step2_ergoscf¶

libra_py.workflows.nbra.step2_ergoscf.do_ovlp(i, params, run)[source]¶

Compute the overlap matrix in the AO basis for two geometries, i and i+1

Parameters

i (int) – index of the time step to be used from the trajectory file
params (dictionary) –
the control parameters of the simulation
- params[“EXE”] ( string ): path to the ERGOSCF executable [ default: ergo ]
- params[“md_file”] ( string ): the name of the xyz file containing the trajectory - the
  file should be in the general xyz format. [default: “md.xyz”]
run (Python function) –
the function that defines the ErgoSCF input generation - the user has to define all the control parameters in it, to be able to run the ErgoSCF calculations

Example

In the example below, the outermost quotes should be tripled

Note: the function should follw the signature shown here

def run(EXE, COORDS):
inp = “#!bin/sh

%s << EOINPUT > /dev/null spin_polarization = 0 molecule_inline %sEOF basis = “STO-3G” scf.create_mtx_file_S = 1 scf.create_mtx_files_S_and_quit = 1 XC.sparse_mode = 1 run “LDA” EOINPUT ” % (EXE, COORDS)

return inp

Returns

(S11, S22, S12), where:

S11 - the matrices of the AO overlaps for the first geometry with itself (normal AO overlaps)

S22 - the matrices of the AO overlaps for the second geometry with itself (normal AO overlaps)

S12 - the matrices of the AO overlaps for the two geometries at the adjacent geometries (for TDM)

where A - is the size of the AO basis

Return type

(CMATRIX(A, A), CMATRIX(A, A), CMATRIX(A, A))

libra_py.workflows.nbra.step2_ergoscf.do_step(i, params, run)[source]¶

Runs a single-point SCF calculation for a given geometry along a trajectory

Parameters

i (int) – index of the time step to be used from the trajectory file
params (dictionary) –
the control parameters of the simulation
- params[“EXE”] ( string ): path to the ErgoSCF executable [ default: ergo ]
- params[“md_file”] ( string ): the name of the xyz file containing the trajectory - the
  file should be in the general xyz format. [default: “md.xyz”]
- params[“mo_active_space”] ( list of ints or None ): indices of the MOs we care about
  The indexing starts from 0, not 1! If set to None - all MOs will be returned. [default: None]
- params[“mo_indexing_convention”] ( string ): orbital indexing convention:
  - ”rel” : relative, with respect to the HOMO position: HOMO = 0, HOMO-1 = -1, LUMO = 1, etc. [default]
  - ”abs” : absolute, with respect to all possible MOs of the system
- params[“direct_MO”] ( int ): a flag to decide to use orbitals as read from
  the ErgoSCF output: - 0 : read in the Fock matrices and diagonalize them internally - 1 : read the MOs produced by ErgoSCF, this is the option to really go
  
  with the linear-scaling costs [ default ]
- params[“spinpolarized”] ( int ): whether the ErgoSCF calculations (and hence the
  following post-processing) are done withing the restricted or unrestricted formulation: - 0 : non-spin-polarized (restricted) [ default ] - 1 : spin-polarized (unrestricted)
run (Python function) –
the function that defines the ErgoSCF input generation - the user has to define all the control parameters in it, to be able to run the ErgoSCF calculations

Example

In the example below, the outermost quotes should be tripled

Note: the function should follw the signature shown here

def run(EXE, COORDS):
inp = “#!bin/sh

%s << EOINPUT > /dev/null spin_polarization = 0 molecule_inline %sEOF basis = “STO-3G” use_simple_starting_guess=1 scf.create_mtx_files_F = 1 scf.create_mtx_file_S = 1 XC.sparse_mode = 1 run “LDA” EOINPUT ” % (EXE, COORDS)

return inp

Returns

(E_sub, MO_sub), where:

E_sub ( list of CMATRIX(M, M) ): the matrix of the converged Hamiltonian eigenvalues (at given geometry)
Here, M = len(params[“mo_active_space”]) - we output only the MO energies that are of interest to us. E_sub[0] is the alpha component (for both restricted and unrestricted calculations) E_sub[1] is the beta component (only for the unrestricted calculations)

MO_sub ( list of CMATRIX(A, M) ): the matrix of the converged Hamiltonian eigenvalues (at given geometry)
Here, M = len(params[“mo_active_space”]) - we output only the MO energies that are of interest to us. A - is the number of AOs in this calculation MO_sub[0] is the alpha component (for both restricted and unrestricted calculations) MO_sub[1] is the beta component (only for the unrestricted calculations)

Return type

(list, list)

libra_py.workflows.nbra.step2_ergoscf.run_step2(params, run1, run2)[source]¶

Calculate the overlaps, transition dipole moments, and vibronic Hamiltonian matrix elements in the AO basis

Parameters

params (dictionary) – the control parameters of the simulation
params["dt"] (*) – nuclear dynamics timestep - as encoded in the trajectory [ units: a.u., default: 41.0 ]
params["isnap"] (*) – initial frame [ default: 0 ]
params["fsnap"] (*) – final frame [ default: 1 ]
params["out_dir"] (*) – the path to the directory that will collect all the results If the directory doesn’t exist, it will be created [ default: “res” ]
params["EXE"] (*) – path to the ErgoSCF executable [ default: ergo ]
params["md_file"] (*) – the name of the xyz file containing the trajectory - the file should be in the general xyz format. [default: “md.xyz”]
params["mo_active_space"] (*) – indices of the MOs we care about The indexing starts from 0, not 1! If set to None - all MOs will be returned. [default: None]
params["mo_indexing_convention"] (*) – orbital indexing convention: - “rel” : relative, with respect to the HOMO position: HOMO = 0, HOMO-1 = -1, LUMO = 1, etc. [default] - “abs” : absolute, with respect to all possible MOs of the system
params["direct_MO"] (*) –
a flag to decide to use orbitals as read from the ErgoSCF output: - 0 : read in the Fock matrices and diagonalize them internally - 1 : read the MOs produced by ErgoSCF, this is the option to really go

with the linear-scaling costs [ default ]
params["spinpolarized"] (*) – whether the ErgoSCF calculations (and hence the following post-processing) are done withing the restricted or unrestricted formulation: - 0 : non-spin-polarized (restricted) [ default ] - 1 : spin-polarized (unrestricted)
SeeAlso – the description of the parameters in `do_ovlp(i, params)` and in `do_step(i, params)`

Returns

but generates the files (S, St, and hvib) indexed in the range [isnap, fsnap), for instance, if isnap = 0, fsnap = 3, we will have files hvib_0, hvib_1, hvib_2

Return type

None