Skip to content

RammVI/Error-Formulation

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

34 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Error-Formulation

Refines grids obtained from MSMS or NanoShaper, based on adjoint error formulations of the Solvation Energy.

Requirements

The following softwares are needed to run this code.

  • python2.7
  • BEMPP v2.0
  • FETK package installed in the Software folder
  • MSMS and NanoShaper installed

Usage

  • Example:
python2 main.py -M=meth_test -D=2.0 -N_it=3 -E=E_u

For more options run

python2 main.py -h

The code allows to change a lot of parameters of the process, which are listed on the help section.

Output data

The main.py rutine requires that at least the user has a .pdb or .pqr file in Molecule/{name}/{name}.pdb or Molecule/{name}/{name}.pqr, then two grids with {dens} and 40.0 elements are created. This last one is used for the smoothing option, and may be replaced in the future by a geometry extrapolation.

This process will generate a sequence of grids in .msh format, and a sequence of local error in .vtk format. Also will save the total electrostatic potential, in both spaces, the marked elements to be refined.

The local error will be saved in a file named as \Molecule{mol_name}{mol_name}_{dens}-{N_it}_N_ref-{N_ref}.vtk

Warnings

Avoid using -N_ref grather than 4. RAM memory usage will be arround x4 times higher each time and the process can crash the computer, also, the number of iterations for solving phi when increasing this factor raises significally.

About

Excecutable files to create optimal grids

Topics

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published