changed pre-commit

.gitignore

@@ -20,7 +20,7 @@ docs/source/api/generated
 
 # Debug
 tmp*
-.coverage
+*.coverage
 
 # Mac stuff
 *.DS_Store*

.pre-commit-config.yaml

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

README.md

@@ -2,21 +2,28 @@
 
 # TODO
 
-[x] Definition of magnetic entities:
+- Definition of magnetic entities:
     * Through simple sequence o forbitals in the unit cell
     * Through atom specification
     * Through atom and orbital specification
-[x] Separation of TR and TRB components of the Hamiltonian, Identification of the exchange field.
-[x] Definition of commutator expressions, old projection matrix elements
-[x] Efficient calculation of Green's functions
-[] Calculation of energy and momentum resolved derivatives
-[] Parallel BZ and serial energy integral
+- Separation of TR and TRB components of the Hamiltonian, Identification of the exchange field.
+- Definition of commutator expressions, old projection matrix elements
+- Efficient calculation of Green's functions
+- Calculation of energy and momentum resolved derivatives
+- Parallel BZ and serial energy integral
 
-# Building wheel 
-https://packaging.python.org/en/latest/tutorials/packaging-projects/
+# Building wheel
+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/*
 
@@ -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
-

all_atoms.txt

@@ -5,16 +5,16 @@ The shape of the Hamiltonian and the Greens function is 84x84.
 
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 ############################### GROGU OUTPUT ###################################
 ================================================================================
-Input file: 
+Input file:
 Not yet specified.
 Number of nodes in the parallel cluster:  4
 ================================================================================
-Cell [Ang]: 
+Cell [Ang]:
 [[ 3.79100000e+00  0.00000000e+00  0.00000000e+00]
  [-1.89550000e+00  3.28310231e+00  0.00000000e+00]
  [ 1.25954923e-15  2.18160327e-15  2.05700000e+01]]
 ================================================================================
-DFT axis: 
+DFT axis:
 [0 0 1]
 Quantization axis and perpendicular rotation directions:
 [1 0 0]  --»  [array([0, 1, 0]), array([0, 0, 1])]
@@ -29,7 +29,7 @@ Ebot:  -30
 Eset:  50
 Esetp:  1000
 ================================================================================
-Atomic informations: 
+Atomic informations:
 
 
 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]
 
 ================================================================================
-Runtime information: 
+Runtime information:
 Total runtime:  37.528785458
 --------------------------------------------------------------------------------
 Initial setup:  0.13668741699999998

lat3_791/BASIS_ENTHALPY

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

lat3_791/BASIS_HARRIS_ENTHALPY

@@ -1,4 +1,4 @@
-  -2878.0654643176349     
- The above number is the electronic (free) harris energy:  -2887.7689582280768     
+  -2878.0654643176349
+ The above number is the electronic (free) harris energy:  -2887.7689582280768
  Plus the pressure :    1.3595453680289311E-005  (   0.20000000000000001       GPa)
-      times the orbital volume (in Bohr**3):    52457.833503994734     
+      times the orbital volume (in Bohr**3):    52457.833503994734

lat3_791/Fe3GeTe2.ORB_INDX

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

lat3_791/Fe3GeTe2.bib

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

lat3_791/Fe3GeTe2.fdf

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

lat3_791/Fe3GeTe2.out

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

lat3_791/Fe3GeTe2.times

@@ -72,4 +72,3 @@ Tot.tot: total CPU time in all programs in one node
 Nod.avg: average calculation time in one program across nodes
 Nod.max: maximum calculation time in one program across nodes
 Calculation time: CPU time excluding communications
-

lat3_791/INPUT_TMP.58436

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

lat3_791/TIMES

@@ -72,4 +72,3 @@ Tot.tot: total CPU time in all programs in one node
 Nod.avg: average calculation time in one program across nodes
 Nod.max: maximum calculation time in one program across nodes
 Calculation time: CPU time excluding communications
- 

lat3_791/fdf-58450.log

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

simmetries.txt

@@ -5,16 +5,16 @@ The shape of the Hamiltonian and the Greens function is 84x84.
 
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 ############################### GROGU OUTPUT ###################################
 ================================================================================
-Input file: 
+Input file:
 Not yet specified.
 Number of nodes in the parallel cluster:  4
 ================================================================================
-Cell [Ang]: 
+Cell [Ang]:
 [[ 3.79100000e+00  0.00000000e+00  0.00000000e+00]
  [-1.89550000e+00  3.28310231e+00  0.00000000e+00]
  [ 1.25954923e-15  2.18160327e-15  2.05700000e+01]]
 ================================================================================
-DFT axis: 
+DFT axis:
 [0 0 1]
 Quantization axis and perpendicular rotation directions:
 [1 0 0]  --»  [array([0, 1, 0]), array([0, 0, 1])]
@@ -29,7 +29,7 @@ Ebot:  -30
 Eset:  50
 Esetp:  1000
 ================================================================================
-Atomic informations: 
+Atomic informations:
 
 
 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]
 
 ================================================================================
-Runtime information: 
+Runtime information:
 Total runtime:  38.489369708
 --------------------------------------------------------------------------------
 Initial setup:  0.141595916

src/grogu/useful.py

@@ -223,7 +223,8 @@ def calculate_exchange_tensor(pair):
     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
     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):
     atomic_indices = ""
@@ -231,17 +232,27 @@ def print_atomic_indices(pair, magnetic_entities, dh):
     if "l" not in atoms.keys():
         atoms["l"] = "all"
     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):
-        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"]]
     if "l" not in atoms.keys():
         atoms["l"] = "all"
     atomic_indices += "    "
     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):
-        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."
-    return atomic_indices
+    return atomic_indices

test.py

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