Metadynamics

Navigation: Documentation / Methods / Metadynamics

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Contents

• MTD:Description
• MTD:Controls
• MTD:Collective variables
• MTD:Post-processing
• MTD:Multiple walkers approach
• MTD:Utilities
• MTD:Examples

Description

Single mode

Single mode of metadynamics follows same common rules as all other PMFLib methods (same definition of CVs, same syntax). It has peculiar sections

SubSection [mtd] in {PMFLIB} section with general metadynamics setup common for whole run (example follows):

 [mtd]
 fmode  1                                                                                                                                  
 fserverkey server.key                                                                                                                      
 fsample 100                                                                                                                                
 fheight 0.01                                                                                                                               
 frestart on

Section {MTD} defining particular configuration for each CV (example follows):

 {MTD}                                                                                                                                      
 [CV]                                                                                                                                       
 name d1                                                                                                                                    
 min_value    5.0                                                                                                                           
 max_value   30.0                                                                                                                           
 nbins      100                                                                                                                             
 width        0.5

Multiple walker mode

Server has to be run and available during all calculation (submit to apropriate queue). Any number of clients that connect to server with results.

Server

mtd-admin - Admin program, is able to connect to server and submit commands to server. Available commands are:

 info     = prints information about registered clients
 flush    = saves accumulated MTD data on server side
 get      = gets accumulated MTD data and saves them locally
 shutdown = stops server execution
 errors   = prints errors from server stack

See mtd-admin help for more info.

mtd-server - is multiple walker metadynamics server program. It requires input file with sections and keywords mentioned below:

Section [server]

Server key file name (serverkey) = server.key

Do not automatically shutdown (donotshutdown) = false (default)

Listening queue length (maxqueuelen) = 30 (default)

Max number of worker threads (maxthreads) = 5 (default)

Section [watcher]

Watcher service is enabled (enabled) = true (default)

Flush dead clients interval (deadinterval) [s] = 3600 (default)

Flush error stack interval (errorinterval) [s] = 30 (default)

Error log file (logname) = errors.log (default)

Section [files]

Input history potential (input) = none (default)

Output history potential (output) = _mtdserver.rst (default)

Client

Client setup is analogous to one in single mode, it contains section [mtd] and extra definition section [mtd-walker] with keyword fserverkey and server key file has to be accesible to client (via it can connect to client):

 [mtd-walker]
 fserverkey server.key