Basic Calculation Plugin¶

The crystal17.basic plugin is the simplest calculation plugin. It takes a pre-written .d12 file as input and (optionally) a .gui file with geometry, for .d12 inputs containing the EXTERNAL keyword.

Command Line Example¶

An example script is available within the examples folder. You also either need to have the runcry17 executable available locally or set the global variable export MOCK_EXECUTABLES=true to use a dummy executable. Then, assuming AiiDA is configured and your database is running, the script can be run within a terminal:

>> verdi daemon start         # make sure the daemon is running
>> cd examples
>> verdi run test_submit_basic.py       # submit test calculation
submitted calculation; calc=Calculation(PK=5)
>> verdi calculation list -a  # check status of calculation
  PK  Creation    State           Sched. state    Computer    Type
----  ----------  --------------  -------------  ----------  ---------------------------
5     1m ago      WITHSCHEDULER                  localhost   crystal17.basic
>> verdi calculation list -a  # after a few seconds
  PK  Creation    State           Sched. state    Computer    Type
----  ----------  --------------  -------------  ----------  ---------------------------
5     1m ago      FINISHED        DONE           localhost   crystal17.basic

Once the calculation has run, it will be linked to the input nodes and a number of output nodes:

>> verdi calculation show 5
-----------  ---------------------------------------------------
type         CryBasicCalculation
pk           5
uuid         3d9f804b-84db-443a-b6f8-69c15d96d244
label        aiida_crystal17 test
description  Test job submission with the aiida_crystal17 plugin
ctime        2018-08-27 15:23:38.670705+00:00
mtime        2018-08-27 15:24:26.516127+00:00
computer     [2] localhost
code         runcry17
-----------  ---------------------------------------------------
##### INPUTS:
Link label       PK    Type
---------------  ----  --------------
input_external   3     SinglefileData
input_file       4     SinglefileData
##### OUTPUTS:
Link label           PK  Type
-----------------  ----  -------------
remote_folder      6     RemoteData
retrieved          7     FolderData
output_parameters  8     ParameterData
output_settings    9     StructSettingsData
output_structure   10    StructureData
##### LOGS:
There are 1 log messages for this calculation
Run 'verdi calculation logshow 5' to see them

The outputs represent:

remote_folder provides a symbolic link to the work directory where the computation was run.
retrieved stores a folder containing the full main output of runcry17 (as main.out)
output_parameters stores a dictionary of key parameters in the database, for later querying.
output_structure stores the final geometry from the calculation
output_settings stores additional information on the structure,

such as the symmetry operations.

For compatibility, parameters are named with the same convention as aiida-quantumespresso:

>> verdi data parameter show 8
{
  "calculation_spin": false,
  "calculation_type": "restricted closed shell",
  "ejplugins_version": "0.9.7",
  "energy": -7380.22160519032,
  "energy_units": "eV",
  "errors": [],
  "mulliken_charges": [
    0.776999999999999,
    -0.776999999999999
  ],
  "mulliken_electrons": [
    11.223,
    8.777
  ],
  "number_of_assymetric": 2,
  "number_of_atoms": 2,
  "parser_class": "CryBasicParser",
  "parser_version": "0.3.0a0",
  "parser_warnings": [
    "no initial structure available, creating new kinds for atoms"
  ],
  "scf_iterations": 7,
  "volume": 18.65461525,
  "wall_time_seconds": 5,
  "warnings": []
}

You can view the structure settings content by (use -c to view the symmetry operations):

>> verdi data cry17-settings show 9
centring_code: 1
crystal_type:  1
num_symops:    48
space_group:   1

The final structure can be directly viewed by a number of different programs (assuming the executables are available):

>> verdi data structure show --format xcrysden 10