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Merge pull request #82 from RMGDFT/develop
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Sync develop with master for 5.1 release.
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@elbriggs
elbriggs authored Mar 29, 2023
2 parents 600a633 + 8c51530 commit 2ff4ca4
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38 changes: 38 additions & 0 deletions Examples/NEGF_Au-benzene-Au_NCPP/3lead_lead1/LCR.dat0
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# orbitals are read from
../lead1/Waves/wave.out

# charge density and potentials are read from
../lead1/Waves/wave.out

# lcr[].NX_GRID, NY_GRID, NZ_GRID
48 72 72

# starting grid point in the orignal grid
0 0 0

# ending grid point in the orignal grid
48 72 72

# starting grid point in the NEGF globla grid
48 0 0

# lcr[].num_ions number of ions in a conductor or a lead
18

#lcr[].state_begin, state_middle, state_end state_middle is dummy
0 0 162

#lcr[].ion_begin
0

#lcr[].bias (eV)
-4.49937761 -4.49937761 0.0

# a_length of this supercell (same as ON2 cal),
# the starting x-coordinate (in the global system)
15.412612 15.412612

# b_length of this supercell (same as ON2 cal),
# the starting y-coordinate (in the global system)
23.118919 0

38 changes: 38 additions & 0 deletions Examples/NEGF_Au-benzene-Au_NCPP/3lead_lead1/LCR.dat1
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# orbitals are read from
../lead1/Waves/wave.out

# charge density and potentials are read from
../lead1/Waves/wave.out

# lcr[].NX_GRID, NY_GRID, NZ_GRID
48 72 72

# starting grid point in the orignal grid
0 0 0

# ending grid point in the orignal grid
48 72 72

# starting grid point in the NEGF globla grid
0 0 0

# lcr[].num_ions number of ions in a conductor or a lead
18

#lcr[].state_begin, state_middle, state_end state_middle is dummy
0 0 162

#lcr[].ion_begin
0

#lcr[].bias (eV)
-4.49937761 -4.49937761 0.0

# a_length of this supercell (same as ON2 cal),
# the starting x-coordinate (in the global system)
15.412612 0

# b_length of this supercell (same as ON2 cal),
# the starting y-coordinate (in the global system)
23.118919 0

38 changes: 38 additions & 0 deletions Examples/NEGF_Au-benzene-Au_NCPP/3lead_lead1/LCR.dat2
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# orbitals are read from
../lead1/Waves/wave.out

# charge density and potentials are read from
../lead1/Waves/wave.out

# lcr[].NX_GRID, NY_GRID, NZ_GRID
48 72 72

# starting grid point in the orignal grid
0 0 0

# ending grid point in the orignal grid
48 72 72

# starting grid point in the NEGF globla grid
96 0 0

# lcr[].num_ions number of ions in a conductor or a lead
18

#lcr[].state_begin, state_middle, state_end state_middle is dummy
0 0 162

#lcr[].ion_begin
0

#lcr[].bias (eV)
-4.49937761 -4.49937761 0.0

# a_length of this supercell (same as ON2 cal),
# the starting x-coordinate (in the global system)
15.412612 30.825225

# b_length of this supercell (same as ON2 cal),
# the starting y-coordinate (in the global system)
23.118919 0

196 changes: 196 additions & 0 deletions Examples/NEGF_Au-benzene-Au_NCPP/3lead_lead1/input
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start_mode_NEGF="111"
start_mode="Random Start"
#space grid and processor grid control

wavefunction_grid ="144 72 72"
num_processor ="12"
processor_grid="3 2 2"
max_nlradius = "6.00000000"

# **** SCF controls ****

max_scf_steps = "12"
rms_convergence_criterion = "1e-12"

# **** Mixing controls ****

charge_density_mixing = "0.1"
charge_mixing_type = "Pulay"
charge_pulay_order = "5"
charge_pulay_scale = "0.5"
charge_pulay_refresh = "100"

# **** Setup ****

description = "3lead Au-mo-Au"
exchange_correlation_type = "LDA"
bravais_lattice_type = "Orthorhombic Primitive"
system_charge = "0.0"

# *****Occupation *****

occupations_type = "Fermi Dirac"
occupation_electron_temperature_eV = "0.1"

# **** Multigrid ****

kohn_sham_mg_levels = "2"
poisson_mg_levels = "2"
kohn_sham_time_step = "1.0"
poisson_time_step = "1.35"

# **** Pseudopotential ****
pseudopotential = "
Au ../Au.UPF"

atomic_orbital_files="
Au ../Au-atom/Wave/wave
"

# **** Units ****

length_units = "Bohr"
atomic_coordinate_type = "Absolute"


# Lattice constants in (x, y, z) directions
# a, b, c, cos(alpha), cos(beta), cos(gamma)
a_length="46.2378372454" b_length="23.1189186227" c_length="23.1189186227"
alpha="0.0" beta="0.0" gamma="0.0"



# atomic coordinates
atoms=
"
Au 0.000000000000e+00 7.706306207564e+00 7.706306207564e+00 1
Au 0.000000000000e+00 1.541261241513e+01 7.706306207564e+00 1
Au 0.000000000000e+00 1.155945931135e+01 1.155945931135e+01 1
Au 0.000000000000e+00 7.706306207564e+00 1.541261241513e+01 1
Au 0.000000000000e+00 1.541261241513e+01 1.541261241513e+01 1
Au 3.853153103782e+00 1.155945931135e+01 7.706306207564e+00 1
Au 3.853153103782e+00 7.706306207564e+00 1.155945931135e+01 1
Au 3.853153103782e+00 1.541261241513e+01 1.155945931135e+01 1
Au 3.853153103782e+00 1.155945931135e+01 1.541261241513e+01 1
Au 7.706306207564e+00 7.706306207564e+00 7.706306207564e+00 1
Au 7.706306207564e+00 1.541261241513e+01 7.706306207564e+00 1
Au 7.706306207564e+00 1.155945931135e+01 1.155945931135e+01 1
Au 7.706306207564e+00 7.706306207564e+00 1.541261241513e+01 1
Au 7.706306207564e+00 1.541261241513e+01 1.541261241513e+01 1
Au 1.155945931135e+01 1.155945931135e+01 7.706306207564e+00 1
Au 1.155945931135e+01 7.706306207564e+00 1.155945931135e+01 1
Au 1.155945931135e+01 1.541261241513e+01 1.155945931135e+01 1
Au 1.155945931135e+01 1.155945931135e+01 1.541261241513e+01 1
Au 1.541261241513e+01 7.706306207564e+00 7.706306207564e+00 1
Au 1.541261241513e+01 1.541261241513e+01 7.706306207564e+00 1
Au 1.541261241513e+01 1.155945931135e+01 1.155945931135e+01 1
Au 1.541261241513e+01 7.706306207564e+00 1.541261241513e+01 1
Au 1.541261241513e+01 1.541261241513e+01 1.541261241513e+01 1
Au 1.926576551891e+01 1.155945931135e+01 7.706306207564e+00 1
Au 1.926576551891e+01 7.706306207564e+00 1.155945931135e+01 1
Au 1.926576551891e+01 1.541261241513e+01 1.155945931135e+01 1
Au 1.926576551891e+01 1.155945931135e+01 1.541261241513e+01 1
Au 2.311891862269e+01 7.706306207564e+00 7.706306207564e+00 1
Au 2.311891862269e+01 1.541261241513e+01 7.706306207564e+00 1
Au 2.311891862269e+01 1.155945931135e+01 1.155945931135e+01 1
Au 2.311891862269e+01 7.706306207564e+00 1.541261241513e+01 1
Au 2.311891862269e+01 1.541261241513e+01 1.541261241513e+01 1
Au 2.697207172647e+01 1.155945931135e+01 7.706306207564e+00 1
Au 2.697207172647e+01 7.706306207564e+00 1.155945931135e+01 1
Au 2.697207172647e+01 1.541261241513e+01 1.155945931135e+01 1
Au 2.697207172647e+01 1.155945931135e+01 1.541261241513e+01 1
Au 3.082522483026e+01 7.706306207564e+00 7.706306207564e+00 1
Au 3.082522483026e+01 1.541261241513e+01 7.706306207564e+00 1
Au 3.082522483026e+01 1.155945931135e+01 1.155945931135e+01 1
Au 3.082522483026e+01 7.706306207564e+00 1.541261241513e+01 1
Au 3.082522483026e+01 1.541261241513e+01 1.541261241513e+01 1
Au 3.467837793404e+01 1.155945931135e+01 7.706306207564e+00 1
Au 3.467837793404e+01 7.706306207564e+00 1.155945931135e+01 1
Au 3.467837793404e+01 1.541261241513e+01 1.155945931135e+01 1
Au 3.467837793404e+01 1.155945931135e+01 1.541261241513e+01 1
Au 3.853153103782e+01 7.706306207564e+00 7.706306207564e+00 1
Au 3.853153103782e+01 1.541261241513e+01 7.706306207564e+00 1
Au 3.853153103782e+01 1.155945931135e+01 1.155945931135e+01 1
Au 3.853153103782e+01 7.706306207564e+00 1.541261241513e+01 1
Au 3.853153103782e+01 1.541261241513e+01 1.541261241513e+01 1
Au 4.238468414160e+01 1.155945931135e+01 7.706306207564e+00 1
Au 4.238468414160e+01 7.706306207564e+00 1.155945931135e+01 1
Au 4.238468414160e+01 1.541261241513e+01 1.155945931135e+01 1
Au 4.238468414160e+01 1.155945931135e+01 1.541261241513e+01 1
"

# orbital centers
orbitals=
"
9 0.000000000000e+00 7.706306207564e+00 7.706306207564e+00 6.5 1 1
9 0.000000000000e+00 1.541261241513e+01 7.706306207564e+00 6.5 1 1
9 0.000000000000e+00 1.155945931135e+01 1.155945931135e+01 6.5 1 1
9 0.000000000000e+00 7.706306207564e+00 1.541261241513e+01 6.5 1 1
9 0.000000000000e+00 1.541261241513e+01 1.541261241513e+01 6.5 1 1
9 3.853153103782e+00 1.155945931135e+01 7.706306207564e+00 6.5 1 1
9 3.853153103782e+00 7.706306207564e+00 1.155945931135e+01 6.5 1 1
9 3.853153103782e+00 1.541261241513e+01 1.155945931135e+01 6.5 1 1
9 3.853153103782e+00 1.155945931135e+01 1.541261241513e+01 6.5 1 1
9 7.706306207564e+00 7.706306207564e+00 7.706306207564e+00 6.5 1 1
9 7.706306207564e+00 1.541261241513e+01 7.706306207564e+00 6.5 1 1
9 7.706306207564e+00 1.155945931135e+01 1.155945931135e+01 6.5 1 1
9 7.706306207564e+00 7.706306207564e+00 1.541261241513e+01 6.5 1 1
9 7.706306207564e+00 1.541261241513e+01 1.541261241513e+01 6.5 1 1
9 1.155945931135e+01 1.155945931135e+01 7.706306207564e+00 6.5 1 1
9 1.155945931135e+01 7.706306207564e+00 1.155945931135e+01 6.5 1 1
9 1.155945931135e+01 1.541261241513e+01 1.155945931135e+01 6.5 1 1
9 1.155945931135e+01 1.155945931135e+01 1.541261241513e+01 6.5 1 1
9 1.541261241513e+01 7.706306207564e+00 7.706306207564e+00 6.5 1 1
9 1.541261241513e+01 1.541261241513e+01 7.706306207564e+00 6.5 1 1
9 1.541261241513e+01 1.155945931135e+01 1.155945931135e+01 6.5 1 1
9 1.541261241513e+01 7.706306207564e+00 1.541261241513e+01 6.5 1 1
9 1.541261241513e+01 1.541261241513e+01 1.541261241513e+01 6.5 1 1
9 1.926576551891e+01 1.155945931135e+01 7.706306207564e+00 6.5 1 1
9 1.926576551891e+01 7.706306207564e+00 1.155945931135e+01 6.5 1 1
9 1.926576551891e+01 1.541261241513e+01 1.155945931135e+01 6.5 1 1
9 1.926576551891e+01 1.155945931135e+01 1.541261241513e+01 6.5 1 1
9 2.311891862269e+01 7.706306207564e+00 7.706306207564e+00 6.5 1 1
9 2.311891862269e+01 1.541261241513e+01 7.706306207564e+00 6.5 1 1
9 2.311891862269e+01 1.155945931135e+01 1.155945931135e+01 6.5 1 1
9 2.311891862269e+01 7.706306207564e+00 1.541261241513e+01 6.5 1 1
9 2.311891862269e+01 1.541261241513e+01 1.541261241513e+01 6.5 1 1
9 2.697207172647e+01 1.155945931135e+01 7.706306207564e+00 6.5 1 1
9 2.697207172647e+01 7.706306207564e+00 1.155945931135e+01 6.5 1 1
9 2.697207172647e+01 1.541261241513e+01 1.155945931135e+01 6.5 1 1
9 2.697207172647e+01 1.155945931135e+01 1.541261241513e+01 6.5 1 1
9 3.082522483026e+01 7.706306207564e+00 7.706306207564e+00 6.5 1 1
9 3.082522483026e+01 1.541261241513e+01 7.706306207564e+00 6.5 1 1
9 3.082522483026e+01 1.155945931135e+01 1.155945931135e+01 6.5 1 1
9 3.082522483026e+01 7.706306207564e+00 1.541261241513e+01 6.5 1 1
9 3.082522483026e+01 1.541261241513e+01 1.541261241513e+01 6.5 1 1
9 3.467837793404e+01 1.155945931135e+01 7.706306207564e+00 6.5 1 1
9 3.467837793404e+01 7.706306207564e+00 1.155945931135e+01 6.5 1 1
9 3.467837793404e+01 1.541261241513e+01 1.155945931135e+01 6.5 1 1
9 3.467837793404e+01 1.155945931135e+01 1.541261241513e+01 6.5 1 1
9 3.853153103782e+01 7.706306207564e+00 7.706306207564e+00 6.5 1 1
9 3.853153103782e+01 1.541261241513e+01 7.706306207564e+00 6.5 1 1
9 3.853153103782e+01 1.155945931135e+01 1.155945931135e+01 6.5 1 1
9 3.853153103782e+01 7.706306207564e+00 1.541261241513e+01 6.5 1 1
9 3.853153103782e+01 1.541261241513e+01 1.541261241513e+01 6.5 1 1
9 4.238468414160e+01 1.155945931135e+01 7.706306207564e+00 6.5 1 1
9 4.238468414160e+01 7.706306207564e+00 1.155945931135e+01 6.5 1 1
9 4.238468414160e+01 1.541261241513e+01 1.155945931135e+01 6.5 1 1
9 4.238468414160e+01 1.155945931135e+01 1.541261241513e+01 6.5 1 1
"

number_of_atoms="54"
number_of_species="1"
number_of_orbitals="486"
metalic="true"
num_blocks="3"
blocks_dim="162 162 162"
potential_compass = "0 48 96 0 72 0 72"
chargedensity_compass = "0 48 96 0 72 0 72"

# **** default parameters for order-n input *****

kpoints_per_processor="1"
potential_grid_refinement="1"
calculation_mode="Quench Electrons"
number_of_kpoints="1"
kpoints= "0.0 0.0 0.0 1.0 "
64 changes: 64 additions & 0 deletions Examples/NEGF_Au-benzene-Au_NCPP/3lead_lead1/trans.in
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#

#num of probes and which block the probe attached to
2 0 2

#num of sub systems and their atomic order in NEGF calculations
#need to edit for multi-probe calclations
3 1 0 2
# num_probe_potential_window & their ranges[in the order of lead 1, 2, 3 ...]
#they are dummy for 2-probe calculations and
#need to edit for multi-probe calclations
4 40 120 40 120 40 120 40 120

# num_dos_axis_window for integration along x,y,z axis
# (required for mode 200)
3 0 110 0 72 0 72

#ncircle
50


#nmax_gq1
50


#nmax_gq2
128


#Enery Low Bound
-30.0


#KT
0.025


#GAMMA
0.5


#DELTA2
2.05


#DELTA
1.0E-6


#Charge density Pulay order
5


#Charge density Pulay refresh steps
100


#Charge density Pulay beta
0.5


#processor grids for block matrix operation
1
1
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