mod_geometry Module Reference

Define a base class geometry and derivatives : sphere or box. More...

Data Types
type	sphere
	Derived class sphere. More...
type	box
	Derived class box. More...
type	geometry
	geometry is a base (common base ) class More...

Functions/Subroutines
subroutine	init_geometry (this, pbc, escape, surface, c_surf, xmin, xmax, ymin, ymax, zmin, zmax, start_pos, record_startpos, min_height, half_sphere)
	Allocate the geometry. More...
subroutine	delete_geometry (this)
	Delete geometry. More...
subroutine	get_parameters (this, params_tmp)
	Get parameters of the geometry object. More...
subroutine	update_translation (this, translation, new_pos, cell)
	Update the translation and apply all border conditions, PBC. Sort of "virtual" function, call the appropiate update of sphere or box. Escape could be checked here. to see later. . More...
subroutine	init_geometry_sphere (this, b_surf, c_surf)
	Create sphere, should be called by geometry. More...
subroutine	get_parameters_sphere (this, param2s)
	Get parameters of the spehere. More...
subroutine	init_geometry_box (this, xmin, xmax, ymin, ymax, zmin, zmax)
	Update translation in case of sphere. More...
subroutine	get_parameters_box (this, params)
	Get parameters in case of box. More...
subroutine	update_translation_box (this, translation, new_pos, pbc, surf, cell)
	Apply the translation with box. Take into account periodicity and surface. More...

Variables
integer, parameter	enum_sphere = 1
	enumeration type More...
integer, parameter	enum_box = 2

Detailed Description

Define a base class geometry and derivatives : sphere or box.

Cannot really define a base and derivatives classes, but creates an gemetry object where only the sphere or the box object will be instanciated

Different border conditions can be applied to the box
Normally PBC apply in 3 dimension ( sdamm case )
It is modified in the presence of a surface

For more details see group PBC

Function/Subroutine Documentation

delete_geometry()

subroutine mod_geometry::delete_geometry

(

type ( geometry )

this

)

Delete geometry.

Delete the appropriate derived class

Parameters

this	: instance of geometry

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get_parameters()

subroutine mod_geometry::get_parameters	(	type ( geometry )	this,
		real ( kind=4 ), dimension(6)	params_tmp
	)

Get parameters of the geometry object.

Call appropriate derived class

Parameters

this	: instance of geometry
params_tmp	: array to store the results

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get_parameters_box()

subroutine mod_geometry::get_parameters_box	(	type ( box )	this,
		real ( kind=4 ), dimension(6), intent(out)	params
	)

Get parameters in case of box.

Should be called by geometry

Parameters

this	: instance of box
params	: return array to store the parameters, use all 6 for sphere

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get_parameters_sphere()

subroutine mod_geometry::get_parameters_sphere	(	type ( sphere )	this,
		real ( kind=4 ), dimension(6), intent(out)	param2s
	)

Get parameters of the spehere.

Should be called by geometry

Parameters

this	: instance of sphere
param2s	: return array with parameters, only 2 over 6 are filed with sphere

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init_geometry()

subroutine mod_geometry::init_geometry	(	type ( geometry )	this,
		logical, intent(in)	pbc,
		logical, intent(in)	escape,
		logical, intent(in)	surface,
		real ( kind=4 ), intent(in)	c_surf,
		real ( kind=4 ), intent(in)	xmin,
		real ( kind=4 ), intent(in)	xmax,
		real ( kind=4 ), intent(in)	ymin,
		real ( kind=4 ), intent(in)	ymax,
		real ( kind=4 ), intent(in)	zmin,
		real ( kind=4 ), intent(in)	zmax,
		real ( kind=4 ), intent(in)	start_pos,
		logical, intent(in)	record_startpos,
		real ( kind=4 ), intent(in)	min_height,
		logical, intent(in)	half_sphere
	)

Allocate the geometry.

The type of geometry type must be setup before the call to this function

It can be set first with enum_sphere or enum_box

Parameters

this	: instance of geometry
pbc	: if periodic boundary conditions should apply
escape	: if solute(s) can escape
surface	: if the simulation contains a surface ( modify the computation of distances )
c_surf	: b and c surface for sphere geometry
xmin,xmax,ymin,ymax,zmin,zmax	: position of the box
start_pos	: if a particular position is needed at start up ( should apply both with box and sphere )
record_startpos	: record the start and end positions of two solute simulations in PDB format

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init_geometry_box()

subroutine mod_geometry::init_geometry_box	(	type ( box )	this,
		real ( kind=4 )	xmin,
		real ( kind=4 )	xmax,
		real ( kind=4 )	ymin,
		real ( kind=4 )	ymax,
		real ( kind=4 )	zmin,
		real ( kind=4 )	zmax
	)

Update translation in case of sphere.

Should be called by geometry
In case of sphere do nothing Create box

Assign the dimension of the box. The sizebox is computed

Parameters

this	: instance of geometry
xmin,xmax,ymin,ymax,zmin,zmax	: the position of the box

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init_geometry_sphere()

subroutine mod_geometry::init_geometry_sphere	(	type ( sphere )	this,
		real ( kind=4 ), intent(in)	b_surf,
		real ( kind=4 ), intent(in)	c_surf
	)

Create sphere, should be called by geometry.

Assign b and c surface

Parameters

this	: instance of sphere
b_surf,c_surf	: values of b and c surfaces

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update_translation()

subroutine mod_geometry::update_translation	(	type ( geometry )	this,
		real ( kind=8 ), dimension (3), intent(in)	translation,
		real ( kind=8 ), dimension (3), intent(out)	new_pos,
		integer, dimension (3), intent(inout)	cell
	)

Update the translation and apply all border conditions, PBC.
Sort of "virtual" function, call the appropiate update of sphere or box.
Escape could be checked here. to see later.
.

Parameters

this	: instance of geometry
translation	: new position of the solute before treatment
new_pos	: new position of the solute after treatment ( PBC or reflective boundaries )
cell	: box information update, used with PBC (box ) of the solute

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update_translation_box()

subroutine mod_geometry::update_translation_box	(	type ( box )	this,
		real ( kind=8 ), dimension (3), intent(in)	translation,
		real ( kind=8 ), dimension (3), intent(out)	new_pos,
		logical, intent(in)	pbc,
		logical, intent(in)	surf,
		integer, dimension (3), intent(inout)	cell
	)

Apply the translation with box. Take into account periodicity and surface.

Normally PBC apply in 3 dimension for box
If a surface is present, there is reflective border on zmax

Function similar in compute_distance.f90. See if we can merge
May add escape ??

Parameters

this	: instance of box
translation	: position of the solute before treatment of periodicity
new_pos	: return the new position after periodicity and border condition
pbc	: if pbc should apply
surf	: if a surface is present
cell	: box information for solutes

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Variable Documentation

enum_box

integer, parameter mod_geometry::enum_box = 2

enum_sphere

integer, parameter mod_geometry::enum_sphere = 1

enumeration type