aiida-crystal17 0.3.0a1

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.

Installation

>> 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 2267
-----------  ---------------------------------------------------
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_arrays      9     ArrayData
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 stdout of runcry17 (as main.out)
• output_parameters stores a dictionary of key parameters in the database, for later querying.
• output_arrays stores keys in the database to array data stored on file (such as symmetry operations and mulliken charges).
• output_structure stores the final geometry from the calculation

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": "0.9.6", 
  "energy": -7380.22160519032, 
  "energy_units": "eV", 
  "errors": [], 
  "number_of_assymetric": 2, 
  "number_of_atoms": 2,
  "number_of_symmops": 48,
  "parser_class": "CryBasicParser", 
  "parser_version": "0.1.0a0", 
  "parser_warnings": [], 
  "scf_iterations": 7, 
  "volume": 18.65461525, 
  "wall_time_seconds": 4, 
  "warnings": []
}

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

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/

Current Development Status

Basic Crystal Calculation

This plugin set is the first to be developed. It provides a basic calculation functionality by:

1. Accepting a (pre-written) input file via a SinglefileData node

2. Initiating a crystal run via the crystal17.basic calculation plugin.

3. Parsing the stdout file into:

   1. an output a SinglefileData node
   2. an output ParameterData node, holding key data, via the crystal17.basic parser plugin.

Future Development

Future development will then focus on:

1. Creation of the input file, via input of
   1. a StructureData node
   2. a main ParamaterData node.
   3. ParamaterData nodes for each atomic basis set
2. Additional output nodes (e.g. TrajectoryData) and extending the data held in the ParamaterData node.
3. Parsing of input files to the input nodes described in (1), for migration of existing computations

License

MIT

Contact

[e-mail]