bem section

The bem section defines parameters for boundary element method (BEM) simulations based on implicit solvation models. This section is mandatory when using the BEM approach.

Valid keywords

Keyword	Type	Allowed Values	Default
mesh file	string	Path to mesh in .msh format (generally obtained from GMSH)	input_file.msh
green function	string	accurate, approximate	approximate
variant	string	dpcm, iefpcm	dpcm
sphere radius	float or string	–	–
normal scalar factor	float	1.0, -1.0 (sign of surface normals)	1.0
permittivity file	string	Path to CSV table with frequency-dependent complex dielectric function	–
permittivity	string	Predefined permittivity functions (see Notes)	–
solvent	string	–	vacuum
solvent epsilon	float	–	–

Notes

• mesh file : 3D molecular surface in .msh format with vertex positions, normals, etc. This is generally obtained from GMSH software. Assumed in Angstrom.

• green function: specifies whether accurate or approximate Green’s function integrals must be computed

  • accurate: full numerical evaluation of Green’s function integrals.

  • approximate: uses simplified expressions (faster, less accurate, centroid-based).

• variant : specifies the right-hand-side formalism.

  • dpcm: Dielectric Polarizable Continuum Model (field, faster).

  • iefpcm: Integral Equation Formalism Polarizable Continuum Model (potential, more stable numerically) .

• sphere radius : radius of enclosing cavity (required for green function: approximate). If it is not given, it is calculated from mesh file.

• normal scalar factor : Orientation of surface normals (-1.0 must only be used for compatibility with other softwares).

• permittivity : Built-in frequency-dependent permittivities . Available models are:

  • silver etchegoin or silver johnson-christy or silver jc : Silver permittivity taken from Phys. Rev. B 1972, 6, 4370

  • silver brendel-bormann or silver bb : Silver permittivity taken from Appl. Opt. 1998, 37, 5271

  • silver palik : Silver permittivity taken from Handbook of Optical Constants of Solids (Elsevier, 1997)

  • gold etchegoin or gold johnson-christy or gold jc : Gold permittivity taken from Phys. Rev. B 1972, 6, 4370

  • gold brendel-bormann or gold bb : Gold permittivity taken from Appl. Opt. 1998, 37, 5271

  • gold palik : Gold permittivity taken from Handbook of Optical Constants of Solids (Elsevier, 1997)

• permittivity file : points to a CSV file with frequency-dependent complex dielectric function of the material. The file must contains 3 columns: frequencies (eV) Re(Eps) Im(Eps)

• solvent : specifies the solvent embedding the nanostructure. Tabulated solvents are given in bem_solvents.

• solvent epsilon : specifies the solvent optical dielectric constant.

Example

bem:
  mesh file: ag_nanocube.msh
  normal scalar factor: 1.0
  permittivity: silver etchegoin
  green function: approximate
  variant: iefpcm
  sphere radius: 5.0
  solvent epsilon: 1.77768