Polarizable Embedding

Penguin leverages the CPPE library[SRK+19] when combined with PySCF[SBB+18] and PyFraMe[ORc21] when combined with VeloxChem[RLV+20] to compute electrostatic and polarization interactions. Polarizable Embedding (PE) is a powerful tool designed to model these interactions, making it a robust choice for embedding-based quantum chemical calculations.
By integrating PE, Penguin ensures that users have access to state-of-the-art methods for incorporating environmental effects into their quantum chemical calculations. This capability enhances the accuracy and reliability of results for complex systems, particularly in cases where environmental interactions play a critical role.

How To Include PE

PE is automatically applied when the @pe section is provided and a valid potential file (POTFILE.pot) is given.
The computational method is then defined as usual with the task keyword.

Example Input File

@method settings  
basis: STO-3G  
@end  

@pe  
potfile: PATH/TO/POTFILE.pot  
@end  

@memory  
max_mem: 1  
@end  

@jobs  
Task: ccs  
@end  

@molecule  
charge: 0  
multiplicity: 1  
units: bohr  
xyz:  
O  0.0000000000  0.0000000000  0.0000000000  
H  0.0000000000  1.4304281903  1.1071565216  
H  0.0000000000 -1.4304281903  1.1071565216  
@end

Example Potential File

@environment  
units: angstrom  
xyz:  
O -1.9957202  0.0160415  1.2422556 water 1  
H -2.4542703 -0.5669741  1.8472817 water 1  
H -1.9377950 -0.4817912  0.4267562 water 1  
@end  

@charges  
O -0.67444408 water  
H  0.33722206 water  
H  0.33722206 water  
@end  

@polarizabilities  
O 5.73935090  0.00000000  0.00000000  5.73935090  0.00000000  5.73935090 water  
H 2.30839051  0.00000000  0.00000000  2.30839051  0.00000000  2.30839051 water  
H 2.30839051  0.00000000  0.00000000  2.30839051  0.00000000  2.30839051 water  
@end

@pe Keywords

General Keywords

potfile
Description	Provide a relative path to the potential file. Doing so turns on PE for the specified calculation.
Type	None
Default	False
Example	An example is given here

CPPE Keywords

iso_pol
Description	Make polarizabilities isotropic.
Type	bool
Default	False

induced_thresh
Description	Threshold for induced moments convergence.
Type	float
Default	1.0E-8

maxiter
Description	Maximum number of iterations for induced moments.
Type	int
Default	50

damp_induced
Description	Enable Thole damping for induced moments.
Type	bool
Default	False

damping_factor_induced
Description	Damping factor for induced moments.
Type	float
Default	2.1304
Requirements	Requires the damp_induced keyword to be True.

damp_multipole
Description	Enable Thole damping for electric fields created by multipole moments.
Type	bool
Default	False

damping_factor_multipole
Description	Damping factor for electric fields created by multipole moments.
Type	float
Default	2.1304
Requirements	Requires the damp_multipole keyword to be True.

pe_border
Description	Enable border options for sites in proximity to the QM/MM border.
Type	bool
Default	False

border_type
Description	Border type, either “remove” or “redist” moments/polarizabilities.
Type	str
Default	remove
Options	remove redist

border_rmin
Description	Min radius in atomic units from QM atoms to MM sites for them to be removed/redistributed.
Type	float
Default	2.2

border_nredist
Description	Number of neighbor sites to redistribute to.
Type	int
Default	-1

border_nredist_order
Description	Order from which moments are removed.
Type	int
Default	1

border_redist_pol
Description	Enable redistribution of polarizabilities.
Type	bool
Default	False

PyFraMe Keywords

threshold
Description	Threshold for the induced dipoles.
Type	float
Default	1.0E-8

max_iterations
Description	Max iterations for the induced dipoles.
Type	int
Default	100

solver
Description	Solver used to obtain the induced dipoles.
Type	str
Default	jacobi
Options	jacobi jidiis dcji dcjidiis

mic
Description	Whether mic scaled coordinates should be used for the dipoles.
Type	bool
Default	False