subtom_renumber_motl

Renumbers the particle indices in a motive list, either sequentially or in a way that preserves particle indices while still making sure there are no duplicates in the list of indices.

This MOTL manipulation script uses one MATLAB compiled scripts below:

subtom_renumber_motl

Options

Directories

scratch_dir: Absolute path to the folder with the input to be processed. Other paths are relative to this one.
mcr_cache_dir: Absolute path to MCR directory for the processing.
exec_dir: Directory for executables

Variables

renumber_motl_exec: Renumber motive list executable

File Options

input_motl_fn: Relative path and name of the input MOTL file to be renumbered.
output_motl_fn: Relative path and name of the output MOTL file.

Renumber Options

sort_row: If you want to have the output MOTL file sorted by a particular field before renumbering then specify it here.
do_sequential: If the following is 1, particles will be completely renumbered from 1 to the number of particles in the motive list. If it is 0, particles will be renumbered in a way that preserves the original index while still removing any duplicate indices. As a guide you probably want to renumber sequentially after cleaning from initial oversampled coordinates, but do not want to renumber sequentially in other cases.

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"

renumber_motl_exec="${exec_dir}/MOTL/subtom_renumber_motl"

input_motl_fn="combinedmotl/allmotl_1.em"

output_motl_fn="combinedmotl/allmotl_unique_1.em"

sort_row="4"

do_sequential="0"