![]() In our case it was 53.Ĭhange the second line of the script depending on your usage: #no of geometry files# Similarly, also change the path for the images that are to be saved.įinally, you will also need to change the number of the geometry files, depending on how many files you have for your animation. add= "file:///C:/Users/manas/Downloads/GeomOptXYZs/geom_"+i+".xyz"Ĭhange the above path based on your own custom usage. If you’re using the files from this tutorial then they will probably be in the Downloads directory. ![]() You will also need to modify the path to the geometry files. Remember, the prefix file:/// is needed irrespective of the path or the operating system. capture transparent "file:///C:/Users/manas/Downloads/GeomOptXYZs/animation.gif" Therefore, you will have to modify the following line to reflect the path where you would want your GIF to be stored. However, this won’t work on your computer because the paths/addresses of the files would be different. The above script will load geom_1.xyz through geom53.xyz and save snapshots as img_1.png through img_53.png. Var PNGaddress="file:///C:/Users/manas/Downloads/GeomOptXYZs/img_"+i+".png" Load 0 1 0 0 -90 #Rotate the molecule 90 degrees about the x-axis instantaneously #no data#Ĭapture transparent "file:///C:/Users/manas/Downloads/GeomOptXYZs/animation.gif"Īdd= "file:///C:/Users/manas/Downloads/GeomOptXYZs/geom_"+i+".xyz" You will need to make a few changes to the script. Paste the following Jmol script in the script editor window. Now that we have the geometry files, we need to open Jmol and run the Jmol script given below. You can download them and extract them and follow the next steps. The Jmol script will iterate through all these files with the given naming pattern and save the snapshots of the structure as image files img_1.png, img_2.png, etc.Īs an example, I have provided the geometry files here –> Geometry_Files_for_animation. The geometry files could be from a geometry optimization calculation or they could be demonstrating a reaction, or even show the electron density dynamics from an RT-TDDFT calculation. The geometry files should ideally be stored in a separate directory and also be named in a serial manner, such as geom_1.xyz, geom_2.xyz, and so on.
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