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fixed openmx_wannier.md
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fixed for new versio
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@DHKiem
DHKiem committed Oct 5, 2023
1 parent 73b41ee commit 5061e23
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8 changes: 4 additions & 4 deletions docs/example_NiO.md
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ julia src/Jx_postprocess.jl --cellvectors 2_2_2 --baseatom1 1 --atom2 1,2 --or
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, +4.9 meV means that current antiferromagnetic ordering is preferred.
> 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.

```sh
Expand Down Expand Up @@ -105,7 +105,7 @@ jx2.col.spin_0.0/jx2.col.spin_nio_atomij_1_2_[all_all]_ChemPdelta_0.0.jld2
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__1.csv
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
Expand All @@ -122,8 +122,8 @@ jx2.col.spin_0.0/jx2.col.spin_nio_atomij_1_2_[all_all]_ChemPdelta_0.0.jld2
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__1.pdf
Writing Plot:Jplot_1_1,2_all_all__1.svg
Writing Plot:Jplot_1_1,2_all_all.pdf
Writing Plot:Jplot_1_1,2_all_all.svg
================ All done =============
```

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75 changes: 38 additions & 37 deletions docs/example_NiO_openmxWannier.md
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Original file line number Diff line number Diff line change
Expand Up @@ -67,64 +67,65 @@ julia src/Jx_postprocess.jl --cellvectors 2_2_2 --baseatom 1 --atom2 1,2 --orb

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, +6 meV means that current antiferromagnetic ordering is preferred.
> 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, +11.0 meV means that current antiferromagnetic ordering is preferred.

The output at terminal would look like bellow:

```sh
Checking the updated version ...
Current version 1.0.1 is the newest version.
DFTforge Version 1.0.1
DFTforge Version 1.3.2
Jx_postprocess started (julia Jx_postprocess.jl --help for inputs)
================ User input =============
baseatom => 1
cellvectors => 2_2_2
baseatom1 => 1
root_dir => jx2.col.spin.wannier_0.0
orbital_name => all_all
atom2 => 1,2
================ Selected result *.jld2 files =============
jx2.col.spin.wannier_0.0/jx2.col.spin.wannier_nio_atomij_1_1_[all_all]_ChemPdelta_0.0.jld2
jx2.col.spin.wannier_0.0/jx2.col.spin.wannier_nio_atomij_1_2_[all_all]_ChemPdelta_0.0.jld2
================ Selected result *.jld2 files =============
[0.0 0.0 0.0; 4.18000019366829 4.18000019366829 4.18000019366829; 2.090000096834145 2.090000096834145 2.090000096834145; 6.270000290502435 6.270000290502435 6.270000290502434]
(1, 2)atom_(i, j):(1, 2) global_xyz:([0.0, 0.0, 0.0] [4.18000019366829, 4.18000019366829, 4.18000019366829])
(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.wannier_nio_atomij_1_2_[all_all]_ChemPdelta_0.0.csv
12×8 DataFrames.DataFrame
│ Row │ Distance │ JmeV │ Rx │ Ry │ Rz │ Dx │ Dy │ Dz │
│ │ Float64 │ Float64 │ Int64 │ Int64 │ Int64 │ Float64 │ Float64 │ Float64 │
├─────┼──────────┼────────────┼───────┼───────┼───────┼─────────────┼─────────────┼─────────────┤
│ 1 │ 2.9557 │ -0.0502568 │ -1 │ -1 │ 0 │ -2.09 │ -2.09 │ -2.64589e-6 │
│ 2 │ 2.9557 │ -0.0501972 │ -1 │ 0 │ -1 │ -2.09 │ -2.64589e-6 │ -2.09 │
│ 3 │ 2.9557 │ -0.0501972 │ 0 │ -1 │ -1 │ -2.64589e-6 │ -2.09 │ -2.09 │
│ 4 │ 2.9557 │ -0.0501653 │ -1 │ 0 │ 0 │ 2.64589e-6 │ 2.09 │ 2.09 │
│ 5 │ 2.9557 │ -0.0501653 │ 0 │ -1 │ 0 │ 2.09 │ 2.64589e-6 │ 2.09 │
│ 6 │ 2.9557 │ -0.0502249 │ 0 │ 0 │ -1 │ 2.09 │ 2.09 │ 2.64589e-6 │
│ 7 │ 4.17999 │ 6.02982 │ -2 │ 0 │ 0 │ -4.17999 │ -2.64589e-6 │ -2.64589e-6 │
│ 8 │ 4.17999 │ 6.02982 │ 0 │ -2 │ 0 │ -2.64589e-6 │ -4.17999 │ -2.64589e-6 │
│ 9 │ 4.17999 │ 6.02954 │ 0 │ 0 │ -2 │ -2.64589e-6 │ -2.64589e-6 │ -4.17999 │
│ 10 │ 4.17999 │ 6.0283 │ -1 │ -1 │ 1 │ 2.64589e-6 │ 2.64589e-6 │ 4.17999 │
│ 11 │ 4.17999 │ 6.02858 │ -1 │ 1 │ -1 │ 2.64589e-6 │ 4.17999 │ 2.64589e-6 │
│ 12 │ 4.17999 │ 6.02858 │ 1 │ -1 │ -1 │ 4.17999 │ 2.64589e-6 │ 2.64589e-6 │
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 │ 2.9557 -0.0771767 1 2 -1 -1 0 -2.09 -2.09 -2.64589e-6
2 │ 2.9557 -0.0769231 1 2 -1 0 -1 -2.09 -2.64589e-6 -2.09
3 │ 2.9557 -0.0769231 1 2 0 -1 -1 -2.64589e-6 -2.09 -2.09
4 │ 2.9557 -0.0769231 1 2 -1 0 0 2.64589e-6 2.09 2.09
5 │ 2.9557 -0.0769231 1 2 0 -1 0 2.09 2.64589e-6 2.09
6 │ 2.9557 -0.0771767 1 2 0 0 -1 2.09 2.09 2.64589e-6
7 │ 4.17999 11.0244 1 2 -2 0 0 -4.17999 -2.64589e-6 -2.64589e-6
8 │ 4.17999 11.0244 1 2 0 -2 0 -2.64589e-6 -4.17999 -2.64589e-6
9 │ 4.17999 11.0233 1 2 0 0 -2 -2.64589e-6 -2.64589e-6 -4.17999
10 │ 4.17999 11.0233 1 2 -1 -1 1 2.64589e-6 2.64589e-6 4.17999
11 │ 4.17999 11.0244 1 2 -1 1 -1 2.64589e-6 4.17999 2.64589e-6
12 │ 4.17999 11.0244 1 2 1 -1 -1 4.17999 2.64589e-6 2.64589e-6
Writing CSV:jx2.col.spin.wannier_nio_atomij_1_1_[all_all]_ChemPdelta_0.0.csv
12×8 DataFrames.DataFrame
│ Row │ Distance │ JmeV │ Rx │ Ry │ Rz │ Dx │ Dy │ Dz │
│ │ Float64 │ Float64 │ Int64 │ Int64 │ Int64 │ Float64 │ Float64 │ Float64 │
├─────┼──────────┼─────────────┼───────┼───────┼───────┼──────────┼──────────┼──────────┤
│ 1 │ 2.9557 │ 0.0277095 │ -1 │ 0 │ 1 │ -2.09 │ 0.0 │ 2.09 │
│ 2 │ 2.9557 │ 0.0274556 │ -1 │ 1 │ 0 │ -2.09 │ 2.09 │ 0.0 │
│ 3 │ 2.9557 │ 0.0277095 │ 0 │ -1 │ 1 │ 0.0 │ -2.09 │ 2.09 │
│ 4 │ 2.9557 │ 0.0277095 │ 0 │ 1 │ -1 │ 0.0 │ 2.09 │ -2.09 │
│ 5 │ 2.9557 │ 0.0274556 │ 1 │ -1 │ 0 │ 2.09 │ -2.09 │ 0.0 │
│ 6 │ 2.9557 │ 0.0277095 │ 1 │ 0 │ -1 │ 2.09 │ 0.0 │ -2.09 │
│ 7 │ 5.11942 │ -0.00451954 │ -2 │ 1 │ 1 │ -4.17999 │ 2.09 │ 2.09 │
│ 8 │ 5.11942 │ -0.00451977 │ -1 │ -1 │ 2 │ -2.09 │ -2.09 │ 4.17999 │
│ 9 │ 5.11942 │ -0.00451936 │ -1 │ 2 │ -1 │ -2.09 │ 4.17999 │ -2.09 │
│ 10 │ 5.11942 │ -0.00451954 │ 1 │ -2 │ 1 │ 2.09 │ -4.17999 │ 2.09 │
│ 11 │ 5.11942 │ -0.00451995 │ 1 │ 1 │ -2 │ 2.09 │ 2.09 │ -4.17999 │
│ 12 │ 5.11942 │ -0.00451936 │ 2 │ -1 │ -1 │ 4.17999 │ -2.09 │ -2.09 │
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 │ 2.9557 0.0696555 1 1 -1 0 1 -2.09 0.0 2.09
2 │ 2.9557 0.0692931 1 1 -1 1 0 -2.09 2.09 0.0
3 │ 2.9557 0.0696555 1 1 0 -1 1 0.0 -2.09 2.09
4 │ 2.9557 0.0696555 1 1 0 1 -1 0.0 2.09 -2.09
5 │ 2.9557 0.0692931 1 1 1 -1 0 2.09 -2.09 0.0
6 │ 2.9557 0.0696555 1 1 1 0 -1 2.09 0.0 -2.09
7 │ 5.11942 -0.00579205 1 1 -2 1 1 -4.17999 2.09 2.09
8 │ 5.11942 -0.0057945 1 1 -1 -1 2 -2.09 -2.09 4.17999
9 │ 5.11942 -0.00579205 1 1 -1 2 -1 -2.09 4.17999 -2.09
10 │ 5.11942 -0.00579205 1 1 1 -2 1 2.09 -4.17999 2.09
11 │ 5.11942 -0.0057945 1 1 1 1 -2 2.09 2.09 -4.17999
12 │ 5.11942 -0.00579205 1 1 2 -1 -1 4.17999 -2.09 -2.09
Writing Plot:Jplot_1_1,2_all_all.pdf
Writing Plot:Jplot_1_1,2_all_all.svg
================ All done =============
```

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