat vec} {\n"
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" set new {}\n"
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" foreach c $mat {\n"
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" lappend new [vecdot $c $vec]\n"
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" }\n"
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" return $new\n"
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" }\n\n"
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" foreach tri $trilist {\n"
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" foreach {vec1 vec2 vec3} $tri {}\n"
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" # rescale to desired radius\n"
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" set rad1 [radscale $radius $vec1]\n"
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" set rad2 [radscale $radius $vec2]\n"
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" set rad3 [radscale $radius $vec3]\n"
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" # get and apply rotation matrix\n"
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" set mat [quattorot $orient]\n"
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" set vec1 [rotvec $mat $vec1]\n"
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" set vec2 [rotvec $mat $vec2]\n"
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" set vec3 [rotvec $mat $vec3]\n"
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" # deform sphereoid and translate\n"
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" set pos1 [vecadd [vecscale $rad1 $vec1] $center]\n"
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" set pos2 [vecadd [vecscale $rad2 $vec2] $center]\n"
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" set pos3 [vecadd [vecscale $rad3 $vec3] $center]\n"
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" # since the original vectors to the vertices are those of\n"
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" # a unit sphere, we can use them directly as surface normals.\n"
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" lappend gid [graphics $mol trinorm $pos1 $pos2 $pos3 $vec1 $vec2 $vec3]\n"
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" }\n"
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" return $gid\n"
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"}\n\n";
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// class that "owns" the file pointer and closes it when going out of scope.
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// this avoids a lot of redundant checks and calls.
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class AutoClose {
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public:
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AutoClose() = delete;
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AutoClose(const AutoClose &) = delete;
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AutoClose(const AutoClose &&) = delete;
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explicit AutoClose(FILE *_fp) : fp(_fp) {};
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~AutoClose()
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{
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if (fp) fclose(fp);
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}
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private:
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FILE *fp;
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};
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/* ---------------------------------------------------------------------- */
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void Region2VMD::command(int narg, char **arg)
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{
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if (narg < 3) utils::missing_cmd_args(FLERR, "region2vmd", error);
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FILE *fp = nullptr;
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if (comm->me == 0) {
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fp = fopen(arg[0], "w");
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if (fp == nullptr) {
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error->one(FLERR, Error::ARGZERO, "Cannot open file {} for writing: {}", arg[0],
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utils::getsyserror());
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} else {
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utils::logmesg(lmp, "Writing region visualizations to VMD Tcl script file {}:\n", arg[0]);
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fputs("# save old top molecule index\nset oldtop [molinfo top]\n", fp);
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}
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}
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// automatically close fp when fpowner goes out of scope
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||||
AutoClose fpowner(fp);
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||||
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||||
// defaults
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||||
std::string color = "silver";
|
||||
std::string material = "Transparent";
|
||||
bool def_ellipsoid_func = false;
|
||||
|
||||
int iarg = 1;
|
||||
std::string thisarg = arg[iarg];
|
||||
while (iarg < narg) {
|
||||
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "region2vmd", error);
|
||||
thisarg = arg[iarg];
|
||||
++iarg;
|
||||
|
||||
if (thisarg == "color") {
|
||||
color = arg[iarg];
|
||||
if (const auto &search = vmdcolors.find(color); search == vmdcolors.end())
|
||||
error->all(FLERR, iarg, "Color {} is not a known VMD color", color);
|
||||
|
||||
} else if (thisarg == "material") {
|
||||
material = arg[iarg];
|
||||
if (const auto &search = vmdmaterials.find(material); search == vmdmaterials.end())
|
||||
error->all(FLERR, iarg, "Material {} is not a known VMD material", material);
|
||||
|
||||
} else if (thisarg == "command") {
|
||||
if (fp) {
|
||||
fputs("\n# custom command\n", fp);
|
||||
fputs(arg[iarg], fp);
|
||||
fputs("\n", fp);
|
||||
}
|
||||
|
||||
} else if (thisarg == "region") {
|
||||
auto *region = domain->get_region_by_id(arg[iarg]);
|
||||
if (!region) {
|
||||
error->all(FLERR, iarg, "Region {} does not exist", arg[iarg]);
|
||||
} else {
|
||||
if (fp) {
|
||||
// add VMD / Tcl function to draw ellipsoids only once
|
||||
if (!def_ellipsoid_func && (strcmp(region->style, "ellipsoid") == 0)) {
|
||||
fputs(draw_ellipsoid_function, fp);
|
||||
def_ellipsoid_func = true;
|
||||
}
|
||||
utils::logmesg(lmp, " writing region {} ...", region->id);
|
||||
utils::print(fp, "\n# region {} of style {}\n", region->id, region->style);
|
||||
|
||||
fputs("# create new empty VMD molecule to store the graphics primitives\n"
|
||||
"set gfxmol [mol new]\nmol top $gfxmol\n",
|
||||
fp);
|
||||
utils::print(fp, "mol rename $gfxmol {{LAMMPS region {}}}\n", region->id);
|
||||
fputs("# set color and material\n", fp);
|
||||
utils::print(fp, "graphics $gfxmol color {}\n", color);
|
||||
utils::print(fp, "graphics $gfxmol material {}\n", material);
|
||||
write_region(fp, region);
|
||||
}
|
||||
}
|
||||
|
||||
} else {
|
||||
error->all(FLERR, iarg - 1, "Unknown region2vmd keyword {}", thisarg);
|
||||
}
|
||||
++iarg;
|
||||
}
|
||||
|
||||
// done. file will be close automatically
|
||||
if (fp) {
|
||||
// reset views and restore previous top molecule
|
||||
fputs("after idle {if {$oldtop >= 0} {mol top $oldtop}; display resetview}\n", fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
write out one region using VMD graphics primitives
|
||||
fp is non-NULL only on MPI rank 0
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void Region2VMD::write_region(FILE *fp, Region *region)
|
||||
{
|
||||
if (!fp || !region) return;
|
||||
|
||||
if (region->rotateflag) {
|
||||
utils::logmesg(lmp, "Cannot (yet) handle rotating region {}. Skipping... ", region->id);
|
||||
return;
|
||||
}
|
||||
|
||||
// compute position offset for moving regions
|
||||
|
||||
double dx = 0.0;
|
||||
double dy = 0.0;
|
||||
double dz = 0.0;
|
||||
if (region->moveflag) {
|
||||
dx = region->dx;
|
||||
dy = region->dy;
|
||||
dz = region->dz;
|
||||
}
|
||||
|
||||
// translate compatible regions to VMD graphics primitives, skip others.
|
||||
|
||||
const std::string regstyle = region->style;
|
||||
if (regstyle == "block") {
|
||||
const auto block = dynamic_cast<RegBlock *>(region);
|
||||
if (!block) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'block'", region->id);
|
||||
} else {
|
||||
// a block is represented by 12 triangles
|
||||
// comment out VMD command when side is open
|
||||
utils::print(fp,
|
||||
"{6}draw triangle {{{0} {2} {4}}} {{{0} {2} {5}}} {{{0} {3} {4}}}\n"
|
||||
"{6}draw triangle {{{0} {3} {4}}} {{{0} {3} {5}}} {{{0} {2} {5}}}\n"
|
||||
"{8}draw triangle {{{0} {2} {4}}} {{{0} {2} {5}}} {{{1} {2} {4}}}\n"
|
||||
"{8}draw triangle {{{1} {2} {4}}} {{{1} {2} {5}}} {{{0} {2} {5}}}\n"
|
||||
"{7}draw triangle {{{1} {2} {4}}} {{{1} {2} {5}}} {{{1} {3} {4}}}\n"
|
||||
"{7}draw triangle {{{1} {3} {4}}} {{{1} {3} {5}}} {{{1} {2} {5}}}\n"
|
||||
"{10}draw triangle {{{0} {2} {4}}} {{{1} {2} {4}}} {{{1} {3} {4}}}\n"
|
||||
"{10}draw triangle {{{0} {2} {4}}} {{{0} {3} {4}}} {{{1} {3} {4}}}\n"
|
||||
"{11}draw triangle {{{0} {2} {5}}} {{{1} {2} {5}}} {{{1} {3} {5}}}\n"
|
||||
"{11}draw triangle {{{0} {2} {5}}} {{{0} {3} {5}}} {{{1} {3} {5}}}\n"
|
||||
"{9}draw triangle {{{0} {3} {4}}} {{{0} {3} {5}}} {{{1} {3} {5}}}\n"
|
||||
"{9}draw triangle {{{0} {3} {4}}} {{{1} {3} {4}}} {{{1} {3} {5}}}\n",
|
||||
block->xlo + dx, block->xhi + dx, block->ylo + dy, block->yhi + dy,
|
||||
block->zlo + dz, block->zhi + dz, block->open_faces[0] ? "# " : "",
|
||||
block->open_faces[1] ? "# " : "", block->open_faces[2] ? "# " : "",
|
||||
block->open_faces[3] ? "# " : "", block->open_faces[4] ? "# " : "",
|
||||
block->open_faces[5] ? "# " : "");
|
||||
}
|
||||
|
||||
} else if (regstyle == "cone") {
|
||||
const auto cone = dynamic_cast<RegCone *>(region);
|
||||
if (!cone) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'cone'", region->id);
|
||||
} else {
|
||||
if (cone->open_faces[0] || cone->open_faces[1])
|
||||
error->warning(FLERR, "Drawing open-faced cones is not supported");
|
||||
// The VMD cone primitive requires one radius set to zero
|
||||
if (cone->radiuslo < SMALL) {
|
||||
// a VMD cone uses a single cone primitive
|
||||
if (cone->axis == 'x') {
|
||||
utils::print(fp, "draw cone {{{1} {2} {3}}} {{{0} {2} {3}}} radius {4} resolution 20\n",
|
||||
cone->lo + dx, cone->hi + dx, cone->c1 + dy, cone->c2 + dz, cone->radiushi);
|
||||
} else if (cone->axis == 'y') {
|
||||
utils::print(fp, "draw cone {{{2} {1} {3}}} {{{2} {0} {3}}} radius {4} resolution 20\n",
|
||||
cone->lo + dy, cone->hi + dy, cone->c1 + dx, cone->c2 + dz, cone->radiushi);
|
||||
} else if (cone->axis == 'z') {
|
||||
utils::print(fp, "draw cone {{{2} {3} {1}}} {{{2} {3} {0}}} radius {4} resolution 20\n",
|
||||
cone->lo + dz, cone->hi + dz, cone->c1 + dx, cone->c2 + dy, cone->radiushi);
|
||||
}
|
||||
} else if (cone->radiushi < SMALL) {
|
||||
// a VMD cone uses a single cone primitive
|
||||
if (cone->axis == 'x') {
|
||||
utils::print(fp, "draw cone {{{0} {2} {3}}} {{{1} {2} {3}}} radius {4} resolution 20\n",
|
||||
cone->lo + dx, cone->hi + dx, cone->c1 + dy, cone->c2 + dz, cone->radiuslo);
|
||||
} else if (cone->axis == 'y') {
|
||||
utils::print(fp, "draw cone {{{2} {0} {3}}} {{{2} {1} {3}}} radius {4} resolution 20\n",
|
||||
cone->lo + dy, cone->hi + dy, cone->c1 + dx, cone->c2 + dz, cone->radiuslo);
|
||||
} else if (cone->axis == 'z') {
|
||||
utils::print(fp, "draw cone {{{2} {3} {0}}} {{{2} {3} {1}}} radius {4} resolution 20\n",
|
||||
cone->lo + dz, cone->hi + dz, cone->c1 + dx, cone->c2 + dy, cone->radiuslo);
|
||||
}
|
||||
} else {
|
||||
utils::logmesg(lmp,
|
||||
"Cannot (yet) translate a truncated cone to VMD graphics. Skipping...\n");
|
||||
}
|
||||
}
|
||||
|
||||
} else if (regstyle == "cylinder") {
|
||||
const auto cylinder = dynamic_cast<RegCylinder *>(region);
|
||||
if (!cylinder) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'cylinder'", region->id);
|
||||
} else {
|
||||
std::string filled = "yes";
|
||||
if (cylinder->open_faces[0] && cylinder->open_faces[1]) {
|
||||
filled = "no";
|
||||
} else if (cylinder->open_faces[0] != cylinder->open_faces[1]) {
|
||||
filled = "no";
|
||||
// we put a single "lid" on an open cylinder by adding a filled cylinder of zero height
|
||||
double lid = cylinder->lo;
|
||||
if (cylinder->open_faces[0]) lid = cylinder->hi;
|
||||
if (cylinder->axis == 'x') {
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{0} {2} {3}}} {{{1:.15} {2} {3}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
lid + dx, lid + dx + DELTA, cylinder->c1 + dy, cylinder->c2 + dz,
|
||||
cylinder->radius);
|
||||
} else if (cylinder->axis == 'y') {
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {0} {3}}} {{{2} {1:.15} {3}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
lid + dy, lid + dy + DELTA, cylinder->c1 + dx, cylinder->c2 + dz,
|
||||
cylinder->radius);
|
||||
} else if (cylinder->axis == 'z') {
|
||||
utils::print(fp,
|
||||
"draw cylinder {{{2} {3} {0}}} {{{2} {3} {1:.15}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
lid + dz, lid + dz + DELTA, cylinder->c1 + dx, cylinder->c2 + dy,
|
||||
cylinder->radius);
|
||||
}
|
||||
}
|
||||
if (cylinder->open_faces[2]) {
|
||||
// need to handle two lids case only. Single lid is already done
|
||||
if (!cylinder->open_faces[0] && !cylinder->open_faces[1]) {
|
||||
if (cylinder->axis == 'x') {
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{0} {2} {3}}} {{{1:.15} {2} {3}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
cylinder->lo + dx, cylinder->lo + dx + DELTA, cylinder->c1 + dy, cylinder->c2 + dz,
|
||||
cylinder->radius);
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{0} {2} {3}}} {{{1:.15} {2} {3}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
cylinder->hi + dx, cylinder->hi + dx + DELTA, cylinder->c1 + dy, cylinder->c2 + dz,
|
||||
cylinder->radius);
|
||||
} else if (cylinder->axis == 'y') {
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{2} {0} {3}}} {{{2} {1:.15} {3}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
cylinder->lo + dy, cylinder->lo + dy + DELTA, cylinder->c1 + dx, cylinder->c2 + dz,
|
||||
cylinder->radius);
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{2} {0} {3}}} {{{2} {1:.15} {3}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
cylinder->hi + dy, cylinder->hi + dy + DELTA, cylinder->c1 + dx, cylinder->c2 + dz,
|
||||
cylinder->radius);
|
||||
} else if (cylinder->axis == 'z') {
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{2} {3} {0}}} {{{2} {3} {1:.15}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
cylinder->lo + dz, cylinder->lo + dz + DELTA, cylinder->c1 + dx, cylinder->c2 + dy,
|
||||
cylinder->radius);
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{2} {3} {0}}} {{{2} {3} {1:.15}}} radius {4} resolution 20 "
|
||||
"filled yes\n",
|
||||
cylinder->hi + dz, cylinder->hi + dz + DELTA, cylinder->c1 + dx, cylinder->c2 + dy,
|
||||
cylinder->radius);
|
||||
}
|
||||
}
|
||||
} else {
|
||||
// a cylinder uses a single cylinder primitive and possibly a single "lid"
|
||||
if (cylinder->axis == 'x') {
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{0} {2} {3}}} {{{1} {2} {3}}} radius {4} resolution 20 filled {5}\n",
|
||||
cylinder->lo + dx, cylinder->hi + dx, cylinder->c1 + dy, cylinder->c2 + dz,
|
||||
cylinder->radius, filled);
|
||||
} else if (cylinder->axis == 'y') {
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{2} {0} {3}}} {{{2} {1} {3}}} radius {4} resolution 20 filled {5}\n",
|
||||
cylinder->lo + dy, cylinder->hi + dy, cylinder->c1 + dx, cylinder->c2 + dz,
|
||||
cylinder->radius, filled);
|
||||
} else if (cylinder->axis == 'z') {
|
||||
utils::print(
|
||||
fp,
|
||||
"draw cylinder {{{2} {3} {0}}} {{{2} {3} {1}}} radius {4} resolution 20 filled {5}\n",
|
||||
cylinder->lo + dz, cylinder->hi + dz, cylinder->c1 + dx, cylinder->c2 + dy,
|
||||
cylinder->radius, filled);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} else if (regstyle == "ellipsoid") {
|
||||
const auto ellipsoid = dynamic_cast<RegEllipsoid *>(region);
|
||||
if (!ellipsoid) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'ellipsoid'", region->id);
|
||||
} else {
|
||||
// for ellipsoid we use a custom VMD function that emulates it using trinorm primitives
|
||||
utils::print(fp, "draw ellipsoid 3 {{{} {} {}}} {{{} {} {}}}\n", ellipsoid->xc + dx,
|
||||
ellipsoid->yc + dy, ellipsoid->zc + dz, ellipsoid->a, ellipsoid->b,
|
||||
ellipsoid->c);
|
||||
}
|
||||
|
||||
} else if (regstyle == "prism") {
|
||||
const auto prism = dynamic_cast<RegPrism *>(region);
|
||||
if (!prism) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'prism'", region->id);
|
||||
} else {
|
||||
// a prism is represented by 12 triangles
|
||||
// comment out VMD command when side is open
|
||||
utils::print(fp,
|
||||
"{14}draw triangle {{{0} {2} {4}}} {{{1} {2} {4}}} {{{7} {3} {4}}}\n"
|
||||
"{14}draw triangle {{{0} {2} {4}}} {{{6} {3} {4}}} {{{7} {3} {4}}}\n"
|
||||
"{16}draw triangle {{{0} {2} {4}}} {{{1} {2} {4}}} {{{8} {9} {5}}}\n"
|
||||
"{16}draw triangle {{{0} {2} {4}}} {{{10} {9} {5}}} {{{8} {9} {5}}}\n"
|
||||
"{19}draw triangle {{{1} {2} {4}}} {{{8} {9} {5}}} {{{7} {3} {4}}}\n"
|
||||
"{19}draw triangle {{{11} {12} {5}}} {{{8} {9} {5}}} {{{7} {3} {4}}}\n"
|
||||
"{18}draw triangle {{{0} {2} {4}}} {{{6} {3} {4}}} {{{13} {12} {5}}}\n"
|
||||
"{18}draw triangle {{{0} {2} {4}}} {{{10} {9} {5}}} {{{13} {12} {5}}}\n"
|
||||
"{15}draw triangle {{{10} {9} {5}}} {{{8} {9} {5}}} {{{11} {12} {5}}}\n"
|
||||
"{15}draw triangle {{{10} {9} {5}}} {{{13} {12} {5}}} {{{11} {12} {5}}}\n"
|
||||
"{17}draw triangle {{{6} {3} {4}}} {{{7} {3} {4}}} {{{11} {12} {5}}}\n"
|
||||
"{17}draw triangle {{{6} {3} {4}}} {{{13} {12} {5}}} {{{11} {12} {5}}}\n",
|
||||
prism->xlo, prism->xhi, prism->ylo, prism->yhi, prism->zlo, prism->zhi,
|
||||
prism->xlo + prism->xy, prism->xhi + prism->xy, prism->xhi + prism->xz,
|
||||
prism->ylo + prism->yz, prism->xlo + prism->xz,
|
||||
prism->xhi + prism->xy + prism->xz, prism->yhi + prism->yz,
|
||||
prism->xlo + prism->xy + prism->xz, prism->open_faces[0] ? "# " : "",
|
||||
prism->open_faces[1] ? "# " : "", prism->open_faces[2] ? "# " : "",
|
||||
prism->open_faces[3] ? "# " : "", prism->open_faces[4] ? "# " : "",
|
||||
prism->open_faces[5] ? "# " : "");
|
||||
}
|
||||
|
||||
} else if (regstyle == "sphere") {
|
||||
const auto sphere = dynamic_cast<RegSphere *>(region);
|
||||
if (!sphere) {
|
||||
error->one(FLERR, Error::NOLASTLINE, "Region {} is not of style 'sphere'", region->id);
|
||||
} else {
|
||||
// a sphere uses a single sphere primitive
|
||||
utils::print(fp, "draw sphere {{{} {} {}}} radius {} resolution 20\n", sphere->xc, sphere->yc,
|
||||
sphere->zc, sphere->radius);
|
||||
}
|
||||
|
||||
} else {
|
||||
utils::logmesg(lmp,
|
||||
"Cannot (yet) translate region {} of style {} to VMD graphics. Skipping... ",
|
||||
region->id, region->style);
|
||||
}
|
||||
utils::logmesg(lmp, " done\n");
|
||||
}
|
||||
41
src/EXTRA-COMMAND/region2vmd.h
Normal file
41
src/EXTRA-COMMAND/region2vmd.h
Normal file
@ -0,0 +1,41 @@
|
||||
/* -*- c++ -*-----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
LAMMPS development team: developers@lammps.org
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMMAND_CLASS
|
||||
// clang-format off
|
||||
CommandStyle(region2vmd,Region2VMD);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_REGION2VMD_H
|
||||
#define LMP_REGION2VMD_H
|
||||
|
||||
#include "command.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class Region;
|
||||
|
||||
class Region2VMD : public Command {
|
||||
public:
|
||||
Region2VMD(class LAMMPS *lmp) : Command(lmp) {};
|
||||
void command(int, char **) override;
|
||||
|
||||
protected:
|
||||
void write_region(FILE *, Region *);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
@ -375,7 +375,7 @@ void Region::options(int narg, char **arg)
|
||||
openflag = 1;
|
||||
iarg += 2;
|
||||
} else
|
||||
error->all(FLERR, "Illegal region command argument: {}", arg[iarg]);
|
||||
error->all(FLERR, iarg, "Unknown region command argument: {}", arg[iarg]);
|
||||
}
|
||||
|
||||
// error check
|
||||
|
||||
@ -26,6 +26,7 @@ namespace LAMMPS_NS {
|
||||
|
||||
class RegBlock : public Region {
|
||||
friend class FixPour;
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegBlock(class LAMMPS *, int, char **);
|
||||
|
||||
@ -25,6 +25,8 @@ RegionStyle(cone,RegCone);
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class RegCone : public Region {
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegCone(class LAMMPS *, int, char **);
|
||||
~RegCone() override;
|
||||
|
||||
@ -26,6 +26,7 @@ namespace LAMMPS_NS {
|
||||
|
||||
class RegCylinder : public Region {
|
||||
friend class FixPour;
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegCylinder(class LAMMPS *, int, char **);
|
||||
|
||||
@ -25,6 +25,8 @@ RegionStyle(ellipsoid,RegEllipsoid);
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class RegEllipsoid : public Region {
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegEllipsoid(class LAMMPS *, int, char **);
|
||||
~RegEllipsoid() override;
|
||||
|
||||
@ -26,6 +26,7 @@ namespace LAMMPS_NS {
|
||||
|
||||
class RegPrism : public Region {
|
||||
friend class CreateBox;
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegPrism(class LAMMPS *, int, char **);
|
||||
|
||||
@ -23,8 +23,9 @@ RegionStyle(sphere,RegSphere);
|
||||
#include "region.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class RegSphere : public Region {
|
||||
friend class Region2VMD;
|
||||
|
||||
public:
|
||||
RegSphere(class LAMMPS *, int, char **);
|
||||
~RegSphere() override;
|
||||
|
||||
Reference in New Issue
Block a user