Module for flexibility.
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subroutine | new_flexible (this, plist_flex) |
| Constructor flexible
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subroutine | delete_flexible (this) |
| Destructor flexible. More...
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subroutine | init_flexible_freq (this) |
| Initialize or reinitialze the time for the next change in conformation : time_next_flex. More...
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subroutine | new_list_flex (this, flex_method_str, list_conf_fname, total_conf, initial_conf, nearest_ngb, frequence, std_freq) |
| Constructor of list_flexible. More...
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subroutine | delete_listflex (this) |
| Delete the full list and the associated sogrid. More...
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subroutine | delete_last_dataflex (this, status) |
| Deleta the last node of the list and the associated sogrid. More...
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subroutine | delete_first_dataflex (this, status) |
| not used until now, to delete ??
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subroutine | insert_sogrid (this, p_sogrid, head, status) |
| Insert a new sogrid and create a new node. More...
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recursive integer function | associate_to_conformation (this, pnew_node, nb_conf, counter, shift_conf) |
| Associate pointer pnew_node to the conformation number. More...
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subroutine | change_conf_flex (this, conf_nb, shift_conf_opt) |
| Update the p_current_node of flex to conformation nb_conf (== -1 random ) or shift_conf ( +/- 1 ) More...
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integer, parameter | flex_intern = 0 |
| enumeration of node's state for the list
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integer, parameter | flex_first = 1 |
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integer, parameter | flex_last = 2 |
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integer, parameter | flex_random = 0 |
| enumeration for the algorithm
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integer, parameter | flex_metropolis = 1 |
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integer, parameter | flex_minimum = 2 |
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integer, parameter | flex_time = 3 |
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Module for flexibility.
Manage a list of possible conformation ( list of set_of_grid ). define type for flexibility : NodeFlex, list_flex_type and flexible
recursive integer function mod_flexibility::associate_to_conformation |
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type ( nodeflex ), target |
this, |
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type ( nodeflex ), pointer |
pnew_node, |
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integer, intent(in) |
nb_conf, |
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integer, intent(out) |
counter, |
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integer, intent(in) |
shift_conf |
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Associate pointer pnew_node to the conformation number.
set pnew_node to nb_conf or shift ( previous or next ) called by change_conf_flex only, which deals with random numbers
if shift_opt is given moved to a neighbour. if shift not given and nb_conf /= -1, moved to nb_conf using recursive function, needed to loop throught the list.
- Parameters
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this | : instance of NodeFlex |
pnew_node | : pointer to the NodeFlex, associated if status == 0 |
nb_conf | : specify the conformation number, used if shift_conf == 0 |
counter | : return the current conformation in the case nb_conf is specified explictely |
shift_conf | : if 1 or -1, points to the next or previous node. if 0 use nb_conf |
subroutine mod_flexibility::change_conf_flex |
( |
type ( flexible ) |
this, |
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integer, intent(in) |
conf_nb, |
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integer, optional |
shift_conf_opt |
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Update the p_current_node of flex to conformation nb_conf (== -1 random ) or shift_conf ( +/- 1 )
if shift_conf_opt present ( +1 / -1) limited to +/- 1 not present, do not use shift both cases if conf_nb == -1 random if shift ( can be the same) full random (can be the same ) if conf_nb /= -1 and shift_conf is not present : specify the conformation number exactly
- Parameters
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this | : instance of flexible |
conf_nb | : new conformation number |
conf_nb | : conformation number, if == -1, random |
shift_conf_opt | : optionaly if conf_nb different of -1 (=0) apply the given shift |
subroutine mod_flexibility::delete_flexible |
( |
type ( flexible ) |
this | ) |
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Destructor flexible.
Deallocate array for statistics, nullify the pointer ( no deletion of sogrid )
- Parameters
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subroutine mod_flexibility::delete_last_dataflex |
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type ( list_flex_type ) |
this, |
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integer, intent(out) |
status |
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Deleta the last node of the list and the associated sogrid.
- Parameters
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subroutine mod_flexibility::delete_listflex |
( |
type ( list_flex_type ) |
this | ) |
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Delete the full list and the associated sogrid.
- Parameters
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subroutine mod_flexibility::init_flexible_freq |
( |
type ( flexible ) |
this | ) |
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Initialize or reinitialze the time for the next change in conformation : time_next_flex.
if std_freq_random > 0, add a random variable else use exactly frequence
- Parameters
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subroutine mod_flexibility::insert_sogrid |
( |
type ( list_flex_type ) |
this, |
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type ( sogrid ), pointer |
p_sogrid, |
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logical, intent(in) |
head, |
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integer |
status |
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Insert a new sogrid and create a new node.
Could increment the size here
- Parameters
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this | : instance of list_flex_type |
p_sogrid | : pointer to the sogrid to insert |
head | : if true insert first position, if false last position |
status | : for error report, not used |
subroutine mod_flexibility::new_flexible |
( |
type ( flexible ) |
this, |
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type ( list_flex_type ), target |
plist_flex |
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Constructor flexible
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Called by mod_protein::set_flexible
The list of conformation should be independently created with new_list_flex
Allocate the array for the statistics
- Parameters
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this | : instance of a flexible |
plist_flex | : the list of sogrid to associate to flexible |
subroutine mod_flexibility::new_list_flex |
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type ( list_flex_type ) |
this, |
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character ( 128 ) |
flex_method_str, |
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character ( 128 ) |
list_conf_fname, |
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integer |
total_conf, |
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integer |
initial_conf, |
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logical |
nearest_ngb, |
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real ( kind=4 ) |
frequence, |
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real ( kind=4 ) |
std_freq |
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Constructor of list_flexible.
- Parameters
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this | : instance of a list_flex_type |
flex_method_str | : "metropolis", "random", "time" or "minimum" |
list_conf_fname | : name of the input file with all conformations |
total_conf | : total number of conformations |
initial_conf | : specifies if a particular conformation is choosen at the start of a new trajectory |
nearest_ngb | : logical, nearest neigbour only |
frequence | : time for changing conformation |
std_freq | : variance in the frequence |
The documentation for this module was generated from the following file: