Merge pull request #117 from siesta-project/Rel1.3.0

Rel1.3.0
siesta-project · Mar 8, 2022 · 932192d · 932192d
2 parents cfbdd13 + 8c083d1
commit 932192d
Show file tree

Hide file tree

Showing 78 changed files with 55,243 additions and 1,661 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,22 @@
 # Changelog
 
+## v1.3.0
+
+Version compatible with aiida-core>=1.3.0,<2.0.0.
+
+### Improvements
+- Introduce dedicated support for optical calculations. In particular,
+  dedicated inputs are created for the `SiestaCalulation` and `SiestaBaseWorkChain`.
+  Moreover a `EpsilonWorkChain` workchain is created to automatically
+  obtain the electronic contribution to the static dielectric constant.
+- Introduce `SiestaBaseNEBWorkChain`, the core building block for the creation of workflows that enable
+  the search of the Minimum Energy Pathway (MEP) connecting two local minima of the potential energy surface
+  through the Nudge Elastic Band (NEB) method.
+
+### Bug fixes
+- Clarify units of stress.
+- The `SiestaBaseWorkChain` now correcty handle LUA inputs.
+
 ## v1.2.0
 
 Version compatible with aiida-core>=1.3.0,<2.0.0.

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,9 +4,8 @@ include CHANGELOG.md
 include PyPI-README.rst
 include LICENSE.txt
 graft aiida_siesta/examples/fixtures
-recursive-include aiida_siesta/examples/ *.txt *.psf *.psml *.cif 00_README
+recursive-include aiida_siesta/examples/ 00_README
 include aiida_siesta/utils/protocols_system/*.yaml
 include aiida_siesta/utils/*.yaml
 prune tests
-prune aiida_siesta/docs/tutorials/first_workchain
-prune aiida_siesta/docs/tutorials/data_icn2_2020
+prune aiida_siesta/docs
diff --git a/PyPI-README.rst b/PyPI-README.rst
@@ -1,7 +1,7 @@
 AiiDA Siesta plugins and workflows
 ==================================
 
-A plugin to interface the `Siesta DFT code <https://icmab.es/siesta/>`_
+A plugin to interface the `Siesta DFT code <https://siesta-project.org/siesta/>`_
 to the `AiiDA system <http://www.aiida.net/>`_.
 
 Documentation can be found in:

diff --git a/README.rst b/README.rst
@@ -1,7 +1,7 @@
 AiiDA Siesta plugins and workflows
 ==================================
 
-A plugin to interface the `Siesta DFT code <https://icmab.es/siesta/>`_
+A plugin to interface the `Siesta DFT code <https://siesta-project.org/siesta/>`_
 to the `AiiDA system <http://www.aiida.net/>`_.
 
 Documentation can be found in:
@@ -14,19 +14,17 @@ this distribution).
 Acknowledgements
 ----------------
 
-This work is supported by the [MARVEL National Centre for Competency
-in Research](<http://nccr-marvel.ch>) funded by the `Swiss National
-Science Foundation <http://www.snf.ch/en>`_, as well as by the `MaX
+This work is supported by the `MaX
 European Centre of Excellence <http://www.max-centre.eu/>`_ funded by
 the Horizon 2020 INFRAEDI-2018-1 program, Grant No. 824143, by the
 `INTERSECT <https://intersect-project.eu/>`_  (Interoperable material-to-device simulation box for
 disruptive electronics) project, funded by Horizon 2020 under grant
 agreement No 814487, and by the Spanish MINECO (projects
 FIS2012-37549-C05-05 and FIS2015-64886-C5-4-P)
+We thank the AiiDA team, who are also supported by the
+`MARVEL National Centre for Competency in Research <http://nccr-marvel.ch>`_
+funded by the `Swiss National Science Foundation <http://www.snf.ch/en>`_
 
-.. figure:: aiida_siesta/docs/miscellaneous/logos/MARVEL.png
-    :alt: MARVEL
-    :target: http://nccr-marvel.ch
 
 .. figure:: aiida_siesta/docs/miscellaneous/logos/MaX.png
     :alt: MaX
@@ -39,3 +37,7 @@ FIS2012-37549-C05-05 and FIS2015-64886-C5-4-P)
 .. figure:: aiida_siesta/docs/miscellaneous/logos/MINECO-AEI.png
     :alt: MINECO-AEI
     :target: http://www.mineco.gob.es/
+
+.. figure:: aiida_siesta/docs/miscellaneous/logos/MARVEL.png
+    :alt: MARVEL
+    :target: http://nccr-marvel.ch
diff --git a/aiida_siesta/__init__.py b/aiida_siesta/__init__.py
@@ -1,2 +1,2 @@
 """The official AiiDA plugin for Siesta."""
-__version__ = '1.2.0'
+__version__ = '1.3.0'
diff --git a/aiida_siesta/calculations/siesta.py b/aiida_siesta/calculations/siesta.py
@@ -47,6 +47,20 @@ def internal_structure(structure, basis_dict=None):
     return tweaked
 
 
+def validate_optical(value, _):
+    """
+    Validate the optical input.
+    """
+    if value:
+        input_params = FDFDict(value.get_dict())
+        if "opticalpolarizationtype" in input_params:
+            if input_params["opticalpolarizationtype"] in ["polarized", "unpolarized"]:
+                if "%block opticalvector" not in input_params:
+                    return "An optical vector must be specified for `polarized` and `unpolarized` polarization types"
+        if "%block opticalmesh" not in input_params:
+            return "An optical-mesh block must always be defined. For molecules set to [1 1 1]"
+
+
 def validate_pseudos(value, _):
     """
     Only used to throw deprecation warnings. Can be deleted in v2.0.0
@@ -107,7 +121,15 @@ def validate_parameters(value, _):
         input_params = FDFDict(value.get_dict())
         for key in input_params:
             if "pao" in key:
-                return "you can't have PAO options in the parameters input port, they belong to the basis input port."
+                return "you can't have PAO options in the parameters input port, they belong to the `basis` input port."
+            #This will return error in v2.0. Now only warning for back compatibility.
+            if "optical" in key:
+                import warnings
+                message = (
+                    "you shouldn't have optical options in the parameters input port, " +
+                    "they belong to the `optical` input port."
+                )
+                warnings.warn(message)  #return message
             if key in SiestaCalculation._aiida_blocked_keywords:
                 message = (
                     f"you can't specify explicitly the '{input_params.get_last_untranslated_key(key)}' flag " +
@@ -191,23 +213,23 @@ def validate_inputs(value, _):
             return "No pseudopotentials nor ions specified in input"
         quantity = 'pseudos'
 
-    if 'basis' in value:
-        structure = internal_structure(value["structure"], value["basis"].get_dict())
-        if structure is None:
-            return "Not possibe to specify `floating_sites` (ghosts) with the same name of a structure kind."
-    else:
-        structure = value["structure"]
-
-    #Check each kind in the structure (including freshly added ghosts) have a corresponding pseudo or ion
-    kinds = [kind.name for kind in structure.kinds]
-    if set(kinds) != set(value[quantity].keys()):
-        ps_io = ', '.join(list(value[quantity].keys()))
-        kin = ', '.join(list(kinds))
-        string_out = (
-            'mismatch between defined pseudos/ions and the list of kinds of the structure\n' +
-            f' pseudos/ions: {ps_io} \n kinds(including ghosts): {kin}'
-        )
-        return string_out
+    if 'structure' in value:  #Some subclasses might make structure optional
+        if 'basis' in value:
+            structure = internal_structure(value["structure"], value["basis"].get_dict())
+            if structure is None:
+                return "Not possibe to specify `floating_sites` (ghosts) with the same name of a structure kind."
+        else:
+            structure = value["structure"]
+        #Check each kind in the structure (including freshly added ghosts) have a corresponding pseudo or ion
+        kinds = [kind.name for kind in structure.kinds]
+        if set(kinds) != set(value[quantity].keys()):
+            ps_io = ', '.join(list(value[quantity].keys()))
+            kin = ', '.join(list(kinds))
+            string_out = (
+                'mismatch between defined pseudos/ions and the list of kinds of the structure\n' +
+                f' pseudos/ions: {ps_io} \n kinds(including ghosts): {kin}'
+            )
+            return string_out
 
 
 class SiestaCalculation(CalcJob):
@@ -255,6 +277,13 @@ def define(cls, spec):
 
         # Input nodes
         spec.input('code', valid_type=orm.Code, help='Input code')
+        spec.input(
+            'optical',
+            valid_type=orm.Dict,
+            help='Specifications for optical properties',
+            required=False,
+            validator=validate_optical
+        )
         spec.input('structure', valid_type=orm.StructureData, help='Input structure', validator=validate_structure)
         spec.input(
             'kpoints', valid_type=orm.KpointsData, help='Input kpoints', required=False, validator=validate_kpoints
@@ -284,7 +313,7 @@ def define(cls, spec):
         # Parameters are in a separate dictionary to enable a reduced set of 'universal' scripts for particular uses.
         # Input files (e.g., image files for NEB) should be packaged in a FolderData object.
         # Files to be retrieved should be specified in a list o# path specifications.
-        spec.input_namespace('lua', help='Script and files for the Lua engine')
+        spec.input_namespace('lua', help='Script and files for the Lua engine', required=False)
         spec.input('lua.script', valid_type=orm.SinglefileData, required=False)
         spec.input('lua.parameters', valid_type=orm.Dict, required=False)
         spec.input('lua.input_files', valid_type=orm.FolderData, required=False)
@@ -306,6 +335,7 @@ def define(cls, spec):
         spec.output('output_structure', valid_type=StructureData, required=False, help='Optional relaxed structure')
         spec.output('bands', valid_type=BandsData, required=False, help='Optional band structure')
         spec.output('forces_and_stress', valid_type=ArrayData, required=False, help='Optional forces and stress')
+        spec.output('optical_eps2', valid_type=ArrayData, required=False, help='Optional eps2 optical data')
         spec.output_namespace('ion_files', valid_type=IonData, dynamic=True, required=False)
 
         # Option that allows access through node.res should be existing output node and a Dict
@@ -314,6 +344,7 @@ def define(cls, spec):
         # Exit codes for specific errors. Useful for error handeling in workchains
         spec.exit_code(453, 'BANDS_PARSE_FAIL', message='Failure while parsing the bands file')
         spec.exit_code(452, 'BANDS_FILE_NOT_PRODUCED', message='Bands analysis was requested, but file is not present')
+        spec.exit_code(454, 'EPS2_FILE_NOT_PRODUCED', message='Optical calculation requested, but file is not present')
         spec.exit_code(450, 'SCF_NOT_CONV', message='Calculation did not reach scf convergence!')
         spec.exit_code(451, 'GEOM_NOT_CONV', message='Calculation did not reach geometry convergence!')
         spec.exit_code(350, 'UNEXPECTED_TERMINATION', message='Statement "Job completed" not detected, unknown error')
@@ -387,6 +418,11 @@ def prepare_for_submission(self, folder):  # noqa: MC0001  - is mccabe too compl
         else:
             bandskpoints = None
 
+        if 'optical' in self.inputs:
+            optical = self.inputs.optical
+        else:
+            optical = None
+
         if 'parent_calc_folder' in self.inputs:
             parent_calc_folder = self.inputs.parent_calc_folder
         else:
@@ -565,6 +601,20 @@ def prepare_for_submission(self, folder):  # noqa: MC0001  - is mccabe too compl
                 fbkpoints_card += "%endblock BandLines\n"
             del bandskpoints_card_list
 
+        # ------------------------------------ OPTICAL-KEYS ----------------------------------
+        # Optical properties info. Again, this is just given in a standard dictionary,
+        # but we make sure that the option is turned on.
+        if optical is not None:
+            optical_dict = FDFDict(optical.get_dict())
+            optical_dict.update({'opticalcalculation': True})
+            #if '%block opticalmesh' not in optical_dict:
+            #    if kpoints is not None:
+            #        mesh, offset = kpoints.get_kpoints_mesh()
+            #        optical_dic["%block optical-mesh"] =
+            #    "{0:6} {1:6} {2:6}\n %endblock optical-mesh".format(mesh[0], mesh[1], mesh[2]))
+            #    else:
+            #       optical_dic["%block optical-mesh"] = "1 1 1\n %endblock optical-mesh"
+
         # ================================= Operations for restart =================================
         # The presence of a 'parent_calc_folder' input node signals that we want to
         # get something from there, as indicated in the self._restart_copy_from attribute.
@@ -597,6 +647,11 @@ def prepare_for_submission(self, folder):  # noqa: MC0001  - is mccabe too compl
                 infile.write("#\n# -- Basis Set Info follows\n#\n")
                 for k, v in basis_dict.items():
                     infile.write("%s %s\n" % (k, v))
+            # Optical properties info.
+            if optical is not None:
+                infile.write("#\n# -- Optical properties Info follows\n#\n")
+                for k, v in optical_dict.items():
+                    infile.write("%s %s\n" % (k, v))
             # Write previously generated cards now
             infile.write("#\n# -- Structural Info follows\n#\n")
             infile.write(atomic_species_card)
@@ -648,9 +703,12 @@ def prepare_for_submission(self, folder):  # noqa: MC0001  - is mccabe too compl
         calcinfo.codes_info = [codeinfo]
         # Retrieve by default: the output file, the xml file, the messages file, and the json timing file.
         # If bandskpoints, also the bands file is added to the retrieve list.
+        # If getting optical props, also the .EPSIMG file is added.
         calcinfo.retrieve_list = []
         xml_file = str(metadataoption.prefix) + ".xml"
         bands_file = str(metadataoption.prefix) + ".bands"
+        eps2_file = str(metadataoption.prefix) + ".EPSIMG"
+
         calcinfo.retrieve_list.append(metadataoption.output_filename)
         calcinfo.retrieve_list.append(xml_file)
         calcinfo.retrieve_list.append(self._JSON_FILE)
@@ -661,6 +719,9 @@ def prepare_for_submission(self, folder):  # noqa: MC0001  - is mccabe too compl
         if bandskpoints is not None:
             calcinfo.retrieve_list.append(bands_file)
 
+        if optical is not None:
+            calcinfo.retrieve_list.append(eps2_file)
+
         if lua_retrieve_list is not None:
             calcinfo.retrieve_list += lua_retrieve_list.get_list()
 

diff --git a/aiida_siesta/docs/conf.py b/aiida_siesta/docs/conf.py
@@ -71,9 +71,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.2.0'
+version = u'1.3.0'
 # The full version, including alpha/beta/rc tags.
-release = u'1.2.0'
+release = u'1.3.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/aiida_siesta/docs/index.rst b/aiida_siesta/docs/index.rst
@@ -9,7 +9,7 @@ Welcome to the AiiDA-Siesta documentation!
 ..
 
 The aiida-siesta python package interfaces the SIESTA DFT code
-(http://icmab.es/siesta) with the AiiDA framework
+(https://siesta-project.org/siesta/) with the AiiDA framework
 (http://www.aiida.net).  The package contains: plugins for SIESTA
 itself and for other utility programs, new data structures, and basic
 workflows. It is distributed under the MIT license and available from
@@ -39,20 +39,29 @@ under the supervision of Alberto Garcia.
 Pol Febrer contributed the SiestaIterator and SiestaConverger workflows, including the underline
 abstract classes system.
 
-We acknowledge partial support from the Spanish Research Agency (projects
-FIS2012-37549-C05-05, FIS2015-64886-C5-4-P and PGC2018-096955-B-C44) and  by the `MaX 
-European Centre of Excellence <http://www.max-centre.eu/>`_ funded by the Horizon 2020 
-INFRAEDI-2018-1 program, Grant No. 824143.
+This work is supported by the `MaX
+European Centre of Excellence <http://www.max-centre.eu/>`_ funded by
+the Horizon 2020 INFRAEDI-2018-1 program, Grant No. 824143, and by the
+`INTERSECT <https://intersect-project.eu/>`_  (Interoperable material-to-device simulation box for
+disruptive electronics) project, funded by Horizon 2020 under grant
+agreement No 814487, as well as by the Spanish MINECO (projects
+FIS2012-37549-C05-05 and FIS2015-64886-C5-4-P)
 
 We thank the AiiDA team, who are also supported by the `MARVEL National Centre for Competency in Research <http://nccr-marvel.ch>`_
 funded by the `Swiss National Science Foundation <http://www.snf.ch/en>`_
 
-.. figure:: miscellaneous/logos/MINECO-AEI.png
-    :alt: MINECO-AEI
 .. figure:: miscellaneous/logos/MaX.png
     :alt: MaX
+    :target: http://www.max-centre.eu/
+.. figure:: miscellaneous/logos/INTERSECT.png
+    :alt: INTERSECT
+    :target: http://intersect-project.eu/
+.. figure:: miscellaneous/logos/MINECO-AEI.png
+    :alt: MINECO-AEI
+    :target: http://www.mineco.gob.es/
 .. figure:: miscellaneous/logos/MARVEL.png
     :alt: MARVEL
+    :target: http://nccr-marvel.ch
 
 Contents:
 ---------

diff --git a/aiida_siesta/docs/installation.rst b/aiida_siesta/docs/installation.rst
@@ -1,5 +1,5 @@
-Installation
-++++++++++++
+Installation and dependences
+++++++++++++++++++++++++++++
 
 It would be a good idea to create and switch to a new python virtual
 environment before the installation.
@@ -29,6 +29,10 @@ in order to configure aiida.
         verdi daemon restart
 
 
+Since version 1.2.0, ``aiida-siesta`` also depends on ``sisl`` (https://github.com/zerothi/sisl). For the moment
+``sisl`` is used only to facilitate the management of basis orbitals, but a closer integration among the
+two packages is foreseen in the future.
+
 For developers
 --------------