Merge pull request #81 from albgar/Rel1.1.1

Rel1.1.1

.gitattributes

@@ -0,0 +1,2 @@
+aiida_siesta/docs/* linguist-documentation
+.ipynb linguist-documentation

.github/workflows/develop.yml

@@ -0,0 +1,81 @@
+name: Nightly Build
+
+on:
+    schedule:
+    -   cron: '0 0 * * *'  # Run every day at midnight
+
+jobs:
+
+    tests:
+
+        if: github.repository == 'albgar/aiida_siesta_plugin'  # Prevent running the builds on forks as well
+
+        runs-on: ubuntu-latest
+
+        strategy:
+            matrix:
+                python-version: [3.6, 3.7, 3.8]
+
+        services:
+            postgres:
+                image: postgres:10
+                env:
+                    POSTGRES_DB: test_${{ matrix.backend }}
+                    POSTGRES_PASSWORD: ''
+                    POSTGRES_HOST_AUTH_METHOD: trust
+                ports:
+                -    5432:5432
+            rabbitmq:
+                image: rabbitmq:latest
+                ports:
+                -   5672:5672
+
+        steps:
+        -   uses: actions/checkout@v2
+
+        -   name: Cache python dependencies
+            id: cache-pip
+            uses: actions/cache@v1
+            with:
+                path: ~/.cache/pip
+                key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
+                restore-keys:
+                    pip-${{ matrix.python-version }}-tests
+
+        -   name: Set up Python ${{ matrix.python-version }}
+            uses: actions/setup-python@v2
+            with:
+                python-version: ${{ matrix.python-version }}
+
+        -   name: Install system dependencies
+            run: |
+                sudo apt update
+                sudo apt install postgresql-10
+
+        -   name: Install python dependencies
+            continue-on-error: true
+            id: install
+            run: |
+                pip install --upgrade setuptools
+                pip install -e .[tests]
+                pip install git+https://github.com/aiidateam/aiida-core@develop
+                reentry scan
+
+        -   name: Run pytest
+            continue-on-error: true
+            id: tests
+            run:
+                pytest -sv tests
+
+        -   name: Slack notification
+            if: steps.install.outcome == 'Failure' || steps.tests.outcome == 'Failure'
+            uses: rtCamp/action-slack-notify@master
+            env:
+                SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
+                SLACK_ICON: https://www.materialscloud.org/discover/images/0ba0a17d.aiida-logo-128.png
+                SLACK_USERNAME: aiida-siesta
+                SLACK_CHANNEL: actions
+                SLACK_COLOR: b60205
+                SLACK_TITLE: "Nightly build against `aiida-core/develop` failed"
+                SLACK_MESSAGE: "The tests fail with the current version of `aiida-core/develop`."
+

.readthedocs.yml

@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: aiida_siesta/docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: aiida_siesta/docs/requirements.txt

CHANGELOG.md

@@ -1,5 +1,46 @@
 # Changelog
 
+## v1.1.1
+
+Version compatible with aiida-core>=1.3.0,<2.0.0.
+
+### Improvements
+- Improvement in the `BandGapWorkChain`. A new feature has been introduced:
+  when no `bandskpoints` are set in input, the workchain automatically calculates the bands
+  using a k-space path automatically selected by SeeK-path.
+  In particular, if a molecular dynamics run was also requested (usually a relaxation),
+  the dynamics is run first and the bands are calculated on a separate Siesta run. This
+  allows to select the k-space path for bands automatically using the output structure.
+  When the `bandskpoints` is selected in input, the behavior is the same of previous versions.
+- Added an output of the `SiestaSequentialConverger` listing, if any,
+  the unconverged parameters. More explicit warnings are returned when a parameter
+  does not converge.
+- A tutorial is now available in the documentation, covering the submission of simple siesta
+  calculations, the use of protocols, the use of the iterator/converger workchains and
+  a simple example on how to create custom workchains.
+
+### Bug fixes
+- A bug was reported regarding the wrong selection of the kpoints path for bands
+  when a relaxation with variable cell was also requested. The energy values were correct,
+  but the distance between kpoints was not corresponding to the one of the Siesta
+  file ".bands". The bug is now fixed.
+- The method `inputs_generator().get_inputs_dict` (available for `SiestaCalculations` and
+  all the workchains in the package) had a minor bug. In case the kpoints or bandskpoints
+  were not requested, the dictionary was anyway returning items for "bandskpoints"
+  and "kpoints" with value "None". This has been fixed.
+  The method `inputs_generator().get_filled_builder` was instead correct.
+- A bug was leading to the failure of `SiestaSequentialConverger` in case one of
+  the parameters to coverge in the sequential process was not reacing convergence.
+  It is now fixed and, in addition, an output listing the unconverged parameters has been
+  added.
+
+### For developers
+- Set up a nightly built in GitHub actions that tests the plugin (run all its tests)
+  against the develop branch of `aiida-core`.
+- The `BandGapWorkChain` has been refactored almost entirely.
+- The abstract class `SequentialConverger` has been modified to fix the bug
+  of `SiestaSequentialConverger` described above.
+
 ## v1.1.0
 
 Version compatible with aiida-core>=1.3.0,<2.0.0. Previous versions of aiida-core do not have a working `BaseRestartWorkChain`, which is the building piece of many workchain in aiida-siesta.

MANIFEST.in

@@ -1,5 +1,7 @@
-include *.rst *.json *.txt *.md
+include *.rst *.json *.txt *.md *.yml
 recursive-include aiida_siesta/docs/ *.rst
 recursive-include aiida_siesta/examples/ *.txt *.psf *.psml *.cif 00_README
 recursive-include aiida_siesta/utils *.yaml
 prune tests
+prune aiida_siesta/docs/tutorialis/first_workchain
+prune aiida_siesta/docs/tutorialis/data_icn2_2020

aiida_siesta/__init__.py

@@ -1,2 +1,2 @@
 """The official AiiDA plugin for Siesta."""
-__version__ = '1.1.0'
+__version__ = '1.1.1'

aiida_siesta/calculations/siesta.py

@@ -29,17 +29,17 @@ class SiestaCalculation(CalcJob):
     ###################################################################
 
     # Parameters stored as class variables
-    # 1) Keywords that cannot be set (need to canonoze this?)
+    # 1) Keywords that cannot be set (already canonized by FDFDict)
     # 2) Filepaths of certain outputs
-    _aiida_blocked_keywords = ['system-name', 'system-label']
-    _aiida_blocked_keywords.append('number-of-species')
-    _aiida_blocked_keywords.append('number-of-atoms')
-    _aiida_blocked_keywords.append('lattice-constant')
-    _aiida_blocked_keywords.append('atomic-coordinates-format')
-    _aiida_blocked_keywords.append('use-tree-timer')
-    _aiida_blocked_keywords.append('xml-write')
-    _aiida_blocked_keywords.append('dm-use-save-dm')
-    _aiida_blocked_keywords.append('geometry-must-converge')
+    _aiida_blocked_keywords = [FDFDict.translate_key('system-name'), FDFDict.translate_key('system-label')]
+    _aiida_blocked_keywords.append(FDFDict.translate_key('number-of-species'))
+    _aiida_blocked_keywords.append(FDFDict.translate_key('number-of-atoms'))
+    _aiida_blocked_keywords.append(FDFDict.translate_key('lattice-constant'))
+    _aiida_blocked_keywords.append(FDFDict.translate_key('atomic-coordinates-format'))
+    _aiida_blocked_keywords.append(FDFDict.translate_key('use-tree-timer'))
+    _aiida_blocked_keywords.append(FDFDict.translate_key('xml-write'))
+    _aiida_blocked_keywords.append(FDFDict.translate_key('dm-use-save-dm'))
+    _aiida_blocked_keywords.append(FDFDict.translate_key('geometry-must-converge'))
     _PSEUDO_SUBFOLDER = './'
     _OUTPUT_SUBFOLDER = './'
     _JSON_FILE = 'time.json'
@@ -169,19 +169,17 @@ def prepare_for_submission(self, folder):  # noqa: MC0001  - is mccabe too compl
         input_params = FDFDict(parameters.get_dict())
 
         # Look for blocked keywords and add the proper values to the dictionary
-        for blocked_key in self._aiida_blocked_keywords:
-            canonical_blocked = FDFDict.translate_key(blocked_key)
-            for key in input_params:
-                if key == canonical_blocked:
-                    raise InputValidationError(
-                        "You cannot specify explicitly the '{}' flag in the "
-                        "input parameters".format(input_params.get_last_untranslated_key(key))
-                    )
-                if "pao" in key:
-                    raise InputValidationError(
-                        "You can not put PAO options in the parameters input port "
-                        "they belong to the basis input port "
-                    )
+        for key in input_params:
+            if "pao" in key:
+                raise InputValidationError(
+                    "You can not put PAO options in the parameters input port "
+                    "they belong to the basis input port "
+                )
+            if key in self._aiida_blocked_keywords:
+                raise InputValidationError(
+                    "You cannot specify explicitly the '{}' flag in the "
+                    "input parameters".format(input_params.get_last_untranslated_key(key))
+                )
 
         input_params.update({'system-name': self.inputs.metadata.options.prefix})
         input_params.update({'system-label': self.inputs.metadata.options.prefix})
@@ -286,13 +284,43 @@ def prepare_for_submission(self, folder):  # noqa: MC0001  - is mccabe too compl
         #BandLinesScale =pi/a is not supported at the moment because currently
         #a=1 always. BandLinesScale ReciprocalLatticeVectors is always set
         if bandskpoints is not None:
+            #first, we check that the user constracted the kpoints using the cell
+            #of the input structure, and not a random cell. This helps parsing
+            kpcell = bandskpoints.get_attribute("cell", None)
+            if kpcell:
+                if kpcell != structure.cell:
+                    raise ValueError(
+                        'The cell used for `bandskpoints` must be the same of the input structure.'
+                        'Alternatively do not set any cell to the bandskpoints.'
+                    )
+            #second we rise a warning about consequences when the cell is relaxed
+            var_cell_keys = [FDFDict.translate_key("md-variable-cell"), FDFDict.translate_key("md-constant-volume")]
+            var_cell_keys.append(FDFDict.translate_key("md-relax-cell-only"))
+            for key in input_params:
+                if key in var_cell_keys:
+                    logline = (
+                        "Requested calculation of bands after a relaxation with variable cell! " +
+                        "If the symmetry of the cell will change, the kpoints path for bands will be wrong. " +
+                        "It is suggested to use the `BandGapWorkChain` instead."
+                    )
+                    if isinstance(input_params[key], str):
+                        if FDFDict.translate_key(input_params[key]) in ["t", "true", "yes"]:
+                            self.logger.warning(logline)
+                            break
+                    else:
+                        if input_params[key] is True:
+                            self.logger.warning(logline)
+                            break
+            #the band line scale
             bandskpoints_card_list = ["BandLinesScale ReciprocalLatticeVectors\n"]
+            #set the BandPoints
             if bandskpoints.labels is None:
                 bandskpoints_card_list.append("%block BandPoints\n")
                 for kpo in bandskpoints.get_kpoints():
                     bandskpoints_card_list.append("{0:8.3f} {1:8.3f} {2:8.3f} \n".format(kpo[0], kpo[1], kpo[2]))
                 fbkpoints_card = "".join(bandskpoints_card_list)
                 fbkpoints_card += "%endblock BandPoints\n"
+            #set the BandLines
             else:
                 bandskpoints_card_list.append("%block BandLines\n")
                 savindx = []

aiida_siesta/calculations/tkdict.py

@@ -43,12 +43,12 @@ def __init__(self, inp_dict=None):  #*args, **kw):
         # _storage is internal dictionary stored as: {<translated_key>: (<value>, <initial_key>), }
         self._storage = {}
 
-        if inp_dict:
+        if inp_dict is not None:
             if not isinstance(inp_dict, dict):
                 message = 'invalid argument for `{}`: it only accepts a dictionary'.format(self.__class__.__name__)
                 raise RuntimeError(message)
 
-        if inp_dict:
+        if inp_dict is not None:
             for inp_key in inp_dict:
                 self[inp_key] = inp_dict[inp_key]
 

aiida_siesta/data/psf.py

@@ -404,7 +404,7 @@ def get_psf_groups(cls, filter_elements=None, user=None):
         query = QueryBuilder()
         query.append(PsfFamily, tag='group', project='*')
 
-        if user:
+        if user is not None:
             query.append(User, filters={'email': {'==': user}}, with_group='group')
 
         if isinstance(filter_elements, str):

aiida_siesta/data/psml.py

@@ -420,7 +420,7 @@ def get_psml_groups(cls, filter_elements=None, user=None):
 
         query.append(PsmlFamily, tag='group', project='*')
 
-        if user:
+        if user is not None:
             query.append(User, filters={'email': {'==': user}}, with_group='group')
 
         if isinstance(filter_elements, str):

aiida_siesta/docs/conf.py

@@ -34,6 +34,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx_copybutton',
     "sphinx_rtd_theme",
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
@@ -70,9 +71,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.1.0'
+version = u'1.1.1'
 # The full version, including alpha/beta/rc tags.
-release = u'1.1.0'
+release = u'1.1.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

aiida_siesta/docs/index.rst

@@ -92,6 +92,15 @@ Workflows
    workflows/index
 ..
    
+Tutorials
+=========
+
+.. toctree::
+   :maxdepth: 4
+
+   tutorials/index
+
+
 
 Indices and tables
 ==================