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complete_fdf.fdf
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#======================================================#
# Script:A complete FDF file for various operations #
# By Pritam Kumar Panda
# Dept. Of Physics and Astronomy
# Materials Theory Group
# Uppsala University
# Email:[email protected]
#------------------------------------------------------#
# -- NAME & LABEL --
SystemName XX unit cell relaxation
SystemLabel bulk
# -- MATERIAL --
NumberOfSpecies XX
NumberOfAtoms XX
%block Chemical_Species_label
1 XX XX
2 XX XX
%endblock Chemical_Species_label
# -- CELL-ATOMIC-POSITION --
LatticeConstant 1.0 Ang
%block LatticeVectors
XXXX XXXX XXXXX
XXXX XXXX XXXXX
XXXX XXXX XXXXX
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
XXX XXXX XXX 1
XXX XXXX XXX 1
XXX XXXX XXX 2
XXX XXXX XXX 2
%endblock AtomicCoordinatesAndAtomicSpecies
# -- MONKHORST-PACK --
%block kgrid_Monkhorst_Pack
XX 0 0 0.0
0 XX 0 0.0
0 0 XX 0.0
%endblock kgrid_Monkhorst_Pack
# -- SELF-CONSISTENT FIELD --
MeshCutoff XX Ry
PAO.BasisType split
PAO.BasisSize DZP
PAO.EnergyShift 0.03 eV
XC.functional GGA
XC.authors PBE
MaxSCFIterations XXX
SolutionMethod diagon
# -- SELF-CONSISTENT FIELD-MIXING --
DM.MixingWeight 0.02
DM.NumberPulay 3
DM.Tolerance 1.d-5
DM.Require.Energy.Convergence T
DM.Energy.Tolerance 1.e-5 eV
SCF.MixAfterConvergence F
DM.FormattedFiles T
DM.FormattedOutput T
# -- MOLECULAR DYNAMICS-CONJUGATE-GRADIENT-METHOD --
MD.TypeOfRun CG
MD.NumCGsteps XXX
MD.MaxForceTol 0.04 eV/Ang
MD.VariableCell T
MD.ConstantVolume F
MD.UseSaveXV T
MD.UseSaveCG T
MD.MaxStressTol 0.0010 eV/Ang**
WriteMDHistory T
WriteMDXMol T
MD.MaxCGDispl 0.02 Bohr
# -- SPIN FIELD --
SpinPolarized F #If spin polarized the use T
FixSpin F #for magnetic systems
NonCollinearSpin F #for magnetic systems
DM.InitSpinAF F #for magnetic systems
# -- SAVING DENSITY-MATRIX & FOR POST RUN --
ON.UseSaveLWF T
DM.UseSaveDM T
UseSaveData T
LongOutput T
# -- SAVING WAVE/BAND/EIGEN/KPOINTS/ANIMATION INFORMATION --
WriteKbands T
WriteBands T
WriteCoorXmol T
WriteCoorStep T
WriteKpoints T
WriteCoorCerius T
WriteHS T
WriteForces T
WriteMullikenPop 1
SaveHS T
XML.Write T
# -- BAND-STRUCTURE-ANALYSIS --
BandLinesScale pi/a
%block BandLines
1 0.0000 0.0000 0.5000 A
20 0.5000 0.0000 0.5000 L
25 0.5000 0.0000 0.0000 M
30 0.0000 0.0000 0.0000 \Gamma
35 0.0000 0.0000 0.5000 A
40 0.6666 0.3333 0.5000 H
45 0.6666 0.3333 0.0000 K
50 0.0000 0.0000 0.0000 \Gamma
%endblock BandLines
# -- WAVEFUNCTIONS-OF-BANDS --
WFS.Write.For.Bands T
COOP.Write T
WriteWaveFunctions T
# -- WAVEFUNCTIONKPOINTS (OPTIONAL) --
%block WaveFuncKPoints
0.0000 0.0000 0.5000 from 1 to 5
0.5000 0.0000 0.5000 from 1 to 5
0.5000 0.0000 0.0000 from 1 to 5
0.0000 0.0000 0.0000 from 1 to 5
0.0000 0.0000 0.5000 from 1 to 5
0.6666 0.3333 0.5000 from 1 to 5
0.6666 0.3333 0.0000 from 1 to 5
0.0000 0.0000 0.0000 from 1 to 5
%endblock WaveFuncKPoints
# -- CHARGE-DENSITIES AND POTENTIALS FOR MACROWAVE --
SaveRho T
SaveDeltaRho T
SaveTotalPotential T
SaveIonicCharge T
SaveElectrostaticPotential T
SaveTotalCharge T
SaveRhoXC T
# -- PSUEDOPOTENTIALS-EXTRAINFO --
WriteIonPlotFiles F
WriteHirshfeldPop F
Atom.Debug.KB.Generation F
# -- GEOMETRY CONSTRAINTS --
%block GeometryConstraints # Constraints impossed on
position X X # the atomic positions
stress X X X # the shear stresses
%endblock GeometryConstraints
# -- PROJECTED DENSITY OF STATES --
LocalDensityOfStates T
%block ProjectedDensityOfStates
-20.00 10.00 0.200 1000 eV
%endblock ProjectedDensityOfStates
%block LocalDensityOfStates
-5.00 0.00 eV
%endblock LocalDensityOfStates
%block PDOS.kgrid_Monkhorst_Pack
XX 0 0 0.0
0 XX 0 0.0
0 0 XX 0.0
%endblock PDOS.kgrid_Monkhorst_Pack
# -- DENCHAR —-
WriteDenchar T
Denchar.TypeOfRun 3D # use 2D if you want 2D
Denchar.PlotCharge T
Denchar.CoorUnits Ang
Denchar.DensityUnits Ele/Ang**3
Denchar.MinX -5.0 bohr
Denchar.MaxX 5.0 bohr
Denchar.MinY -5.0 bohr
Denchar.MaxY 5.0 bohr
Denchar.NumberPointsX 40
Denchar.NumberPointsY 40
Denchar.PlaneGeneration ThreeAtomicIndices
Denchar.PlotWaveFunctions T
%block Denchar.Indices3Atoms
1 2 3
%endblock Denchar.Indices3Atoms
# -- EXTRA PARAMETERS FOR VARIOUS CALCULATIONS --
# -- VARIABLES FOR CONTANT DISPLACEMENT FIELD AT EVERY SCF CYCLE TO COMPENSTAE DIPOLE —-
SlabDipoleCorrection T
LatticeDielectricConstant T
# -- POLARIZATION --
%block PolarizationGrids
20 4 4 yes
4 20 4 yes
4 4 20 yes
%endblock PolarizationGrids
# -- PHONON EIGENVALUES AND EIGENVECTORS --
Eigenvectors T
# -- SYNTHETIC ATOMS IF ANY --
%block SyntheticAtoms
4
2 2 3 4
2.000000 3.950000 0.000000 0.000000
5
2 2 3 4
2.000000 4.050000 0.000000 0.000000
%endblock SyntheticAtoms
# -- FOR MOLECULES e.g. BENZENE --
%block PS.lmax
C 3
H 3
%endblock PS.lmax
AtomicCoordinatesFormat NotScaledCartesianAng
ZM.ForceTolLength 0.01 eV/Ang
ZM.ForceTolAngle 0.0001 eV/deg
ZM.MaxDisplLength 0.1 Ang
ZM.MaxDisplAngle 20.0 deg
%block Zmatrix
molecule
2 0 0 0 xm1 ym1 zm1 0 0 0
2 1 0 0 CC 90.0 60.0 0 0 0
2 2 1 0 CC CCC 90.0 0 0 0
2 3 2 1 CC CCC 0.0 0 0 0
2 4 3 2 CC CCC 0.0 0 0 0
2 5 4 3 CC CCC 0.0 0 0 0
1 1 2 3 CH CCH 180.0 0 0 0
1 2 1 7 CH CCH 0.0 0 0 0
1 3 2 8 CH CCH 0.0 0 0 0
1 4 3 9 CH CCH 0.0 0 0 0
1 5 4 10 CH CCH 0.0 0 0 0
1 6 5 11 CH CCH 0.0 0 0 0
constants
ym1 5.00
zm1 0.00
CCC 120.0
CCH 120.0
variables
CC 1.390
CH 1.090
constraints
xm1 CC -1.0 3.903229
%endblock Zmatrix
ZM.UnitsLength Ang
ZM.UnitsAngle deg
# -- BASIS SET DEFINITION e.g.Graphene --
%block PAO.Basis # Define Basis set
C 2 # Species label, number of l-shells
n=2 0 1 # n, l, Nzeta
4.088
1.000
n=2 1 1 # n, l, Nzeta
4.870
1.000
Ghost-H 1
n=1 0 1 # n, l, Nzeta
5.000
1.000
%endblock PAO.Basis
# -- BASIS SET DEFINITION e.g.SrTiO3 --
%block PAO.Basis
Sr 5 1.64000
n=4 0 1 E 155.00000 6.00000
6.49993
1.00000
n=5 0 2 E 149.48000 6.50000
6.99958 5.49957
1.00000 1.00000
n=4 1 1 E 148.98000 5.61000
6.74964
1.00000
n=5 1 1 E 4.57000 1.20000
4.00000
1.00000
n=4 2 1 E 146.26000 6.09000
6.63062
1.00000
Ti 5 1.91
n=3 0 1 E 93.95 5.20
5.69946662616249
1.00000000000000
n=3 1 1 E 95.47 5.20
5.69941339465994
1.00000000000000
n=4 0 2 E 96.47 5.60
6.09996398975307 5.09944363262274
1.00000000000000 1.00000000000000
n=3 2 2 E 46.05 4.95
5.94327035784617 4.70009988294302
1.00000000000000 1.00000000000000
n=4 1 1 E 0.50 1.77
3.05365979938936
1.00000000000000
O 3 -0.28
n=2 0 2 E 40.58 3.95
4.95272270428712 3.60331408800389
1.00000000000000 1.00000000000000
n=2 1 2 E 36.78 4.35
4.99990228025066 3.89745395068600
1.00000000000000 1.00000000000000
n=3 2 1 E 21.69 0.93
2.73276990670788
1.00000000000000
%endblock PAO.Basis
# -- LDA+U CALCULATIONS e.g NiO --
LDAU.FirstIteration .false.
LDAU.ThresholdTol 1.0d-3
LDAU.PopTol 4.0d-4
LDAU.ProjectorGenerationMethod 2
LDAU.CutoffNorm 0.90
%block LDAU.proj
Ni 1 # number of shells of projectors
n=3 2 # n, l
4.600 0.000 # U(eV), J(eV)
0.000 0.000 # rc, \omega (default values)
%endblock LDAU.proj
# -- FERMI SURFACE CALCULATIONS --
Siesta2Wannier90.WriteMmn .true.
Siesta2Wannier90.WriteAmn .true.
Siesta2Wannier90.WriteEig .true.
Siesta2Wannier90.WriteUnk .true.
Siesta2Wannier90.NumberOfBands 23
Siesta2Wannier90.UnkGrid1 20
Siesta2Wannier90.UnkGrid2 20
Siesta2Wannier90.UnkGrid3 20
NumberOfBandManifoldsForWannier 3
#RBetweenManifolds .true.
%block WannierProjections
1 # Sequential index of the manifold, from 1 to NumberOfBandManifoldsForWannier
12 20 # Indices of the initial and final band of the manifold
9 # Number of bands for Wannier transformation
36 37 38 49 50 51 62 63 64 # Indices of the orbitals that will be used as localized trial orbitals
num_iter 0 # Number of iterations for the minimization of \Omega
wannier_plot 3 # Plot the Wannier function
fermi_surface_plot # Plot the Fermi surface
write_hr # Write the Hamiltonian in the WF basis
write_tb # Write lattice vectors, Hamiltonian, and position operator in WF basis
2 # Sequential index of the manifold, from 1 to NumberOfBandManifoldsForWannier
21 23 # Indices of the initial and final band of the manifold
3 # Number of bands for Wannier transformation
24 25 27 # Indices of the orbitals that will be used as localized trial orbitals
num_iter 0 # Number of iterations for the minimization of \Omega
wannier_plot 3 # Plot the Wannier function
fermi_surface_plot # Plot the Fermi surface
write_hr # Write the Hamiltonian in the WF basis
write_tb # Write lattice vectors, Hamiltonian, and position operator in WF basis
3 # Sequential index of the manifold, from 1 to NumberOfBandManifoldsForWannier
12 23 # Indices of the initial and final band of the manifold
12 # Number of bands for Wannier transformation
24 25 27 36 37 38 49 50 51 62 63 64 # Indices of the orbitals that will be used as localized trial orbitals
num_iter 0 # Number of iterations for the minimization of \Omega
wannier_plot 3 # Plot the Wannier function
fermi_surface_plot # Plot the Fermi surface
write_hr # Write the Hamiltonian in the WF basis
write_tb # Write lattice vectors, Hamiltonian, and position operator in WF basis
%endblock WannierProjections
%block kMeshforWannier
6 6 6
%endblock kMeshforWannier
# -- MOLECULAR DYNAMICS USING VERLET --
MD.TypeOfRun Verlet
MD.InitialTemperature 300 K
MD.Initial.Time.Step 1
MD.Final.Time.Step 100
MD.Length.Time.Step 1.00 fs