NiO (OpenMX full Hamiltonian) example
This is the NiO with OpenMX example. After the electronic structure is given, the MFT calculation procedures consist of two processes process of calculating J(q) and converting J(q) to J(R).
The required files for Jx MFT calculation (with OpenMX)
These files are provided in the following example script.
Automated script
Run following script:
./example_NiO_OpenMX.sh
- It will automatically unzip pre calculated OpenMX Hamilton file
NiO.scfoutand Jx inputnio_J_openmx.tomlatexamples/NiO_G-AFM.OpenMx/. - Then, Jx will perform J(q) calculation (The most time-consuming part. Roughly 5-10 min depending on CPU).
- After J(q) calculation done, the J(q) -> J(R) transformation will run.
J(q) calculation
julia -p 4 src/Jx_col_spin_exchange.jl -T examples/NiO_G-AFM.OpenMx/nio_J_openmx.toml
This is the main MFT procedure.
This is the most time-consuming part.
The output path is jx2.col.spin_0.0 and inside the output path two files jx2.col.spin_nio_atomij_1_1_[all_all]_ChemPdelta_0.0.jld2,jx2.col.spin_nio_atomij_1_2_[all_all]_ChemPdelta_0.0.jld2 will be generated.
The parallel option can be given by
-p #of cpu coreor--machine-file #PBS_NODES. See Julia parallel computing for detailed options.
J(q)->J(R) transformation
julia src/Jx_postprocess.jl --cellvectors 2_2_2 --baseatom1 1 --atom2 1,2 --orbital_name all_all examples/NiO_G-AFM.OpenMx/jx2.col.spin_0.0
For MFT with Wannier Hamiltonians, the output path is jx2.col.spin_0.0.
The output files are jx2.col.spin.wannier_nio_atomij_1_1_[all_all]_ChemPdelta_0.0.csv
jx2.col.spin.wannier_nio_atomij_1_2_[all_all]_ChemPdelta_0.0.csv and the ploted image Jplot_1_1,2_all_all.pdf.
Note that the raw sign of the MFT results contains information about whether a system likes or dislikes the current spin order. So, at the second nearest (4.18 Å) between 1-2 spins, +8.5 meV means that current antiferromagnetic ordering is preferred.
DFTforge Version 1.3.4
Jx_postprocess started (julia Jx_postprocess.jl --help for inputs)
================ User input =============
cellvectors => 2_2_2
baseatom1 => 1
root_dir => jx2.col.spin_0.0
orbital_name => all_all
atom2 => 1,2
================ Selected result *.jld2 files =============
jx2.col.spin_0.0/jx2.col.spin_nio_atomij_1_1_[all_all]_ChemPdelta_0.0.jld2
jx2.col.spin_0.0/jx2.col.spin_nio_atomij_1_2_[all_all]_ChemPdelta_0.0.jld2
================ Selected result *.jld2 files =============
[0.0 0.0 0.0; 4.1799999990685945 4.1799999990685945 4.1799999990685945; 2.0899999995342973 2.0899999995342973 2.0899999995342973; 6.269999998602892 6.269999998602892 6.269999998602892]
(1, 2)atom_(i, j):(1, 2) global_xyz:([0.0, 0.0, 0.0] [4.1799999990685945, 4.1799999990685945, 4.1799999990685945])
(1, 1)atom_(i, j):(1, 1) global_xyz:([0.0, 0.0, 0.0] [0.0, 0.0, 0.0])
================ Writing CSV & Plotfile =============
2 2
Writing CSV:jx2.col.spin_nio_atomij_1_2_[all_all]_ChemPdelta_0.0__1.csv
12×10 DataFrame
Row │ Distance JmeV Atom1 Atom2 Rx Ry Rz Dx Dy Dz
│ Float64 Float64 Int64 Int64 Int64 Int64 Int64 Float64 Float64 Float64
─────┼─────────────────────────────────────────────────────────────────────────────────────────────
1 │ 2.95571 -0.238341 1 2 -1 -1 0 -2.09 -2.09 0.0
2 │ 2.95571 -0.238341 1 2 -1 0 -1 -2.09 0.0 -2.09
3 │ 2.95571 -0.238341 1 2 0 -1 -1 0.0 -2.09 -2.09
4 │ 2.95571 -0.238341 1 2 -1 0 0 0.0 2.09 2.09
5 │ 2.95571 -0.238341 1 2 0 -1 0 2.09 0.0 2.09
6 │ 2.95571 -0.238341 1 2 0 0 -1 2.09 2.09 0.0
7 │ 4.18 8.54461 1 2 -2 0 0 -4.18 0.0 0.0
8 │ 4.18 8.5446 1 2 -1 -1 1 8.88178e-16 8.88178e-16 4.18
9 │ 4.18 8.54461 1 2 -1 1 -1 0.0 4.18 0.0
10 │ 4.18 8.54461 1 2 0 -2 0 0.0 -4.18 0.0
11 │ 4.18 8.5446 1 2 0 0 -2 0.0 0.0 -4.18
12 │ 4.18 8.54461 1 2 1 -1 -1 4.18 0.0 0.0
Writing CSV:jx2.col.spin_nio_atomij_1_1_[all_all]_ChemPdelta_0.0.csv
12×10 DataFrame
Row │ Distance JmeV Atom1 Atom2 Rx Ry Rz Dx Dy Dz
│ Float64 Float64 Int64 Int64 Int64 Int64 Int64 Float64 Float64 Float64
─────┼────────────────────────────────────────────────────────────────────────────────────
1 │ 2.95571 0.160754 1 1 -1 0 1 -2.09 0.0 2.09
2 │ 2.95571 0.160753 1 1 -1 1 0 -2.09 2.09 0.0
3 │ 2.95571 0.160754 1 1 0 -1 1 0.0 -2.09 2.09
4 │ 2.95571 0.160754 1 1 0 1 -1 0.0 2.09 -2.09
5 │ 2.95571 0.160753 1 1 1 -1 0 2.09 -2.09 0.0
6 │ 2.95571 0.160754 1 1 1 0 -1 2.09 0.0 -2.09
7 │ 5.11943 0.00673793 1 1 -2 1 1 -4.18 2.09 2.09
8 │ 5.11943 0.00673793 1 1 -1 2 -1 -2.09 4.18 -2.09
9 │ 5.11943 0.00673793 1 1 1 -2 1 2.09 -4.18 2.09
10 │ 5.11943 0.00673793 1 1 2 -1 -1 4.18 -2.09 -2.09
11 │ 5.11943 0.00673793 1 1 -1 -1 2 -2.09 -2.09 4.18
12 │ 5.11943 0.00624584 1 1 -1 0 0 -4.18 -2.09 -2.09
Writing Plot:Jplot_1_1,2_all_all.pdf
Writing Plot:Jplot_1_1,2_all_all.svg
================ All done =============
The files provided in the example script
NiO.dat
#
# output Hamiltonian and overlap
#
HS.fileout on # on|off, default=off
nio_J_openmx.toml
# This is the DFT-forge TOML file
HamiltonianType = "OpenMX" # OpenMX, OpenMXWannier, Wannier90
spintype = "co_spin" #Set Spin type, para, co_spin, nc_spin
result_file = "nio.scfout"
atom12 = [[1,1],[1,2]]
# k,q for calculation. Using the same k,q points number is recommended
k_point_num = [6,6,6]
q_point_num = [6,6,6]
[orbitals]
##################################################################################################
#In OpenMX inputfile NiO.dat
#<Definition.of.Atomic.Species
#Ni Ni6.0S-s2p2d2f1 Ni_PBE13S
##################################################################################################
# s2p2d2f1 represents 2 s orbitals, 2 p orbitals, 2 d orbitals, and 1 f orbital for the Ni.
# Therefore, orbital indexs 1,2 standsfor s1, s2
# 3,4,5: p1 5,6,7: p2
# 9,10,11,12,13: d1 14,15,16,17,18: d2
# 19,20,21,22,23,24,25: f1
#
# If we want to calculate the interaction between d orbitals of Ni,
# you can choose [9-13] orbital.
# Each orbital index name is as follows:
# 9:dz2, 10:dx2y2, 11:dxy, 12:dyz, 13:dxz
# You can check it through nio.out file.
##################################################################################################
orbitalselection = false # true,false
orbital_mask1_list = [[9],[10],[11],[12],[13]]
orbital_mask2_list = [[9],[10],[11],[12],[13]]
orbital_mask1_names = "[dz2,dx2y2,dxy,dxz,dyz]"
orbital_mask2_names = "[dz2,dx2y2,dxy,dxz,dyz]"
./example_NiO_OpenMX.sh:
#!/bin/bash
RED='\033[0;31m'
BLUE='\033[0;34m'
GREEN='\033[0;32m'
NC='\033[0m'
JX_ROOT=`pwd`
source ~/.profile # to add Julia to path
printf "${BLUE} 0. Unzip the example ${NC} \n"
printf "${BLUE} examples/NiO_G-AFM.OpenMx ${NC} \n"
cd "examples/NiO_G-AFM.OpenMx"
# Unzip dft result
# nio.scf : OpenMX full Hamiltonian info
# nio.HWR : Wannier Hamiltonian from OpenMX
tar xvf nio_dft_result.tar.gz
# cd "../../"
# obtain J(q) long execution
printf "${BLUE} 1. Calculate J(q) ${NC} \n"
printf "${GREEN} julia -p 4 src/Jx_col_spin_exchange.jl -T examples/NiO_G-AFM.OpenMx/nio_J_openmx.toml ${NC} \n"
printf "${GREEN} 'julia --machine-file <file>' instead of 'julia -p 4' is also possible ${NC} \n"
sleep 2
#julia -p 4 src/Jx_col_spin_exchange.jl -T nio_J_openmx.toml
julia -p 4 $JX_ROOT/src/Jx_col_spin_exchange.jl -T nio_J_openmx.toml
# J(q) -> J(R) short post processing
printf "${BLUE} 2. Transform J(q) -> J(Rij) ${NC} \n"
printf "${GREEN} julia src/Jx_postprocess.jl --cellvectors 2_2_2 --baseatom1 1 --atom2 1,2 --orbital_name all_all examples/NiO_G-AFM.OpenMx/jx2.col.spin_0.0 ${NC} \n"
sleep 2
julia $JX_ROOT/src/Jx_postprocess.jl --cellvectors 2_2_2 --baseatom1 1 --atom2 1,2 --orbital_name all_all jx2.col.spin_0.0