mod_grid.f90 File Reference

Data Types
type	mod_grid::type_uhbd_grid
type	mod_grid::type_dtgrid
type	mod_grid::type_grid
	Contains all data related to grid. More...

Modules
module	mod_grid
	Module for dealing with 3 dimensional grids.

Functions/Subroutines
subroutine	mod_grid::allocate_grid (this, xmax, ymax, zmax, opt_logical)
	Allocate grid.
subroutine	mod_grid::allocate_grid_uhbd (this, xmax, ymax, zmax, be_logical)
	Allocate the 3d imensional uhbd grid.
subroutine	mod_grid::allocate_dtgrid (this, filename, scfct, be_logical)
subroutine	mod_grid::delete_grid (this)
	Delete the grid.
subroutine	mod_grid::delete_uhbd_grid (this)
	Delete UHBD grid Called by delete_grid.
subroutine	mod_grid::delete_dtgrid (this, be_logical)
logical function	mod_grid::is_associated (this)
	function to test if the 3d grid is correctly initiliazed
integer function	mod_grid::is_associated_int (this)
	function to test the type of grid variant return type_of_grid
subroutine	mod_grid::read_grid (this, filename, grid_type_opt, scfct_opt, read_header_only_opt, iform_opt)
	Read grid file.
real(kind=8) function	mod_grid::get_value_real_uhbd (this, i, j, k)
	Test for uhbd and dtgrid.
real(kind=8) function	mod_grid::get_value_dtgrid (this, i, j, k)
	Get the value at a point of a dtgrid.
logical function	mod_grid::get_value_exclusion_dtgrid (this, i, j, k)
subroutine	mod_grid::get_voxel_dtgrid (this, i, j, k, voxel)
real(kind=8) function	mod_grid::get_value (this, i, j, k)
	Test function.
subroutine	mod_grid::copy_grid (this, outgrid, opt_form)
	Copy a grid.
subroutine	mod_grid::grid_scale (this, scaling)
	Multiply all grid points by a scaling factor.
subroutine	mod_grid::exclude (this, exclud_grid)
	Exclude potential interior of grid solute.
subroutine	mod_grid::make_sphere (this)
	Set to 0. all points further than a cutoff. The cutoff is the maximum shpere we can include inside the cube.
subroutine	mod_grid::set_grid_zero (this)
subroutine	mod_grid::test_format_grid (this, io_unit)
	Error in make ep_grid, grdflag is a good variable for binary or ascii, but works only if created by module no rules for uhbd ( 1 ) or apbs ( -1 ) use title of electrostatic grid to decide by default in sda, force to read in binary, can be changed now.
subroutine	mod_grid::read_header_grid (this, io_unit, status)
	Read header of the file.
subroutine	mod_grid::write_grid (this, filename, opt_modif_name, opt_pgrid4)
	Write a grid to a file.
subroutine	mod_grid::write_uhbd_grid (this, base, filename, opt_pgrid4)
	Write UHBD grid to a file Called by write_grid.
subroutine	mod_grid::read_excl_grid (this, filename, prot_cm, param_probe, status)
	Specific function for reading an exclusion grid.
subroutine	mod_grid::write_excl_grid (this, filename, prot_cm, param_probe)
	Write exclusion grid.
subroutine	mod_grid::write_grid_dx (this, filename, opt_modif_name)
	Write grid to dx format.
subroutine	mod_grid::print_grid (this, io_unit)
	Print information about the grid into a log file.
integer function	mod_grid::get_gridtype (this)
	Return the grid type as defined in mod_gridtype.
subroutine	mod_grid::shift_origin (this, center)
	Shift the origin of the grid to the given position.
subroutine	mod_grid::print_origin (this)
	Print origin, for debug.
subroutine	mod_grid::info_grid (this)
	Print information about the grid, may extend.

Variables
integer, parameter	mod_grid::enum_uhbd = 1
integer, parameter	mod_grid::enum_dtgrid = 2

Detailed Description

Version

{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Please send your contact address to get information on updates and new features to "mcmsoft@h-its.org". Questions will be answered as soon as possible.

References: see also http://mcm.h-its.org/sda7/do:c/doc_sda7/references.html:

Brownian dynamics simulation of protein-protein diffusional encounter. (1998) Methods, 14, 329-341.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of computational chemistry 36.21 (2015): 1631-1645.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, X. Yu, M. Ozboyaci, M. Reinhardt, P. Friedrich, R.R.Gabdoulline, S.Richter and R.C.Wade

---

Define 3D UHBD