ERGO_methods¶
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libra_py.ERGO_methods.energies(en, nocc, nvirt, act_space=None)[source]¶ This function creates a diagonal matrix of energies of the states included in the active space.
- Parameters
en (list of floats) – energies of all (occupied + unoccupied) orbitals as read from the ErgoSCF
nocc (int) – the number of occupied orbitals in the pool of the printed out MO files
nvirt (int) – the number of unoccupied (virtual) orbitals in the pool of the printed out MO files
act_space (list of ints) – indices of the orbitals we are interested in The indexing convention is relative to HOMO, that is 0 is HOMO, -1 is HOMO-1, 1 is LUMO, etc.
- Returns
- matrix with orbital energies (ordered from lowest to highest)
Here, N is the size of the active space
- Return type
( CMATRIX(N,N) )
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libra_py.ERGO_methods.find_last_file(prefix, suffix)[source]¶ This functions searches for the last file in a series of files named prefix`%i`suffix, for instance “A1.txt”, “A2.txt”, “A3.txt”, etc.
- Parameters
prefix (string) – the prefix of the filenames
suffix (string) – the suffix of the filenames
- Returns
(i, filename), where:
i : the largest index of the existing file
filename : the name of the last existing file
- Return type
(int, string)
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libra_py.ERGO_methods.get_mtx_matrices(filename, act_sp1=None, act_sp2=None)[source]¶ Get the matrices printed out by the DFTB+
- Parameters
filename (string) – the name of the file to read. In the MatrixMarket (mtx) format
act_sp1 (list of ints or None) – the row active space to extract from the original files Indices here start from 0. If set to None - the number of AOs will be determined automatically from the file. [default: None]
act_sp2 (list of ints or None) – the cols active space to extract from the original files Indices here start from 0. If set to None - the number of AOs will be determined automatically from the file. [default: None]
- Returns
- X: where N = len(act_sp1) and M = len(act_sp2)
These are the corresponding property matrices (converted to the complex type)
- Return type
list of CMATRIX(N, M)
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libra_py.ERGO_methods.read_mo_restricted(nocc, nvirt, act_space=None)[source]¶ This function reads the MO files produced by ErgoSCF in the case of spin-unpolarized (restricted) formulation. The names of the files are known, so the we do not need to specify that
- Parameters
nocc (int) – the number of occupied orbitals in the pool of the printed out MO files
nvirt (int) – the number of unoccupied (virtual) orbitals in the pool of the printed out MO files
act_space (list of ints) – indices of the orbitals we are interested in The indexing convention is relative to HOMO, that is 0 is HOMO, -1 is HOMO-1, 1 is LUMO, etc.
- Returns
( [mo_a] )
mo_a ( CMATRIX(nao, nocc+nvirt) ): alpha orbitals
- Return type
( list )
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libra_py.ERGO_methods.read_mo_unrestricted(nocc, nvirt, act_space=None)[source]¶ This function reads the MO files produced by ErgoSCF in the case of spin-polarized (unrestricted) formulation. The names of the files are known, so the we do not need to specify that
- Parameters
nocc (int) – the number of occupied orbitals in the pool of the printed out MO files
nvirt (int) – the number of unoccupied (virtual) orbitals in the pool of the printed out MO files
act_space (list of ints) – indices of the orbitals we are interested in The indexing convention is relative to HOMO, that is 0 is HOMO, -1 is HOMO-1, 1 is LUMO, etc.
- Returns
( [mo_a, mo_b] )
mo_a ( CMATRIX(nao, nocc+nvirt) ): alpha orbitals
mo_b ( CMATRIX(nao, nocc+nvirt) ): beta orbitals
- Return type
( list )
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libra_py.ERGO_methods.read_spectrum_restricted()[source]¶ This function reads the eigenspectrum files produced by ErgoSCF in the case of spin-unpolarized (restricted) formulation. The names of the files are known, so the we do not need any arguments
Note: the ordering of the orbitals in the ErgoSCF is:
H L H-1 L+1 … …
So, the occupied orbitals order is reverted in the created array
Args: None
- Returns
( [e_a], [nocc, nvirt])
- e_a ( list of floats ): energies of the alpha orbitals printed out
this list contains both occupied and unoccupied orbitals
- nocc ( int ): the number of occupied orbitals, it should be less than
len(e_a) and len(e_b)
- nvirt ( int ): the number of unoccupied orbitals, it should be less than
len(e_a) and len(e_b)
- Return type
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libra_py.ERGO_methods.read_spectrum_unrestricted()[source]¶ This function reads the eigenspectrum files produced by ErgoSCF in the case of spin-polarized (unrestricted) formulation. The names of the files are known, so the we do not need any arguments
Note: the ordering of the orbitals in the ErgoSCF is:
H L H-1 L+1 … …
So, the occupied orbitals order is reverted in the created array
Args: None
- Returns
( [e_a, e_b], [nocc, nvirt])
- e_a ( list of floats ): energies of the alpha orbitals printed out
this list contains both occupied and unoccupied orbitals
- e_b ( list of floats ): energies of the beta orbitals printed out
this list contains both occupied and unoccupied orbitals
- nocc ( int ): the number of occupied orbitals, it should be less than
len(e_a) and len(e_b)
- nvirt ( int ): the number of unoccupied orbitals, it should be less than
len(e_a) and len(e_b)
- Return type
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libra_py.ERGO_methods.xyz_traj2gen_ovlp(infile, md_iter1, md_iter2)[source]¶ This file converts the xyz trajectory file to a string that contains the superimposed geometries of the
`md_iter1`and`md_step2`steps that can be used to setup the input for the ErgoSCF calculations
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libra_py.ERGO_methods.xyz_traj2gen_sp(infile, md_iter)[source]¶ This file converts the xyz trajectory file to a string that contains the geometry of the
`md_iter`step that can be used to setup the input for the ErgoSCF calculations- Parameters
infile (string) – the name of the input xyz trajectory file
md_iter (int) – index of the timeframe to extract
- Returns
atoms and coordinates section [ units: same as in xyz file ]
- Return type
string