Contents

Basic Calculation

The crystal17.basic plugin is the simplest calculation plugin. It accepts as input:

  • a pre-written main.d12 file and,

  • (optionally) a main.gui file with geometry, to accompany a main.d12 file containing the EXTERNAL keyword.

Initial Setup

To run a computation, first ensure AiiDA is running:

!verdi status

 ✓ profile:     On profile test_profile
 ✓ repository:  /var/folders/dm/b2qnkb_n3r72slmpxlfmcjvm00lbnd/T/tmpt_morsq7/test_repo
 ✓ postgres:    Connected as aiida@localhost:51390
 ✓ rabbitmq:    Connected to amqp://127.0.0.1?heartbeat=600
 ✓ daemon:      Daemon is running as PID 96578 since 2019-08-12 14:08:06

See also

AiiDA documentation: Getting Started

If aiida-crystal17 is installed, the crystal17.basic computation should be available:

!verdi plugin list aiida.calculations crystal17.basic

-/|\-/|Inputs
            code:  required  Code            The Code to use for this job.
      input_file:  required  SinglefileData  the input .d12 file content.
  input_external:  optional  SinglefileData  optional input fort.34 (gui) file content (for use with EXTERNAL keyword).
        metadata:  optional                  
Outputs
   remote_folder:  required  RemoteData      Input files necessary to run the process will be stored in this folder node ...
         results:  required  Dict            the data extracted from the main output file
       retrieved:  required  FolderData      Files that are retrieved by the daemon will be stored in this node. By defa ...
       structure:  optional  StructureData   the structure output from the calculation
        symmetry:  optional  SymmetryData    the symmetry data from the calculation
Exit codes
               1:  The process has failed with an unspecified error.
               2:  The process failed with legacy failure mode.
              10:  The process returned an invalid output.
              11:  The process did not register a required output.
             200:  The retrieved folder data node could not be accessed.
             210:  The main (stdout) output file was not found
             211:  The temporary retrieved folder was not found
             300:  An error was flagged trying to parse the crystal exec stdout file
             301:  An error occurred parsing the 'opta'/'optc' geometry files
             302:  The crystal exec stdout file denoted that the run was a testgeom
             350:  The input file could not be read by crystal
             351:  Crystal could not find the required wavefunction file
             400:  The calculation stopped prematurely because it ran out of walltime.
             401:  The calculation stopped prematurely because it ran out of memory.
             402:  The calculation stopped prematurely because it ran out of virtual memory.
             411:  Scf convergence did not finalise (usually due to reaching step limit)
             412:  Geometry convergence did not finalise (usually due to reaching step limit)
             413:  An error encountered usually during geometry optimisation
             414:  An error was encountered during an scf computation
             415:  An unknown error was encountered, causing the mpi to abort
             499:  The main crystal output file flagged an unhandled error
             510:  Inconsistency in the input and output symmetry
             520:  Primitive symmops were not found in the output file

To use the python interface, first ensure a profile is loaded in the python kernel, and import the required modules:

from aiida import load_profile
profile = load_profile()
profile.name

'test_crystal17'

import os
from aiida_crystal17.common import display_json
from aiida_crystal17.tests import open_resource_binary
from aiida.orm import Code
from aiida.engine import run_get_node
from aiida.plugins import DataFactory

Input Creation

See also

AiiDA documentation: How to run external codes

CRYSTAL17 Manual

An Code node should be set up in advance, to use the crystal17.basic calculation plugin, and call the runcry17 executable (or mock_runcry17 used here for test purposes).

from aiida_crystal17.tests.utils import get_or_create_local_computer, get_or_create_code
computer = get_or_create_local_computer('work_directory', 'localhost')
code = get_or_create_code('crystal17.basic', computer, 'mock_crystal17')
code.get_full_text_info()

[['PK', 1],
 ['UUID', '9bbbc497-a8d5-4265-a3f9-6eda89c14a1c'],
 ['Label', 'crystal17.basic-mock_crystal17@localhost'],
 ['Description', ''],
 ['Default plugin', 'crystal17.basic'],
 ['Type', 'remote'],
 ['Remote machine', 'localhost'],
 ['Remote absolute path',
  '//anaconda/envs/aiida_crystal17/bin/mock_crystal17'],
 ['Prepend text', 'No prepend text'],
 ['Append text', 'No append text']]

An SinglefileData node is then set containing the main input file.

SinglefileData = DataFactory('singlefile')
with open_resource_binary('crystal', 'mgo_sto3g_scf', 'INPUT') as handle:
   infile = SinglefileData(file=handle)

with infile.open() as handle:
    print(handle.read())

MgO bulk
CRYSTAL
0 0 0
 225
4.21
2
 12 0.    0.    0.
  8 0.5   0.5   0.5
END
12 3
1 0 3  2.  0.
1 1 3  8.  0.
1 1 3  2.  0.
8 2
1 0 3  2.  0.
1 1 3  6.  0.
99   0
END
SHRINK
8 8
END

Setting Up and Running the Calculation

See also

AiiDA documentation: Processes

A builder can be obtained from the Code node, which will define all the required input nodes and settings:

builder = code.get_builder()
builder.metadata.options.withmpi = False
builder.metadata.options.resources = {
    "num_machines": 1,
    "num_mpiprocs_per_machine": 1}
builder.input_file = infile
display_json(builder)

{
  "metadata": {
    "options": {
      "withmpi": false,
      "resources": {
        "num_machines": 1,
        "num_mpiprocs_per_machine": 1
      }
    }
  },
  "code": [
    "Remote code 'crystal17.basic-mock_crystal17@localhost' on localhost,",
    "pk: 1, uuid: 9bbbc497-a8d5-4265-a3f9-6eda89c14a1c"
  ],
  "input_file": [
    "uuid: a2aa4ddf-d438-426e-9b1b-f6b7ba3ea7b6 (unstored)"
  ]
}

In order to run the computation, the builder can be parsed to one of the AiiDA run (blocking execution) or submit (non-blocking execution) functions:

result, calcnode = run_get_node(builder)

The process can be monitored on the command line:

!verdi process list -a -l 1 -D desc

-/|\-/|\  PK  Created    Process label        Process State    Process status
----  ---------  -------------------  ---------------  ----------------
   3  16s ago    CryBasicCalculation  ⏹ Finished [0]

Total results: 1

Info: last time an entry changed state: 2s ago (at 13:08:30 on 2019-08-12)

Once the calculation is complete, a CalcJobNode will be created, to store the settings and outcome of the computation. Crucially, if the computation has completed successfully, the exit_status will be 0.

This can be assessed on the command line or with the python API.

!verdi process show {calcnode.pk}

-/|\-/|Property       Value
-------------  ------------------------------------
type           CalcJobNode
pk             3
uuid           22f461b9-1fa6-46ce-980b-5be137a985db
label
description
ctime          2019-08-12 13:08:16.459048+00:00
mtime          2019-08-12 13:08:30.163635+00:00
process state  Finished
exit status    0
computer       [1] localhost

Inputs        PK  Type
----------  ----  --------------
code           1  Code
input_file     2  SinglefileData

Outputs          PK  Type
-------------  ----  -------------
remote_folder     4  RemoteData
results           6  Dict
retrieved         5  FolderData
structure         7  StructureData
symmetry          8  SymmetryData

print(calcnode.is_finished_ok)
print(calcnode.process_state)
print(calcnode.exit_status)

True
ProcessState.FINISHED
0

If the calculation fails, there are three things that should be checked:

  1. The calculation’s exit_message

  2. The calculation’s log messages and scheduler output

  3. The results output node (if available)

print("Exit Message:", calcnode.exit_message)
from aiida.cmdline.utils.common import get_calcjob_report
print(get_calcjob_report(calcnode))

Exit Message: None
*** 3: None
*** (empty scheduler output file)
*** (empty scheduler errors file)
*** 0 LOG MESSAGES

!verdi process report {calcnode.pk}

-/|\-/|*** 3: None
*** (empty scheduler output file)
*** (empty scheduler errors file)
*** 0 LOG MESSAGES

Analysis of Outputs

The aiida.tools.visualization.graph.Graph can be used to visualise the calculations provenance graph:

from aiida.tools.visualization import Graph
graph = Graph(graph_attr={'size': "6,8!", "rankdir": "LR"})
graph.add_node(calcnode)
graph.add_incoming(calcnode, annotate_links="both")
graph.add_outgoing(calcnode, annotate_links="both")
graph.graphviz
../_images/calc_basic_33_0.svg

The retrieved FolderData output node contains the CRYSTAL17 main output file.

calcnode.outputs.retrieved.list_object_names()

['_scheduler-stderr.txt', '_scheduler-stdout.txt', 'main.out']

The results Dict output node contains key values extracted from the CRYSTAL17 main output file.

display_json(calcnode.outputs.results.attributes)

{
  "units": {
    "angle": "degrees",
    "energy": "eV",
    "length": "angstrom",
    "conversion": "CODATA2014"
  },
  "energy": -7380.2216051903,
  "errors": [],
  "header": {
    "crystal_version": 17,
    "crystal_subversion": "1.0.1"
  },
  "volume": 18.65461525,
  "warnings": [],
  "calculation": {
    "n_ao": 14,
    "spin": false,
    "type": "restricted closed shell",
    "n_atoms": 2,
    "n_shells": 5,
    "n_symops": 48,
    "n_core_el": 12,
    "n_electrons": 20,
    "n_kpoints_ibz": 29,
    "n_kpoints_gilat": 29
  },
  "energy_units": "eV",
  "parser_class": "CryMainParser",
  "parser_errors": [],
  "parser_version": "0.11.0",
  "scf_iterations": 7,
  "number_of_atoms": 2,
  "parser_warnings": [
    "no initial structure available, creating new kinds for atoms"
  ],
  "parser_exceptions": [],
  "number_of_assymetric": 2,
  "execution_time_seconds": 3
}

The structure StructureData output node contains the final structure, obtained from the CRYSTAL17 main output file.

%matplotlib inline
import matplotlib.pyplot as plt
from ase.visualize.plot import plot_atoms
atoms = calcnode.outputs.structure.get_ase()
fig, ax = plt.subplots()
plot_atoms(atoms.repeat((4,4,4)),
           ax, radii=0.8, show_unit_cell=True,
           rotation=('45x,0y,0z'));
../_images/calc_basic_39_0.png

The symmetry SymmetryData output node contains the symmetry of the final structure, obtained from the CRYSTAL17 main output file.

print(calcnode.outputs.symmetry.attributes)
calcnode.outputs.symmetry.data.operations

{'basis': 'fractional', 'num_symops': 48, 'hall_number': None}

[[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, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0],
 [-1.0, -1.0, -1.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, 1.0, -1.0, -1.0, -1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [1.0, 0.0, 0.0, 0.0, 0.0, 1.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0],
 [1.0, 0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
 [-1.0, -1.0, -1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, 1.0, 0.0, 1.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0],
 [0.0, 1.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0],
 [-1.0, -1.0, -1.0, 1.0, 0.0, 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, 0.0, 0.0, 0.0],
 [-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, -1.0, 1.0, 1.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
 [1.0, 1.0, 1.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 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],
 [0.0, 0.0, -1.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
 [1.0, 1.0, 1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, -1.0, 0.0, 1.0, 1.0, 1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
 [1.0, 1.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
 [-1.0, 0.0, 0.0, 1.0, 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, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
 [0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
 [1.0, 1.0, 1.0, 0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, -1.0, 1.0, 1.0, 1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, -1.0, 0.0, 0.0, 0.0, -1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [-1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
 [-1.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
 [1.0, 1.0, 1.0, 0.0, -1.0, 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, -1.0, 0.0, -1.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
 [0.0, -1.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
 [1.0, 1.0, 1.0, -1.0, 0.0, 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, 0.0, 0.0, 0.0],
 [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, 1.0, -1.0, -1.0, -1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
 [-1.0, -1.0, -1.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 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],
 [0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 0.0, 1.0, 1.0, 0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0],
 [-1.0, -1.0, -1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 1.0, 0.0, -1.0, -1.0, -1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
 [0.0, 1.0, 0.0, 0.0, 0.0, 1.0, -1.0, -1.0, -1.0, 0.0, 0.0, 0.0],
 [-1.0, -1.0, -1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0],
 [1.0, 0.0, 0.0, -1.0, -1.0, -1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0]]
Installation Main Calculation