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cleaning up repository and trying packaging

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class-solution
Daniel Pozsar 2 months ago
parent 44292e02a3
commit 51fdb95eb9
58 changed files with 29 additions and 86409 deletions
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17
.pre-commit-config.yaml
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@ -10,13 +10,6 @@ repos:
- L-HEADER - L-HEADER
- --update-year - --update-year
- --verbose - --verbose
#- repo: https://github.com/pre-commit/pre-commit-hooks
# rev: v4.6.0
# hooks:
# - id: trailing-whitespace
# - id: end-of-file-fixer
# - id: check-added-large-files
# - id: check-yaml
- repo: https://github.com/pycqa/isort - repo: https://github.com/pycqa/isort
rev: 5.13.2 rev: 5.13.2
hooks: hooks:
@ -31,4 +24,12 @@ repos:
rev: 24.4.2 rev: 24.4.2
hooks: hooks:
- id: black-jupyter - id: black-jupyter
language_version: python3.9 language_version: python3.9
#- repo: https://github.com/pre-commit/pre-commit-hooks
# rev: v4.6.0
# hooks:
# - id: trailing-whitespace
# - id: end-of-file-fixer
# - id: check-added-large-files
# - id: check-yaml

2
L-HEADER
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Copyright (c) [2024] [Daniel Pozsar] Copyright (c) [2024] []
Permission is hereby granted, free of charge, to any person obtaining a copy Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal of this software and associated documentation files (the "Software"), to deal

268
LATEST_RUN_ON_KOMONDOR_AND_GROGU_MATLAB
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Total charge: 39.93682211852279
Total charge: 39.937913835302076
Total charge: 40.012607110907126
Magnetic entities integrated.
Pairs integrated.
Magnetic parameters calculated.
##################################################################### GROGU OUTPUT #############################################################################
================================================================================================================================================================
Input file:
./lat3_791/Fe3GeTe2.fdf
Output file:
./Fe3GeTe2_benchmark_on_100k_600eset_final_test.pickle
Number of nodes in the parallel cluster: 8
================================================================================================================================================================
Cell [Ang]:
[[ 3.79100000e+00 0.00000000e+00 0.00000000e+00]
[-1.89550000e+00 3.28310231e+00 0.00000000e+00]
[ 1.25954923e-15 2.18160327e-15 2.05700000e+01]]
================================================================================================================================================================
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
[0 1 0] --» [array([1, 0, 0]), array([0, 0, 1])]
[0 0 1] --» [array([1, 0, 0]), array([0, 1, 0])]
================================================================================================================================================================
Parameters for the contour integral:
Number of k points: 100
k point directions: xy
Ebot: -15
Eset: 600
Esetp: 10000
================================================================================================================================================================
Atomic information:
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[atom index]Element(orbitals) x [Ang] y [Ang] z [Ang] Sx Sy Sz Q Lx Ly Lz Jx Jy Jz
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[3]Fe(2) -7.339158738013707e-06 4.149278510690423e-06 11.657585837928032
[4]Fe(2) -7.326987662162937e-06 4.158274523275774e-06 8.912422537596708
[5]Fe(2) 1.8954667088117545 1.0943913231921656 10.285002698393109
================================================================================================================================================================
Exchange [meV]
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Magnetic entity1 Magnetic entity2 [i j k] d [Ang]
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[3]Fe(2) [4]Fe(2) [0 0 0] d [Ang] 2.745163300331324
Isotropic: -86.34442888188431
DMI: [ 1.26959080e-01 -6.68807559e-04 -3.62770994e-07]
Symmetric-anisotropy: [ 6.77397756e-01 -8.36063246e-05 -7.29981887e-05 -8.36063246e-05
6.84252238e-01 -2.46503172e-04 -7.29981887e-05 -2.46503172e-04
-1.36164999e+00]
J: [-8.56670311e+01 -8.36063246e-05 -7.29981887e-05 -8.36063246e-05
-8.56601766e+01 -2.46503172e-04 -7.29981887e-05 -2.46503172e-04
-8.77060789e+01]
Energies for debugging:
array([[-8.76976821e-02, 1.27205583e-04, -1.26712576e-04,
-8.78732914e-02],
[-8.77144756e-02, 7.41805748e-07, -5.95809371e-07,
-8.78869396e-02],
[-8.34470619e-02, 8.32435536e-08, 8.39690956e-08,
-8.34471227e-02]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([-0.08788694, -0.08344706, -0.08769768])
Test J_xx = E(y,z) = E(z,y)
-0.08788693955919667 -0.08344712269177329
[3]Fe(2) [5]Fe(2) [0 0 0] d [Ang] 2.5835033632437767
Isotropic: -42.135738635547185
DMI: [ 1.14985913 -1.98675214 0.0109073 ]
Symmetric-anisotropy: [ 0.11829377 0.13803139 -0.06754341 0.13803139 -0.1258364 -0.04029948
-0.06754341 -0.04029948 0.00754263]
J: [-4.20174449e+01 1.38031387e-01 -6.75434084e-02 1.38031387e-01
-4.22615750e+01 -4.02994850e-02 -6.75434084e-02 -4.02994850e-02
-4.21281960e+01]
Energies for debugging:
array([[-0.04223303, 0.00119016, -0.00110956, -0.04240784],
[-0.04202336, 0.0020543 , -0.00191921, -0.04207956],
[-0.04211531, -0.00012712, -0.00014894, -0.04195533]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([-0.04207956, -0.04211531, -0.04223303])
Test J_xx = E(y,z) = E(z,y)
-0.04207956278909725 -0.04195532693971167
[4]Fe(2) [5]Fe(2) [0 0 0] d [Ang] 2.583501767937866
Isotropic: -42.13756331215063
DMI: [-1.14605424 2.04251866 0.01090899]
Symmetric-anisotropy: [ 0.11988385 0.13803161 0.0551642 0.13803161 -0.12943909 0.03047108
0.0551642 0.03047108 0.00955523]
J: [-4.20176795e+01 1.38031610e-01 5.51641982e-02 1.38031610e-01
-4.22670024e+01 3.04710785e-02 5.51641982e-02 3.04710785e-02
-4.21280081e+01]
Energies for debugging:
array([[-0.04223534, -0.00117653, 0.00111558, -0.04241802],
[-0.04202068, -0.00209768, 0.00198735, -0.04207936],
[-0.04211599, -0.00012712, -0.00014894, -0.041956 ]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([-0.04207936, -0.04211599, -0.04223534])
Test J_xx = E(y,z) = E(z,y)
-0.04207935696294549 -0.0419560019581248
[3]Fe(2) [5]Fe(2) [-1 -1 0] d [Ang] 2.5834973202859075
Isotropic: -42.14772703529168
DMI: [-2.31377877e+00 1.31005845e-03 -1.17939618e-02]
Symmetric-anisotropy: [-2.67391508e-01 -2.42945028e-04 9.46271135e-04 -2.42945028e-04
2.59883170e-01 7.17582186e-02 9.46271135e-04 7.17582186e-02
7.50833764e-03]
J: [-4.24151185e+01 -2.42945028e-04 9.46271135e-04 -2.42945028e-04
-4.18878439e+01 7.17582186e-02 9.46271135e-04 7.17582186e-02
-4.21402187e+01]
Energies for debugging:
array([[-4.18938511e-02, -2.38553699e-03, 2.24202055e-03,
-4.18980295e-02],
[-4.23865863e-02, -2.25632958e-06, 3.63787311e-07,
-4.26334620e-02],
[-4.18776582e-02, -1.15510168e-05, 1.20369068e-05,
-4.21967751e-02]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([-0.04263346, -0.04187766, -0.04189385])
Test J_xx = E(y,z) = E(z,y)
-0.04263346199013239 -0.04219677509632287
[4]Fe(2) [5]Fe(2) [-1 -1 0] d [Ang] 2.583495745338251
Isotropic: -42.145453555729674
DMI: [ 2.31622405e+00 1.01134560e-03 -1.17956355e-02]
Symmetric-anisotropy: [-2.65342856e-01 -2.43008373e-04 3.22482902e-04 -2.43008373e-04
2.58475375e-01 -7.16741491e-02 3.22482902e-04 -7.16741491e-02
6.86748114e-03]
J: [-4.24107964e+01 -2.43008373e-04 3.22482902e-04 -2.43008373e-04
-4.18869782e+01 -7.16741491e-02 3.22482902e-04 -7.16741491e-02
-4.21385861e+01]
Energies for debugging:
array([[-4.18915056e-02, 2.38789820e-03, -2.24454990e-03,
-4.18956238e-02],
[-4.23856665e-02, -1.33382850e-06, 6.88862698e-07,
-4.26241428e-02],
[-4.18783326e-02, -1.15526271e-05, 1.20386439e-05,
-4.21974500e-02]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([-0.04262414, -0.04187833, -0.04189151])
Test J_xx = E(y,z) = E(z,y)
-0.0426241428261591 -0.04219744999692707
[3]Fe(2) [5]Fe(2) [-1 0 0] d [Ang] 2.5835414446413725
Isotropic: -42.129623558740505
DMI: [1.14621946e+00 1.98931941e+00 8.94174395e-04]
Symmetric-anisotropy: [ 0.11573153 -0.13810044 0.06662932 -0.13810044 -0.12877265 -0.03057518
0.06662932 -0.03057518 0.01304111]
J: [-4.20138920e+01 -1.38100436e-01 6.66293166e-02 -1.38100436e-01
-4.22583962e+01 -3.05751769e-02 6.66293166e-02 -3.05751769e-02
-4.21165824e+01]
Energies for debugging:
array([[-0.04221921, 0.00117679, -0.00111564, -0.04240089],
[-0.04201396, -0.00205595, 0.00192269, -0.04207138],
[-0.0421159 , 0.00013899, 0.00013721, -0.0419564 ]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([-0.04207138, -0.0421159 , -0.04221921])
Test J_xx = E(y,z) = E(z,y)
-0.04207138043334055 -0.04195640361455671
[4]Fe(2) [5]Fe(2) [-1 0 0] d [Ang] 2.5835398672184064
Isotropic: -42.12730921546265
DMI: [-1.14743982e+00 -2.03983518e+00 8.95442025e-04]
Symmetric-anisotropy: [ 0.11306029 -0.13810087 -0.05589985 -0.13810087 -0.12635809 0.04017865
-0.05589985 0.04017865 0.0132978 ]
J: [-4.20142489e+01 -1.38100866e-01 -5.58998501e-02 -1.38100866e-01
-4.22536673e+01 4.01786543e-02 -5.58998501e-02 4.01786543e-02
-4.21140114e+01]
Energies for debugging:
array([[-0.04221703, -0.00118762, 0.00110726, -0.04239074],
[-0.04201099, 0.00209574, -0.00198394, -0.04207141],
[-0.04211659, 0.000139 , 0.00013721, -0.04195709]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([-0.04207141, -0.04211659, -0.04221703])
Test J_xx = E(y,z) = E(z,y)
-0.04207140711748633 -0.04195709073578825
[4]Fe(2) [5]Fe(2) [-2 0 0] d [Ang] 5.951322298958084
Isotropic: -1.8232451301996326
DMI: [ 0.02705666 0.33317704 -0.59092579]
Symmetric-anisotropy: [ 0.13387827 0.05652754 0.02339254 0.05652754 -0.12675634 -0.0364858
0.02339254 -0.0364858 -0.00712192]
J: [-1.68936686 0.05652754 0.02339254 0.05652754 -1.95000147 -0.0364858
0.02339254 -0.0364858 -1.83036705]
Energies for debugging:
array([[-1.84775366e-03, 6.35424602e-05, 9.42913717e-06,
-2.05719754e-03],
[-1.81298045e-03, -3.56569571e-04, 3.09784500e-04,
-1.78595999e-03],
[-1.84280541e-03, -6.47453327e-04, 5.34398256e-04,
-1.59277373e-03]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([-0.00178596, -0.00184281, -0.00184775])
Test J_xx = E(y,z) = E(z,y)
-0.0017859599945927644 -0.0015927737292729515
[4]Fe(2) [5]Fe(2) [-3 0 0] d [Ang] 9.638732176310562
Isotropic: 0.08415238341059932
DMI: [ 0.02765926 -0.01193683 -0.08860892]
Symmetric-anisotropy: [-0.01463505 -0.02335298 -0.0115624 -0.02335298 0.01019026 -0.00490545
-0.0115624 -0.00490545 0.00444478]
J: [ 0.06951734 -0.02335298 -0.0115624 -0.02335298 0.09434264 -0.00490545
-0.0115624 -0.00490545 0.08859717]
Energies for debugging:
array([[ 7.78485206e-05, 3.25647165e-05, -2.27538126e-05,
1.23484184e-04],
[ 9.93458145e-05, 2.34992299e-05, -3.74434418e-07,
6.87808473e-05],
[ 6.52011050e-05, -6.52559373e-05, 1.11961900e-04,
7.02538287e-05]])
J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)
array([6.87808473e-05, 6.52011050e-05, 7.78485206e-05])
Test J_xx = E(y,z) = E(z,y)
6.878084728235458e-05 7.025382868651086e-05
================================================================================================================================================================
Runtime information:
Total runtime: 3558.681470017007 s
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Initial setup: 1.776719820976723 s
Hamiltonian conversion and XC field extraction: 0.413 s
Pair and site datastructure creatrions: 0.008 s
k set cration and distribution: 0.047 s
Rotating XC potential: 0.284 s
Greens function inversion: 3555.639 s
Calculate energies and magnetic components: 0.515 s
k loop: 0%| | 0/1250 [00:00<?, ?it/s]
k loop: 0%| | 0/1250 [00:00<?, ?it/s]
k loop: 0%| | 0/1250 [00:00<?, ?it/s]
k loop: 0%| | 0/1250 [00:00<?, ?it/s]
k loop: 0%| | 0/1250 [00:00<?, ?it/s]
k loop: 0%| | 0/1250 [00:00<?, ?it/s]
k loop: 0%| | 0/1250 [00:00<?, ?it/s]
real 59m32.849s
user 0m0.011s
sys 0m0.020s
========================================
Atom Angstrom
# Label, x y z Sx Sy Sz #Q Lx Ly Lz Jx Jy Jz
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Te1 1.8955 1.0943 13.1698 -0.0000 0.0000 -0.1543 # 5.9345 -0.0000 0.0000 -0.0537 -0.0000 0.0000 -0.2080
Te2 1.8955 1.0943 7.4002 0.0000 -0.0000 -0.1543 # 5.9345 0.0000 -0.0000 -0.0537 0.0000 -0.0000 -0.2080
Ge3 -0.0000 2.1887 10.2850 0.0000 0.0000 -0.1605 # 3.1927 -0.0000 0.0000 0.0012 0.0000 0.0000 -0.1593
Fe4 -0.0000 0.0000 11.6576 0.0001 -0.0001 2.0466 # 8.3044 0.0000 -0.0000 0.1606 0.0001 -0.0001 2.2072
Fe5 -0.0000 0.0000 8.9124 -0.0001 0.0001 2.0466 # 8.3044 -0.0000 0.0000 0.1606 -0.0001 0.0001 2.2072
Fe6 1.8955 1.0944 10.2850 0.0000 0.0000 1.5824 # 8.3296 -0.0000 -0.0000 0.0520 -0.0000 0.0000 1.6344
==================================================================================================================================
Exchange meV
--------------------------------------------------------------------------------
# at1 at2 i j k # d (Ang)
--------------------------------------------------------------------------------
Fe4 Fe5 0 0 0 # 2.7452
Isotropic -82.0854
DMI 0.12557 -0.00082199 6.9668e-08
Symmetric-anisotropy -0.60237 -0.83842 -0.00032278 -1.2166e-05 -3.3923e-05
--------------------------------------------------------------------------------
Fe4 Fe6 0 0 0 # 2.5835
Isotropic -41.9627
DMI 1.1205 -1.9532 0.0018386
Symmetric-anisotropy 0.26007 -0.00013243 0.12977 -0.069979 -0.042066
--------------------------------------------------------------------------------

2
LICENSE
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MIT License MIT License
Copyright (c) [2024] [Daniel Pozsar] Copyright (c) [2024] []
Permission is hereby granted, free of charge, to any person obtaining a copy Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal of this software and associated documentation files (the "Software"), to deal

1
data/lat3_791/0_NORMAL_EXIT
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SIESTA completed, MPI exit: 0

4
data/lat3_791/BASIS_ENTHALPY
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-2878.0655830244073
The above number is the electronic (free)energy: -2887.7690769348492
Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa)
times the orbital volume (in Bohr**3): 52457.833503994734

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data/lat3_791/BASIS_HARRIS_ENTHALPY
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-2878.0654643176349
The above number is the electronic (free) harris energy: -2887.7689582280768
Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa)
times the orbital volume (in Bohr**3): 52457.833503994734

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data/lat3_791/CLOCK
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Start of run 0.000
-------------- end of scf step 56.978
-------------- end of scf step 64.924
-------------- end of scf step 72.987
-------------- end of scf step 80.904
-------------- end of scf step 88.821
-------------- end of scf step 96.737
-------------- end of scf step 104.683
-------------- end of scf step 112.640
-------------- end of scf step 120.582
-------------- end of scf step 128.524
-------------- end of scf step 136.457
-------------- end of scf step 144.411
-------------- end of scf step 152.358
-------------- end of scf step 160.363
-------------- end of scf step 168.352
-------------- end of scf step 176.304
-------------- end of scf step 184.251
-------------- end of scf step 192.213
-------------- end of scf step 200.170
-------------- end of scf step 208.114
-------------- end of scf step 216.053
-------------- end of scf step 224.017
-------------- end of scf step 231.935
-------------- end of scf step 239.863
-------------- end of scf step 248.322
-------------- end of scf step 256.303
-------------- end of scf step 264.256
-------------- end of scf step 272.206
-------------- end of scf step 280.150
-------------- end of scf step 288.089
-------------- end of scf step 296.045
-------------- end of scf step 304.008
-------------- end of scf step 311.961
-------------- end of scf step 319.913
-------------- end of scf step 327.867
-------------- end of scf step 335.825
-------------- end of scf step 343.802
-------------- end of scf step 351.752
-------------- end of scf step 359.706
-------------- end of scf step 367.668
-------------- end of scf step 375.740
-------------- end of scf step 383.726
-------------- end of scf step 391.662
-------------- end of scf step 399.569
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-------------- end of scf step 487.047
-------------- end of scf step 495.021
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-------------- end of scf step 790.051
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-------------- end of scf step 806.009
-------------- end of scf step 813.963
--- end of geometry step 1009.026
-------------- end of scf step 1035.442
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-------------- end of scf step 1058.453
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-------------- end of scf step 1226.641
-------------- end of scf step 1234.333
-------------- end of scf step 1241.929
--- end of geometry step 1437.577
-------------- end of scf step 1463.543
-------------- end of scf step 1470.916
-------------- end of scf step 1478.372
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-------------- end of scf step 1493.108
-------------- end of scf step 1500.480
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4 Fe 2.5750 Ang. Really at: 7.1640 0.0000 21.8231
4 Fe 2.5750 Ang. Really at: 3.5820 6.2042 21.8231
4 Fe 2.5750 Ang. Really at: -0.0000 0.0000 21.8231
6 Fe 2.6198 Ang. Really at: 3.5820 2.0681 19.4358
Neighbors of: 2 Te at: 3.5820 2.0681 14.4850
5 Fe 2.5750 Ang. Really at: 7.1640 0.0000 17.0486
5 Fe 2.5750 Ang. Really at: 3.5820 6.2042 17.0486
5 Fe 2.5750 Ang. Really at: -0.0000 0.0000 17.0486
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Neighbors of: 3 Ge at: -0.0000 4.1361 19.4358
6 Fe 2.1887 Ang. Really at: -3.5820 2.0681 19.4358
6 Fe 2.1887 Ang. Really at: 0.0000 8.2722 19.4358
6 Fe 2.1887 Ang. Really at: 3.5820 2.0681 19.4358
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5 Fe 2.5271 Ang. Really at: 3.5820 6.2042 17.0486
4 Fe 2.5271 Ang. Really at: 3.5820 6.2042 21.8231
4 Fe 2.5271 Ang. Really at: -0.0000 0.0000 21.8231
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Neighbors of: 4 Fe at: 0.0000 0.0000 21.8231
5 Fe 2.5266 Ang. Really at: 0.0000 0.0000 17.0486
3 Ge 2.5271 Ang. Really at: 3.5820 -2.0681 19.4358
6 Fe 2.5271 Ang. Really at: -3.5820 2.0681 19.4358
3 Ge 2.5271 Ang. Really at: -3.5820 -2.0681 19.4358
6 Fe 2.5271 Ang. Really at: 3.5820 2.0681 19.4358
3 Ge 2.5271 Ang. Really at: -0.0000 4.1361 19.4358
6 Fe 2.5271 Ang. Really at: 0.0000 -4.1361 19.4358
1 Te 2.5750 Ang. Really at: -3.5820 2.0681 24.3866
1 Te 2.5750 Ang. Really at: 3.5820 2.0681 24.3866
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Neighbors of: 5 Fe at: 0.0000 0.0000 17.0486
4 Fe 2.5266 Ang. Really at: 0.0000 0.0000 21.8231
3 Ge 2.5271 Ang. Really at: 3.5820 -2.0681 19.4358
6 Fe 2.5271 Ang. Really at: -3.5820 2.0681 19.4358
3 Ge 2.5271 Ang. Really at: -3.5820 -2.0681 19.4358
3 Ge 2.5271 Ang. Really at: -0.0000 4.1361 19.4358
6 Fe 2.5271 Ang. Really at: 0.0000 -4.1361 19.4358
6 Fe 2.5271 Ang. Really at: 3.5820 2.0681 19.4358
2 Te 2.5750 Ang. Really at: -3.5820 2.0681 14.4850
2 Te 2.5750 Ang. Really at: 3.5820 2.0681 14.4850
2 Te 2.5750 Ang. Really at: 0.0000 -4.1361 14.4850
Neighbors of: 6 Fe at: 3.5820 2.0681 19.4358
3 Ge 2.1887 Ang. Really at: 3.5820 -2.0681 19.4358
3 Ge 2.1887 Ang. Really at: 7.1640 4.1361 19.4358
3 Ge 2.1887 Ang. Really at: -0.0000 4.1361 19.4358
5 Fe 2.5271 Ang. Really at: 7.1640 0.0000 17.0486
4 Fe 2.5271 Ang. Really at: 7.1640 0.0000 21.8231
4 Fe 2.5271 Ang. Really at: -0.0000 0.0000 21.8231
4 Fe 2.5271 Ang. Really at: 3.5820 6.2042 21.8231
5 Fe 2.5271 Ang. Really at: 3.5820 6.2042 17.0486
5 Fe 2.5271 Ang. Really at: -0.0000 0.0000 17.0486
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54
data/lat3_791/Fe3GeTe2.BONDS_FINAL
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4 Fe 2.6603 Ang. Really at: 7.1639 0.0000 22.0296
4 Fe 2.6603 Ang. Really at: 3.5820 6.2042 22.0296
4 Fe 2.6603 Ang. Really at: -0.0000 0.0000 22.0296
6 Fe 2.8848 Ang. Really at: 3.5819 2.0681 19.4358
Neighbors of: 2 Te at: 3.5821 2.0680 13.9844
5 Fe 2.6603 Ang. Really at: 7.1639 0.0000 16.8420
5 Fe 2.6603 Ang. Really at: 3.5820 6.2042 16.8420
5 Fe 2.6603 Ang. Really at: -0.0000 0.0000 16.8420
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Neighbors of: 3 Ge at: -0.0001 4.1361 19.4358
6 Fe 2.1887 Ang. Really at: 3.5819 2.0681 19.4358
6 Fe 2.1887 Ang. Really at: -3.5820 2.0681 19.4358
6 Fe 2.1887 Ang. Really at: -0.0001 8.2723 19.4358
4 Fe 2.5835 Ang. Really at: -3.5820 6.2042 22.0296
5 Fe 2.5835 Ang. Really at: -3.5820 6.2042 16.8420
4 Fe 2.5835 Ang. Really at: -0.0000 0.0000 22.0296
5 Fe 2.5835 Ang. Really at: -0.0000 0.0000 16.8420
4 Fe 2.5835 Ang. Really at: 3.5820 6.2042 22.0296
5 Fe 2.5835 Ang. Really at: 3.5820 6.2042 16.8420
Neighbors of: 4 Fe at: -0.0000 0.0000 22.0296
3 Ge 2.5835 Ang. Really at: 3.5819 -2.0680 19.4358
6 Fe 2.5835 Ang. Really at: -0.0001 -4.1361 19.4358
6 Fe 2.5835 Ang. Really at: 3.5819 2.0681 19.4358
3 Ge 2.5835 Ang. Really at: -0.0001 4.1361 19.4358
3 Ge 2.5835 Ang. Really at: -3.5820 -2.0680 19.4358
6 Fe 2.5835 Ang. Really at: -3.5820 2.0681 19.4358
1 Te 2.6603 Ang. Really at: -3.5819 2.0680 24.8872
1 Te 2.6603 Ang. Really at: 0.0001 -4.1362 24.8872
1 Te 2.6603 Ang. Really at: 3.5821 2.0680 24.8872
5 Fe 2.7452 Ang. Really at: -0.0000 0.0000 16.8420
Neighbors of: 5 Fe at: -0.0000 0.0000 16.8420
3 Ge 2.5835 Ang. Really at: 3.5819 -2.0680 19.4358
6 Fe 2.5835 Ang. Really at: -0.0001 -4.1361 19.4358
6 Fe 2.5835 Ang. Really at: 3.5819 2.0681 19.4358
3 Ge 2.5835 Ang. Really at: -0.0001 4.1361 19.4358
3 Ge 2.5835 Ang. Really at: -3.5820 -2.0680 19.4358
6 Fe 2.5835 Ang. Really at: -3.5820 2.0681 19.4358
2 Te 2.6603 Ang. Really at: -3.5819 2.0680 13.9844
2 Te 2.6603 Ang. Really at: 0.0001 -4.1362 13.9844
2 Te 2.6603 Ang. Really at: 3.5821 2.0680 13.9844
4 Fe 2.7452 Ang. Really at: -0.0000 0.0000 22.0296
Neighbors of: 6 Fe at: 3.5819 2.0681 19.4358
3 Ge 2.1887 Ang. Really at: -0.0001 4.1361 19.4358
3 Ge 2.1887 Ang. Really at: 7.1639 4.1361 19.4358
3 Ge 2.1887 Ang. Really at: 3.5819 -2.0680 19.4358
5 Fe 2.5835 Ang. Really at: 3.5820 6.2042 16.8420
4 Fe 2.5835 Ang. Really at: 3.5820 6.2042 22.0296
5 Fe 2.5835 Ang. Really at: -0.0000 0.0000 16.8420
4 Fe 2.5835 Ang. Really at: -0.0000 0.0000 22.0296
5 Fe 2.5835 Ang. Really at: 7.1639 0.0000 16.8420
4 Fe 2.5835 Ang. Really at: 7.1639 0.0000 22.0296
2 Te 2.8848 Ang. Really at: 3.5821 2.0680 13.9844
1 Te 2.8848 Ang. Really at: 3.5821 2.0680 24.8872

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373 0.131558E+00 0.531687E+00 0.000000E+00 0.250000E-02
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375 0.219264E+00 0.582323E+00 0.000000E+00 0.250000E-02
376 0.263117E+00 0.607642E+00 0.000000E+00 0.250000E-02
377 0.306969E+00 0.632960E+00 0.000000E+00 0.250000E-02
378 0.350822E+00 0.658279E+00 0.000000E+00 0.250000E-02
379 0.394675E+00 0.683597E+00 0.000000E+00 0.250000E-02
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389 -0.438528E-01 0.481050E+00 0.000000E+00 0.250000E-02
390 0.000000E+00 0.506368E+00 0.000000E+00 0.250000E-02
391 0.438528E-01 0.531687E+00 0.000000E+00 0.250000E-02
392 0.877055E-01 0.557005E+00 0.000000E+00 0.250000E-02
393 0.131558E+00 0.582323E+00 0.000000E+00 0.250000E-02
394 0.175411E+00 0.607642E+00 0.000000E+00 0.250000E-02
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data/lat3_791/Fe3GeTe2.ORB_INDX
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data/lat3_791/Fe3GeTe2.STRUCT_NEXT_ITER
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3.791000000 0.000000000 0.000000000
-1.895500000 3.283102306 0.000000000
0.000000000 0.000000000 20.570000000
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3 52 0.666673605 0.333326450 0.640241032
3 52 0.666673626 0.333326450 0.359758985
2 32 0.333327644 0.666670477 0.500000043
1 26 -0.000001304 0.000001264 0.566727331
1 26 -0.000001299 0.000001267 0.433272678
1 26 0.666661257 0.333340476 0.499999932

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data/lat3_791/Fe3GeTe2.STRUCT_OUT
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3.791000000 0.000000000 0.000000000
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3 52 0.666673626 0.333326450 0.359758985
2 32 0.333327644 0.666670477 0.500000043
1 26 -0.000001304 0.000001264 0.566727331
1 26 -0.000001299 0.000001267 0.433272678
1 26 0.666661257 0.333340476 0.499999932

10
data/lat3_791/Fe3GeTe2.XV
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7.163954594 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
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0.000000000 0.000000000 38.871681876 0.000000000 0.000000000 0.000000000
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3 52 3.582051658 2.068012852 24.887245724 0.000000000 0.000000000 0.000000000
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2 32 -0.000054407 4.136134751 19.435842617 0.000000000 0.000000000 0.000000000
1 26 -0.000013869 0.000007841 22.029644508 0.000000000 0.000000000 0.000000000
1 26 -0.000013846 0.000007858 16.842037703 0.000000000 0.000000000 0.000000000
1 26 3.581912958 2.068099874 19.435838291 0.000000000 0.000000000 0.000000000

23
data/lat3_791/Fe3GeTe2.bib
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# This file contains articles we encourage you to cite in case of publishing a paper.
# Each entry corresponds to using a feature that has been enabled via FDF-flags
# and which is based on a development paper as indicated.
# Primary SIESTA paper
@article{Soler2002,
journal = {{Journal of Physics: Condensed Matter}},
year = {2002},
volume = {14},
issue = {11},
doi = {10.1088/0953-8984/14/11/302},
}
# Spin-orbit coupling (off-site approximation)
@article{Cuadrado2012,
author = {{Cuadrado, R. and Cerda, J. I.}},
title = {{Fully relativistic pseudopotential formalism under an atomic orbital basis: spin–orbit splittings and magnetic anisotropies}},
journal = {{Journal of Physics: Condensed Matter}},
year = {2012},
volume = {24},
issue = {086005},
doi = {10.1088/0953-8984/24/8/086005},
}

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data/lat3_791/Fe3GeTe2.fdf
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# --------------------------
# GENERAL SYSTEM DESCRIPTORS
# --------------------------
SystemLabel Fe3GeTe2
SystemName Fe3GeTe2
NumberOfAtoms 6
NumberOfSpecies 3
%block ChemicalSpeciesLabel
1 26 Fe
2 32 Ge
3 52 Te
%endblock ChemicalSpeciesLabel
# ----------------
# BASIS DEFINITION
# ----------------
PAO.Basis DZP
PAO.EnergyShift 0.001 Ry
# --------------------------------
# ATOMIC COORDINATES
# --------------------------------
LatticeConstant 1.0 Ang
%block LatticeParameters
3.791 3.791 20.57 90.0 90.0 120.0
%endblock LatticeParameters
%block kgrid_Monkhorst_Pack
20 0 0 0
0 20 0 0
0 0 1 0
%endblock kgrid_Monkhorst_Pack
AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
0.66666667 0.33333333 0.62736262 3
0.66666667 0.33333333 0.37263738 3
0.33333333 0.66666667 0.5 2
0. 0. 0.56141409 1
0. 0. 0.43858591 1
0.66666667 0.33333333 0.5 1
%endblock AtomicCoordinatesAndAtomicSpecies
# --------------
# SPIN
# --------------
Spin spin-orbit
SpinOrbitStrength 1.0
WriteOrbMom T
%block DM.InitSpin
4 +
5 +
6 +
%endblock DM.InitSpin
# --------------
# XC
# --------------
xc.functional GGA
xc.authors PBE
# --------------
# GRID
# --------------
MeshCutoff 1000. Ry
GridCellSampling [ 2 2 2 ]
# --------------
# Solution Method
# --------------
SolutionMethod diagon
ElectronicTemperature 0.1 K
# --------------
# SCF
# --------------
SCF.DM.Tolerance 1.E-5
SCF.H.Tolerance 1.E-4 eV
SCF.Mix Hamiltonian
SCF.Mix.Spin all
SCF.Mixer.Method Pulay
SCF.Mixer.Weight 0.1
SCF.Mixer.History 6
SCF.Mixer.Kick 20
MaxSCFIterations 1000
DM.UseSaveDM T
# --------------
# MD
# --------------
MD.TypeOfRun CG
MD.Steps 1000
MD.MaxCGDispl 0.05 Ang
MD.MaxForceTol 0.005 eV/Ang
MD.VariableCell F
MD.UseSaveXV T
MD.UseSaveCG T
MD.MaxStressTol 0.01 GPa
#MD.TargetPressure 0.01 GPa
MD.PreconditionVariableCell 5.0 Ang
# --------------
# OUTPUT OPTIONS
# --------------
WriteMullikenPop 1
WriteEigenvalues T
WriteForces T
WriteCoorStep T
SaveHS T
Write.DM.NetCDF T
Write.DMHS.NetCDF T
CDF.Grid.Precision double
CDF.Save T
DM.UseSaveDM T
WriteCoorXmol T
Diag.ParallelOverK T

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data/lat3_791/Fe3GeTe2.out
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data/lat3_791/Fe3GeTe2.times
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timer: Number of nodes = 20
timer: Busiest calculating node was node = 18
timer: Times refer to node = 18
timer: Total elapsed wall-clock time (sec) = 4921.130
timer: CPU times (sec):
Calc: Sum, Avge, myNode, Avg/Max = 98310.798 4915.540 4921.325 0.999
No communications time available. Compile with -DMPI_TIMING
Tot: Sum, Avge, myNode, Avg/Max = 98310.798 4915.540 4921.325 0.999
Program times printed if > 0.000E+00 of total
Program Calls Prg.com Prg.com Prg.tot Prg.tot Nod.avg
/Tot.com /Tot.tot/Nod.max
siesta 1 0.000 0.0000 4921.325 1.0000 0.999
Setup 1 0.000 0.0000 0.511 0.0001 0.984
bands 1 0.000 0.0000 0.000 0.0000 0.858
KSV_init 1 0.000 0.0000 0.000 0.0000 0.917
IterGeom 10 0.000 0.0000 4920.527 0.9998 0.999
state_init 10 0.000 0.0000 1.272 0.0003 0.989
hsparse 10 0.000 0.0000 0.081 0.0000 0.576
overlap 10 0.000 0.0000 0.279 0.0001 0.658
Setup_H0 10 0.000 0.0000 161.354 0.0328 1.000
naefs 20 0.000 0.0000 0.011 0.0000 0.886
MolMec 20 0.000 0.0000 0.000 0.0000 0.098
kinefsm 20 0.000 0.0000 0.278 0.0001 0.606
nlefsm 20 0.000 0.0000 48.182 0.0098 0.745
DHSCF_Init 90 0.000 0.0000 1163.358 0.2364 0.944
DHSCF1 90 0.000 0.0000 82.443 0.0168 0.994
INITMESH 270 0.000 0.0000 369.066 0.0750 0.554
DHSCF2 90 0.000 0.0000 1080.910 0.2196 0.940
REMESH 90 0.000 0.0000 469.449 0.0954 0.865
SPLOAD 180 0.000 0.0000 369.038 0.0750 0.554
REORD 1140 0.000 0.0000 0.206 0.0000 0.941
PHION 90 0.000 0.0000 426.782 0.0867 0.873
COMM_BSC 7602 0.000 0.0000 105.291 0.0214 0.536
POISON 552 0.000 0.0000 14.244 0.0029 0.987
fft 1104 0.000 0.0000 13.151 0.0027 0.969
IterSCF 372 0.000 0.0000 2858.456 0.5808 0.998
setup_H 382 0.000 0.0000 2051.209 0.4168 1.000
DHSCF 462 0.000 0.0000 2821.010 0.5732 0.961
DHSCF3 462 0.000 0.0000 2266.686 0.4606 1.000
rhoofd 462 0.000 0.0000 1029.321 0.2092 0.914
XC 462 0.000 0.0000 113.504 0.0231 0.998
GXC-CellXC 462 0.000 0.0000 109.178 0.0222 0.991
cellXC 462 0.000 0.0000 108.908 0.0221 0.990
vmat 392 0.000 0.0000 976.532 0.1984 0.999
writeHSX 392 0.000 0.0000 33.003 0.0067 0.993
compute_dm 372 0.000 0.0000 730.565 0.1484 0.996
diagon 372 0.000 0.0000 629.148 0.1278 1.000
cdiag 14880 0.000 0.0000 91.288 0.0185 0.986
cdiag1 14880 0.000 0.0000 4.822 0.0010 0.986
cdiag2 14880 0.000 0.0000 17.911 0.0036 0.981
cdiag3 14880 0.000 0.0000 65.579 0.0133 0.986
cdiag4 7440 0.000 0.0000 1.677 0.0003 0.977
MIXER 362 0.000 0.0000 3.093 0.0006 0.858
PostSCF 10 0.000 0.0000 1898.042 0.3857 1.000
DHSCF4 80 0.000 0.0000 554.322 0.1126 0.838
dfscf 80 0.000 0.0000 499.182 0.1014 0.823
overfsm 10 0.000 0.0000 0.035 0.0000 0.636
state_analysis 10 0.000 0.0000 1.382 0.0003 0.951
siesta_move 10 0.000 0.0000 0.005 0.0000 0.876
Analysis 1 0.000 0.0000 0.284 0.0001 0.970
No communications time available. Compile with -DMPI_TIMING
Definitions:
Program: Name of a time-profiled routine (or code section)
Calls: Number of profiled calls to a program
Prg.com: CPU time in communications in one program in one node
Tot.com: CPU time in communications in all progs. in one node
Prg.tot: total CPU time in one program in one node
Tot.tot: total CPU time in all programs in one node
Nod.avg: average calculation time in one program across nodes
Nod.max: maximum calculation time in one program across nodes
Calculation time: CPU time excluding communications

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data/lat3_791/Fe3GeTe2.xyz
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6
Te 1.895539 1.094345 13.169758
Te 1.895539 1.094345 7.400242
Ge -0.000029 2.188747 10.285001
Fe -0.000007 0.000004 11.657581
Fe -0.000007 0.000004 8.912419
Fe 1.895466 1.094391 10.284999

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data/lat3_791/Ge.ion
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data/lat3_791/Ge.ion.nc
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data/lat3_791/Ge.ion.xml
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data/lat3_791/Ge.psf
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data/lat3_791/INPUT_TMP.58436
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# --------------------------
# GENERAL SYSTEM DESCRIPTORS
# --------------------------
SystemLabel Fe3GeTe2
SystemName Fe3GeTe2
NumberOfAtoms 6
NumberOfSpecies 3
%block ChemicalSpeciesLabel
1 26 Fe
2 32 Ge
3 52 Te
%endblock ChemicalSpeciesLabel
# ----------------
# BASIS DEFINITION
# ----------------
PAO.Basis DZP
PAO.EnergyShift 0.001 Ry
# --------------------------------
# ATOMIC COORDINATES
# --------------------------------
LatticeConstant 1.0 Ang
%block LatticeParameters
3.791 3.791 20.57 90.0 90.0 120.0
%endblock LatticeParameters
%block kgrid_Monkhorst_Pack
20 0 0 0
0 20 0 0
0 0 1 0
%endblock kgrid_Monkhorst_Pack
AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
0.66666667 0.33333333 0.62736262 3
0.66666667 0.33333333 0.37263738 3
0.33333333 0.66666667 0.5 2
0. 0. 0.56141409 1
0. 0. 0.43858591 1
0.66666667 0.33333333 0.5 1
%endblock AtomicCoordinatesAndAtomicSpecies
# --------------
# SPIN
# --------------
Spin spin-orbit
SpinOrbitStrength 1.0
WriteOrbMom T
%block DM.InitSpin
4 +
5 +
6 +
%endblock DM.InitSpin
# --------------
# XC
# --------------
xc.functional GGA
xc.authors PBE
# --------------
# GRID
# --------------
MeshCutoff 1000. Ry
GridCellSampling [ 2 2 2 ]
# --------------
# Solution Method
# --------------
SolutionMethod diagon
ElectronicTemperature 0.1 K
# --------------
# SCF
# --------------
SCF.DM.Tolerance 1.E-5
SCF.H.Tolerance 1.E-4 eV
SCF.Mix Hamiltonian
SCF.Mix.Spin all
SCF.Mixer.Method Pulay
SCF.Mixer.Weight 0.1
SCF.Mixer.History 6
SCF.Mixer.Kick 20
MaxSCFIterations 1000
DM.UseSaveDM T
# --------------
# MD
# --------------
MD.TypeOfRun CG
MD.Steps 1000
MD.MaxCGDispl 0.05 Ang
MD.MaxForceTol 0.005 eV/Ang
MD.VariableCell F
MD.UseSaveXV T
MD.UseSaveCG T
MD.MaxStressTol 0.01 GPa
#MD.TargetPressure 0.01 GPa
MD.PreconditionVariableCell 5.0 Ang
# --------------
# OUTPUT OPTIONS
# --------------
WriteMullikenPop 1
WriteEigenvalues T
WriteForces T
WriteCoorStep T
SaveHS T
Write.DM.NetCDF T
Write.DMHS.NetCDF T
CDF.Grid.Precision double
CDF.Save T
DM.UseSaveDM T
WriteCoorXmol T
Diag.ParallelOverK T

1
data/lat3_791/MESSAGES
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INFO: Job completed

44
data/lat3_791/OUTVARS.yml
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%YAML 1.2
---
siesta:
version: "master-post-4.1-268"
arch: "x86_64_MPI"
compiler: "GNU Fortran (GCC) 8.3.0"
fflags: "mpif90 -O2 -fPIC -ftree-vectorize -march=native"
fppflags: "-DFC_HAVE_ABORT -DMPI -DSIESTA__FLOOK -DCDF -DNCDF -DNCDF_4"
libs: "libfdict.a libncdf.a libfdict.a -lflookall -ldl -lnetcdff -lnetcdf -lhdf5_hhl -lhdf5 -lz -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl"
build: "mpi"
openmp: "no"
gemm3m: "no"
netcdf: "yes"
netcdf4: "yes"
netcdf4_mpi: "no"
metis: "no"
chess: "no"
elpa: "no"
flook: "yes"
pexsi: "no"
energies:
Ebs: -0.28235793E+02
Eions: 0.21377222E+03
Ena: 0.16680972E+02
Ekin: 0.18204901E+03
Enl: -0.10039819E+03
Eso: -0.16945358E-01
Edftu: 0.00000000E+00
DEna: -0.23487505E+01
DUscf: 0.40057219E+00
DUext: 0.00000000E+00
Exc: -0.94839892E+02
Ecorrec: 0.00000000E+00
Emadel: 0.00000000E+00
Emeta: 0.00000000E+00
Emolmec: 0.00000000E+00
Ekinion: 0.00000000E+00
Eharris: -0.21224544E+03
Etot: -0.21224545E+03
FreeEng: -0.21224545E+03
...

20
data/lat3_791/PARALLEL_DIST
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@ -1,20 +0,0 @@
Node 0 handles 8 orbitals.
Node 1 handles 4 orbitals.
Node 2 handles 4 orbitals.
Node 3 handles 4 orbitals.
Node 4 handles 4 orbitals.
Node 5 handles 4 orbitals.
Node 6 handles 4 orbitals.
Node 7 handles 4 orbitals.
Node 8 handles 4 orbitals.
Node 9 handles 4 orbitals.
Node 10 handles 4 orbitals.
Node 11 handles 4 orbitals.
Node 12 handles 4 orbitals.
Node 13 handles 4 orbitals.
Node 14 handles 4 orbitals.
Node 15 handles 4 orbitals.
Node 16 handles 4 orbitals.
Node 17 handles 4 orbitals.
Node 18 handles 4 orbitals.
Node 19 handles 4 orbitals.

74
data/lat3_791/TIMES
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@ -1,74 +0,0 @@
timer: Number of nodes = 20
timer: Busiest calculating node was node = 18
timer: Times refer to node = 18
timer: Total elapsed wall-clock time (sec) = 4921.130
timer: CPU times (sec):
Calc: Sum, Avge, myNode, Avg/Max = 98310.798 4915.540 4921.325 0.999
No communications time available. Compile with -DMPI_TIMING
Tot: Sum, Avge, myNode, Avg/Max = 98310.798 4915.540 4921.325 0.999
Program times printed if > 0.000E+00 of total
Program Calls Prg.com Prg.com Prg.tot Prg.tot Nod.avg
/Tot.com /Tot.tot/Nod.max
siesta 1 0.000 0.0000 4921.325 1.0000 0.999
Setup 1 0.000 0.0000 0.511 0.0001 0.984
bands 1 0.000 0.0000 0.000 0.0000 0.858
KSV_init 1 0.000 0.0000 0.000 0.0000 0.917
IterGeom 10 0.000 0.0000 4920.527 0.9998 0.999
state_init 10 0.000 0.0000 1.272 0.0003 0.989
hsparse 10 0.000 0.0000 0.081 0.0000 0.576
overlap 10 0.000 0.0000 0.279 0.0001 0.658
Setup_H0 10 0.000 0.0000 161.354 0.0328 1.000
naefs 20 0.000 0.0000 0.011 0.0000 0.886
MolMec 20 0.000 0.0000 0.000 0.0000 0.098
kinefsm 20 0.000 0.0000 0.278 0.0001 0.606
nlefsm 20 0.000 0.0000 48.182 0.0098 0.745
DHSCF_Init 90 0.000 0.0000 1163.358 0.2364 0.944
DHSCF1 90 0.000 0.0000 82.443 0.0168 0.994
INITMESH 270 0.000 0.0000 369.066 0.0750 0.554
DHSCF2 90 0.000 0.0000 1080.910 0.2196 0.940
REMESH 90 0.000 0.0000 469.449 0.0954 0.865
SPLOAD 180 0.000 0.0000 369.038 0.0750 0.554
REORD 1140 0.000 0.0000 0.206 0.0000 0.941
PHION 90 0.000 0.0000 426.782 0.0867 0.873
COMM_BSC 7602 0.000 0.0000 105.291 0.0214 0.536
POISON 552 0.000 0.0000 14.244 0.0029 0.987
fft 1104 0.000 0.0000 13.151 0.0027 0.969
IterSCF 372 0.000 0.0000 2858.456 0.5808 0.998
setup_H 382 0.000 0.0000 2051.209 0.4168 1.000
DHSCF 462 0.000 0.0000 2821.010 0.5732 0.961
DHSCF3 462 0.000 0.0000 2266.686 0.4606 1.000
rhoofd 462 0.000 0.0000 1029.321 0.2092 0.914
XC 462 0.000 0.0000 113.504 0.0231 0.998
GXC-CellXC 462 0.000 0.0000 109.178 0.0222 0.991
cellXC 462 0.000 0.0000 108.908 0.0221 0.990
vmat 392 0.000 0.0000 976.532 0.1984 0.999
writeHSX 392 0.000 0.0000 33.003 0.0067 0.993
compute_dm 372 0.000 0.0000 730.565 0.1484 0.996
diagon 372 0.000 0.0000 629.148 0.1278 1.000
cdiag 14880 0.000 0.0000 91.288 0.0185 0.986
cdiag1 14880 0.000 0.0000 4.822 0.0010 0.986
cdiag2 14880 0.000 0.0000 17.911 0.0036 0.981
cdiag3 14880 0.000 0.0000 65.579 0.0133 0.986
cdiag4 7440 0.000 0.0000 1.677 0.0003 0.977
MIXER 362 0.000 0.0000 3.093 0.0006 0.858
PostSCF 10 0.000 0.0000 1898.042 0.3857 1.000
DHSCF4 80 0.000 0.0000 554.322 0.1126 0.838
dfscf 80 0.000 0.0000 499.182 0.1014 0.823
overfsm 10 0.000 0.0000 0.035 0.0000 0.636
state_analysis 10 0.000 0.0000 1.382 0.0003 0.951
siesta_move 10 0.000 0.0000 0.005 0.0000 0.876
Analysis 1 0.000 0.0000 0.284 0.0001 0.970
No communications time available. Compile with -DMPI_TIMING
Definitions:
Program: Name of a time-profiled routine (or code section)
Calls: Number of profiled calls to a program
Prg.com: CPU time in communications in one program in one node
Tot.com: CPU time in communications in all progs. in one node
Prg.tot: total CPU time in one program in one node
Tot.tot: total CPU time in all programs in one node
Nod.avg: average calculation time in one program across nodes
Nod.max: maximum calculation time in one program across nodes
Calculation time: CPU time excluding communications

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1
data/lat3_791/error.err
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@ -1 +0,0 @@
Job completed

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7
data/lat3_791/run-siesta.mpi
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@ -1,7 +0,0 @@
#!/bin/bash
#PBS -N Fe3GeTe2-uu
#PBS -e error.err
#PBS -q cola_d
#PBS -l select=1:ncpus=20:mpiprocs=20
cd $PBS_O_WORKDIR
mpirun siesta < Fe3GeTe2.fdf > Fe3GeTe2.out

8
pyproject.toml
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@ -3,8 +3,8 @@ requires = ["hatchling"]
build-backend = "hatchling.build" build-backend = "hatchling.build"
[project] [project]
name = "grogu_magn" name = "grogupy"
version = "0.0.3" version = "0.2.0"
authors = [ authors = [
{ name="Daniel Pozsar", email="danielpozsar@student.elte.hu" }, { name="Daniel Pozsar", email="danielpozsar@student.elte.hu" },
{ name="Laszlo Oroszlany", email="laszlo.oroszlany@ttk.elte.hu" }, { name="Laszlo Oroszlany", email="laszlo.oroszlany@ttk.elte.hu" },
@ -25,6 +25,10 @@ dependencies = [
"netcdf4", "netcdf4",
"openmpi", "openmpi",
"mpi4py", "mpi4py",
"threadpoolctl"
]
optional-dependencies = [
"tqdm"
] ]
classifiers = [ classifiers = [

19
src/grogu_magn/example.py
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@ -1,19 +0,0 @@
# Copyright (c) [2024] [Daniel Pozsar]
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

10
src/grogu_magn/__init__.py → src/grogupy/__init__.py
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@ -1,4 +1,4 @@
# Copyright (c) [2024] [Daniel Pozsar] # Copyright (c) [2024] []
# #
# Permission is hereby granted, free of charge, to any person obtaining a copy # Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal # of this software and associated documentation files (the "Software"), to deal
@ -18,10 +18,10 @@
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE. # SOFTWARE.
from grogu_magn.core import * from grogupy.core import *
from grogu_magn.io import * from grogupy.io import *
from grogu_magn.magnetism import * from grogupy.magnetism import *
from grogu_magn.utils import * from grogupy.utils import *
try: try:
from tqdm import tqdm from tqdm import tqdm

4
src/grogu_magn/core.py → src/grogupy/core.py
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@ -1,4 +1,4 @@
# Copyright (c) [2024] [Daniel Pozsar] # Copyright (c) [2024] []
# #
# Permission is hereby granted, free of charge, to any person obtaining a copy # Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal # of this software and associated documentation files (the "Software"), to deal
@ -21,7 +21,7 @@
import numpy as np import numpy as np
from numpy.linalg import inv from numpy.linalg import inv
from grogu_magn.utils import blow_up_orbindx, commutator, parse_magnetic_entity from grogupy.utils import blow_up_orbindx, commutator, parse_magnetic_entity
def parallel_Gk(HK, SK, eran, eset): def parallel_Gk(HK, SK, eran, eset):

4
src/grogu_magn/grogu.py → src/grogupy/grogu.py
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@ -1,4 +1,4 @@
# Copyright (c) [2024] [Daniel Pozsar] # Copyright (c) [2024] []
# #
# Permission is hereby granted, free of charge, to any person obtaining a copy # Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal # of this software and associated documentation files (the "Software"), to deal
@ -40,7 +40,7 @@ from sys import getsizeof
import sisl import sisl
from mpi4py import MPI from mpi4py import MPI
from src.grogu_magn import * from src.grogupy import *
# input output stuff # input output stuff
###################################################################### ######################################################################

2
src/grogu_magn/io.py → src/grogupy/io.py
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@ -1,4 +1,4 @@
# Copyright (c) [2024] [Daniel Pozsar] # Copyright (c) [2024] []
# #
# Permission is hereby granted, free of charge, to any person obtaining a copy # Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal # of this software and associated documentation files (the "Software"), to deal

2
src/grogu_magn/magnetism.py → src/grogupy/magnetism.py
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@ -1,4 +1,4 @@
# Copyright (c) [2024] [Daniel Pozsar] # Copyright (c) [2024] []
# #
# Permission is hereby granted, free of charge, to any person obtaining a copy # Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal # of this software and associated documentation files (the "Software"), to deal

2
src/grogu_magn/utils.py → src/grogupy/utils.py
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@ -1,4 +1,4 @@
# Copyright (c) [2024] [Daniel Pozsar] # Copyright (c) [2024] []
# #
# Permission is hereby granted, free of charge, to any person obtaining a copy # Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal # of this software and associated documentation files (the "Software"), to deal

475
test.py
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@ -1,475 +0,0 @@
# Copyright (c) [2024] [Daniel Pozsar]
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import os
os.environ["OMP_NUM_THREADS"] = "1" # export OMP_NUM_THREADS=1
os.environ["OPENBLAS_NUM_THREADS"] = "1" # export OPENBLAS_NUM_THREADS=1
os.environ["MKL_NUM_THREADS"] = "1" # export MKL_NUM_THREADS=1
os.environ["VECLIB_MAXIMUM_THREADS"] = "1" # export VECLIB_MAXIMUM_THREADS=1
os.environ["NUMEXPR_NUM_THREADS"] = "1" # export NUMEXPR_NUM_THREADS=1
from timeit import default_timer as timer
# runtime information
times = dict()
times["start_time"] = timer()
import warnings
from sys import getsizeof
import sisl
from mpi4py import MPI
from src.grogu_magn import *
# input output stuff
######################################################################
######################################################################
######################################################################
infile = (
"/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf"
)
outfile = "./Fe3GeTe2_notebook"
magnetic_entities = [
dict(atom=3, l=2),
dict(atom=4, l=2),
dict(atom=5, l=2),
]
pairs = [
dict(ai=0, aj=1, Ruc=np.array([0, 0, 0])),
dict(ai=0, aj=2, Ruc=np.array([0, 0, 0])),
dict(ai=1, aj=2, Ruc=np.array([0, 0, 0])),
dict(ai=0, aj=2, Ruc=np.array([-1, -1, 0])),
dict(ai=1, aj=2, Ruc=np.array([-1, -1, 0])),
dict(ai=0, aj=2, Ruc=np.array([-1, 0, 0])),
dict(ai=1, aj=2, Ruc=np.array([-1, 0, 0])),
dict(ai=1, aj=2, Ruc=np.array([-2, 0, 0])),
dict(ai=1, aj=2, Ruc=np.array([-3, 0, 0])),
]
simulation_parameters = default_args
simulation_parameters["infile"] = infile
simulation_parameters["outfile"] = outfile
simulation_parameters["kset"] = 20
simulation_parameters["kdirs"] = "xy"
simulation_parameters["eset"] = 600
simulation_parameters["esetp"] = 10000
fdf = sisl.io.fdfSileSiesta("input.fdf")
fdf.get("XCF_Rotation")
######################################################################
######################################################################
######################################################################
# MPI parameters
comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()
root_node = 0
# include parallel size in simulation parameters
simulation_parameters["parallel_size"] = size
# check versions for debugging
if rank == root_node:
try:
print("sisl version: ", sisl.__version__)
except:
print("sisl version unknown.")
try:
print("numpy version: ", np.__version__)
except:
print("numpy version unknown.")
# rename outfile
if not simulation_parameters["outfile"].endswith(".pickle"):
simulation_parameters["outfile"] += ".pickle"
# if ebot is not given put it 0.1 eV under the smallest energy
if simulation_parameters["ebot"] is None:
try:
eigfile = simulation_parameters["infile"][:-3] + "EIG"
simulation_parameters["ebot"] = read_siesta_emin(eigfile) - 0.1
simulation_parameters["automatic_ebot"] = True
except:
print("Could not determine ebot.")
print("Parameter was not given and .EIG file was not found.")
# read sile
fdf = sisl.get_sile(simulation_parameters["infile"])
# read in hamiltonian
dh = fdf.read_hamiltonian()
# read unit cell vectors
simulation_parameters["cell"] = fdf.read_geometry().cell
# unit cell index
uc_in_sc_idx = dh.lattice.sc_index([0, 0, 0])
if rank == root_node:
print("\n\n\n\n\n")
print(
"#################################################################### JOB INFORMATION ###########################################################################"
)
print_job_description(simulation_parameters)
print(
"################################################################################################################################################################"
)
print("\n\n\n\n\n")
times["setup_time"] = timer()
print(f"Setup done. Elapsed time: {times['setup_time']} s")
print(
"================================================================================================================================================================"
)
# reformat Hamltonian and Overlap matrix for manipulations
hh, ss, NO = build_hh_ss(dh)
# symmetrizing Hamiltonian and Overlap matrix to make them hermitian
for i in range(dh.lattice.sc_off.shape[0]):
j = dh.lattice.sc_index(-dh.lattice.sc_off[i])
h1, h1d = hh[i], hh[j]
hh[i], hh[j] = (h1 + h1d.T.conj()) / 2, (h1d + h1.T.conj()) / 2
s1, s1d = ss[i], ss[j]
ss[i], ss[j] = (s1 + s1d.T.conj()) / 2, (s1d + s1.T.conj()) / 2
# identifying TRS and TRB parts of the Hamiltonian
TAUY = np.kron(np.eye(NO), tau_y)
hTR = np.array([TAUY @ hh[i].conj() @ TAUY for i in range(dh.lattice.nsc.prod())])
hTRS = (hh + hTR) / 2
hTRB = (hh - hTR) / 2
# extracting the exchange field
traced = [spin_tracer(hTRB[i]) for i in range(dh.lattice.nsc.prod())] # equation 77
XCF = np.array(
[
np.array([f["x"] / 2 for f in traced]),
np.array([f["y"] / 2 for f in traced]),
np.array([f["z"] / 2 for f in traced]),
]
)
# check if exchange field has scalar part
max_xcfs = abs(np.array(np.array([f["c"] / 2 for f in traced]))).max()
if max_xcfs > 1e-12:
warnings.warn(
f"Exchange field has non negligible scalar part. Largest value is {max_xcfs}"
)
if rank == root_node:
times["H_and_XCF_time"] = timer()
print(
f"Hamiltonian and exchange field rotated. Elapsed time: {times['H_and_XCF_time']} s"
)
print(
"================================================================================================================================================================"
)
# initialize pairs and magnetic entities based on input information
pairs, magnetic_entities = setup_pairs_and_magnetic_entities(
magnetic_entities, pairs, dh, simulation_parameters
)
if rank == root_node:
times["site_and_pair_dictionaries_time"] = timer()
print(
f"Site and pair dictionaries created. Elapsed time: {times['site_and_pair_dictionaries_time']} s"
)
print(
"================================================================================================================================================================"
)
# generate k space sampling
kset = make_kset(
dirs=simulation_parameters["kdirs"], NUMK=simulation_parameters["kset"]
)
# generate weights for k points
wkset = np.ones(len(kset)) / len(kset)
# split the k points based on MPI size
kpcs = np.array_split(kset, size)
# use progress bar if available
if rank == root_node and tqdm_imported:
kpcs[root_node] = tqdm(kpcs[root_node], desc="k loop")
if rank == root_node:
times["k_set_time"] = timer()
print(f"k set created. Elapsed time: {times['k_set_time']} s")
print(
"================================================================================================================================================================"
)
# this will contain the three Hamiltonian in the
# reference directions needed to calculate the energy
# variations upon rotation
hamiltonians = []
# iterate over the reference directions (quantization axes)
for i, orient in enumerate(simulation_parameters["ref_xcf_orientations"]):
# obtain rotated exchange field and Hamiltonian
R = RotMa2b(simulation_parameters["scf_xcf_orientation"], orient["o"])
rot_XCF = np.einsum("ij,jklm->iklm", R, XCF)
rot_H_XCF = sum(
[np.kron(rot_XCF[i], tau) for i, tau in enumerate([tau_x, tau_y, tau_z])]
)
rot_H_XCF_uc = rot_H_XCF[uc_in_sc_idx]
# obtain total Hamiltonian with the rotated exchange field
rot_H = hTRS + rot_H_XCF # equation 76
# store the relevant information of the Hamiltonian
hamiltonians.append(dict(orient=orient["o"], H=rot_H))
if simulation_parameters["calculate_charge"]:
hamiltonians[-1]["GS"] = np.zeros(
(simulation_parameters["eset"], rot_H.shape[1], rot_H.shape[2]),
dtype="complex128",
)
hamiltonians[-1]["GS_tmp"] = np.zeros(
(simulation_parameters["eset"], rot_H.shape[1], rot_H.shape[2]),
dtype="complex128",
)
# these are the rotations (for now) perpendicular to the quantization axis
for u in orient["vw"]:
# section 2.H
Tu = np.kron(np.eye(NO, dtype=int), tau_u(u))
Vu1, Vu2 = calc_Vu(rot_H_XCF_uc, Tu)
for mag_ent in magnetic_entities:
idx = mag_ent["spin_box_indices"]
# fill up the perturbed potentials (for now) based on the on-site projections
mag_ent["Vu1"][i].append(onsite_projection(Vu1, idx, idx))
mag_ent["Vu2"][i].append(onsite_projection(Vu2, idx, idx))
if rank == root_node:
times["reference_rotations_time"] = timer()
print(
f"Rotations done perpendicular to quantization axis. Elapsed time: {times['reference_rotations_time']} s"
)
print(
"================================================================================================================================================================"
)
# provide helpful information to estimate the runtime and memory
# requirements of the Greens function calculations
if rank == root_node:
print("Starting matrix inversions.")
if simulation_parameters["padawan_mode"]:
print("Padawan mode: ")
print(f"Total number of k points: {kset.shape[0]}")
print(f"Number of energy samples per k point: {simulation_parameters['eset']}")
print(f"Total number of directions: {len(hamiltonians)}")
print(
f"Total number of matrix inversions: {kset.shape[0] * len(hamiltonians) * simulation_parameters['eset']}"
)
print(
f"The shape of the Hamiltonian and the Greens function is {NO}x{NO}={NO*NO}"
)
# https://stackoverflow.com/questions/70746660/how-to-predict-memory-requirement-for-np-linalg-inv
# memory is O(64 n**2) for complex matrices
memory_size = getsizeof(hamiltonians[0]["H"].base) / 1024
print(
f"Memory taken by a single Hamiltonian is: {getsizeof(hamiltonians[0]['H'].base) / 1024} KB"
)
print(f"Expected memory usage per matrix inversion: {memory_size * 32} KB")
print(
f"Expected memory usage per k point for parallel inversion: {memory_size * len(hamiltonians) * simulation_parameters['eset'] * 32} KB"
)
print(
f"Expected memory usage on root node: {len(np.array_split(kset, size)[0]) * memory_size * len(hamiltonians) * simulation_parameters['eset'] * 32 / 1024} MB"
)
print(
"================================================================================================================================================================"
)
# MPI barrier
comm.Barrier()
# make energy contour
cont = make_contour(
emin=simulation_parameters["ebot"],
enum=simulation_parameters["eset"],
p=simulation_parameters["esetp"],
)
eran = cont.ze
# sampling the integrand on the contour and the BZ
for k in kpcs[rank]:
# weight of k point in BZ integral
wk = wkset[rank]
# iterate over reference directions
for i, hamiltonian_orientation in enumerate(hamiltonians):
# calculate Hamiltonian and Overlap matrix in a given k point
H = hamiltonian_orientation["H"]
HK, SK = hsk(H, ss, dh.sc_off, k)
if simulation_parameters["parallel_solver_for_Gk"]:
Gk = parallel_Gk(HK, SK, eran, simulation_parameters["eset"])
else:
# solve Greens function sequentially for the energies, because of memory bound
Gk = sequential_GK(HK, SK, eran, simulation_parameters["eset"])
# saving this for total charge
if simulation_parameters["calculate_charge"]:
hamiltonian_orientation["GS_tmp"] += Gk @ SK * wk
# store the Greens function slice of the magnetic entities
for mag_ent in magnetic_entities:
idx = mag_ent["spin_box_indices"]
mag_ent["Gii_tmp"][i] += onsite_projection(Gk, idx, idx) * wk
for pair in pairs:
# add phase shift based on the cell difference
phase = np.exp(1j * 2 * np.pi * k @ pair["Ruc"].T)
# get the pair orbital sizes from the magnetic entities
ai = magnetic_entities[pair["ai"]]["spin_box_indices"]
aj = magnetic_entities[pair["aj"]]["spin_box_indices"]
# store the Greens function slice of the magnetic entities
pair["Gij_tmp"][i] += onsite_projection(Gk, ai, aj) * phase * wk
pair["Gji_tmp"][i] += onsite_projection(Gk, aj, ai) / phase * wk
# summ reduce partial results of mpi nodes
for i in range(len(hamiltonians)):
# for total charge calculation
if simulation_parameters["calculate_charge"]:
comm.Reduce(hamiltonians[i]["GS_tmp"], hamiltonians[i]["GS"], root=root_node)
for mag_ent in magnetic_entities:
comm.Reduce(mag_ent["Gii_tmp"][i], mag_ent["Gii"][i], root=root_node)
for pair in pairs:
comm.Reduce(pair["Gij_tmp"][i], pair["Gij"][i], root=root_node)
comm.Reduce(pair["Gji_tmp"][i], pair["Gji"][i], root=root_node)
if rank == root_node:
times["green_function_inversion_time"] = timer()
print(
f"Calculated Greens functions. Elapsed time: {times['green_function_inversion_time']} s"
)
print(
"================================================================================================================================================================"
)
if rank == root_node:
# Calculate total charge
if simulation_parameters["calculate_charge"]:
for hamiltonian in hamiltonians:
GS = hamiltonian["GS"]
traced = np.trace((GS), axis1=1, axis2=2)
simulation_parameters["charges"].append(int_de_ke(traced, cont.we))
# iterate over the magnetic entities
for tracker, mag_ent in enumerate(magnetic_entities):
# iterate over the quantization axes
for i, Gii in enumerate(mag_ent["Gii"]):
storage = []
# iterate over the first and second order local perturbations
for Vu1, Vu2 in zip(mag_ent["Vu1"][i], mag_ent["Vu2"][i]):
# The Szunyogh-Lichtenstein formula
traced = np.trace(
(Vu2 @ Gii + 0.5 * Gii @ Vu1 @ Gii), axis1=1, axis2=2
) # this is the on site projection
# evaluation of the contour integral
storage.append(int_de_ke(traced, cont.we))
# fill up the magnetic entities dictionary with the energies
magnetic_entities[tracker]["energies"].append(storage)
# convert to np array
magnetic_entities[tracker]["energies"] = np.array(
magnetic_entities[tracker]["energies"]
)
# iterate over the pairs
for tracker, pair in enumerate(pairs):
# iterate over the quantization axes
for i, (Gij, Gji) in enumerate(zip(pair["Gij"], pair["Gji"])):
site_i = magnetic_entities[pair["ai"]]
site_j = magnetic_entities[pair["aj"]]
storage = []
# iterate over the first order local perturbations in all possible orientations for the two sites
for Vui in site_i["Vu1"][i]:
for Vuj in site_j["Vu1"][i]:
# The Szunyogh-Lichtenstein formula
traced = np.trace(
(Vui @ Gij @ Vuj @ Gji), axis1=1, axis2=2
) # this is the on site projection
# evaluation of the contour integral
storage.append(int_de_ke(traced, cont.we))
# fill up the pairs dictionary with the energies
pairs[tracker]["energies"].append(storage)
# convert to np array
pairs[tracker]["energies"] = np.array(pairs[tracker]["energies"])
# calculate magnetic parameters
for mag_ent in magnetic_entities:
Kxx, Kyy, Kzz, consistency = calculate_anisotropy_tensor(mag_ent)
mag_ent["K"] = np.array([Kxx, Kyy, Kzz]) * sisl.unit_convert("eV", "meV")
mag_ent["K_consistency"] = consistency
for pair in pairs:
J_iso, J_S, D, J = calculate_exchange_tensor(pair)
pair["J_iso"] = J_iso * sisl.unit_convert("eV", "meV")
pair["J_S"] = J_S * sisl.unit_convert("eV", "meV")
pair["D"] = D * sisl.unit_convert("eV", "meV")
pair["J"] = J * sisl.unit_convert("eV", "meV")
times["end_time"] = timer()
print("\n\n\n\n\n")
print(
"##################################################################### GROGU OUTPUT #############################################################################"
)
print_parameters(simulation_parameters)
print_atoms_and_pairs(magnetic_entities, pairs)
print(
"################################################################################################################################################################"
)
print_runtime_information(times)
print("")
# remove unwanted stuff before saving
pairs, magnetic_entities = remove_clutter_for_save(pairs, magnetic_entities)
# create output dictionary with all the relevant data
results = dict(
parameters=simulation_parameters,
magnetic_entities=magnetic_entities,
pairs=pairs,
runtime=times,
)
# save results
save_pickle(simulation_parameters["outfile"], results)
print("\n\n\n\n\n")
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