Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Messages - Alexander Stukowski

Pages: 1 [2] 3 4 ... 21
Support Forum / Re: rendering quality
« on: March 12, 2018, 11:09:40 AM »
Dear Kyu,

Yes, you can specify the resolution of the image or movie to be rendered in pixels. It is done by settings the size attribute of the RenderSettings object as shown here:

You might have to adjust the zoom level as well to make the simulation box fill the entire picture. This is done through the Viewport.fov attribute.


Support Forum / Re: atomic strain
« on: March 12, 2018, 11:04:52 AM »
Dear Hui,

it is not exactly what Atomeye does, but I think it is close to what you have in mind. The 'Elastic Strain Calculation' function of OVITO calculates the per-atom elastic strain tensor. This tensor describes the elastic distortion of the lattice with respect to an ideal crystal state, which doesn't have to be explicitly specified in terms of atomic positions:

Note the following important limitation: The elastic deformation can only be calculated for atoms that form a elastically distorted, but otherwise perfect lattice. For atoms that are part of crystal defects, the elastic strain is not well defined and OVITO won't calculate a value for them.

Best regards,

Support Forum / Re: How to visualize bonds?
« on: March 11, 2018, 12:09:21 PM »
Dear Young,

I'm not sure what exactly you mean with "create bonds as the configuration itself". Are you looking for a function to manually create bonds between selected particles within the program?

OVITO can read bonding information from LAMMPS data files and PDB files. The PSF format, however, is not supported yet.


Support Forum / Re: Python script modifiers
« on: March 05, 2018, 03:03:53 PM »
Looks like the manual editing of the HTML page requires some more care. I think I've fixed the problem now. Please try again.

Support Forum / Re: Python script modifiers
« on: March 05, 2018, 01:58:30 PM »
I just realised that you stumbled over an old documentation bug. The last line of the orientation colouring script has been cut off in the user manual. This error has been fixed some time ago in the development version of OVITO, but it is still present in the documentation of OVITO 2.9.0. I now manually added the missing script line to the online version of the scripting manual:

I'm sorry for the confusion.

Support Forum / Re: Python script modifiers
« on: March 01, 2018, 05:49:58 PM »

You don't need the Color Coding modifier. The Python script should directly assign colors to the atoms. Don't you see any colors? Make sure that the "Output - Lattice orientation" option is activated in the PTM modifier. If you still don't see any colors being assigned, please check if the Python script modifier displays any error messages.


Support Forum / Re: segmentation fault
« on: February 28, 2018, 09:27:21 PM »
Hi Emile,

I could not reproduce the segfault under macOS using Ovito 2.8.1. Which operating system do you use? And have you tried newer versions of Ovito already?


Support Forum / Re: how to import_file with specified dump files
« on: February 27, 2018, 09:27:54 AM »
Hi Kevin,

I don't think that this can be done with any of the current program versions. You need to live with the fact that OVITO will read in all the files in the series.

But I like the idea and agree that, in general, this would be a useful feature that would bring additional flexibility. I added a corresponding feature request to the GitLab project and hope to find some time to implement this extension in the future:


Support Forum / Re: Combine Particle Set Modifier issue.
« on: February 22, 2018, 10:01:03 AM »
Thanks for sending the data files. Now it became clear what the issue is.

It turned out that the 'Combine particle sets' modifier in the current Ovito version is still too dumb to combine datasets with different atom types. I worked on the modifier code yesterday to make it smarter. Please download the latest development version of Ovito (3.0.0-dev123), which is able to merge datasets correctly that do not have the same set of particle types:

Let me know if you still experience any problems.


Support Forum / Re: How to make ovito write data file in a modify way
« on: February 21, 2018, 10:11:46 PM »
Just to let you know: The latest development version of OVITO (3.0.0-dev123) lets you set the desired numeric precision for file export.

Support Forum / Re: Combine Particle Set Modifier issue.
« on: February 20, 2018, 03:03:31 PM »
Can you please post the data files with the two atom sets? I would like to reproduce the problem that you are facing. Right now, I still don't understand what you are doing and what is happening. On one hand you write that atom IDs are not correct, on the other hand you talk about chemical types not being as expected. Note that, in Ovito, all particles have two different properties: "Particle Type" and "Particle Identifier", which have nothing to do with each other. The first property describes the chemical type of an atom while the second property is a numeric identifier, which is unique throughout a system. The particle type determines the display color of particles, while the particle identifier is a non-visual property, which is used by Ovito behind the scenes to track particles over time.

My suspicion is that there might be problem with the particle types. Note that Ovito encodes the chemical types using numbers, e.g. Li=1, Ni=2, O=3. if this mapping differs in the two input files, a problem may arise when the datasets are merged into one.

Support Forum / Re: Combine Particle Set Modifier issue.
« on: February 19, 2018, 10:31:34 PM »
I don't understand what you mean with the "labels of the atoms". Do you mean the atom types, the atom IDs, or some other property? Please clarify.

If you mean the atom IDs, please note the following statement from the user manual:

The IDs of particles loaded from the second file are newly assigned by the modifier to ensure that they do not conflict with the existing particle IDs in the current dataset.

This is to ensure the uniqueness of the particle IDs.


Support Forum / Re: how to display dumbbells through W-S defect analysis
« on: February 19, 2018, 04:14:35 PM »
Ok, I took the time today to implement the new output mode and extend the W-S modifier as described above. You can find the extension in the latest development version (dev120).
Note that the user manual hasn't been updated yet, but the scripting documentation already reflects the addition:

Let me know if it works (or not).

Support Forum / Re: How can we get a bond angle distribution in ovito?
« on: February 16, 2018, 04:17:41 PM »
Hi there,

Here is a script I wrote some time ago for Ovito 2.9.0 to calculate the bond-angle distribution for a system (for demonstration purposes). It may serve you as a starting point to develop a solution for your specific problem. Disclaimer: I never used the script for real-word analyses and I never verified that it is working correctly. So use with caution.


I can only guess, but the discrepancy between the results obtained within the GUI and with ovitos are likely due to different modifier settings. In general, when you use a modifier in a script executed with ovitos, its parameters are initialized to hard-coded default values, which are all documented in the Python scripting reference. In contrast to that, when you insert a modifier into the pipeline using the GUI, some its parameters are typically initialized the most-recently used values (Ovito memorizes them in a config file in the user's home directory). Remaining parameter are always initialized to the same hard-coded values as in ovitos.

So please make sure that the WignerSeitzAnalysisModifier.eliminate_cell_deformation setting has been set consistently in the GUI and in the script. Note that, in Ovito 3.0, this parameter has been deprecated and replaced by the ReferenceConfigurationModifier.affine_mapping parameter.

Pages: 1 [2] 3 4 ... 21