Sorry, I am a bit confused. Does JDFTx enable ab-initio molecular dynamics?
Although in the website I saw JDFTx can use Atomic Simulation Environment developed for phonons and ab-initio molecular dynamics, I didn't see ab-initio molecular dynamics related parameters in Command documentation.
Thanks a lot,
Jovis Yang
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The ASE interface is distinct from the main JDFTx code. The command documentation is only for the commands directly accessible in an input file to JDFTx. MD through the ASE interface works by having JDFTx calculate forces at fixed atomic positions, so you will needto lookup the documentation for that within ASE. Maybe Deniz can post an example of MD using ASE?
We also have recently built MD directly into JDFTx, and we will update the online command documentation to reflect this soon. Meanwhile, you can see the documentation of commands ion-vel and ionic-dynamics in the output of "jdftx -t". Yalcin, can you post an example of using the in-built MD?
Best,
Shankar
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jdftx supports ab-initio molecular dynamics in two different ways: You can either use ASE as your integrator and just use jdftx as your force and enegy calculator. Or alternatively you can use the internal verlet implementation. ASE supports a much wider range of features, but the internal implementation is likely more efficient.
As for the internal implementation, Yalcin's the one who knows it the best. He is busy for the next week or so, but I'm sure he'll get back after that.
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The page you point to does not have the commands from the most recent svn revision. We are halfway through transitioning the documentation system and website, so that version of the page is out of date.
You can access the most recent command documentation by downloading and compiling the code, and then either using "make doc" to generate HTML documentation using doxygen, or running "jdftx -t" which will output the command documentation on the shell. (You can do something like "jdftx -t > ref.txt" to save that output to a file.)
Shankar
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Sorry, I am a bit confused. Does JDFTx enable ab-initio molecular dynamics?
Although in the website I saw JDFTx can use Atomic Simulation Environment developed for phonons and ab-initio molecular dynamics, I didn't see ab-initio molecular dynamics related parameters in Command documentation.
Thanks a lot,
Jovis Yang
The ASE interface is distinct from the main JDFTx code. The command documentation is only for the commands directly accessible in an input file to JDFTx. MD through the ASE interface works by having JDFTx calculate forces at fixed atomic positions, so you will needto lookup the documentation for that within ASE. Maybe Deniz can post an example of MD using ASE?
We also have recently built MD directly into JDFTx, and we will update the online command documentation to reflect this soon. Meanwhile, you can see the documentation of commands ion-vel and ionic-dynamics in the output of "jdftx -t". Yalcin, can you post an example of using the in-built MD?
Best,
Shankar
Hello Chi-Ta,
jdftx supports ab-initio molecular dynamics in two different ways: You can either use ASE as your integrator and just use jdftx as your force and enegy calculator. Or alternatively you can use the internal verlet implementation. ASE supports a much wider range of features, but the internal implementation is likely more efficient.
For setting up the ASE interface with jdftx, you can read: https://sourceforge.net/p/jdftx/wiki/ASE%20Interface/
And for performing molecular dynamics with ASE, there is a wide range of documentation available at the ASE website (for example: https://wiki.fysik.dtu.dk/ase/tutorials/md/md.html , simply replace the EMT() calculator with JDFTx )
As for the internal implementation, Yalcin's the one who knows it the best. He is busy for the next week or so, but I'm sure he'll get back after that.
Shankar and Deniz ,thank you lot for your helps !!!
BTW, Shankar...
"you can see the documentation of commands ion-vel and ionic-dynamics in the output of "jdftx -t" "
do you mean http://svn.code.sf.net/p/jdftx/code/trunk/jdftx/commands/man.html ?
Thanks a lot,
Chi-Ta
Hi Chi-Ta,
The page you point to does not have the commands from the most recent svn revision. We are halfway through transitioning the documentation system and website, so that version of the page is out of date.
You can access the most recent command documentation by downloading and compiling the code, and then either using "make doc" to generate HTML documentation using doxygen, or running "jdftx -t" which will output the command documentation on the shell. (You can do something like "jdftx -t > ref.txt" to save that output to a file.)
Shankar
Thank you a lot Shankar ~