mod_flexibility::list_flex_type Type Reference

List of set of grid. More...

Collaboration diagram for mod_flexibility::list_flex_type:

Public Attributes
character(128)	list_conf_fname
	in case of dynamical allocation keep copy of list_name_conf and factor grid, may change
real(kind=8)	distance_max
	store the maximum over all sogrid
logical	implicit
	related to the format of list_conformation.dat should belong to the module, because of reload
integer	max_size_movable_charge
	need to know the maximum size to not reallocate every time should be allocated when reading input,
integer	max_size_movable_atom
type(nodeflex), pointer	p_first
	pointer on first and last node of the list
type(nodeflex), pointer	p_last
real(kind=4)	frequence
	keep all data for update, minimal in term of memory all same type of proteins have the same frequency because sdamm=> asynchroneous update, add own time_frequence to flexible ( each protein ) and use std_freq_random
real(kind=4)	std_freq_random
integer	method_flex
	to deal with the different methods of update, add option for nearest_neighbour
logical	nearest_ngb
integer	total_conf
	for setting total number of conformation and the initial nb at the start of the trajectory
integer	initial_conf
logical	internal
	for turning internal energy calculation on/off
real(kind=8), dimension(:), allocatable	stationary_distribution
	store stationary distribution for internal energy calculations the stationary distribution corresponds to the given weights given each conformation or to the eigenvector with eigenvalue=1 of the transition matrix
logical	imarkov
	to deal with different methods of internal energy calculations
real(kind=8), dimension(:,:), allocatable	transition_matrix
	store transition matrix from markov model

Detailed Description

List of set of grid.

Each group of proteins will point indirectly, by a flexible, to one unique list

Member Data Documentation

distance_max

real ( kind=8 ) mod_flexibility::list_flex_type::distance_max

store the maximum over all sogrid

frequence

real ( kind=4 ) mod_flexibility::list_flex_type::frequence

keep all data for update, minimal in term of memory all same type of proteins have the same frequency because sdamm=> asynchroneous update, add own time_frequence to flexible ( each protein ) and use std_freq_random

imarkov

logical mod_flexibility::list_flex_type::imarkov

to deal with different methods of internal energy calculations

implicit

logical mod_flexibility::list_flex_type::implicit

related to the format of list_conformation.dat should belong to the module, because of reload

initial_conf

integer mod_flexibility::list_flex_type::initial_conf

internal

logical mod_flexibility::list_flex_type::internal

for turning internal energy calculation on/off

list_conf_fname

character ( 128 ) mod_flexibility::list_flex_type::list_conf_fname

in case of dynamical allocation keep copy of list_name_conf and factor grid, may change

max_size_movable_atom

integer mod_flexibility::list_flex_type::max_size_movable_atom

max_size_movable_charge

integer mod_flexibility::list_flex_type::max_size_movable_charge

need to know the maximum size to not reallocate every time should be allocated when reading input,

Todo

need to add max_atom_lj or already included ? to check

method_flex

integer mod_flexibility::list_flex_type::method_flex

to deal with the different methods of update, add option for nearest_neighbour

nearest_ngb

logical mod_flexibility::list_flex_type::nearest_ngb

p_first

type ( nodeflex ), pointer mod_flexibility::list_flex_type::p_first

pointer on first and last node of the list

p_last

type ( nodeflex ), pointer mod_flexibility::list_flex_type::p_last

stationary_distribution

real ( kind = 8 ), dimension(:), allocatable mod_flexibility::list_flex_type::stationary_distribution

store stationary distribution for internal energy calculations the stationary distribution corresponds to the given weights given each conformation or to the eigenvector with eigenvalue=1 of the transition matrix

std_freq_random

real ( kind=4 ) mod_flexibility::list_flex_type::std_freq_random

total_conf

integer mod_flexibility::list_flex_type::total_conf

for setting total number of conformation and the initial nb at the start of the trajectory

transition_matrix

real ( kind = 8 ), dimension(:,:), allocatable mod_flexibility::list_flex_type::transition_matrix

store transition matrix from markov model

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The documentation for this type was generated from the following file:

• mod_flexibility.f90