mod_grid Module Reference

Module for dealing with 3 dimensional grids. More...

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

Functions/Subroutines
subroutine	allocate_grid (this, xmax, ymax, zmax, opt_logical)
	Allocate grid. More...
subroutine	allocate_grid_uhbd (this, xmax, ymax, zmax, be_logical)
	Allocate the 3d imensional uhbd grid. More...
subroutine	allocate_dtgrid (this, filename, scfct, be_logical)
subroutine	delete_grid (this)
	Delete the grid. More...
subroutine	delete_uhbd_grid (this)
	Delete UHBD grid Called by delete_grid. More...
subroutine	delete_dtgrid (this, be_logical)
logical function	is_associated (this)
	function to test if the 3d grid is correctly initiliazed More...
integer function	is_associated_int (this)
	function to test the type of grid variant return type_of_grid More...
subroutine	read_grid (this, filename, grid_type_opt, scfct_opt, read_header_only_opt, iform_opt)
	Read grid file. More...
real(kind=8) function	get_value_real_uhbd (this, i, j, k)
	Test for uhbd and dtgrid. More...
real(kind=8) function	get_value_dtgrid (this, i, j, k)
	Get the value at a point of a dtgrid. More...
logical function	get_value_exclusion_dtgrid (this, i, j, k)
subroutine	get_voxel_dtgrid (this, i, j, k, voxel)
real(kind=8) function	get_value (this, i, j, k)
	Test function. More...
subroutine	copy_grid (this, outgrid, opt_form)
	Copy a grid. More...
subroutine	grid_scale (this, scaling)
	Multiply all grid points by a scaling factor. More...
subroutine	exclude (this, exclud_grid)
	Exclude potential interior of grid solute. More...
subroutine	make_sphere (this)
	Set to 0. all points further than a cutoff. The cutoff is the maximum shpere we can include inside the cube. More...
subroutine	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. More...
subroutine	read_header_grid (this, io_unit, status)
	Read header of the file. More...
subroutine	write_grid (this, filename, opt_modif_name, opt_pgrid4)
	Write a grid to a file. More...
subroutine	write_uhbd_grid (this, base, filename, opt_pgrid4)
	Write UHBD grid to a file Called by write_grid. More...
subroutine	read_excl_grid (this, filename, prot_cm, param_probe, status)
	Specific function for reading an exclusion grid. More...
subroutine	write_excl_grid (this, filename, prot_cm, param_probe)
	Write exclusion grid. More...
subroutine	write_grid_dx (this, filename, opt_modif_name)
	Write grid to dx format. More...
subroutine	print_grid (this, io_unit)
	Print information about the grid into a log file. More...
integer function	get_gridtype (this)
	Return the grid type as defined in mod_gridtype. More...
subroutine	shift_origin (this, center)
	Shift the origin of the grid to the given position. More...
subroutine	print_origin (this)
	Print origin, for debug. More...
subroutine	info_grid (this)
	Print information about the grid, may extend. More...

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

Detailed Description

Module for dealing with 3 dimensional grids.

Function/Subroutine Documentation

allocate_dtgrid()

subroutine mod_grid::allocate_dtgrid	(	type ( type_dtgrid )	this,
		character*128	filename,
		real ( kind=8 )	scfct,
		logical	be_logical
	)

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allocate_grid()

subroutine mod_grid::allocate_grid	(	type ( type_grid ), intent(inout)	this,
		integer, intent(in)	xmax,
		integer, intent(in)	ymax,
		integer, intent(in)	zmax,
		logical, intent(in), optional	opt_logical
	)

Allocate grid.

Parameters

this	: instance of type_grid
xmax,ymax,zmax	: size of the grid in number of cells
opt_logical	: if values stored are logical. Default real*4 in disk, real*8 in memory

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allocate_grid_uhbd()

subroutine mod_grid::allocate_grid_uhbd	(	type (type_uhbd_grid), intent(inout)	this,
		integer, intent(in)	xmax,
		integer, intent(in)	ymax,
		integer, intent(in)	zmax,
		logical, intent(in)	be_logical
	)

Allocate the 3d imensional uhbd grid.

Called by allocate_grid

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copy_grid()

subroutine mod_grid::copy_grid	(	type ( type_grid )	this,
		type ( type_grid )	outgrid,
		integer, optional	opt_form
	)

Copy a grid.

Used by tools only
Not a real copy, only the members are copied
The pointer will use the original grid
The new grid can modify some data members ( iform, origin ) and write a new version

May add an option real copy, or internal % real_copy, to known if need to delete

Parameters

this	: instance of type_grid, source grid
outgrid	: instance of the target grid
opt_form	: optionaly provides the new format. By default use the source format

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delete_dtgrid()

subroutine mod_grid::delete_dtgrid	(	type ( type_dtgrid )	this,
		logical	be_logical
	)

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delete_grid()

subroutine mod_grid::delete_grid

(

type ( type_grid )

this

)

Delete the grid.

deallocate 3 dimensional grid

Parameters

this	: instance of type_grid

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delete_uhbd_grid()

subroutine mod_grid::delete_uhbd_grid

(

type ( type_uhbd_grid )

this

)

Delete UHBD grid Called by delete_grid.

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exclude()

subroutine mod_grid::exclude	(	type ( type_grid )	this,
		type ( type_grid )	exclud_grid
	)

Exclude potential interior of grid solute.

this is a pointer to the input grid, can be overloaded in this case

Parameters

this	: instance of type_grid, pointer to the input grid called by convert_grid -exclude can be overloaded in this case
exclud_grid	: grid already loaded in convert grid

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get_gridtype()

integer function mod_grid::get_gridtype

(

type (type_grid)

this

)

Return the grid type as defined in mod_gridtype.

get_value()

real ( kind=8 ) function mod_grid::get_value	(	type ( type_grid ), intent(in)	this,
		integer, intent(in)	i,
		integer, intent(in)	j,
		integer, intent(in)	k
	)

Test function.

keep as intermediate, efficient call get directly the value

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get_value_dtgrid()

real ( kind=8 ) function mod_grid::get_value_dtgrid	(	type ( type_dtgrid ), intent(in)	this,
		integer, intent(in)	i,
		integer, intent(in)	j,
		integer, intent(in)	k
	)

Get the value at a point of a dtgrid.

Need a call to C++ function

Parameters

this	: instance of type_dtgrid
i,j,k	: position of the cell

Returns

value : energy

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get_value_exclusion_dtgrid()

logical function mod_grid::get_value_exclusion_dtgrid	(	type ( type_dtgrid ), intent(in)	this,
		integer, intent(in)	i,
		integer, intent(in)	j,
		integer, intent(in)	k
	)

get_value_real_uhbd()

real ( kind=8 ) function mod_grid::get_value_real_uhbd	(	type ( type_uhbd_grid ), intent(in)	this,
		integer, intent(in)	i,
		integer, intent(in)	j,
		integer, intent(in)	k
	)

Test for uhbd and dtgrid.

get_voxel_dtgrid()

subroutine mod_grid::get_voxel_dtgrid	(	type ( type_dtgrid ), intent(in)	this,
		integer, intent(in)	i,
		integer, intent(in)	j,
		integer, intent(in)	k,
		real ( kind=8 ), dimension ( 8 ), intent(inout)	voxel
	)

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grid_scale()

subroutine mod_grid::grid_scale	(	type ( type_grid )	this,
		real ( kind=8 )	scaling
	)

Multiply all grid points by a scaling factor.

Apply only to UHBD grid

Parameters

this	: instance of type_grid
scaling	: multiplicative factor

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info_grid()

subroutine mod_grid::info_grid

(

type (type_grid)

this

)

Print information about the grid, may extend.

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is_associated()

logical function mod_grid::is_associated

(

type ( type_grid ), intent(in)

this

)

function to test if the 3d grid is correctly initiliazed

Will check if the correct pointer is associated

Parameters

this	: instance of type_grid

Returns

is : true or false

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is_associated_int()

integer function mod_grid::is_associated_int

(

type ( type_grid ), intent(in)

this

)

function to test the type of grid variant return type_of_grid

Parameters

this	: instance of type_grid

Returns

is : 1 is UHBD, 2 is dtgrid

make_sphere()

subroutine mod_grid::make_sphere

(

type ( type_grid )

this

)

Set to 0. all points further than a cutoff.
The cutoff is the maximum shpere we can include inside the cube.

Parameters

this	: instance of type_grid

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print_grid()

subroutine mod_grid::print_grid	(	type ( type_grid ), intent(in)	this,
		integer, intent(in)	io_unit
	)

Print information about the grid into a log file.

Write slice of potential in fort.77 as before and convenient for comparing methods

Parameters

this	: instance of type_grid
io_unit	: file descriptor of the output file. Use a log file in sda

print_origin()

subroutine mod_grid::print_origin

(

type (type_grid)

this

)

Print origin, for debug.

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read_excl_grid()

subroutine mod_grid::read_excl_grid	(	type ( type_grid )	this,
		character, dimension(*)	filename,
		real ( kind = 8 ), dimension ( 3 )	prot_cm,
		type ( probe_type )	param_probe,
		logical	status
	)

Specific function for reading an exclusion grid.

Shortcut for exclusion grid. Always logical values Can read UHBD or dtgrid format

Parameters

this	: instance of type_grid
filename	: name of the file
prot_cm	: center of geometry of the pdb file. used to recenter the grid ?? needed ??
param_probe	: instance of probe_type
status	: for error report

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read_grid()

subroutine mod_grid::read_grid	(	type ( type_grid )	this,
		character*128	filename,
		integer, intent(in), optional	grid_type_opt,
		real ( kind=8 ), intent(in), optional	scfct_opt,
		logical, intent(in), optional	read_header_only_opt,
		integer, intent(in), optional	iform_opt
	)

Read grid file.

Parameters

this	: instance of type_grid
filename	: name of the file
grid_type_opt	: optionaly the grid number, mod_gridtype
scfct_opt	: optionaly if a multiplicative factor must be applied to all grid points. Default 1
read_header_only_opt	: optionaly just print information of the header file. Do not load the grid
iform_opt	: optionaly if the file is ascii ( 1 ) or binary ( 0 ). Not necessary for uhbd, will call test_format_grid

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read_header_grid()

subroutine mod_grid::read_header_grid	(	type ( type_grid )	this,
		integer, intent(in)	io_unit,
		integer	status
	)

Read header of the file.

Fill data member with information of the header iform should be set correctly before calling the function

Parameters

this	: instance of type_grid
io_unit	: file descriptor
status	: return error code

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shift_origin()

subroutine mod_grid::shift_origin	(	type (type_grid), intent(inout)	this,
		real ( kind=8 ), dimension(3), intent(in)	center
	)

Shift the origin of the grid to the given position.

Center is the new position of the origin. UHBD uses origin at the lower left corner of the grid

Parameters

this	: instance of type_grid
center	: position of the new origin

test_format_grid()

subroutine mod_grid::test_format_grid	(	type ( type_grid )	this,
		integer	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.

Test the format of a grid file

Test if the grid is writen in binary or ascii format Trick : I use the filed 4 ( called grdflag ) to store this information in the grid writen by this software
Does not apply to electrostatic grids produced by UHBD or APBS. Need to use header content

Parameters

this	: instance of type_grid
io_unit	: file descriptor of the file

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write_excl_grid()

subroutine mod_grid::write_excl_grid	(	type ( type_grid )	this,
		character, dimension(*)	filename,
		real ( kind = 8 ), dimension ( 3 )	prot_cm,
		type ( probe_type )	param_probe
	)

Write exclusion grid.

Parameters

this	: instance of type_grid
filename	: name of the file
prot_cm	: center of geometry of the solute
param_probe	: instance of probe_type

write_grid()

subroutine mod_grid::write_grid	(	type ( type_grid )	this,
		character*128	filename,
		logical, optional	opt_modif_name,
		real ( kind=4 ), dimension (:, :, :), optional, pointer	opt_pgrid4
	)

Write a grid to a file.

If a pointer to a real*4 3d grid is provided in option, its content will be printed into the file
It avoids the conversion and copy from real*4 to real*8
Apply only to UHBD grids

Parameters

this	: instance of type_grid
filename	: name of the file
opt_modif_name	: optionaly if true append a suffix ".bin.grd" or ".ascii.grd"
opt_pgrid4	: optionaly use an external pointer to 3d dimensional grid. Default use type_grid::p_grid

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write_grid_dx()

subroutine mod_grid::write_grid_dx	(	type ( type_grid )	this,
		character*128	filename,
		logical, optional	opt_modif_name
	)

Write grid to dx format.

Used only by the tool read_record

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write_uhbd_grid()

subroutine mod_grid::write_uhbd_grid	(	type ( type_uhbd_grid ), intent(in)	this,
		type ( type_grid ), intent(in)	base,
		character*128, intent(in)	filename,
		real ( kind=4 ), dimension (:, :, :), optional, pointer	opt_pgrid4
	)

Write UHBD grid to a file Called by write_grid.

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Variable Documentation

enum_dtgrid

integer, parameter mod_grid::enum_dtgrid = 2

enum_uhbd

integer, parameter mod_grid::enum_uhbd = 1