Command Line Interface¶
Example Script Execution¶
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_main.py # submit test calculation
submitted calculation; calc=Calculation(PK=1)
>> verdi calculation list -a # check status of calculation
PK Creation State Sched. state Computer Type
---- ---------- -------------- ------------- -------------- -----------------
1 1m ago WITHSCHEDULER RUNNING localhost-test crystal17.main
>> verdi calculation list -a # after completion (~30 minutes if using runcry17)
PK Creation State Sched. state Computer Type
---- ---------- -------------- ------------- -------------- -----------------
1 4m ago FINISHED DONE localhost-test crystal17.main
Once the calculation has run, it will be linked to the input nodes and a number of output nodes:
verdi calculation show 1
----------- ---------------------------------------------------
type CryMainCalculation
pk 1
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 [1] localhost-test
code runcry17
----------- ---------------------------------------------------
##### INPUTS:
Link label PK Type
------------ ---- -------------
parameters 4 ParameterData
settings 5 StructSettingsData
basis_Ni 2 BasisSetData
basis_O 3 BasisSetData
structure 6 StructureData
##### OUTPUTS:
Link label PK Type
----------------- ---- -------------
remote_folder 7 RemoteData
retrieved 8 FolderData
output_parameters 9 ParameterData
output_structure 10 StructureData
##### LOGS:
There are 1 log messages for this calculation
Run 'verdi calculation logshow 1' to see them
The inputs represent:
parametersis a dictionary of (structure independent) data,- used to create the main.d12 file.
structurestores the initial atomic configuration for the calculation.settingsstores additional data related to the initial atomic- configuration, such as symmetry operations and initial spin.
basis_store the basis set for each element
The outputs represent:
remote_folderprovides a symbolic link to the work directory where the computation was run.retrievedstores a folder containing the full stdout ofruncry17(as main.out)output_parametersstores a dictionary of key parameters in the database, for later querying.output_structurestores the final geometry from the calculation
Input and Output Parameters¶
Both can be viewed at the command line:
>> verdi data parameter show 4
{
"geometry": {
"optimise": {
"type": "FULLOPTG"
}
},
"scf": {
"k_points": [
8,
8
],
"numerical": {
"FMIXING": 30
},
"post_scf": [
"PPAN"
],
"single": "UHF",
"spinlock": {
"SPINLOCK": [
0,
15
]
}
},
"title": "NiO Bulk with AFM spin"
}
For compatibility, output parameters are named with the same convention as in aiida-quantumespresso.pw
>> verdi data parameter show 9
{
"calculation_spin": true,
"calculation_type": "unrestricted open shell",
"ejplugins_version": "0.9.7",
"energy": -85124.8936673389,
"energy_units": "eV",
"errors": [],
"mulliken_spin_total": 0.0,
"mulliken_spins": [
3.057,
-3.057,
-0.072,
0.072
],
"number_of_assymetric": 4,
"number_of_atoms": 4,
"number_of_symmops": 16,
"parser_class": "CryBasicParser",
"parser_version": "0.2.0a0",
"parser_warnings": [],
"scf_iterations": 13,
"volume": 36.099581472,
"wall_time_seconds": 187,
"warnings": []
}
Input and Output Structures¶
The structures can be directly opened by a number of different programs (assuming the executables are available):
>> verdi data structure show --format xcrysden 10
Note
The output structure will only be present for optimisations, and not SCF computations, i.e. only when the input structure has changed
Structure Settings Data¶
This node contains data to create the main.d12, which is specific to the structure:
>> verdi data cry17-settings show -symmetries 5
centring_code: 1
computation_class: Symmetrise3DStructure
computation_version: 0.3.0a0
crystal_type: 4
kinds:
spin_alpha: [Ni1]
spin_beta: [Ni2]
operations: [[1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0,
0.0], [-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 1.0,
6.6613e-16, 0.0], [0.0, -1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0,
1.0, 2.2204e-16, 4.4409e-16, 0.0], [0.0, 1.0, 0.0, -1.0,
0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 2.2204e-16, 6.163e-33],
[-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 1.0,
6.6613e-16, 0.0], [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
-1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0,
0.0, 1.0, 1.0, 2.2204e-16, 6.163e-33], [0.0, -1.0, 0.0,
1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 2.2204e-16, 4.4409e-16,
0.0], [1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0,
6.6613e-16, 0.0], [-1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0,
1.0, 1.0, 0.0, 0.0], [0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0,
0.0, -1.0, 2.2204e-16, 2.2204e-16, 0.0], [0.0, 1.0, 0.0,
1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 4.4409e-16, 6.163e-33],
[-1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0,
0.0], [1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0,
6.6613e-16, 0.0], [0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0,
-1.0, 1.0, 4.4409e-16, 6.163e-33], [0.0, -1.0, 0.0, -1.0,
0.0, 0.0, 0.0, 0.0, 1.0, 2.2204e-16, 2.2204e-16, 0.0]]
space_group: 123
symmetry_program: spglib
symmetry_version: 1.9.10
In this case the symmetry operations, have been pre computed
by the Symmetrise3DStructure workflow,
which will be discussed in Python API Walk-through.
Basis Sets¶
Basis sets are stored as individual nodes:
>> verdi data cry17-basis show -c 2
atomic_number: 28
author: John Smith
basis_type: all-electron
class: sto3g
element: Ni
filename: sto3g_Ni.basis
md5: fd341c4056cffcbd63ab92a94dea80e4
num_shells: 5
year: 1999
28 5
1 0 3 2. 0.
1 1 3 8. 0.
1 1 3 8. 0.
1 1 3 2. 0.
1 3 3 8. 0.
They can also (preferably) be grouped into families:
>> verdi data cry17-basis listfamilies
Family Num Basis Sets
-------- ----------------
sto3g 3
Families can be created from a folder of individual basis set files, optionally with a yaml meta-data header (see Basis Sets):
>> verdi data cry17-basis uploadfamily --help
Usage: verdi data cry17-basis uploadfamily [OPTIONS]
Upload a family of CRYSTAL Basis Set files.
Options:
--path PATH Path to a folder containing the Basis Set files
--ext TEXT the file extension to filter by
--name TEXT Name of the BasisSet family [required]
-D, --description TEXT A description for the family
--stop-if-existing Abort when encountering a previously uploaded Basis
Set file
--dry-run do not commit to database or modify configuration
files
--help Show this message and exit.