kaist-elst / dftforge.jl Goto Github PK

Easy install of JX.

• Easy install of Julia
• Easy install of JX with DFTforge

Consider a non-Bash shell environment.

Currently, the J(r) output is printed as
Distance,J(r)
=>
Distance,J(r),x,y,z,Rx,Ry,Rz
where [x,y,z] is displacement in angstronm and [Rx,Ry,Rz] is cell vectors in integer numbers ex: (0,0,0), (0,1,0)

Consider data save format from https://github.com/JuliaIO/MAT.jl -> https://github.com/simonster/JLD2.jl .
MAT is good as this could be read from MATLAB, but JLD2 can save Julia Dataformat more natively.

Rename Wannier90type -> Wanniertype as Wannier90 is one of Wannier function option.

0.5, 0.5, -0.1 should be treated as 0.5, 0.5, 0.9.

Though HDF5 is a helpful format, Julia in Linux system asks for libHDF5 install by root privilege (such as apt-get install libhdf5-dev).
Currently, DFTforge only needs HDF5 for MMAP (result export type is replaced MAT ->JLD2).

Julia MMAP can be done without HDF5, so removing HDF5 dependency may help user for easier install (HPC cluster account without root privilege is very common situation).

MMAP Julia Reference
https://docs.julialang.org/en/v1/stdlib/Mmap/index.html

This issue is used to trigger TagBot; feel free to unsubscribe.

If you haven't already, you should update your TagBot.yml to include issue comment triggers.
Please see this post on Discourse for instructions and more details.

If you'd like for me to do this for you, comment TagBot fix on this issue.
I'll open a PR within a few hours, please be patient!

Let's support Hamiltonian results from DMFT with OpenMX @jhsim4279 .

When the eigenvalue of the overlap matrix (S) value is very small (like 1.0E-8), the small value of S should be handled very carefully.

Previously, it was based on OpenMX, VASP but filename convention according to spin, up down may differ from Wien2K.
Input toml should be more flexible.

Be sure to at least notify that the user needs to update it.
An automatic update would be great, but It would need some engineering.

When alat is not 1.88973 (Bohr radius) position is incorrectly read.
The scaling of pos by alat is required.

Currently, input argument takes

3_1,3_2,3_3 --baseatom 3

that means, from atom number 3 is center and obtain J for between 3 and [1,2,3].
So we may simplify as

1,2,3 --baseatom 3

Waiting for JuliaIO/HDF5.jl#512 to be fixed.

https://julialang.org/blog/2018/08/one-point-zero

For EcalJ PostCommon, the orbital rotation was not implemented.

Merge [77b6020] branch into master?

Remove unnecessary outputs from all codes.

Explain the meaning of the orbital index in examples.

For an exmaple,

<Definition.of.Atomic.Species
Ni     Ni6.0S-s2p2d2f1  Ni_PBE13S

s2p2d2f1 represent 2 s orbitals, 2 p orbitals, 2 d orbitals, and 1 f orbital.
In this case, orbital index will be

1: s1
2: s2

px,py,pz
3,4,5: p1 
6,7,8: p2 

dz2,dx2y2,dxy,dyz,dxz
9,10,11,12,13: d1 
14,15,16,17,18: d2

19,20,21,22,23,24,25: f1

As the registered TOML Pkg is Old.
This https://github.com/wildart/TOML.jl/ works good but not registered project.
Therefore import TOML is not simple. User have to execute such as

julia>
import Pkg
Pkg.add("https://github.com/wildart/TOML.jl/")

, which is not favourable.

So make an ext folder and will clone it.