##Parameters for semi-infinite electrode calculation using ASE## Format= Keyword : {Default Value,Type} : Explaination of Keyword : Options/Context
Keywords That Generaly Need Be Defined Each Calculation
output : {pyruqt_results,str} : Sets the filename to be used for all calculation outputfiles : Define uniquely for each new calculation to avoid overwriting data
exmol_dir : {None,str} : Defines location of extended molecular region geometry xyz file for pySCF or MolEl.dat for MOLCAS : Always needed
elec_dir : {None,str} : Defines location of the left electrode xyz file or MolEl.dat : Not needed if elec_prog type is "supercell", Replaced by "elec_size"
elec2_dir : {None,str} : Defines location of right electrode xyz/MolEl.dat if not same as left electrode : Can be omitted if electrodes are superimposable mirror images of each other
Calculation Dependent or Optional Keywords
Keywords that define the electronic structure programs to be used
exmol_prog : {"molcas",str} : Defines what electronic structure program is used for the extended molecular region : Options are currently "molcas" or "pyscf"
elec_prog : {"molcas",str} : Same as exmol_prog but for the left and right electrodes : Additional option of "supercell" which activates the supercell method (no separate electrode calc)
pyRUQT transport keywords
*Transport Keywords
min_trans_energy : {-2.0,float} : Lowest transmission energy to be calculated in eV :
max_trans_energy : {2.0,float} : Highest transmission energy to be calculated in eV :
delta_energy : {0.01,float} : Energy difference between transmission points to be calculated in eV :
min_bias : {-2.0,float} : Lowest voltage bias to be calculated in Volts : Not needed for transmission calculations
max_bias : {2.0,float} : Highest bias voltage to be calculated in Volts : Not needed for transmission calculations
delta_bias : {0.1,float} : Difference between bias voltage points in Volts : Not needed for transmission calculations
spin_pol : {False,logical} : Sets the current to 2*value when using data from 1-electron spin orbitals : Use if input data is from single electron orbitals vs double electron (standard for MOLCAS)
dos_calc : {False,bool} : Generates the density of states using ASE : Currently non-functional
fd_change : {0.001,float} : Finite difference to be used when calculating the difference conductance :
ase_current : {False,bool} : Use ASE's inbuilt current calculator instead of pyRUQT : Recommended to keep False as pyRUQT routine uses an improved numerical integration technique over ASE
*Alignment/Electrode Keywords
full_align : {True,bool} : Uses improved wieghed average alignment routine in pyRUQT over ASE's default alignment (align_elec) : Recommended to always use unless using ASE's align_elec instead
align_elec : {0,int} : Default ASE alignment routine to align electrode/extended molecular regions based a selected element : Not recommended, replaced by "full_align"
coupling_calc : {None,str} : Improve coupling interactions defining coupling elements in off-diagonal paritioned Green's functions set to zero in ASE : Use "Fock_EX" value to activate
coupled : {"molecule",str} : Defines how much of the extended molecular region should receive the additional Fock_EX coupling with electrode : Options are "molecule" or "extended_molecule"
n_elec_units : {2,int} : Number of repeating electrode units in the electrode regions : Only default of 2 currently supported
*Supercell Calculations
elec_size : {None,[int,int]} : Basis functions to be placed in the electrode regions for a supercell calculation in list format, [left,right] : Required if elec_prog="supercell"
Molcas specific keywords,Use if either exmol_prog or elec_prog equal "molcas"
state_num : {1,int} : Select CI state to be used for transport calculations : Values other than 1 need a corresponding Effective Hamiltonian matrix to be in MolEl.dat
state_num_e : {1,int} : Select excited CI state to be used for transport calculations : Unused for now
PySCF specific keywords, Use if either exmol_prog or elec_prog equal "pyscf"
exmol_geo : {None,str} : Define the full xyz file name for extended molecular region : Be sure to include any extensions in name (ex. exmol_geo="geo_file.xyz")
elec_geo : {None,str} : Define the full xyz file name for left electrode : Can be omitted if elec_prog="supercell"
elec2_geo : {None,str} : Define the full xyz file name for right electrode (if not same as left electrode) : Can be omitted if electrodes are superimposable mirror images of each other
dft_functional : {"pbe",str} : Defines the DFT functional to be used by PySCF : See pySCF manual for a full list of options
basis_set : {None,str} : Defines basis set to be used by PySCF : See PySCF manual for full list of keywords
ecp : {None,str} : If your basis set has an ECP (or auxbasis for PBC PySCF) it must be defined separately using this keyword : Can be left empty for non-ECP Gaussian basis like 6-31G
pyscf_pbc : {False,logical} : Uses periodic basis set for pySCF calculations instead of Gaussian orbitals : Requires "lattice_v" to be defined with a list of the 3 lattice vectors, [a1,b2,c3]
conv_tol : {1E-7,float} : Defines the SCF convergence of PySCF in Hartees :
max_iter : {100,int} : Max number of PySCF iterations allowed before SCF termination :
*PySCF Keywords when using Periodic Boundary Conditions (Along X-Axis)
pyscf_pbc : {False,logical} : Use periodic basis set for pySCF calculations instead of Gaussian orbitals : Requires "lattice_v" to be defined with a list of the 3 lattice vectors: [a1,a2,a3]
lattice_v : {None,float} : List of the 3 lattice vectors in 1-D list format of [a1,a2,a3] : Required to be Defined for PBC pySCF
meshum : {10,float} : # of mesh points used by pySCF per lattice vector : Highly recommended to adjust from default verbosity : {4,int} : Degree of pySCF output : Recommended to use 2 for no output and 4 for useable output (must pipe script output to file via command line)