2-Configuration

Configuration of DFTTK

Content

• Preparation
• Configure all with one command
• Configure separately
  • Configuration for atomate
  • Configuration for pymatgen
• Example
• Validation for configuration
• Help for dfttk config command

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Preparation

For configure dfttk, the following file you need to prepare.

current_folder
├── psp                          [specified by -psp]
│   ├── pseudopotential_content  [required if you didnot configurate pymatgen]
│   └── ...
├── config                       [specified by -c parameter]
│   ├── db.json                  [required]
│   ├── my_launchpad.yaml        [required]
│   ├── FW_config.yaml           [optional]
│   ├── my_fworker.yaml          [optional]
│   └── my_qadapter.yaml         [optional]
└── vaspjob.pbs                  [optional, specified by -q parameter]

After prepared the above required file, simply run dfttk config -all to finish the configuration. If such command successes, you can skip all of the reset part of this documents. If not, please reading the following parts.

• pseudopotential_content:** The vasp pseudopotential.

  • PRL Group Notes: For PRL group, if you use ACI at PSU, you can skip this part, using -aci parameter

  • It can be compressed file (*.tar.gz) or uncompressed folder. The name is handled as follows:

    

    Note: 1. The split can recognize.,-,_,+,=,* and space .

    ​ 2. After split, the name will be a list. The condition e.g contain 52 is the elements' level. It means 52 should be a elements of the list. But US is string level, which means US only need be a sub-string of the elements of the list.

    ​ 3. For compressed file, it support *.tar.gz and *.tar

    ​ e.g. potpaw_PBE, PBE.tar.gz and potpaw_PBE_5254 will be recognized as PBE.

    ​ potpaw_PBE.52 and potpaw_PBE_52 will be recognized as PBE_52

    ​ potUSPP_LDA and POT_LDA_US will be recognized as LDA_US

    After prepare, the file structure should look like as follows:

    Click for details

    e.g. psp
         ├── potpaw_LDA.54.tar.gz
         ├── potpaw_PBE.54.tar.gz
         └── ...
     or: psp
         ├── potpaw_LDA_54
         │   ├── Ac
         │   └── ...
         ├── potpaw_PBE_54
         │   ├── Ac
         │   └── ...
         └── ...

    The original pseudopotential file, please ask those who are in charge of vasp in your group.

• MAPI_KEY: The API key of Materials Project, ref. API KEY

• vaspjob.pbs: The submitting script of your queue system. Currently, only pbs system is supported

• other config files: At least, you need prepare two files, db.json and my_launchpad.yaml. The template is shown in the config folder.

  • For more details, please ref. Configure database connections and computing center parameters

• PRL GROUP NOTES:

  • For db.json and my_launchpad.yaml file, please ask Brandon for help.
  • vaspjob.pbs for ACI can be download from github
  • For pseudopotential, two choices: 1. using the pseudopotentials in ACI account (Using -aci parameter). 2. Download the pseudopotential from group's box(Group Documents/VASP_potential note: only PBE_54 and LDA_54).

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Configure all with one command

• dfttk config -all

• For ACI at PSU user, please use dfttk config -all -aci

  usage: dfttk config [-h] [-all] [-p PATH_TO_STORE_CONFIG] [-a]
                      [-c CONFIG_FOLDER] [-q QUEUE_SCRIPT] [-qt QUEUE_TYPE]
                      [-v VASP_CMD_FLAG] [-mp] [-aci] [-psp VASP_PSP_DIR]
                      [-mapi MAPI_KEY] [-df DEFAULT_FUNCTIONAL]

  The meaning of the parameters, please ref Help for dfttk config command or just run dfttk config -h

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Configure separately

Configuration for atomate

• Config manual, ref Configure database connections and computing center parameters

• dfttk config -a

  usage: dfttk config -a [-p PATH_TO_STORE_CONFIG] [-c CONFIG_FOLDER] [-q QUEUE_SCRIPT] 
                         [-qt QUEUE_TYPE] [-v VASP_CMD_FLAG] 

  The meaning of the parameters, please ref Help for dfttk config command or just run dfttk config -h

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Configuration for pymatgen

• Config manual, ref POTCAR setup in pymatgen

• dfttk config -mp

  usage: dfttk config -mp [-aci] [-p PATH_TO_STORE_CONFIG] [-psp VASP_PSP_DIR] [-mapi MAPI_KEY] 
                      [-df DEFAULT_FUNCTIONAL]

  The meaning of the parameters, please ref Help for dfttk config command or just run dfttk config -h

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Example

dfttk config -all -p test_config -mapi test_api

In test_config folder

test_config
├── config
│   ├── db.json
│   ├── FW_config.yaml
│   ├── my_fworker.yaml
│   ├── my_launchpad.yaml
│   └── my_qadapter.yaml
├── logs
└── vasp_psp
    ├── POT_GGA_PAW_PBE_54
    │   ├──Ac
    │   └── ...
    └── POT_LDA_PAW_54
        ├──Ac
        └── ...

In ~/.bashrc

export FW_CONFIG_FILE=/gpfs/scratch/mjl6505/test/dfttk/tutorial/config/test_config/config/FW_config.yaml

in ~/.pmgrc.yaml

PMG_DEFAULT_FUNCTIONAL: PBE
PMG_MAPI_KEY: test_api
PMG_VASP_PSP_DIR: /gpfs/scratch/mjl6505/test/dfttk/tutorial/config/test_config/vasp_psp

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Validation for configuration

• dfttk config -t

  This command will validate the configuration, and give some error or tips for the incorrect configuration

  dfttk config -t [{all,pymatgen,atomate,none}]

  • Currently only support validation for the configuration of pymatgen

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Help for dfttk config command

dfttk config -h

DFTTK version: 0.1+121.g8fddda3.dirty
Copyright © Phases Research Lab (https://www.phaseslab.com/)

usage: dfttk config [-h] [-all] [-p PATH_TO_STORE_CONFIG] [-a]
                    [-c CONFIG_FOLDER] [-q QUEUE_SCRIPT] [-qt QUEUE_TYPE]
                    [-v VASP_CMD_FLAG] [-mp] [-aci] [-psp VASP_PSP_DIR]
                    [-mapi MAPI_KEY]
                    [-df {LDA,LDA_52,LDA_54,LDA_US,PBE,PBE_52,PBE_54,PW91,PW91_US,Perdew-Zunger81}]
                    [-t [{all,pymatgen,atomate}]]

optional arguments:
  -h, --help            show this help message and exit
  -all, --all           Configure atomate and pymatgen.
  -p PATH_TO_STORE_CONFIG, --prefix PATH_TO_STORE_CONFIG
                        The folder to store the config files. Default: .
                        (current folder)
  -a, --atomate         Configure atomate.
  -c CONFIG_FOLDER, --config_folder CONFIG_FOLDER
                        The folder containing config files, at least contain
                        db.json and my_launchpad.yaml. Default: '.'
  -q QUEUE_SCRIPT, --queue_script QUEUE_SCRIPT
                        The filename of the script for sumitting vasp job. It
                        will search in current folder and sub-folders.
                        Default: vaspjob.pbs
  -qt QUEUE_TYPE, --queue_type QUEUE_TYPE
                        The type of queue system. Note, only pbs is supported
                        now. Default: pbs
  -v VASP_CMD_FLAG, --vasp_cmd_flg VASP_CMD_FLAG
                        The flag to distinguish vasp_cmd to othe commands in
                        queue_script. Default: vasp_std
  -mp, --pymatgen       Configure pymatgen.
  -aci, --aci           Using the pesudopotential on the ACI cluster at PSU.
  -psp VASP_PSP_DIR, --vasp_psp_dir VASP_PSP_DIR
                        The path of pseudopotentials. Default: psp
  -mapi MAPI_KEY, --mapi_key MAPI_KEY
                        The API key of Materials Projects
  -df {LDA,LDA_52,LDA_54,LDA_US,PBE,PBE_52,PBE_54,PW91,PW91_US,Perdew-Zunger81}, --default_functional {LDA,LDA_52,LDA_54,LDA_US,PBE,PBE_52,PBE_54,PW91,PW91_US,Perdew-Zunger81}
                        The default functional. Default: PBE
  -t [{all,pymatgen,atomate}], --test_config [{all,pymatgen,atomate}]
                        Test for configurations. Note: currently only support
                        for pymatgen.