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Libra-X program

Due to the increased volume of technical questions about installing and using the Libra, Libra-X, Pyxaid and Pyxaid2 codes, I have decided to create a convenient public forum for all users with the intent:

a) to share my replies with not only a single user that have a trouble, but also other potential users who may found that information useful; b) so that the users/developers who have had some experience with the code would be able to share their knowledge and skills with others;

Among different platforms I found that the Google Group Forum is perhaps the best option. https://groups.google.com/forum/#!forum/quantum-dynamics-hub

So, since Aug. 31, 2017, please post your questions about Libra, Libra-X, Pyxaid, or Pyxaid2 there.

This is only a test practice, I don't know how well it'll go, but lets try it. If you have ideas and suggestions for a better forum platform, please email me.

This file introduces how to execute Libra-X_program

  1. Install Libra and GAMESS on your PC or server. For installation, access the websites below: Libra: http://www.acsu.buffalo.edu/~alexeyak/libra/index.html GAMESS: http://www.msg.ameslab.gov/gamess/

  2. Create a working directory,say, /home/work .

  3. There, create input files(*.inp).(H2O.inp and 23waters.inp in ".../libra-gamess_interface/run" are the simple examples.) For more details about how to create that, please see the website http://www.msg.ameslab.gov/gamess/GAMESS_Manual/input.pdf . Here, Keep in mind 3 things. A. Only semi-empirical methods have been connected to libra so far; set GBASIS=MNDO, AM1, PM3, or RM1 in $BASIS section. B. Set RUNTYP=GRADIENT in $CONTROL section. C. Use cartesian coordinates in $DATA section like this:

    Cn 1

    C 6.000000 4.377921 -4.769170 -2.758971 C 6.000000 3.858116 -4.331728 -3.995136 C 6.000000 2.478331 -4.387937 -4.267327 . . .

    • set blank line between "Cn 1" and 1st coordinate line.

  4. For convinience, copy run_gms.py in ".../libra-gamess_interface/run" to the working place.

  5. Modify copied run_gms.py for calculation. Concretely, set variables for GAMESS, Molecular Dynamics(MD), excited electron dynamics, and debugs. See the input manual in ".../libra-gamess_interface/run" to know more about the variables.

  6. copy elements.txt in ".../libra-gamess_interface/run" to the working directory.

  7. Create "res" and "sd_ham" directories under the working place, where the results will be output.

  8. When the precedures above are finished, it is the time to execute this program. Here, 2 types of execution can be used. A. Only invoke "python run_gms.py" in the working place. B. Use queuing system. submit_templ_gms.lsf or submit_templ_gms.slurm in ".../libra-gamess_interface/run" are the simple examples for using this. Modify the files following your queuing system.

  9. After the calculation finished, the results will be set in "res" directory.