Input File Format

In this file, the format for the input files is detailed. To run, PyGBe needs two input files: a config file and a parameters file. You can find samples of these files in the examples directory.

Config file format

This file has two parts:

FILE: indicates in that line a mesh file will be specified. This code interfaces with the MSMS format, which generates a filename.vert and filename.face files. Each filename has the information for the mesh of one surface. To account for more than one surface (ie. for Stern layers, solvent filled cavities, several proteins), more than one FILE line is needed. After filename, the user must specify what kind of surface filename is. It can be:

  • stern_layer: surface interfacer stern layer with solvent.

  • dielectric_interface:

    • In Poisson Boltzmann applications: surface interfaces low dielectric (inside protein) and high dielectric (outside protein).
    • In LSPR applications: surface interfaces dielectric inside the particle and the dielectric of the medium.

  • internal_cavity: surface is an internal cavity (a result of ‘-all_components’ flag in MSMS). This is important to specify because by default MSMS changes the vertex ordering for internal cavities.

  • dirichlet_surface: surface of specified potential. The value of this potential is read from a text file which has to be specified next to ‘dirichlet_surface’. (See .phi0 file in example).

  • neumann_surface: surface of specified potential. The value of this potential is read from a text file which has to be specified next to ‘neumann_surface’. (See .phi0 file in example).

FIELD: specifies physical parameters of the different regions. Parameters:

  • LorY: 1: Laplace, 2: Yukawa
  • E?: 1: calculate the energy in this region 0: don’t calculate energy in this region Note: if region is surrounded by a dirichlet or neumann surface, surface energy will be calculated.
  • Dielec: Dielectric constant
  • kappa: reciprocal of Debye length
  • charges?: 0: No charges inside this region 1: There are charges in this region
  • coulomb?: 0: don’t calculate coulomb energy in this region 1: calculate coulomb energy in this region
  • charge_file: location of the ‘.pqr’ file with the location of the charges
  • Nparent: Number of ‘parent’ surfaces (surface containing this region) Of course, this is either 1 of 0 (if it corresponds to the infinite region)
  • parent: file of the parent surface mesh, according to their position in the FILE list, starting from 0 (eg. if the mesh file for the parent is the third one specified in the FILE section, parent=2)
  • Nchild: number of child surfaces (surfaces completely contained in this region).
  • children: position of the mesh files for the children surface in the FILE section

WAVE: Only applicable in LSPR problems. It specifies physical parameters of the incoming electric field in LSPR applications. Parameters:

  • Efield: electric field intensity, it is in the ‘z’ direction, ‘-‘ indicates ‘-z’.
  • Wavelength: wavelength of the incident electric field, in Ångström.

Parameters file format

  • Precision: double or float. (float not supported yet!).
  • K: number of Gauss points per element (1, 3, 4, and 7 are supported).
  • Nk: number of Gauss points per triangle edge for semi-analytical integration.
  • K_fine: number of Gauss points per element for near singular integrals.
  • threshold: defines region near singularity where semi-analytical technique is used. if sqrt(2*Area)/r > threshold, integration is done semi-analytically.
  • BSZ: CUDA block size.
  • restart: number of iterations for GMRES to do restart.
  • tolerance: GMRES tolerance.
  • max_iter: maximum number of GMRES iterations.
  • P: order of expansion in treecode.
  • eps: epsilon machine.
  • NCRIT: maximum number of boundary elements per twig box of tree structure.
  • theta: multipole acceptance criterion of treecode.
  • GPU: 0: don’t use GPU. 1: use GPU.