mod_ljgrid Module Reference

Module to define lennard-jones interaction. More...

Data Types
type	type_ljgrid
type	type_position_atom
	independent, used by other modules could extend with charges More...

Functions/Subroutines
subroutine	allocate_position_atom (this, nb_atoms)
	Allocate array for position of the atoms.
subroutine	copy_position_atom (this, pdest)
	Copy atom position.
subroutine	deallocate_position_atom (this)
	Deallocate p_pos_atom.
subroutine	allocate_ljgrid (this, nb_grids)
	Constructor.
subroutine	copy_ljgrid (this, pdest)
subroutine	deallocate_ljgrid (this, opt_copy_omp)
	Delete lj grid.
subroutine	set_ljgrid (this, filename, nb, fct)
	Set one lennard-jones grid, assign to the nb element of the array.
subroutine	set_atom_lj (this, filename, nb, atom_type)
	Set one atom_type, assign to element nb in array.
subroutine	print_info_ljgrid (this)

Detailed Description

Module to define lennard-jones interaction.

Function/Subroutine Documentation

allocate_ljgrid()

subroutine mod_ljgrid::allocate_ljgrid	(	type ( type_ljgrid )	this,
		integer, intent(in)	nb_grids
	)

Constructor.

Allocate arrays of pointers, nullified by default and still empty New do not allocate the array, easier for tests Will be correctly allocated in function set_lj_X

First allocate both arrays, but asymetric by default, need to test if null or not Later, allocate only needed ?

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allocate_position_atom()

subroutine mod_ljgrid::allocate_position_atom	(	type ( type_position_atom )	this,
		integer, intent(in)	nb_atoms
	)

Allocate array for position of the atoms.

Parameters

this	: instance of mod_ljgrid
nb_atoms	: size of the array, always (3 , nb_atoms )

copy_ljgrid()

subroutine mod_ljgrid::copy_ljgrid	(	type ( type_ljgrid ), intent(in)	this,
		type ( type_ljgrid ), pointer	pdest
	)

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copy_position_atom()

subroutine mod_ljgrid::copy_position_atom	(	type ( type_position_atom ), intent(in)	this,
		type ( type_position_atom ), pointer	pdest
	)

Copy atom position.

Parameters

this	: instance of type_position_atom
pdest	: pointer to the destination of type_position

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deallocate_ljgrid()

subroutine mod_ljgrid::deallocate_ljgrid	(	type ( type_ljgrid )	this,
		logical, intent(in), optional	opt_copy_omp
	)

Delete lj grid.

Parameters

this	: instance of type_ljgrid
opt_copy_omp	: optionaly do not delete the associated sogrid and flexible. Default delete all

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deallocate_position_atom()

subroutine mod_ljgrid::deallocate_position_atom

(

type ( type_position_atom )

this

)

Deallocate p_pos_atom.

Check if associated done inside the destructor

Parameters

this	: instance of type_position_atom

print_info_ljgrid()

subroutine mod_ljgrid::print_info_ljgrid

(

type ( type_ljgrid )

this

)

set_atom_lj()

subroutine mod_ljgrid::set_atom_lj	(	type ( type_ljgrid )	this,
		character, dimension(*), intent(in)	filename,
		integer, intent(in)	nb,
		character, dimension(*), intent(in)	atom_type
	)

Set one atom_type, assign to element nb in array.

First version, read the pdb and extract the psotiosion of the atom

later should accept array from read_pdb, prepare_atom_protein

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set_ljgrid()

subroutine mod_ljgrid::set_ljgrid	(	type ( type_ljgrid )	this,
		character, dimension(*), intent(in)	filename,
		integer, intent(in)	nb,
		real ( kind=8 )	fct
	)

Set one lennard-jones grid, assign to the nb element of the array.

nb indicates which place in array, filename, only the filename

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