aiida-crystal17 0.4.0

AiiDA plugin for running the CRYSTAL17 code

aiida-crystal17

AiiDA plugin for running the CRYSTAL17 code. The code is principally tested against CRYSTAL17, but the output parsing has also been tested against CRYSTAL14.

Documentation: https://readthedocs.org/projects/aiida-crystal17

Installation

To install from pypi:

>> pip install aiida-crystal17

To install the development version:

>> git clone https://github.com/chrisjsewell/aiida-crystal17 .
>> cd aiida-crystal17
>> pip install -e .  # also installs aiida, if missing (but not postgres)
>> #pip install -e .[pre-commit,testing] # install extras for more features
>> verdi quicksetup  # set up a new profile
>> verdi calculation plugins  # should now show the calclulation plugins (with prefix crystal17.)

Usage

Basic Calculation

The crystal17.basic 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. Assuming AiiDA is configured and your database is running:

>> 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:

.. code:: shell

>> 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

Main Calculation

The crystal17.main plugin is designed with a more programmatic input interface. It creates the input .d12 and .gui files, from a set of AiiDa nodes.

>> 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:

• parameters is a dictionary of (structure independent) data, used to create the main.d12 file.
• structure stores the initial atomic configuration for the calculation.
• settings stores additional data related to the initial atomic configuration, such as symmetry operations and initial spin.
• basis_ store the basis set for each element.

Tests

The following will discover and run all unit test:

>> pip install -e .[testing]
>> reentry scan -r aiida
>> pytest -v

To omit tests which call runcry17:

>> pytest -v -m "not process_execution"

or alternatively to call the mock_runcry17 executable, first set the global environmental variable:

>> export MOCK_EXECUTABLES=true

Development and Testing Notes

The original plugin template was created from the aiida-plugin-cutter .

Coding Style Requirements

The code style is tested using prospector, with the configuration set in .prospector.yaml, and yapf.

Installing with aiida-crystal17[pre-commit] makes the pre-commit package available, which will ensure these tests are passed by reformatting the code and testing for lint errors before submitting a commit. It can be setup by:

>> cd aiida-crystal17
>> pre-commit install

Optionally you can run yapf and prospector separately:

>> yapf -r -i .  # recusivel find and format files in-place
>> prospector 

Editors like PyCharm also have automatic code reformat utilities, which should adhere to this standard.

Testing against mock CRYSTAL17 executables

Because CRYSTAL17 is a licensed software, it is not possible to source a copy of the executable on Travis CI. Therefore, a mock executable (mock_runcry17) has been created for testing purposes (which also speeds up test runs).

This executable computes the md5 hash of the supplied input file and tries to match it against a dictionary of precomputed hashes. If found, the executable will write the matching output (from test/output_files) to stdout.

To use this mock executable when running tests, set the global variable MOCK_EXECUTABLES=true.

Setting up CRYSTAL17 locally

To set up local version of CRYSTAL17 on a mac (after downloading a copy from the distributor), I had to:

1. Remove the quarantine from the executable permissions:

   xattr -c crystal 
   xattr -c properties
   

2. Create versions of the lapack/blas libraries in the expected folders:

   sudo port install lapack
   sudo cp /opt/local/lib/lapack/liblapack.3.dylib /usr/local/opt/lapack/lib/liblapack.3.dylib
   sudo cp /opt/local/lib/lapack/libblas.3.dylib /usr/local/opt/lapack/lib/libblas.3.dylib
   

3. Define environmental variables in ~/.bashrc, as detailed in cry17_scripts/cry17.bashrc

4. Copy or symlink the cry17_scripts/runcry17 script into /usr/local/bin/

License

MIT

Contact

[e-mail]