shunsunsun / simupkgs Goto Github PK

[UPDATE] at 2020/12/26: A basic Hartree-fock program that transcode from FORTRAN code written by Szabo is uploaded, for further generalization, I divide whole program into several subroutines:
A_Szabo_RHF_HeH.py: main program that contains initialization of integrals, and SCF procedure
hf_propagation.py: subroutine that has been partially generalized can be used to solve other HF equations
diag_numpy.py: subroutine that has been fully generalized can be used to perform diagonalization and rearrange transforming matrix and matrix diagonalized
basisReadIn.py: subroutine that read external basis-contained files, format required is shown in basis.dat file
GauInteLib.py: subroutine that can calculate s-orbital integrals, has not bebn generalized yet

several simple optimizers will come soon.

[UPDATE] at 2020/12/24:
A basic framework of Hartree-Fock method is added into directory. Modules support function-integration, more specificly, one-electron integrator, two-, three and four will be coded and upload. For I am busy recently so this will be a long process.
Also there seem some module that I just code them in several month ago but failed to upload them.

[UPDATE] at 2020/12:
Two cp2k scripts are uploaded, alter.sh and grep.sh, for performing cutoff convergence tests on supercomputer where batch subscribing is not allowed or, not a good choice. To use alter.sh, you need to delete all space in front of parameters CUTOFF, REL_CUTOFF, R_CUTOFF and KPOINTS. An input script named cutofftest.inp should be placed in the same directory in advance or, you can modify these two shell whatever you want.
These two auxillary shell will not be incorperated into main.py of SIMUPKGS.

[UPDATE] at 2020/6:
SIMUPKGS is a integrated module that contains some basic functions such as:

1. supercell duplication
2. free energy calculation of isolated molecule (based on frequencies result yiedled by other software, but I will add frequency calculation into my package in the future)
3. finite cell x-ray diffraction simulation
4. q4-order parameter analysis

To run this package, you only need to open main.py and run it. Note: numpy, matplotlib package are needed, please install them in advance:

1. pip install numpy (for most modules)
2. pip install matplotlib (for XRD related modules)
3. pip install pandas (for absToolkit)

There is also another way to use this package, if you have understood how this package works, you can run all subroutine of it, for instance, pp_smooth.py provides easy-to-use smmoth function to smooth any 1 or 2 dimensional graphs, so you can directy import this module in you OWN program.

As this package is just I write in my spare time (yes this is only one of my hobbies), update may be somehow slow, so if you are not satisfied with it you can also have contribution in this package, it is welcome, certainly!

Footnote: calculation of distance matrix has just been implemented, so the next function that will come soon is dynamics simulation based on classical mechanics. I also have plan to write static calculation based on quantum mechanics, but maybe large amount of time is required.