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Topics - jatink

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1
Support Forum / Updating Molecule IDs in Replicate Copies
« on: November 16, 2018, 12:40:32 AM »
Hello All,

I have one question, please pardon me if I am missing anything. Let's say I have a system in which I have 10 atoms in which first five atoms had molecule ID 1 and next five has molecule ID as 2. And now if I replicate 1 copy in any direction, then why it doesn't assign updated molecule IDs to the newly generated atoms as it does for atom IDs i.e. new 10 atoms still have molecule IDs as 1 and 2 instead of 3 and 4.

Thanks a lot for your time.

2
Support Forum / Not Able to Print a Variable While Looping Over Frames
« on: October 06, 2018, 01:09:24 AM »
Dear All,

I'm trying to find out maximum Z coordinate in my dump file and then print it which I ultimatly want to write to a text file. I'm following snippets given at "https://ovito.org/manual/python/modules/ovito_io.html" for looping over multiple frames which looks likes below:

import ovito
print("Hello, this is OVITO %i.%i.%i" % ovito.version)

from ovito.io import *

node = import_file("/Users/kashyap/Google_Drive/NJIT/graphene_h2o/redo/angle_6/variable_gap/1_h2o/main/stress/dry/200000/dump_*.cfg")
frames = node.source.num_frames
print("The total number of dump frames are:",frames)

for frame in range(node.source.num_frames):
   node.compute(frame)
   coordinates = node.output.particle_properties.position.array
   zl = max(coordinates[:,2])
   print("The highest z-coordinate in reference frame is:",zl)



But all it's printing is the variable value only processed for the first frame for number of times equal to number of frames in that directory as below:

Hello, this is OVITO 3.0.0
The total number of dump frames are: 11
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664
The highest z-coordinate in reference frame is: 17.81900825664


Can anybody please help me to understand why the new dump files are not being loaded instead it's just repeating the variable value evaluated for first frame.
Thank you.


3
Support Forum / Loading the dump file error in python script
« on: September 25, 2018, 11:48:13 PM »
Dear OVITO Users,

I'm new to python scripting in OVITO. And I'm banging my head just to solve a simple begining step problem. How to load the file? Can anybody please help me to solve it. It looks like the solution is very simple but I'm constantly missing it while reading this webpage "https://ovito.org/manual/python/introduction/overview.html#loading-data-and-applying-modifiers" Anyhelp to locate the answer will be much appreciated.

This is my sample script:

from ovito.io import *
node = import_file("dump.mix")

from ovito.modifiers import *
node.modifiers.append(SelectExpressionModifier(expression="PotentialEnergy<-3.9"))
node.modifiers.append(DeleteSelectedParticlesModifier())

export_file(node, "outputdata.dump", "lammps_dump", columns = ["Position.X", "Position.Y", "Position.Z", "Structure Type"])


And this is script output:

The Python script has exited with an error.
Traceback (most recent call last):
  File "<string>", line 2, in <module>
  File "/Applications/Ovito.app/Contents/MacOS/../Resources/python/ovito/io/import_file.py", line 121, in import_file
    importer = FileImporter.autodetect_format(ovito.dataset, first_location)
RuntimeError: File does not exist:
dump.mix

4
Support Forum / Calculating the velocity of a, or group of atoms.
« on: September 14, 2018, 12:22:44 AM »
Hello,

I want to calculate the x-velocity of a particle between two given frames. I'm following this doc "https://www.ovito.org/manual_testing/particles.modifiers.compute_property.html" but I'm unable to help my self to find out the definition of all "Available input variables" given on the right side of the webpage so that I can make expression of velocity. Can anybody please give me the corresponding page or any short similar example to calculate the velocity of a group or single particle.

Thanks a lot!

5
Support Forum / Shifting the System Along an Axis
« on: September 10, 2018, 05:57:17 PM »
Hello,

Can anybody please tell me, is there a feature in OVITO by which we can shift the system along a axis so that we can see a feature in the system in it's center instead of watching it half split at one corner and wrapping around at the other corner. I'm attaching the screenshot of my system which is showing a wrinkle in graphene sheet at its corner which I want to see in the center of the system.

Thank you.

6
Support Forum / Unable to create animation
« on: September 23, 2017, 02:16:36 AM »
Hello OVITOians,

I'm having around 10 CFG files that I dumped from LAMMPS. I'm using macSierra. I'm using this webpage "https://ovito.org/manual/usage.rendering.html" to create movie out of given CFG files it says "QuickTime Player can't open “movie.avi”." Is their any hint whats going around in here. This issue is giving me hard time.

Thank a lot for your time.

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