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Run dfttk with dfttk run command

usage: dfttk run [-h] [-f STRUCTURE_FOLDER] [-mh MATCH_PATTERN] [-s SETTINGS]
                 [-r] [-wf WORKFLOW] [-l] [-m [MAX_JOB]] [-o]

The help of dfttk run command, please ref. Help for dfttk run command or simply run dfttk run -h

All the examples is run under current folder (get_started)

get_started
 NaCl.cif
 NotSupportFile
 POSCAR
 test_folder
     Fe3Ni.cif
     Fe3Ni-settings.yaml
     POSCAR
     POSCAR-2
     SETTINGS-POSCAR.yaml
     SETTINGS.yaml
     sub_folder
         POSCAR

Run dfttk for a single structure or a single folder

-f parameter, specify the structure or folder containing structure

dfttk run -f STRUCTURE/STRUCTURE_FOLDER

  • When the parameter value of -f is a file it run this file; if it is a folder, it will search all supported files in the specified folder.

  • It support POSCAR, CONTCAR, CHGCAR, LOCPOT, cif, vasprun.xml, pymatgens structures, mcsqs’s structure, more details, ref pymatgen.core.structure.IStructure.from_file

    • For POSCAR or CONTCAR, the name should be *POSCAR* or *CONTCAR* or *.vasp

    • For CHGCAR or LOCPOT, the name should be *CHGCAR* or *LOCPOT*

    • For cif, the name should be *.cif* or *.mcif*

    • For vasprun.xml, the name should be vasprun*.xml*

    • For pymatgen’s structure, the name shold be *.json or *.yaml

    • For atat’s structure, the name should be *rndstr.in* or *lat.in* or *bestsqs*

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Write out the workflow

-o parameter, write out work flow

  • When add -o parameter, the work flow for every structure will be write out

  • The file name of the work flow is dfttk_wf- + filename of the structure + .yaml (e.g. dfttk_wf-POSCAR.yaml)

    dfttk run -f POSCAR -o

    It will write out the work flow in current folder as dfttk_wf-POSCAR.yaml

  • The file will write out in the same folder with corresponding structure.

    dfttk run -f ./test_folder/POSCAR -o

    It will write out the work flow as ./test_folder/dfttk_wf-POSCAR.yaml

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Run dfttk for a folder and its sub-folder

-r parameter, recursive the folder

-mh parameter, specify the match pattern

  • Add -r parameter, it will searching the folder (specified by -f parameter) and its sub-folder

    dfttk run -f . -r

    It will run the following structure

    get_started/NaCl.cif
get_started/POSCAR
get_started/test_folder/Fe3Ni.cif
get_started/test_folder/POSCAR
get_started/test_folder/POSCAR-2
get_started/test_folder/sub_folder/POSCAR

  • Add -mh parameter, it will filter the filename by the value of -mh, the pattern should be placed in quotes (’’ or “”)

dfttk run -r -mh '*.cif'

It will run the following structure

get_started/NaCl.cif
get_started/test_folder/Fe3Ni.cif

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Run dfttk with individual settings

-s parameter, specify the name for settings, default: SETTINGS

  • SETTINGS.yaml or SETTINGS.json: The global settings for current folder

  • SETTINGS-*.yaml(json) or *-SETTINGS.yaml(json): The individual settings, * is the name of the structure (without ext)

  • Case insensitive. (both SETTINGS and settings are OK)

  • The value of -s parameter will replace SETTINGS.

  • Examples:

    dfttk run -f test_folder -s set

    It will take ./test_folder/Fe3Ni-SET.yaml as setting file, and ./test_folder/Fe3Ni-settings.yaml will not taken as setting file.

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Submit job to launchpad and queue system

-l parameter, launch to launchpad

-m parameter, launch to queue system and determine the number of jobs

  • Add -l parameter, it will submit the job to launchpad

  • Add -m N parameter, it will submit the job to queue system. N specifies the number of jobs run at the same time. (Note: This only work when -l parameter is added.)

    dfttk run -l
dfttk run -l -m 1
dfttk run -l -m 2

    • When -m 1, it will run qlaunch singleshot (fireworks command)

    • When -m N (N>1), it will run qlaunch rapidfire -m N (fireworks command)

    • For more details, please ref. Fireworks: Launch Rockets through a queue

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Run dfttk with python script

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Help for dfttk run command

dfttk run -h

DFTTK version: 0.1+98.ge7aa39c.dirty
Copyright  Phases Research Lab (https://www.phaseslab.com/)

usage: dfttk run [-h] [-f STRUCTURE_FOLDER] [-mh MATCH_PATTERN] [-s SETTINGS]
                 [-r] [-wf WORKFLOW] [-l] [-m [MAX_JOB]] [-o]

optional arguments:
  -h, --help            show this help message and exit
  -f STRUCTURE_FOLDER, --structure_folder STRUCTURE_FOLDER
                        The folder/file containing the structure, Default: '.'
  -mh MATCH_PATTERN, --match_pattern MATCH_PATTERN
                        The match pattern for structure file, e.g. *POSCAR*,
                        Default: * -- everything except SETTING files, ref. -s
  -s SETTINGS, --setting SETTINGS
                        Specify the name of SETTINGS files (yaml or json file)
                        Default: SETTINGS (case insensitive and without ext)
                        The following filename will be treat as SETTINGS file
                        SETTINGS (global settings in the folder) Start with
                        SETTINGS- (individual settings for struct) End with
                        -SETTINGS (individual settings)
  -r, --recursive       Recursive the path.
  -wf WORKFLOW, --workflow WORKFLOW
                        Specify the workflow to run. Default: get_wf_gibbs
                        (NOTE: currently, only get_wf_gibbs is supported.)
  -l, --launch          Launch the wf to launchpad
  -m [MAX_JOB], --max_job [MAX_JOB]
                        Run the job, only works when -l is specified. Default:
                        0 (Not submit to queue) 1: qlaunch singleshot (single
                        job) N(N>1): qlaunch rapidfire -m N
  -o, --write_out_wf    Write out the workflow

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