TABLE OF CONTENTS
::pwtk::neb_refine
SYNOPSIS
proc ::pwtk::neb_refine {args} {
USAGE
::pwtk::neb_refine ?OPTIONS? FIRST_IMAGE LAST_IMAGE 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.
This command is typically called after a converged neb.x calculation (called previous-NEB).
This command is similar to the ::pwtk::neb_refine_auto command. The difference is that images to be used in the refined NEB calculation are not automatically determined. Instead, the portion of MEP to be refined needs to be explicitly specified with the FIRST_IMAGE and LAST_IMAGE indices.
ARGUMENTS
- FIRST_IMAGE -- take the image #.firstImage from previous-NEB as the FIRST_IMAGE of the new refinement neb.x calculation
- LAST_IMAGE -- take the image #.lastImage from previous-NEB as the LAST_IMAGE of the new refinement neb.x calculation
- 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
RETURN VALUE
- the name of the neb.x output file, which is neb.$NEW_PREFIX.$CI_scheme.out
SOURCE
printTitle NEB "Refining neb.x MEP" set narg 4 set usage "FIRST_IMAGE LAST_IMAGE NEW_PREFIX NUM_OF_IMAGES" ::pwtk::neb_refine_parse_and_load_ lassign $args firstImage lastImage new_prefix num_of_images # get iTS, Emax, and E(i) foreach {var value} [::pwtk::path::energies $pathFile] { set $var $value } ::pwtk::neb_refine_exe_ }