mirror of https://gitlab.com/scemama/eplf
104 lines
3.1 KiB
Org Mode
104 lines
3.1 KiB
Org Mode
#+TITLE: EPLF
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#+AUTHOR: Anthony Scemama
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#+EMAIL: scemama@irsamc.ups-tlse.fr
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#+date: 2020-06-02
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Computes the Electron Pair Localization Function.
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* Dependencies
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- Python3
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- resultsFile : https://gitlab.com/scemama/resultsFile
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- IRPF90 : http://irpf90.ups-tlse.fr
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- GFortran or Intel Fortran =resultsFile= and =IRPF90= can both be installed with pip.
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#+begin_src shell
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python3 -m pip install resultsFile
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python3 -m pip install irpf90
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#+end_src =./configure= should detect suitable defaults for your system. You can
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update the =make.config= file if you want. It is important to give the
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Fortran compiler the option to accept infinitely long lines (with
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gfortran, the option is =-ffree-line-length-none=).
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The =configure= script will also create a file =$HOME/.eplfrc= that you
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will need to source before running the program.
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* Using EPLF
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GAMESS or Gaussian can be used to produce the wave function.
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With Gaussian, the following keywords are required:
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#+begin_example
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# GFPRINT pop=Full 6d 10f
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#+end_example
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Go into the =test= directory and execute the following commands to make
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a test run with an Gaussian output file.
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1. Run the =to_ezfio.py= script to convert the output file into an
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EZFIO directory containing all the data required for the
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computation:
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#+begin_src shell
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to_ezfio.py c2h.out
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#+end_src
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The =c2h.out.ezfio= directory is produced.
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2. Edit the parameters by running =eplf_edit.py=
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#+begin_src shell
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eplf_edit.py c2h.out.ezfio
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#+end_src
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The editor defined with the =$EDITOR= environment variable will open
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and let you change the parameters. To compute the density and the
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EPLF, just add an =X= character between the brackets next to =eplf=
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and =density=:
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#+begin_example
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( ) density -> (X) density
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( ) eplf -> (X) eplf
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#+end_example
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3. Run the program to compute the data and save it in the EZFIO directory
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#+begin_src shell
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eplf c2h.out.ezfio
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#+end_src
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If the program is compiled with MPI, run
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#+begin_src shell
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mpirun eplf c2h.out.ezfio
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#+end_src
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4. Now you can convert the data into cube files as:
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#+begin_src shell
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to_cube.py c2h.out.ezfio density
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to_cube.py c2h.out.ezfio eplf
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#+end_src
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The parameters of the grid can be changed by first clearing the
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data, and the updating the grid parameters. This can be done with =eplf_edit.py= by un-commenting the lines =clear(all)=
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and =edit(grid_parameters)=.
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* References
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Scemama, A., Chaquin, P., Caffarel, M. (2004).
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"Electron pair localization function: A practical tool to visualize electron
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localization in molecules from quantum Monte Carlo data". /J. Chem. Phys./ *121* (4), 1725–1735.
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[[https://dx.doi.org/10.1063/1.1765098][doi:10.1063/1.1765098]]
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Scemama, A., Caffarel, M., Chaudret, R., & Piquemal, J.-P. (2011),
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"Electron Pair Localization Function (EPLF) for Density Functional
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Theory and ab Initio Wave Function-Based Methods: A New Tool for
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Chemical Interpretation". /J. Chem. Theory Comput./ *7* (3), 618–624.
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[[https://dx.doi.org/10.1021/ct1005938][doi:10.1021/ct1005938]]
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