diff --git a/Fe3GeTe2_benchmark_on_15k_300eset.log b/Fe3GeTe2_benchmark_on_15k_300eset.log
index f92ed38..675fdb4 100644
--- a/Fe3GeTe2_benchmark_on_15k_300eset.log
+++ b/Fe3GeTe2_benchmark_on_15k_300eset.log
@@ -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
diff --git a/Fe3GeTe2_benchmark_on_15k_300eset_orb_test.log b/Fe3GeTe2_benchmark_on_15k_300eset_orb_test.log
index f54a424..0759261 100644
--- a/Fe3GeTe2_benchmark_on_15k_300eset_orb_test.log
+++ b/Fe3GeTe2_benchmark_on_15k_300eset_orb_test.log
@@ -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
diff --git a/Fe3GeTe2_benchmark_on_15k_300eset_orb_test2.log b/Fe3GeTe2_benchmark_on_15k_300eset_orb_test2.log
index 7a5553c..fb7e858 100644
--- a/Fe3GeTe2_benchmark_on_15k_300eset_orb_test2.log
+++ b/Fe3GeTe2_benchmark_on_15k_300eset_orb_test2.log
@@ -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
diff --git a/Fe3GeTe2_benchmark_on_15k_300eset_orb_test3.log b/Fe3GeTe2_benchmark_on_15k_300eset_orb_test3.log
index 9debbf9..28d1a0b 100644
--- a/Fe3GeTe2_benchmark_on_15k_300eset_orb_test3.log
+++ b/Fe3GeTe2_benchmark_on_15k_300eset_orb_test3.log
@@ -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
diff --git a/Fe3GeTe2_final_test.pickle b/Fe3GeTe2_final_test.pickle
new file mode 100644
index 0000000..bde045a
Binary files /dev/null and b/Fe3GeTe2_final_test.pickle differ
diff --git a/Fe3GeTe2_notebook.pickle b/Fe3GeTe2_notebook.pickle
index 6e413b1..2cbfd51 100644
Binary files a/Fe3GeTe2_notebook.pickle and b/Fe3GeTe2_notebook.pickle differ
diff --git a/LATEST_RUN_ON_KOMONDOR_AND_GROGU_MATLAB b/LATEST_RUN_ON_KOMONDOR_AND_GROGU_MATLAB
index 92b3a78..b0d95b1 100644
--- a/LATEST_RUN_ON_KOMONDOR_AND_GROGU_MATLAB
+++ b/LATEST_RUN_ON_KOMONDOR_AND_GROGU_MATLAB
@@ -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)
diff --git a/data/lat3_791/BASIS_ENTHALPY b/data/lat3_791/BASIS_ENTHALPY
index 52034ee..3a0a70f 100644
--- a/data/lat3_791/BASIS_ENTHALPY
+++ b/data/lat3_791/BASIS_ENTHALPY
@@ -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
diff --git a/data/lat3_791/BASIS_HARRIS_ENTHALPY b/data/lat3_791/BASIS_HARRIS_ENTHALPY
index 5cfbca1..64db155 100644
--- a/data/lat3_791/BASIS_HARRIS_ENTHALPY
+++ b/data/lat3_791/BASIS_HARRIS_ENTHALPY
@@ -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
diff --git a/data/lat3_791/Fe.ion b/data/lat3_791/Fe.ion
index 5436107..0570f70 100644
--- a/data/lat3_791/Fe.ion
+++ b/data/lat3_791/Fe.ion
@@ -6,25 +6,25 @@ 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: 9.6494 6.8853
- lambdas: 1.0000 1.0000
+ rcs: 9.6494 6.8853
+ 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: 6.6319 2.5648
- lambdas: 1.0000 1.0000
+ rcs: 6.6319 2.5648
+ lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=2 erefs: 0.17977+309 0.17977+309
@@ -35,237 +35,237 @@ L=3 Nkbl=1 erefs: 0.17977+309
Fe pb rel pcec
- ATM3.3 17-MAR-14 Troullier-Martins
- 4s 1.00r r= 2.00/4p 0.00r r= 2.00/3d 7.00r r= 2.00/4f 0.00r r= 2.00/
+ ATM3.3 17-MAR-14 Troullier-Martins
+ 4s 1.00r r= 2.00/4p 0.00r r= 2.00/3d 7.00r r= 2.00/4f 0.00r r= 2.00/
Fe # Symbol
Fe # Label
26 # Atomic number
8.00000000000 # Valence charge
- 55.8500000000 # Mass
- 52.4107105251 # Self energy
- 2 5 # Lmax for basis, no. of nl orbitals
+ 55.8500000000 # Mass
+ 52.4107105251 # Self energy
+ 2 5 # Lmax for basis, no. of nl orbitals
3 9 T # Lmax for projectors, no. of nl KB projectors, LJ projs?
# PAOs:__________________________
0 4 1 0 2.000000 #orbital l, n, z, is_polarized, population
500 0.1933743327183080E-01 9.649379202643571 # npts, delta, cutoff
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@@ -549,7 +549,7 @@ Fe # Label
9.591366902828078 0.1939165774133531E-03
9.610704336099909 0.1290064010187526E-03
9.630041769371740 0.6437027860662103E-04
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0 4 2 0 0.000000 #orbital l, n, z, is_polarized, population
500 0.1379820896943888E-01 6.885306275750000 # npts, delta, cutoff
0.000000000000000 0.8912522727590136E-01
@@ -578,267 +578,267 @@ Fe # Label
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@@ -1553,329 +1553,329 @@ Fe # Label
6.592014007715606 0.4579999954711445E-05
6.605304358537612 0.3034791708703095E-05
6.618594709359620 0.1508225058083222E-05
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@@ -2055,127 +2055,127 @@ Fe # Label
2.549344129432304 0.1143801066149498E-04
2.554483936144870 0.5058226523641859E-05
2.559623742857435 0.1254296233929513E-05
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1 4 1 1 0.000000 #orbital l, n, z, is_polarized, population
500 0.1933743327183080E-01 9.649379202643571 # npts, delta, cutoff
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@@ -2557,436 +2557,436 @@ Fe # Label
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# KBs:__________________________
0 0.5 1 4.0239553167632671 #kb l, j, n (sequence number), Reference energy
500 0.4104180526713427E-02 2.047986082830000 # npts, delta, cutoff
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2.035673541249860 -0.3623808412418252E-04
2.039777721776573 -0.3872685668640974E-04
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1 1.5 1 3.2566811235052211 #kb l, j, n (sequence number), Reference energy
500 0.4104180526713427E-02 2.047986082830000 # npts, delta, cutoff
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@@ -7076,187 +7076,187 @@ Fe # Label
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# Vna:__________________________
500 0.1933743327183080E-01 9.649379202643571 # npts, delta, cutoff
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@@ -8080,188 +8080,188 @@ Fe # Label
3.075115548197195 0.8216913031644819E-05
3.081315377931463 0.5985994306827748E-05
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# Core:__________________________
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diff --git a/data/lat3_791/Fe.ion.xml b/data/lat3_791/Fe.ion.xml
index b2bff15..56e673c 100644
--- a/data/lat3_791/Fe.ion.xml
+++ b/data/lat3_791/Fe.ion.xml
@@ -1,15 +1,15 @@
- Fe
-
- 26
- 8.00000000000
- 55.8500000000
- 52.4107105251
- 2
- 5
- 3
- 9
- true
+ Fe
+
+ 26
+ 8.00000000000
+ 55.8500000000
+ 52.4107105251
+ 2
+ 5
+ 3
+ 9
+ true
@@ -18,25 +18,25 @@ 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: 9.6494 6.8853
- lambdas: 1.0000 1.0000
+ rcs: 9.6494 6.8853
+ 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: 6.6319 2.5648
- lambdas: 1.0000 1.0000
+ rcs: 6.6319 2.5648
+ lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=2 erefs: 0.17977+309 0.17977+309
@@ -47,239 +47,239 @@ L=3 Nkbl=1 erefs: 0.17977+309
Fe pb rel pcec
- ATM3.3 17-MAR-14 Troullier-Martins
- 4s 1.00r r= 2.00/4p 0.00r r= 2.00/3d 7.00r r= 2.00/4f 0.00r r= 2.00/
+ ATM3.3 17-MAR-14 Troullier-Martins
+ 4s 1.00r r= 2.00/4p 0.00r r= 2.00/3d 7.00r r= 2.00/4f 0.00r r= 2.00/
-
- 500
- 0.193374332718E-01
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diff --git a/data/lat3_791/Fe.psf b/data/lat3_791/Fe.psf
index 7e2890d..f2f747d 100644
--- a/data/lat3_791/Fe.psf
+++ b/data/lat3_791/Fe.psf
@@ -1,7 +1,7 @@
Fe pb rel pcec
- ATM3.3 17-MAR-14 Troullier-Martins
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- 4 3 1123 0.953366221795E-04 0.125000000000E-01 8.00000000000
+ ATM3.3 17-MAR-14 Troullier-Martins
+ 4s 1.00r r= 2.00/4p 0.00r r= 2.00/3d 7.00r r= 2.00/4f 0.00r r= 2.00/
+ 4 3 1123 0.953366221795E-04 0.125000000000E-01 8.00000000000
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+ 6.59299167315 6.51404420927 6.42717470528 6.33286154514
+ 6.23162087918 6.12400173999 6.01058081380 5.89195694691
+ 5.76874547107 5.64157243471 5.51106882796 5.37786488776
+ 5.24258456634 5.10584024123 4.96822773776 4.83032172682
+ 4.69267154831 4.55579751282 4.42018769533 4.28629525370
+ 4.15453627512 4.02528814782 3.89888844455 3.77563429540
+ 3.65578221912 3.53954837602 3.42710920050 3.31860236837
+ 3.21412805253 3.11375042140 3.01749933624 2.92537220761
+ 2.83733597617 2.75332918964 2.67326415496 2.59702915315
+ 2.52449071251 2.45549594441 2.38987495368 2.32744334190
+ 2.26800482683 2.21135400288 2.15727926564 2.10556591728
+ 2.05599945762 2.00836904718 1.96247110329 1.91811295716
+ 1.87511645948 1.83332137456 1.79258835132 1.75280118736
+ 1.71386807676 1.67572147725 1.63831549304 1.60162280722
+ 1.56562587738 1.53030937435 1.49565780905 1.46165553912
+ 1.42828672332 1.39553542243 1.36338566988 1.33182153658
+ 1.30082719660 1.27038698912 1.24048547776 1.21110750702
+ 1.18223825550 1.15386328584 1.12596859108 1.09854063662
+ 1.07156640331 1.04503340526 1.01892976764 0.993244168894
+ 0.967965970623 0.943085237675 0.918592688484 0.894479651447
+ 0.870738128569 0.847360777334 0.824340925215 0.801672565750
+ 0.779350352957 0.757369590957 0.735726219697 0.714416797062
+ 0.693438477657 0.672788988523 0.652466601998 0.632470105969
+ 0.612798771708 0.593452319502 0.574430882290 0.555734967519
+ 0.537365417427 0.519323367998 0.501610206807 0.484227530029
+ 0.467177098860 0.450460795636 0.434080579935 0.418038444976
+ 0.402336374612 0.386976301241 0.371960064954 0.357289374233
+ 0.342965768508 0.328990582869 0.315364915211 0.302089596047
+ 0.289165161260 0.276591827922 0.264369473369 0.252497617635
+ 0.240975409306 0.229801614832 0.218974611266 0.208492382370
+ 0.198352517987 0.188552216541 0.179088290490 0.169957174531
+ 0.161154936322 0.152677289498 0.144519608692 0.136676946313
+ 0.129144050813 0.121915386145 0.114985152187 0.108347305835
0.101995582559 0.959235181711E-01 0.901244706052E-01 0.845916415293E-01
0.793180976123E-01 0.742967913123E-01 0.695205810648E-01 0.649822507742E-01
0.606745285393E-01 0.565901045578E-01 0.527216481827E-01 0.490618241161E-01
@@ -2829,4 +2829,3 @@
0.159623499658E-47 0.394685762244E-48 0.959152537476E-49 0.229037992853E-49
0.537289950000E-50 0.123783348782E-50 0.280097688343E-51 0.624177220781E-52
0.136516118863E-52 0.292975523658E-53 0.616797664740E-54
-
diff --git a/data/lat3_791/Fe3GeTe2.ORB_INDX b/data/lat3_791/Fe3GeTe2.ORB_INDX
index d99f38f..3ae1fc2 100644
--- a/data/lat3_791/Fe3GeTe2.ORB_INDX
+++ b/data/lat3_791/Fe3GeTe2.ORB_INDX
@@ -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
-
diff --git a/data/lat3_791/Fe3GeTe2.bib b/data/lat3_791/Fe3GeTe2.bib
index 410d980..42a612a 100644
--- a/data/lat3_791/Fe3GeTe2.bib
+++ b/data/lat3_791/Fe3GeTe2.bib
@@ -21,4 +21,3 @@
issue = {086005},
doi = {10.1088/0953-8984/24/8/086005},
}
-
diff --git a/data/lat3_791/Fe3GeTe2.fdf b/data/lat3_791/Fe3GeTe2.fdf
index 66cd1c1..88f1bd7 100644
--- a/data/lat3_791/Fe3GeTe2.fdf
+++ b/data/lat3_791/Fe3GeTe2.fdf
@@ -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
diff --git a/data/lat3_791/Fe3GeTe2.out b/data/lat3_791/Fe3GeTe2.out
index a7bdf47..3fed38f 100644
--- a/data/lat3_791/Fe3GeTe2.out
+++ b/data/lat3_791/Fe3GeTe2.out
@@ -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(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -1262,7 +1262,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.035 -0.000 0.000 0.035
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -1283,7 +1283,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.033 -0.000 -0.000 -0.033
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -1325,7 +1325,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -1715,7 +1715,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.039 -0.000 0.000 0.039
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -1736,7 +1736,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.034 -0.000 -0.000 -0.034
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -1778,7 +1778,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -2207,7 +2207,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.047 -0.000 0.000 0.047
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -2228,7 +2228,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.039 0.000 0.000 -0.039
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -2270,7 +2270,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -2641,7 +2641,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.047 0.000 -0.000 0.047
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -2662,7 +2662,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.041 -0.000 0.000 -0.041
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -2704,7 +2704,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -3135,7 +3135,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.044 -0.000 0.000 0.044
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -3156,7 +3156,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.045 -0.000 -0.000 -0.045
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -3198,7 +3198,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -3584,7 +3584,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.038 0.000 -0.000 0.038
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -3605,7 +3605,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.045 -0.000 0.000 -0.045
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -3647,7 +3647,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4033,7 +4033,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.040 -0.000 0.000 0.040
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4054,7 +4054,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.046 -0.000 -0.000 -0.046
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4096,7 +4096,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4480,7 +4480,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.043 -0.000 -0.000 0.043
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4501,7 +4501,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.046 0.000 -0.000 -0.046
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4543,7 +4543,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4929,7 +4929,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.031 0.000 -0.000 0.031
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4950,7 +4950,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.044 0.000 -0.000 -0.044
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -4992,7 +4992,7 @@ Atom Orb sqrt(^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:
^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -5378,7 +5378,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
6 Total 0.041 0.000 -0.000 0.041
-Species: Ge
+Species: Ge
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -5399,7 +5399,7 @@ Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
3 Total 0.046 0.000 0.000 -0.046
-Species: Te
+Species: Te
Atom Orb sqrt(^2) <(Lx,Ly,Lz)>
----------------------------------------------------------------------------------------------------
@@ -5441,7 +5441,7 @@ Atom Orb sqrt(^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
diff --git a/data/lat3_791/Fe3GeTe2.times b/data/lat3_791/Fe3GeTe2.times
index 7769405..a738da3 100644
--- a/data/lat3_791/Fe3GeTe2.times
+++ b/data/lat3_791/Fe3GeTe2.times
@@ -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
-
diff --git a/data/lat3_791/Ge.ion b/data/lat3_791/Ge.ion
index fb5ffba..f6c53c9 100644
--- a/data/lat3_791/Ge.ion
+++ b/data/lat3_791/Ge.ion
@@ -6,24 +6,24 @@ 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: 6.5814 4.4116
- lambdas: 1.0000 1.0000
+ rcs: 6.5814 4.4116
+ 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: 9.3395 5.6647
- lambdas: 1.0000 1.0000
+ rcs: 9.3395 5.6647
+ lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
@@ -33,280 +33,280 @@ L=3 Nkbl=1 erefs: 0.17977+309
- Ge pb rel nc
- ATM3 17-OCT-13 Troullier-Martins
- 4s 2.00r r= 2.81/4p 2.00r r= 2.11/4d 0.00r r= 2.71/4f 0.00r r= 2.45/
+ Ge pb rel nc
+ ATM3 17-OCT-13 Troullier-Martins
+ 4s 2.00r r= 2.81/4p 2.00r r= 2.11/4d 0.00r r= 2.71/4f 0.00r r= 2.45/
Ge # Symbol
Ge # Label
32 # Atomic number
4.00000000000 # Valence charge
- 72.6100000000 # Mass
- 10.2968736702 # Self energy
- 2 5 # Lmax for basis, no. of nl orbitals
+ 72.6100000000 # Mass
+ 10.2968736702 # Self energy
+ 2 5 # Lmax for basis, no. of nl orbitals
3 7 T # Lmax for projectors, no. of nl KB projectors, LJ projs?
# PAOs:__________________________
0 4 1 0 2.000000 #orbital l, n, z, is_polarized, population
500 0.1318924217901012E-01 6.581431847326051 # npts, delta, cutoff
- 0.000000000000000 0.4925955660973397
- 0.1318924217901012E-01 0.4925946066275391
- 0.2637848435802025E-01 0.4925926761097314
- 0.3956772653703037E-01 0.4925894585891435
- 0.5275696871604049E-01 0.4925849540201773
- 0.6594621089505062E-01 0.4925791622739624
- 0.7913545307406074E-01 0.4925720830718455
- 0.9232469525307085E-01 0.4925637158960844
- 0.1055139374320810 0.4925540598826844
- 0.1187031796110911 0.4925431137024222
- 0.1318924217901012 0.4925308754040023
- 0.1450816639691113 0.4925173422723871
- 0.1582709061481215 0.4925025106340048
- 0.1714601483271316 0.4924863756623983
- 0.1846493905061417 0.4924689311757336
- 0.1978386326851518 0.4924501693857117
- 0.2110278748641620 0.4924300806737634
- 0.2242171170431721 0.4924086533095576
- 0.2374063592221822 0.4923858731818772
- 0.2505956014011924 0.4923617235048020
- 0.2637848435802025 0.4923361845139130
- 0.2769740857592126 0.4923092331364302
- 0.2901633279382227 0.4922808426703321
- 0.3033525701172328 0.4922509824332339
- 0.3165418122962430 0.4922196174027662
- 0.3297310544752531 0.4921867078578955
- 0.3429202966542632 0.4921522089926740
- 0.3561095388332733 0.4921160705417209
- 0.3692987810122834 0.4920782363739323
- 0.3824880231912935 0.4920386441005540
- 0.3956772653703037 0.4919972246608040
- 0.4088665075493138 0.4919539019141759
- 0.4220557497283239 0.4919085922194202
- 0.4352449919073341 0.4918612040131836
- 0.4484342340863442 0.4918116373893657
- 0.4616234762653543 0.4917597836676872
- 0.4748127184443645 0.4917055249737500
- 0.4880019606233745 0.4916487338108162
- 0.5011912028023847 0.4915892726355772
- 0.5143804449813948 0.4915269934417212
- 0.5275696871604050 0.4914617373356303
- 0.5407589293394151 0.4913933341334485
- 0.5539481715184251 0.4913216019480913
- 0.5671374136974353 0.4912463467960936
- 0.5803266558764454 0.4911673622086563
- 0.5935158980554556 0.4910844288489797
- 0.6067051402344656 0.4909973141498394
- 0.6198943824134758 0.4909057719522243
- 0.6330836245924859 0.4908095421708160
- 0.6462728667714960 0.4907083504645133
- 0.6594621089505062 0.4906019079258687
- 0.6726513511295162 0.4904899107938812
- 0.6858405933085264 0.4903720401771161
- 0.6990298354875365 0.4902479618067795
- 0.7122190776665467 0.4901173258032162
- 0.7254083198455568 0.4899797664729972
- 0.7385975620245668 0.4898349021268892
- 0.7517868042035770 0.4896823349240523
- 0.7649760463825871 0.4895216507470951
- 0.7781652885615973 0.4893524191012051
- 0.7913545307406074 0.4891741930498413
- 0.8045437729196175 0.4889865091758034
- 0.8177330150986276 0.4887888875807138
- 0.8309222572776378 0.4885808319167308
- 0.8441114994566479 0.4883618294536097
- 0.8573007416356579 0.4881313511853752
- 0.8704899838146681 0.4878888519743656
- 0.8836792259936782 0.4876337707325381
- 0.8968684681726884 0.4873655306488121
- 0.9100577103516985 0.4870835394538545
- 0.9232469525307087 0.4867871897321491
- 0.9364361947097187 0.4864758592741887
- 0.9496254368887289 0.4861489114797989
- 0.9628146790677390 0.4858056957998269
- 0.9760039212467491 0.4854455482340855
- 0.9891931634257592 0.4850677918688864
- 1.002382405604769 0.4846717374716872
- 1.015571647783780 0.4842566841213121
- 1.028760889962790 0.4838219199112300
- 1.041950132141800 0.4833667226736278
- 1.055139374320810 0.4828903607758953
- 1.068328616499820 0.4823920939635620
- 1.081517858678830 0.4818711742405001
- 1.094707100857840 0.4813268468155532
- 1.107896343036850 0.4807583511000969
- 1.121085585215861 0.4801649217327413
- 1.134274827394871 0.4795457896684093
- 1.147464069573881 0.4789001833326840
- 1.160653311752891 0.4782273297876469
- 1.173842553931901 0.4775264559650906
- 1.187031796110911 0.4767967899402690
- 1.200221038289921 0.4760375622542943
- 1.213410280468931 0.4752480072633141
- 1.226599522647941 0.4744273645325361
- 1.239788764826952 0.4735748802799917
- 1.252978007005962 0.4726898088357472
- 1.266167249184972 0.4717714141431139
- 1.279356491363982 0.4708189712934249
- 1.292545733542992 0.4698317680621934
- 1.305734975722002 0.4688091065068420
- 1.318924217901012 0.4677503045519223
- 1.332113460080022 0.4666546976010933
- 1.345302702259032 0.4655216401610931
- 1.358491944438043 0.4643505074710110
- 1.371681186617053 0.4631406971393734
- 1.384870428796063 0.4618916307735627
- 1.398059670975073 0.4606027556086046
- 1.411248913154083 0.4592735461241073
- 1.424438155333093 0.4579035056423044
- 1.437627397512103 0.4564921679108414
- 1.450816639691114 0.4550390986595855
- 1.464005881870124 0.4535438971244602
- 1.477195124049134 0.4520061975314552
- 1.490384366228144 0.4504256705493749
- 1.503573608407154 0.4488020246898650
- 1.516762850586164 0.4471350077319557
- 1.529952092765174 0.4454244075435797
- 1.543141334944184 0.4436700544064935
- 1.556330577123195 0.4418718238784292
- 1.569519819302205 0.4400296197796514
- 1.582709061481215 0.4381434246175583
- 1.595898303660225 0.4362132901332276
- 1.609087545839235 0.4342392281555796
- 1.622276788018245 0.4322213153990712
- 1.635466030197255 0.4301597162696305
- 1.648655272376265 0.4280546269206528
- 1.661844514555276 0.4259062942843529
- 1.675033756734286 0.4237150160020696
- 1.688222998913296 0.4214811388838985
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@@ -548,352 +548,352 @@ Ge # Label
6.541864120789021 0.2594870914340458E-03
6.555053362968031 0.1726244834128768E-03
6.568242605147042 0.8613318983104734E-04
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0 4 2 0 0.000000 #orbital l, n, z, is_polarized, population
500 0.8840962247575150E-02 4.411640161540000 # npts, delta, cutoff
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# KBs:__________________________
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diff --git a/data/lat3_791/Ge.ion.xml b/data/lat3_791/Ge.ion.xml
index 307dbb3..77987fc 100644
--- a/data/lat3_791/Ge.ion.xml
+++ b/data/lat3_791/Ge.ion.xml
@@ -1,15 +1,15 @@
- Ge
-
- 32
- 4.00000000000
- 72.6100000000
- 10.2968736702
- 2
- 5
- 3
- 7
- true
+ Ge
+
+ 32
+ 4.00000000000
+ 72.6100000000
+ 10.2968736702
+ 2
+ 5
+ 3
+ 7
+ true
@@ -18,24 +18,24 @@ 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: 6.5814 4.4116
- lambdas: 1.0000 1.0000
+ rcs: 6.5814 4.4116
+ 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: 9.3395 5.6647
- lambdas: 1.0000 1.0000
+ rcs: 9.3395 5.6647
+ lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
@@ -45,282 +45,282 @@ L=3 Nkbl=1 erefs: 0.17977+309
- Ge pb rel nc
- ATM3 17-OCT-13 Troullier-Martins
- 4s 2.00r r= 2.81/4p 2.00r r= 2.11/4d 0.00r r= 2.71/4f 0.00r r= 2.45/
+ Ge pb rel nc
+ ATM3 17-OCT-13 Troullier-Martins
+ 4s 2.00r r= 2.81/4p 2.00r r= 2.11/4d 0.00r r= 2.71/4f 0.00r r= 2.45/
-
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diff --git a/data/lat3_791/Ge.psf b/data/lat3_791/Ge.psf
index 50f8e99..9748c82 100644
--- a/data/lat3_791/Ge.psf
+++ b/data/lat3_791/Ge.psf
@@ -1,7 +1,7 @@
- Ge pb rel nc
- ATM3 17-OCT-13 Troullier-Martins
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- 4 3 1140 0.774610055208E-04 0.125000000000E-01 4.00000000000
+ Ge pb rel nc
+ ATM3 17-OCT-13 Troullier-Martins
+ 4s 2.00r r= 2.81/4p 2.00r r= 2.11/4d 0.00r r= 2.71/4f 0.00r r= 2.45/
+ 4 3 1140 0.774610055208E-04 0.125000000000E-01 4.00000000000
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+ 0.836784609997 0.860093575733 0.883900515334 0.908196201683
+ 0.932968933216 0.958204337085 0.983885170182 1.00999112004
+ 1.03649860793 1.06338059693 1.09060640791 1.11814154689
+ 1.14594754741 1.17398183217 1.20219759793 1.23054372859
+ 1.25896474090 1.28740076785 1.31578758446 1.34405668070
+ 1.37213538610 1.39994705004 1.42741128139 1.45444425025
+ 1.48095905374 1.50686614675 1.53207383730 1.55648884466
+ 1.58001691701 1.60256350357 1.62403447451 1.64433688023
+ 1.66337973961 1.68107484549 1.69733757393 1.71208768265
+ 1.72525008324 1.73675557127 1.74654149860 1.75455237339
+ 1.76074037487 1.76506577330 1.76749724970 1.76801211606
+ 1.76659644469 1.76324512562 1.75796188402 1.75075930543
+ 1.74165893667 1.73069153194 1.71789736018 1.70332615664
+ 1.68703660605 1.66909586008 1.64957882640 1.62856734135
+ 1.60614922897 1.58241725718 1.55746801530 1.53140073597
+ 1.50431608898 1.47631497696 1.44749736445 1.41796117378
+ 1.38780128197 1.35710865313 1.32596964153 1.29446548932
+ 1.26267210328 1.23066004694 1.19849495657 1.16623800282
+ 1.13394713597 1.10167804724 1.06948437798 1.03741766714
+ 1.00552722298 0.973860117352 0.942461025032 0.911372139308
+ 0.880633202194 0.850281594355 0.820352204834 0.790877473264
+ 0.761887361616 0.733409364160 0.705468521488 0.678087445431
+ 0.651286353280 0.625083110748 0.599493283048 0.574530193430
+ 0.550204988515 0.526526709764 0.503502370419 0.481137037245
+ 0.459433916417 0.438394442902 0.418018372696 0.398303877268
+ 0.379247639615 0.360844951311 0.343089809972 0.325975016590
+ 0.309492272189 0.293632273314 0.278384805883 0.263738836966
+ 0.249682604098 0.236203701780 0.223289164836 0.210925548376
+ 0.199099004115 0.187795352876 0.177000153124 0.166698765413
+ 0.156876412706 0.147518236497 0.138609348766 0.130134879795
+ 0.122080021884 0.114430069091 0.107170453077 0.100286775205
0.937648350379E-01 0.875906554053E-01 0.817505042156E-01 0.762309132040E-01
0.710186938174E-01 0.661009504386E-01 0.614650911584E-01 0.570988363074E-01
0.529902249546E-01 0.491276195817E-01 0.454997091354E-01 0.420955106525E-01
diff --git a/data/lat3_791/INPUT_TMP.58436 b/data/lat3_791/INPUT_TMP.58436
index 146c3e1..a08a816 100644
--- a/data/lat3_791/INPUT_TMP.58436
+++ b/data/lat3_791/INPUT_TMP.58436
@@ -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
# --------------
diff --git a/data/lat3_791/TIMES b/data/lat3_791/TIMES
index 51e1607..a738da3 100644
--- a/data/lat3_791/TIMES
+++ b/data/lat3_791/TIMES
@@ -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
-
diff --git a/data/lat3_791/Te.ion b/data/lat3_791/Te.ion
index 95be034..ab6a5fa 100644
--- a/data/lat3_791/Te.ion
+++ b/data/lat3_791/Te.ion
@@ -6,24 +6,24 @@ 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: 6.1950 4.2049
- lambdas: 1.0000 1.0000
+ rcs: 6.1950 4.2049
+ 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: 8.1560 5.0091
- lambdas: 1.0000 1.0000
+ rcs: 8.1560 5.0091
+ lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
@@ -33,291 +33,291 @@ L=3 Nkbl=1 erefs: 0.17977+309
- Te pb rel nc
- ATM4.2.7 24-JAN-23 Troullier-Martins
- 5s 2.00r r= 2.58/5p 4.00r r= 2.82/5d 0.00r r= 2.82/4f 0.00r r= 2.49/
+ Te pb rel nc
+ ATM4.2.7 24-JAN-23 Troullier-Martins
+ 5s 2.00r r= 2.58/5p 4.00r r= 2.82/5d 0.00r r= 2.82/4f 0.00r r= 2.49/
Te # Symbol
Te # Label
52 # Atomic number
6.00000000000 # Valence charge
- 127.600000000 # Mass
- 23.1216080840 # Self energy
- 2 5 # Lmax for basis, no. of nl orbitals
+ 127.600000000 # Mass
+ 23.1216080840 # Self energy
+ 2 5 # Lmax for basis, no. of nl orbitals
3 7 T # Lmax for projectors, no. of nl KB projectors, LJ projs?
# PAOs:__________________________
0 5 1 0 2.000000 #orbital l, n, z, is_polarized, population
500 0.1241490503954237E-01 6.195037614731642 # npts, delta, cutoff
- 0.000000000000000 0.3573803062851749
- 0.1241490503954237E-01 0.3573918266786729
- 0.2482981007908474E-01 0.3574270240586601
- 0.3724471511862711E-01 0.3574856909702223
- 0.4965962015816947E-01 0.3575678342713688
- 0.6207452519771184E-01 0.3576734634780225
- 0.7448943023725421E-01 0.3578025906696790
- 0.8690433527679657E-01 0.3579552303745482
- 0.9931924031633894E-01 0.3581313994274686
- 0.1117341453558813 0.3583311168055666
- 0.1241490503954237 0.3585544034299830
- 0.1365639554349661 0.3588012819538679
- 0.1489788604745084 0.3590717765125120
- 0.1613937655140508 0.3593659124609877
- 0.1738086705535931 0.3596837160725347
- 0.1862235755931355 0.3600252142232608
- 0.1986384806326779 0.3603904340470923
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- 0.2234682907117626 0.3611921462756988
- 0.2358831957513050 0.3616286907644199
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+ 1.687874554394509 -0.1102740147226906
+ 1.694519729805511 -0.1087342443333207
+ 1.701164905216513 -0.1072025320538348
+ 1.707810080627515 -0.1056790331454889
+ 1.714455256038517 -0.1041639014376688
+ 1.721100431449519 -0.1026572892667442
+ 1.727745606860521 -0.1011593474148447
1.734390782271523 -0.9967022504858204E-01
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1.747681133093527 -0.9671902699422893E-01
diff --git a/data/lat3_791/Te.ion.xml b/data/lat3_791/Te.ion.xml
index c4018d3..613e40b 100644
--- a/data/lat3_791/Te.ion.xml
+++ b/data/lat3_791/Te.ion.xml
@@ -1,15 +1,15 @@
- Te
-
- 52
- 6.00000000000
- 127.600000000
- 23.1216080840
- 2
- 5
- 3
- 7
- true
+ Te
+
+ 52
+ 6.00000000000
+ 127.600000000
+ 23.1216080840
+ 2
+ 5
+ 3
+ 7
+ true
@@ -18,24 +18,24 @@ 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: 6.1950 4.2049
- lambdas: 1.0000 1.0000
+ rcs: 6.1950 4.2049
+ 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: 8.1560 5.0091
- lambdas: 1.0000 1.0000
+ rcs: 8.1560 5.0091
+ lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
@@ -45,293 +45,293 @@ L=3 Nkbl=1 erefs: 0.17977+309
- Te pb rel nc
- ATM4.2.7 24-JAN-23 Troullier-Martins
- 5s 2.00r r= 2.58/5p 4.00r r= 2.82/5d 0.00r r= 2.82/4f 0.00r r= 2.49/
+ Te pb rel nc
+ ATM4.2.7 24-JAN-23 Troullier-Martins
+ 5s 2.00r r= 2.58/5p 4.00r r= 2.82/5d 0.00r r= 2.82/4f 0.00r r= 2.49/
-
- 500
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- 6.19503761473
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diff --git a/data/lat3_791/Te.psf b/data/lat3_791/Te.psf
index dee0663..484faf5 100644
--- a/data/lat3_791/Te.psf
+++ b/data/lat3_791/Te.psf
@@ -1,7 +1,7 @@
- Te pb rel nc
- ATM4.2.7 24-JAN-23 Troullier-Martins
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- 4 3 1179 0.476683110897E-04 0.125000000000E-01 6.00000000000
+ Te pb rel nc
+ ATM4.2.7 24-JAN-23 Troullier-Martins
+ 5s 2.00r r= 2.58/5p 4.00r r= 2.82/5d 0.00r r= 2.82/4f 0.00r r= 2.49/
+ 4 3 1179 0.476683110897E-04 0.125000000000E-01 6.00000000000
Radial grid follows
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Valence charge follows
0.913978654024E-13 0.370204496830E-12 0.843492378500E-12 0.151854232068E-11
0.240284910186E-11 0.350412725837E-11 0.483031702525E-11 0.638959043233E-11
@@ -2859,53 +2859,53 @@
0.628849136629E-01 0.648685229072E-01 0.669219761932E-01 0.690480112293E-01
0.712494816680E-01 0.735293621691E-01 0.758907536756E-01 0.783368889118E-01
0.808711381105E-01 0.834970149775E-01 0.862181829006E-01 0.890384614117E-01
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- 0.168382440133 0.155984784658 0.144342315493 0.133421089933
+ 0.919618329102E-01 0.949924496545E-01 0.981346410300E-01 0.101392921101
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+ 0.226221743494 0.210453941299 0.195581836970 0.181569793618
+ 0.168382440133 0.155984784658 0.144342315493 0.133421089933
0.123187811608 0.113609896975 0.104655531666 0.962937174350E-01
0.884943104559E-01 0.812280517648E-01 0.744665905987E-01 0.681825013920E-01
0.623492951494E-01 0.569414258833E-01 0.519342927515E-01 0.473042384827E-01
diff --git a/data/lat3_791/fdf-58450.log b/data/lat3_791/fdf-58450.log
index 9674992..6e9d0c3 100644
--- a/data/lat3_791/fdf-58450.log
+++ b/data/lat3_791/fdf-58450.log
@@ -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
diff --git a/input.fdf b/input.fdf
new file mode 100644
index 0000000..aabdb0d
--- /dev/null
+++ b/input.fdf
@@ -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
\ No newline at end of file
diff --git a/out with HK = HK + Ef * SK.txt b/out with HK = HK + Ef * SK.txt
index 5016a88..321b5ad 100644
--- a/out with HK = HK + Ef * SK.txt
+++ b/out with HK = HK + Ef * SK.txt
@@ -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
\ No newline at end of file
+Calculate energies and magnetic components: 0.248 s
diff --git a/test.ipynb b/test.ipynb
index 3ee66cb..65186e2 100644
--- a/test.ipynb
+++ b/test.ipynb
@@ -2,14 +2,14 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
- "[Mac:75276] shmem: mmap: an error occurred while determining whether or not /var/folders/yh/dx7xl94n3g52ts3td8qcxjcc0000gn/T//ompi.Mac.501/jf.0/1847132160/sm_segment.Mac.501.6e190000.0 could be created.\n"
+ "[Daniels-Air:78400] shmem: mmap: an error occurred while determining whether or not /var/folders/yh/dx7xl94n3g52ts3td8qcxjcc0000gn/T//ompi.Daniels-Air.501/jf.0/412614656/sm_segment.Daniels-Air.501.18980000.0 could be created.\n"
]
},
{
@@ -24,113 +24,48 @@
}
],
"source": [
- "from tqdm import tqdm\n",
"from sys import getsizeof\n",
"from timeit import default_timer as timer\n",
"\n",
- "import numpy as np\n",
"import sisl\n",
"import sisl.viz\n",
- "from src.grogu_magn.utils import *\n",
+ "from src.grogu_magn import *\n",
"from mpi4py import MPI\n",
- "import pickle\n",
- "from numpy.linalg import inv\n",
"import warnings\n",
"\n",
- "\"\"\" \n",
- "# Some input parsing\n",
- "parser = argparse.ArgumentParser()\n",
- "parser.add_argument('--kset' , dest = 'kset' , default = 2 , type=int , help = 'k-space resolution of Jij calculation')\n",
- "parser.add_argument('--kdirs' , dest = 'kdirs' , default = 'xyz' , help = 'Definition of k-space dimensionality')\n",
- "parser.add_argument('--eset' , dest = 'eset' , default = 42 , type=int , help = 'Number of energy points on the contour')\n",
- "parser.add_argument('--eset-p' , dest = 'esetp' , default = 10 , type=int , help = 'Parameter tuning the distribution on the contour')\n",
- "parser.add_argument('--input' , dest = 'infile' , required = True , help = 'Input file name')\n",
- "parser.add_argument('--output' , dest = 'outfile', required = True , help = 'Output file name')\n",
- "parser.add_argument('--Ebot' , dest = 'Ebot' , default = -20.0 , type=float, help = 'Bottom energy of the contour')\n",
- "parser.add_argument('--npairs' , dest = 'npairs' , default = 1 , type=int , help = 'Number of unitcell pairs in each direction for Jij calculation')\n",
- "parser.add_argument('--adirs' , dest = 'adirs' , default = False , help = 'Definition of pair directions')\n",
- "parser.add_argument('--use-tqdm', dest = 'usetqdm', default = 'not' , help = 'Use tqdm for progressbars or not')\n",
- "parser.add_argument('--cutoff' , dest = 'cutoff' , default = 100.0 , type=float, help = 'Real space cutoff for pair generation in Angs')\n",
- "parser.add_argument('--pairfile', dest = 'pairfile', default = False , help = 'File to read pair information')\n",
- "args = parser.parse_args()\n",
- "\"\"\"\n",
"# runtime information\n",
"times = dict()\n",
"times[\"start_time\"] = timer()\n",
"########################\n",
"# it works if data is in downloads folder\n",
"########################\n",
- "sisl.__version__"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "file = open(\"Fe3GeTe2_benchmark_on_15k_300eset.pickle\", \"rb\")\n",
- "object_file = pickle.load(file)\n",
- "object_file"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "dat = sisl.io.siesta.eigSileSiesta(\n",
- " \"/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.EIG\"\n",
- ")\n",
- "siesta_eigs = dat.read_data()\n",
- "siesta_eigs.min()"
+ "sisl.__version__\n",
+ "\n",
+ "try:\n",
+ " print(sisl.__version__)\n",
+ "except:\n",
+ " print(\"sisl version unknown.\")\n",
+ "\n",
+ "try:\n",
+ " print(np.__version__)\n",
+ "except:\n",
+ " print(\"numpy version unknown.\")"
]
},
{
- "cell_type": "markdown",
+ "cell_type": "code",
+ "execution_count": 20,
"metadata": {},
+ "outputs": [],
"source": [
- "Ef = dat.read_fermi_level()\n",
- "Ef"
+ "sisl.io.Sile(\"input.fdf\").read(\"scfOrientation\")"
]
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "================================================================================================================================================================\n",
- "Input file: \n",
- "/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf\n",
- "Output file: \n",
- "./Fe3GeTe2_notebook.pickle\n",
- "Number of nodes in the parallel cluster: 1\n",
- "================================================================================================================================================================\n",
- "Cell [Ang]: \n",
- "[[ 3.79100000e+00 0.00000000e+00 0.00000000e+00]\n",
- " [-1.89550000e+00 3.28310231e+00 0.00000000e+00]\n",
- " [ 1.25954923e-15 2.18160327e-15 2.05700000e+01]]\n",
- "================================================================================================================================================================\n",
- "DFT axis: \n",
- "[0 0 1]\n",
- "Quantization axis and perpendicular rotation directions:\n",
- "[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]\n",
- "[0 1 0] --» [array([1, 0, 0]), array([0, 0, 1])]\n",
- "[0 0 1] --» [array([1, 0, 0]), array([0, 1, 0])]\n",
- "================================================================================================================================================================\n",
- "Parameters for the contour integral:\n",
- "Number of k points: 10\n",
- "k point directions: xy\n",
- "Ebot: -13\n",
- "Eset: 300\n",
- "Esetp: 1000\n",
- "================================================================================================================================================================\n",
- "Setup done. Elapsed time: 4.909605666 s\n",
- "================================================================================================================================================================\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"################################################################################\n",
"#################################### INPUT #####################################\n",
@@ -167,16 +102,59 @@
" dict(ai=1, aj=2, Ruc=np.array([-2, 0, 0])),\n",
" dict(ai=1, aj=2, Ruc=np.array([-3, 0, 0])),\n",
"]\n",
+ "\n",
"# Brilloun zone sampling and Green function contour integral\n",
- "kset = 10\n",
+ "kset = 3\n",
"kdirs = \"xy\"\n",
"ebot = -13\n",
"eset = 300\n",
"esetp = 1000\n",
"################################################################################\n",
"#################################### INPUT #####################################\n",
- "################################################################################\n",
- "\n",
+ "################################################################################"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "================================================================================================================================================================\n",
+ "Input file: \n",
+ "/Users/danielpozsar/Downloads/nojij/Fe3GeTe2/monolayer/soc/lat3_791/Fe3GeTe2.fdf\n",
+ "Output file: \n",
+ "./Fe3GeTe2_notebook.pickle\n",
+ "Number of nodes in the parallel cluster: 1\n",
+ "================================================================================================================================================================\n",
+ "Cell [Ang]: \n",
+ "[[ 3.79100000e+00 0.00000000e+00 0.00000000e+00]\n",
+ " [-1.89550000e+00 3.28310231e+00 0.00000000e+00]\n",
+ " [ 1.25954923e-15 2.18160327e-15 2.05700000e+01]]\n",
+ "================================================================================================================================================================\n",
+ "DFT axis: \n",
+ "[0 0 1]\n",
+ "Quantization axis and perpendicular rotation directions:\n",
+ "[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]\n",
+ "[0 1 0] --» [array([1, 0, 0]), array([0, 0, 1])]\n",
+ "[0 0 1] --» [array([1, 0, 0]), array([0, 1, 0])]\n",
+ "================================================================================================================================================================\n",
+ "Parameters for the contour integral:\n",
+ "Number of k points: 3\n",
+ "k point directions: xy\n",
+ "Ebot: -13\n",
+ "Eset: 300\n",
+ "Esetp: 1000\n",
+ "================================================================================================================================================================\n",
+ "Setup done. Elapsed time: 2.303232 s\n",
+ "================================================================================================================================================================\n"
+ ]
+ }
+ ],
+ "source": [
"# MPI parameters\n",
"comm = MPI.COMM_WORLD\n",
"size = comm.Get_size()\n",
@@ -188,8 +166,8 @@
" outfile += \".pickle\"\n",
"\n",
"simulation_parameters = dict(\n",
- " path=path,\n",
- " outpath=outfile,\n",
+ " infile=path,\n",
+ " outfile=outfile,\n",
" scf_xcf_orientation=scf_xcf_orientation,\n",
" ref_xcf_orientations=ref_xcf_orientations,\n",
" kset=kset,\n",
@@ -200,9 +178,17 @@
" parallel_size=size,\n",
")\n",
"\n",
+ "# if ebot is not given put it 0.1 eV under the smallest energy\n",
+ "if simulation_parameters[\"ebot\"] is None:\n",
+ " try:\n",
+ " eigfile = simulation_parameters[\"infile\"][:-3] + \"EIG\"\n",
+ " simulation_parameters[\"ebot\"] = read_siesta_emin(eigfile) - 0.1\n",
+ " except:\n",
+ " print(\"Could not determine ebot.\")\n",
+ " print(\"Parameter was not given and .EIG file was not found.\")\n",
"# digestion of the input\n",
"# read sile\n",
- "fdf = sisl.get_sile(path)\n",
+ "fdf = sisl.get_sile(simulation_parameters[\"infile\"])\n",
"# read in hamiltonian\n",
"dh = fdf.read_hamiltonian()\n",
"simulation_parameters[\"cell\"] = fdf.read_geometry().cell\n",
@@ -219,62 +205,6 @@
" )"
]
},
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "import matplotlib.pyplot as plt\n",
- "\n",
- "plt.figure(figsize=(15, 5))\n",
- "plt.subplot(121)\n",
- "plt.plot(np.sort(dh.eigh()), marker=\"o\", linestyle=\" \", label=\"sisl\")\n",
- "plt.plot(np.sort(siesta_eigs[0, 0]), marker=\"o\", linestyle=\" \", label=\"siesta\")\n",
- "plt.ylim(None, 10)\n",
- "plt.xlim(None, 75)\n",
- "plt.legend()\n",
- "plt.grid()\n",
- "plt.subplot(122)\n",
- "DOS = sisl.physics.electron.DOS(np.linspace(-15, 85, 1000), dh.eigh())\n",
- "plt.plot(DOS, np.linspace(-15, 85, 1000))\n",
- "DOS = sisl.physics.electron.DOS(np.linspace(-15, 85, 1000), siesta_eigs[0, 0])\n",
- "plt.plot(DOS, np.linspace(-15, 85, 1000))\n",
- "plt.ylim(None, 10)\n",
- "\n",
- "coords = dh.xyz[-3:]\n",
- "\n",
- "shift = np.array([-1, 0, 0]) @ simulation_parameters[\"cell\"]\n",
- "\n",
- "\n",
- "plt.figure(figsize=(15, 5))\n",
- "plt.subplot(131)\n",
- "plt.scatter(coords[:, 0], coords[:, 2], color=[\"r\", \"g\", \"b\"])\n",
- "plt.scatter(\n",
- " (coords + shift)[:, 0], (coords + shift)[:, 2], color=[\"r\", \"g\", \"b\"], marker=\"x\"\n",
- ")\n",
- "plt.xlabel(\"x\")\n",
- "plt.ylabel(\"z\")\n",
- "plt.subplot(132)\n",
- "plt.scatter(coords[:, 1], coords[:, 2], color=[\"r\", \"g\", \"b\"])\n",
- "plt.scatter(\n",
- " (coords + shift)[:, 1], (coords + shift)[:, 2], color=[\"r\", \"g\", \"b\"], marker=\"x\"\n",
- ")\n",
- "plt.xlabel(\"y\")\n",
- "plt.ylabel(\"z\")\n",
- "plt.subplot(133)\n",
- "plt.scatter(coords[:, 0], coords[:, 1], color=[\"r\", \"g\", \"b\"])\n",
- "plt.scatter(\n",
- " (coords + shift)[:, 0], (coords + shift)[:, 1], color=[\"r\", \"g\", \"b\"], marker=\"x\"\n",
- ")\n",
- "plt.xlabel(\"x\")\n",
- "plt.ylabel(\"y\")\n",
- "print(\"xyz[-3:]: red, green, blue\")\n",
- "\n",
- "print(np.linalg.norm(coords[0] - coords[1]))\n",
- "print(np.linalg.norm(coords[0] - coords[2]))\n",
- "print(np.linalg.norm(coords[2] - coords[1]))\n",
- "print(np.linalg.norm(coords[0] - (coords + shift)[2]))"
- ]
- },
{
"cell_type": "code",
"execution_count": 3,
@@ -284,63 +214,13 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Hamiltonian and exchange field rotated. Elapsed time: 5.473272791 s\n",
+ "Hamiltonian and exchange field rotated. Elapsed time: 2.914966208 s\n",
"================================================================================================================================================================\n"
]
}
],
"source": [
- "NO = dh.no # shorthand for number of orbitals in the unit cell\n",
- "\n",
- "# preprocessing Hamiltonian and overlap matrix elements\n",
- "h11 = dh.tocsr(dh.M11r)\n",
- "h11 += dh.tocsr(dh.M11i) * 1.0j\n",
- "h11 = h11.toarray().reshape(NO, dh.n_s, NO).transpose(0, 2, 1).astype(\"complex128\")\n",
- "\n",
- "h22 = dh.tocsr(dh.M22r)\n",
- "h22 += dh.tocsr(dh.M22i) * 1.0j\n",
- "h22 = h22.toarray().reshape(NO, dh.n_s, NO).transpose(0, 2, 1).astype(\"complex128\")\n",
- "\n",
- "h12 = dh.tocsr(dh.M12r)\n",
- "h12 += dh.tocsr(dh.M12i) * 1.0j\n",
- "h12 = h12.toarray().reshape(NO, dh.n_s, NO).transpose(0, 2, 1).astype(\"complex128\")\n",
- "\n",
- "h21 = dh.tocsr(dh.M21r)\n",
- "h21 += dh.tocsr(dh.M21i) * 1.0j\n",
- "h21 = h21.toarray().reshape(NO, dh.n_s, NO).transpose(0, 2, 1).astype(\"complex128\")\n",
- "\n",
- "sov = (\n",
- " dh.tocsr(dh.S_idx)\n",
- " .toarray()\n",
- " .reshape(NO, dh.n_s, NO)\n",
- " .transpose(0, 2, 1)\n",
- " .astype(\"complex128\")\n",
- ")\n",
- "\n",
- "\n",
- "# Reorganization of Hamiltonian and overlap matrix elements to SPIN BOX representation\n",
- "U = np.vstack(\n",
- " [np.kron(np.eye(NO, dtype=int), [1, 0]), np.kron(np.eye(NO, dtype=int), [0, 1])]\n",
- ")\n",
- "# This is the permutation that transforms ud1ud2 to u12d12\n",
- "# That is this transforms FROM SPIN BOX to ORBITAL BOX => U\n",
- "# the inverse transformation is U.T u12d12 to ud1ud2\n",
- "# That is FROM ORBITAL BOX to SPIN BOX => U.T\n",
- "\n",
- "# From now on everything is in SPIN BOX!!\n",
- "hh, ss = np.array(\n",
- " [\n",
- " U.T @ np.block([[h11[:, :, i], h12[:, :, i]], [h21[:, :, i], h22[:, :, i]]]) @ U\n",
- " for i in range(dh.lattice.nsc.prod())\n",
- " ]\n",
- "), np.array(\n",
- " [\n",
- " U.T\n",
- " @ np.block([[sov[:, :, i], sov[:, :, i] * 0], [sov[:, :, i] * 0, sov[:, :, i]]])\n",
- " @ U\n",
- " for i in range(dh.lattice.nsc.prod())\n",
- " ]\n",
- ")\n",
+ "hh, ss, NO = build_hh_ss(dh)\n",
"\n",
"\n",
"# symmetrizing Hamiltonian and overlap matrix to make them hermitian\n",
@@ -352,9 +232,6 @@
" ss[i], ss[j] = (s1 + s1d.T.conj()) / 2, (s1d + s1.T.conj()) / 2\n",
"\n",
"\n",
- "###################################################################################\n",
- "# either this is shit\n",
- "\n",
"# identifying TRS and TRB parts of the Hamiltonian\n",
"TAUY = np.kron(np.eye(NO), tau_y)\n",
"hTR = np.array([TAUY @ hh[i].conj() @ TAUY for i in range(dh.lattice.nsc.prod())])\n",
@@ -371,8 +248,6 @@
" ]\n",
") # equation 77\n",
"\n",
- "###################################################################################\n",
- "\n",
"\n",
"# Check if exchange field has scalar part\n",
"max_xcfs = abs(np.array(np.array([f[\"c\"] / 2 for f in traced]))).max()\n",
@@ -400,154 +275,15 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "R [[1. 0. 0.]\n",
- " [0. 1. 0.]\n",
- " [0. 0. 1.]]\n",
- "Z rot doesnt change anything in XCF: True\n",
- "MAX(myhk - sislhk) 2.974862582050264e-06 this is zero as should be\n",
- "MAX(myhk_rot - sislhk) 2.974862582050264e-06 rotation fucks it up\n",
- "MAX(rot_H - sislhk) 8.881784197001252e-16 rotation fucks it up\n"
- ]
- }
- ],
- "source": [
- "myhk, sk = hsk(hh, ss, dh.sc_off, np.array([0.5, 0, 0]))\n",
- "sislhk = dh.Hk(np.array([0.5, 0, 0])).toarray()\n",
- "\n",
- "R = RotMa2b(scf_xcf_orientation, ref_xcf_orientations[2][\"o\"])\n",
- "print(\"R\", R)\n",
- "rot_XCF = np.einsum(\"ij,jklm->iklm\", R, XCF)\n",
- "print(\"Z rot doesnt change anything in XCF: \", np.allclose(XCF, rot_XCF))\n",
- "\n",
- "###################################################################################\n",
- "# either this is shit\n",
- "rot_H_XCF = sum(\n",
- " [np.kron(rot_XCF[i], tau) for i, tau in enumerate([tau_x, tau_y, tau_z])]\n",
- ")\n",
- "rot_H = hTRS + rot_H_XCF # equation 76\n",
- "###################################################################################\n",
- "\n",
- "\n",
- "myhk_rot, sk = hsk(rot_H, ss, dh.sc_off, np.array([0.5, 0, 0]))\n",
- "\n",
- "print(\"MAX(myhk - sislhk)\", np.max(abs(myhk - sislhk)), \"this is zero as should be\")\n",
- "print(\"MAX(myhk_rot - sislhk)\", np.max(abs(myhk_rot - sislhk)), \"rotation fucks it up\")\n",
- "print(\"MAX(rot_H - sislhk)\", np.max(abs(rot_H - hh)), \"rotation fucks it up\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Site and pair dictionaries created. Elapsed time: 5.680114458 s\n",
+ "Site and pair dictionaries created. Elapsed time: 2.944875791 s\n",
"================================================================================================================================================================\n"
]
}
],
"source": [
- "# for every site we have to store 3 Greens function (and the associated _tmp-s) in the 3 reference directions\n",
- "for mag_ent in magnetic_entities:\n",
- " parsed = parse_magnetic_entity(dh, **mag_ent) # parse orbital indexes\n",
- " mag_ent[\"orbital_indeces\"] = parsed\n",
- " mag_ent[\"spin_box_indeces\"] = blow_up_orbindx(parsed) # calculate spin box indexes\n",
- " # if orbital is not set use all\n",
- " if \"l\" not in mag_ent.keys():\n",
- " mag_ent[\"l\"] = \"all\"\n",
- " if isinstance(mag_ent[\"atom\"], int):\n",
- " mag_ent[\"tags\"] = [\n",
- " f\"[{mag_ent['atom']}]{dh.atoms[mag_ent['atom']].tag}({mag_ent['l']})\"\n",
- " ]\n",
- " mag_ent[\"xyz\"] = [dh.xyz[mag_ent[\"atom\"]]]\n",
- " if isinstance(mag_ent[\"atom\"], list):\n",
- " mag_ent[\"tags\"] = []\n",
- " mag_ent[\"xyz\"] = []\n",
- " # iterate over atoms\n",
- " for atom_idx in mag_ent[\"atom\"]:\n",
- " mag_ent[\"tags\"].append(\n",
- " f\"[{atom_idx}]{dh.atoms[atom_idx].tag}({mag_ent['l']})\"\n",
- " )\n",
- " mag_ent[\"xyz\"].append(dh.xyz[atom_idx])\n",
- "\n",
- " # calculate size for Greens function generation\n",
- " spin_box_shape = len(mag_ent[\"spin_box_indeces\"])\n",
- "\n",
- " mag_ent[\"energies\"] = [] # we will store the second order energy derivations here\n",
- "\n",
- " # These will be the perturbed potentials from eq. 100\n",
- " mag_ent[\"Vu1\"] = [] # so they are independent in memory\n",
- " mag_ent[\"Vu2\"] = []\n",
- "\n",
- " mag_ent[\"Gii\"] = [] # Greens function\n",
- " mag_ent[\"Gii_tmp\"] = [] # Greens function for parallelization\n",
- " for i in ref_xcf_orientations:\n",
- " # Rotations for every quantization axis\n",
- " mag_ent[\"Vu1\"].append([])\n",
- " mag_ent[\"Vu2\"].append([])\n",
- " # Greens functions for every quantization axis\n",
- " mag_ent[\"Gii\"].append(\n",
- " np.zeros((eset, spin_box_shape, spin_box_shape), dtype=\"complex128\")\n",
- " )\n",
- " mag_ent[\"Gii_tmp\"].append(\n",
- " np.zeros((eset, spin_box_shape, spin_box_shape), dtype=\"complex128\")\n",
- " )\n",
- "\n",
- "# for every site we have to store 2x3 Greens function (and the associated _tmp-s)\n",
- "# in the 3 reference directions, because G_ij and G_ji are both needed\n",
- "for pair in pairs:\n",
- " # calculate distance\n",
- " xyz_ai = magnetic_entities[pair[\"ai\"]][\"xyz\"]\n",
- " xyz_aj = magnetic_entities[pair[\"aj\"]][\"xyz\"]\n",
- " xyz_aj = xyz_aj + pair[\"Ruc\"] @ simulation_parameters[\"cell\"]\n",
- " pair[\"dist\"] = np.linalg.norm(xyz_ai - xyz_aj)\n",
- "\n",
- " # calculate size for Greens function generation\n",
- " spin_box_shape_i = len(magnetic_entities[pair[\"ai\"]][\"spin_box_indeces\"])\n",
- " spin_box_shape_j = len(magnetic_entities[pair[\"aj\"]][\"spin_box_indeces\"])\n",
- " pair[\"tags\"] = []\n",
- " for mag_ent in [magnetic_entities[pair[\"ai\"]], magnetic_entities[pair[\"aj\"]]]:\n",
- " tag = \"\"\n",
- " # get atoms of magnetic entity\n",
- " atoms_idx = mag_ent[\"atom\"]\n",
- " orbitals = mag_ent[\"l\"]\n",
- "\n",
- " # if magnetic entity contains one atoms\n",
- " if isinstance(atoms_idx, int):\n",
- " tag += f\"[{atoms_idx}]{dh.atoms[atoms_idx].tag}({orbitals})\"\n",
- "\n",
- " # if magnetic entity contains more than one atoms\n",
- " if isinstance(atoms_idx, list):\n",
- " # iterate over atoms\n",
- " atom_group = \"{\"\n",
- " for atom_idx in atoms_idx:\n",
- " atom_group += f\"[{atom_idx}]{dh.atoms[atom_idx].tag}({orbitals})--\"\n",
- " # end {} of the atoms in the magnetic entity\n",
- " tag += atom_group[:-2] + \"}\"\n",
- " pair[\"tags\"].append(tag)\n",
- " pair[\"energies\"] = [] # we will store the second order energy derivations here\n",
- "\n",
- " pair[\"Gij\"] = [] # Greens function\n",
- " pair[\"Gji\"] = []\n",
- " pair[\"Gij_tmp\"] = [] # Greens function for parallelization\n",
- " pair[\"Gji_tmp\"] = []\n",
- " for i in ref_xcf_orientations:\n",
- " # Greens functions for every quantization axis\n",
- " pair[\"Gij\"].append(\n",
- " np.zeros((eset, spin_box_shape_i, spin_box_shape_j), dtype=\"complex128\")\n",
- " )\n",
- " pair[\"Gij_tmp\"].append(\n",
- " np.zeros((eset, spin_box_shape_i, spin_box_shape_j), dtype=\"complex128\")\n",
- " )\n",
- " pair[\"Gji\"].append(\n",
- " np.zeros((eset, spin_box_shape_j, spin_box_shape_i), dtype=\"complex128\")\n",
- " )\n",
- " pair[\"Gji_tmp\"].append(\n",
- " np.zeros((eset, spin_box_shape_j, spin_box_shape_i), dtype=\"complex128\")\n",
- " )\n",
+ "pairs, magnetic_entities = setup_pairs_and_magnetic_entities(\n",
+ " magnetic_entities, pairs, dh, simulation_parameters\n",
+ ")\n",
"\n",
"if rank == root_node:\n",
" times[\"site_and_pair_dictionaries_time\"] = timer()\n",
@@ -561,30 +297,34 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
- "k loop: 0%| | 0/100 [00:00iklm\", R, XCF)\n",
" rot_H_XCF = sum(\n",
" [np.kron(rot_XCF[i], tau) for i, tau in enumerate([tau_x, tau_y, tau_z])]\n",
@@ -629,8 +369,14 @@
" dict(\n",
" orient=orient[\"o\"],\n",
" H=rot_H,\n",
- " GS=np.zeros((eset, rot_H.shape[1], rot_H.shape[2]), dtype=\"complex128\"),\n",
- " GS_tmp=np.zeros((eset, rot_H.shape[1], rot_H.shape[2]), dtype=\"complex128\"),\n",
+ " GS=np.zeros(\n",
+ " (simulation_parameters[\"eset\"], rot_H.shape[1], rot_H.shape[2]),\n",
+ " dtype=\"complex128\",\n",
+ " ),\n",
+ " GS_tmp=np.zeros(\n",
+ " (simulation_parameters[\"eset\"], rot_H.shape[1], rot_H.shape[2]),\n",
+ " dtype=\"complex128\",\n",
+ " ),\n",
" )\n",
" ) # store orientation and rotated Hamiltonian\n",
"\n",
@@ -638,8 +384,7 @@
" for u in orient[\"vw\"]:\n",
" Tu = np.kron(np.eye(NO, dtype=int), tau_u(u)) # section 2.H\n",
"\n",
- " Vu1 = 1j / 2 * commutator(rot_H_XCF_uc, Tu) # equation 100\n",
- " Vu2 = 1 / 8 * commutator(commutator(Tu, rot_H_XCF_uc), Tu) # equation 100\n",
+ " Vu1, Vu2 = calc_Vu(rot_H_XCF_uc, Tu)\n",
"\n",
" for mag_ent in magnetic_entities:\n",
" idx = mag_ent[\"spin_box_indeces\"]\n",
@@ -659,23 +404,23 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "Starting matrix inversions\n",
- "Total number of k points: 100\n",
+ "Starting matrix inversions.\n",
+ "Total number of k points: 9\n",
"Number of energy samples per k point: 300\n",
"Total number of directions: 3\n",
- "Total number of matrix inversions: 90000\n",
+ "Total number of matrix inversions: 8100\n",
"The shape of the Hamiltonian and the Greens function is 84x84=7056\n",
"Memory taken by a single Hamiltonian is: 0.015625 KB\n",
"Expected memory usage per matrix inversion: 0.5 KB\n",
"Expected memory usage per k point for parallel inversion: 450.0 KB\n",
- "Expected memory usage on root node: 43.9453125 MB\n",
+ "Expected memory usage on root node: 3.955078125 MB\n",
"================================================================================================================================================================\n"
]
},
@@ -683,14 +428,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "k loop: 100%|██████████| 100/100 [03:17<00:00, 1.97s/it]"
+ "k loop: 100%|██████████| 9/9 [00:31<00:00, 3.50s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
- "Calculated Greens functions. Elapsed time: 203.218047166 s\n",
+ "Calculated Greens functions. Elapsed time: 34.685783333 s\n",
"================================================================================================================================================================\n"
]
},
@@ -704,12 +449,12 @@
],
"source": [
"if rank == root_node:\n",
- " print(\"Starting matrix inversions\")\n",
+ " print(\"Starting matrix inversions.\")\n",
" print(f\"Total number of k points: {kset.shape[0]}\")\n",
- " print(f\"Number of energy samples per k point: {eset}\")\n",
+ " print(f\"Number of energy samples per k point: {simulation_parameters['eset']}\")\n",
" print(f\"Total number of directions: {len(hamiltonians)}\")\n",
" print(\n",
- " f\"Total number of matrix inversions: {kset.shape[0] * len(hamiltonians) * eset}\"\n",
+ " f\"Total number of matrix inversions: {kset.shape[0] * len(hamiltonians) * simulation_parameters['eset']}\"\n",
" )\n",
" print(f\"The shape of the Hamiltonian and the Greens function is {NO}x{NO}={NO*NO}\")\n",
" # https://stackoverflow.com/questions/70746660/how-to-predict-memory-requirement-for-np-linalg-inv\n",
@@ -720,10 +465,10 @@
" )\n",
" print(f\"Expected memory usage per matrix inversion: {memory_size * 32} KB\")\n",
" print(\n",
- " f\"Expected memory usage per k point for parallel inversion: {memory_size * len(hamiltonians) * eset * 32} KB\"\n",
+ " f\"Expected memory usage per k point for parallel inversion: {memory_size * len(hamiltonians) * simulation_parameters['eset'] * 32} KB\"\n",
" )\n",
" print(\n",
- " f\"Expected memory usage on root node: {len(np.array_split(kset, size)[0]) * memory_size * len(hamiltonians) * eset * 32 / 1024} MB\"\n",
+ " f\"Expected memory usage on root node: {len(np.array_split(kset, size)[0]) * memory_size * len(hamiltonians) * simulation_parameters['eset'] * 32 / 1024} MB\"\n",
" )\n",
" print(\n",
" \"================================================================================================================================================================\"\n",
@@ -735,7 +480,11 @@
"# make energy contour\n",
"# we are working in eV now !\n",
"# and sisl shifts E_F to 0 !\n",
- "cont = make_contour(emin=ebot, enum=eset, p=esetp)\n",
+ "cont = make_contour(\n",
+ " emin=simulation_parameters[\"ebot\"],\n",
+ " enum=simulation_parameters[\"eset\"],\n",
+ " p=simulation_parameters[\"esetp\"],\n",
+ ")\n",
"eran = cont.ze\n",
"\n",
"# ----------------------------------------------------------------------\n",
@@ -749,9 +498,7 @@
" HK, SK = hsk(H, ss, dh.sc_off, k)\n",
"\n",
" # solve Greens function sequentially for the energies, because of memory bound\n",
- " Gk = np.zeros(shape=(eset, HK.shape[0], HK.shape[1]), dtype=\"complex128\")\n",
- " for j in range(eset):\n",
- " Gk[j] = inv(SK * eran[j] - HK)\n",
+ " Gk = sequential_GK(HK, SK, eran, simulation_parameters[\"eset\"])\n",
"\n",
" # saving this for total charge\n",
" hamiltonian_orientation[\"GS_tmp\"] += Gk @ SK * wk\n",
@@ -799,16 +546,16 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "Total charge: 39.857798089095745\n",
- "Total charge: 39.85779799083869\n",
- "Total charge: 39.95778482001014\n",
+ "Total charge: 39.98745949985201\n",
+ "Total charge: 39.987459508326964\n",
+ "Total charge: 40.098563331816784\n",
"Magnetic entities integrated.\n",
"Pairs integrated.\n",
"Magnetic parameters calculated.\n",
@@ -833,7 +580,7 @@
"[0 0 1] --» [array([1, 0, 0]), array([0, 1, 0])]\n",
"================================================================================================================================================================\n",
"Parameters for the contour integral:\n",
- "Number of k points: 10\n",
+ "Number of k points: 3\n",
"k point directions: xy\n",
"Ebot: -13\n",
"Eset: 300\n",
@@ -855,16 +602,16 @@
"Magnetic entity x [Ang] y [Ang] z [Ang]\n",
"----------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"[3]Fe(2) -7.339158738013707e-06 4.149278510690423e-06 11.657585837928032\n",
- "Consistency check: 6.818420305920725e-05\n",
- "Anisotropy diag: [-0.07482326 -0.00552873 0. ]\n",
+ "Consistency check: 2.3860081328264116e-05\n",
+ "Anisotropy diag: [0.02546754 0.00208022 0. ]\n",
"\n",
"[4]Fe(2) -7.326987662162937e-06 4.158274523275774e-06 8.912422537596708\n",
- "Consistency check: 7.686025895869975e-05\n",
- "Anisotropy diag: [ 0.0004411 -0.07750451 0. ]\n",
+ "Consistency check: 7.768349833381372e-05\n",
+ "Anisotropy diag: [-0.06673164 0.01049614 0. ]\n",
"\n",
"[5]Fe(2) 1.8954667088117545 1.0943913231921656 10.285002698393109\n",
- "Consistency check: 5.268649241663148e-05\n",
- "Anisotropy diag: [ 0.01120506 -0.0414785 0. ]\n",
+ "Consistency check: 1.2052892692793193e-06\n",
+ "Anisotropy diag: [-0.01943729 -0.0206467 0. ]\n",
"\n",
"================================================================================================================================================================\n",
"Exchange [meV]\n",
@@ -872,185 +619,171 @@
"Magnetic entity1 Magnetic entity2 [i j k] d [Ang]\n",
"----------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
"[3]Fe(2) [4]Fe(2) [0 0 0] d [Ang] 2.745163300331324\n",
- "Isotropic: -84.46399731420344\n",
- "DMI: [ 1.88620081e-01 -7.64018484e-04 -4.37922496e-07]\n",
- "Symmetric-anisotropy: [ 2.38296852e+00 1.42209663e-04 -6.68866203e-05 1.42209663e-04\n",
- " 2.40029619e+00 -8.14152579e-06 -6.68866203e-05 -8.14152579e-06\n",
- " -4.78326471e+00]\n",
- "J: [-8.20810288e+01 1.42209663e-04 -6.68866203e-05 1.42209663e-04\n",
- " -8.20637011e+01 -8.14152579e-06 -6.68866203e-05 -8.14152579e-06\n",
- " -8.92472620e+01]\n",
+ "Isotropic: -39.96748066866786\n",
+ "DMI: [-4.16373454e-04 -8.52759845e-04 2.22666054e-07]\n",
+ "Symmetric-anisotropy: [ 7.85170293e-01 -2.01786552e-05 -2.73439476e-07 -2.01786552e-05\n",
+ " 7.85623794e-01 -9.79265975e-07 -2.73439476e-07 -9.79265975e-07\n",
+ " -1.57079409e+00]\n",
+ "J: [-3.91823104e+01 -2.01786552e-05 -2.73439476e-07 -2.01786552e-05\n",
+ " -3.91818569e+01 -9.79265975e-07 -2.73439476e-07 -9.79265975e-07\n",
+ " -4.15382748e+01]\n",
"Energies for debugging: \n",
- "array([[-8.92399658e-02, 1.88628223e-04, -1.88611940e-04,\n",
- " -8.91429459e-02],\n",
- " [-8.92545582e-02, 8.30905104e-07, -6.97131863e-07,\n",
- " -8.91774451e-02],\n",
- " [-7.49844563e-02, -1.42647586e-07, -1.41771741e-07,\n",
- " -7.49846125e-02]])\n",
+ "[[-4.15381735e-02 -4.15394188e-07 4.17352720e-07 -4.17291610e-02]\n",
+ " [-4.15383760e-02 8.53033284e-07 -8.52486405e-07 -4.17300740e-02]\n",
+ " [-3.66345528e-02 2.04013212e-08 1.99559891e-08 -3.66345467e-02]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.08917745, -0.07498446, -0.08923997])\n",
+ "[-0.04173007 -0.03663455 -0.04153817]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.08917744514035186 -0.07498461245605947\n",
+ "-0.04173007401441678 -0.036634546737597175\n",
"\n",
"[3]Fe(2) [5]Fe(2) [0 0 0] d [Ang] 2.5835033632437767\n",
- "Isotropic: -41.629965239513076\n",
- "DMI: [ 1.16104440e+00 -2.02989607e+00 1.42007213e-04]\n",
- "Symmetric-anisotropy: [-0.3583508 0.2300684 -0.0464857 0.2300684 -0.60812243 -0.03183621\n",
- " -0.0464857 -0.03183621 0.96647323]\n",
- "J: [-4.19883160e+01 2.30068404e-01 -4.64857039e-02 2.30068404e-01\n",
- " -4.22380877e+01 -3.18362116e-02 -4.64857039e-02 -3.18362116e-02\n",
- " -4.06634920e+01]\n",
+ "Isotropic: -54.8678926276239\n",
+ "DMI: [ 8.10240490e-01 -1.36608099e+00 3.25215454e-05]\n",
+ "Symmetric-anisotropy: [ 0.12903943 0.14426756 -0.06549931 0.14426756 -0.20896588 -0.05975815\n",
+ " -0.06549931 -0.05975815 0.07992645]\n",
+ "J: [-54.7388532 0.14426756 -0.06549931 0.14426756 -55.07685851\n",
+ " -0.05975815 -0.06549931 -0.05975815 -54.78796617]\n",
"Energies for debugging: \n",
- "array([[-0.04075812, 0.00119288, -0.00112921, -0.04080062],\n",
- " [-0.04056886, 0.00207638, -0.00198341, -0.04056711],\n",
- " [-0.04367555, -0.00022993, -0.00023021, -0.04340952]])\n",
+ "[[-0.05497624 0.00087 -0.00075048 -0.0552075 ]\n",
+ " [-0.0545997 0.00143158 -0.00130058 -0.05469815]\n",
+ " [-0.05494622 -0.00014424 -0.0001443 -0.05477956]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.04056711, -0.04367555, -0.04075812])\n",
+ "[-0.05469815 -0.05494622 -0.05497624]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.04056710918296237 -0.04340952290351278\n",
+ "-0.05469814671520505 -0.05477955968564471\n",
"\n",
"[4]Fe(2) [5]Fe(2) [0 0 0] d [Ang] 2.583501767937866\n",
- "Isotropic: -41.63818539049319\n",
- "DMI: [-1.15569804e+00 2.01131866e+00 1.42813172e-04]\n",
- "Symmetric-anisotropy: [-0.35474671 0.23007014 0.03254717 0.23007014 -0.61181222 0.01758968\n",
- " 0.03254717 0.01758968 0.96655893]\n",
- "J: [-4.19929321e+01 2.30070141e-01 3.25471741e-02 2.30070141e-01\n",
- " -4.22499976e+01 1.75896770e-02 3.25471741e-02 1.75896770e-02\n",
- " -4.06716265e+01]\n",
+ "Isotropic: -54.86287528016134\n",
+ "DMI: [-8.08522805e-01 1.36388593e+00 3.14077512e-05]\n",
+ "Symmetric-anisotropy: [ 0.12501449 0.14426595 0.05678873 0.14426595 -0.20956489 0.04990479\n",
+ " 0.05678873 0.04990479 0.08455041]\n",
+ "J: [-5.47378608e+01 1.44265952e-01 5.67887254e-02 1.44265952e-01\n",
+ " -5.50724402e+01 4.99047869e-02 5.67887254e-02 4.99047869e-02\n",
+ " -5.47783249e+01]\n",
"Energies for debugging: \n",
- "array([[-0.04076979, -0.00117329, 0.00113811, -0.04082375],\n",
- " [-0.04057347, -0.00204387, 0.00197877, -0.04057565],\n",
- " [-0.04367625, -0.00022993, -0.00023021, -0.04341022]])\n",
+ "[[-0.05496666 -0.00085843 0.00075862 -0.05519787]\n",
+ " [-0.05458999 -0.00142067 0.0013071 -0.05469537]\n",
+ " [-0.05494701 -0.00014423 -0.0001443 -0.05478035]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.04057565, -0.04367625, -0.04076979])\n",
+ "[-0.05469537 -0.05494701 -0.05496666]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.04057564848089523 -0.043410215712362775\n",
+ "-0.054695368426152975 -0.05478035315936865\n",
"\n",
"[3]Fe(2) [5]Fe(2) [-1 -1 0] d [Ang] 2.5834973202859075\n",
- "Isotropic: -41.66159765171782\n",
- "DMI: [-2.33447929e+00 5.88920633e-05 -4.25773045e-05]\n",
- "Symmetric-anisotropy: [-7.33142752e-01 -1.52756996e-04 1.46307682e-04 -1.52756996e-04\n",
- " -2.16761810e-01 4.07813099e-02 1.46307682e-04 4.07813099e-02\n",
- " 9.49904562e-01]\n",
- "J: [-4.23947404e+01 -1.52756996e-04 1.46307682e-04 -1.52756996e-04\n",
- " -4.18783595e+01 4.07813099e-02 1.46307682e-04 4.07813099e-02\n",
- " -4.07116931e+01]\n",
+ "Isotropic: -54.86725213337313\n",
+ "DMI: [-1.55587908e+00 1.48356799e-05 -4.55339161e-05]\n",
+ "Symmetric-anisotropy: [-3.76175058e-01 -2.58204985e-05 -2.58761719e-05 -2.58204985e-05\n",
+ " 2.92919450e-01 4.97693839e-02 -2.58761719e-05 4.97693839e-02\n",
+ " 8.32556083e-02]\n",
+ "J: [-5.52434272e+01 -2.58204985e-05 -2.58761719e-05 -2.58204985e-05\n",
+ " -5.45743327e+01 4.97693839e-02 -2.58761719e-05 4.97693839e-02\n",
+ " -5.47839965e+01]\n",
"Energies for debugging: \n",
- "array([[-4.05161871e-02, -2.37526060e-03, 2.29369798e-03,\n",
- " -4.04786366e-02],\n",
- " [-4.09071991e-02, -2.05199745e-07, -8.74156186e-08,\n",
- " -4.09798629e-02],\n",
- " [-4.32780824e-02, 1.10179692e-07, 1.95334301e-07,\n",
- " -4.38096179e-02]])\n",
+ "[[-5.44093670e-02 -1.60564846e-03 1.50610969e-03 -5.44511949e-02]\n",
+ " [-5.51586260e-02 1.10404920e-08 4.07118518e-08 -5.54561691e-02]\n",
+ " [-5.46974705e-02 -1.97134176e-08 7.13544147e-08 -5.50306852e-02]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.04097986, -0.04327808, -0.04051619])\n",
+ "[-0.05545617 -0.05469747 -0.05440937]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.040979862867913205 -0.043809617939982115\n",
+ "-0.0554561691350627 -0.05503068524779923\n",
"\n",
"[4]Fe(2) [5]Fe(2) [-1 -1 0] d [Ang] 2.583495745338251\n",
- "Isotropic: -41.651354364546386\n",
- "DMI: [ 2.33450755e+00 -3.01207900e-04 -4.35448493e-05]\n",
- "Symmetric-anisotropy: [-7.24739149e-01 -1.52908277e-04 1.43933638e-04 -1.52908277e-04\n",
- " -2.27695138e-01 -4.07805826e-02 1.43933638e-04 -4.07805826e-02\n",
- " 9.52434287e-01]\n",
- "J: [-4.23760935e+01 -1.52908277e-04 1.43933638e-04 -1.52908277e-04\n",
- " -4.18790495e+01 -4.07805826e-02 1.43933638e-04 -4.07805826e-02\n",
- " -4.06989201e+01]\n",
+ "Isotropic: -54.87173513590157\n",
+ "DMI: [ 1.55588615e+00 -3.50135692e-04 -4.46128995e-05]\n",
+ "Symmetric-anisotropy: [-3.79737241e-01 -2.60848380e-05 -4.45024497e-05 -2.60848380e-05\n",
+ " 2.96608300e-01 -4.97778119e-02 -4.45024497e-05 -4.97778119e-02\n",
+ " 8.31289413e-02]\n",
+ "J: [-5.52514724e+01 -2.60848380e-05 -4.45024497e-05 -2.60848380e-05\n",
+ " -5.45751268e+01 -4.97778119e-02 -4.45024497e-05 -4.97778119e-02\n",
+ " -5.47886062e+01]\n",
"Energies for debugging: \n",
- "array([[-4.05168794e-02, 2.37528813e-03, -2.29372696e-03,\n",
- " -4.04793245e-02],\n",
- " [-4.08809608e-02, 1.57274262e-07, -4.45141537e-07,\n",
- " -4.09418727e-02],\n",
- " [-4.32787745e-02, 1.09363428e-07, 1.96453126e-07,\n",
- " -4.38103143e-02]])\n",
+ "[[-5.44101654e-02 1.60566396e-03 -1.50610834e-03 -5.44519935e-02]\n",
+ " [-5.51670469e-02 3.94638142e-07 -3.05633242e-07 -5.54714740e-02]\n",
+ " [-5.46982601e-02 -1.85280615e-08 7.06977375e-08 -5.50314708e-02]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.04094187, -0.04327877, -0.04051688])\n",
+ "[-0.05547147 -0.05469826 -0.05441017]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.04094187270410039 -0.04381031432397496\n",
+ "-0.05547147397315911 -0.05503147078078048\n",
"\n",
"[3]Fe(2) [5]Fe(2) [-1 0 0] d [Ang] 2.583541444641373\n",
- "Isotropic: -41.622961610451405\n",
- "DMI: [ 1.15553716e+00 2.03004764e+00 -1.00662008e-04]\n",
- "Symmetric-anisotropy: [-0.35259845 -0.22988479 0.04629996 -0.22988479 -0.61302608 -0.01757494\n",
- " 0.04629996 -0.01757494 0.96562453]\n",
- "J: [-4.19755601e+01 -2.29884795e-01 4.62999578e-02 -2.29884795e-01\n",
- " -4.22359877e+01 -1.75749425e-02 4.62999578e-02 -1.75749425e-02\n",
- " -4.06573371e+01]\n",
+ "Isotropic: -54.8543539372674\n",
+ "DMI: [8.08531830e-01 1.36653494e+00 1.23153243e-05]\n",
+ "Symmetric-anisotropy: [ 0.12565256 -0.14422424 0.06554219 -0.14422424 -0.2071834 -0.04991746\n",
+ " 0.06554219 -0.04991746 0.08153084]\n",
+ "J: [-5.47287014e+01 -1.44224241e-01 6.55421872e-02 -1.44224241e-01\n",
+ " -5.50615373e+01 -4.99174557e-02 6.55421872e-02 -4.99174557e-02\n",
+ " -5.47728231e+01]\n",
"Energies for debugging: \n",
- "array([[-0.04075738, 0.00117311, -0.00113796, -0.04081079],\n",
- " [-0.04055729, -0.00207635, 0.00198375, -0.0405554 ],\n",
- " [-0.04366118, 0.00022978, 0.00022999, -0.04339572]])\n",
+ "[[-0.0549559 0.00085845 -0.00075861 -0.05518723]\n",
+ " [-0.05458975 -0.00143208 0.00130099 -0.05468811]\n",
+ " [-0.05493584 0.00014424 0.00014421 -0.05476929]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.0405554 , -0.04366118, -0.04075738])\n",
+ "[-0.05468811 -0.05493584 -0.0549559 ]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.040555403759627504 -0.043395716365454126\n",
+ "-0.05468810820091341 -0.054769294557366933\n",
"\n",
"[4]Fe(2) [5]Fe(2) [-1 0 0] d [Ang] 2.5835398672184064\n",
- "Isotropic: -41.62008807379083\n",
- "DMI: [-1.16093102e+00 -2.01118580e+00 -9.97040031e-05]\n",
- "Symmetric-anisotropy: [-0.36016123 -0.22988672 -0.03265224 -0.22988672 -0.60539869 0.03182552\n",
- " -0.03265224 0.03182552 0.96555993]\n",
- "J: [-4.19802493e+01 -2.29886721e-01 -3.26522393e-02 -2.29886721e-01\n",
- " -4.22254868e+01 3.18255164e-02 -3.26522393e-02 3.18255164e-02\n",
- " -4.06545281e+01]\n",
+ "Isotropic: -54.85632586904892\n",
+ "DMI: [-8.10252027e-01 -1.36402738e+00 1.40111262e-05]\n",
+ "Symmetric-anisotropy: [ 0.12852618 -0.14422269 -0.05676095 -0.14422269 -0.21124941 0.05978565\n",
+ " -0.05676095 0.05978565 0.08272322]\n",
+ "J: [-54.72779968 -0.14422269 -0.05676095 -0.14422269 -55.06757527\n",
+ " 0.05978565 -0.05676095 0.05978565 -54.77360265]\n",
"Energies for debugging: \n",
- "array([[-0.04074714, -0.00119276, 0.00112911, -0.04078908],\n",
- " [-0.04056191, 0.00204384, -0.00197853, -0.04056407],\n",
- " [-0.04366189, 0.00022979, 0.00022999, -0.04339642]])\n",
+ "[[-0.05496711 -0.00087004 0.00075047 -0.0551985 ]\n",
+ " [-0.05458009 0.00142079 -0.00130727 -0.05468549]\n",
+ " [-0.05493665 0.00014424 0.00014421 -0.05477011]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.04056407, -0.04366189, -0.04074714])\n",
+ "[-0.05468549 -0.05493665 -0.05496711]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.04056407415889504 -0.043396424451279274\n",
+ "-0.05468549220244033 -0.05477010716669793\n",
"\n",
"[4]Fe(2) [5]Fe(2) [-2 0 0] d [Ang] 5.951322298958084\n",
- "Isotropic: -1.7294071924601657\n",
- "DMI: [-0.08510436 0.24159561 1.44684598]\n",
- "Symmetric-anisotropy: [ 0.09622056 0.08175665 0.02144594 0.08175665 -0.06049024 -0.0414623\n",
- " 0.02144594 -0.0414623 -0.03573033]\n",
- "J: [-1.63318663 0.08175665 0.02144594 0.08175665 -1.78989743 -0.0414623\n",
- " 0.02144594 -0.0414623 -1.76513752]\n",
+ "Isotropic: 0.7670124122315716\n",
+ "DMI: [-2.53243316e-01 2.68939617e-04 -1.43892049e-04]\n",
+ "Symmetric-anisotropy: [ 8.10949387e-02 -1.65488077e-05 -4.52585019e-05 -1.65488077e-05\n",
+ " -3.13833695e-01 -2.50031263e-01 -4.52585019e-05 -2.50031263e-01\n",
+ " 2.32738756e-01]\n",
+ "J: [ 8.48107351e-01 -1.65488077e-05 -4.52585019e-05 -1.65488077e-05\n",
+ " 4.53178717e-01 -2.50031263e-01 -4.52585019e-05 -2.50031263e-01\n",
+ " 9.99751168e-01]\n",
"Energies for debugging: \n",
- "array([[-1.72606525e-03, -4.36420623e-05, 1.26566667e-04,\n",
- " -1.82716801e-03],\n",
- " [-1.80420979e-03, -2.63041556e-04, 2.20149672e-04,\n",
- " -1.73934458e-03],\n",
- " [-1.75262685e-03, 1.36508933e-03, -1.52860262e-03,\n",
- " -1.52702868e-03]])\n",
+ "[[ 1.27357111e-03 -3.21205279e-06 5.03274580e-04 6.56773632e-04]\n",
+ " [ 7.25931228e-04 -2.23681115e-07 3.14198119e-07 7.58339032e-04]\n",
+ " [ 2.49583803e-04 -1.27343241e-07 1.60440856e-07 9.37875670e-04]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.00173934, -0.00175263, -0.00172607])\n",
+ "[0.00075834 0.00024958 0.00127357]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.0017393445796559598 -0.0015270286786416\n",
+ "0.0007583390322003737 0.0009378756696001232\n",
"\n",
"[4]Fe(2) [5]Fe(2) [-3 0 0] d [Ang] 9.638732176310562\n",
- "Isotropic: -0.4535195863892767\n",
- "DMI: [ 0.04836847 0.05429183 -0.15906095]\n",
- "Symmetric-anisotropy: [ 0.14297234 -0.0154665 0.00345288 -0.0154665 0.19102043 0.01270769\n",
- " 0.00345288 0.01270769 -0.33399277]\n",
- "J: [-0.31054725 -0.0154665 0.00345288 -0.0154665 -0.26249915 0.01270769\n",
- " 0.00345288 0.01270769 -0.78751236]\n",
+ "Isotropic: -54.86287528016134\n",
+ "DMI: [-8.08522805e-01 1.36388593e+00 3.14077512e-05]\n",
+ "Symmetric-anisotropy: [ 0.12501449 0.14426595 0.05678873 0.14426595 -0.20956489 0.04990479\n",
+ " 0.05678873 0.04990479 0.08455041]\n",
+ "J: [-5.47378608e+01 1.44265952e-01 5.67887254e-02 1.44265952e-01\n",
+ " -5.50724402e+01 4.99047869e-02 5.67887254e-02 4.99047869e-02\n",
+ " -5.47783249e+01]\n",
"Energies for debugging: \n",
- "array([[-7.80081681e-04, 3.56607876e-05, -6.10761579e-05,\n",
- " -7.42232776e-04],\n",
- " [-7.94943031e-04, -5.77447108e-05, 5.08389441e-05,\n",
- " -8.34582436e-04],\n",
- " [ 2.17234470e-04, -1.43594444e-04, 1.74527450e-04,\n",
- " 2.13487935e-04]])\n",
+ "[[-0.05496666 -0.00085843 0.00075862 -0.05519787]\n",
+ " [-0.05458999 -0.00142067 0.0013071 -0.05469537]\n",
+ " [-0.05494701 -0.00014423 -0.0001443 -0.05478035]]\n",
"J_ii for debugging: (check if this is the same as in calculate_exchange_tensor)\n",
- "array([-0.00083458, 0.00021723, -0.00078008])\n",
+ "[-0.05469537 -0.05494701 -0.05496666]\n",
"Test J_xx = E(y,z) = E(z,y)\n",
- "-0.0008345824358667467 0.0002134879350515751\n",
+ "-0.05469536842615297 -0.05478035315936865\n",
"\n",
"================================================================================================================================================================\n",
"Runtime information: \n",
- "Total runtime: 198.828617583 s\n",
+ "Total runtime: 32.859570917000006 s\n",
"----------------------------------------------------------------------------------------------------------------------------------------------------------------\n",
- "Initial setup: 0.12195141599999992 s\n",
- "Hamiltonian conversion and XC field extraction: 0.564 s\n",
- "Pair and site datastructure creatrions: 0.207 s\n",
- "k set cration and distribution: 0.036 s\n",
- "Rotating XC potential: 0.358 s\n",
- "Greens function inversion: 197.144 s\n",
- "Calculate energies and magnetic components: 0.398 s\n"
+ "Initial setup: 0.10918341700000012 s\n",
+ "Hamiltonian conversion and XC field extraction: 0.612 s\n",
+ "Pair and site datastructure creatrions: 0.030 s\n",
+ "k set cration and distribution: 0.030 s\n",
+ "Rotating XC potential: 0.278 s\n",
+ "Greens function inversion: 31.432 s\n",
+ "Calculate energies and magnetic components: 0.368 s\n"
]
}
],
@@ -1060,8 +793,7 @@
" for hamiltonian in hamiltonians:\n",
" GS = hamiltonian[\"GS\"]\n",
" traced = np.trace((GS), axis1=1, axis2=2)\n",
- " integral = np.trapz(-1 / np.pi * np.imag(traced * cont.we))\n",
- " print(\"Total charge: \", integral)\n",
+ " print(\"Total charge: \", int_de_ke(traced, cont.we))\n",
"\n",
" # iterate over the magnetic entities\n",
" for tracker, mag_ent in enumerate(magnetic_entities):\n",
@@ -1073,7 +805,7 @@
" # The Szunyogh-Lichtenstein formula\n",
" traced = np.trace((Vu2 @ Gii + 0.5 * Gii @ Vu1 @ Gii), axis1=1, axis2=2)\n",
" # evaluation of the contour integral\n",
- " storage.append(np.trapz(-1 / np.pi * np.imag(traced * cont.we)))\n",
+ " storage.append(int_de_ke(traced, cont.we))\n",
"\n",
" # fill up the magnetic entities dictionary with the energies\n",
" magnetic_entities[tracker][\"energies\"].append(storage)\n",
@@ -1097,7 +829,7 @@
" # The Szunyogh-Lichtenstein formula\n",
" traced = np.trace((Vui @ Gij @ Vuj @ Gji), axis1=1, axis2=2)\n",
" # evaluation of the contour integral\n",
- " storage.append(np.trapz(-1 / np.pi * np.imag(traced * cont.we)))\n",
+ " storage.append(int_de_ke(traced, cont.we))\n",
" # fill up the pairs dictionary with the energies\n",
" pairs[tracker][\"energies\"].append(storage)\n",
" # convert to np array\n",
@@ -1129,17 +861,7 @@
" print_atoms_and_pairs(magnetic_entities, pairs)\n",
" print_runtime_information(times)\n",
"\n",
- " # remove clutter from magnetic entities and pair information\n",
- " for pair in pairs:\n",
- " del pair[\"Gij\"]\n",
- " del pair[\"Gij_tmp\"]\n",
- " del pair[\"Gji\"]\n",
- " del pair[\"Gji_tmp\"]\n",
- " for mag_ent in magnetic_entities:\n",
- " del mag_ent[\"Gii\"]\n",
- " del mag_ent[\"Gii_tmp\"]\n",
- " del mag_ent[\"Vu1\"]\n",
- " del mag_ent[\"Vu2\"]\n",
+ " pairs, magnetic_entities = remove_clutter_for_save(pairs, magnetic_entities)\n",
" # create output dictionary with all the relevant data\n",
" results = dict(\n",
" parameters=simulation_parameters,\n",
@@ -1147,14 +869,13 @@
" pairs=pairs,\n",
" runtime=times,\n",
" )\n",
- " # save dictionary\n",
- " with open(outfile, \"wb\") as output_file:\n",
- " pickle.dump(results, output_file)"
+ "\n",
+ " save_pickle(simulation_parameters[\"outfile\"], results)"
]
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 9,
"metadata": {},
"outputs": [
{
@@ -1162,7 +883,7 @@
"evalue": "invalid syntax (3105939143.py, line 1)",
"output_type": "error",
"traceback": [
- "\u001b[0;36m Cell \u001b[0;32mIn[10], line 1\u001b[0;36m\u001b[0m\n\u001b[0;31m ========================================\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
+ "\u001b[0;36m Cell \u001b[0;32mIn[9], line 1\u001b[0;36m\u001b[0m\n\u001b[0;31m ========================================\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
]
}
],
diff --git a/test.py b/test.py
index 8a5e94b..4e5aa93 100644
--- a/test.py
+++ b/test.py
@@ -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)