mod_onecomplexe Module Reference

Module to define one_complexe Theses objects are stored in record. More...

Data Types
type	one_complexe
	Objects stored in the list ( for complexes ) or in the array ( for trajectory ). More...

Functions/Subroutines
subroutine, public	new_onecomplexe (this, nb_int, nb_real, nb_other_real, opt_ibox)
	Allocate an instance of one_complexe Need only size of variable fields, optional ibox for sdamm.
subroutine	delete_onecomplexe (this)
	Delete onecomplexe.
subroutine	set_onecomplexe (this, position, box, orient_x, orient_y, array_int_compl, array_real_compl, other_real, size_other_real, bit_integer, bit_energy, opt_sum, nb_to_sum)
	Set values of an one_complexe instance.
subroutine	return_compatible_array (this, array_int, array_real, other_real, size_other_real, bit_integer, bit_energy, opt_sum, nb_to_sum)
	Return arrays of data of fixed size.
subroutine	return_array_int (this, array_int, bit_integer)
	Same as return compatible array, only for int_ocompl.
subroutine	return_array_real (this, array_real, bit_energy, opt_sum, nb_to_sum)
	Same as return_compatible_array, only for real_ocompl.
subroutine	update_statistics (this, previous, opt_other_real)
	Update statistics for complexes : occurency, average and std deviation.
subroutine	print_onecomplexe (this)
	Test function, convenient for debug.
subroutine	make_ascii_string (this, string, format_str)
	Make string, send back a string, only for ascii.
subroutine	read_ascii_string (this, string, format_str)
	reading file is done by record or derived, same logic than for writting for binary should change, for both reading and writting....
subroutine	read_binary_string (this, io_file, box_info, io_err)
	For reading binary.
subroutine	write_binary_string (this, io_file, io_err)
	For writing binary.

Detailed Description

Module to define one_complexe Theses objects are stored in record.

Function/Subroutine Documentation

delete_onecomplexe()

subroutine mod_onecomplexe::delete_onecomplexe

(

type ( one_complexe )

this

)

Delete onecomplexe.

Deallocate all arrays

Parameters

this	: instance of one_complexe

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make_ascii_string()

subroutine mod_onecomplexe::make_ascii_string	(	type ( one_complexe )	this,
		character, dimension(*), intent(out)	string,
		character, dimension(*), intent(in)	format_str )

Make string, send back a string, only for ascii.

Give the format string as input, computed only once
Binary need an other function

Parameters

this	: instance of one_complexe
string	: return value
format_str	: format of one line

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new_onecomplexe()

subroutine, public mod_onecomplexe::new_onecomplexe	(	type ( one_complexe )	this,
		integer, intent(in)	nb_int,
		integer, intent(in)	nb_real,
		integer, intent(in)	nb_other_real,
		logical, optional	opt_ibox )

Allocate an instance of one_complexe
Need only size of variable fields, optional ibox for sdamm.

Parameters

this	: instance of one_complexe
nb_int	: size of int_ocompl
nb_real	: size of real_ocompl
nb_other_real	: size of other_real_ocompl
opt_ibox	: optionaly activate the box information

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print_onecomplexe()

subroutine mod_onecomplexe::print_onecomplexe

(

type ( one_complexe )

this

)

Test function, convenient for debug.

Parameters

this	: instance of one_complexe

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read_ascii_string()

subroutine mod_onecomplexe::read_ascii_string	(	type ( one_complexe )	this,
		character, dimension(*), intent(in)	string,
		character, dimension(*), intent(in)	format_str )

reading file is done by record or derived, same logic than for writting for binary should change, for both reading and writting....

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read_binary_string()

subroutine mod_onecomplexe::read_binary_string	(	type ( one_complexe )	this,
		integer, intent(in)	io_file,
		logical, intent(in)	box_info,
		integer, intent(out)	io_err )

For reading binary.

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return_array_int()

subroutine mod_onecomplexe::return_array_int	(	type ( one_complexe )	this,
		integer, dimension ( : ), intent(out)	array_int,
		integer ( kind = 2 ), intent(in)	bit_integer )

Same as return compatible array, only for int_ocompl.

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return_array_real()

subroutine mod_onecomplexe::return_array_real	(	type ( one_complexe )	this,
		real ( kind=8), dimension ( : ), intent(out)	array_real,
		integer ( kind = 2 ), intent(in)	bit_energy,
		logical, intent(in)	opt_sum,
		integer, intent(in)	nb_to_sum )

Same as return_compatible_array, only for real_ocompl.

Extended with nb_types. Convenient if allocate the array inside.
The array should have the correct size, safer if allocated with mod::record::get_nbterms_energy_compatible.

Parameters

this	: instance of one_complexe
array_real	: array to fill, store only valid data
bit_energy	: indicates which information are stored in one_complexe object
opt_sum	: indicates if the sum of the terms must be given or all
nb_to_sum	: number of types of grids

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return_compatible_array()

subroutine mod_onecomplexe::return_compatible_array	(	type ( one_complexe )	this,
		integer, dimension ( : ), intent(out)	array_int,
		real ( kind=8 ), dimension( : ), intent(out)	array_real,
		real ( kind=8 ), dimension( : ), intent(out)	other_real,
		integer, intent(in)	size_other_real,
		integer ( kind=2 ), intent(in)	bit_integer,
		integer ( kind=2 ), intent(in)	bit_energy,
		logical, intent(in)	opt_sum,
		integer, intent(in)	nb_to_sum )

Return arrays of data of fixed size.

Sort of inverse of set_onecomplexe, allow to extract easily the data
bit_integer and bit_energy will provide the information to select the returned data
Extract data from this one_complexe, order and size are fixed ( ntraj, nstep, nprot, nconf...) value is null by default, if not present in one_complexe

Easier to use record % return_compatible_array_wrapper.

Todo

add box information

Need to extend with nb_to_sum, keep same variable name May add aprameter for size of other_real

Parameters

this	: instance of one_complexe
array_int,array_real,other_real	: array filled by the function
size_other_real	: size of array other_real
bit_integer,bit_energy	: information wanted in return of the function
opt_sum	: if the energy terms should be added are kept separate
nb_to_sum	: equal the number of types of solutes

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set_onecomplexe()

subroutine mod_onecomplexe::set_onecomplexe	(	type ( one_complexe )	this,
		real ( kind=8 ), dimension( 3 ), intent(in)	position,
		integer, dimension ( 3 )	box,
		real ( kind=8 ), dimension( 3 ), intent(in)	orient_x,
		real ( kind=8 ), dimension( 3 ), intent(in)	orient_y,
		integer, dimension ( : ), intent(in)	array_int_compl,
		real ( kind=8 ), dimension( : ), intent(in)	array_real_compl,
		real ( kind=8 ), dimension( : ), intent(in)	other_real,
		integer, intent(in)	size_other_real,
		integer ( kind=2 )	bit_integer,
		integer ( kind=2 )	bit_energy,
		logical	opt_sum,
		integer, intent(in)	nb_to_sum )

Set values of an one_complexe instance.

Should be allocated before
Input array from record have a fixed size, only the relevent informations ( gieven by the bits ) are stored in internal array of one_complexe

Parameters

this	: instance of one_complexe
position,box	: position of the complex and box information ( default ( 0, 0, 0) )
orient_x,orient_y	: orientation of the complex
array_int_compl	: to store in int_ocompl
array_real_compl	: to store in real_ocompl
other_real	: to store in other_real_ocompl
size_other_real	: size of array other_real
bit_integer,bit_energy	: bits information
opt_sum	: if the sum of energy terms is required
nb_to_sum	: equal to the number of types in the simulation

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update_statistics()

subroutine mod_onecomplexe::update_statistics	(	type ( one_complexe )	this,
		type ( one_complexe ), pointer	previous,
		real ( kind=8 ), dimension ( : ), optional	opt_other_real )

Update statistics for complexes : occurency, average and std deviation.

By default increase occurency by one with the last energy
if used from merge_trajectory, take into account correctly the previous data ( sum of the square of the energy )
should improve, general occurency, average.,.. and only one loop

Parameters

this	: instance of one_complexe
previous	: pointer to the original one_complexe to be merged in, if not associated update this
opt_other_real	: optional update the other_real terms.

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write_binary_string()

subroutine mod_onecomplexe::write_binary_string	(	type ( one_complexe )	this,
		integer	io_file,
		integer	io_err )

For writing binary.

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