et209d
/
grogu
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

WARNING: ran pre commit hooks on these, this may break stuff...

Browse Source
class-solution
Daniel Pozsar 2 months ago
parent 49d2be4982
commit 0db938aa50
30 changed files with 29329 additions and 29929 deletions
Show Stats Download Patch File Download Diff File

38
Fe3GeTe2_benchmark_on_15k_300eset.log
Unescape View File

@ -1,16 +1,16 @@
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_15k_300eset.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -52,18 +52,18 @@ Pairs integrated.
Magnetic parameters calculated.
##################################################################### GROGU OUTPUT #############################################################################
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_15k_300eset.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -77,7 +77,7 @@ Ebot: -13
Eset: 300
Esetp: 1000
================================================================================================================================================================
Atomic information:
Atomic information:
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[atom index]Element(orbitals) x [Ang] y [Ang] z [Ang] Sx Sy Sz Q Lx Ly Lz Jx Jy Jz
----------------------------------------------------------------------------------------------------------------------------------------------------------------
@ -101,7 +101,7 @@ Symmetric-anisotropy: [-2.32809260e+00 1.41154602e-06 -9.40957764e-09 1.41154
J: [-4.22458475e+01 1.41154602e-06 -9.40957764e-09 1.41154602e-06
-4.12721879e+01 5.63570534e-07 -9.40957764e-09 5.63570534e-07
-3.62352293e+01]
Energies for debugging:
Energies for debugging:
array([[-3.52462334e-02, 5.22790048e-06, -5.22902762e-06,
-3.50238913e-02],
[-3.72242252e-02, 1.25410885e-08, -1.25222693e-08,
@ -121,7 +121,7 @@ Symmetric-anisotropy: [ 0.90424825 0.05359555 -0.07541288 0.05359555 0.51675
J: [-6.32993411e+01 5.35955501e-02 -7.54128755e-02 5.35955501e-02
-6.36868334e+01 -3.66014961e-02 -7.54128755e-02 -3.66014961e-02
-6.56245935e+01]
Energies for debugging:
Energies for debugging:
array([[-6.59077017e-02, 3.37863278e-03, -3.30542979e-03,
-6.63454261e-02],
[-6.53414853e-02, 5.87819515e-03, -5.72736940e-03,
@ -141,7 +141,7 @@ Symmetric-anisotropy: [ 0.9024007 0.05359252 0.07068773 0.05359252 0.51528
J: [-6.32966646e+01 5.35925196e-02 7.06877343e-02 5.35925196e-02
-6.36837832e+01 3.23646213e-02 7.06877343e-02 3.23646213e-02
-6.56167480e+01]
Energies for debugging:
Energies for debugging:
array([[-6.58989484e-02, -3.39791181e-03, 3.33318257e-03,
-6.63392511e-02],
[-6.53345476e-02, -5.88748024e-03, 5.74610477e-03,
@ -162,7 +162,7 @@ Symmetric-anisotropy: [ 2.81689694e-01 -9.99033947e-05 1.00133116e-04 -9.99033
J: [-6.41257790e+01 -9.99033947e-05 1.00133116e-04 -9.99033947e-05
-6.31697101e+01 9.79547273e-02 1.00133116e-04 9.79547273e-02
-6.59269169e+01]
Energies for debugging:
Energies for debugging:
array([[-6.51429577e-02, -6.76632987e-03, 6.57042041e-03,
-6.54030227e-02],
[-6.67108762e-02, -4.56940315e-07, 2.56674082e-07,
@ -183,7 +183,7 @@ Symmetric-anisotropy: [ 2.81831507e-01 -9.95864576e-05 7.28304048e-05 -9.95864
J: [-6.41271745e+01 -9.95864576e-05 7.28304048e-05 -9.95864576e-05
-6.31698065e+01 -9.79655745e-02 7.28304048e-05 -9.79655745e-02
-6.59300371e+01]
Energies for debugging:
Energies for debugging:
array([[-6.51430169e-02, 6.76649535e-03, -6.57056420e-03,
-6.54030961e-02],
[-6.67170573e-02, 6.60963771e-07, -8.06624581e-07,
@ -203,7 +203,7 @@ Symmetric-anisotropy: [ 0.9015663 -0.05345052 0.07536033 -0.05345052 0.51805
J: [-6.32853372e+01 -5.34505248e-02 7.53603270e-02 -5.34505248e-02
-6.36688505e+01 -3.23998894e-02 7.53603270e-02 -3.23998894e-02
-6.56065227e+01]
Energies for debugging:
Energies for debugging:
array([[-6.58846583e-02, 3.39716065e-03, -3.33236087e-03,
-6.63246913e-02],
[-6.53283870e-02, -5.87805205e-03, 5.72733140e-03,
@ -223,7 +223,7 @@ Symmetric-anisotropy: [ 0.90467906 -0.05344778 -0.07078134 -0.05344778 0.51541
J: [-6.32828201e+01 -5.34477814e-02 -7.07813383e-02 -5.34477814e-02
-6.36720845e+01 3.66227144e-02 -7.07813383e-02 3.66227144e-02
-6.56075929e+01]
Energies for debugging:
Energies for debugging:
array([[-6.58936437e-02, -3.37805282e-03, 3.30480739e-03,
-6.63310120e-02],
[-6.53215421e-02, 5.88691588e-03, -5.74535321e-03,
@ -242,7 +242,7 @@ Symmetric-anisotropy: [-0.02046716 -0.0444248 -0.03977157 -0.0444248 0.43165
-0.03977157 -0.07442493 -0.41118888]
J: [ 4.57908344 -0.0444248 -0.03977157 -0.0444248 5.03120664 -0.07442493
-0.03977157 -0.07442493 4.18836172]
Energies for debugging:
Energies for debugging:
array([[ 0.00472963, 0.00046075, -0.0003119 , 0.00466184],
[ 0.00364709, -0.00085554, 0.00093509, 0.0036577 ],
[ 0.00540057, -0.00061296, 0.00070181, 0.00550046]])
@ -258,7 +258,7 @@ Symmetric-anisotropy: [-0.08681631 0.00193669 -0.00538302 0.00193669 -0.07518
-0.00538302 -0.03449947 0.162005 ]
J: [-0.31785424 0.00193669 -0.00538302 0.00193669 -0.30622661 -0.03449947
-0.00538302 -0.03449947 -0.06903292]
Energies for debugging:
Energies for debugging:
array([[ 9.75938878e-06, 1.25731290e-04, -5.67323532e-05,
-1.49392424e-04],
[-1.47825232e-04, -3.25058913e-04, 3.35824948e-04,
@ -271,7 +271,7 @@ Test J_xx = E(y,z) = E(z,y)
-0.00022355248815234167 -0.00041215598873809247
================================================================================================================================================================
Runtime information:
Runtime information:
Total runtime: 295.33235375 s
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Initial setup: 0.09973091699999992 s

38
Fe3GeTe2_benchmark_on_15k_300eset_orb_test.log
Unescape View File

@ -1,16 +1,16 @@
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_15k_300eset_orb_test.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -52,18 +52,18 @@ Pairs integrated.
Magnetic parameters calculated.
##################################################################### GROGU OUTPUT #############################################################################
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_15k_300eset_orb_test.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -77,7 +77,7 @@ Ebot: -13
Eset: 300
Esetp: 1000
================================================================================================================================================================
Atomic information:
Atomic information:
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[atom index]Element(orbitals) x [Ang] y [Ang] z [Ang] Sx Sy Sz Q Lx Ly Lz Jx Jy Jz
----------------------------------------------------------------------------------------------------------------------------------------------------------------
@ -101,7 +101,7 @@ Symmetric-anisotropy: [ 3.04085587e-04 6.89183595e-08 -2.49215900e-07 6.89183
J: [ 3.48138853e-01 6.89183595e-08 -2.49215900e-07 6.89183595e-08
3.47340831e-01 5.24663366e-05 -2.49215900e-07 5.24663366e-05
3.48024619e-01]
Energies for debugging:
Energies for debugging:
array([[ 3.46973270e-04, 5.01274226e-07, -6.06206899e-07,
3.50103963e-04],
[ 3.49075968e-04, 1.06857880e-10, 3.91573921e-10,
@ -120,7 +120,7 @@ Symmetric-anisotropy: [ 0.00063826 -0.00205346 0.00155526 -0.00205346 0.00126
0.00155526 0.00091559 -0.00190362]
J: [ 0.21394658 -0.00205346 0.00155526 -0.00205346 0.21457368 0.00091559
0.00155526 0.00091559 0.2114047 ]
Energies for debugging:
Energies for debugging:
array([[ 2.09552786e-04, 8.85836233e-06, -1.06895444e-05,
2.12830226e-04],
[ 2.13256611e-04, 1.55953293e-05, -1.87058404e-05,
@ -140,7 +140,7 @@ Symmetric-anisotropy: [ 0.9024007 0.05359252 0.07068773 0.05359252 0.51528
J: [-6.32966646e+01 5.35925196e-02 7.06877343e-02 5.35925196e-02
-6.36837832e+01 3.23646213e-02 7.06877343e-02 3.23646213e-02
-6.56167480e+01]
Energies for debugging:
Energies for debugging:
array([[-6.58989484e-02, -3.39791181e-03, 3.33318257e-03,
-6.63392511e-02],
[-6.53345476e-02, -5.88748024e-03, 5.74610477e-03,
@ -161,7 +161,7 @@ Symmetric-anisotropy: [ 2.14788484e-03 6.88789785e-07 -6.77046017e-07 6.88789
J: [ 2.15033668e-01 6.88789785e-07 -6.77046017e-07 6.88789785e-07
2.12525607e-01 -1.77759079e-03 -6.77046017e-07 -1.77759079e-03
2.11098073e-01]
Energies for debugging:
Energies for debugging:
array([[ 2.12888094e-04, -1.83008074e-05, 2.18559890e-05,
2.12284870e-04],
[ 2.09308053e-04, -3.35069315e-10, 1.68916135e-09,
@ -182,7 +182,7 @@ Symmetric-anisotropy: [ 2.81831507e-01 -9.95864576e-05 7.28304048e-05 -9.95864
J: [-6.41271745e+01 -9.95864576e-05 7.28304048e-05 -9.95864576e-05
-6.31698065e+01 -9.79655745e-02 7.28304048e-05 -9.79655745e-02
-6.59300371e+01]
Energies for debugging:
Energies for debugging:
array([[-6.51430169e-02, 6.76649535e-03, -6.57056420e-03,
-6.54030961e-02],
[-6.67170573e-02, 6.60963771e-07, -8.06624581e-07,
@ -201,7 +201,7 @@ Symmetric-anisotropy: [ 0.00072503 0.0020527 -0.00155485 0.0020527 0.00098
-0.00155485 0.00102463 -0.00171383]
J: [ 0.21393071 0.0020527 -0.00155485 0.0020527 0.21419448 0.00102463
-0.00155485 0.00102463 0.21149184]
Energies for debugging:
Energies for debugging:
array([[ 2.09743450e-04, 8.87062962e-06, -1.09198949e-05,
2.12089719e-04],
[ 2.13240238e-04, -1.55974916e-05, 1.87071826e-05,
@ -221,7 +221,7 @@ Symmetric-anisotropy: [ 0.90467906 -0.05344778 -0.07078134 -0.05344778 0.51541
J: [-6.32828201e+01 -5.34477814e-02 -7.07813383e-02 -5.34477814e-02
-6.36720845e+01 3.66227144e-02 -7.07813383e-02 3.66227144e-02
-6.56075929e+01]
Energies for debugging:
Energies for debugging:
array([[-6.58936437e-02, -3.37805282e-03, 3.30480739e-03,
-6.63310120e-02],
[-6.53215421e-02, 5.88691588e-03, -5.74535321e-03,
@ -240,7 +240,7 @@ Symmetric-anisotropy: [-0.02046716 -0.0444248 -0.03977157 -0.0444248 0.43165
-0.03977157 -0.07442493 -0.41118888]
J: [ 4.57908344 -0.0444248 -0.03977157 -0.0444248 5.03120664 -0.07442493
-0.03977157 -0.07442493 4.18836172]
Energies for debugging:
Energies for debugging:
array([[ 0.00472963, 0.00046075, -0.0003119 , 0.00466184],
[ 0.00364709, -0.00085554, 0.00093509, 0.0036577 ],
[ 0.00540057, -0.00061296, 0.00070181, 0.00550046]])
@ -256,7 +256,7 @@ Symmetric-anisotropy: [-0.08681631 0.00193669 -0.00538302 0.00193669 -0.07518
-0.00538302 -0.03449947 0.162005 ]
J: [-0.31785424 0.00193669 -0.00538302 0.00193669 -0.30622661 -0.03449947
-0.00538302 -0.03449947 -0.06903292]
Energies for debugging:
Energies for debugging:
array([[ 9.75938878e-06, 1.25731290e-04, -5.67323532e-05,
-1.49392424e-04],
[-1.47825232e-04, -3.25058913e-04, 3.35824948e-04,
@ -269,7 +269,7 @@ Test J_xx = E(y,z) = E(z,y)
-0.00022355248815234167 -0.00041215598873809247
================================================================================================================================================================
Runtime information:
Runtime information:
Total runtime: 340.88071287500003 s
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Initial setup: 0.11835845800000011 s

38
Fe3GeTe2_benchmark_on_15k_300eset_orb_test2.log
Unescape View File

@ -1,16 +1,16 @@
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_15k_300eset_orb_test2.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -52,18 +52,18 @@ Pairs integrated.
Magnetic parameters calculated.
##################################################################### GROGU OUTPUT #############################################################################
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_15k_300eset_orb_test2.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -77,7 +77,7 @@ Ebot: -13
Eset: 300
Esetp: 1000
================================================================================================================================================================
Atomic information:
Atomic information:
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[atom index]Element(orbitals) x [Ang] y [Ang] z [Ang] Sx Sy Sz Q Lx Ly Lz Jx Jy Jz
----------------------------------------------------------------------------------------------------------------------------------------------------------------
@ -101,7 +101,7 @@ Symmetric-anisotropy: [-2.32043212e+00 2.53801348e-06 -1.08593736e-06 2.53801
J: [-4.31923232e+01 2.53801348e-06 -1.08593736e-06 2.53801348e-06
-4.22223518e+01 7.74258719e-05 -1.08593736e-06 7.74258719e-05
-3.72009983e+01]
Energies for debugging:
Energies for debugging:
array([[-3.62152318e-02, 6.08744793e-06, -6.24229967e-06,
-3.59883911e-02],
[-3.81867648e-02, -2.07836820e-09, 4.25024293e-09,
@ -121,7 +121,7 @@ Symmetric-anisotropy: [ 0.90811936 0.04789656 -0.07353011 0.04789656 0.52317
J: [-6.11208170e+01 4.78965641e-02 -7.35301053e-02 4.78965641e-02
-6.15057604e+01 -3.53313894e-02 -7.35301053e-02 -3.53313894e-02
-6.34602317e+01]
Energies for debugging:
Energies for debugging:
array([[-6.37479933e-02, 3.26584482e-03, -3.19518204e-03,
-6.41681572e-02],
[-6.31724700e-02, 5.68317362e-03, -5.53611341e-03,
@ -141,7 +141,7 @@ Symmetric-anisotropy: [ 0.9024007 0.05359252 0.07068773 0.05359252 0.51528
J: [-6.32966646e+01 5.35925196e-02 7.06877343e-02 5.35925196e-02
-6.36837832e+01 3.23646213e-02 7.06877343e-02 3.23646213e-02
-6.56167480e+01]
Energies for debugging:
Energies for debugging:
array([[-6.58989484e-02, -3.39791181e-03, 3.33318257e-03,
-6.63392511e-02],
[-6.53345476e-02, -5.88748024e-03, 5.74610477e-03,
@ -162,7 +162,7 @@ Symmetric-anisotropy: [ 2.91447198e-01 -1.04541004e-04 1.02420326e-04 -1.04541
J: [-6.19437002e+01 -1.04541004e-04 1.02420326e-04 -1.04541004e-04
-6.09961853e+01 9.61259121e-02 1.02420326e-04 9.61259121e-02
-6.37655566e+01]
Energies for debugging:
Energies for debugging:
array([[-6.29770048e-02, -6.54086391e-03, 6.34861208e-03,
-6.32308800e-02],
[-6.45541084e-02, -4.72318891e-07, 2.67478238e-07,
@ -183,7 +183,7 @@ Symmetric-anisotropy: [ 2.81831507e-01 -9.95864576e-05 7.28304048e-05 -9.95864
J: [-6.41271745e+01 -9.95864576e-05 7.28304048e-05 -9.95864576e-05
-6.31698065e+01 -9.79655745e-02 7.28304048e-05 -9.79655745e-02
-6.59300371e+01]
Energies for debugging:
Energies for debugging:
array([[-6.51430169e-02, 6.76649535e-03, -6.57056420e-03,
-6.54030961e-02],
[-6.67170573e-02, 6.60963771e-07, -8.06624581e-07,
@ -203,7 +203,7 @@ Symmetric-anisotropy: [ 0.90589405 -0.04774783 0.07347635 -0.04774783 0.52393
J: [-6.11067929e+01 -4.77478280e-02 7.34763489e-02 -4.77478280e-02
-6.14887510e+01 -3.17998960e-02 7.34763489e-02 -3.17998960e-02
-6.34425170e+01]
Energies for debugging:
Energies for debugging:
array([[-6.37256875e-02, 3.28370499e-03, -3.22010520e-03,
-6.41494027e-02],
[-6.31593465e-02, -5.68293772e-03, 5.53598502e-03,
@ -223,7 +223,7 @@ Symmetric-anisotropy: [ 0.90467906 -0.05344778 -0.07078134 -0.05344778 0.51541
J: [-6.32828201e+01 -5.34477814e-02 -7.07813383e-02 -5.34477814e-02
-6.36720845e+01 3.66227144e-02 -7.07813383e-02 3.66227144e-02
-6.56075929e+01]
Energies for debugging:
Energies for debugging:
array([[-6.58936437e-02, -3.37805282e-03, 3.30480739e-03,
-6.63310120e-02],
[-6.53215421e-02, 5.88691588e-03, -5.74535321e-03,
@ -242,7 +242,7 @@ Symmetric-anisotropy: [-0.02046716 -0.0444248 -0.03977157 -0.0444248 0.43165
-0.03977157 -0.07442493 -0.41118888]
J: [ 4.57908344 -0.0444248 -0.03977157 -0.0444248 5.03120664 -0.07442493
-0.03977157 -0.07442493 4.18836172]
Energies for debugging:
Energies for debugging:
array([[ 0.00472963, 0.00046075, -0.0003119 , 0.00466184],
[ 0.00364709, -0.00085554, 0.00093509, 0.0036577 ],
[ 0.00540057, -0.00061296, 0.00070181, 0.00550046]])
@ -258,7 +258,7 @@ Symmetric-anisotropy: [-0.08681631 0.00193669 -0.00538302 0.00193669 -0.07518
-0.00538302 -0.03449947 0.162005 ]
J: [-0.31785424 0.00193669 -0.00538302 0.00193669 -0.30622661 -0.03449947
-0.00538302 -0.03449947 -0.06903292]
Energies for debugging:
Energies for debugging:
array([[ 9.75938878e-06, 1.25731290e-04, -5.67323532e-05,
-1.49392424e-04],
[-1.47825232e-04, -3.25058913e-04, 3.35824948e-04,
@ -271,7 +271,7 @@ Test J_xx = E(y,z) = E(z,y)
-0.00022355248815234167 -0.00041215598873809247
================================================================================================================================================================
Runtime information:
Runtime information:
Total runtime: 376.47007308300005 s
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Initial setup: 0.10374624999999993 s

38
Fe3GeTe2_benchmark_on_15k_300eset_orb_test3.log
Unescape View File

@ -1,16 +1,16 @@
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_15k_300eset_orb_test3.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -52,18 +52,18 @@ Pairs integrated.
Magnetic parameters calculated.
##################################################################### GROGU OUTPUT #############################################################################
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_15k_300eset_orb_test3.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -77,7 +77,7 @@ Ebot: -13
Eset: 300
Esetp: 1000
================================================================================================================================================================
Atomic information:
Atomic information:
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[atom index]Element(orbitals) x [Ang] y [Ang] z [Ang] Sx Sy Sz Q Lx Ly Lz Jx Jy Jz
----------------------------------------------------------------------------------------------------------------------------------------------------------------
@ -101,7 +101,7 @@ Symmetric-anisotropy: [-2.32809260e+00 1.41154602e-06 -9.40957764e-09 1.41154
J: [-4.22458475e+01 1.41154602e-06 -9.40957764e-09 1.41154602e-06
-4.12721879e+01 5.63570534e-07 -9.40957764e-09 5.63570534e-07
-3.62352293e+01]
Energies for debugging:
Energies for debugging:
array([[-3.52462334e-02, 5.22790048e-06, -5.22902762e-06,
-3.50238913e-02],
[-3.72242252e-02, 1.25410885e-08, -1.25222693e-08,
@ -121,7 +121,7 @@ Symmetric-anisotropy: [ 0.00118024 -0.00059551 0.00215378 -0.00059551 0.00208
J: [ 8.88196640e-01 -5.95511036e-04 2.15378323e-03 -5.95511036e-04
8.89105004e-01 1.17990204e-03 2.15378323e-03 1.17990204e-03
8.83747559e-01]
Energies for debugging:
Energies for debugging:
array([[ 8.83744987e-04, -7.99390205e-06, 5.63409797e-06,
8.79698388e-04],
[ 8.83750131e-04, -1.46860980e-05, 1.03785316e-05,
@ -141,7 +141,7 @@ Symmetric-anisotropy: [ 0.00121184 -0.00059549 -0.00251075 -0.00059549 0.00196
J: [ 8.88030729e-01 -5.95487820e-04 -2.51075463e-03 -5.95487820e-04
8.88784872e-01 -1.53973241e-03 -2.51075463e-03 -1.53973241e-03
8.83641063e-01]
Energies for debugging:
Energies for debugging:
array([[ 8.83607807e-04, 8.40203736e-06, -5.32257253e-06,
8.79039963e-04],
[ 8.83674318e-04, 1.51089504e-05, -1.00874412e-05,
@ -162,7 +162,7 @@ Symmetric-anisotropy: [ 1.81701265e-03 3.64387859e-07 -3.98367585e-07 3.64387
J: [ 8.89205217e-01 3.64387859e-07 -3.98367585e-07 3.64387859e-07
8.88484078e-01 -2.68591644e-03 -3.98367585e-07 -2.68591644e-03
8.84475317e-01]
Energies for debugging:
Energies for debugging:
array([[ 8.85246673e-04, 1.60298046e-05, -1.06579717e-05,
8.79437935e-04],
[ 8.83703961e-04, -2.70801139e-09, 3.50474656e-09,
@ -183,7 +183,7 @@ Symmetric-anisotropy: [ 2.04264547e-03 3.37868118e-07 -1.11445852e-07 3.37868
J: [ 8.89577626e-01 3.37868118e-07 -1.11445852e-07 3.37868118e-07
8.88482966e-01 2.68621558e-03 -1.11445852e-07 2.68621558e-03
8.84544350e-01]
Energies for debugging:
Energies for debugging:
array([[ 8.85244669e-04, -1.60326937e-05, 1.06602626e-05,
8.79436556e-04],
[ 8.83844032e-04, 2.25306766e-09, -2.03017595e-09,
@ -203,7 +203,7 @@ Symmetric-anisotropy: [ 0.00131884 0.00059514 -0.00215344 0.00059514 0.00188
J: [ 8.88137090e-01 5.95135152e-04 -2.15344168e-03 5.95135152e-04
8.88706732e-01 1.53937991e-03 -2.15344168e-03 1.53937991e-03
8.83610919e-01]
Energies for debugging:
Energies for debugging:
array([[ 8.83530441e-04, -8.40658406e-06, 5.32782424e-06,
8.78961554e-04],
[ 8.83691396e-04, 1.46897672e-05, -1.03828838e-05,
@ -223,7 +223,7 @@ Symmetric-anisotropy: [ 0.00107296 0.0005951 0.00251098 0.0005951 0.00216
J: [ 8.87970741e-01 5.95103772e-04 2.51097668e-03 5.95103772e-04
8.89062777e-01 -1.18003269e-03 2.51097668e-03 -1.18003269e-03
8.83659823e-01]
Energies for debugging:
Energies for debugging:
array([[ 8.83704519e-04, 7.99924309e-06, -5.63917770e-06,
8.79656541e-04],
[ 8.83615126e-04, -1.51117047e-05, 1.00897514e-05,
@ -242,7 +242,7 @@ Symmetric-anisotropy: [-0.00042022 -0.00062904 -0.0002685 -0.00062904 -0.00046
-0.0002685 -0.00021878 0.00088328]
J: [-0.00088759 -0.00062904 -0.0002685 -0.00062904 -0.00093043 -0.00021878
-0.0002685 -0.00021878 0.0004159 ]
Energies for debugging:
Energies for debugging:
array([[-7.73059157e-07, -5.77850763e-06, 6.21607755e-06,
-4.49512876e-07],
[ 1.60486730e-06, 2.66304599e-06, -2.12605204e-06,
@ -263,7 +263,7 @@ Symmetric-anisotropy: [-7.05667939e-04 -3.63676406e-06 6.10574306e-05 -3.63676
J: [-1.23948374e-03 -3.63676406e-06 6.10574306e-05 -3.63676406e-06
6.05619321e-04 1.11677253e-04 6.10574306e-05 1.11677253e-04
-9.67582986e-04]
Energies for debugging:
Energies for debugging:
array([[ 1.09205519e-06, -6.26479989e-07, 4.03125483e-07,
1.08736474e-06],
[-3.02722116e-06, -1.80253356e-07, 5.81384945e-08,
@ -276,7 +276,7 @@ Test J_xx = E(y,z) = E(z,y)
-2.6416569513028827e-06 1.6268947133712035e-07
================================================================================================================================================================
Runtime information:
Runtime information:
Total runtime: 313.759723375 s
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Initial setup: 0.11209495800000013 s

BIN
Fe3GeTe2_final_test.pickle
View File

Binary file not shown.

BIN
Fe3GeTe2_notebook.pickle
View File

Binary file not shown.

46
LATEST_RUN_ON_KOMONDOR_AND_GROGU_MATLAB
Unescape View File

@ -6,18 +6,18 @@ Pairs integrated.
Magnetic parameters calculated.
##################################################################### GROGU OUTPUT #############################################################################
================================================================================================================================================================
Input file:
Input file:
./lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_benchmark_on_100k_600eset_final_test.pickle
Number of nodes in the parallel cluster: 8
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -31,7 +31,7 @@ Ebot: -15
Eset: 600
Esetp: 10000
================================================================================================================================================================
Atomic information:
Atomic information:
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[atom index]Element(orbitals) x [Ang] y [Ang] z [Ang] Sx Sy Sz Q Lx Ly Lz Jx Jy Jz
----------------------------------------------------------------------------------------------------------------------------------------------------------------
@ -55,7 +55,7 @@ Symmetric-anisotropy: [ 6.77397756e-01 -8.36063246e-05 -7.29981887e-05 -8.36063
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:
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,
@ -75,7 +75,7 @@ Symmetric-anisotropy: [ 0.11829377 0.13803139 -0.06754341 0.13803139 -0.12583
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:
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]])
@ -92,7 +92,7 @@ Symmetric-anisotropy: [ 0.11988385 0.13803161 0.0551642 0.13803161 -0.12943
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:
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 ]])
@ -110,7 +110,7 @@ Symmetric-anisotropy: [-2.67391508e-01 -2.42945028e-04 9.46271135e-04 -2.42945
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:
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,
@ -131,7 +131,7 @@ Symmetric-anisotropy: [-2.65342856e-01 -2.43008373e-04 3.22482902e-04 -2.43008
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:
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,
@ -151,7 +151,7 @@ Symmetric-anisotropy: [ 0.11573153 -0.13810044 0.06662932 -0.13810044 -0.12877
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:
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 ]])
@ -168,7 +168,7 @@ Symmetric-anisotropy: [ 0.11306029 -0.13810087 -0.05589985 -0.13810087 -0.12635
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:
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]])
@ -184,7 +184,7 @@ Symmetric-anisotropy: [ 0.13387827 0.05652754 0.02339254 0.05652754 -0.12675
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:
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,
@ -203,7 +203,7 @@ Symmetric-anisotropy: [-0.01463505 -0.02335298 -0.0115624 -0.02335298 0.01019
-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:
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,
@ -216,7 +216,7 @@ Test J_xx = E(y,z) = E(z,y)
6.878084728235458e-05 7.025382868651086e-05
================================================================================================================================================================
Runtime information:
Runtime information:
Total runtime: 3558.681470017007 s
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Initial setup: 1.776719820976723 s
@ -240,18 +240,18 @@ 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
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)

6
data/lat3_791/BASIS_ENTHALPY
Unescape View File

@ -1,4 +1,4 @@
-2878.0655830244073
The above number is the electronic (free)energy: -2887.7690769348492
-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
times the orbital volume (in Bohr**3): 52457.833503994734

6
data/lat3_791/BASIS_HARRIS_ENTHALPY
Unescape View File

@ -1,4 +1,4 @@
-2878.0654643176349
The above number is the electronic (free) harris energy: -2887.7689582280768
-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
times the orbital volume (in Bohr**3): 52457.833503994734

10342
data/lat3_791/Fe.ion
View File

File diff suppressed because it is too large Load Diff

11192
data/lat3_791/Fe.ion.xml
View File

File diff suppressed because it is too large Load Diff

2775
data/lat3_791/Fe.psf
View File

File diff suppressed because it is too large Load Diff

1
data/lat3_791/Fe3GeTe2.ORB_INDX
Unescape View File

@ -6823,4 +6823,3 @@ spec = Atomic species label
isc = Unit cell indexes to which orbital belongs:
center(io) = center(iuo) + sum_(i=1:3) cell_vec(i) * isc(i)
iuo = Equivalent orbital in first unit cell

1
data/lat3_791/Fe3GeTe2.bib
Unescape View File

@ -21,4 +21,3 @@
issue = {086005},
doi = {10.1088/0953-8984/24/8/086005},
}

14
data/lat3_791/Fe3GeTe2.fdf
Unescape View File

@ -31,7 +31,7 @@ LatticeConstant 1.0 Ang
%block kgrid_Monkhorst_Pack
%block kgrid_Monkhorst_Pack
20 0 0 0
0 20 0 0
0 0 1 0
@ -70,20 +70,20 @@ WriteOrbMom T
# --------------
# XC
# --------------
xc.functional GGA
xc.authors PBE
xc.functional GGA
xc.authors PBE
# --------------
# GRID
# --------------
MeshCutoff 1000. Ry
GridCellSampling [ 2 2 2 ]
GridCellSampling [ 2 2 2 ]
# --------------
# Solution Method
# --------------
SolutionMethod diagon
ElectronicTemperature 0.1 K
ElectronicTemperature 0.1 K
# --------------
# SCF
@ -102,7 +102,7 @@ DM.UseSaveDM T
# --------------
# MD
# --------------
MD.TypeOfRun CG
MD.TypeOfRun CG
MD.Steps 1000
MD.MaxCGDispl 0.05 Ang
MD.MaxForceTol 0.005 eV/Ang
@ -134,4 +134,4 @@ DM.UseSaveDM T
WriteCoorXmol T
Diag.ParallelOverK T
Diag.ParallelOverK T

328
data/lat3_791/Fe3GeTe2.out
Unescape View File

@ -13,9 +13,9 @@ Lua support
* Running on 20 nodes in parallel
>> Start of run: 17-APR-2024 11:41:22
***********************
* WELCOME TO SIESTA *
***********************
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.58436
@ -72,18 +72,18 @@ WriteOrbMom T
# --------------
# XC
# --------------
xc.functional GGA
xc.authors PBE
xc.functional GGA
xc.authors PBE
# --------------
# GRID
# --------------
MeshCutoff 1000. Ry
GridCellSampling [ 2 2 2 ]
GridCellSampling [ 2 2 2 ]
# --------------
# Solution Method
# --------------
SolutionMethod diagon
ElectronicTemperature 0.1 K
ElectronicTemperature 0.1 K
# --------------
# SCF
# --------------
@ -185,25 +185,25 @@ Fe Z= 26 Mass= 55.850 Charge= 0.17977+309
Lmxo=2 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=4
i=1 nzeta=2 polorb=1 (4s)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=4
L=2 Nsemic=0 Cnfigmx=3
i=1 nzeta=2 polorb=0 (3d)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=2 erefs: 0.17977+309 0.17977+309
@ -215,7 +215,7 @@ L=3 Nkbl=1 erefs: 0.17977+309
atom: Called for Fe (Z = 26)
read_vps: Pseudopotential generation method:
read_vps: ATM3.3 Troullier-Martins
read_vps: ATM3.3 Troullier-Martins
Valence charge for ps generation: 8.00000
read_vps: Pseudopotential includes a core correction:
@ -236,7 +236,7 @@ atom: Estimated core radius 2.79930
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 3.09372
atom: Maximum radius for r*vlocal+2*Zval: 2.83451
KBgen: Kleinman-Bylander projectors:
KBgen: Kleinman-Bylander projectors:
GHOST: No ghost state for L = 0
l= 0 rc= 2.047986 el= -0.311923 Ekb= 4.023955 kbcos= 0.247515
j- l= 1 rc= 2.047986 el= -0.065197 Ekb= 2.985458 kbcos= 0.163279
@ -258,7 +258,7 @@ KBgen: Total number of Kleinman-Bylander projectors: 37
atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split
atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0
@ -319,9 +319,9 @@ POLgen: Polarization orbital for state 4s
atom: Total number of Sankey-type orbitals: 15
atm_pop: Valence configuration (for local Pseudopot. screening):
4s( 2.00)
4p( 0.00)
3d( 6.00)
4s( 2.00)
4p( 0.00)
3d( 6.00)
Vna: chval, zval: 8.00000 8.00000
Vna: Cut-off radius for the neutral-atom potential: 9.649379
@ -335,24 +335,24 @@ Ge Z= 32 Mass= 72.610 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=4
i=1 nzeta=2 polorb=0 (4s)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=4
i=1 nzeta=2 polorb=1 (4p)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
@ -364,7 +364,7 @@ L=3 Nkbl=1 erefs: 0.17977+309
atom: Called for Ge (Z = 32)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 4.00000
xc_check: Exchange-correlation functional:
@ -382,7 +382,7 @@ VLOCAL1: 99.9% of the norm of Vloc inside 12.819 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 3.30931
atom: Maximum radius for r*vlocal+2*Zval: 2.88417
KBgen: Kleinman-Bylander projectors:
KBgen: Kleinman-Bylander projectors:
GHOST: No ghost state for L = 0
l= 0 rc= 3.435772 el= -0.860281 Ekb= 2.253895 kbcos= 0.346706
GHOST: No ghost state for L = 1
@ -402,7 +402,7 @@ KBgen: Total number of Kleinman-Bylander projectors: 31
atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split
atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0
@ -463,8 +463,8 @@ POLgen: Polarization orbital for state 4p
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
4s( 2.00)
4p( 2.00)
4s( 2.00)
4p( 2.00)
Vna: chval, zval: 4.00000 4.00000
Vna: Cut-off radius for the neutral-atom potential: 9.339529
@ -477,24 +477,24 @@ Te Z= 52 Mass= 127.60 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=5
i=1 nzeta=2 polorb=0 (5s)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=5
i=1 nzeta=2 polorb=1 (5p)
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
@ -506,7 +506,7 @@ L=3 Nkbl=1 erefs: 0.17977+309
atom: Called for Te (Z = 52)
read_vps: Pseudopotential generation method:
read_vps: ATM4.2.7 Troullier-Martins
read_vps: ATM4.2.7 Troullier-Martins
Valence charge for ps generation: 6.00000
xc_check: Exchange-correlation functional:
@ -524,7 +524,7 @@ VLOCAL1: 99.9% of the norm of Vloc inside 12.767 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 3.31594
atom: Maximum radius for r*vlocal+2*Zval: 2.92630
KBgen: Kleinman-Bylander projectors:
KBgen: Kleinman-Bylander projectors:
GHOST: No ghost state for L = 0
l= 0 rc= 3.619164 el= -1.105853 Ekb= 3.973827 kbcos= 0.331834
GHOST: No ghost state for L = 1
@ -544,7 +544,7 @@ KBgen: Total number of Kleinman-Bylander projectors: 31
atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split
atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0
@ -605,8 +605,8 @@ POLgen: Polarization orbital for state 5p
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
5s( 2.00)
5p( 4.00)
5s( 2.00)
5p( 4.00)
Vna: chval, zval: 6.00000 6.00000
Vna: Cut-off radius for the neutral-atom potential: 8.155972
@ -615,7 +615,7 @@ atom: _________________________________________________________________________
prinput: Basis input ----------------------------------------------------------
PAO.BasisType split
PAO.BasisType split
%block ChemicalSpeciesLabel
1 26 Fe # Species index, atomic number, species label
@ -626,25 +626,25 @@ PAO.BasisType split
%block PAO.Basis # Define Basis set
Fe 2 # Species label, number of l-shells
n=4 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
9.649 6.885
1.000 1.000
n=3 2 2 # n, l, Nzeta
6.632 2.565
1.000 1.000
9.649 6.885
1.000 1.000
n=3 2 2 # n, l, Nzeta
6.632 2.565
1.000 1.000
Ge 2 # Species label, number of l-shells
n=4 0 2 # n, l, Nzeta
6.581 4.412
1.000 1.000
n=4 0 2 # n, l, Nzeta
6.581 4.412
1.000 1.000
n=4 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
9.340 5.665
1.000 1.000
9.340 5.665
1.000 1.000
Te 2 # Species label, number of l-shells
n=5 0 2 # n, l, Nzeta
6.195 4.205
1.000 1.000
n=5 0 2 # n, l, Nzeta
6.195 4.205
1.000 1.000
n=5 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
8.156 5.009
1.000 1.000
8.156 5.009
1.000 1.000
%endblock PAO.Basis
prinput: ----------------------------------------------------------------------
@ -664,11 +664,11 @@ siesta: 0.00000 0.00000 21.82311 1 4
siesta: 0.00000 0.00000 17.04857 1 5
siesta: 3.58198 2.06806 19.43584 1 6
siesta: System type = slab
siesta: System type = slab
initatomlists: Number of atoms, orbitals, and projectors: 6 84 204
coxmol: Writing XMOL coordinates into file Fe3GeTe2.xyz
coxmol: Writing XMOL coordinates into file Fe3GeTe2.xyz
siesta: ******************** Simulation parameters ****************************
siesta:
@ -826,7 +826,7 @@ ts: **************************************************************
Begin CG opt. move = 0
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66666667 0.33333333 0.62736262 3 1 Te
0.66666667 0.33333333 0.37263738 3 2 Te
0.33333333 0.66666667 0.50000000 2 3 Ge
@ -1203,7 +1203,7 @@ Target enthalpy (eV/cell) -2887.3781
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -1262,7 +1262,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.035 -0.000 0.000 0.035
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -1283,7 +1283,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.033 -0.000 -0.000 -0.033
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -1325,7 +1325,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -1384,7 +1384,7 @@ Atom Orb Charge Spin Svec
Total 25.03161 5.20582 -0.000 0.000 5.206
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -1407,7 +1407,7 @@ Atom Orb Charge Spin Svec
Total 28.19264 5.13266 -0.000 0.000 5.133
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -1451,7 +1451,7 @@ cgvc: WARNING: CG file not found
Begin CG opt. move = 1
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66666736 0.33333257 0.62895986 3 1 Te
0.66666736 0.33333257 0.37104015 3 2 Te
0.33333155 0.66666849 0.50000000 2 3 Ge
@ -1478,7 +1478,7 @@ refcount: 1>
new_DM -- step: 2
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -1656,7 +1656,7 @@ Target enthalpy (eV/cell) -2887.4795
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -1715,7 +1715,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.039 -0.000 0.000 0.039
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -1736,7 +1736,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.034 -0.000 -0.000 -0.034
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -1778,7 +1778,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -1837,7 +1837,7 @@ Atom Orb Charge Spin Svec
Total 25.02154 5.28348 -0.000 0.000 5.283
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -1860,7 +1860,7 @@ Atom Orb Charge Spin Svec
Total 28.18575 5.20433 -0.000 0.000 5.204
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -1902,7 +1902,7 @@ Total 40.00000 5.05233 -0.000 0.000 5.052
Begin CG opt. move = 2
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66666842 0.33333142 0.63139058 3 1 Te
0.66666842 0.33333142 0.36860945 3 2 Te
0.33332884 0.66667125 0.50000001 2 3 Ge
@ -1929,7 +1929,7 @@ refcount: 1>
new_DM -- step: 3
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -2148,7 +2148,7 @@ Target enthalpy (eV/cell) -2887.6020
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -2207,7 +2207,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.047 -0.000 0.000 0.047
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -2228,7 +2228,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.039 0.000 0.000 -0.039
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -2270,7 +2270,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -2329,7 +2329,7 @@ Atom Orb Charge Spin Svec
Total 25.00210 5.44061 -0.000 0.000 5.441
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -2352,7 +2352,7 @@ Atom Orb Charge Spin Svec
Total 28.17223 5.34996 -0.000 0.000 5.350
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -2394,7 +2394,7 @@ Total 40.00000 5.19246 -0.000 0.000 5.192
Begin CG opt. move = 3
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66666948 0.33333027 0.63382131 3 1 Te
0.66666948 0.33333027 0.36617874 3 2 Te
0.33332613 0.66667402 0.50000002 2 3 Ge
@ -2421,7 +2421,7 @@ refcount: 1>
new_DM -- step: 4
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -2582,7 +2582,7 @@ Target enthalpy (eV/cell) -2887.6878
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -2641,7 +2641,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.047 0.000 -0.000 0.047
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -2662,7 +2662,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.041 -0.000 0.000 -0.041
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -2704,7 +2704,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -2763,7 +2763,7 @@ Atom Orb Charge Spin Svec
Total 24.98507 5.49344 -0.000 0.000 5.493
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -2786,7 +2786,7 @@ Atom Orb Charge Spin Svec
Total 28.16009 5.38968 -0.000 0.000 5.390
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -2828,7 +2828,7 @@ Total 40.00000 5.21298 -0.000 0.000 5.213
Begin CG opt. move = 4
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66667053 0.33332911 0.63625203 3 1 Te
0.66667053 0.33332911 0.36374803 3 2 Te
0.33332342 0.66667678 0.50000003 2 3 Ge
@ -2855,7 +2855,7 @@ refcount: 1>
new_DM -- step: 5
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -3076,7 +3076,7 @@ Target enthalpy (eV/cell) -2887.7394
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -3135,7 +3135,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.044 -0.000 0.000 0.044
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -3156,7 +3156,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.045 -0.000 -0.000 -0.045
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -3198,7 +3198,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -3257,7 +3257,7 @@ Atom Orb Charge Spin Svec
Total 24.96519 5.59565 -0.000 0.000 5.596
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -3280,7 +3280,7 @@ Atom Orb Charge Spin Svec
Total 28.14610 5.47374 -0.000 0.000 5.474
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -3322,7 +3322,7 @@ Total 40.00000 5.26648 -0.000 0.000 5.266
Begin CG opt. move = 5
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66667159 0.33332796 0.63868276 3 1 Te
0.66667159 0.33332796 0.36131733 3 2 Te
0.33332071 0.66667955 0.50000003 2 3 Ge
@ -3349,7 +3349,7 @@ refcount: 1>
new_DM -- step: 6
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -3525,7 +3525,7 @@ Target enthalpy (eV/cell) -2887.7640
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -3584,7 +3584,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.038 0.000 -0.000 0.038
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -3605,7 +3605,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.045 -0.000 0.000 -0.045
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -3647,7 +3647,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -3706,7 +3706,7 @@ Atom Orb Charge Spin Svec
Total 24.94861 5.63367 -0.000 0.000 5.634
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -3729,7 +3729,7 @@ Atom Orb Charge Spin Svec
Total 28.13607 5.48673 -0.000 0.000 5.487
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -3771,7 +3771,7 @@ Total 40.00000 5.21162 -0.000 0.000 5.212
Begin CG opt. move = 6
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66667265 0.33332680 0.64111348 3 1 Te
0.66667265 0.33332680 0.35888662 3 2 Te
0.33331800 0.66668232 0.50000004 2 3 Ge
@ -3798,7 +3798,7 @@ refcount: 1>
new_DM -- step: 7
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -3974,7 +3974,7 @@ Target enthalpy (eV/cell) -2887.7677
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4033,7 +4033,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.040 -0.000 0.000 0.040
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4054,7 +4054,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.046 -0.000 -0.000 -0.046
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4096,7 +4096,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -4155,7 +4155,7 @@ Atom Orb Charge Spin Svec
Total 24.92888 5.67926 -0.000 0.000 5.679
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -4178,7 +4178,7 @@ Atom Orb Charge Spin Svec
Total 28.12497 5.51147 -0.000 0.000 5.511
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -4220,7 +4220,7 @@ Total 40.00000 5.17734 -0.000 0.000 5.177
Begin CG opt. move = 7
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66667229 0.33332719 0.64030278 3 1 Te
0.66667229 0.33332719 0.35969732 3 2 Te
0.33331891 0.66668139 0.50000004 2 3 Ge
@ -4247,7 +4247,7 @@ refcount: 1>
new_DM -- step: 8
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -4421,7 +4421,7 @@ Target enthalpy (eV/cell) -2887.7688
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4480,7 +4480,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.043 -0.000 -0.000 0.043
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4501,7 +4501,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.046 0.000 -0.000 -0.046
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4543,7 +4543,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -4602,7 +4602,7 @@ Atom Orb Charge Spin Svec
Total 24.93523 5.65918 -0.000 0.000 5.659
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -4625,7 +4625,7 @@ Atom Orb Charge Spin Svec
Total 28.12904 5.49796 -0.000 0.000 5.498
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -4669,7 +4669,7 @@ cgvc: Finished line minimization 1. Mean atomic displacement = 0.0580
Begin CG opt. move = 8
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66669105 0.33331661 0.63941912 3 1 Te
0.66669135 0.33331661 0.36057985 3 2 Te
0.33344392 0.66652517 0.50000010 2 3 Ge
@ -4696,7 +4696,7 @@ refcount: 1>
new_DM -- step: 9
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -4870,7 +4870,7 @@ Target enthalpy (eV/cell) -2887.7399
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4929,7 +4929,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.031 0.000 -0.000 0.031
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4950,7 +4950,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.044 0.000 -0.000 -0.044
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -4992,7 +4992,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -5051,7 +5051,7 @@ Atom Orb Charge Spin Svec
Total 24.98627 5.61671 0.000 -0.000 5.617
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -5074,7 +5074,7 @@ Atom Orb Charge Spin Svec
Total 28.16844 5.46830 0.000 -0.000 5.468
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -5116,7 +5116,7 @@ Total 40.00000 5.24200 0.000 -0.000 5.242
Begin CG opt. move = 9
====================================
outcoor: Atomic coordinates (fractional):
outcoor: Atomic coordinates (fractional):
0.66667360 0.33332645 0.64024103 3 1 Te
0.66667363 0.33332645 0.35975899 3 2 Te
0.33332764 0.66667048 0.50000004 2 3 Ge
@ -5143,7 +5143,7 @@ refcount: 1>
new_DM -- step: 10
Re-using DM from previous geometries...
Number of DMs in history: 1
DM extrapolation coefficients:
DM extrapolation coefficients:
1 1.00000
New DM after history re-use:
<dSpData2D:SpM extrapolated using coords
@ -5319,7 +5319,7 @@ Target enthalpy (eV/cell) -2887.7691
moments: Magnetic moments from orbital angular momenta:
Species: Fe
Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -5378,7 +5378,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.041 0.000 -0.000 0.041
Species: Ge
Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -5399,7 +5399,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.046 0.000 0.000 -0.046
Species: Te
Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@ -5441,7 +5441,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations:
Species: Fe
Species: Fe
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -5500,7 +5500,7 @@ Atom Orb Charge Spin Svec
Total 24.93834 5.67564 -0.000 0.000 5.676
Species: Ge
Species: Ge
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -5523,7 +5523,7 @@ Atom Orb Charge Spin Svec
Total 28.13105 5.51515 -0.000 0.000 5.515
Species: Te
Species: Te
Atom Orb Charge Spin Svec
----------------------------------------------------------------
@ -5561,7 +5561,7 @@ Atom Orb Charge Spin Svec
Total 40.00000 5.20655 -0.000 0.000 5.207
outcoor: Relaxed atomic coordinates (fractional):
outcoor: Relaxed atomic coordinates (fractional):
0.66667360 0.33332645 0.64024103 3 1 Te
0.66667363 0.33332645 0.35975899 3 2 Te
0.33332764 0.66667048 0.50000004 2 3 Ge
@ -5569,7 +5569,7 @@ outcoor: Relaxed atomic coordinates (fractional):
-0.00000130 0.00000127 0.43327268 1 5 Fe
0.66666126 0.33334048 0.49999993 1 6 Fe
coxmol: Writing XMOL coordinates into file Fe3GeTe2.xyz
coxmol: Writing XMOL coordinates into file Fe3GeTe2.xyz
siesta: Eigenvalues (eV):
ik = 1

1
data/lat3_791/Fe3GeTe2.times
Unescape View File

@ -72,4 +72,3 @@ 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

6128
data/lat3_791/Ge.ion
View File

File diff suppressed because it is too large Load Diff

7046
data/lat3_791/Ge.ion.xml
View File

File diff suppressed because it is too large Load Diff

2854
data/lat3_791/Ge.psf
View File

File diff suppressed because it is too large Load Diff

8
data/lat3_791/INPUT_TMP.58436
Unescape View File

@ -50,18 +50,18 @@ WriteOrbMom T
# --------------
# XC
# --------------
xc.functional GGA
xc.authors PBE
xc.functional GGA
xc.authors PBE
# --------------
# GRID
# --------------
MeshCutoff 1000. Ry
GridCellSampling [ 2 2 2 ]
GridCellSampling [ 2 2 2 ]
# --------------
# Solution Method
# --------------
SolutionMethod diagon
ElectronicTemperature 0.1 K
ElectronicTemperature 0.1 K
# --------------
# SCF
# --------------

1
data/lat3_791/TIMES
Unescape View File

@ -72,4 +72,3 @@ 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

6480
data/lat3_791/Te.ion
View File

File diff suppressed because it is too large Load Diff

7418
data/lat3_791/Te.ion.xml
View File

File diff suppressed because it is too large Load Diff

2988
data/lat3_791/Te.psf
View File

File diff suppressed because it is too large Load Diff

60
data/lat3_791/fdf-58450.log
Unescape View File

@ -1,5 +1,5 @@
SystemName Fe3GeTe2
SystemLabel Fe3GeTe2
SystemName Fe3GeTe2
SystemLabel Fe3GeTe2
MPI.Nprocs.SIESTA 20 # default value
SpinPolarized F # default value
NonCollinearSpin F # default value
@ -10,7 +10,7 @@ SpinOrbit F # default value
#:defined? NonCollinearSpin F
#:block? SpinOrbit F
#:defined? SpinOrbit F
Spin spin-orbit
Spin spin-orbit
DebugObjects.Node 0 # default value
DebugObjects F # default value
XML.Write F # default value
@ -20,8 +20,8 @@ UseTreeTimer F # default value
timing-split-scf-steps F # default value
alloc_report_level 0 # default value
alloc_report_threshold 0.000000000 # default value
xc.functional GGA
xc.authors PBE
xc.functional GGA
xc.authors PBE
MM.Cutoff 30.00000000 Bohr # default value
MM.UnitsEnergy eV # default value
MM.UnitsDistance Ang # default value
@ -70,10 +70,10 @@ DFTU.FirstIteration F # default value
FilterCutoff 0.000000000 Ry # default value
FilterTol 0.000000000 Ry # default value
keep-npotu-bug F # default value
spin-orbit-strength 1.000000000
spin-orbit-strength 1.000000000
KB.Rmax 6.000000000 Bohr # default value
PAO.EnergyShift 0.1000000000E-02 Ry
# above item originally: PAO.EnergyShift 0.1000000000E-02 Ry
# above item originally: PAO.EnergyShift 0.1000000000E-02 Ry
PAO.SplitTailNorm F # default value
PAO.FixSplitTable F # default value
PAO.NewSplitCode F # default value
@ -92,10 +92,10 @@ PCC.Filter F # default value
FilterCutoff 0.000000000 Ry # default value
FilterTol 0.000000000 Ry # default value
keep-npotu-bug F # default value
spin-orbit-strength 1.000000000
spin-orbit-strength 1.000000000
KB.Rmax 6.000000000 Bohr # default value
PAO.EnergyShift 0.1000000000E-02 Ry
# above item originally: PAO.EnergyShift 0.1000000000E-02 Ry
# above item originally: PAO.EnergyShift 0.1000000000E-02 Ry
PAO.SplitTailNorm F # default value
PAO.FixSplitTable F # default value
PAO.NewSplitCode F # default value
@ -112,10 +112,10 @@ Vna.Filter F # default value
FilterCutoff 0.000000000 Ry # default value
FilterTol 0.000000000 Ry # default value
keep-npotu-bug F # default value
spin-orbit-strength 1.000000000
spin-orbit-strength 1.000000000
KB.Rmax 6.000000000 Bohr # default value
PAO.EnergyShift 0.1000000000E-02 Ry
# above item originally: PAO.EnergyShift 0.1000000000E-02 Ry
# above item originally: PAO.EnergyShift 0.1000000000E-02 Ry
PAO.SplitTailNorm F # default value
PAO.FixSplitTable F # default value
PAO.NewSplitCode F # default value
@ -134,13 +134,13 @@ Atom-Setup-Only F # default value
UseStructFile F # default value
MD.UseStructFile F # default value
LatticeConstant 1.889726878 Bohr
# above item originally: LatticeConstant 1.000000000 Ang
# above item originally: LatticeConstant 1.000000000 Ang
#:block? LatticeParameters T
#:block? LatticeVectors F
%block LatticeParameters
3.791 3.791 20.57 90.0 90.0 120.0
%endblock LatticeParameters
AtomicCoordinatesFormat Fractional
AtomicCoordinatesFormat Fractional
NumberOfAtoms 6
#:block? AtomicCoordinatesOrigin F
#:defined? AtomicCoordinatesOrigin F
@ -162,11 +162,11 @@ ZM.CalcAllForces F # default value
MD.UseSaveXV T
MD.UseSaveZM F # default value
WriteCoorInitial T # default value
MD.TypeOfRun CG
MD.TypeOfRun CG
MD.TypeOfRun CG
MD.TypeOfRun CG
MD.InitialTimeStep 1 # default value
MD.FinalTimeStep 1 # default value
MD.TypeOfRun CG
MD.TypeOfRun CG
MaxBondDistance 6.000000000 Bohr # default value
Output-Structure-Only F # default value
WriteCoorXmol T
@ -184,7 +184,7 @@ WriteVoronoiPop F # default value
PartialChargesAtEveryGeometry F # default value
PartialChargesAtEveryScfStep F # default value
MeshCutoff 1000.000000 Ry
# above item originally: MeshCutoff 1000.000000 Ry
# above item originally: MeshCutoff 1000.000000 Ry
NetCharge 0.000000000 # default value
MinSCFIterations 0 # default value
MaxSCFIterations 1000
@ -198,7 +198,7 @@ SCF.MustConverge T # default value
TS.MixH T # default value
MixHamiltonian T # default value
MixCharge F # default value
SCF.Mix Hamiltonian
SCF.Mix Hamiltonian
Compat-pre-v4-DM-H F # default value
SCF.MixAfterConvergence F # default value
SCF.Recompute-H-After-Scf F # default value
@ -224,7 +224,7 @@ SCF.EDM.Converge F # default value
SCF.EDM.Tolerance 0.7349806700E-04 Ry # default value
SCF.H.Converge T # default value
SCF.H.Tolerance 0.7349798845E-05 Ry
# above item originally: SCF.H.Tolerance 0.1000000000E-03 eV
# above item originally: SCF.H.Tolerance 0.1000000000E-03 eV
DM.RequireEnergyConvergence F # default value
SCF.FreeE.Converge F # default value
DM.EnergyTolerance 0.7349806700E-05 Ry # default value
@ -234,9 +234,9 @@ SCF.MonitorForces F # default value
UseSaveData F # default value
DM.UseSaveDM T
NeglNonOverlapInt F # default value
SolutionMethod diagon
SolutionMethod diagon
ElectronicTemperature 0.6333564230E-06 Ry
# above item originally: ElectronicTemperature 0.1000000000 K
# above item originally: ElectronicTemperature 0.1000000000 K
FixSpin F # default value
Spin.Fix F # default value
SOC.Split.SR.SO T # default value
@ -267,7 +267,7 @@ TDED.Inverse.Linear T # default value
TDED.WF.Save F # default value
MD.VariableCell F
compat-pre-v4-dynamics F # default value
MD.TypeOfRun CG
MD.TypeOfRun CG
MD.UseSaveCG T
Optim.Broyden F # default value
#:block? Optim.Broyden F
@ -275,12 +275,12 @@ Optim.Broyden F # default value
MD.NumCGsteps 0 # default value
MD.Steps 1000
MD.MaxCGDispl 0.9448634389E-01 Bohr
# above item originally: MD.MaxCGDispl 0.5000000000E-01 Ang
# above item originally: MD.MaxCGDispl 0.5000000000E-01 Ang
MD.MaxDispl 0.9448634389E-01 Bohr # default value
MD.MaxForceTol 0.1944674385E-03 Ry/Bohr
# above item originally: MD.MaxForceTol 0.5000000000E-02 eV/Ang
# above item originally: MD.MaxForceTol 0.5000000000E-02 eV/Ang
MD.MaxStressTol 0.6797726840E-06 Ry/Bohr**3
# above item originally: MD.MaxStressTol 0.1000000000E-01 GPa
# above item originally: MD.MaxStressTol 0.1000000000E-01 GPa
GeometryMustConverge F # default value
MD.InitialTimeStep 1 # default value
#:defined? MD.Steps T
@ -301,7 +301,7 @@ MD.FCfirst 1 # default value
MD.FClast 6 # default value
UseSpatialDecomposition F # default value
UseDomainDecomposition F # default value
SCF.Mix.Spin all
SCF.Mix.Spin all
Mixer.Debug F # default value
Mixer.Debug.MPI F # default value
DM.NumberPulay 2 # default value
@ -312,12 +312,12 @@ DM.KickMixingWeight 0.5000000000 # default value
SCF.LinearMixingAfterPulay F # default value
SCF.MixingWeightAfterPulay 0.2500000000 # default value
SCF.Mixer.History 6
SCF.Mixer.Weight 0.1000000000
SCF.Mixer.Weight 0.1000000000
SCF.Mixer.Kick 20
SCF.Mixer.Kick.Weight 0.5000000000 # default value
SCF.Mixer.Restart 0 # default value
SCF.Mixer.Restart.Save 1 # default value
SCF.Mixer.Method Pulay
SCF.Mixer.Method Pulay
SCF.Mixer.Variant original # default value
SCF.Mixer.Linear.After -1 # default value
SCF.Mixer.Linear.After.Weight 0.2500000000 # default value
@ -460,10 +460,10 @@ TimeReversalSymmetryForKpoints F # default value
#:defined? TS.kgrid.File F
LUA.Interactive F # default value
LUA.Script # default value
AtomicCoordinatesFormat Fractional
AtomicCoordinatesFormat Fractional
AtomCoorFormatOut Fractional # default value
LatticeConstant 1.889726878 Bohr
# above item originally: LatticeConstant 1.000000000 Ang
# above item originally: LatticeConstant 1.000000000 Ang
debug-folding F # default value
Save.Overlap.Gradient F # default value
Sonly F # default value

47
input.fdf
Unescape View File

@ -0,0 +1,47 @@
InputFile /Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
OutputFile ./Fe3GeTe2_notebook
ScfOrientation [ 0 0 1 ]
%block XCF_Rotation
1 0 0
0 1 0
0 0 1
%endblock XCFRotation
%block XCF_Rotation
0 1 0
1 0 0
0 0 1
%endblock XCFRotation
%block XCF_Rotation
0 0 1
1 0 0
0 1 0
%endblock XCFRotation
%block MagneticEntites # atom index and orbital index
3 2
4 2
5 2
%endblock MagneticEntites
%Pairsblock # MagneticEntites index ai and aj, supercell offset
0 1 0 0 0
0 2 0 0 0
1 2 0 0 0
0 2 -1 -1 0
1 2 -1 -1 0
0 2 -1 0 0
1 2 -1 0 0
1 2 -2 0 0
1 2 -3 0 0
%endPairsblock
INTEGRAL.Kset 3
INTEGRAL.Kdirs xy
INTEGRAL.Ebot -13
INTEGRAL.Eset 300
INTEGRAL.Esetp 1000

32
out with HK = HK + Ef * SK.txt
Unescape View File

@ -3,18 +3,18 @@ Pairs integrated.
Magnetic parameters calculated.
##################################################################### GROGU OUTPUT #############################################################################
================================================================================================================================================================
Input file:
Input file:
/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf
Output file:
Output file:
./Fe3GeTe2_notebook.pickle
Number of nodes in the parallel cluster: 1
================================================================================================================================================================
Cell [Ang]:
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:
DFT axis:
[0 0 1]
Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -28,7 +28,7 @@ Ebot: -13
Eset: 300
Esetp: 1000
================================================================================================================================================================
Atomic information:
Atomic information:
----------------------------------------------------------------------------------------------------------------------------------------------------------------
[atom index]Element(orbitals) x [Ang] y [Ang] z [Ang] Sx Sy Sz Q Lx Ly Lz Jx Jy Jz
----------------------------------------------------------------------------------------------------------------------------------------------------------------
@ -52,7 +52,7 @@ Symmetric-anisotropy: [ 7.51357435e-02 -7.11950712e-07 3.59136771e-08 -7.11950
J: [ 3.81154345e+00 -7.11950712e-07 3.59136771e-08 -7.11950712e-07
3.81154015e+00 3.13082991e-08 3.59136771e-08 3.13082991e-08
3.58613951e+00]
Energies for debugging:
Energies for debugging:
array([[ 3.58613658e-03, 1.50649068e-07, -1.50711685e-07,
3.58823154e-03],
[ 3.58614245e-03, -6.66917293e-09, 6.59734558e-09,
@ -72,7 +72,7 @@ Symmetric-anisotropy: [ 0.00046905 0.00297291 -0.00117676 0.00297291 -0.00302
J: [ 1.36697602e+00 2.97290780e-03 -1.17675699e-03 2.97290780e-03
1.36348532e+00 -6.33095832e-04 -1.17675699e-03 -6.33095832e-04
1.36905957e+00]
Energies for debugging:
Energies for debugging:
array([[ 1.36869655e-03, 6.07996330e-05, -5.95334413e-05,
1.36354141e-03],
[ 1.36942260e-03, 1.05300334e-04, -1.02946820e-04,
@ -92,7 +92,7 @@ Symmetric-anisotropy: [ 0.0004341 0.00297286 0.00136618 0.00297286 -0.00305
J: [1.36699315e+00 2.97285931e-03 1.36618160e-03 2.97285931e-03
1.36350704e+00 8.31592395e-04 1.36618160e-03 8.31592395e-04
1.36917697e+00]
Energies for debugging:
Energies for debugging:
array([[ 1.36884061e-03, -6.09739008e-05, 5.93107160e-05,
1.36356111e-03],
[ 1.36951332e-03, -1.05470361e-04, 1.02737998e-04,
@ -113,7 +113,7 @@ Symmetric-anisotropy: [-4.78793224e-03 -5.40296355e-06 4.35410484e-06 -5.40296
J: [ 1.36183963e+00 -5.40296355e-06 4.35410484e-06 -5.40296355e-06
1.36880565e+00 1.46954942e-03 4.35410484e-06 1.46954942e-03
1.36923739e+00]
Energies for debugging:
Energies for debugging:
array([[ 1.36990885e-03, -1.21632799e-04, 1.18693700e-04,
1.36893010e-03],
[ 1.36856594e-03, -8.08368896e-10, -7.89984078e-09,
@ -134,7 +134,7 @@ Symmetric-anisotropy: [-4.76680949e-03 -5.40568363e-06 4.15669294e-06 -5.40568
J: [ 1.36184799e+00 -5.40568363e-06 4.15669294e-06 -5.40568363e-06
1.36881823e+00 -1.46945257e-03 4.15669294e-06 -1.46945257e-03
1.36917819e+00]
Energies for debugging:
Energies for debugging:
array([[ 1.36992100e-03, 1.21632465e-04, -1.18693560e-04,
1.36894224e-03],
[ 1.36843538e-03, 2.07139714e-09, -1.03847830e-08,
@ -154,7 +154,7 @@ Symmetric-anisotropy: [ 0.00044657 -0.00296955 0.00117251 -0.00296955 -0.00303
J: [ 1.36681306e+00 -2.96954847e-03 1.17250768e-03 -2.96954847e-03
1.36332921e+00 -8.31759183e-04 1.17250768e-03 -8.31759183e-04
1.36895719e+00]
Energies for debugging:
Energies for debugging:
array([[ 1.36864715e-03, 6.09736506e-05, -5.93101323e-05,
1.36338366e-03],
[ 1.36926723e-03, -1.05302174e-04, 1.02957159e-04,
@ -174,7 +174,7 @@ Symmetric-anisotropy: [ 0.00045093 -0.00296959 -0.00137041 -0.00296959 -0.00302
J: [ 1.36680784e+00 -2.96958730e-03 -1.37041361e-03 -2.96958730e-03
1.36333151e+00 6.33143106e-04 -1.37041361e-03 6.33143106e-04
1.36893138e+00]
Energies for debugging:
Energies for debugging:
array([[ 1.36852649e-03, -6.08031071e-05, 5.95368209e-05,
1.36338712e-03],
[ 1.36933627e-03, 1.05475941e-04, -1.02735114e-04,
@ -195,7 +195,7 @@ Symmetric-anisotropy: [ 1.71572275e-04 -1.64462154e-04 -6.17520368e-05 -1.64462
J: [-3.30303816e-03 -1.64462154e-04 -6.17520368e-05 -1.64462154e-04
-3.42142919e-03 2.26715191e-04 -6.17520368e-05 2.26715191e-04
-3.69936395e-03]
Energies for debugging:
Energies for debugging:
array([[-3.70537194e-06, -5.86835019e-06, 5.41491981e-06,
-3.68176164e-06],
[-3.69335596e-06, -1.84488317e-06, 1.96838725e-06,
@ -214,7 +214,7 @@ Symmetric-anisotropy: [ 0.00095486 -0.00049048 -0.00010491 -0.00049048 -0.00065
-0.00010491 -0.00015335 -0.00030483]
J: [ 0.00652769 -0.00049048 -0.00010491 -0.00049048 0.0049228 -0.00015335
-0.00010491 -0.00015335 0.00526801]
Energies for debugging:
Energies for debugging:
array([[ 5.39229066e-06, -2.91508841e-06, 3.22178614e-06,
4.70355358e-06],
[ 5.14372081e-06, -3.12647464e-06, 3.33630142e-06,
@ -227,7 +227,7 @@ Test J_xx = E(y,z) = E(z,y)
6.553735898142947e-06 6.501653779660145e-06
================================================================================================================================================================
Runtime information:
Runtime information:
Total runtime: 350.25778825 s
----------------------------------------------------------------------------------------------------------------------------------------------------------------
Initial setup: 0.13192529200000003 s
@ -236,4 +236,4 @@ Pair and site datastructure creatrions: 0.060 s
k set cration and distribution: 0.045 s
Rotating XC potential: 0.247 s
Greens function inversion: 349.010 s
Calculate energies and magnetic components: 0.248 s
Calculate energies and magnetic components: 0.248 s

799
test.ipynb
View File

File diff suppressed because it is too large Load Diff

533
test.py
Unescape View File

@ -1,61 +1,52 @@
import pickle
import warnings
from sys import getsizeof
# 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.
from timeit import default_timer as timer
import numpy as np
import sisl
import sisl.viz
from mpi4py import MPI
from numpy.linalg import inv
from tqdm import tqdm
from grogu_magn.utils import *
"""
# Some input parsing
parser = argparse.ArgumentParser()
parser.add_argument('--kset' , dest = 'kset' , default = 2 , type=int , help = 'k-space resolution of Jij calculation')
parser.add_argument('--kdirs' , dest = 'kdirs' , default = 'xyz' , help = 'Definition of k-space dimensionality')
parser.add_argument('--eset' , dest = 'eset' , default = 42 , type=int , help = 'Number of energy points on the contour')
parser.add_argument('--eset-p' , dest = 'esetp' , default = 10 , type=int , help = 'Parameter tuning the distribution on the contour')
parser.add_argument('--input' , dest = 'infile' , required = True , help = 'Input file name')
parser.add_argument('--output' , dest = 'outfile', required = True , help = 'Output file name')
parser.add_argument('--Ebot' , dest = 'Ebot' , default = -20.0 , type=float, help = 'Bottom energy of the contour')
parser.add_argument('--npairs' , dest = 'npairs' , default = 1 , type=int , help = 'Number of unitcell pairs in each direction for Jij calculation')
parser.add_argument('--adirs' , dest = 'adirs' , default = False , help = 'Definition of pair directions')
parser.add_argument('--use-tqdm', dest = 'usetqdm', default = 'not' , help = 'Use tqdm for progressbars or not')
parser.add_argument('--cutoff' , dest = 'cutoff' , default = 100.0 , type=float, help = 'Real space cutoff for pair generation in Angs')
parser.add_argument('--pairfile', dest = 'pairfile', default = False , help = 'File to read pair information')
args = parser.parse_args()
"""
# runtime information
times = dict()
times["start_time"] = timer()
################################################################################
#################################### INPUT #####################################
################################################################################
import warnings
from sys import getsizeof
import sisl
from mpi4py import MPI
from src.grogu_magn import *
# input output stuff
######################################################################
######################################################################
######################################################################
path = (
"/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf"
)
outfile = "./Fe3GeTe2_benchmark_on_15k_300eset_orb_test3"
# this information needs to be given at the input!!
scf_xcf_orientation = np.array([0, 0, 1]) # z
# list of reference directions for around which we calculate the derivatives
# o is the quantization axis, v and w are two axes perpendicular to it
# at this moment the user has to supply o,v,w on the input.
# we can have some default for this
ref_xcf_orientations = [
dict(o=np.array([1, 0, 0]), vw=[np.array([0, 1, 0]), np.array([0, 0, 1])]),
dict(o=np.array([0, 1, 0]), vw=[np.array([1, 0, 0]), np.array([0, 0, 1])]),
dict(o=np.array([0, 0, 1]), vw=[np.array([1, 0, 0]), np.array([0, 1, 0])]),
]
outfile = "./Fe3GeTe2_notebook"
magnetic_entities = [
dict(atom=3, l=2),
dict(atom=4, l=2),
dict(atom=5, l=1),
dict(atom=5, l=2),
]
pairs = [
dict(ai=0, aj=1, Ruc=np.array([0, 0, 0])),
@ -68,15 +59,12 @@ pairs = [
dict(ai=1, aj=2, Ruc=np.array([-2, 0, 0])),
dict(ai=1, aj=2, Ruc=np.array([-3, 0, 0])),
]
# Brilloun zone sampling and Green function contour integral
kset = 15
kdirs = "xy"
ebot = -13
eset = 300
esetp = 1000
################################################################################
#################################### INPUT #####################################
################################################################################
simulation_parameters = default_args
######################################################################
######################################################################
######################################################################
# MPI parameters
comm = MPI.COMM_WORLD
@ -84,28 +72,37 @@ size = comm.Get_size()
rank = comm.Get_rank()
root_node = 0
# check versions for debugging
if rank == root_node:
try:
print(sisl.__version__)
except:
print("sisl version unknown.")
try:
print(np.__version__)
except:
print("numpy version unknown.")
# rename outfile
if not outfile.endswith(".pickle"):
outfile += ".pickle"
simulation_parameters = dict(
path=path,
outpath=outfile,
scf_xcf_orientation=scf_xcf_orientation,
ref_xcf_orientations=ref_xcf_orientations,
kset=kset,
kdirs=kdirs,
ebot=ebot,
eset=eset,
esetp=esetp,
parallel_size=size,
)
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
except:
print("Could not determine ebot.")
print("Parameter was not given and .EIG file was not found.")
# digestion of the input
# read sile
fdf = sisl.get_sile(path)
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
@ -119,60 +116,11 @@ if rank == root_node:
"================================================================================================================================================================"
)
NO = dh.no # shorthand for number of orbitals in the unit cell
# preprocessing Hamiltonian and overlap matrix elements
h11 = dh.tocsr(dh.M11r)
h11 += dh.tocsr(dh.M11i) * 1.0j
h11 = h11.toarray().reshape(NO, dh.n_s, NO).transpose(0, 2, 1).astype("complex128")
h22 = dh.tocsr(dh.M22r)
h22 += dh.tocsr(dh.M22i) * 1.0j
h22 = h22.toarray().reshape(NO, dh.n_s, NO).transpose(0, 2, 1).astype("complex128")
h12 = dh.tocsr(dh.M12r)
h12 += dh.tocsr(dh.M12i) * 1.0j
h12 = h12.toarray().reshape(NO, dh.n_s, NO).transpose(0, 2, 1).astype("complex128")
h21 = dh.tocsr(dh.M21r)
h21 += dh.tocsr(dh.M21i) * 1.0j
h21 = h21.toarray().reshape(NO, dh.n_s, NO).transpose(0, 2, 1).astype("complex128")
sov = (
dh.tocsr(dh.S_idx)
.toarray()
.reshape(NO, dh.n_s, NO)
.transpose(0, 2, 1)
.astype("complex128")
)
# reformat Hamltonian and Overlap matrix for manipulations
hh, ss, NO = build_hh_ss(dh)
# Reorganization of Hamiltonian and overlap matrix elements to SPIN BOX representation
U = np.vstack(
[np.kron(np.eye(NO, dtype=int), [1, 0]), np.kron(np.eye(NO, dtype=int), [0, 1])]
)
# This is the permutation that transforms ud1ud2 to u12d12
# That is this transforms FROM SPIN BOX to ORBITAL BOX => U
# the inverse transformation is U.T u12d12 to ud1ud2
# That is FROM ORBITAL BOX to SPIN BOX => U.T
# From now on everything is in SPIN BOX!!
hh, ss = np.array(
[
U.T @ np.block([[h11[:, :, i], h12[:, :, i]], [h21[:, :, i], h22[:, :, i]]]) @ U
for i in range(dh.lattice.nsc.prod())
]
), np.array(
[
U.T
@ np.block([[sov[:, :, i], sov[:, :, i] * 0], [sov[:, :, i] * 0, sov[:, :, i]]])
@ U
for i in range(dh.lattice.nsc.prod())
]
)
# symmetrizing Hamiltonian and overlap matrix to make them hermitian
# 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]
@ -194,9 +142,9 @@ XCF = np.array(
np.array([f["y"] / 2 for f in traced]),
np.array([f["z"] / 2 for f in traced]),
]
) # equation 77
)
# Check if exchange field has scalar part
# 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(
@ -212,104 +160,10 @@ if rank == root_node:
"================================================================================================================================================================"
)
# for every site we have to store 3 Greens function (and the associated _tmp-s) in the 3 reference directions
for mag_ent in magnetic_entities:
parsed = parse_magnetic_entity(dh, **mag_ent) # parse orbital indexes
mag_ent["orbital_indeces"] = parsed
mag_ent["spin_box_indeces"] = blow_up_orbindx(parsed) # calculate spin box indexes
# if orbital is not set use all
if "l" not in mag_ent.keys():
mag_ent["l"] = "all"
if isinstance(mag_ent["atom"], int):
mag_ent["tags"] = [
f"[{mag_ent['atom']}]{dh.atoms[mag_ent['atom']].tag}({mag_ent['l']})"
]
mag_ent["xyz"] = [dh.xyz[mag_ent["atom"]]]
if isinstance(mag_ent["atom"], list):
mag_ent["tags"] = []
mag_ent["xyz"] = []
# iterate over atoms
for atom_idx in mag_ent["atom"]:
mag_ent["tags"].append(
f"[{atom_idx}]{dh.atoms[atom_idx].tag}({mag_ent['l']})"
)
mag_ent["xyz"].append(dh.xyz[atom_idx])
# calculate size for Greens function generation
spin_box_shape = len(mag_ent["spin_box_indeces"])
mag_ent["energies"] = [] # we will store the second order energy derivations here
# These will be the perturbed potentials from eq. 100
mag_ent["Vu1"] = [] # so they are independent in memory
mag_ent["Vu2"] = []
mag_ent["Gii"] = [] # Greens function
mag_ent["Gii_tmp"] = [] # Greens function for parallelization
for i in ref_xcf_orientations:
# Rotations for every quantization axis
mag_ent["Vu1"].append([])
mag_ent["Vu2"].append([])
# Greens functions for every quantization axis
mag_ent["Gii"].append(
np.zeros((eset, spin_box_shape, spin_box_shape), dtype="complex128")
)
mag_ent["Gii_tmp"].append(
np.zeros((eset, spin_box_shape, spin_box_shape), dtype="complex128")
)
# for every site we have to store 2x3 Greens function (and the associated _tmp-s)
# in the 3 reference directions, because G_ij and G_ji are both needed
for pair in pairs:
# calculate distance
xyz_ai = magnetic_entities[pair["ai"]]["xyz"]
xyz_aj = magnetic_entities[pair["aj"]]["xyz"]
xyz_aj = xyz_aj + pair["Ruc"] @ simulation_parameters["cell"]
pair["dist"] = np.linalg.norm(xyz_ai - xyz_aj)
# calculate size for Greens function generation
spin_box_shape_i = len(magnetic_entities[pair["ai"]]["spin_box_indeces"])
spin_box_shape_j = len(magnetic_entities[pair["aj"]]["spin_box_indeces"])
pair["tags"] = []
for mag_ent in [magnetic_entities[pair["ai"]], magnetic_entities[pair["aj"]]]:
tag = ""
# get atoms of magnetic entity
atoms_idx = mag_ent["atom"]
orbitals = mag_ent["l"]
# if magnetic entity contains one atoms
if isinstance(atoms_idx, int):
tag += f"[{atoms_idx}]{dh.atoms[atoms_idx].tag}({orbitals})"
# if magnetic entity contains more than one atoms
if isinstance(atoms_idx, list):
# iterate over atoms
atom_group = "{"
for atom_idx in atoms_idx:
atom_group += f"[{atom_idx}]{dh.atoms[atom_idx].tag}({orbitals})--"
# end {} of the atoms in the magnetic entity
tag += atom_group[:-2] + "}"
pair["tags"].append(tag)
pair["energies"] = [] # we will store the second order energy derivations here
pair["Gij"] = [] # Greens function
pair["Gji"] = []
pair["Gij_tmp"] = [] # Greens function for parallelization
pair["Gji_tmp"] = []
for i in ref_xcf_orientations:
# Greens functions for every quantization axis
pair["Gij"].append(
np.zeros((eset, spin_box_shape_i, spin_box_shape_j), dtype="complex128")
)
pair["Gij_tmp"].append(
np.zeros((eset, spin_box_shape_i, spin_box_shape_j), dtype="complex128")
)
pair["Gji"].append(
np.zeros((eset, spin_box_shape_j, spin_box_shape_i), dtype="complex128")
)
pair["Gji_tmp"].append(
np.zeros((eset, spin_box_shape_j, spin_box_shape_i), dtype="complex128")
)
# 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()
@ -320,10 +174,15 @@ if rank == root_node:
"================================================================================================================================================================"
)
kset = make_kset(dirs=kdirs, NUMK=kset) # generate k space sampling
# generate k space sampling
kset = make_kset(
dirs=simulation_parameters["kdirs"], NUMK=simulation_parameters["kset"]
)
wkset = np.ones(len(kset)) / len(kset) # generate weights for k points
kpcs = np.array_split(kset, size) # split the k points based on MPI size
kpcs[root_node] = tqdm(kpcs[root_node], desc="k loop")
if tqdm_imported:
kpcs[root_node] = tqdm(kpcs[root_node], desc="k loop")
if rank == root_node:
times["k_set_time"] = timer()
@ -331,225 +190,3 @@ if rank == root_node:
print(
"================================================================================================================================================================"
)
# this will contain the three hamiltonians 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(ref_xcf_orientations):
# obtain rotated exchange field
R = RotMa2b(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 #######################################################################################
hamiltonians.append(
dict(orient=orient["o"], H=rot_H)
) # store orientation and rotated Hamiltonian
# these are the rotations (for now) perpendicular to the quantization axis
for u in orient["vw"]:
Tu = np.kron(np.eye(NO, dtype=int), tau_u(u)) # section 2.H
Vu1 = 1j / 2 * commutator(rot_H_XCF_uc, Tu) # equation 100
Vu2 = 1 / 8 * commutator(commutator(Tu, rot_H_XCF_uc), Tu) # equation 100
for mag_ent in magnetic_entities:
idx = mag_ent["spin_box_indeces"]
# fill up the perturbed potentials (for now) based on the on-site projections
mag_ent["Vu1"][i].append(Vu1[:, idx][idx, :])
mag_ent["Vu2"][i].append(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(
"================================================================================================================================================================"
)
if rank == root_node:
print("Starting matrix inversions")
print(f"Total number of k points: {kset.shape[0]}")
print(f"Number of energy samples per k point: {eset}")
print(f"Total number of directions: {len(hamiltonians)}")
print(
f"Total number of matrix inversions: {kset.shape[0] * len(hamiltonians) * 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) * eset * 32} KB"
)
print(
f"Expected memory usage on root node: {len(np.array_split(kset, size)[0]) * memory_size * len(hamiltonians) * eset * 32 / 1024} MB"
)
print(
"================================================================================================================================================================"
)
comm.Barrier()
# ----------------------------------------------------------------------
# make energy contour
# we are working in eV now !
# and sisl shifts E_F to 0 !
cont = make_contour(emin=ebot, enum=eset, p=esetp)
eran = cont.ze
# ----------------------------------------------------------------------
# sampling the integrand on the contour and the BZ
for k in kpcs[rank]:
wk = wkset[rank] # weight of k point in BZ integral
# iterate over reference directions
for i, hamiltonian_orientation in enumerate(hamiltonians):
# calculate Greens function
H = hamiltonian_orientation["H"]
HK, SK = hsk(H, ss, dh.sc_off, k)
# Gk = inv(SK * eran.reshape(eset, 1, 1) - HK)
# solve Greens function sequentially for the energies, because of memory bound
Gk = np.zeros(shape=(eset, HK.shape[0], HK.shape[1]), dtype="complex128")
for j in range(eset):
Gk[j] = inv(SK * eran[j] - HK)
# store the Greens function slice of the magnetic entities (for now) based on the on-site projections
for mag_ent in magnetic_entities:
mag_ent["Gii_tmp"][i] += (
Gk[:, mag_ent["spin_box_indeces"], :][:, :, mag_ent["spin_box_indeces"]]
* 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_indeces"]
aj = magnetic_entities[pair["aj"]]["spin_box_indeces"]
# store the Greens function slice of the magnetic entities (for now) based on the on-site projections
pair["Gij_tmp"][i] += Gk[:, ai][..., aj] * phase * wk
pair["Gji_tmp"][i] += Gk[:, aj][..., ai] / phase * wk
# summ reduce partial results of mpi nodes
for i in range(len(hamiltonians)):
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:
# 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)
# evaluation of the contour integral
storage.append(np.trapz(-1 / np.pi * np.imag(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"]
)
print("Magnetic entities integrated.")
# 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)
# evaluation of the contour integral
storage.append(np.trapz(-1 / np.pi * np.imag(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"])
print("Pairs integrated.")
# 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")
print("Magnetic parameters calculated.")
times["end_time"] = timer()
print(
"##################################################################### GROGU OUTPUT #############################################################################"
)
print_parameters(simulation_parameters)
print_atoms_and_pairs(magnetic_entities, pairs)
print_runtime_information(times)
# remove clutter from magnetic entities and pair information
for pair in pairs:
del pair["Gij"]
del pair["Gij_tmp"]
del pair["Gji"]
del pair["Gji_tmp"]
for mag_ent in magnetic_entities:
del mag_ent["Gii"]
del mag_ent["Gii_tmp"]
del mag_ent["Vu1"]
del mag_ent["Vu2"]
# create output dictionary with all the relevant data
results = dict(
parameters=simulation_parameters,
magnetic_entities=magnetic_entities,
pairs=pairs,
runtime=times,
)
# save dictionary
with open(outfile, "wb") as output_file:
pickle.dump(results, output_file)

Write Preview
Loading…
Cancel
Save