TABLE OF CONTENTS


::pwtk::neb_refine_auto

SYNOPSIS

proc ::pwtk::neb_refine_auto {args} {

USAGE

   ::pwtk::neb_refine_auto ?OPTIONS?  NEW_PREFIX  NUM_OF_IMAGES

   where OPTIONS are:

      -nebi NEBI
      -crd  CRD
      -path PATH
      -CI_scheme SCHEME
      -CI        INDEXES
      -CI_thr    THRESHOLD

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., PREFIX.path, where the PREFIX is obtained from the value of the 'prefix' variable in the current CONTROL namelist (if the -nebi option was given, then 'prefix' is taken from the provided input).

For the refined NEB calculation, 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 files of the 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

OPTIONS

Rules:

RETURN VALUE

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_ 
}