TABLE OF CONTENTS
::pwtk::neb_refine
SYNOPSIS
proc ::pwtk::neb_refine {args} {
USAGE
::pwtk::neb_refine ?-nebi NEBI ?-crd CRD? ?-path PATH? \
?-CI_scheme SCHEME? ?-CI INDEXES? ?-CI_thr THRESHOLD? \
FIRST_IMAGE LAST_IMAGE NEW_PREFIX NUM_OF_IMAGES
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 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
- NEW_PREFIX -- prefix used for the new refinement neb.x calculation
- NUM_OF_IMAGES -- number of images for the new refinement neb.x calculation
- 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
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
set narg 4 set usage "firstImage lastImage 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_ }