![]() (The Index, ResID, and type numbers correspond to the Atom-ID, Molecule-ID, and Type numbers in the LAMMPS data file. USEFUL FEATURE: If you press the % button, you can click on the atoms in your system, and the coordinates, atom-ID, molecule-ID, and atom type will printed to the terminal that you used to start VMD.Select the “File”->“Render” menu option and click on “Snapshot” and change it to “Tachyon (in-memory rendering” option.Select the “Display”->“Display Settings” menu option to enable ambient occlusion and change the field of view.Optional: Select the “Display”->“Render Mode”->“GSL” menu option (to improve the frame rate).For example, “ResID” refers to the LAMMPS Molecule-ID number, and “Index” refers to the LAMMPS Atom-ID. Use the “Graphics->Representations” menu and change the appearance using the ("Draw Style, “Coloring Method”, “Periodic”, “Create Rep” and “Delete Rep” buttons) Some of options for the draw styles and coloring methods use terminology which were originally intended for proteins.(I assume you are using “atom_style full”) Sometimes VMD prints useful information to the terminal from which it was invoked.))ī) Select the “Extensions”->“Tk Console” menu option ![]() To do thatĪ) Start VMD (preferably from a terminal, by entering “vmd”. Then, use topotools to load the data file into VMD.If not, use the LAMMPS “write_data” command to create one. I assume you are using a LAMMPS data file.So here’s a more detailed reply to your question with VMD-specific instructions, if you want to try VMD: VMD can’t render ellipsoids, dipoles or handle trajectories with bonds breaking and forming. VMD is a older and it is more confusing to use because it was designed for rendering proteins (which most LAMMPS users don’t care about). They both use the tachyon rendering engine. I’m not sure if VMD makes images which are better than the free version of OVITO. I have never seen a scientific journal reject a paper because the authors did not use the latest ray-tracing methods to produce prettier pictures. The free version makes pretty good images also. It’s hard to get funding to feed yourself when writing software like this.) Don’t feel bad if you are a graduate student and you can’t afford a license (currently $420). (For what it’s worth, I support them for doing that. OVITO has the ability to make really beautiful ray traced images, but they charge money for some of the ray-tracing features. They are currently determined by atom type and distance, I think.) The only limitation I’ve noticed is the ability to specify the bonds between specific pairs of atoms. (I actually usually prefer OVITO over VMD. I’m curious to know what feature you would like to see in OVITO? Also try “Display”->“Render Mode”->“GSL” (to improve the frame rate), and “Display”->“Display Settings”, where you can change the field-of-view, and add shadows and ambient occlusion “Amb. (Play with the settings in the “Graphics->Representations” menu, including the "Draw Style, “Periodic”, “Create Rep” and “Delete Rep” buttons. But with some experimentation, you can make some really great images and movies. I’ve used VMD a lot, but it has some limitations, and the default colors, field-of-view, and rendering settings are kind of ugly (in my opinion). VMD, AtomEye, and LAMMPS own dump image feature can generate publication quality images. Now open up the terminal and go to the directory, where the images from the movie maker are saved.Along with OVITO, is there any other paid/open source code for visualization/plotting that can work with LAMMPS outputs and produce high quality images? You can either write the path to a folder in either “Selection” or manually select the path to that folder using your mouse. Also, to change the location of a folder that will have and save all the JPEG pictures, press on “Set working directory:” button which is shown below. Lastly, make sure to put a title on your movie in a box on next to “Name of movie”. This will take take many spanshots of your movie amd save with a “.jpeg” extension. The last button that you should press is “Format” and select “JPEG frames(ImageMagick)”. Next press on the “Movie Setting” and select “Trajectory”, these steps are shown below: ![]() In that window, press on the “Renderer” button and select “Internal Tachyon(Ray Tracer)” from the dropdown menu. Those steps should take you to a window called “VMD Movie Generator” shown below. This following image shows the steps you chose: After loading your files to VMD, press on a Window called VMD Main and press on Extension menu and select “Visualization”, and “Movie Maker” from the dropdown menu.
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