The official repo is now github.com/MaterialDesigner/JorG.

JorGπ (Georgie Pie) is an automatic scheme of mapping an ab-initio system (so far using VASP) onto the Heisenberg model.

Workflow

1. Find a ground state of your magnetic structure.
2. Run JorGpi-startup
   • You can check the options using JorGpi-startup --help.
   • We suggest that for complicated structures you do not use the minimal-set mode.
   • Note that ICHARG=1 will be added to all generated INCARS.
3. Run the calculations using your version of VASP.
   1. We recommend running the noFlip cell (enlarged cell provided in the previous step) and save the resultant CHGCAR file.
   2. Next use our tool JorGpi-demagnetize to extract the non-magnetic part of CHGCAR.
   3. Copy the file obtained above to the directories with the flipped states. With ICHARG=1 and no magnetic terms in CHGCAR VASP will use the charge-density with magnetic moments obtained from MAGMOM line.
   • The above is not necessary , yet it seems to speed-up the convergence.
   • It is also recommended to save your CHGCAR files as the excited magnetic states (flipped) might take significantly more electronic steps to converge.
4. Run JorGpi-pickup
   • You can check the options using JorGpi-pickup --help.
   • We suggest to check the flipped states for convergence.
   • The solver either solves the system of equations (if a minimal set of excided states is provided) or finds an optimal fit to the model using the least-squares method (thus canceling out the numerical error).

General Scheme of JorG workflow

Options

JorGpi-startup

 JorGpi-startup --help
usage: JorGpi-startup [-h] [--input INPUT] [--incar INCAR] [--output OUTPUT]
                      [--cutOff CUTOFF | --neighbor NEIGHBOR] [--Wyckoffs WYCKOFFS]
                      [--reference REFERENCE] [--elements ELEMENTS]
                      [--group {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18} [{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18} ...]]
                      [--period {2p,3p,4p,5p,6p,3d,4d,5d,4f,5f} [{2p,3p,4p,5p,6p,3d,4d,5d,4f,5f} ...]]
                      [--block {P,D,F} [{P,D,F} ...]] [--minimal-set] [--buffer-cases BUFFER_CASES]
                      [--extra-dimentions EXTRA-DIMENTIONS] [--carthesian-output] [--symmetry]
                      [--refined]

Find minimal number of unique spin-flips

optional arguments:
  -h, --help            show this help message and exit
  --input INPUT, -i INPUT
                        input POSCAR file
  --incar INCAR, --INCAR INCAR, -I INCAR
                        input INCAR file
  --output OUTPUT, -o OUTPUT
                        output directory
  --cutOff CUTOFF, -R CUTOFF
                        a cut-off distance (in Å) for calculations
  --neighbor NEIGHBOR, -N NEIGHBOR
                        a rank of the last Neighbor taken into account
  --Wyckoffs WYCKOFFS, -W WYCKOFFS
                        narrows down the atomic selection to the atoms in positions defined by string
                        (eg. 'abc')
  --reference REFERENCE, -r REFERENCE
                        number of reference atom in inputFile
  --elements ELEMENTS, -E ELEMENTS
                        string of all elements taken into account (eg. 'CuO')
  --group {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18} [{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18} ...]
                        group number (eg. 1 <=> 'HLiNaKRbCsFr')
  --period {2p,3p,4p,5p,6p,3d,4d,5d,4f,5f} [{2p,3p,4p,5p,6p,3d,4d,5d,4f,5f} ...]
                        period name (eg. 3d <=> '$Sc$Ti$V$Cr$Mn$Fe$Co$Ni$Cu$Zn$')
  --block {P,D,F} [{P,D,F} ...]
                        block name (eg. P <=>
                        '$B$C$N$O$F$Al$Si$P$S$Cl$Ga$Ge$As$Se$Br$In$Sn$Sb$Te$I$Tl$Pb$Bi$Po$At$')
  --minimal-set         creates a minimal-set system of equations for final calculation of the
                        Heisenberg exchange interaction (default False)
  --buffer-cases BUFFER_CASES, -B BUFFER_CASES
                        The number of additional solutions of the Ising model (above the twice the
                        number of exchange interacions, (i.e., the ASA solver finds 2*J+B excited
                        states (default 4)
  --extra-dimentions EXTRA-DIMENTIONS, -X EXTRA-DIMENTIONS
                        string "X Y Z" of extra cell copies in each directions (eg. "0 0 1")
  --carthesian-output   Sets output cells to carthesian coordinates (default False, i.e., using direct
  --symmetry, -S        symmetry run only (default False)
  --refined             should use refined supercell (default False)

New in version 0.3.0

  --nmpi NUM_MPI_PROC
                        Enable the Ising model solver to run in parallel using
                        the given number of MPI processes
  --mpicompiler MPI_COMPILER
                        MPI compiler to use if nmpi > 0.  Supported compilers:
                        mpicxx, mpiCC, mpic++. By default, set to the MPI compiler
                        saved in the CC or CXX environment variable, or to mpicxx

JorGpi-pickup

usage: JorGpi-pickup [-h] [--number-of-interactions #J] --reference dir
                     [--units {eV,meV,Ry,mRy,He,mHe,K}] --elements symbol [symbol ...] --directories
                     dir [dir ...]

Finding Js

optional arguments:
  -h, --help            show this help message and exit
  --number-of-interactions #J, -J #J
                        number of exchange-interaction magnitudes to-be-included in calculations
  --reference dir, --noFlip dir, -R dir
                        reference directory (usually noFlip/)
  --units {eV,meV,Ry,mRy,He,mHe,K}, -U {eV,meV,Ry,mRy,He,mHe,K}
                        units of energy
  --elements symbol [symbol ...], --atoms symbol [symbol ...], -E symbol [symbol ...]
                        Symbol of elements taken into account in calculations
  --directories dir [dir ...], -D dir [dir ...]
                        Directories containing flipped configurations (eg. flip00000/)

Additional utilities

JorGpi-demagnetize

An awk-based tool for removing the information on the magnetization from the CHGCAR. Redirect standart output if you want to save the result (JorGpi-demagnetize > newCHGCAR or JorGpi-demagnetize PATH_TO_CHAGCAR > newCHGCAR)!

JorGpi-KPOINTS

A tool usefull for the non-diagonal cells -> provides with the propositions on the reciprocal space mesh. Use JorGpi-KPOINTS POSCAR1 POSCAR2 ...

JorGpi-POSCAR

A POSCAR unit converter

Options

usage: JorGpi-POSCAR [-h] [--convert-to {d,c,k,D,C,K,Direct,Carthesian}] --files POSCAR_file
                     [POSCAR_file ...]

Converting POSCAR files

optional arguments:
  -h, --help            show this help message and exit
  --convert-to {d,c,k,D,C,K,Direct,Carthesian}, -T {d,c,k,D,C,K,Direct,Carthesian}
                        Convertion To
  --files POSCAR_file [POSCAR_file ...], -F POSCAR_file [POSCAR_file ...]
                        POSCAR files to convert

Exemplary flips

by A.P. Kądzielawa using Jmol: an open-source Java viewer for chemical structures in 3D. www.jmol.org

_{^{This work was supported by The Ministry of Education, Youth and Sports from the Large Infrastructures for Research, Experimental Development and Innovations project IT4Innovations National Supercomputing Center – LM2015070.}}