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region2vmd command
Syntax
region2vmd file keyword arg ...
filename = name of file to write VMD script commands to
zero or more keyword/arg pairs may be appended
keyword = region or color or material or command
region region-ID = name of region to translate to VMD graphics color color-name = set color for following visualized objects material material-name = set material for following visualized objects command string = string with custom VMD script command (in quotes)
Examples
region2vmd regions.vmd material Opaque color red region c1 color green region c2
region2vmd vizbox.vmd command "mol new system.lammpstrj waitfor all" region box
region2vmd regdefs.vmd region upper region lower region hole
Description
Added in version 2Apr2025.
Write a VMD Tcl script file with commands that aim to create a visualization of regions. There may be multiple region visualizations stored in a single file.
The visualization is implemented by creating a new (and empty) “VMD molecule” and then assigning a sequence of VMD graphics primitives to represent the region in VMD. Each region will be stored in a separate “VMD molecule” with the name “LAMMPS region <region ID>”.
The region2vmd command is following by the filename for the resulting VMD script and an arbitrary number of keyword argument pairs to either write out a new region visualization, change the color or material setting, or to insert arbitrary VMD script commands. The keywords and arguments are processed in sequence.
The region keyword must be followed by a previously defined LAMMPS region. Only a limited set region styles and region settings are currently supported. See Restrictions below. Unsupported region styles or regions with unsupported settings will be skipped and a corresponding message is printed.
The color keyword must be followed by a color name that is defined in VMD. This color will be used by all following region visualizations. The default setting is ‘silver’. VMD has the following colors pre-defined:
blue |
red |
gray |
orange |
yellow |
tan |
silver |
green |
white |
pink |
cyan |
purple |
lime |
mauve |
ochre |
iceblue |
black |
yellow2 |
yellow3 |
green2 |
green3 |
cyan2 |
cyan3 |
blue2 |
blue3 |
violet |
violet2 |
magenta |
magenta2 |
red2 |
red3 |
orange2 |
orange3 |
The material keyword must be followed by a material name that is defined in VMD. This material will be used by all following visualizations. The default setting is ‘Transparent’. VMD has the following materials pre-defined:
Opaque |
Transparent |
BrushedMetal |
Diffuse |
Ghost |
Glass1 |
Glass2 |
Glass3 |
Glossy |
HardPlastic |
MetallicPastel |
Steel |
Translucent |
Edgy |
EdgyShiny |
EdgyGlass |
Goodsell |
AOShiny |
AOChalky |
AOEdgy |
BlownGlass |
GlassBubble |
RTChrome |
The command keyword must be followed by a VMD script command as a single string in quotes. This VMD command will be directly inserted into the created VMD script.
The created file can be loaded into VMD either from the command line with the ‘-e’ flag, or from the command prompt with ‘play <script file>’, or from the File menu via “Load VMD visualization state”.
Setting the “top” molecule in VMD
It is usually desirable to have the “molecule” with the LAMMPS
trajectory set at “top” molecule in VMD and not one of the “region
molecules”. The VMD script generated by this region2vmd assumes that
this molecule is already loaded and set as the current “top”
molecule. Thus at the beginning of the script the index of the top
molecule is stored in the VMD variable ‘oldtop’ and at the end of the
script, that “top” molecule is restored. If no molecule is loaded,
this can be inserted into the script with a custom command. The
molecule index to this new molecules should be assigned to the oldtop
variable. This can be done with e.g. set oldtop [mol new
{regions.vmd} waitfor all]
Restrictions
This command is part of the EXTRA-COMMAND package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.
Only the following region styles are currently supported: block, cone, cylinder, ellipsoid, prism, and sphere. Regions formed from unions or intersections of other regions are not supported.
Rotating regions are currently not supported.
Defaults
color = silver, material = Transparent