Usage (gui version)

For windows, find Data Postprocessing (ml_post_ui.exe) in marlowe_ui group and click it. Or, type ml_post_ui or ml_post_ui.py on console.

On GUI, select .lst file to be expanded and push Expand button.

Usage (command line version)

To run postprocesseor,

$ ml_post marlowe_result.lst

, or

$ ml_post.py marlowe_result.lst

marlowe_result.lst is the output data by MARLOWE. ml_post.py parses marlowe_result.lst and extracts some contents into marlowe_result.post directory (the output directory is automatically created at same directory of input file).

Data Preview using ParaView

In order to preview the parsed data, a state file for ParaView (http://www.paraview.org) is provided as marlowe_result.post/summary.pvsm. To review it, select File -> Load State to load summary.pvsm file, or, from command line,

$ paraview --state=summary.psvm

usage: ml_post.py [-h] [--cascade-directory-format CASCADE_DIRECTORY_FORMAT]
                  input [output]

positional arguments:
  input                 Input file. '-' for stdin
  output                output data directory to output parsed data. If
                        ommitted, INPUT.post is set for INPUT.lst data file. If
                        input is stdin, this option should be given.

optional arguments:
  -h, --help            show this help message and exit
  --cascade-directory-format CASCADE_DIRECTORY_FORMAT
                        directory form to store data for each cascade, which
                        is created under OUTPUT directory
                        (default: casc{Cascade:05d}-gr{Group:05d}-num{Number:05d})
  -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --logging {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        choose logging level (default : INFO)
  --skip-verbose-textblock-output
                          skip output of verbose text block
  --cascade-table-output {BUNDLE,SEPARATE,BOTH}
                        Select output form for large cascade data tables
                        (ex. description_of_cascade{_all}.csv) (default: BUNDLE)
                          BUNDLE: output as <root>/xxx_all.csv
                          SEPARATE: output as <root>/CASCADE_DIRECTORY_FORMAT/xxx.csv
                          BOTH: BUNDLE and SEPARATE
  --ignore-block-parse-error
                        ignore errors during parsing each text block. This is useful
                        to test whether the blockseparater runs correctly to the end.

  --old-inline-parser   use old inline parser

Output Data Files

The structure of output data is following. Each file is optional and might be missing depending on the configuration of output file.

|
+- RESULT.lst
|      Marlowe Output File (input file for ml_post.py)
|
+- RESULT.post/
    |    Output directory generated by ml_post.py
    |
    +- summary.json
    |      JSON packed data of parsed object.
    |
    +- summary.pvsm
    |      Paraview state file to preview results.
    |
    +- analysis_of_primary_recoil_ranges.csv
    |      Table from "Analysis of Primary Recoil Ranges ( ##### Stopped Particles)"
    |      section.
    |
    +- statistical_analysis_of_data.csv
    |      Table from "Statistical Analysis of Data from  ##### Cascades" section.
    |
    +- description_of_cascade_all.csv
    |      Concatenated data of description_of_cascade.csv for each cascade detail.
    |      (available when --cascade-table-output == {BUNDLE or BOTH}, similar for the below *_all.csv files)
    |
    +- description_of_cascade_primary_recoil_all.csv
    |      Concatenated data of description_of_cascade_primary_recoil.csv for each cascade detail.
    |
    +- distant_iv_pairs_all.csv
    |      Concatenated data of distant_iv_pairs.csv for each cascade detail.
    |
    +- lattice_sites_all.csv
    |      Concatenated data of lattice_sites.csv for each cascade detail.
    |
    +- primary_recoil_ranges_all.csv
    |      Concatenated data of primary_recoil_ranges.csv for each cascade detail.
    |
    +- 00.config.txt
    |      Raw text block data describing configuration data
    |      (this files is always output regardless of --skip-verbose-textblock-output)
    |
    +- 00.final_rangex.txt
    |      (suppressed when --skip-verbose-textblock-output is set, similar for the below 00.*.txt)
    |
    +- 00.final_slavex.txt
    |
    |
    +- 00.final_slavex_atom.txt
    |
    |
    +- 00.final_seqex.txt
    |
    |
    +- 00.final_orgex.txt
    |
    |
    +- casc#####-gr####-num####/
             Detail data for each cascade section. The section starts like,
             "Cascade     1:     Group    1      Number  1"

The content of each cascade directory is ...

|
+- RESULT.lst
|
+- RESULT.post/
    |
    +- casc#####-gr#####-num#####/
        |
        +- cascade.json
        |      JSON packed data of cascade specific information
        |
        +- description_of_cascade.csv
        |      Table entitled with "Detailed Description of the Cascade part {1,2,3} of 3",
        |      which includes the initial and final position and other states of the
        |      knocked-on atoms
        |      (available when --cascade-table-output == {SEPARATE or BOTH}, similar for the below .csv files)
        |
        +- description_of_cascade_primary_recoil.csv
        |      The first line content of description_of_cascade.csv
        |
        +- distant_iv_pairs.csv
        |      Table entitles with "Separations of Distant Interstitial-Vacancy Pairs".
        |      Interstitial and vacancy file numbers are related with those in
        |      description_of_cascade.csv and lattice_sites.csv.
        |      The coordinates of int. and vac. are also shown in this file.
        |
        +- initial_defect_atom.csv
        |      Rasidual defect atoms before collision
        |
        +- initial_defect_lattice.csv
        |      Rasidual defect lattice sites before collision
        |
        +- lattice_sites.csv
        |      Table entitled with "Locations of the Cascade Lattice Sites", which includes
        |      the coordinate of lattice sites involved into the entire cascade process.
        |
        +- primary_recoil_ranges.csv
        |      Taken from "XX Primary Recoil Ranges" section, simple result on final status
        |      of primary recoil
        |
        +- 00.cascade_summary.txt
        |      Raw text data block starts with 'Cascade{d6}:     Group{d5}     Number{d3}'
        |      (suppressed when --skip-verbose-textblock-output is set, similar for the below 00.*.txt)
        |
        +- 00.cascade_detail_initial_defect_lattice.txt
        |
        +- 00.cascade_detail_initial_defect_atom.txt
        |
        +- 00.cascade_detail_projectile.txt
        |
        +- 00.cascade_report_summary.txt
        |
        +- 00.cascade_report_atom.txt
        |
        +- 00.cascade_report_detail_1.txt
        |
        +- 00.cascade_report_detail_2.txt
        |
        +- 00.cascade_report_detail_3.txt
        |
        +- 00.cascade_report_lattice_sites.txt
        |
        +- 00.cascade_rangex.txt
        |
        +- 00.cascade_sequin.txt
        |
        +- 00.cascade_orgiv.txt

The old output form (with --old-inline-parser) is following

|
+- RESULT.lst
|      Marlowe Output File (input file for ml_post.py)
|
+- RESULT.post
    |    Output directory generated by ml_post.py
    |
    +- analysis_of_primary_recoil_ranges.csv
    |      Table from "Analysis of Primary Recoil Ranges ( ##### Stopped Particles)"
    |      section.
    |
    +- description_of_cascade_all.csv
    |      Concatenated data of description_of_cascade.csv for each cascade detail.
    |
    +- distant_iv_pairs_all.csv
    |      Concatenated data of distant_iv_pairs.csv for each cascade detail.
    |
    +- lattice_sites_all.csv
    |      Concatenated data of lattice_sites.csv for each cascade detail.
    |
    +- primary_recoil_ranges_all.csv
    |      Concatenated data of primary_recoil_ranges.csv for each cascade detail.
    |
    +- statistical_analysis_of_data.csv
    |      Table from "Statistical Analysis of Data from  ##### Cascades" section.
    |
    +- summary.json
    |      JSON packed data of parsed object.
    |
    +- summary.pvsm
    |      Paraview state file to preview results.
    |
    +- summary_of_cascade_all.csv
    |      Concatenated data of summary_of_cascade.csv for each cascade detail.
    |
    +- summary_of_cascade_each_atom_all.csv
    |      Concatenated data of summary_of_cascade_each_atom.csv for each cascade detail.
    |
    +- casc#####-gr####-num####
        |    Detail data for each cascade section. The section starts like,
        |    "Cascade     1:     Group    1      Number  1"
        |
        +- cascade_summary.json
        |      JSON packed data of cascade specific information
        |
        +- description_of_cascade.csv
        |      Table entitled with "Detailed Description of the Cascade part 1-3 of 3",
        |      which includes the initial and final position and other states of the
        |      knocked-on atoms
        |
        +- distant_iv_pairs.csv
        |      Table entitles with "Separations of Distant Interstitial-Vacancy Pairs".
        |      Interstitial and vacancy file numbers are related with those in
        |      description_of_cascade.csv and lattice_sites.csv.
        |      The coordinates of int. and vac. are also shown in this file.
        |
        +- lattice_sites.csv
        |      Table entitled with "Locations of the Cascade Lattice Sites", which includes
        |      the coordinate of lattice sites involved into the entire cascade process.
        |
        +- primary_recoil_ranges.csv
        |      Taken from "XX Primary Recoil Ranges" section, simple result on final status
        |      of primary recoil
        |
        +- summary_of_cascade.csv
        |      Taken from "Summary of Cascade  ####:  Group ### Number ###" section.
        |      This table includes summarized data of the single cascade on various numbers
        |      and energies
        |
        +- summary_of_cascade_each_atom.csv
               Taken from "Cascade Summary for XX atoms" section.
               This table shows decomposed data in summary_of_cascade.csv for each atom.

Notes

$ ml_post marlowe_output.lst c:\temp\malrowe_results\20141201-01