neb_utils.tcl

::pwtk::neb_refine_auto

::pwtk::neb_refine_auto

SYNOPSIS

proc ::pwtk::neb_refine_auto {args} {

USAGE

   ::pwtk::neb_refine_auto ?-nebi NEBI  ?-crd CRD?  ?-path PATH?  \
                           ?-CI_scheme SCHEME?  ?-CI INDEXES?  ?-CI_thr THRESHOLD?  \
                           NEW_PREFIX NUM_OF_IMAGES

PURPOSE

Refine an existing neb.x minimum-energy path (MEP) by using a denser MEP discretezation around the transition-state (TS) image.

This command is typically called after a converged neb.x calculation (called previous-NEB).

The TS image is determined from the previous-NEB path file, i.e., the previous-NEB TS-1, TS, TS+1 images are taken for the new refinement calculation. The algorithm is the following: 1. use the previous-NEB TS-1, TS, TS+1 images as the new

      FIRST_IMAGE, INTERMEDIATE_IMAGE, and LAST_IMAGE

2. fix the FIRST_IMAGE and LAST_IMAGE (aka first_last_opt = .false.) 3. perform a new neb.x calculation with NUM_OF_IMAGES, which

      is specified as the command-line argument.

This command needs the crd and path file of previous-NEB. They can be specified with the command line options. If no options are provided, then all the needed data are taken from the current input data (as specified in the PWTK script prior to calling this command). Otherwise, the options have the following meaning.

ARGUMENTS

NEW_PREFIX -- prefix used for the new refinement neb.x calculation
NUM_OF_IMAGES -- number of images for the new refinement neb.x calculation

OPTIONS

-nebi NEBI ... the neb.x input file of previous-NEB
-crd CRD ... the neb.x crd file of previous-NEB
-path PATH ... the neb.x path file of previous-NEB
-CI_scheme SCHEME ... CI_scheme for the new refined neb.x calculation
-CI INDEXES ... list of indexes of CLIMBING_IMAGES for the new refined neb.x calculation (only used for CI_scheme = 'manual'
-CI_thr THRESHOLD ... the value of path_thr the new refined neb.x calculation

Rules:

'prefix' is obtained from the current CONTROL namelist (if the -nebi option was given, then 'prefix' is taken from the provided input).
if the -crd option was not given, the prefix.crd is assumed for the crd file
if the -path option was not given, the prefix.path is assumed for the path file
if the -CI_scheme option was not given, the current value of CI_scheme is used
if the -CI option was not given, the current CLIMBING_IMAGES card is used
if the -CI_thr option was not given, the current value of path_thr is used

RETURN VALUE

the name of the neb.x output file, which is neb.$NEW_PREFIX.$CI_scheme.out

SOURCE

    printTitle NEB "Auto-refining neb.x MEP"
    
    set narg 2
    set usage "new_prefix num_of_images"

    ::pwtk::neb_refine_parse_and_load_
    lassign $args new_prefix num_of_images

    # get iTS, Emax, and E(i)
    foreach {var datum} [::pwtk::path::energies $pathFile] { set $var $datum }

    set firstImage [expr { $iTS > 1 ? $iTS-1 : $iTS }]
    set lastImage  [expr { $iTS < $nImages ? $iTS+1 : $iTS }]

    ::pwtk::neb_refine_exe_ 
}

TABLE OF CONTENTS

::pwtk::neb_refine_auto