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changed pre-commit

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class-solution
Daniel Pozsar 3 months ago
parent 18d42b11c8
commit 21ab0dca84
26 changed files with 28962 additions and 28908 deletions
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2
.gitignore vendored
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@ -20,7 +20,7 @@ docs/source/api/generated
# Debug # Debug
tmp* tmp*
.coverage *.coverage
# Mac stuff # Mac stuff
*.DS_Store* *.DS_Store*

26
.pre-commit-config.yaml
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@ -22,16 +22,16 @@ repos:
hooks: hooks:
- id: isort - id: isort
args: ["--profile", "black", "--filter-files"] args: ["--profile", "black", "--filter-files"]
- repo: https://github.com/psf/black-pre-commit-mirror #- repo: https://github.com/psf/black-pre-commit-mirror
rev: 24.4.2 # rev: 24.4.2
hooks: # hooks:
- id: black # - id: black
language_version: python3.9 # language_version: python3.9
- repo: local #- repo: local
hooks: # hooks:
- id: pytest-check # - id: pytest-check
name: pytest-check # name: pytest-check
entry: ./.venv/bin/pytest # entry: ./.venv/bin/pytest
language: system # language: system
pass_filenames: false # pass_filenames: false
always_run: true # always_run: true

26
README.md
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@ -2,21 +2,28 @@
# TODO # TODO
[x] Definition of magnetic entities: - Definition of magnetic entities:
* Through simple sequence o forbitals in the unit cell * Through simple sequence o forbitals in the unit cell
* Through atom specification * Through atom specification
* Through atom and orbital specification * Through atom and orbital specification
[x] Separation of TR and TRB components of the Hamiltonian, Identification of the exchange field. - Separation of TR and TRB components of the Hamiltonian, Identification of the exchange field.
[x] Definition of commutator expressions, old projection matrix elements - Definition of commutator expressions, old projection matrix elements
[x] Efficient calculation of Green's functions - Efficient calculation of Green's functions
[] Calculation of energy and momentum resolved derivatives - Calculation of energy and momentum resolved derivatives
[] Parallel BZ and serial energy integral - Parallel BZ and serial energy integral
# Building wheel # Building wheel
https://packaging.python.org/en/latest/tutorials/packaging-projects/ See detailed documentation on [PYPI](https://packaging.python.org/en/latest/tutorials/packaging-projects/).
Use the following commands for a quick setup:
Build wheel: python -m build - Build wheel
```
python -m build
```
Build wheel:
Push to pypi(testpypi for beginners): python3 -m twine upload --repository testpypi dist/* Push to pypi(testpypi for beginners): python3 -m twine upload --repository testpypi dist/*
@ -25,4 +32,3 @@ You will be prompted for a username and password. For the username, use __token_
Végfelhasználóknak (egyelőre testpypi): python3 -m pip install --index-url https://test.pypi.org/simple/ example-package-YOUR-USERNAME-HERE Végfelhasználóknak (egyelőre testpypi): python3 -m pip install --index-url https://test.pypi.org/simple/ example-package-YOUR-USERNAME-HERE

10
all_atoms.txt
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@ -5,16 +5,16 @@ The shape of the Hamiltonian and the Greens function is 84x84.
k loop: 1% 1/100 [00:01<01:48, 1.10s/it] k loop: 2% 2/100 [00:01<01:05, 1.51it/s] k loop: 3% 3/100 [00:01<00:53, 1.80it/s] k loop: 4% 4/100 [00:02<00:43, 2.19it/s] k loop: 5% 5/100 [00:02<00:38, 2.50it/s] k loop: 6% 6/100 [00:02<00:34, 2.74it/s] k loop: 7% 7/100 [00:03<00:32, 2.90it/s] k loop: 8% 8/100 [00:03<00:30, 3.03it/s] k loop: 9% 9/100 [00:03<00:29, 3.12it/s] k loop: 10% 10/100 [00:04<00:28, 3.13it/s] k loop: 11% 11/100 [00:04<00:28, 3.14it/s] k loop: 12% 12/100 [00:04<00:27, 3.15it/s] k loop: 13% 13/100 [00:04<00:27, 3.16it/s] k loop: 14% 14/100 [00:05<00:27, 3.17it/s] k loop: 15% 15/100 [00:05<00:26, 3.19it/s] k loop: 16% 16/100 [00:05<00:26, 3.21it/s] k loop: 17% 17/100 [00:06<00:25, 3.22it/s] k loop: 18% 18/100 [00:06<00:25, 3.21it/s] k loop: 19% 19/100 [00:06<00:25, 3.21it/s] k loop: 20% 20/100 [00:07<00:24, 3.23it/s] k loop: 21% 21/100 [00:07<00:24, 3.22it/s] k loop: 22% 22/100 [00:07<00:24, 3.21it/s] k loop: 23% 23/100 [00:08<00:24, 3.19it/s] k loop: 24% 24/100 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############################### GROGU OUTPUT ################################### ############################### GROGU OUTPUT ###################################
================================================================================ ================================================================================
Input file: Input file:
Not yet specified. Not yet specified.
Number of nodes in the parallel cluster: 4 Number of nodes in the parallel cluster: 4
================================================================================ ================================================================================
Cell [Ang]: Cell [Ang]:
[[ 3.79100000e+00 0.00000000e+00 0.00000000e+00] [[ 3.79100000e+00 0.00000000e+00 0.00000000e+00]
[-1.89550000e+00 3.28310231e+00 0.00000000e+00] [-1.89550000e+00 3.28310231e+00 0.00000000e+00]
[ 1.25954923e-15 2.18160327e-15 2.05700000e+01]] [ 1.25954923e-15 2.18160327e-15 2.05700000e+01]]
================================================================================ ================================================================================
DFT axis: DFT axis:
[0 0 1] [0 0 1]
Quantization axis and perpendicular rotation directions: Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])] [1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -29,7 +29,7 @@ Ebot: -30
Eset: 50 Eset: 50
Esetp: 1000 Esetp: 1000
================================================================================ ================================================================================
Atomic informations: Atomic informations:
Not yet specified. Not yet specified.
@ -73,7 +73,7 @@ DMI: [ 1.80242372e-01 -1.58918940e-01 -3.86257106e-05 -4.61370582e-06
Symmetric-anisotropy: [-5.89003655e-02 -2.55180972e-05 1.55753104e-03] Symmetric-anisotropy: [-5.89003655e-02 -2.55180972e-05 1.55753104e-03]
================================================================================ ================================================================================
Runtime information: Runtime information:
Total runtime: 37.528785458 Total runtime: 37.528785458
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
Initial setup: 0.13668741699999998 Initial setup: 0.13668741699999998

6
lat3_791/BASIS_ENTHALPY
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@ -1,4 +1,4 @@
-2878.0655830244073 -2878.0655830244073
The above number is the electronic (free)energy: -2887.7690769348492 The above number is the electronic (free)energy: -2887.7690769348492
Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa) Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa)
times the orbital volume (in Bohr**3): 52457.833503994734 times the orbital volume (in Bohr**3): 52457.833503994734

6
lat3_791/BASIS_HARRIS_ENTHALPY
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@ -1,4 +1,4 @@
-2878.0654643176349 -2878.0654643176349
The above number is the electronic (free) harris energy: -2887.7689582280768 The above number is the electronic (free) harris energy: -2887.7689582280768
Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa) 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

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lat3_791/Fe.ion
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lat3_791/Fe.ion.xml
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lat3_791/Fe.psf
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1
lat3_791/Fe3GeTe2.ORB_INDX
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@ -6823,4 +6823,3 @@ spec = Atomic species label
isc = Unit cell indexes to which orbital belongs: isc = Unit cell indexes to which orbital belongs:
center(io) = center(iuo) + sum_(i=1:3) cell_vec(i) * isc(i) center(io) = center(iuo) + sum_(i=1:3) cell_vec(i) * isc(i)
iuo = Equivalent orbital in first unit cell iuo = Equivalent orbital in first unit cell

1
lat3_791/Fe3GeTe2.bib
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@ -21,4 +21,3 @@
issue = {086005}, issue = {086005},
doi = {10.1088/0953-8984/24/8/086005}, doi = {10.1088/0953-8984/24/8/086005},
} }

14
lat3_791/Fe3GeTe2.fdf
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@ -31,7 +31,7 @@ LatticeConstant 1.0 Ang
%block kgrid_Monkhorst_Pack %block kgrid_Monkhorst_Pack
20 0 0 0 20 0 0 0
0 20 0 0 0 20 0 0
0 0 1 0 0 0 1 0
@ -70,20 +70,20 @@ WriteOrbMom T
# -------------- # --------------
# XC # XC
# -------------- # --------------
xc.functional GGA xc.functional GGA
xc.authors PBE xc.authors PBE
# -------------- # --------------
# GRID # GRID
# -------------- # --------------
MeshCutoff 1000. Ry MeshCutoff 1000. Ry
GridCellSampling [ 2 2 2 ] GridCellSampling [ 2 2 2 ]
# -------------- # --------------
# Solution Method # Solution Method
# -------------- # --------------
SolutionMethod diagon SolutionMethod diagon
ElectronicTemperature 0.1 K ElectronicTemperature 0.1 K
# -------------- # --------------
# SCF # SCF
@ -102,7 +102,7 @@ DM.UseSaveDM T
# -------------- # --------------
# MD # MD
# -------------- # --------------
MD.TypeOfRun CG MD.TypeOfRun CG
MD.Steps 1000 MD.Steps 1000
MD.MaxCGDispl 0.05 Ang MD.MaxCGDispl 0.05 Ang
MD.MaxForceTol 0.005 eV/Ang MD.MaxForceTol 0.005 eV/Ang
@ -134,4 +134,4 @@ DM.UseSaveDM T
WriteCoorXmol T WriteCoorXmol T
Diag.ParallelOverK T Diag.ParallelOverK T

328
lat3_791/Fe3GeTe2.out
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@ -13,9 +13,9 @@ Lua support
* Running on 20 nodes in parallel * Running on 20 nodes in parallel
>> Start of run: 17-APR-2024 11:41:22 >> Start of run: 17-APR-2024 11:41:22
*********************** ***********************
* WELCOME TO SIESTA * * WELCOME TO SIESTA *
*********************** ***********************
reinit: Reading from standard input reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.58436 reinit: Dumped input in INPUT_TMP.58436
@ -72,18 +72,18 @@ WriteOrbMom T
# -------------- # --------------
# XC # XC
# -------------- # --------------
xc.functional GGA xc.functional GGA
xc.authors PBE xc.authors PBE
# -------------- # --------------
# GRID # GRID
# -------------- # --------------
MeshCutoff 1000. Ry MeshCutoff 1000. Ry
GridCellSampling [ 2 2 2 ] GridCellSampling [ 2 2 2 ]
# -------------- # --------------
# Solution Method # Solution Method
# -------------- # --------------
SolutionMethod diagon SolutionMethod diagon
ElectronicTemperature 0.1 K ElectronicTemperature 0.1 K
# -------------- # --------------
# SCF # SCF
# -------------- # --------------
@ -185,25 +185,25 @@ Fe Z= 26 Mass= 55.850 Charge= 0.17977+309
Lmxo=2 Lmxkb= 3 BasisType=split Semic=F Lmxo=2 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=4 L=0 Nsemic=0 Cnfigmx=4
i=1 nzeta=2 polorb=1 (4s) i=1 nzeta=2 polorb=1 (4s)
splnorm: 0.15000 splnorm: 0.15000
vcte: 0.0000 vcte: 0.0000
rinn: 0.0000 rinn: 0.0000
qcoe: 0.0000 qcoe: 0.0000
qyuk: 0.0000 qyuk: 0.0000
qwid: 0.10000E-01 qwid: 0.10000E-01
rcs: 0.0000 0.0000 rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000 lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=4 L=1 Nsemic=0 Cnfigmx=4
L=2 Nsemic=0 Cnfigmx=3 L=2 Nsemic=0 Cnfigmx=3
i=1 nzeta=2 polorb=0 (3d) i=1 nzeta=2 polorb=0 (3d)
splnorm: 0.15000 splnorm: 0.15000
vcte: 0.0000 vcte: 0.0000
rinn: 0.0000 rinn: 0.0000
qcoe: 0.0000 qcoe: 0.0000
qyuk: 0.0000 qyuk: 0.0000
qwid: 0.10000E-01 qwid: 0.10000E-01
rcs: 0.0000 0.0000 rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000 lambdas: 1.0000 1.0000
------------------------------------------------------------------------------- -------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309 L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=2 erefs: 0.17977+309 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) atom: Called for Fe (Z = 26)
read_vps: Pseudopotential generation method: read_vps: Pseudopotential generation method:
read_vps: ATM3.3 Troullier-Martins read_vps: ATM3.3 Troullier-Martins
Valence charge for ps generation: 8.00000 Valence charge for ps generation: 8.00000
read_vps: Pseudopotential includes a core correction: 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 4*pi*r*r*local-pseudopot. charge 3.09372
atom: Maximum radius for r*vlocal+2*Zval: 2.83451 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 GHOST: No ghost state for L = 0
l= 0 rc= 2.047986 el= -0.311923 Ekb= 4.023955 kbcos= 0.247515 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 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: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS: atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0 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 atom: Total number of Sankey-type orbitals: 15
atm_pop: Valence configuration (for local Pseudopot. screening): atm_pop: Valence configuration (for local Pseudopot. screening):
4s( 2.00) 4s( 2.00)
4p( 0.00) 4p( 0.00)
3d( 6.00) 3d( 6.00)
Vna: chval, zval: 8.00000 8.00000 Vna: chval, zval: 8.00000 8.00000
Vna: Cut-off radius for the neutral-atom potential: 9.649379 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 Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=4 L=0 Nsemic=0 Cnfigmx=4
i=1 nzeta=2 polorb=0 (4s) i=1 nzeta=2 polorb=0 (4s)
splnorm: 0.15000 splnorm: 0.15000
vcte: 0.0000 vcte: 0.0000
rinn: 0.0000 rinn: 0.0000
qcoe: 0.0000 qcoe: 0.0000
qyuk: 0.0000 qyuk: 0.0000
qwid: 0.10000E-01 qwid: 0.10000E-01
rcs: 0.0000 0.0000 rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000 lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=4 L=1 Nsemic=0 Cnfigmx=4
i=1 nzeta=2 polorb=1 (4p) i=1 nzeta=2 polorb=1 (4p)
splnorm: 0.15000 splnorm: 0.15000
vcte: 0.0000 vcte: 0.0000
rinn: 0.0000 rinn: 0.0000
qcoe: 0.0000 qcoe: 0.0000
qyuk: 0.0000 qyuk: 0.0000
qwid: 0.10000E-01 qwid: 0.10000E-01
rcs: 0.0000 0.0000 rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000 lambdas: 1.0000 1.0000
------------------------------------------------------------------------------- -------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309 L=0 Nkbl=1 erefs: 0.17977+309
L=1 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) atom: Called for Ge (Z = 32)
read_vps: Pseudopotential generation method: read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins read_vps: ATM3 Troullier-Martins
Valence charge for ps generation: 4.00000 Valence charge for ps generation: 4.00000
xc_check: Exchange-correlation functional: 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 4*pi*r*r*local-pseudopot. charge 3.30931
atom: Maximum radius for r*vlocal+2*Zval: 2.88417 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 GHOST: No ghost state for L = 0
l= 0 rc= 3.435772 el= -0.860281 Ekb= 2.253895 kbcos= 0.346706 l= 0 rc= 3.435772 el= -0.860281 Ekb= 2.253895 kbcos= 0.346706
GHOST: No ghost state for L = 1 GHOST: No ghost state for L = 1
@ -402,7 +402,7 @@ KBgen: Total number of Kleinman-Bylander projectors: 31
atom: ------------------------------------------------------------------------- atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS: atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0 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 atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening): atm_pop: Valence configuration (for local Pseudopot. screening):
4s( 2.00) 4s( 2.00)
4p( 2.00) 4p( 2.00)
Vna: chval, zval: 4.00000 4.00000 Vna: chval, zval: 4.00000 4.00000
Vna: Cut-off radius for the neutral-atom potential: 9.339529 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 Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=5 L=0 Nsemic=0 Cnfigmx=5
i=1 nzeta=2 polorb=0 (5s) i=1 nzeta=2 polorb=0 (5s)
splnorm: 0.15000 splnorm: 0.15000
vcte: 0.0000 vcte: 0.0000
rinn: 0.0000 rinn: 0.0000
qcoe: 0.0000 qcoe: 0.0000
qyuk: 0.0000 qyuk: 0.0000
qwid: 0.10000E-01 qwid: 0.10000E-01
rcs: 0.0000 0.0000 rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000 lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=5 L=1 Nsemic=0 Cnfigmx=5
i=1 nzeta=2 polorb=1 (5p) i=1 nzeta=2 polorb=1 (5p)
splnorm: 0.15000 splnorm: 0.15000
vcte: 0.0000 vcte: 0.0000
rinn: 0.0000 rinn: 0.0000
qcoe: 0.0000 qcoe: 0.0000
qyuk: 0.0000 qyuk: 0.0000
qwid: 0.10000E-01 qwid: 0.10000E-01
rcs: 0.0000 0.0000 rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000 lambdas: 1.0000 1.0000
------------------------------------------------------------------------------- -------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309 L=0 Nkbl=1 erefs: 0.17977+309
L=1 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) atom: Called for Te (Z = 52)
read_vps: Pseudopotential generation method: 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 Valence charge for ps generation: 6.00000
xc_check: Exchange-correlation functional: 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 4*pi*r*r*local-pseudopot. charge 3.31594
atom: Maximum radius for r*vlocal+2*Zval: 2.92630 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 GHOST: No ghost state for L = 0
l= 0 rc= 3.619164 el= -1.105853 Ekb= 3.973827 kbcos= 0.331834 l= 0 rc= 3.619164 el= -1.105853 Ekb= 3.973827 kbcos= 0.331834
GHOST: No ghost state for L = 1 GHOST: No ghost state for L = 1
@ -544,7 +544,7 @@ KBgen: Total number of Kleinman-Bylander projectors: 31
atom: ------------------------------------------------------------------------- atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS: atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0 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 atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening): atm_pop: Valence configuration (for local Pseudopot. screening):
5s( 2.00) 5s( 2.00)
5p( 4.00) 5p( 4.00)
Vna: chval, zval: 6.00000 6.00000 Vna: chval, zval: 6.00000 6.00000
Vna: Cut-off radius for the neutral-atom potential: 8.155972 Vna: Cut-off radius for the neutral-atom potential: 8.155972
@ -615,7 +615,7 @@ atom: _________________________________________________________________________
prinput: Basis input ---------------------------------------------------------- prinput: Basis input ----------------------------------------------------------
PAO.BasisType split PAO.BasisType split
%block ChemicalSpeciesLabel %block ChemicalSpeciesLabel
1 26 Fe # Species index, atomic number, species label 1 26 Fe # Species index, atomic number, species label
@ -626,25 +626,25 @@ PAO.BasisType split
%block PAO.Basis # Define Basis set %block PAO.Basis # Define Basis set
Fe 2 # Species label, number of l-shells Fe 2 # Species label, number of l-shells
n=4 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol n=4 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
9.649 6.885 9.649 6.885
1.000 1.000 1.000 1.000
n=3 2 2 # n, l, Nzeta n=3 2 2 # n, l, Nzeta
6.632 2.565 6.632 2.565
1.000 1.000 1.000 1.000
Ge 2 # Species label, number of l-shells Ge 2 # Species label, number of l-shells
n=4 0 2 # n, l, Nzeta n=4 0 2 # n, l, Nzeta
6.581 4.412 6.581 4.412
1.000 1.000 1.000 1.000
n=4 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol n=4 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
9.340 5.665 9.340 5.665
1.000 1.000 1.000 1.000
Te 2 # Species label, number of l-shells Te 2 # Species label, number of l-shells
n=5 0 2 # n, l, Nzeta n=5 0 2 # n, l, Nzeta
6.195 4.205 6.195 4.205
1.000 1.000 1.000 1.000
n=5 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol n=5 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
8.156 5.009 8.156 5.009
1.000 1.000 1.000 1.000
%endblock PAO.Basis %endblock PAO.Basis
prinput: ---------------------------------------------------------------------- prinput: ----------------------------------------------------------------------
@ -664,11 +664,11 @@ siesta: 0.00000 0.00000 21.82311 1 4
siesta: 0.00000 0.00000 17.04857 1 5 siesta: 0.00000 0.00000 17.04857 1 5
siesta: 3.58198 2.06806 19.43584 1 6 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 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: ******************** Simulation parameters ****************************
siesta: siesta:
@ -826,7 +826,7 @@ ts: **************************************************************
Begin CG opt. move = 0 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 0.62736262 3 1 Te
0.66666667 0.33333333 0.37263738 3 2 Te 0.66666667 0.33333333 0.37263738 3 2 Te
0.33333333 0.66666667 0.50000000 2 3 Ge 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: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -1262,7 +1262,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.035 -0.000 0.000 0.035 6 Total 0.035 -0.000 0.000 0.035
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -1283,7 +1283,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.033 -0.000 -0.000 -0.033 3 Total 0.033 -0.000 -0.000 -0.033
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -1325,7 +1325,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 25.03161 5.20582 -0.000 0.000 5.206
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.19264 5.13266 -0.000 0.000 5.133
Species: Te Species: Te
Atom Orb Charge Spin Svec Atom Orb Charge Spin Svec
---------------------------------------------------------------- ----------------------------------------------------------------
@ -1451,7 +1451,7 @@ cgvc: WARNING: CG file not found
Begin CG opt. move = 1 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 0.62895986 3 1 Te
0.66666736 0.33333257 0.37104015 3 2 Te 0.66666736 0.33333257 0.37104015 3 2 Te
0.33333155 0.66666849 0.50000000 2 3 Ge 0.33333155 0.66666849 0.50000000 2 3 Ge
@ -1478,7 +1478,7 @@ refcount: 1>
new_DM -- step: 2 new_DM -- step: 2
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -1656,7 +1656,7 @@ Target enthalpy (eV/cell) -2887.4795
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -1715,7 +1715,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.039 -0.000 0.000 0.039 6 Total 0.039 -0.000 0.000 0.039
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -1736,7 +1736,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.034 -0.000 -0.000 -0.034 3 Total 0.034 -0.000 -0.000 -0.034
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -1778,7 +1778,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 25.02154 5.28348 -0.000 0.000 5.283
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.18575 5.20433 -0.000 0.000 5.204
Species: Te Species: Te
Atom Orb Charge Spin Svec 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 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 0.63139058 3 1 Te
0.66666842 0.33333142 0.36860945 3 2 Te 0.66666842 0.33333142 0.36860945 3 2 Te
0.33332884 0.66667125 0.50000001 2 3 Ge 0.33332884 0.66667125 0.50000001 2 3 Ge
@ -1929,7 +1929,7 @@ refcount: 1>
new_DM -- step: 3 new_DM -- step: 3
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -2148,7 +2148,7 @@ Target enthalpy (eV/cell) -2887.6020
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -2207,7 +2207,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.047 -0.000 0.000 0.047 6 Total 0.047 -0.000 0.000 0.047
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -2228,7 +2228,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.039 0.000 0.000 -0.039 3 Total 0.039 0.000 0.000 -0.039
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -2270,7 +2270,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 25.00210 5.44061 -0.000 0.000 5.441
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.17223 5.34996 -0.000 0.000 5.350
Species: Te Species: Te
Atom Orb Charge Spin Svec 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 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 0.63382131 3 1 Te
0.66666948 0.33333027 0.36617874 3 2 Te 0.66666948 0.33333027 0.36617874 3 2 Te
0.33332613 0.66667402 0.50000002 2 3 Ge 0.33332613 0.66667402 0.50000002 2 3 Ge
@ -2421,7 +2421,7 @@ refcount: 1>
new_DM -- step: 4 new_DM -- step: 4
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -2582,7 +2582,7 @@ Target enthalpy (eV/cell) -2887.6878
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -2641,7 +2641,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.047 0.000 -0.000 0.047 6 Total 0.047 0.000 -0.000 0.047
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -2662,7 +2662,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.041 -0.000 0.000 -0.041 3 Total 0.041 -0.000 0.000 -0.041
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -2704,7 +2704,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 24.98507 5.49344 -0.000 0.000 5.493
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.16009 5.38968 -0.000 0.000 5.390
Species: Te Species: Te
Atom Orb Charge Spin Svec 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 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 0.63625203 3 1 Te
0.66667053 0.33332911 0.36374803 3 2 Te 0.66667053 0.33332911 0.36374803 3 2 Te
0.33332342 0.66667678 0.50000003 2 3 Ge 0.33332342 0.66667678 0.50000003 2 3 Ge
@ -2855,7 +2855,7 @@ refcount: 1>
new_DM -- step: 5 new_DM -- step: 5
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -3076,7 +3076,7 @@ Target enthalpy (eV/cell) -2887.7394
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -3135,7 +3135,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.044 -0.000 0.000 0.044 6 Total 0.044 -0.000 0.000 0.044
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -3156,7 +3156,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.045 -0.000 -0.000 -0.045 3 Total 0.045 -0.000 -0.000 -0.045
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -3198,7 +3198,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 24.96519 5.59565 -0.000 0.000 5.596
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.14610 5.47374 -0.000 0.000 5.474
Species: Te Species: Te
Atom Orb Charge Spin Svec 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 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 0.63868276 3 1 Te
0.66667159 0.33332796 0.36131733 3 2 Te 0.66667159 0.33332796 0.36131733 3 2 Te
0.33332071 0.66667955 0.50000003 2 3 Ge 0.33332071 0.66667955 0.50000003 2 3 Ge
@ -3349,7 +3349,7 @@ refcount: 1>
new_DM -- step: 6 new_DM -- step: 6
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -3525,7 +3525,7 @@ Target enthalpy (eV/cell) -2887.7640
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -3584,7 +3584,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.038 0.000 -0.000 0.038 6 Total 0.038 0.000 -0.000 0.038
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -3605,7 +3605,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.045 -0.000 0.000 -0.045 3 Total 0.045 -0.000 0.000 -0.045
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -3647,7 +3647,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 24.94861 5.63367 -0.000 0.000 5.634
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.13607 5.48673 -0.000 0.000 5.487
Species: Te Species: Te
Atom Orb Charge Spin Svec 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 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 0.64111348 3 1 Te
0.66667265 0.33332680 0.35888662 3 2 Te 0.66667265 0.33332680 0.35888662 3 2 Te
0.33331800 0.66668232 0.50000004 2 3 Ge 0.33331800 0.66668232 0.50000004 2 3 Ge
@ -3798,7 +3798,7 @@ refcount: 1>
new_DM -- step: 7 new_DM -- step: 7
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -3974,7 +3974,7 @@ Target enthalpy (eV/cell) -2887.7677
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4033,7 +4033,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.040 -0.000 0.000 0.040 6 Total 0.040 -0.000 0.000 0.040
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4054,7 +4054,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.046 -0.000 -0.000 -0.046 3 Total 0.046 -0.000 -0.000 -0.046
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4096,7 +4096,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 24.92888 5.67926 -0.000 0.000 5.679
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.12497 5.51147 -0.000 0.000 5.511
Species: Te Species: Te
Atom Orb Charge Spin Svec 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 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 0.64030278 3 1 Te
0.66667229 0.33332719 0.35969732 3 2 Te 0.66667229 0.33332719 0.35969732 3 2 Te
0.33331891 0.66668139 0.50000004 2 3 Ge 0.33331891 0.66668139 0.50000004 2 3 Ge
@ -4247,7 +4247,7 @@ refcount: 1>
new_DM -- step: 8 new_DM -- step: 8
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -4421,7 +4421,7 @@ Target enthalpy (eV/cell) -2887.7688
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4480,7 +4480,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.043 -0.000 -0.000 0.043 6 Total 0.043 -0.000 -0.000 0.043
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4501,7 +4501,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.046 0.000 -0.000 -0.046 3 Total 0.046 0.000 -0.000 -0.046
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4543,7 +4543,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 24.93523 5.65918 -0.000 0.000 5.659
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.12904 5.49796 -0.000 0.000 5.498
Species: Te Species: Te
Atom Orb Charge Spin Svec Atom Orb Charge Spin Svec
---------------------------------------------------------------- ----------------------------------------------------------------
@ -4669,7 +4669,7 @@ cgvc: Finished line minimization 1. Mean atomic displacement = 0.0580
Begin CG opt. move = 8 Begin CG opt. move = 8
==================================== ====================================
outcoor: Atomic coordinates (fractional): outcoor: Atomic coordinates (fractional):
0.66669105 0.33331661 0.63941912 3 1 Te 0.66669105 0.33331661 0.63941912 3 1 Te
0.66669135 0.33331661 0.36057985 3 2 Te 0.66669135 0.33331661 0.36057985 3 2 Te
0.33344392 0.66652517 0.50000010 2 3 Ge 0.33344392 0.66652517 0.50000010 2 3 Ge
@ -4696,7 +4696,7 @@ refcount: 1>
new_DM -- step: 9 new_DM -- step: 9
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -4870,7 +4870,7 @@ Target enthalpy (eV/cell) -2887.7399
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4929,7 +4929,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.031 0.000 -0.000 0.031 6 Total 0.031 0.000 -0.000 0.031
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4950,7 +4950,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.044 0.000 -0.000 -0.044 3 Total 0.044 0.000 -0.000 -0.044
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -4992,7 +4992,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 24.98627 5.61671 0.000 -0.000 5.617
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.16844 5.46830 0.000 -0.000 5.468
Species: Te Species: Te
Atom Orb Charge Spin Svec 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 Begin CG opt. move = 9
==================================== ====================================
outcoor: Atomic coordinates (fractional): outcoor: Atomic coordinates (fractional):
0.66667360 0.33332645 0.64024103 3 1 Te 0.66667360 0.33332645 0.64024103 3 1 Te
0.66667363 0.33332645 0.35975899 3 2 Te 0.66667363 0.33332645 0.35975899 3 2 Te
0.33332764 0.66667048 0.50000004 2 3 Ge 0.33332764 0.66667048 0.50000004 2 3 Ge
@ -5143,7 +5143,7 @@ refcount: 1>
new_DM -- step: 10 new_DM -- step: 10
Re-using DM from previous geometries... Re-using DM from previous geometries...
Number of DMs in history: 1 Number of DMs in history: 1
DM extrapolation coefficients: DM extrapolation coefficients:
1 1.00000 1 1.00000
New DM after history re-use: New DM after history re-use:
<dSpData2D:SpM extrapolated using coords <dSpData2D:SpM extrapolated using coords
@ -5319,7 +5319,7 @@ Target enthalpy (eV/cell) -2887.7691
moments: Magnetic moments from orbital angular momenta: moments: Magnetic moments from orbital angular momenta:
Species: Fe Species: Fe
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -5378,7 +5378,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
6 Total 0.041 0.000 -0.000 0.041 6 Total 0.041 0.000 -0.000 0.041
Species: Ge Species: Ge
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -5399,7 +5399,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
3 Total 0.046 0.000 0.000 -0.046 3 Total 0.046 0.000 0.000 -0.046
Species: Te Species: Te
Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)> Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
---------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------
@ -5441,7 +5441,7 @@ Atom Orb sqrt(<L>^2) <(Lx,Ly,Lz)>
mulliken: Atomic and Orbital Populations: mulliken: Atomic and Orbital Populations:
Species: Fe Species: Fe
Atom Orb Charge Spin Svec 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 Total 24.93834 5.67564 -0.000 0.000 5.676
Species: Ge Species: Ge
Atom Orb Charge Spin Svec 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 Total 28.13105 5.51515 -0.000 0.000 5.515
Species: Te Species: Te
Atom Orb Charge Spin Svec 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 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 0.66667360 0.33332645 0.64024103 3 1 Te
0.66667363 0.33332645 0.35975899 3 2 Te 0.66667363 0.33332645 0.35975899 3 2 Te
0.33332764 0.66667048 0.50000004 2 3 Ge 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 -0.00000130 0.00000127 0.43327268 1 5 Fe
0.66666126 0.33334048 0.49999993 1 6 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): siesta: Eigenvalues (eV):
ik = 1 ik = 1

1
lat3_791/Fe3GeTe2.times
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@ -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.avg: average calculation time in one program across nodes
Nod.max: maximum calculation time in one program across nodes Nod.max: maximum calculation time in one program across nodes
Calculation time: CPU time excluding communications Calculation time: CPU time excluding communications

6128
lat3_791/Ge.ion
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lat3_791/Ge.ion.xml
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lat3_791/Ge.psf
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lat3_791/INPUT_TMP.58436
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@ -50,18 +50,18 @@ WriteOrbMom T
# -------------- # --------------
# XC # XC
# -------------- # --------------
xc.functional GGA xc.functional GGA
xc.authors PBE xc.authors PBE
# -------------- # --------------
# GRID # GRID
# -------------- # --------------
MeshCutoff 1000. Ry MeshCutoff 1000. Ry
GridCellSampling [ 2 2 2 ] GridCellSampling [ 2 2 2 ]
# -------------- # --------------
# Solution Method # Solution Method
# -------------- # --------------
SolutionMethod diagon SolutionMethod diagon
ElectronicTemperature 0.1 K ElectronicTemperature 0.1 K
# -------------- # --------------
# SCF # SCF
# -------------- # --------------

1
lat3_791/TIMES
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@ -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.avg: average calculation time in one program across nodes
Nod.max: maximum calculation time in one program across nodes Nod.max: maximum calculation time in one program across nodes
Calculation time: CPU time excluding communications Calculation time: CPU time excluding communications

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lat3_791/Te.ion
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lat3_791/Te.ion.xml
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lat3_791/Te.psf
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lat3_791/fdf-58450.log
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@ -1,5 +1,5 @@
SystemName Fe3GeTe2 SystemName Fe3GeTe2
SystemLabel Fe3GeTe2 SystemLabel Fe3GeTe2
MPI.Nprocs.SIESTA 20 # default value MPI.Nprocs.SIESTA 20 # default value
SpinPolarized F # default value SpinPolarized F # default value
NonCollinearSpin F # default value NonCollinearSpin F # default value
@ -10,7 +10,7 @@ SpinOrbit F # default value
#:defined? NonCollinearSpin F #:defined? NonCollinearSpin F
#:block? SpinOrbit F #:block? SpinOrbit F
#:defined? SpinOrbit F #:defined? SpinOrbit F
Spin spin-orbit Spin spin-orbit
DebugObjects.Node 0 # default value DebugObjects.Node 0 # default value
DebugObjects F # default value DebugObjects F # default value
XML.Write F # default value XML.Write F # default value
@ -20,8 +20,8 @@ UseTreeTimer F # default value
timing-split-scf-steps F # default value timing-split-scf-steps F # default value
alloc_report_level 0 # default value alloc_report_level 0 # default value
alloc_report_threshold 0.000000000 # default value alloc_report_threshold 0.000000000 # default value
xc.functional GGA xc.functional GGA
xc.authors PBE xc.authors PBE
MM.Cutoff 30.00000000 Bohr # default value MM.Cutoff 30.00000000 Bohr # default value
MM.UnitsEnergy eV # default value MM.UnitsEnergy eV # default value
MM.UnitsDistance Ang # default value MM.UnitsDistance Ang # default value
@ -70,10 +70,10 @@ DFTU.FirstIteration F # default value
FilterCutoff 0.000000000 Ry # default value FilterCutoff 0.000000000 Ry # default value
FilterTol 0.000000000 Ry # default value FilterTol 0.000000000 Ry # default value
keep-npotu-bug F # 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 KB.Rmax 6.000000000 Bohr # default value
PAO.EnergyShift 0.1000000000E-02 Ry 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.SplitTailNorm F # default value
PAO.FixSplitTable F # default value PAO.FixSplitTable F # default value
PAO.NewSplitCode F # default value PAO.NewSplitCode F # default value
@ -92,10 +92,10 @@ PCC.Filter F # default value
FilterCutoff 0.000000000 Ry # default value FilterCutoff 0.000000000 Ry # default value
FilterTol 0.000000000 Ry # default value FilterTol 0.000000000 Ry # default value
keep-npotu-bug F # 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 KB.Rmax 6.000000000 Bohr # default value
PAO.EnergyShift 0.1000000000E-02 Ry 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.SplitTailNorm F # default value
PAO.FixSplitTable F # default value PAO.FixSplitTable F # default value
PAO.NewSplitCode F # default value PAO.NewSplitCode F # default value
@ -112,10 +112,10 @@ Vna.Filter F # default value
FilterCutoff 0.000000000 Ry # default value FilterCutoff 0.000000000 Ry # default value
FilterTol 0.000000000 Ry # default value FilterTol 0.000000000 Ry # default value
keep-npotu-bug F # 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 KB.Rmax 6.000000000 Bohr # default value
PAO.EnergyShift 0.1000000000E-02 Ry 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.SplitTailNorm F # default value
PAO.FixSplitTable F # default value PAO.FixSplitTable F # default value
PAO.NewSplitCode F # default value PAO.NewSplitCode F # default value
@ -134,13 +134,13 @@ Atom-Setup-Only F # default value
UseStructFile F # default value UseStructFile F # default value
MD.UseStructFile F # default value MD.UseStructFile F # default value
LatticeConstant 1.889726878 Bohr LatticeConstant 1.889726878 Bohr
# above item originally: LatticeConstant 1.000000000 Ang # above item originally: LatticeConstant 1.000000000 Ang
#:block? LatticeParameters T #:block? LatticeParameters T
#:block? LatticeVectors F #:block? LatticeVectors F
%block LatticeParameters %block LatticeParameters
3.791 3.791 20.57 90.0 90.0 120.0 3.791 3.791 20.57 90.0 90.0 120.0
%endblock LatticeParameters %endblock LatticeParameters
AtomicCoordinatesFormat Fractional AtomicCoordinatesFormat Fractional
NumberOfAtoms 6 NumberOfAtoms 6
#:block? AtomicCoordinatesOrigin F #:block? AtomicCoordinatesOrigin F
#:defined? AtomicCoordinatesOrigin F #:defined? AtomicCoordinatesOrigin F
@ -162,11 +162,11 @@ ZM.CalcAllForces F # default value
MD.UseSaveXV T MD.UseSaveXV T
MD.UseSaveZM F # default value MD.UseSaveZM F # default value
WriteCoorInitial T # default value WriteCoorInitial T # default value
MD.TypeOfRun CG MD.TypeOfRun CG
MD.TypeOfRun CG MD.TypeOfRun CG
MD.InitialTimeStep 1 # default value MD.InitialTimeStep 1 # default value
MD.FinalTimeStep 1 # default value MD.FinalTimeStep 1 # default value
MD.TypeOfRun CG MD.TypeOfRun CG
MaxBondDistance 6.000000000 Bohr # default value MaxBondDistance 6.000000000 Bohr # default value
Output-Structure-Only F # default value Output-Structure-Only F # default value
WriteCoorXmol T WriteCoorXmol T
@ -184,7 +184,7 @@ WriteVoronoiPop F # default value
PartialChargesAtEveryGeometry F # default value PartialChargesAtEveryGeometry F # default value
PartialChargesAtEveryScfStep F # default value PartialChargesAtEveryScfStep F # default value
MeshCutoff 1000.000000 Ry MeshCutoff 1000.000000 Ry
# above item originally: MeshCutoff 1000.000000 Ry # above item originally: MeshCutoff 1000.000000 Ry
NetCharge 0.000000000 # default value NetCharge 0.000000000 # default value
MinSCFIterations 0 # default value MinSCFIterations 0 # default value
MaxSCFIterations 1000 MaxSCFIterations 1000
@ -198,7 +198,7 @@ SCF.MustConverge T # default value
TS.MixH T # default value TS.MixH T # default value
MixHamiltonian T # default value MixHamiltonian T # default value
MixCharge F # default value MixCharge F # default value
SCF.Mix Hamiltonian SCF.Mix Hamiltonian
Compat-pre-v4-DM-H F # default value Compat-pre-v4-DM-H F # default value
SCF.MixAfterConvergence F # default value SCF.MixAfterConvergence F # default value
SCF.Recompute-H-After-Scf 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.EDM.Tolerance 0.7349806700E-04 Ry # default value
SCF.H.Converge T # default value SCF.H.Converge T # default value
SCF.H.Tolerance 0.7349798845E-05 Ry 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 DM.RequireEnergyConvergence F # default value
SCF.FreeE.Converge F # default value SCF.FreeE.Converge F # default value
DM.EnergyTolerance 0.7349806700E-05 Ry # default value DM.EnergyTolerance 0.7349806700E-05 Ry # default value
@ -234,9 +234,9 @@ SCF.MonitorForces F # default value
UseSaveData F # default value UseSaveData F # default value
DM.UseSaveDM T DM.UseSaveDM T
NeglNonOverlapInt F # default value NeglNonOverlapInt F # default value
SolutionMethod diagon SolutionMethod diagon
ElectronicTemperature 0.6333564230E-06 Ry ElectronicTemperature 0.6333564230E-06 Ry
# above item originally: ElectronicTemperature 0.1000000000 K # above item originally: ElectronicTemperature 0.1000000000 K
FixSpin F # default value FixSpin F # default value
Spin.Fix F # default value Spin.Fix F # default value
SOC.Split.SR.SO T # 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 TDED.WF.Save F # default value
MD.VariableCell F MD.VariableCell F
compat-pre-v4-dynamics F # default value compat-pre-v4-dynamics F # default value
MD.TypeOfRun CG MD.TypeOfRun CG
MD.UseSaveCG T MD.UseSaveCG T
Optim.Broyden F # default value Optim.Broyden F # default value
#:block? Optim.Broyden F #:block? Optim.Broyden F
@ -275,12 +275,12 @@ Optim.Broyden F # default value
MD.NumCGsteps 0 # default value MD.NumCGsteps 0 # default value
MD.Steps 1000 MD.Steps 1000
MD.MaxCGDispl 0.9448634389E-01 Bohr 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.MaxDispl 0.9448634389E-01 Bohr # default value
MD.MaxForceTol 0.1944674385E-03 Ry/Bohr 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 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 GeometryMustConverge F # default value
MD.InitialTimeStep 1 # default value MD.InitialTimeStep 1 # default value
#:defined? MD.Steps T #:defined? MD.Steps T
@ -301,7 +301,7 @@ MD.FCfirst 1 # default value
MD.FClast 6 # default value MD.FClast 6 # default value
UseSpatialDecomposition F # default value UseSpatialDecomposition F # default value
UseDomainDecomposition F # default value UseDomainDecomposition F # default value
SCF.Mix.Spin all SCF.Mix.Spin all
Mixer.Debug F # default value Mixer.Debug F # default value
Mixer.Debug.MPI F # default value Mixer.Debug.MPI F # default value
DM.NumberPulay 2 # default value DM.NumberPulay 2 # default value
@ -312,12 +312,12 @@ DM.KickMixingWeight 0.5000000000 # default value
SCF.LinearMixingAfterPulay F # default value SCF.LinearMixingAfterPulay F # default value
SCF.MixingWeightAfterPulay 0.2500000000 # default value SCF.MixingWeightAfterPulay 0.2500000000 # default value
SCF.Mixer.History 6 SCF.Mixer.History 6
SCF.Mixer.Weight 0.1000000000 SCF.Mixer.Weight 0.1000000000
SCF.Mixer.Kick 20 SCF.Mixer.Kick 20
SCF.Mixer.Kick.Weight 0.5000000000 # default value SCF.Mixer.Kick.Weight 0.5000000000 # default value
SCF.Mixer.Restart 0 # default value SCF.Mixer.Restart 0 # default value
SCF.Mixer.Restart.Save 1 # 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.Variant original # default value
SCF.Mixer.Linear.After -1 # default value SCF.Mixer.Linear.After -1 # default value
SCF.Mixer.Linear.After.Weight 0.2500000000 # default value SCF.Mixer.Linear.After.Weight 0.2500000000 # default value
@ -460,10 +460,10 @@ TimeReversalSymmetryForKpoints F # default value
#:defined? TS.kgrid.File F #:defined? TS.kgrid.File F
LUA.Interactive F # default value LUA.Interactive F # default value
LUA.Script # default value LUA.Script # default value
AtomicCoordinatesFormat Fractional AtomicCoordinatesFormat Fractional
AtomCoorFormatOut Fractional # default value AtomCoorFormatOut Fractional # default value
LatticeConstant 1.889726878 Bohr LatticeConstant 1.889726878 Bohr
# above item originally: LatticeConstant 1.000000000 Ang # above item originally: LatticeConstant 1.000000000 Ang
debug-folding F # default value debug-folding F # default value
Save.Overlap.Gradient F # default value Save.Overlap.Gradient F # default value
Sonly F # default value Sonly F # default value

10
simmetries.txt
Unescape View File

@ -5,16 +5,16 @@ The shape of the Hamiltonian and the Greens function is 84x84.
k loop: 1% 1/100 [00:00<01:34, 1.05it/s] k loop: 2% 2/100 [00:01<00:57, 1.71it/s] k loop: 3% 3/100 [00:01<00:44, 2.17it/s] k loop: 4% 4/100 [00:01<00:38, 2.51it/s] k loop: 5% 5/100 [00:02<00:35, 2.71it/s] k loop: 6% 6/100 [00:02<00:33, 2.83it/s] k loop: 7% 7/100 [00:02<00:31, 2.92it/s] k loop: 8% 8/100 [00:03<00:30, 2.98it/s] k loop: 9% 9/100 [00:03<00:29, 3.07it/s] k loop: 10% 10/100 [00:03<00:28, 3.12it/s] k loop: 11% 11/100 [00:04<00:28, 3.17it/s] k loop: 12% 12/100 [00:04<00:27, 3.21it/s] k loop: 13% 13/100 [00:04<00:27, 3.22it/s] k loop: 14% 14/100 [00:05<00:26, 3.24it/s] k loop: 15% 15/100 [00:05<00:28, 2.99it/s] k loop: 16% 16/100 [00:05<00:32, 2.59it/s] k loop: 17% 17/100 [00:06<00:31, 2.63it/s] k loop: 18% 18/100 [00:06<00:31, 2.62it/s] k loop: 19% 19/100 [00:07<00:30, 2.67it/s] k loop: 20% 20/100 [00:07<00:29, 2.75it/s] k loop: 21% 21/100 [00:07<00:29, 2.72it/s] k loop: 22% 22/100 [00:08<00:28, 2.75it/s] k loop: 23% 23/100 [00:08<00:26, 2.86it/s] k loop: 24% 24/100 [00:08<00:26, 2.92it/s] k loop: 25% 25/100 [00:09<00:25, 2.97it/s] k loop: 26% 26/100 [00:09<00:24, 3.01it/s] k loop: 27% 27/100 [00:09<00:24, 3.04it/s] k loop: 28% 28/100 [00:10<00:23, 3.07it/s] k loop: 29% 29/100 [00:10<00:22, 3.10it/s] k loop: 30% 30/100 [00:10<00:22, 3.13it/s] k loop: 31% 31/100 [00:10<00:22, 3.12it/s] k loop: 32% 32/100 [00:11<00:21, 3.10it/s] k loop: 33% 33/100 [00:11<00:21, 3.11it/s] k loop: 34% 34/100 [00:11<00:21, 3.11it/s] k loop: 35% 35/100 [00:12<00:20, 3.12it/s] k loop: 36% 36/100 [00:12<00:20, 3.11it/s] k loop: 37% 37/100 [00:12<00:20, 3.11it/s] k loop: 38% 38/100 [00:13<00:20, 3.10it/s] k loop: 39% 39/100 [00:13<00:19, 3.11it/s] k loop: 40% 40/100 [00:13<00:19, 3.10it/s] k loop: 41% 41/100 [00:14<00:19, 3.09it/s] k loop: 42% 42/100 [00:14<00:18, 3.07it/s] k loop: 43% 43/100 [00:14<00:18, 3.06it/s] k loop: 44% 44/100 [00:15<00:21, 2.62it/s] k loop: 45% 45/100 [00:16<00:29, 1.85it/s] k loop: 46% 46/100 [00:16<00:28, 1.87it/s] k loop: 47% 47/100 [00:17<00:26, 2.04it/s] k loop: 48% 48/100 [00:17<00:24, 2.11it/s] k loop: 49% 49/100 [00:18<00:23, 2.14it/s] k loop: 50% 50/100 [00:18<00:23, 2.15it/s] k loop: 51% 51/100 [00:18<00:22, 2.17it/s] k loop: 52% 52/100 [00:19<00:20, 2.29it/s] k loop: 53% 53/100 [00:19<00:19, 2.37it/s] k loop: 54% 54/100 [00:20<00:19, 2.36it/s] k loop: 55% 55/100 [00:20<00:18, 2.42it/s] k loop: 56% 56/100 [00:20<00:17, 2.46it/s] k loop: 57% 57/100 [00:21<00:16, 2.60it/s] k loop: 58% 58/100 [00:21<00:15, 2.70it/s] k loop: 59% 59/100 [00:21<00:14, 2.77it/s] k loop: 60% 60/100 [00:22<00:14, 2.82it/s] k loop: 61% 61/100 [00:22<00:13, 2.86it/s] k loop: 62% 62/100 [00:23<00:13, 2.85it/s] k loop: 63% 63/100 [00:23<00:13, 2.83it/s] k loop: 64% 64/100 [00:23<00:12, 2.82it/s] k loop: 65% 65/100 [00:24<00:12, 2.85it/s] k loop: 66% 66/100 [00:24<00:11, 2.84it/s] k loop: 67% 67/100 [00:24<00:11, 2.85it/s] k loop: 68% 68/100 [00:25<00:11, 2.83it/s] k loop: 69% 69/100 [00:25<00:10, 2.87it/s] k loop: 70% 70/100 [00:25<00:10, 2.84it/s] k loop: 71% 71/100 [00:26<00:10, 2.69it/s] k loop: 72% 72/100 [00:26<00:10, 2.69it/s] k loop: 73% 73/100 [00:26<00:09, 2.74it/s] k loop: 74% 74/100 [00:27<00:09, 2.80it/s] k loop: 75% 75/100 [00:27<00:08, 2.83it/s] k loop: 76% 76/100 [00:27<00:08, 2.83it/s] k loop: 77% 77/100 [00:28<00:08, 2.80it/s] k loop: 78% 78/100 [00:28<00:07, 2.76it/s] k loop: 79% 79/100 [00:29<00:07, 2.79it/s] k loop: 80% 80/100 [00:29<00:07, 2.76it/s] k loop: 81% 81/100 [00:29<00:06, 2.79it/s] k loop: 82% 82/100 [00:30<00:06, 2.80it/s] k loop: 83% 83/100 [00:30<00:06, 2.68it/s] k loop: 84% 84/100 [00:30<00:05, 2.75it/s] k loop: 85% 85/100 [00:31<00:05, 2.81it/s] k loop: 86% 86/100 [00:31<00:04, 2.82it/s] k loop: 87% 87/100 [00:31<00:04, 2.78it/s] k loop: 88% 88/100 [00:32<00:04, 2.77it/s] k loop: 89% 89/100 [00:32<00:04, 2.64it/s] k loop: 90% 90/100 [00:33<00:04, 2.41it/s] k loop: 91% 91/100 [00:33<00:03, 2.45it/s] k loop: 92% 92/100 [00:34<00:03, 2.45it/s] k loop: 93% 93/100 [00:34<00:02, 2.53it/s] k loop: 94% 94/100 [00:34<00:02, 2.50it/s] k loop: 95% 95/100 [00:35<00:02, 2.46it/s] k loop: 96% 96/100 [00:35<00:01, 2.50it/s] k loop: 97% 97/100 [00:36<00:01, 2.52it/s] k loop: 98% 98/100 [00:36<00:00, 2.55it/s] k loop: 99% 99/100 [00:36<00:00, 2.59it/s] k loop: 100% 100/100 [00:37<00:00, 2.65it/s] k loop: 100% 100/100 [00:37<00:00, 2.69it/s] k loop: 1% 1/100 [00:00<01:34, 1.05it/s] k loop: 2% 2/100 [00:01<00:57, 1.71it/s] k loop: 3% 3/100 [00:01<00:44, 2.17it/s] k loop: 4% 4/100 [00:01<00:38, 2.51it/s] k loop: 5% 5/100 [00:02<00:35, 2.71it/s] k loop: 6% 6/100 [00:02<00:33, 2.83it/s] k loop: 7% 7/100 [00:02<00:31, 2.92it/s] k loop: 8% 8/100 [00:03<00:30, 2.98it/s] k loop: 9% 9/100 [00:03<00:29, 3.07it/s] k loop: 10% 10/100 [00:03<00:28, 3.12it/s] k loop: 11% 11/100 [00:04<00:28, 3.17it/s] k loop: 12% 12/100 [00:04<00:27, 3.21it/s] k loop: 13% 13/100 [00:04<00:27, 3.22it/s] k loop: 14% 14/100 [00:05<00:26, 3.24it/s] k loop: 15% 15/100 [00:05<00:28, 2.99it/s] k loop: 16% 16/100 [00:05<00:32, 2.59it/s] k loop: 17% 17/100 [00:06<00:31, 2.63it/s] k loop: 18% 18/100 [00:06<00:31, 2.62it/s] k loop: 19% 19/100 [00:07<00:30, 2.67it/s] k loop: 20% 20/100 [00:07<00:29, 2.75it/s] k loop: 21% 21/100 [00:07<00:29, 2.72it/s] k loop: 22% 22/100 [00:08<00:28, 2.75it/s] k loop: 23% 23/100 [00:08<00:26, 2.86it/s] k loop: 24% 24/100 [00:08<00:26, 2.92it/s] k loop: 25% 25/100 [00:09<00:25, 2.97it/s] k loop: 26% 26/100 [00:09<00:24, 3.01it/s] k loop: 27% 27/100 [00:09<00:24, 3.04it/s] k loop: 28% 28/100 [00:10<00:23, 3.07it/s] k loop: 29% 29/100 [00:10<00:22, 3.10it/s] k loop: 30% 30/100 [00:10<00:22, 3.13it/s] k loop: 31% 31/100 [00:10<00:22, 3.12it/s] k loop: 32% 32/100 [00:11<00:21, 3.10it/s] k loop: 33% 33/100 [00:11<00:21, 3.11it/s] k loop: 34% 34/100 [00:11<00:21, 3.11it/s] k loop: 35% 35/100 [00:12<00:20, 3.12it/s] k loop: 36% 36/100 [00:12<00:20, 3.11it/s] k loop: 37% 37/100 [00:12<00:20, 3.11it/s] k loop: 38% 38/100 [00:13<00:20, 3.10it/s] k loop: 39% 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[00:23<00:13, 2.85it/s] k loop: 63% 63/100 [00:23<00:13, 2.83it/s] k loop: 64% 64/100 [00:23<00:12, 2.82it/s] k loop: 65% 65/100 [00:24<00:12, 2.85it/s] k loop: 66% 66/100 [00:24<00:11, 2.84it/s] k loop: 67% 67/100 [00:24<00:11, 2.85it/s] k loop: 68% 68/100 [00:25<00:11, 2.83it/s] k loop: 69% 69/100 [00:25<00:10, 2.87it/s] k loop: 70% 70/100 [00:25<00:10, 2.84it/s] k loop: 71% 71/100 [00:26<00:10, 2.69it/s] k loop: 72% 72/100 [00:26<00:10, 2.69it/s] k loop: 73% 73/100 [00:26<00:09, 2.74it/s] k loop: 74% 74/100 [00:27<00:09, 2.80it/s] k loop: 75% 75/100 [00:27<00:08, 2.83it/s] k loop: 76% 76/100 [00:27<00:08, 2.83it/s] k loop: 77% 77/100 [00:28<00:08, 2.80it/s] k loop: 78% 78/100 [00:28<00:07, 2.76it/s] k loop: 79% 79/100 [00:29<00:07, 2.79it/s] k loop: 80% 80/100 [00:29<00:07, 2.76it/s] k loop: 81% 81/100 [00:29<00:06, 2.79it/s] k loop: 82% 82/100 [00:30<00:06, 2.80it/s] k loop: 83% 83/100 [00:30<00:06, 2.68it/s] k loop: 84% 84/100 [00:30<00:05, 2.75it/s] k loop: 85% 85/100 [00:31<00:05, 2.81it/s] k loop: 86% 86/100 [00:31<00:04, 2.82it/s] k loop: 87% 87/100 [00:31<00:04, 2.78it/s] k loop: 88% 88/100 [00:32<00:04, 2.77it/s] k loop: 89% 89/100 [00:32<00:04, 2.64it/s] k loop: 90% 90/100 [00:33<00:04, 2.41it/s] k loop: 91% 91/100 [00:33<00:03, 2.45it/s] k loop: 92% 92/100 [00:34<00:03, 2.45it/s] k loop: 93% 93/100 [00:34<00:02, 2.53it/s] k loop: 94% 94/100 [00:34<00:02, 2.50it/s] k loop: 95% 95/100 [00:35<00:02, 2.46it/s] k loop: 96% 96/100 [00:35<00:01, 2.50it/s] k loop: 97% 97/100 [00:36<00:01, 2.52it/s] k loop: 98% 98/100 [00:36<00:00, 2.55it/s] k loop: 99% 99/100 [00:36<00:00, 2.59it/s] k loop: 100% 100/100 [00:37<00:00, 2.65it/s] k loop: 100% 100/100 [00:37<00:00, 2.69it/s]
############################### GROGU OUTPUT ################################### ############################### GROGU OUTPUT ###################################
================================================================================ ================================================================================
Input file: Input file:
Not yet specified. Not yet specified.
Number of nodes in the parallel cluster: 4 Number of nodes in the parallel cluster: 4
================================================================================ ================================================================================
Cell [Ang]: Cell [Ang]:
[[ 3.79100000e+00 0.00000000e+00 0.00000000e+00] [[ 3.79100000e+00 0.00000000e+00 0.00000000e+00]
[-1.89550000e+00 3.28310231e+00 0.00000000e+00] [-1.89550000e+00 3.28310231e+00 0.00000000e+00]
[ 1.25954923e-15 2.18160327e-15 2.05700000e+01]] [ 1.25954923e-15 2.18160327e-15 2.05700000e+01]]
================================================================================ ================================================================================
DFT axis: DFT axis:
[0 0 1] [0 0 1]
Quantization axis and perpendicular rotation directions: Quantization axis and perpendicular rotation directions:
[1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])] [1 0 0] --» [array([0, 1, 0]), array([0, 0, 1])]
@ -29,7 +29,7 @@ Ebot: -30
Eset: 50 Eset: 50
Esetp: 1000 Esetp: 1000
================================================================================ ================================================================================
Atomic informations: Atomic informations:
Not yet specified. Not yet specified.
@ -105,7 +105,7 @@ DMI: [ 0.31014172 0.23111069 -0.03120608 4.2460402 -0.09698692]
Symmetric-anisotropy: [6.19497698 4.23351577 6.50855465] Symmetric-anisotropy: [6.19497698 4.23351577 6.50855465]
================================================================================ ================================================================================
Runtime information: Runtime information:
Total runtime: 38.489369708 Total runtime: 38.489369708
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
Initial setup: 0.141595916 Initial setup: 0.141595916

23
src/grogu/useful.py
Unescape View File

@ -223,7 +223,8 @@ def calculate_exchange_tensor(pair):
J_ii = np.array([o2[-1], o3[0], o1[0]]) # xx, yy, zz J_ii = np.array([o2[-1], o3[0], o1[0]]) # xx, yy, zz
J_S = -0.5 * np.array([o3[1] + o3[2], o2[1] + o2[1], o1[1] + o1[2]]) # yz, zx, xy J_S = -0.5 * np.array([o3[1] + o3[2], o2[1] + o2[1], o1[1] + o1[2]]) # yz, zx, xy
D = 0.5 * np.array([o1[1] - o1[2], o2[2] - o2[1], o3[1] - o3[2]]) # x, y, z D = 0.5 * np.array([o1[1] - o1[2], o2[2] - o2[1], o3[1] - o3[2]]) # x, y, z
return J_ii.sum() / 3, D, np.concatenate([J_ii[:2] - J_ii.sum()/3, J_S]).flatten() return J_ii.sum() / 3, D, np.concatenate([J_ii[:2] - J_ii.sum() / 3, J_S]).flatten()
def print_atomic_indices(pair, magnetic_entities, dh): def print_atomic_indices(pair, magnetic_entities, dh):
atomic_indices = "" atomic_indices = ""
@ -231,17 +232,27 @@ def print_atomic_indices(pair, magnetic_entities, dh):
if "l" not in atoms.keys(): if "l" not in atoms.keys():
atoms["l"] = "all" atoms["l"] = "all"
if isinstance(atoms["atom"], int): if isinstance(atoms["atom"], int):
atomic_indices += f"[{atoms['atom']}]{dh.atoms[atoms['atom']].tag}({atoms['l']})" atomic_indices += (
f"[{atoms['atom']}]{dh.atoms[atoms['atom']].tag}({atoms['l']})"
)
if isinstance(atoms, list): if isinstance(atoms, list):
atomic_indices += [f"[{atoms['atom']}]{dh.atoms[atom['atom']].tag}({atom['l']})" for atom in atoms["atom"]] atomic_indices += [
f"[{atoms['atom']}]{dh.atoms[atom['atom']].tag}({atom['l']})"
for atom in atoms["atom"]
]
atoms = magnetic_entities[pair["aj"]] atoms = magnetic_entities[pair["aj"]]
if "l" not in atoms.keys(): if "l" not in atoms.keys():
atoms["l"] = "all" atoms["l"] = "all"
atomic_indices += " " atomic_indices += " "
if isinstance(atoms["atom"], int): if isinstance(atoms["atom"], int):
atomic_indices += f"[{atoms['atom']}]{dh.atoms[atoms['atom']].tag}({atoms['l']})" atomic_indices += (
f"[{atoms['atom']}]{dh.atoms[atoms['atom']].tag}({atoms['l']})"
)
if isinstance(atoms, list): if isinstance(atoms, list):
atomic_indices += [f"[{atoms['atom']}]{dh.atoms[atom['atom']].tag}({atom['l']})" for atom in atoms["atom"]] atomic_indices += [
f"[{atoms['atom']}]{dh.atoms[atom['atom']].tag}({atom['l']})"
for atom in atoms["atom"]
]
atomic_indices += f" {pair['Ruc']} d [Ang] Not yet." atomic_indices += f" {pair['Ruc']} d [Ang] Not yet."
return atomic_indices return atomic_indices

124
test.py
Unescape View File

@ -1,27 +1,28 @@
import os import os
from sys import stdout from sys import stdout
from tqdm import tqdm
from timeit import default_timer as timer from timeit import default_timer as timer
from tqdm import tqdm
os.environ["OMP_NUM_THREADS"] = "1" # export OMP_NUM_THREADS=4 os.environ["OMP_NUM_THREADS"] = "1" # export OMP_NUM_THREADS=4
os.environ["OPENBLAS_NUM_THREADS"] = "1" # export OPENBLAS_NUM_THREADS=4 os.environ["OPENBLAS_NUM_THREADS"] = "1" # export OPENBLAS_NUM_THREADS=4
os.environ["MKL_NUM_THREADS"] = "1" # export MKL_NUM_THREADS=6 os.environ["MKL_NUM_THREADS"] = "1" # export MKL_NUM_THREADS=6
os.environ["VECLIB_MAXIMUM_THREADS"] = "1" # export VECLIB_MAXIMUM_THREADS=4 os.environ["VECLIB_MAXIMUM_THREADS"] = "1" # export VECLIB_MAXIMUM_THREADS=4
os.environ["NUMEXPR_NUM_THREADS"] = "1" # export NUMEXPR_NUM_THREADS=6 os.environ["NUMEXPR_NUM_THREADS"] = "1" # export NUMEXPR_NUM_THREADS=6
import warnings
import numpy as np import numpy as np
import sisl import sisl
from grogu.useful import *
from mpi4py import MPI from mpi4py import MPI
from numpy.linalg import inv from numpy.linalg import inv
import warnings
from grogu.useful import *
start_time = timer() start_time = timer()
# this cell mimicks an input file # this cell mimicks an input file
fdf = sisl.get_sile( fdf = sisl.get_sile("./lat3_791/Fe3GeTe2.fdf")
"./lat3_791/Fe3GeTe2.fdf"
)
# this information needs to be given at the input!! # this information needs to be given at the input!!
scf_xcf_orientation = np.array([0, 0, 1]) # z scf_xcf_orientation = np.array([0, 0, 1]) # z
# list of reference directions for around which we calculate the derivatives # list of reference directions for around which we calculate the derivatives
@ -35,22 +36,22 @@ ref_xcf_orientations = [
] ]
# human readable definition of magnetic entities # human readable definition of magnetic entities
#magnetic_entities = [ # magnetic_entities = [
# dict(atom=0, ), # dict(atom=0, ),
# dict(atom=1, ), # dict(atom=1, ),
# dict(atom=2, ), # dict(atom=2, ),
# dict(atom=3, l=2), # dict(atom=3, l=2),
# dict(atom=4, l=2), # dict(atom=4, l=2),
# dict(atom=5, l=2), # dict(atom=5, l=2),
#] # ]
#pairs = [ # pairs = [
# dict(ai=3, aj=4, Ruc=np.array([0, 0, 0])), # isotropic should be -82 meV # dict(ai=3, aj=4, Ruc=np.array([0, 0, 0])), # isotropic should be -82 meV
# dict(ai=3, aj=5, Ruc=np.array([0, 0, 0])), # these should all be around -41.9 in the isotropic part # dict(ai=3, aj=5, Ruc=np.array([0, 0, 0])), # these should all be around -41.9 in the isotropic part
# dict(ai=4, aj=5, Ruc=np.array([0, 0, 0])), # dict(ai=4, aj=5, Ruc=np.array([0, 0, 0])),
# dict(ai=3, aj=0, Ruc=np.array([0, 0, 0])), # dict(ai=3, aj=0, Ruc=np.array([0, 0, 0])),
# dict(ai=3, aj=1, Ruc=np.array([0, 0, 0])), # dict(ai=3, aj=1, Ruc=np.array([0, 0, 0])),
# dict(ai=3, aj=2, Ruc=np.array([0, 0, 0])), # dict(ai=3, aj=2, Ruc=np.array([0, 0, 0])),
#] # ]
magnetic_entities = [ magnetic_entities = [
dict(atom=3, l=2), dict(atom=3, l=2),
dict(atom=4, l=2), dict(atom=4, l=2),
@ -60,7 +61,9 @@ magnetic_entities = [
# pair information # pair information
pairs = [ pairs = [
dict(ai=0, aj=1, Ruc=np.array([0, 0, 0])), # isotropic should be -82 meV dict(ai=0, aj=1, Ruc=np.array([0, 0, 0])), # isotropic should be -82 meV
dict(ai=0, aj=2, Ruc=np.array([0, 0, 0])), # these should all be around -41.9 in the isotropic part dict(
ai=0, aj=2, Ruc=np.array([0, 0, 0])
), # these should all be around -41.9 in the isotropic part
dict(ai=1, aj=2, Ruc=np.array([0, 0, 0])), dict(ai=1, aj=2, Ruc=np.array([0, 0, 0])),
dict(ai=0, aj=1, Ruc=np.array([-1, 0, 0])), dict(ai=0, aj=1, Ruc=np.array([-1, 0, 0])),
dict(ai=0, aj=2, Ruc=np.array([-1, 0, 0])), dict(ai=0, aj=2, Ruc=np.array([-1, 0, 0])),
@ -89,15 +92,17 @@ root_node = 0
if rank == root_node: if rank == root_node:
print("Number of nodes in the parallel cluster: ", size) print("Number of nodes in the parallel cluster: ", size)
simulation_parameters = dict(path="Not yet specified.", simulation_parameters = dict(
scf_xcf_orientation=scf_xcf_orientation, path="Not yet specified.",
ref_xcf_orientations=ref_xcf_orientations, scf_xcf_orientation=scf_xcf_orientation,
kset=kset, ref_xcf_orientations=ref_xcf_orientations,
kdirs=kdirs, kset=kset,
ebot=ebot, kdirs=kdirs,
eset=eset, ebot=ebot,
esetp=esetp, eset=eset,
parallel_size=size) esetp=esetp,
parallel_size=size,
)
# digestion of the input # digestion of the input
# read in hamiltonian # read in hamiltonian
@ -265,7 +270,7 @@ site_and_pair_dictionaries_time = timer()
kset = make_kset(dirs=kdirs, NUMK=kset) # generate k space sampling kset = make_kset(dirs=kdirs, NUMK=kset) # generate k space sampling
wkset = np.ones(len(kset)) / len(kset) # generate weights for k points 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 = np.array_split(kset, size) # split the k points based on MPI size
kpcs[root_node] = tqdm(kpcs[root_node], desc='k loop', file=stdout) kpcs[root_node] = tqdm(kpcs[root_node], desc="k loop", file=stdout)
k_set_time = timer() k_set_time = timer()
@ -411,63 +416,100 @@ if rank == root_node:
end_time = timer() end_time = timer()
print("############################### GROGU OUTPUT ###################################") print(
print("================================================================================") "############################### GROGU OUTPUT ###################################"
)
print(
"================================================================================"
)
print("Input file: ") print("Input file: ")
print(simulation_parameters["path"]) print(simulation_parameters["path"])
print("Number of nodes in the parallel cluster: ", simulation_parameters["parallel_size"]) print(
print("================================================================================") "Number of nodes in the parallel cluster: ",
simulation_parameters["parallel_size"],
)
print(
"================================================================================"
)
try: try:
print("Cell [Ang]: ") print("Cell [Ang]: ")
print(simulation_parameters["geom"].cell) print(simulation_parameters["geom"].cell)
except: except:
print("Geometry could not be read.") print("Geometry could not be read.")
print("================================================================================") print(
"================================================================================"
)
print("DFT axis: ") print("DFT axis: ")
print(simulation_parameters["scf_xcf_orientation"]) print(simulation_parameters["scf_xcf_orientation"])
print("Quantization axis and perpendicular rotation directions:") print("Quantization axis and perpendicular rotation directions:")
for ref in ref_xcf_orientations: for ref in ref_xcf_orientations:
print(ref["o"], " --» ", ref["vw"]) print(ref["o"], " --» ", ref["vw"])
print("================================================================================") print(
"================================================================================"
)
print("number of k points: ", simulation_parameters["kset"]) print("number of k points: ", simulation_parameters["kset"])
print("k point directions: ", simulation_parameters["kdirs"]) print("k point directions: ", simulation_parameters["kdirs"])
print("================================================================================") print(
"================================================================================"
)
print("Parameters for the contour integral:") print("Parameters for the contour integral:")
print("Ebot: ", simulation_parameters["ebot"]) print("Ebot: ", simulation_parameters["ebot"])
print("Eset: ", simulation_parameters["eset"]) print("Eset: ", simulation_parameters["eset"])
print("Esetp: ", simulation_parameters["esetp"]) print("Esetp: ", simulation_parameters["esetp"])
print("================================================================================") print(
"================================================================================"
)
print("Atomic informations: ") print("Atomic informations: ")
print("") print("")
print("") print("")
print("Not yet specified.") print("Not yet specified.")
print("") print("")
print("") print("")
print("================================================================================") print(
"================================================================================"
)
print("Exchange [meV]") print("Exchange [meV]")
print("--------------------------------------------------------------------------------") print(
"--------------------------------------------------------------------------------"
)
print("Atom1 Atom2 [i j k] d [Ang]") print("Atom1 Atom2 [i j k] d [Ang]")
print("--------------------------------------------------------------------------------") print(
"--------------------------------------------------------------------------------"
)
for pair in pairs: for pair in pairs:
J_iso, J_S, D = calculate_exchange_tensor(pair) J_iso, J_S, D = calculate_exchange_tensor(pair)
J_iso = J_iso * sisl.unit_convert("eV", "meV") J_iso = J_iso * sisl.unit_convert("eV", "meV")
J_S = J_S * sisl.unit_convert("eV", "meV") J_S = J_S * sisl.unit_convert("eV", "meV")
D = D * sisl.unit_convert("eV", "meV") D = D * sisl.unit_convert("eV", "meV")
print(print_atomic_indices(pair, magnetic_entities, dh)) print(print_atomic_indices(pair, magnetic_entities, dh))
print("Isotropic: ", J_iso) print("Isotropic: ", J_iso)
print("DMI: ", D) print("DMI: ", D)
print("Symmetric-anisotropy: ", J_S) print("Symmetric-anisotropy: ", J_S)
print("") print("")
print("================================================================================") print(
"================================================================================"
)
print("Runtime information: ") print("Runtime information: ")
print("Total runtime: ", end_time - start_time) print("Total runtime: ", end_time - start_time)
print("--------------------------------------------------------------------------------") print(
"--------------------------------------------------------------------------------"
)
print("Initial setup: ", setup_time - start_time) print("Initial setup: ", setup_time - start_time)
print(f"Hamiltonian conversion and XC field extraction: {H_and_XCF_time - setup_time:.3f} s") print(
print(f"Pair and site datastructure creatrions: {site_and_pair_dictionaries_time - H_and_XCF_time:.3f} s") f"Hamiltonian conversion and XC field extraction: {H_and_XCF_time - setup_time:.3f} s"
print(f"k set cration and distribution: {k_set_time - site_and_pair_dictionaries_time:.3f} s") )
print(
f"Pair and site datastructure creatrions: {site_and_pair_dictionaries_time - H_and_XCF_time:.3f} s"
)
print(
f"k set cration and distribution: {k_set_time - site_and_pair_dictionaries_time:.3f} s"
)
print(f"Rotating XC potential: {reference_rotations_time - k_set_time:.3f} s") print(f"Rotating XC potential: {reference_rotations_time - k_set_time:.3f} s")
print(f"Greens function inversion: {green_function_inversion_time - reference_rotations_time:.3f} s") print(
print(f"Calculate energies and magnetic components: {end_time - green_function_inversion_time:.3f} s") f"Greens function inversion: {green_function_inversion_time - reference_rotations_time:.3f} s"
)
print(
f"Calculate energies and magnetic components: {end_time - green_function_inversion_time:.3f} s"
)

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