explanation of QCLObot YAML File

QCLObot playbook is separated by following two parts:

• “vars” section

  definition of variables

• “tasks” section

  definition of task for general and for frame molecule

“vars” section

Declare the variable. The declared variables can be used with with_items and so on.

vars:
  residues: [27, 28, 48, 97, 101, 108, 248, 547, 558, 559]

tasks:
  - name: frame_{{ item }}
    sp: true
    fragments:
      - name: AA_{{ item }}
        brd_select: /model_1/A/{{ item }}/
      - name: ACE_{{ item }}
        add_ACE: true
        brd_select: /model_1/A/{{ item -1 }}/
      - name: NME_{{ item }}
        add_NME: true
        brd_select: /model_1/A/{{ item +1 }}/
    with_items: residues

Warning

Note that when using templates, especially when operating within a template, there is a distinction between strings and numbers.

“tasks” section

The “tasks” section is consist of three parts:

• condition

• task

• frame definition

condition

with_items

repeat the task.

when

do the task if the condition is satisfied.

include

Insert an external file. Fill in the external file with the “tasks” statement.

tasks:
  - name: include_step1
    include_tasks: "step1.yaml"

task

mail

Send mail.

- name: send_mail
  mail:
    smtp_server: xxx.xxx.xxx.xxx
    smtp_port: xx
    use_SSL: yes
    smtp_account: xxxx
    smtp_password: xxxx
    from_address: xxxx@xxxx.xxxx
    to_address: xxxx@xxxx.xxxx
    subject: 'test mail'
    msg: 'job finished.'

debug

do nothing.

frame

frame definition

name(mandatory)

All frame require the name. Based of this name value, the working directory is created on the current directory.

cmd_alias

Accept values of the dictionary type. Replaces the default external commands. The following commands are currently supported:

• archive

• mat-extend

• mat-mul

• mat-select

• mat-symetrize

• mat-transpose

• mat-diagonal

fragments

A frame molecule consists of fragment(s). The fragment is defined by following keywords. All fragment requires the “name” attribute, which is used as name of the fragment.

• atomlist

atomlist directive makes fragment from atom list

- name: N2
  sp: true
  fragments:
    - name: N2
      atomlist:
        - "N  0.000000   0.000000   0.000000"
        - "N  1.000000   0.000000   0.000000"

The atomlist is an array object. Each atom is defined by string separated white space, or by array object as following:

- name: OH
  sp: true
  fragments:
    - name: OH
      atomlist:
        - [O, -7.328, -30.909,  17.923]
        - [H, -6.026, -31.757,  17.909]

• add_CH3

  If the keyword is defined as yes, a methyl group is add as fragment.

  • displacement

    This atom is substitute with methyl carbon. This value is specified by string as Bridge path.

  • root

    This atom is indicated to the next atom of the displacement atom. This value is specified by string as Bridge path.

    - name: small_mol
      sp: true
      fragments:
        - name: frag1
          add_CH3: true
          displacement: "/model_1/A/100/100_C1"
          root: "/model_1/A/100/100_C2"
    

• add_ACE

Place the acetyl group in the specified place and add it as a fragment.

- name: res_3
  sp: true
  fragments:
    - name: res_3
      brd_select: /model_1/A/3/
    - name: ACE_3
      add_ACE: true
      brd_select: /model_1/A/2/

• add_NME

Place the N-methyl group in the specified place and add it as a fragment.

- name: res_3
  sp: true
  fragments:
    - name: res_3
      brd_select: /model_1/A/3/
    - name: NME_3
      add_NME: true
      brd_select: /model_1/A/4/

• reference

The fragment is created by using the previous calculation result.

• frame

  This value indicates the name of the frame molecule.

• fragment

  The name of the fragment in the frame molecule.

- name: frame_3
  sp: true
  fragments:
    - name: AA_3
      brd_select: /model_1/A/3/
    - name: ACE_3
      add_ACE: true
      brd_select: /model_1/A/3/
    - name: NME_3
      add_NME: true
      brd_select: /model_1/A/3/

- name: frame_3-7
  sp: true
  guess: QCLO
  fragments:
    - name: AA_3
      reference:
        frame: frame_3
        fragment: AA_3

• brd_select

The group which is indicated by the value of brd_select keyword is add as fragment. This value is specified by string as Bridge path.

New in version 2022.10: dict type supported.

parameters

parameter	type	comment
path	string	Specify the group of atoms to be included.
except	string	Specify the path to exclude from the atom group specified by `path` .

- name: frame_HEM4
  sp: true
  fragments:
    - name: HEM4
      brd_select:
        path: /model_1/A/204/
        except: /model_1/A/204/*_FE
    - name: S-CH3_B
      add_CH3: true
      root: /model_1/A/100/1476_SG
      displacement: /model_1/A/100/1475_CB
    - name: S-CH3_C
      add_CH3: true
      root: /model_1/A/105/1548_SG
      displacement: /model_1/A/105/1547_CB
    - name: HEM3X
      atomlist:
        - "X  -11.048   6.729   4.106 +1"
        - "X   -5.968   5.999   7.701 +1"
  charge: -2

frame action

The following keyword indicates for the frame object to do.

• pre_scf

  If pre_scf is defined as yes , then the processing calculation before SCF loop is carried out in the frame molecule.

• guess

  Creation of the initial guess is executed. How to create guess depends on the value of “guess” keyword. Use mapping format in “guess” section.

  • method

    Specified method for guess. Possible values are as follows.

    • harris

      The initial guess is created by using Harris functional method. This is default.

    • QCLO

      The inigial guess is made of the QCLOs of corresponding fragments by using QCLO method. If the QCLO of the child fragment has not been created, it is computed automatically.

  • force

    boolean. The default value is False. If you want to force execution even if it has already been done, specify True.

• sp

  If the sp is defined as yes , the single-point calculation of the frame molecule is carried out. If pre_scf and guess keywords are not indicated, these operations are automatically performed.

• force

  If the force is defined as yes , the energy force is gained in the frame molecule.

  - name: res_3-7
    pre_scf: yes
    guess: QCLO
    sp: yes
    force: yes
  

• summary

  Displays a summary of the calculation. There are three different methods depending on the data format.

  • boolean

    Outputs a standard summary (True).

    - name: res_3-7
      pre_scf: yes
      guess: QCLO
      sp: yes
      summary: yes
    

  • string

    Output according to the given string. Specific strings are replaced by the corresponding content.

    keyword	content
    {NUM_OF_ATOMS}	number of atoms
    {NUM_OF_AO}	number of AOs
    {NUM_OF_MO}	number of MOs
    {METHOD}	method
    {IS_CONVERGED}	Whether the SCF is converged or not
    {ITERATION}	iteration
    {TOTAL_ENERGY}	total energy
    {GRADIENT_RMS}	gradient RMS

    - name: res_3-7
    pre_scf: yes
    guess: QCLO
    sp: yes
    summary: "atoms: {NUM_OF_ATOMS} iterations: {ITERATION}"
    

  • dict

    If you want to export to a file, you can use this format. The output file is written in appendix mode.

    • format

      Output according to the format string.

    • filepath

      Specify the file path to be output.

      - name: res_3-7
        pre_scf: yes
        guess: QCLO
        sp: yes
        summary:
          format: "atoms: {NUM_OF_ATOMS} iterations: {ITERATION}"
          filepath: "summary.txt"
      

default frame

The default frame is a special frame.

If the name section is “default”, this frame parameters are used as default values.

In the following example, the frame is calculated as DZVP2 as the basisset and the exchange correlation functional is used by B3LYP.

tasks:
  - name: default
    brd_file: sample.brd
    basis_set: DZVP2
    XC_functional: B3LYP

  - name: N2
    atomlist:
      - "N  0.000000   0.000000   0.000000"
      - "N  1.000000   0.000000   0.000000"