Merge pull request #8 from chrisjsewell/develop

v0.6.0b3 release

README.md

@@ -1,13 +1,13 @@
 [![Build Status](https://travis-ci.org/chrisjsewell/aiida-crystal17.svg?branch=master)](https://travis-ci.org/chrisjsewell/aiida-crystal17)
 [![Coverage Status](https://coveralls.io/repos/github/chrisjsewell/aiida-crystal17/badge.svg?branch=master)](https://coveralls.io/github/chrisjsewell/aiida-crystal17?branch=master)
-[![Docs status](https://readthedocs.org/projects/aiida-crystal17/badge)](http://aiida-crystal17.readthedocs.io/) 
+[![Docs status](https://readthedocs.org/projects/aiida-crystal17/badge)](http://aiida-crystal17.readthedocs.io/)
 [![PyPI](https://img.shields.io/pypi/v/aiida-crystal17.svg)](https://pypi.python.org/pypi/aiida-crystal17/)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/aiida-crystal17/badges/version.svg)](https://anaconda.org/conda-forge/aiida-crystal17)
 
 # aiida-crystal17
 
 AiiDA plugin for running the [CRYSTAL17](http://www.crystal.unito.it/) code.
-The code is principally tested against CRYSTAL17, 
+The code is principally tested against CRYSTAL17,
 but the output parsing has also been tested against CRYSTAL14.
 
 **Documentation**: https://readthedocs.org/projects/aiida-crystal17
@@ -17,8 +17,7 @@ but the output parsing has also been tested against CRYSTAL14.
 To install from Conda (recommended)::
 
 ```shell
->> conda install -c conda-forge aiida-crystal17
->> conda install -c bioconda chainmap==1.0.2
+>> conda install -c conda-forge aiida-crystal17 aiida-core.services
 ```
 
 To install from pypi::
@@ -54,7 +53,7 @@ To omit tests which call `runcry17`:
 >> pytest -v -m "not process_execution"
 ```
 
-or alternatively to call the `mock_runcry17` executable, 
+or alternatively to call the `mock_runcry17` executable,
 first set the global environmental variable:
 
 ```shell

aiida_crystal17/__init__.py

@@ -4,4 +4,4 @@
 AiiDA plugin for running the CRYSTAL17 code
 """
 
-__version__ = "0.5.0b3"
+__version__ = "0.6.0b3"

aiida_crystal17/calculations/cry_abstract.py

@@ -48,21 +48,46 @@ def define(cls, spec):
             message=('An error was flagged trying to parse the '
                      'main crystal output file'))
 
+        spec.exit_code(
+            350, 'ERROR_CRYSTAL_INPUT',
+            message='the input file was could not be read by CRYSTAL')
+        spec.exit_code(
+            351, 'ERROR_WAVEFUNCTION_NOT_FOUND',
+            message='CRYSTAL could not find the required wavefunction file')
+
         # Significant errors but calculation can be used to restart
         spec.exit_code(
-            400, 'ERROR_CRYSTAL_RUN',
-            message='The main crystal output file flagged an error')
+            401, 'UNCONVERGED_SCF',
+            message='SCF convergence did not finalise (usually due to reaching step limit)')
+        spec.exit_code(
+            402, 'UNCONVERGED_GEOMETRY',
+            message='Geometry convergence did not finalise (usually due to reaching step limit)')
+        spec.exit_code(
+            410, 'ERROR_SCF_ABNORMAL_END',
+            message='an error was encountered during an SCF computation')
+        spec.exit_code(
+            411, 'BASIS_SET_LINEARLY_DEPENDENT',
+            message='an error encountered usually during geometry optimisation')
+        spec.exit_code(
+            412, 'ERROR_MPI_ABORT',
+            message='an unknown error was encountered, causing the MPI to abort')
+        spec.exit_code(
+            499, 'ERROR_CRYSTAL_RUN',
+            message='The main crystal output file flagged an unhandled error')
+
+        # errors in symmetry node consistency check
         spec.exit_code(
-            410, 'ERROR_SYMMETRY_INCONSISTENCY',
+            510, 'ERROR_SYMMETRY_INCONSISTENCY',
             message=('inconsistency in the input and output symmetry'))
         spec.exit_code(
-            420, 'ERROR_SYMMETRY_NOT_FOUND',
+            520, 'ERROR_SYMMETRY_NOT_FOUND',
             message=('primitive symmops were not found in the output file'))
 
         spec.output(cls.link_output_results,
                     valid_type=DataFactory('dict'),
                     required=True,
                     help='the data extracted from the main output file')
+        spec.default_output_node = cls.link_output_results
         spec.output(cls.link_output_structure,
                     valid_type=DataFactory('structure'),
                     required=False,

aiida_crystal17/calculations/cry_main.py

@@ -11,8 +11,8 @@
 from aiida.plugins import DataFactory
 
 from aiida_crystal17.calculations.cry_abstract import CryAbstractCalculation
-from aiida_crystal17.parsers.gui_parse import gui_file_write
-from aiida_crystal17.parsers.inputd12_write import (
+from aiida_crystal17.parsers.raw.gui_parse import gui_file_write
+from aiida_crystal17.parsers.raw.inputd12_write import (
     write_input, create_atom_properties)
 
 

aiida_crystal17/calculations/tests/test_cry_basic.py

@@ -52,7 +52,6 @@ def test_calcjob_submission(db_test_app):
     ('mgo_sto3g_opt.crystal.d12', None),
     ('mgo_sto3g_external.crystal.d12', 'mgo_sto3g_external.crystal.gui')
 ))
-@pytest.mark.timeout(60)
 @pytest.mark.process_execution
 def test_calcjob_run(db_test_app, inpath_main, inpath_gui):
     # type: (AiidaTestApp, str, str) -> None

aiida_crystal17/calculations/tests/test_cry_main.py

@@ -4,42 +4,34 @@
 import os
 from textwrap import dedent  # noqa: F401
 
-from ase.spacegroup import crystal
 import ejplugins
 from jsonextended import edict
 import pytest
 from aiida.engine import run_get_node
+from aiida.plugins import CalculationFactory, DataFactory, WorkflowFactory
 import aiida_crystal17
 from aiida_crystal17.tests import TEST_DIR
 from aiida_crystal17.tests.utils import AiidaTestApp  # noqa: F401
 
 
-def test_create_builder(db_test_app):
+def test_create_builder(db_test_app, get_structure):
     # type: (AiidaTestApp) -> None
     """test preparation of inputs"""
     db_test_app.get_or_create_code('crystal17.main')
 
     inparams = {"scf.k_points": (8, 8)}
 
-    from aiida.plugins import DataFactory, CalculationFactory
     structure_data_cls = DataFactory('structure')
     basis_data_cls = DataFactory('crystal17.basisset')
 
-    atoms = crystal(
-        symbols=[12, 8],
-        basis=[[0, 0, 0], [0.5, 0.5, 0.5]],
-        spacegroup=225,
-        cellpar=[4.21, 4.21, 4.21, 90, 90, 90])
-    instruct = structure_data_cls(ase=atoms)
+    instruct = get_structure("MgO")
     mg_basis, _ = basis_data_cls.get_or_create(
         os.path.join(TEST_DIR, "input_files", "sto3g", 'sto3g_Mg.basis'))
     o_basis, _ = basis_data_cls.get_or_create(
         os.path.join(TEST_DIR, "input_files", "sto3g", 'sto3g_O.basis'))
 
-    from aiida_crystal17.workflows.symmetrise_3d_struct import (
-        Symmetrise3DStructure)
     sym_calc = run_get_node(
-        Symmetrise3DStructure, structure=instruct, symprec=0.01,
+        WorkflowFactory("crystal17.sym3d"), structure=instruct, symprec=0.01,
         compute={"primitive": True}).node
     instruct = sym_calc.get_outgoing().get_node_by_label("structure")
     symmetry = sym_calc.get_outgoing().get_node_by_label("symmetry")
@@ -57,12 +49,11 @@ def test_create_builder(db_test_app):
     "input_symmetry",
     (False, True)
 )
-def test_calcjob_submit_mgo(db_test_app, input_symmetry):
+def test_calcjob_submit_mgo(db_test_app, input_symmetry, get_structure):
     # type: (AiidaTestApp, bool) -> None
     """Test submitting a calculation"""
-    from aiida.plugins import DataFactory
+
     param_data_cls = DataFactory('crystal17.parameters')
-    structure_data_cls = DataFactory('structure')
     basis_data_cls = DataFactory('crystal17.basisset')
 
     code = db_test_app.get_or_create_code('crystal17.main')
@@ -75,18 +66,10 @@ def test_calcjob_submit_mgo(db_test_app, input_symmetry):
         }
     })
 
-    # MgO
-    atoms = crystal(
-        symbols=[12, 8],
-        basis=[[0, 0, 0], [0.5, 0.5, 0.5]],
-        spacegroup=225,
-        cellpar=[4.21, 4.21, 4.21, 90, 90, 90])
-    instruct = structure_data_cls(ase=atoms)
+    instruct = get_structure("MgO")
 
-    from aiida_crystal17.workflows.symmetrise_3d_struct import (
-        Symmetrise3DStructure)
     sym_calc = run_get_node(
-        Symmetrise3DStructure, structure=instruct, symprec=0.01,
+        WorkflowFactory("crystal17.sym3d"), structure=instruct, symprec=0.01,
         compute={"primitive": True}).node
     instruct = sym_calc.get_outgoing().get_node_by_label("structure")
     symmetry = sym_calc.get_outgoing().get_node_by_label("symmetry")
@@ -164,12 +147,10 @@ def test_calcjob_submit_mgo(db_test_app, input_symmetry):
     # assert gui_content == expected_gui
 
 
-def test_calcjob_submit_nio_afm(db_test_app):
+def test_calcjob_submit_nio_afm(db_test_app, get_structure):
     # type: (AiidaTestApp) -> None
     """Test submitting a calculation"""
-    from aiida.engine import run_get_node
-    from aiida.plugins import DataFactory
-    structure_data_cls = DataFactory('structure')
+
     kind_data_cls = DataFactory('crystal17.kinds')
     basis_data_cls = DataFactory('crystal17.basisset')
     upload_basisset_family = basis_data_cls.upload_basisset_family
@@ -187,23 +168,14 @@ def test_calcjob_submit_nio_afm(db_test_app):
         "scf.post_scf": ["PPAN"]
     }
 
-    # Ni0
-    atoms = crystal(
-        symbols=[28, 8],
-        basis=[[0, 0, 0], [0.5, 0.5, 0.5]],
-        spacegroup=225,
-        cellpar=[4.164, 4.164, 4.164, 90, 90, 90])
-    atoms.set_tags([1, 1, 2, 2, 0, 0, 0, 0])
-    instruct = structure_data_cls(ase=atoms)
+    instruct = get_structure("NiO_afm")
 
     kind_data = kind_data_cls(data={
         "kind_names": ["Ni1", "Ni2", "O"],
         "spin_alpha": [True, False, False], "spin_beta": [False, True, False]})
 
-    from aiida_crystal17.workflows.symmetrise_3d_struct import (
-        Symmetrise3DStructure)
     sym_calc = run_get_node(
-        Symmetrise3DStructure, structure=instruct, symprec=0.01,
+        WorkflowFactory("crystal17.sym3d"), structure=instruct, symprec=0.01,
         compute={"primitive": True}).node
     instruct = sym_calc.get_outgoing().get_node_by_label("structure")
     symmetry = sym_calc.get_outgoing().get_node_by_label("symmetry")
@@ -291,13 +263,10 @@ def test_calcjob_submit_nio_afm(db_test_app):
     # assert gui_content == expected_gui
 
 
-@pytest.mark.timeout(60)
-def test_run_nio_afm_scf(db_test_app):
+def test_run_nio_afm_scf(db_test_app, get_structure):
     # type: (AiidaTestApp) -> None
     """Test running a calculation"""
-    from aiida.engine import run_get_node
-    from aiida.plugins import DataFactory
-    structure_data_cls = DataFactory('structure')
+
     kind_data_cls = DataFactory('crystal17.kinds')
     basisset_data_cls = DataFactory('crystal17.basisset')
     upload_basisset_family = basisset_data_cls.upload_basisset_family
@@ -315,23 +284,14 @@ def test_run_nio_afm_scf(db_test_app):
         "scf.post_scf": ["PPAN"]
     }
 
-    # Ni0
-    atoms = crystal(
-        symbols=[28, 8],
-        basis=[[0, 0, 0], [0.5, 0.5, 0.5]],
-        spacegroup=225,
-        cellpar=[4.164, 4.164, 4.164, 90, 90, 90])
-    atoms.set_tags([1, 1, 2, 2, 0, 0, 0, 0])
-    instruct = structure_data_cls(ase=atoms)
+    instruct = get_structure("NiO_afm")
 
     kind_data = kind_data_cls(data={
         "kind_names": ["Ni1", "Ni2", "O"],
         "spin_alpha": [True, False, False], "spin_beta": [False, True, False]})
 
-    from aiida_crystal17.workflows.symmetrise_3d_struct import (
-        Symmetrise3DStructure)
     sym_calc = run_get_node(
-        Symmetrise3DStructure, structure=instruct, symprec=0.01,
+        WorkflowFactory("crystal17.sym3d"), structure=instruct, symprec=0.01,
         compute={"primitive": True}).node
     instruct = sym_calc.get_outgoing().get_node_by_label("structure")
     symmetry = sym_calc.get_outgoing().get_node_by_label("symmetry")
@@ -395,14 +355,11 @@ def test_run_nio_afm_scf(db_test_app):
     assert edict.diff(attributes, expected_results, np_allclose=True) == {}
 
 
-@pytest.mark.timeout(60)
 @pytest.mark.process_execution
-def test_run_nio_afm_fullopt(db_test_app):
+def test_run_nio_afm_fullopt(db_test_app, get_structure):
     # type: (AiidaTestApp) -> None
     """Test running a calculation"""
-    from aiida.engine import run_get_node
-    from aiida.plugins import DataFactory
-    structure_data_cls = DataFactory('structure')
+
     kind_data_cls = DataFactory('crystal17.kinds')
     basis_data_cls = DataFactory('crystal17.basisset')
     upload_basisset_family = basis_data_cls.upload_basisset_family
@@ -420,23 +377,14 @@ def test_run_nio_afm_fullopt(db_test_app):
         "scf.post_scf": ["PPAN"]
     }
 
-    # Ni0
-    atoms = crystal(
-        symbols=[28, 8],
-        basis=[[0, 0, 0], [0.5, 0.5, 0.5]],
-        spacegroup=225,
-        cellpar=[4.164, 4.164, 4.164, 90, 90, 90])
-    atoms.set_tags([1, 1, 2, 2, 0, 0, 0, 0])
-    instruct = structure_data_cls(ase=atoms)
+    instruct = get_structure("NiO_afm")
 
     kind_data = kind_data_cls(data={
         "kind_names": ["Ni1", "Ni2", "O"],
         "spin_alpha": [True, False, False], "spin_beta": [False, True, False]})
 
-    from aiida_crystal17.workflows.symmetrise_3d_struct import (
-        Symmetrise3DStructure)
     sym_calc = run_get_node(
-        Symmetrise3DStructure, structure=instruct, symprec=0.01,
+        WorkflowFactory("crystal17.sym3d"), structure=instruct, symprec=0.01,
         compute={"primitive": True}).node
     instruct = sym_calc.get_outgoing().get_node_by_label("structure")
     symmetry = sym_calc.get_outgoing().get_node_by_label("symmetry")

aiida_crystal17/data/symmetry.py

@@ -3,6 +3,7 @@
 
 from jsonschema import ValidationError as SchemeError
 import numpy as np
+import spglib
 
 from aiida.common.utils import classproperty
 # from aiida.common.exceptions import ValidationError
@@ -169,6 +170,16 @@ def num_symops(self):
     def hall_number(self):
         return self.get_attribute("hall_number", None)
 
+    @property
+    def spacegroup_info(self):
+        """ Translate Hall number to space group type information.
+        Returned as an attribute dict
+        """
+        info = spglib.get_spacegroup_type(self.hall_number)
+        if info is None:
+            raise ValueError("the hall number could not be converted")
+        return AttributeDict(info)
+
     def add_path(self, src_abs, dst_path):
         from aiida.common.exceptions import ModificationNotAllowed
 

aiida_crystal17/gulp/calculations/gulp_abstract.py

@@ -45,7 +45,7 @@ def define(cls, spec):
             help=('atomic structure used to create the '
                   'geometry section of .gin file content.'))
         spec.input(
-            'potential', valid_type=DataFactory('dict'),
+            'potential', valid_type=DataFactory('gulp.potential'),
             required=True,
             help=('parameters to create the '
                   'potential section of the .gin file content.'))
@@ -74,12 +74,16 @@ def define(cls, spec):
         # Significant errors but calculation can be used to restart
         spec.exit_code(
             400, 'ERROR_GULP_RUN',
-            message='The main gulp output file flagged an error')
+            message='The main gulp output file flagged an unknown error')
+        spec.exit_code(
+            410, 'ERROR_NOT_OPTIMISED',
+            message='The main gulp output file did not signal that an expected optimisation completed')
 
         spec.output(cls.link_output_results,
                     valid_type=DataFactory('dict'),
                     required=True,
                     help='the data extracted from the main output file')
+        spec.default_output_node = cls.link_output_results
 
     def prepare_for_submission(self, tempfolder):
         """