project	author	email
ecalj README at https://github.com/tkotani/ecalj	takao kotani	takaokotani@gmail.com

LICENCE: AGPLv3

ecalj: a suite of first-principles elecronic structure calculations

What can we do in ecalj package? (on github)

1. All electron full-potential PMT method

   Here the PMT method means; a mixed basis method of two kinds of augmented waves, that is, APW+MTO. In other words, the PMT method= the linearized (APW+MTO) method, which is unique except the Questaal having the same origin with ecalj. Our recent research shows that very localized MTOs (damping factor exp(-kappa r) where kappa \sim 1 a.u), together with APW (cutoff is \approx 3 Ry) works well to get reasonable convergences. We can perform atomic-position rexalxation at GGA/LDA level. Because of including APWs, we can describe the scattering states very well.

   The current PMT formulation is given in

   [1]KotaniKinoAkai2015, PMT formalism
   [2]KotaniKino2013, PMT applied to diatomic molecules.

   Since we have automatic settings for basis set paremeters, we don't need to be bothered with the parameter settings. Just crystal structure (cif,POSCAR) are needed for calculation. (In 2022, we implemented a command, job_mp, to perform automatic calculations only from the id of material project. job_mp seems working well, although we need some further developments.)

   In principle, it is possible to perform reasonable calculations just from crystal structures and very minimum setting. We have documents included about how to confirm calculations to be publicaiton quality. (but someghing still in progress..)

2. the PMT-QSGW method

   The PMT-QSGW means the Quasiparticle self-consistent GW method (QSGW) based on the PMT method. We can perform QSGW with litte settings by hand (for nonmag case, virtually no settings by hand). After converged, we can easily make band plots of the QSGW calculaiton without the Wanneir interpolation. This is because an interpolation scheme of self-energy is internally built in. We can handle even metals, Fermi surface as well. This may be an unique feature differenciate ecalj GW from those implemeneted in other packages.

   Paralellization is minimum and we now working on it on GPU. Roughly speaking, our current PMT-QSGW is applicable upto ~16 atoms a cell (light atoms are easier to handle) for research purpose.

   [3]Kotani2014,Formulation of PMT-QSGW method

   [4]PMT-QSGW applied to a variety of insulators

3. The Model Hamiltonian with Wannier functions

   We can generate the effective model (Maxloc Wannier and effective interaction between Wannier funcitons). This is originally from codes by Dr.Miyake, Dr.Sakuma, and Dr.Kino. The cRPA given by Juelich group is implemented. We are now replacing this with a new version MLO (Muffin-Tin-orbail-based localized orbital).

4. Dielectric functions and magnetic susceptibilities

   We can calculate GW-related quantities such as dielectric functions, spectrum function of the Green's functions and so on (some of functions are obsolate. Need fixing).Magnetic fluctuation and so on are implemented but not documented well (ask us). See papers by TK.

5. Utilitys are included

   For example, a converter between POSCAR(VASP) and our crystal strucrue file 'ctrls.*' are included. A command job_mp [num of cores] [mp id] access to material project to get crystal structure, and perform LDA/GGA calculaitons, showing DOS and BAND automatically. As it is combined with seekpath and spglib, Brillowin Zone and symmetry lines are automatically drawn with matplotlib (we need minor fixing...).

Install and automatic test

After we get package from github, together with some standard tools, we do execute an automatic installer and test system. This is just by a command. Tests are for Linux with gfortran and ifort. See README_Install.org.

Manuals, Documents, Samples for ecalj

We have manuals and presentations of ecalj at .Document/. Especially, ecaljmanual.pdf is the main manual. Read "LDA/GGA calculations and Plots" at first (but some part become obsolate---I have to revise) QSGW calculations can be performed easily after you learend the procedure. Band plot and so on are in the same manner of the LDA calculations, althogh QSGW is computationally expensive (roughly 100~1000 times expensive. We ara going to use GPU now.).

It is instractive to reproduce samples in ./Document/PAPERandPRESENTATION/deguchi2016.pdf. We can set up templates for your calculations. Ask us.

• How to perform paper quality calculations with minimum costs? See ./README_hints.org
• Usage minimum. QSGW for Si See Section.4. of ./Document/Manual/ecaljmanual.pdf.

Very minimum to run ecalj

In Japanese, see a page by Dr.Gomi at http://gomisai.blog75.fc2.com/blog-entry-675.html (and others. Use search engine.)

1. write structure file ctrls.si by hand (you can generate ctrls from POSCAR(VASP) with vasp2ctrl in ecalj/StructureTool/, thus cif --> POSCAR ---> ctrls is also possible.)

2. conver ctrls.si to ctrl.si by ctrlgenM1.py si (without argument, it gives a help). Then you have default ctrl.si (rename ctrlgenM1.ctr.si to ctrl.si). Edit number of k points, spin (nsp=0 or 1) and so on if necessary.

3. Run "lmfa si" to prepare atoms (very quick).Then run 'mpirun -np 4 lmf-MPIK si'. This generates rst.si, which contains self-consistent density in LDA. Postprocessing for energy bands are job_band si, job_tdos, job_pdos are also available. For job_band, you need symmetry line file syml.si, which can be generated at the method implemented in GetSyml/

NOTE: If you like to skip steps (1)-(3), run ./job_materials.py Si at ./MATERIALS/. Then

>cd Si
>cp ../syml.si
>job_band si

This shows energy bands in LDA in gnuplot. To generate syml.si, we can use ecalj/GetSyml/getsyml.py. When it is correctly installed (see below),

>getsyml si

should generate a syml.si from ctrl.si. You can edit it and run job_band.

4. For PMT-QSGW, make GWinput.tmp by mkGWIN_v2 si. Copy GWinput.tmp as GWinput.

5. Then run a script gwsc, e.g. "gwsc 2 si -np 3" (2+1 iteration with 3 nodes).

6. To continue calculation do "gwsc 5 si -np 3" again. To start, you need ctrl.si rst.si QGpsi sigm.si. Latest gwsc is given in python3 (adopted from that by Dr.suzuki)

7. For band, dos, and pdos plot, we have scripts which almost automatically makes these plot in gnuplot. Thus easy to modify these plots at your desposal. For example, job_band is for band plot. But symmetry line path file syml.si is required. The syml can be generated by getsyml.py, which also visualise the pathes in the BZ.

Memo for StructureTool/ and Getsyml/

In any calculations, we first need to supply crystal structure correctly. In the case of ecalj, we write it ctrls.*. All calculaitons can be performed from it.

For this purpose, we have converters between POSCAR (VASP's crystal structure file, Cartesian setting is needed; 'conversion bug for Fractional aug2019') and ctrls.*(that for ecalj). In addition, we have a simple script to invoke crystal strucrure viewer, usually VESTA. It is in [[file:StructureTool/README.txt][StructureTool/]].

Furthermore, we have a tool to generate BZ and symmetry lines on it for band plot in ./GetSyml/ The symmetry line is written into syml.* and used for the band plot mode, job_band. The BZ and the lines are visualized.

Install the viever at StructureTool/

---

Here we use VESTA at http://jp-minerals.org/vesta/. Download it, and expand it to a directory. VESTA can handle kinds of format of crystal structure.

Then make a softlike by

ln -s ~/ecalj/StructureTool/viewvesta.py ~/bin/viewvesta
ln -s ~/ecalj/StructureTool/ctrl2vasp.py ~/bin/ctrl2vasp
ln -s ~/ecalj/StructureTool/vasp2ctrl.py ~/bin/vasp2ctrl

With this procedure we can run command viewvesta, ctrl2vasp, vasp2ctrl from console as long as you have ~/bin/ in the command search path. In my case, .bashrc have a line export PATH=$HOME/bin:$HOME/VESTA-x86_64:$PATH

It depends on your machine. (after editing .bashrc, you have to do "source ~/.bashrc" to reflect changes).

Set the variable of VESTA=, at the begining of ~/ecalj/StructureTool/viewvesta.py to let it know where is VESTA.

Symmetry line finder at GetSyml/

---

This is to generate symmetry lines. syml.* from ctrl.* in ecalj/GetSyml/ In the directory, we have getsyml.py, which is based on the seekpath https://github.com/giovannipizzi/seekpath/ and spglib. See Lincence.txt in it. Folllowing citations are required. 1.Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Band structure diagram paths based on crystallography, Comp. Mat. Sci. 128, 140 (2017) 2.You should also cite spglib that is an essential library used in the implementation.

How to do version up? minimum for git

Be careful to do version up. It may cause another problem. But it is not so difficult to move it back to original version if you have knowledge of git. An important things is keeping your changes by yourself.

cd ecalj
git log
This shows what version you use now.

git diff > gitdiff_backup
This is to save your changes added to the original (to a file git_diff_backup ) for safe. I recommend you do take git diff >foobar as backup.
git stash also move your changes to stash.

git checkout -f
CAUTION!!!: this delete your changes in ecalj/. This recover files controlled by git to the original which was just downloaded.

git pull
This takes all new changes.

I think it is recommended to use

gitk --all

and read this document. Difference can be easily taken, e.g. by

git diff d2281:README 81d27:README (here d2281 and 81d27 are several digits of the begining of its version id).

git show 81d27:README

is also useful.

Licence

• AGPLv3

• For publications, we hope to make a citation cleary to this homepage such as;

  [foobar] ecalj package available from https://github.com/tkotani/ecalj/.