From 77c790f4d79a56f624d4069a334ec2f97a9bb5cc Mon Sep 17 00:00:00 2001 From: Bosoni Date: Wed, 6 Nov 2019 18:10:07 +0100 Subject: [PATCH 01/10] Improved documentation for input bandskpoint First commit for the improvement of the documentation related to the bands calculation part. Mostly interested in looking at the appearence of the changing as I'm using .rst for the first time. Missing the part about outputs. --- aiida_siesta/docs/plugins/siesta.rst | 69 +++++++++++++++++++++++++--- 1 file changed, 63 insertions(+), 6 deletions(-) diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index 09783229..f55647f0 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -125,12 +125,66 @@ If this node is not present, only the Gamma point is used for sampling. * **bandskpoints**, class :py:class:`KpointsData ` -Reciprocal space points for the calculation of bands. They can be -given as a simple list of k-points, as segments with start and end -point and number of points, or as a complete automatic path, using the -functionality of modern versions of the class. - -If this node is not present, no band structure is computed. +Reciprocal space points for the calculation of bands. +This keyword is meant to facilitate the management of kpoints +exploiting the functionality +of the class :py:class:`KpointsData `. +The full list of kpoints must be passed to the class +and they must be in units of the reciprocal lattice vectors. +Moreover the cell must be set in the :py:class:`KpointsData ` +class. + +This can be achieved manually listing a set of kpoints:: + bandskpoints.set_cell(structure.cell, structure.pbc) + kpp = [(0.500, 0.250, 0.750), (0.500, 0.500, 0.500), (0., 0., 0.)] + bandskpoints.set_kpoints(kpp) +In this case Siesta will create the BandPoints block. + +Alternatively (recommended) the high-symmetry path associated to the +structure under investigation can be +automatically generated through the aiida tool 'get_explicit_kpoints_path'. +Here how to use it:: + from aiida.tools import get_explicit_kpoints_path + symmpath_parameters = Dict(dict={ + 'reference_distance': 0.02, + 'symprec': 0.0001 + }) + kpresult = get_explicit_kpoints_path(s, **symmpath_parameters.get_dict()) + bandskpoints = kpresult['explicit_kpoints'] +Where 's' in the input structure and 'reference_distance' is +the distance between two subsequent kpoints. 'symprec' is the precision +in calculating the + +In this case the block BandLines is set in the Siesta +calculation. + +.. note:: 'get_explicit_kpoints_path' make use of "SeeK-path". + Please cite the `HPKOT paper`_. if you use this tool. + Warning: as explained in the `aiida documentation`_., SeekPath + might modify the structure to follow particular conventions + and the generated kpoints might only + apply on the internally generated 'primitive_structure' and not + on the input structure that was provided. The correct + way to use this tool is to use the generated 'primitive_structure' also for the + Siesta calculation:: + structure = kpresult['primitive_structure'] + +The final option (unrecommended) covers the situation +when one really needs to maintain a specific convention for the +structure or one needs to calculate the bands on a specific path +that is not a high-symmetry direction, the following (very involved) +option is available:: + from aiida.tools.data.array.kpoints.legacy import get_explicit_kpoints_path as legacy_path + kpp = [('A', (0.500, 0.250, 0.750), 'B', (0.500, 0.500, 0.500), 40), + ('B', (0.500, 0.500, 0.500), 'C', (0., 0., 0.), 40)] + tmp=legacy_path(kpp) + bandskpoints.set_cell(structure.cell, structure.pbc) + bandskpoints.set_kpoints(tmp[3]) + bandskpoints.labels=tmp[4] +The legacy "get_explicit_kpoints_path" shares only the name with the function in +"aiida.tools", but it is very different in scope. + +If the keyword node is not present, no band structure is computed. * **settings**, class :py:class:`Dict ` @@ -275,3 +329,6 @@ those files as a list as follows:: settings_dict = { 'additional_retrieve_list': ['aiida.EIG', 'aiida.ORB_INDX'], } + +.. _HPKOT paper: http://dx.doi.org/10.1016/j.commatsci.2016.10.015 +.. _aiida documentation: https://aiida.readthedocs.io/projects/aiida-core/en/latest/apidoc/aiida.tools.html#aiida.tools.get_explicit_kpoints_path From 43b3573d7d404beaa5f9eb2bb46083902d153aea Mon Sep 17 00:00:00 2001 From: Bosoni Date: Thu, 7 Nov 2019 11:03:59 +0100 Subject: [PATCH 02/10] Bandskpoints documentation part 2 Concludes the documentation regarding the bandskpoints part adding a warning about the use of labels. Few information are added to the output bands part. --- aiida_siesta/docs/plugins/siesta.rst | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index f55647f0..bede7aff 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -135,6 +135,7 @@ Moreover the cell must be set in the :py:class:`KpointsData `. + Refrain from the use of 'bandskpoints.labels= ..' in any other + situation apart from the one described above. An incorrect use of the labels + might result in an incorrect parsing of the bands. + * **settings**, class :py:class:`Dict ` @@ -262,9 +270,12 @@ positions refer to the last configuration. Present only if a band calculation is requested (signaled by the presence of a **bandskpoints** input node of class KpointsData) -Contains an array with the list of electronic energies for every +Contains an array with the list of electronic energies (in eV) for every kpoint. For spin-polarized calculations, there is an extra dimension -for spin. +for spin. In this class also the full list of kpoints is stored and they are +in units of 1/Angstrom. Therefore a direct comparison with the Siesta output +SystLabel.bands is possible only after the conversion of Angstrom to Bohr. +The bands are not rescaled by the Fermi energy. No trajectories have been implemented yet. From 3210a5528627f6ace55479cb79d2725babc49ff9 Mon Sep 17 00:00:00 2001 From: Bosoni Date: Thu, 7 Nov 2019 15:46:08 +0100 Subject: [PATCH 03/10] Final details of bandskpoint documentation Added a sentence in the inputs structure part to clirify the need of passing the structure in Angstrom units. Fixed a small error in the bandskpoints part. --- aiida_siesta/docs/plugins/siesta.rst | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index bede7aff..ce1e3941 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -49,6 +49,8 @@ implemented through the 'name' attribute of the Site objects. For example:: s.append_atom(position=(0.000,0.000,4.442),symbols=['C']) s.append_atom(position=(0.000,0.000,5.604),symbols=['H']) +The class :py:class:`StructureData ` uses Angstrom +as internal units, the cell and atom positions must be specified in Angstrom. * **parameters**, class :py:class:`Dict ` @@ -146,15 +148,11 @@ structure under investigation can be automatically generated through the aiida tool 'get_explicit_kpoints_path'. Here how to use it:: from aiida.tools import get_explicit_kpoints_path - symmpath_parameters = Dict(dict={ - 'reference_distance': 0.02, - 'symprec': 0.0001 - }) + symmpath_parameters = Dict(dict={'reference_distance': 0.02}) kpresult = get_explicit_kpoints_path(s, **symmpath_parameters.get_dict()) bandskpoints = kpresult['explicit_kpoints'] Where 's' in the input structure and 'reference_distance' is -the distance between two subsequent kpoints. 'symprec' is the precision -in calculating the +the distance between two subsequent kpoints. In this case the block BandLines is set in the Siesta calculation. From 337e23b1119b3aa6a06dd62746a4c83ffc776a3f Mon Sep 17 00:00:00 2001 From: Bosoni Date: Fri, 8 Nov 2019 15:24:45 +0100 Subject: [PATCH 04/10] Explanded documentation Introduced a section about "submitting the calculation". More extensive explanetion of inputs. Improved the visual impression. Also added reference to example, but in an incomplete way as I want to test the example before pull request --- aiida_siesta/docs/plugins/siesta.rst | 477 ++++++++++++++++----------- 1 file changed, 291 insertions(+), 186 deletions(-) diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index ce1e3941..948e8ba4 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -17,52 +17,65 @@ can be found in the development platform Inputs ------ -* **code**, class :py:class:`Code ` - -A code object linked to a Siesta executable. - -* **structure**, class :py:class:`StructureData ` - -A structure. Siesta employs "species labels" to implement special -conditions (such as basis set characteristics) for specific atoms -(e.g., surface atoms might have a richer basis set). This is -implemented through the 'name' attribute of the Site objects. For example:: - - alat = 15. # angstrom - cell = [[alat, 0., 0.,], - [0., alat, 0.,], - [0., 0., alat,], - ] - - # Benzene molecule with a special carbon atom - s = StructureData(cell=cell) - s.append_atom(position=(0.000,0.000,0.468),symbols=['H']) - s.append_atom(position=(0.000,0.000,1.620),symbols=['C']) - s.append_atom(position=(0.000,-2.233,1.754),symbols=['H']) - s.append_atom(position=(0.000,2.233,1.754),symbols=['H']) - s.append_atom(position=(0.000,-1.225,2.327),symbols='C',name="Cred") - s.append_atom(position=(0.000,1.225,2.327),symbols=['C']) - s.append_atom(position=(0.000,-1.225,3.737),symbols=['C']) - s.append_atom(position=(0.000,1.225,3.737),symbols=['C']) - s.append_atom(position=(0.000,-2.233,4.311),symbols=['H']) - s.append_atom(position=(0.000,2.233,4.311),symbols=['H']) - s.append_atom(position=(0.000,0.000,4.442),symbols=['C']) - s.append_atom(position=(0.000,0.000,5.604),symbols=['H']) - -The class :py:class:`StructureData ` uses Angstrom -as internal units, the cell and atom positions must be specified in Angstrom. - -* **parameters**, class :py:class:`Dict ` - -A dictionary with scalar fdf variables and blocks, which are the -basic elements of any Siesta input file. A given Siesta fdf file -can be cast almost directly into this dictionary form, except that -some items (for structure data) are blocked. Any units are -specified for now as part of the value string. Blocks are entered -by using an appropriate key and Python's multiline string -constructor. For example:: - - { +* **code**, class :py:class:`Code `, *Mandatory* + + A code object linked to a Siesta executable. + If you setup the code ``Siesta4.0.1`` on machine ``kelvin`` following the `aiida guidelines`_, + then the code is selected in this way:: + + codename = 'Siesta4.0.1@kelvin' + from aiida.orm import Code + code = Code.get_from_string(codename) + + +* **structure**, class :py:class:`StructureData `, *Mandatory* + + A structure. Siesta employs "species labels" to implement special + conditions (such as basis set characteristics) for specific atoms + (e.g., surface atoms might have a richer basis set). This is + implemented through the 'name' attribute of the Site objects. For example:: + from aiida.orm import StructureData + + alat = 15. # angstrom + cell = [[alat, 0., 0.,], + [0., alat, 0.,], + [0., 0., alat,], + ] + + # Benzene molecule with a special carbon atom + s = StructureData(cell=cell) + s.append_atom(position=(0.000,0.000,0.468),symbols=['H']) + s.append_atom(position=(0.000,0.000,1.620),symbols=['C']) + s.append_atom(position=(0.000,-2.233,1.754),symbols=['H']) + s.append_atom(position=(0.000,2.233,1.754),symbols=['H']) + s.append_atom(position=(0.000,-1.225,2.327),symbols='C',name="Cred") + s.append_atom(position=(0.000,1.225,2.327),symbols=['C']) + s.append_atom(position=(0.000,-1.225,3.737),symbols=['C']) + s.append_atom(position=(0.000,1.225,3.737),symbols=['C']) + s.append_atom(position=(0.000,-2.233,4.311),symbols=['H']) + s.append_atom(position=(0.000,2.233,4.311),symbols=['H']) + s.append_atom(position=(0.000,0.000,4.442),symbols=['C']) + s.append_atom(position=(0.000,0.000,5.604),symbols=['H']) + + The class :py:class:`StructureData ` uses Angstrom + as internal units, the cell and atom positions must be specified in Angstrom. + + The :py:class:`StructureData ` can also import + ase structure or pymatgen structures. This two tools can be used to load + structure from files. See example in .... + +* **parameters**, class :py:class:`Dict `, *Mandatory* + A dictionary with scalar fdf variables and blocks, which are the + basic elements of any Siesta input file. A given Siesta fdf file + can be cast almost directly into this dictionary form, except that + some items (for structure data) are blocked. Any units are + specified for now as part of the value string. Blocks are entered + by using an appropriate key and Python's multiline string + constructor. For example:: + + from aiida.orm import Dict + + parameters = Dict(dict={ "mesh-cutoff": "200 Ry", "dm-tolerance": "0.0001", "%block example-block": @@ -70,132 +83,221 @@ constructor. For example:: first line second line %endblock example-block""", - } + }) -Note that Siesta fdf keywords allow '.', '-', (or nothing) as internal -separators. AiiDA does not allow the use of '.' in nodes to be -inserted in the database, so it should not be used in the input script -(or removed before assigning the dictionary to the Dict -instance). For legibility, a single dash ('-') is suggested, as in the -examples above. + Note that Siesta fdf keywords allow '.', '-', (or nothing) as internal + separators. AiiDA does not allow the use of '.' in nodes to be + inserted in the database, so it should not be used in the input script + (or removed before assigning the dictionary to the Dict + instance). For legibility, a single dash ('-') is suggested, as in the + examples above. * **pseudos**, input namespace of class :py:class:`PsfData ` - OR class :py:class:`PsmlData ` + OR class :py:class:`PsmlData `, *Mandatory* + + The PsfData and PsmlData classes have been implemented along the lines of the Upf class for QE. + + One pseudopotential file per atomic element. Several species (in the + Siesta sense, which allows the same element to be treated differently + according to its environment) can share the same pseudopotential. For the example + above:: + + import os + from aiida_siesta.data.psf import PsfData + + pseudo_file_to_species_map = [ ("C.psf", ['C', 'Cred']),("H.psf", 'H')] + pseudos_dict = {} + for fname, kinds, in pseudo_file_to_species_map: + absname = os.path.realpath(os.path.join("path/to/file",fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + for j in kinds: + pseudos_dict[j]=pseudo + + Alternatively, a pseudo for every atomic species can be set with the + **use_pseudos_from_family** method, if a family of pseudopotentials + has been installed. (But the family approach does not yet support + multiple species sharing the same pseudopotential.) For an example ... + + .. note:: The verdi command-line interface now supports entry points + defined by external packages. We have implemented `verdi data + psf` and `verdi data psml` suites of commands: `uploadfamily`, `exportfamily`, and + `listfamilies`. + + It can be argued that a single `SiestaPseudo` class, with psf and psml + subclasses, might have been implemented. But the `PsmlData` class aims + to transcend Siesta and to be used by other codes. + +* **basis**, class :py:class:`Dict `, *Optional* + + A dictionary specifically intended for basis set information. It + follows the same structure as the **parameters** element, including + the allowed use of fdf-block items. This raw interface allows a + direct translation of the myriad basis-set options supported by the + Siesta program. In future we might have a more structured input for + basis-set information. + An example:: + + from aiida.orm import Dict + + basis_dict = { + 'pao-basistype': + 'split', + 'pao-splitnorm': + 0.150, + 'pao-energyshift': + '0.020 Ry', + '%block pao-basis-sizes': + """ + C SZP + Cred SZ + H SZP + %endblock pao-basis-sizes""", + } + + basis = Dict(dict=basis_dict) + + In case no basis is set, the Siesta calculation will not include + any basis specification and it will run with the default DZP. + +* **kpoints**, class :py:class:`KpointsData `, *Optional* + Reciprocal space points for the full sampling of the BZ during the + self-consistent-field iteration. It must be given in mesh form. There is no support + yet for Siesta's kgrid-cutoff keyword:: + from aiida.orm import KpointsData + kpoints=KpointsData() + kpoints_mesh = 5 + kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) + + If this node is not present, only the Gamma point is used for sampling. + +* **bandskpoints**, class :py:class:`KpointsData `, *Optional* + Reciprocal space points for the calculation of bands. + This keyword is meant to facilitate the management of kpoints + exploiting the functionality + of the class :py:class:`KpointsData `. + The full list of kpoints must be passed to the class + and they must be in units of the reciprocal lattice vectors. + Moreover the cell must be set in the :py:class:`KpointsData ` + class. + + This can be achieved manually listing a set of kpoints:: + + from aiida.orm import KpointsData + bandskpoints=KpointsData() + bandskpoints.set_cell(structure.cell, structure.pbc) + kpp = [(0.500, 0.250, 0.750), (0.500, 0.500, 0.500), (0., 0., 0.)] + bandskpoints.set_kpoints(kpp) + In this case the Siesta input will present the BandPoints block. + + Alternatively (recommended) the high-symmetry path associated to the + structure under investigation can be + automatically generated through the aiida tool 'get_explicit_kpoints_path'. + Here how to use it:: + from aiida.orm import KpointsData + bandskpoints=KpointsData() + from aiida.tools import get_explicit_kpoints_path + symmpath_parameters = Dict(dict={'reference_distance': 0.02}) + kpresult = get_explicit_kpoints_path(s, **symmpath_parameters.get_dict()) + bandskpoints = kpresult['explicit_kpoints'] + Where 's' in the input structure and 'reference_distance' is + the distance between two subsequent kpoints. + In this case the block BandLines is set in the Siesta + calculation. + + .. note:: 'get_explicit_kpoints_path' make use of "SeeK-path". + Please cite the `HPKOT paper`_ if you use this tool. + Warning: as explained in the `aiida documentation`_, SeekPath + might modify the structure to follow particular conventions + and the generated kpoints might only + apply on the internally generated 'primitive_structure' and not + on the input structure that was provided. The correct + way to use this tool is to use the generated 'primitive_structure' also for the + Siesta calculation:: + structure = kpresult['primitive_structure'] + + + + The final option (unrecommended) covers the situation + when one really needs to maintain a specific convention for the + structure or one needs to calculate the bands on a specific path + that is not a high-symmetry direction, the following (very involved) + option is available:: + from aiida.orm import KpointsData + bandskpoints=KpointsData() + from aiida.tools.data.array.kpoints.legacy import get_explicit_kpoints_path as legacy_path + kpp = [('A', (0.500, 0.250, 0.750), 'B', (0.500, 0.500, 0.500), 40), + ('B', (0.500, 0.500, 0.500), 'C', (0., 0., 0.), 40)] + tmp=legacy_path(kpp) + bandskpoints.set_cell(structure.cell, structure.pbc) + bandskpoints.set_kpoints(tmp[3]) + bandskpoints.labels=tmp[4] + The legacy "get_explicit_kpoints_path" shares only the name with the function in + "aiida.tools", but it is very different in scope. -The PsfData and PsmlData classes have been implemented along the lines of the Upf class for QE. + The full list of cases can be explored looking at the example ... -One pseudopotential file per atomic element. Several species (in the -Siesta sense, which allows the same element to be treated differently -according to its environment) can share the same pseudopotential. For the example -above:: + If the keyword node **bandskpoints** is not present, no band structure is computed. - pseudo_file_to_species_map = [ ("C.psf", ['C', 'Cred']), - ("H.psf", 'H') - ] + .. warning:: The implementation relies on the correct description of + the labels in the class :py:class:`KpointsData `. + Refrain from the use of 'bandskpoints.labels' in any other + situation apart from the one described above. An incorrect use of the labels + might result in an incorrect parsing of the bands. -Alternatively, a pseudo for every atomic species can be set with the -**use_pseudos_from_family** method, if a family of pseudopotentials -has been installed. (But the family approach does not yet support -multiple species sharing the same pseudopotential.) +* **settings**, class :py:class:`Dict ` , *Optional* + An optional dictionary that activates non-default operations. For a list of possible + values to pass, see the section on :ref:`advanced features `. -.. note:: The verdi command-line interface now supports entry points - defined by external packages. We have implemented `verdi data - psf` and `verdi data psml` suites of commands: `uploadfamily`, `exportfamily`, and - `listfamilies`. +Submitting the calculation +-------------------------- -It can be argued that a single `SiestaPseudo` class, with psf and psml -subclasses, might have been implemented. But the `PsmlData` class aims -to transcend Siesta and to be used by other codes. +Once all the inputs above are set, the subsequent step consists in passing them to the +calculation class and run/submit it. -* **basis**, class :py:class:`Dict ` - -A dictionary specifically intended for basis set information. It -follows the same structure as the **parameters** element, including -the allowed use of fdf-block items. This raw interface allows a -direct translation of the myriad basis-set options supported by the -Siesta program. In future we might have a more structured input for -basis-set information. - -* **kpoints**, class :py:class:`KpointsData ` - -Reciprocal space points for the full sampling of the BZ during the -self-consistent-field iteration. It must be given in mesh form. There is no support -yet for Siesta's kgrid-cutoff keyword. +First, the Siesta calculation class is loaded:: + from aiida_siesta.calculations.siesta import SiestaCalculation + builder = SiestaCalculation.get_builder() -If this node is not present, only the Gamma point is used for sampling. +The inputs (defined as in the previous section) are passed to the builder:: + builder.code = code + builder.structure = structure + builder.parameters = parameters + builder.pseudos = pseudos_dict + builder.basis = basis + builder.kpoints = kpoints + builder.bandskpoints = bandskpoints -* **bandskpoints**, class :py:class:`KpointsData ` - -Reciprocal space points for the calculation of bands. -This keyword is meant to facilitate the management of kpoints -exploiting the functionality -of the class :py:class:`KpointsData `. -The full list of kpoints must be passed to the class -and they must be in units of the reciprocal lattice vectors. -Moreover the cell must be set in the :py:class:`KpointsData ` -class. +Finally the resources for the calculation must be set, for instance:: + builder.metadata.options.resources = {'num_machines': 1} + builder.metadata.options.max_wallclock_seconds = 1800 -This can be achieved manually listing a set of kpoints:: +Optionally, label and description:: + builder.metadata.label = 'My generic title' + builder.metadata.description 'My more detailed description' - bandskpoints.set_cell(structure.cell, structure.pbc) - kpp = [(0.500, 0.250, 0.750), (0.500, 0.500, 0.500), (0., 0., 0.)] - bandskpoints.set_kpoints(kpp) -In this case Siesta will create the BandPoints block. - -Alternatively (recommended) the high-symmetry path associated to the -structure under investigation can be -automatically generated through the aiida tool 'get_explicit_kpoints_path'. -Here how to use it:: - from aiida.tools import get_explicit_kpoints_path - symmpath_parameters = Dict(dict={'reference_distance': 0.02}) - kpresult = get_explicit_kpoints_path(s, **symmpath_parameters.get_dict()) - bandskpoints = kpresult['explicit_kpoints'] -Where 's' in the input structure and 'reference_distance' is -the distance between two subsequent kpoints. - -In this case the block BandLines is set in the Siesta -calculation. - -.. note:: 'get_explicit_kpoints_path' make use of "SeeK-path". - Please cite the `HPKOT paper`_ if you use this tool. - Warning: as explained in the `aiida documentation`_, SeekPath - might modify the structure to follow particular conventions - and the generated kpoints might only - apply on the internally generated 'primitive_structure' and not - on the input structure that was provided. The correct - way to use this tool is to use the generated 'primitive_structure' also for the - Siesta calculation:: - structure = kpresult['primitive_structure'] - -The final option (unrecommended) covers the situation -when one really needs to maintain a specific convention for the -structure or one needs to calculate the bands on a specific path -that is not a high-symmetry direction, the following (very involved) -option is available:: - from aiida.tools.data.array.kpoints.legacy import get_explicit_kpoints_path as legacy_path - kpp = [('A', (0.500, 0.250, 0.750), 'B', (0.500, 0.500, 0.500), 40), - ('B', (0.500, 0.500, 0.500), 'C', (0., 0., 0.), 40)] - tmp=legacy_path(kpp) - bandskpoints.set_cell(structure.cell, structure.pbc) - bandskpoints.set_kpoints(tmp[3]) - bandskpoints.labels=tmp[4] -The legacy "get_explicit_kpoints_path" shares only the name with the function in -"aiida.tools", but it is very different in scope. +Run the calculation for interactive run:: + from aiida.engine import run + results = run(builder) +where the results variable will contain a dictionary containing all the nodes that were produced as output. -If the keyword node **bandskpoints** is not present, no band structure is computed. +Or submit it to the deamon to run in backround:: + from aiida.engine import run + calc = submit(builder) +In this case, calc is the calculation node, and not the result dictionary. -.. note:: The implementation relies on the correct description of - the labels in the class :py:class:`KpointsData `. - Refrain from the use of 'bandskpoints.labels= ..' in any other - situation apart from the one described above. An incorrect use of the labels - might result in an incorrect parsing of the bands. +.. note:: In order to inspect the inputs created by AiiDA without + actually running the calculation, we can perform a dry run of the submission process:: + builder.metadata.dry_run = True + builder.metadata.store_provenance = False + This will create the input files, that are available for inspection. +.. note:: The use of the builder makes the process more intuitive, but it + is not mandatory. The inputs can be provided as keywords argument when you + launch the calculation, passing the calculation class as the first argument:: + run(SiestaCalculation, structure=s, pseudos=pseudos, kpoints = kpoints, ...) -* **settings**, class :py:class:`Dict ` - -An optional dictionary that activates non-default operations. For a list of possible -values to pass, see the section on :ref:`advanced features `. +Examples in the folder ... Outputs ------- @@ -210,10 +312,10 @@ functionality should be compiled in and active in the run! * **output_parameters** :py:class:`Dict ` -A dictionary with metadata, scalar result values, a warnings -list, and possibly a timing section. -Units are specified by means of an extra item with '_units' -appended to the key:: + A dictionary with metadata, scalar result values, a warnings + list, and possibly a timing section. + Units are specified by means of an extra item with '_units' + appended to the key:: { "siesta:Version": "siesta-4.0.2", @@ -235,45 +337,45 @@ appended to the key:: "warnings": [ "INFO: Job Completed"] } -The scalar quantities to include are specified in a global-variable -in the parser. Currently they are the Kohn-Sham, Free, Band, and Fermi -energies, and the total spin. These are converted to 'float'. -As this dictionary is sorted, keys for program values and metadata are -intermixed. - -The timing information (if present), includes the global walltime in -seconds, and a decomposition by sections of the code. Most relevant -are typically the `compute_DM` and `setup_H` sections. - -The 'warnings' list contains program messages, labeled as INFO, -WARNING, or FATAL, read directly from a MESSAGES file produced by -Siesta, which include items from the execution of the program and -also a possible 'out of time' condition. This is implemented by -passing to the program the wallclock time specified in the script, -and checking at each scf step for the walltime consumed. This -'warnings' list can be examined by the parser itself to raise an -exception in the FATAL case. + The scalar quantities to include are specified in a global-variable + in the parser. Currently they are the Kohn-Sham, Free, Band, and Fermi + energies, and the total spin. These are converted to 'float'. + As this dictionary is sorted, keys for program values and metadata are + intermixed. + + The timing information (if present), includes the global walltime in + seconds, and a decomposition by sections of the code. Most relevant + are typically the `compute_DM` and `setup_H` sections. + + The 'warnings' list contains program messages, labeled as INFO, + WARNING, or FATAL, read directly from a MESSAGES file produced by + Siesta, which include items from the execution of the program and + also a possible 'out of time' condition. This is implemented by + passing to the program the wallclock time specified in the script, + and checking at each scf step for the walltime consumed. This + 'warnings' list can be examined by the parser itself to raise an + exception in the FATAL case. * **forces_and_stress** :py:class:`ArrayData ` -Contains the final forces (eV/Angstrom) and stresses (GPa) in array form. + Contains the final forces (eV/Angstrom) and stresses (GPa) in array form. * **output_structure** :py:class:`StructureData ` -Present only if the calculation is moving the ions. Cell and ionic -positions refer to the last configuration. + Present only if the calculation is moving the ions. Cell and ionic + positions refer to the last configuration. * **bands**, :py:class:`BandsData ` -Present only if a band calculation is requested (signaled by the -presence of a **bandskpoints** input node of class KpointsData) -Contains an array with the list of electronic energies (in eV) for every -kpoint. For spin-polarized calculations, there is an extra dimension -for spin. In this class also the full list of kpoints is stored and they are -in units of 1/Angstrom. Therefore a direct comparison with the Siesta output -SystLabel.bands is possible only after the conversion of Angstrom to Bohr. -The bands are not rescaled by the Fermi energy. + Present only if a band calculation is requested (signaled by the + presence of a **bandskpoints** input node of class KpointsData) + Contains an array with the list of electronic energies (in eV) for every + kpoint. For spin-polarized calculations, there is an extra dimension + for spin. In this class also the full list of kpoints is stored and they are + in units of 1/Angstrom. Therefore a direct comparison with the Siesta output + SystLabel.bands is possible only after the conversion of Angstrom to Bohr. + The bands are not rescaled by the Fermi energy. No trajectories have been implemented yet. @@ -299,6 +401,8 @@ This approach enables continuation of runs which have failed due to lack of time or insufficient convergence in the allotted number of steps. +Examples are in ... + .. _siesta-advanced-features: Additional advanced features @@ -339,5 +443,6 @@ those files as a list as follows:: 'additional_retrieve_list': ['aiida.EIG', 'aiida.ORB_INDX'], } +.. _aiida guidelines: https://aiida-core.readthedocs.io/en/latest/get_started/computers.html .. _HPKOT paper: http://dx.doi.org/10.1016/j.commatsci.2016.10.015 .. _aiida documentation: https://aiida.readthedocs.io/projects/aiida-core/en/latest/apidoc/aiida.tools.html#aiida.tools.get_explicit_kpoints_path From c64520f729c919210357f0b5909e42dc65ec97d6 Mon Sep 17 00:00:00 2001 From: Bosoni Date: Mon, 11 Nov 2019 10:54:07 +0100 Subject: [PATCH 05/10] Restructure of tests and example folder. From the files in the folder example I selected 14 that covers all the important situation for the understanding of the aiida_siesta plugin. I renamed them example_. In the future, on top of the didactic purpose, they could be used for "integreted" tests that requires the use of a siesta installation. The other files previously in /example are more "unit" tests. I will move them to a folder tests in the main folder of aiida_siesta_plugin. They are not added to this commit, as they are not usable, at the moment, as "unit" tests in the sense we discussed with Sebastian and Giovanni. I'll work on that after the release of b1. Final part of this effort is to run this 14 example to make sure that everithing is fine. This is the priority of the next commit! --- .../examples/plugins/siesta/example_bands.py | 190 ++++++++++++ .../plugins/siesta/example_cif_bands.py | 173 +++++++++++ .../examples/plugins/siesta/example_first.py | 146 +++++++++ .../plugins/siesta/example_geom_fail.py | 144 +++++++++ .../examples/plugins/siesta/example_ldos.py | 199 +++++++++++++ .../plugins/siesta/example_magnetic_bands.py | 142 +++++++++ .../plugins/siesta/example_molecule.py | 233 +++++++++++++++ .../plugins/siesta/example_psf_family.py | 185 ++++++++++++ .../examples/plugins/siesta/example_psml.py | 193 ++++++++++++ .../examples/plugins/siesta/example_relax.py | 276 ++++++++++++++++++ .../plugins/siesta/example_restart.py | 91 ++++++ .../plugins/siesta/example_scf_fail.py | 179 ++++++++++++ .../plugins/siesta/example_soc_bands.py | 166 +++++++++++ .../plugins/siesta/example_varcell.py | 169 +++++++++++ 14 files changed, 2486 insertions(+) create mode 100755 aiida_siesta/examples/plugins/siesta/example_bands.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_cif_bands.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_first.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_geom_fail.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_ldos.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_magnetic_bands.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_molecule.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_psf_family.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_psml.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_relax.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_restart.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_scf_fail.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_soc_bands.py create mode 100755 aiida_siesta/examples/plugins/siesta/example_varcell.py diff --git a/aiida_siesta/examples/plugins/siesta/example_bands.py b/aiida_siesta/examples/plugins/siesta/example_bands.py new file mode 100755 index 00000000..daa4302e --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_bands.py @@ -0,0 +1,190 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- +from __future__ import absolute_import +from __future__ import print_function + +import os.path as op +import sys +from aiida.tools import get_explicit_kpoints_path + +#In this example we will calculate the band structure of Si. +#Thanks to SeeK-path we can automatically generate the +#high symmetry points path where to calculate the bands. +#Alternatively, a manual list of k-points can be set. + +################################################################ + +from aiida.engine import submit +from aiida.orm import load_code +from aiida.orm import (Dict, StructureData, KpointsData) +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory + +PsfData = DataFactory('siesta.psf') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta4.0.1@kelvin' + +##-------------------Structure----------------------------------- +##Manually set the structure, all the quantities must be in Ang. +##Then, we pass through SeeK-path, to get the standardized cell, +##necessary for the automatic choice of the bands path. + +alat = 5.430 # angstrom +cell = [ + [ + 0.5 * alat, + 0.5 * alat, + 0., + ], + [ + 0., + 0.5 * alat, + 0.5 * alat, + ], + [ + 0.5 * alat, + 0., + 0.5 * alat, + ], +] + +s = StructureData(cell=cell) +s.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), + symbols=['Si']) +s.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), + symbols=['Si']) + +elements = list(s.get_symbols_set()) + +seekpath_parameters = Dict(dict={ + 'reference_distance': 0.02, + 'symprec': 0.0001 +}) +result = get_explicit_kpoints_path(s, **seekpath_parameters.get_dict()) +structure = result['primitive_structure'] + +code = load_code(codename) + +parameters = Dict( + dict={ + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'max-scfiterations': 50, + 'dm-numberpulay': 4, + 'dm-mixingweight': 0.3, + 'dm-tolerance': 1.e-3, + 'Solution-method': 'diagon', + 'electronic-temperature': '25 meV', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 3, + 'md-maxcgdispl': '0.1 Ang', + 'md-maxforcetol': '0.04 eV/Ang', + 'write-forces': True, + # 'xml-write': True + }) + +basis = Dict( + dict={ + 'pao-energy-shift': '300 meV', + '%block pao-basis-sizes': """ +Si DZP +%endblock pao-basis-sizes""", + }) + +kpoints = KpointsData() +kpoints.set_kpoints_mesh([4, 4, 4]) + +##-------------------K-points for bands -------------------- +bandskpoints = KpointsData() +##Uncomment your favourite, two options: + +##1) +##.....Making use of SeeK-path for the automatic path...... +##The choice of the distance between kpoints is in the call seekpath_parameters +##All high symmetry points included, labels already included +##This calls BandLine in siesta +bandskpoints = result['explicit_kpoints'] + +##2) +##.....Only points, no labels....... +##Mandatory to set cell and pbc +##This calls BandsPoint +#kpp = [(0.500, 0.250, 0.750), (0.500, 0.500, 0.500), (0., 0., 0.)] +#bandskpoints.set_cell(structure.cell, structure.pbc) +#bandskpoints.set_kpoints(kpp) + +#Note: The option to define a path touching specific kpoints +#for instance: +#kpp = [('W', (0.500, 0.250, 0.750), 'L', (0.500, 0.500, 0.500), 40), +# ('L', (0.500, 0.500, 0.500), 'G', (0., 0., 0.), 40)] +#Now is not easy to set. I'll study more on that + +pseudos_list = [] +raw_pseudos = [("Si.psf", 'Si')] +for fname, kind in raw_pseudos: + absname = op.realpath( + op.join(op.dirname(__file__), "data/sample-psf-family", fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + if created: + print("\nCreated the pseudo for {}".format(kind)) + else: + print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) + pseudos_list.append(pseudo) + +options = { + "max_wallclock_seconds": 600, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} + +inputs = { + 'structure': structure, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'kpoints': kpoints, + 'bandskpoints': bandskpoints, + 'pseudos': { + 'Si': pseudos_list[0], + }, + 'metadata': { + "label": "TestOnSiliconBandsLines", + 'options': options, + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + # subfolder, script_filename = calc.submit_test() + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") +# I could't find a way to access the actual folder (subfolder of submit_test) +# from the calculation node. So I can't print the exact location + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_cif_bands.py b/aiida_siesta/examples/plugins/siesta/example_cif_bands.py new file mode 100755 index 00000000..d89c37ea --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_cif_bands.py @@ -0,0 +1,173 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +from __future__ import absolute_import +from __future__ import print_function + +import sys + +import pymatgen as mg + +from aiida.engine import submit +from aiida.orm import load_code +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida_siesta.data.psf import get_pseudos_from_structure +from aiida.plugins import DataFactory +from aiida.tools import get_explicit_kpoints_path + +# This script will send a Siesta calculation on a structure taken from +# a cif file. +# The band structure is calculated and the kpoint path is automatically +# generated using seekpath. + +PsfData = DataFactory('siesta.psf') +Dict = DataFactory('dict') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'siesta4.0.1@parsons' + +# +#------------------Code and computer options --------------------------- +# +code = load_code(codename) + +options = { + "queue_name": "debug", + "max_wallclock_seconds": 1700, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} +# +settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +settings = Dict(dict=settings_dict) +#--------------------------------------------------------------------- + +# +# Structure ----------------------------------------- +# +# Passing through SeeK-path first, to get the standardized cell. +# Necessary for the automatic choice of the bands path. +# +structure = mg.Structure.from_file("data/O2_ICSD_173933.cif", primitive=False) +s = StructureData(pymatgen_structure=structure) + +seekpath_parameters = {'reference_distance': 0.02, 'symprec': 0.0001} +result = get_explicit_kpoints_path(s, **seekpath_parameters) +newstructure = result['primitive_structure'] + +# +# Parameters --------------------------------------------------- +# +params_dict = { + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'spin-polarized': True, + 'noncollinearspin': False, + 'mesh-cutoff': '200.000 Ry', + 'max-scfiterations': 1000, + 'dm-numberpulay': 5, + 'dm-mixingweight': 0.050, + 'dm-tolerance': 1.e-4, + 'dm-mixscf1': True, + 'negl-nonoverlap-int': False, + 'solution-method': 'diagon', + 'electronic-temperature': '100.000 K', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 2, + 'md-maxcgdispl': '0.200 bohr', + 'md-maxforcetol': '0.050 eV/Ang', + 'writeforces': True, + 'writecoorstep': True, + 'write-mulliken-pop': 1 +} +# +parameters = Dict(dict=params_dict) + +#---------------------------------------------------------- +# +# Basis Set Info ------------------------------------------ +# The basis dictionary follows the 'parameters' convention +# +basis_dict = { + 'pao-basistype': 'split', + 'pao-splitnorm': 0.150, + 'pao-energyshift': '0.020 Ry', + '%block pao-basis-sizes': """ +O SZP +%endblock pao-basis-sizes""", +} +# +basis = Dict(dict=basis_dict) +#-------------------------------------------------------------- + +#--------------------- Pseudopotentials --------------------------------- +# +# FIXME: The family name is hardwired +# +pseudos_dict = get_pseudos_from_structure(s, 'sample_psf_family') +print(pseudos_dict) +#----------------------------------------------------------------------- + +# K-points for scf cycle ------------------------------------------- +kts = KpointsData() +kpoints_mesh = 4 +kts.set_kpoints_mesh([kpoints_mesh, kpoints_mesh, kpoints_mesh]) + +# +bandskpoints = KpointsData() + +# Making use of SeeK-path for the automatic path +# The choice of the distance between kpoints is in the call seekpath_parameters +# All high symmetry points included, labels already included +bandskpoints = result['explicit_kpoints'] + +# +#--All the inputs of a Siesta calculations are listed in a dictionary-- +# +inputs = { + 'structure': newstructure, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'kpoints': kts, + 'bandskpoints': bandskpoints, + 'pseudos': pseudos_dict, + 'metadata': { + 'options': options, + 'label': "O_el_cell_spin from CIF" + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_first.py b/aiida_siesta/examples/plugins/siesta/example_first.py new file mode 100755 index 00000000..2f2b2155 --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_first.py @@ -0,0 +1,146 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- +from __future__ import absolute_import +from __future__ import print_function + +import os.path as op +import sys + +from aiida.engine import submit +from aiida.orm import load_code +from aiida.orm import (Dict, StructureData, KpointsData) +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory + +PsfData = DataFactory('siesta.psf') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta4.0.1@kelvin' + +# Si diamond structure +alat = 5.430 # angstrom +cell = [ + [ + 0.5 * alat, + 0.5 * alat, + 0., + ], + [ + 0., + 0.5 * alat, + 0.5 * alat, + ], + [ + 0.5 * alat, + 0., + 0.5 * alat, + ], +] + +# Si +# This was originally given in the "ScaledCartesian" format +# +structure = StructureData(cell=cell) +structure.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), + symbols=['Si']) +structure.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), + symbols=['Si']) + +code = load_code(codename) + +parameters = Dict( + dict={ + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'max-scfiterations': 50, + 'dm-numberpulay': 4, + 'dm-mixingweight': 0.3, + 'dm-tolerance': 1.e-3, + 'Solution-method': 'diagon', + 'electronic-temperature': '25 meV', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 3, + 'md-maxcgdispl': '0.1 Ang', + 'md-maxforcetol': '0.04 eV/Ang', + 'write-forces': True, + # 'xml-write': True + }) + +basis = Dict( + dict={ + 'pao-energy-shift': '300 meV', + '%block pao-basis-sizes': """ +Si DZP +%endblock pao-basis-sizes""", + }) + +kpoints = KpointsData() +kpoints.set_kpoints_mesh([4, 4, 4]) + +pseudos_list = [] +raw_pseudos = [("Si.psf", 'Si')] +for fname, kind in raw_pseudos: + absname = op.realpath( + op.join(op.dirname(__file__), "data/sample-psf-family", fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + if created: + print("\nCreated the pseudo for {}".format(kind)) + else: + print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) + pseudos_list.append(pseudo) + +options = { + "max_wallclock_seconds": 360, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} + +inputs = { + 'structure': structure, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'kpoints': kpoints, + 'pseudos': { + 'Si': pseudos_list[0], + }, + 'metadata': { + "label": "TestOnSiliconBulk", + 'options': options, + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + # subfolder, script_filename = calc.submit_test() + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") +# I could't find a way to access the actual folder (subfolder of submit_test) +# from the calculation node. So I can't print the exact location + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_geom_fail.py b/aiida_siesta/examples/plugins/siesta/example_geom_fail.py new file mode 100755 index 00000000..aad4d5aa --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_geom_fail.py @@ -0,0 +1,144 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +from __future__ import absolute_import +from __future__ import print_function + +import sys + +from aiida.engine import submit +from aiida.orm import load_code +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida_siesta.data.psf import get_pseudos_from_structure +from aiida.plugins import DataFactory + +# Siesta calculation on Water molecule -- to fail in geom relaxation + +PsfData = DataFactory('siesta.psf') +Dict = DataFactory('dict') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) +# +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta4.0.1@kelvin' + +# +#------------------Code and computer options --------------------------- +# +code = load_code(codename) + +options = { + "queue_name": "debug", + "max_wallclock_seconds": 1700, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} +# +#-------------------------- Settings --------------------------------- +# +settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +settings = Dict(dict=settings_dict) +# +# Structure ----------------------------------------- +# +alat = 10.0 # angstrom +cell = [ + [ + alat, + 0., + 0., + ], + [ + 0., + alat, + 0., + ], + [ + 0., + 0., + alat, + ], +] + +# Water molecule +# One of the H atoms is sligthy moved + +s = StructureData(cell=cell) +s.append_atom(position=(0.000, 0.000, 0.00), symbols=['O']) +s.append_atom(position=(0.757, 0.586, 0.00), symbols=['H']) +s.append_atom(position=(-0.780, 0.600, 0.00), symbols=['H']) + +# ----------------------Parameters ------------------------------------- + +params_dict = { + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'mesh-cutoff': '100.000 Ry', + 'max-scfiterations': 30, + 'dm-numberpulay': 4, + 'dm-mixingweight': 0.1, + 'dm-tolerance': 1.e-4, + 'md-typeofrun': 'cg', + 'md-numcgsteps': 8, + 'md-maxcgdispl': '0.200 bohr', + 'md-maxforcetol': '0.020 eV/Ang', + 'geometry-must-converge': True +} + +parameters = Dict(dict=params_dict) +#------------------------------------------------------------------------ +# +# No basis set spec in this calculation (default) +# +#--------------------- Pseudopotentials --------------------------------- +# +# FIXME: The family name is hardwired +# +pseudos_dict = get_pseudos_from_structure(s, 'sample_psf_family') +#----------------------------------------------------------------------- + +# +#--All the inputs of a Siesta calculations are listed in a dictionary-- +# +inputs = { + 'structure': s, + 'parameters': parameters, + 'code': code, + 'pseudos': pseudos_dict, + 'metadata': { + 'options': options, + 'label': "Water molecule -- geom fail" + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_ldos.py b/aiida_siesta/examples/plugins/siesta/example_ldos.py new file mode 100755 index 00000000..97e4220a --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_ldos.py @@ -0,0 +1,199 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +from __future__ import absolute_import +from __future__ import print_function + +import sys +import os + +from aiida.engine import submit +from aiida.orm import load_code +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory + +################################################################ + +PsfData = DataFactory('siesta.psf') +Dict = DataFactory('dict') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta-4.0@rinaldo' + +# +#------------------Code and computer options --------------------------- +# +code = load_code(codename) + +options = { + "queue_name": "debug", + "max_wallclock_seconds": 1700, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} +# +#----Settings first ----------------------------- +# +settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +settings = Dict(dict=settings_dict) +#--------------------------------------------------- + +# +# Structure ----------------------------------------- +# +alat = 15. # angstrom +cell = [ + [ + alat, + 0., + 0., + ], + [ + 0., + alat, + 0., + ], + [ + 0., + 0., + alat, + ], +] + +# Benzene molecule +# Note an atom tagged (for convenience) with a different label +# +s = StructureData(cell=cell) +s.append_atom(position=(0.000, 0.000, 0.468), symbols=['H']) +s.append_atom(position=(0.000, 0.000, 1.620), symbols=['C']) +s.append_atom(position=(0.000, -2.233, 1.754), symbols=['H']) +s.append_atom(position=(0.000, 2.233, 1.754), symbols=['H']) +s.append_atom(position=(0.000, -1.225, 2.327), symbols='C', name="Cred") +s.append_atom(position=(0.000, 1.225, 2.327), symbols=['C']) +s.append_atom(position=(0.000, -1.225, 3.737), symbols=['C']) +s.append_atom(position=(0.000, 1.225, 3.737), symbols=['C']) +s.append_atom(position=(0.000, -2.233, 4.311), symbols=['H']) +s.append_atom(position=(0.000, 2.233, 4.311), symbols=['H']) +s.append_atom(position=(0.000, 0.000, 4.442), symbols=['C']) +s.append_atom(position=(0.000, 0.000, 5.604), symbols=['H']) + +#------------------------------------------------------------- +# +# Parameters --------------------------------------------------- +# +ldos_block_content = "\n {e1} {e2} eV".format(e1=-5.0, e2=1.0) + +params_dict = { + 'xc-functional': + 'LDA', + 'xc-authors': + 'CA', + 'mesh-cutoff': + '200.000 Ry', + 'dm-numberpulay': + 5, + 'dm-mixingweight': + 0.050, + 'dm-tolerance': + 1.e-4, + 'electronic-temperature': + '100.000 K', + '%block local-density-of-states': + """ + -5.0 1.0 eV +%endblock local-density-of-states """ +} +parameters = Dict(dict=params_dict) +# +# Basis Set Info ------------------------------------------ +# The basis dictionary follows the 'parameters' convention +# +basis_dict = { + 'pao-basistype': + 'split', + 'pao-splitnorm': + 0.150, + 'pao-energyshift': + '0.020 Ry', + '%block pao-basis-sizes': + """ +C SZP +Cred SZ +H SZP +%endblock pao-basis-sizes""" +} +basis = Dict(dict=basis_dict) +#-------------------------------------------------------------- + +#--------------------- Pseudopotentials --------------------------------- +# +# This exemplifies the handling of pseudos for different species +# Those sharing the same pseudo should be indicated. +# +pseudos_list = [] +raw_pseudos = [("C.psf", ['C', 'Cred']), ("H.psf", 'H')] + +for fname, kinds, in raw_pseudos: + absname = os.path.realpath( + os.path.join(os.path.dirname(__file__), "data/sample-psf-family", + fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + if created: + print("Created the pseudo for {}".format(kinds)) + else: + print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + pseudos_list.append(pseudo) + +#----------------------------------------------------------------------- +#--All the inputs of a Siesta calculations are listed in a dictionary-- +# +inputs = { + 'structure': s, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'pseudos': { + 'C': pseudos_list[0], + 'Cred': pseudos_list[0], + 'H': pseudos_list[1], + }, + 'metadata': { + 'options': options, + 'label': "Benzene molecule", + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + # subfolder, script_filename = calc.submit_test() + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_magnetic_bands.py b/aiida_siesta/examples/plugins/siesta/example_magnetic_bands.py new file mode 100755 index 00000000..412d94c2 --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_magnetic_bands.py @@ -0,0 +1,142 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." +__license__ = "MIT license, see LICENSE.txt file" +__version__ = "0.7.0" +__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" + +import sys +import os + +from aiida.common.example_helpers import test_and_get_code +from aiida.common.exceptions import NotExistent + +# Calculation on Iron, collinear spin polarization applied + +################################################################ + +PsfData = DataFactory('siesta.psf') +ParameterData = DataFactory('parameter') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print >> sys.stderr, ("The first parameter can only be either " + "--send or --dont-send") + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'siesta4.0.1@parsons' + +code = test_and_get_code(codename, expected_code_type='siesta.siesta') +# +# Set up calculation object first +# +calc = code.new_calc() +calc.label = "Siesta-Fe-bulk-spin" +calc.description = "Test Siesta calculation. Fe bulk spin-polarized" + +# +# Structure ----------------------------------------- +# +# BCC +alat = 2.87 # angstrom +cell = [[alat/2, alat/2, alat/2,], + [alat/2, -alat/2, alat/2,], + [alat/2, alat/2, -alat/2,], + ] + +# +s = StructureData(cell=cell) +s.append_atom(position=(0.000,0.000,0.000),symbols=['Fe']) + +elements = list(s.get_symbols_set()) +calc.use_structure(s) +#------------------------------------------------------------- +# +# Parameters --------------------------------------------------- +# +# Note the use of '.' in some entries. This will be fixed below. +# Note also that some entries have ':' as separator. This is not +# allowed in Siesta, and will be fixed by the plugin itself. The +# latter case is an unfortunate historical choice. It should not +# be used in modern scripts. +# +params_dict= { +'xc.functional': 'GGA', +'xc.authors': 'PBE', +'spin-polarized': True, +'noncollinearspin': False, +'mesh-cutoff': '150.000 Ry', +'max-scfiterations': 40, +'dm-numberpulay': 4, +'dm-mixingweight': 0.1, +'dm-tolerance': 1.e-3, +'electronic-temperature': '300.000 K' +} +# +# Sanitize, as '.' is not kosher for the database handlers +# +params_dict = { k.replace('.','-') :v for k,v in params_dict.iteritems() } +# +parameters = ParameterData(dict=params_dict) +calc.use_parameters(parameters) +# +kpoints = KpointsData() +kpoints_mesh = 6 +kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) +calc.use_kpoints(kpoints) +# +# Pseudopotentials ---------------------------------------------- +# +# This exemplifies the handling of pseudos for different species +# Those sharing the same pseudo should be indicated. +# Families support is not yet available for this. +# +raw_pseudos = [ ("Fe.psf", 'Fe')] + +for fname, kinds, in raw_pseudos: + absname = os.path.realpath(os.path.join(os.path.dirname(__file__), + "data",fname)) + pseudo, created = PsfData.get_or_create(absname,use_first=True) + if created: + print "Created the pseudo for {}".format(kinds) + else: + print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) + + # Attach pseudo node to the calculation + calc.use_pseudo(pseudo,kind=kinds) +#------------------------------------------------------------------- + +calc.set_max_wallclock_seconds(30*60) # 30 min + +calc.set_resources({"num_machines": 1}) +#------------------ + +if submit_test: + subfolder, script_filename = calc.submit_test() + print "Test_submit for calculation (uuid='{}')".format( + calc.uuid) + print "Submit file in {}".format(os.path.join( + os.path.relpath(subfolder.abspath), + script_filename + )) +else: + calc.store_all() + print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( + calc.uuid,calc.dbnode.pk) + calc.submit() + print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( + calc.uuid,calc.dbnode.pk) + diff --git a/aiida_siesta/examples/plugins/siesta/example_molecule.py b/aiida_siesta/examples/plugins/siesta/example_molecule.py new file mode 100755 index 00000000..02f50648 --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_molecule.py @@ -0,0 +1,233 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +from __future__ import absolute_import +from __future__ import print_function + +import sys +import os + +from aiida.engine import submit +from aiida.orm import load_code +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory + +# Siesta calculation on benzene molecule + +PsfData = DataFactory('siesta.psf') +Dict = DataFactory('dict') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) +# +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta4.0.1@kelvin' + +# +#------------------Code and computer options --------------------------- +# +code = load_code(codename) + +options = { + "queue_name": "debug", + "max_wallclock_seconds": 1700, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} + +#TO DO: +# A Siesta executable compiled in serial mode might not work properly +# on a computer set up for MPI operation. +# This snippet can be used to check whether a code has been compiled +# with mpi support, and act accordingly +# For this to work, the user has to manually add the record in the +# database. In the verdi shell: +# +# code = load_node(code_PK) +# code.set_extra("mpi",True) +#code_mpi_enabled = False +#try: +# code_mpi_enabled = code.get_extra("mpi") +#except AttributeError: +# pass +#calc.set_withmpi(code_mpi_enabled) +#----------------------------------------------------------------------- + +# +#-------------------------- Settings --------------------------------- +# +settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +settings = Dict(dict=settings_dict) +#--------------------------------------------------------------------- + +# +#-------------------------- Structure -------------------------------- +# +alat = 15. # angstrom +cell = [ + [ + alat, + 0., + 0., + ], + [ + 0., + alat, + 0., + ], + [ + 0., + 0., + alat, + ], +] + +# Note an atom tagged (for convenience) with a different label + +s = StructureData(cell=cell) +s.append_atom(position=(0.000, 0.000, 0.468), symbols=['H']) +s.append_atom(position=(0.000, 0.000, 1.620), symbols=['C']) +s.append_atom(position=(0.000, -2.233, 1.754), symbols=['H']) +s.append_atom(position=(0.000, 2.233, 1.754), symbols=['H']) +s.append_atom(position=(0.000, -1.225, 2.327), symbols='C', name="Cred") +s.append_atom(position=(0.000, 1.225, 2.327), symbols=['C']) +s.append_atom(position=(0.000, -1.225, 3.737), symbols=['C']) +s.append_atom(position=(0.000, 1.225, 3.737), symbols=['C']) +s.append_atom(position=(0.000, -2.233, 4.311), symbols=['H']) +s.append_atom(position=(0.000, 2.233, 4.311), symbols=['H']) +s.append_atom(position=(0.000, 0.000, 4.442), symbols=['C']) +s.append_atom(position=(0.000, 0.000, 5.604), symbols=['H']) + +elements = list(s.get_symbols_set()) +#----------------------------------------------------------------------- + +# +# ----------------------Parameters ------------------------------------- +# +# Note the use of '.' in some entries. This will be fixed below. +# Note also that some entries have ':' as separator. This is not +# allowed in Siesta, and will be fixed by the plugin itself. The +# latter case is an unfortunate historical choice. It should not +# be used in modern scripts. +# +params_dict = { + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'spin-polarized': True, + 'noncollinearspin': False, + 'mesh-cutoff': '200.000 Ry', + 'max-scfiterations': 1000, + 'dm-numberpulay': 5, + 'dm-mixingweight': 0.050, + 'dm-tolerance': 1.e-4, + 'dm-mixscf1': True, + 'negl-nonoverlap-int': False, + 'solution-method': 'diagon', + 'electronic-temperature': '100.000 K', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 2, + 'md-maxcgdispl': '0.200 bohr', + 'md-maxforcetol': '0.050 eV/Ang', + 'writeforces': True, + 'writecoorstep': True, + 'write-mulliken-pop': 1, +} + +parameters = Dict(dict=params_dict) +#------------------------------------------------------------------------ + +# +# ---------------------Basis Set Info ----------------------------------- +# The basis dictionary follows the 'parameters' convention +# +basis_dict = { + 'pao-basistype': + 'split', + 'pao-splitnorm': + 0.150, + 'pao-energyshift': + '0.020 Ry', + '%block pao-basis-sizes': + """ +C SZP +Cred SZ +H SZP +%endblock pao-basis-sizes""", +} + +basis = Dict(dict=basis_dict) +#------------------------------------------------------------------------ + +#--------------------- Pseudopotentials --------------------------------- +# +# This exemplifies the handling of pseudos for different species +# Those sharing the same pseudo should be indicated. +# +pseudos_list = [] +raw_pseudos = [("C.psf", ['C', 'Cred']), ("H.psf", 'H')] + +for fname, kinds, in raw_pseudos: + absname = os.path.realpath( + os.path.join(os.path.dirname(__file__), "data/sample-psf-family", + fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + if created: + print("Created the pseudo for {}".format(kinds)) + else: + print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + pseudos_list.append(pseudo) + +#----------------------------------------------------------------------- + +# +#--All the inputs of a Siesta calculations are listed in a dictionary-- +# +inputs = { + 'structure': s, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'pseudos': { + 'C': pseudos_list[0], + 'Cred': pseudos_list[0], + 'H': pseudos_list[1], + }, + 'metadata': { + 'options': options, + 'label': "Benzene molecule", + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + # subfolder, script_filename = calc.submit_test() + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") +# I could't find a way to access the actual folder (subfolder of submit_test) +# from the calculation node. So I can't print the exact location + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_psf_family.py b/aiida_siesta/examples/plugins/siesta/example_psf_family.py new file mode 100755 index 00000000..b8a8d662 --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_psf_family.py @@ -0,0 +1,185 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +from __future__ import absolute_import +from __future__ import print_function + +import sys + +from aiida.engine import submit +from aiida.orm import load_code +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida_siesta.data.psf import get_pseudos_from_structure +from aiida.plugins import DataFactory + +#----------------- Example of the use of a pseudopotential family + +PsfData = DataFactory('siesta.psf') +Dict = DataFactory('dict') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) +# +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta4.0.1@kelvin' + +# +#------------------Code and computer options --------------------------- +# +code = load_code(codename) + +options = { + "queue_name": "debug", + "max_wallclock_seconds": 1700, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} +# +settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +settings = Dict(dict=settings_dict) +#--------------------------------------------------------------------- + +# +#-------------------------- Structure -------------------------------- +# +alat = 15. # angstrom +cell = [ + [ + alat, + 0., + 0., + ], + [ + 0., + alat, + 0., + ], + [ + 0., + 0., + alat, + ], +] + +# Note an atom tagged (for convenience) with a different label + +s = StructureData(cell=cell) +s.append_atom(position=(0.000, 0.000, 0.468), symbols=['H']) +s.append_atom(position=(0.000, 0.000, 1.620), symbols=['C']) +s.append_atom(position=(0.000, -2.233, 1.754), symbols=['H']) +s.append_atom(position=(0.000, 2.233, 1.754), symbols=['H']) +s.append_atom(position=(0.000, -1.225, 2.327), symbols='C', name="Cred") +s.append_atom(position=(0.000, 1.225, 2.327), symbols=['C']) +s.append_atom(position=(0.000, -1.225, 3.737), symbols=['C']) +s.append_atom(position=(0.000, 1.225, 3.737), symbols=['C']) +s.append_atom(position=(0.000, -2.233, 4.311), symbols=['H']) +s.append_atom(position=(0.000, 2.233, 4.311), symbols=['H']) +s.append_atom(position=(0.000, 0.000, 4.442), symbols=['C']) +s.append_atom(position=(0.000, 0.000, 5.604), symbols=['H']) + +#----------------------------------------------------------------------- + +# +# ----------------------Parameters ------------------------------------- +# +params_dict = { + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'spin-polarized': True, + 'noncollinearspin': False, + 'mesh-cutoff': '200.000 Ry', + 'max-scfiterations': 1000, + 'dm-numberpulay': 5, + 'dm-mixingweight': 0.050, + 'dm-tolerance': 1.e-4, + 'dm-mixscf1': True, + 'negl-nonoverlap-int': False, + 'solution-method': 'diagon', + 'electronic-temperature': '100.000 K', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 2, + 'md-maxcgdispl': '0.200 bohr', + 'md-maxforcetol': '0.050 eV/Ang', + 'writeforces': True, + 'writecoorstep': True, + 'write-mulliken-pop': 1, +} + +parameters = Dict(dict=params_dict) +#------------------------------------------------------------------------ + +# +# ---------------------Basis Set Info ----------------------------------- +# The basis dictionary follows the 'parameters' convention +# +basis_dict = { + 'pao-basistype': + 'split', + 'pao-splitnorm': + 0.150, + 'pao-energyshift': + '0.020 Ry', + '%block pao-basis-sizes': + """ +C SZP +Cred SZ +H SZP +%endblock pao-basis-sizes""", +} + +basis = Dict(dict=basis_dict) +#------------------------------------------------------------------------ + +#--------------------- Pseudopotentials --------------------------------- +# +# FIXME: The family name is hardwired +# +pseudos_dict = get_pseudos_from_structure(s, 'sample_psf_family') +print(pseudos_dict) +#----------------------------------------------------------------------- + +# +#--All the inputs of a Siesta calculations are listed in a dictionary-- +# +inputs = { + 'structure': s, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'pseudos': pseudos_dict, + 'metadata': { + 'options': options, + 'label': "Benzene molecule with pseudo family", + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_psml.py b/aiida_siesta/examples/plugins/siesta/example_psml.py new file mode 100755 index 00000000..b635f597 --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_psml.py @@ -0,0 +1,193 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +from __future__ import absolute_import +from __future__ import print_function + +import sys +import os + +from aiida.engine import submit +from aiida.orm import load_code +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory + +########################################################## +# # +# Siesta calculation on benzene molecule, first to try # +# # +########################################################## + +PsmlData = DataFactory('siesta.psml') +Dict = DataFactory('dict') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) +# +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta4.0.1@kelvin' + +# +#------------------Code and computer options --------------------------- +# +code = load_code(codename) + +options = { + "queue_name": "debug", + "max_wallclock_seconds": 1700, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} + +# +#-------------------------- Settings --------------------------------- +# +settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +settings = Dict(dict=settings_dict) +#--------------------------------------------------------------------- + +# +#-------------------------- Structure -------------------------------- +# +alat = 5.430 # angstrom +cell = [ + [ + 0.5 * alat, + 0.5 * alat, + 0., + ], + [ + 0., + 0.5 * alat, + 0.5 * alat, + ], + [ + 0.5 * alat, + 0., + 0.5 * alat, + ], +] + +s = StructureData(cell=cell) +s.append_atom( + position=(0.000 * alat, 0.000 * alat, 0.000 * alat), symbols=['Si']) +s.append_atom( + position=(0.250 * alat, 0.250 * alat, 0.250 * alat), symbols=['Si']) + +#----------------------------------------------------------------------- + +# +# ----------------------Parameters ------------------------------------- +# +# Note the use of '.' in some entries. This will be fixed below. +# Note also that some entries have ':' as separator. This is not +# allowed in Siesta, and will be fixed by the plugin itself. The +# latter case is an unfortunate historical choice. It should not +# be used in modern scripts. +# +params_dict = { + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'spin': 'SO', + 'mesh-cutoff': '200.000 Ry', + 'max-scfiterations': 1000, + 'dm-numberpulay': 5, + 'dm-mixingweight': 0.050, + 'dm-tolerance': 1.e-4, + 'dm-mixscf1': True, + 'negl-nonoverlap-int': False, + 'solution-method': 'diagon', + 'electronic-temperature': '100.000 K', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 2, + 'md-maxcgdispl': '0.200 bohr', + 'md-maxforcetol': '0.050 eV/Ang', + 'writeforces': True, + 'writecoorstep': True, + 'write-mulliken-pop': 1, +} + +parameters = Dict(dict=params_dict) +#------------------------------------------------------------------------ + +# +# ---------------------Basis Set Info ----------------------------------- +# The basis dictionary follows the 'parameters' convention +# +basis_dict = { + 'pao-basistype': 'split', + 'pao-splitnorm': 0.150, + 'pao-energyshift': '0.020 Ry' +} + +basis = Dict(dict=basis_dict) +#------------------------------------------------------------------------ + +#--------------------- Pseudopotentials --------------------------------- +# +# This exemplifies the handling of pseudos for different species +# Those sharing the same pseudo should be indicated. +# +pseudos_list = [] +raw_pseudos = [("Si.psml", 'Si')] + +for fname, kinds, in raw_pseudos: + absname = os.path.realpath( + os.path.join(os.path.dirname(__file__), "data/sample-psml-family", fname)) + pseudo, created = PsmlData.get_or_create(absname, use_first=True) + if created: + print("Created the pseudo for {}".format(kinds)) + else: + print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + pseudos_list.append(pseudo) + +#----------------------------------------------------------------------- + +# +#--All the inputs of a Siesta calculations are listed in a dictionary-- +# +inputs = { + 'structure': s, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'pseudos': { + 'Si': pseudos_list[0] + }, + 'metadata': { + 'options': options, + 'label': "Si crystal with PSML pseudos", + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + # subfolder, script_filename = calc.submit_test() + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_relax.py b/aiida_siesta/examples/plugins/siesta/example_relax.py new file mode 100755 index 00000000..02c616fb --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_relax.py @@ -0,0 +1,276 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." +__license__ = "MIT license, see LICENSE.txt file" +__version__ = "0.7.0" +__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" + +import sys +import os + +from aiida.common.example_helpers import test_and_get_code +from aiida.common.exceptions import NotExistent + +# Another molecule +# Pseudo families introduced + +################################################################ + +PsfData = DataFactory('siesta.psf') +ParameterData = DataFactory('parameter') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print >> sys.stderr, ("The first parameter can only be either " + "--send or --dont-send") + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'siesta4.0.1@parsons' + + + +queue = None +settings = None + +code = test_and_get_code(codename, expected_code_type='siesta.siesta') +## For remote codes, it is not necessary to manually set the computer, +## since it is set automatically by new_calc +#computer = code.get_remote_computer() +#calc = code.new_calc(computer=computer) + +calc = code.new_calc() +calc.label = "SiH_spin" +calc.description = "Test calculation with the Siesta code. SiH spin" +calc.set_max_wallclock_seconds(30*60) # 30 min + +#------------ clarify this +# Valid only for Slurm and PBS (using default values for the +# number_cpus_per_machine), change for SGE-like schedulers +## Otherwise, to specify a given # of cpus per machine, uncomment the following: +# calc.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 8}) +#calc.set_resources({"parallel_env": 'openmpi',"tot_num_mpiprocs": 1,"num_machines": 1,"num_cpus": 2}) +#------------ clarify this +calc.set_resources({"num_machines": 1}) + +#calc.set_custom_scheduler_commands("#SBATCH --account=ch3") + +if queue is not None: + calc.set_queue_name(queue) + + +##----Structure--- + +alat = 5.430 # angstrom +cell = [[2*alat, 0., 0.,], + [0., 2*alat, 0.,], + [0., 0., 2*alat,], + ] + +# SiH coordinates +# This was originally given in the "ScaledCartesian" format +# +s = StructureData(cell=cell) +s.append_atom(position=(0.000*alat,0.000*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,0.250*alat,0.250*alat),symbols=['Si']) +s.append_atom(position=(0.000*alat,0.500*alat,0.500*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,0.750*alat,0.750*alat),symbols=['Si']) +s.append_atom(position=(0.500*alat,0.000*alat,0.500*alat),symbols=['Si']) +s.append_atom(position=(0.750*alat,0.250*alat,0.750*alat),symbols=['Si']) +s.append_atom(position=(0.500*alat,0.500*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(0.750*alat,0.750*alat,0.250*alat),symbols=['Si']) +s.append_atom(position=(1.000*alat,0.000*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(1.250*alat,0.250*alat,0.250*alat),symbols=['Si']) +s.append_atom(position=(1.000*alat,0.500*alat,0.500*alat),symbols=['Si']) +s.append_atom(position=(1.250*alat,0.750*alat,0.750*alat),symbols=['Si']) +s.append_atom(position=(1.500*alat,0.000*alat,0.500*alat),symbols=['Si']) +s.append_atom(position=(1.750*alat,0.250*alat,0.750*alat),symbols=['Si']) +s.append_atom(position=(1.500*alat,0.500*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(1.750*alat,0.750*alat,0.250*alat),symbols=['Si']) +s.append_atom(position=(0.000*alat,1.000*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,1.250*alat,0.250*alat),symbols=['Si']) +s.append_atom(position=(0.000*alat,1.500*alat,0.500*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,1.750*alat,0.750*alat),symbols=['Si']) +s.append_atom(position=(0.500*alat,1.000*alat,0.500*alat),symbols=['Si']) +s.append_atom(position=(0.750*alat,1.250*alat,0.750*alat),symbols=['Si']) +s.append_atom(position=(0.500*alat,1.500*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(0.750*alat,1.750*alat,0.250*alat),symbols=['Si']) +s.append_atom(position=(0.000*alat,0.000*alat,1.000*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,0.250*alat,1.250*alat),symbols=['Si']) +s.append_atom(position=(0.000*alat,0.500*alat,1.500*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,0.750*alat,1.750*alat),symbols=['Si']) +s.append_atom(position=(0.500*alat,0.000*alat,1.500*alat),symbols=['Si']) +s.append_atom(position=(0.750*alat,0.250*alat,1.750*alat),symbols=['Si']) +s.append_atom(position=(0.500*alat,0.500*alat,1.000*alat),symbols=['Si']) +s.append_atom(position=(0.750*alat,0.750*alat,1.250*alat),symbols=['Si']) +s.append_atom(position=(1.000*alat,1.000*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(1.250*alat,1.250*alat,0.250*alat),symbols=['Si']) +s.append_atom(position=(1.000*alat,1.500*alat,0.500*alat),symbols=['Si']) +s.append_atom(position=(1.250*alat,1.750*alat,0.750*alat),symbols=['Si']) +s.append_atom(position=(1.500*alat,1.000*alat,0.500*alat),symbols=['Si']) +s.append_atom(position=(1.750*alat,1.250*alat,0.750*alat),symbols=['Si']) +s.append_atom(position=(1.500*alat,1.500*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(1.750*alat,1.750*alat,0.250*alat),symbols=['Si']) +s.append_atom(position=(1.000*alat,0.000*alat,1.000*alat),symbols=['Si']) +s.append_atom(position=(1.250*alat,0.250*alat,1.250*alat),symbols=['Si']) +s.append_atom(position=(1.000*alat,0.500*alat,1.500*alat),symbols=['Si']) +s.append_atom(position=(1.250*alat,0.750*alat,1.750*alat),symbols=['Si']) +s.append_atom(position=(1.500*alat,0.000*alat,1.500*alat),symbols=['Si']) +s.append_atom(position=(1.750*alat,0.250*alat,1.750*alat),symbols=['Si']) +s.append_atom(position=(1.500*alat,0.500*alat,1.000*alat),symbols=['Si']) +s.append_atom(position=(1.750*alat,0.750*alat,1.250*alat),symbols=['Si']) +s.append_atom(position=(0.000*alat,1.000*alat,1.000*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,1.250*alat,1.250*alat),symbols=['Si']) +s.append_atom(position=(0.000*alat,1.500*alat,1.500*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,1.750*alat,1.750*alat),symbols=['Si']) +s.append_atom(position=(0.500*alat,1.000*alat,1.500*alat),symbols=['Si']) +s.append_atom(position=(0.750*alat,1.250*alat,1.750*alat),symbols=['Si']) +s.append_atom(position=(0.500*alat,1.500*alat,1.000*alat),symbols=['Si']) +s.append_atom(position=(0.750*alat,1.750*alat,1.250*alat),symbols=['Si']) +s.append_atom(position=(1.000*alat,1.000*alat,1.000*alat),symbols=['Si']) +s.append_atom(position=(1.250*alat,1.250*alat,1.250*alat),symbols=['Si']) +s.append_atom(position=(1.000*alat,1.500*alat,1.500*alat),symbols=['Si']) +s.append_atom(position=(1.250*alat,1.750*alat,1.750*alat),symbols=['Si']) +s.append_atom(position=(1.500*alat,1.000*alat,1.500*alat),symbols=['Si']) +s.append_atom(position=(1.750*alat,1.250*alat,1.750*alat),symbols=['Si']) +s.append_atom(position=(1.500*alat,1.500*alat,1.000*alat),symbols=['Si']) +s.append_atom(position=(1.750*alat,1.750*alat,1.250*alat),symbols=['Si']) +s.append_atom(position=(1.125*alat,1.125*alat,1.125*alat),symbols=['H']) + +elements = list(s.get_symbols_set()) + +calc.use_structure(s) + + +###-----Pseudos------ + +# If True, load the pseudos from the family specified below +# Otherwise, use static files provided +auto_pseudos = False + +if auto_pseudos: + valid_pseudo_groups = PsfData.get_psf_groups(filter_elements=elements) + + try: + pseudo_family = sys.argv[3] + except IndexError: + print >> sys.stderr, "Error, auto_pseudos set to True. You therefore need to pass as second parameter" + print >> sys.stderr, "the pseudo family name." + print >> sys.stderr, "Valid PSF families are:" + print >> sys.stderr, "\n".join("* {}".format(i.name) for i in valid_pseudo_groups) + sys.exit(1) + + try: + PsfData.get_psf_group(pseudo_family) + except NotExistent: + print >> sys.stderr, "auto_pseudos is set to True and pseudo_family='{}',".format(pseudo_family) + print >> sys.stderr, "but no group with such a name found in the DB." + print >> sys.stderr, "Valid PSF groups are:" + print >> sys.stderr, ",".join(i.name for i in valid_pseudo_groups) + sys.exit(1) + + +if auto_pseudos: + try: + calc.use_pseudos_from_family(pseudo_family) + print "Pseudos successfully loaded from family {}".format(pseudo_family) + except NotExistent: + print ("Pseudo or pseudo family not found. You may want to load the " + "pseudo family, or set auto_pseudos to False.") + raise +else: + raw_pseudos = [("Si.psf", 'Si'), + ("H.psf", 'H')] + + for fname, kinds, in raw_pseudos: + absname = os.path.realpath(os.path.join(os.path.dirname(__file__), + "data",fname)) + pseudo, created = PsfData.get_or_create(absname,use_first=True) + if created: + print "Created the pseudo for {}".format(kinds) + else: + print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) + + # Attach pseudo node to the calculation + calc.use_pseudo(pseudo,kind=kinds) + + +##-----Parameters----------- + +parameters = ParameterData(dict={ + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'spinpolarized': True, + 'meshcutoff': '40.000 Ry', + 'max-scfiterations': 50, + 'dm-numberpulay': 4, + 'dm-mixingweight': 0.3, + 'dm-tolerance': 1.e-3, + 'solution-method': 'diagon', + 'electronic-temperature': '25 meV', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 3, + 'md-maxcgdispl': '0.1 Ang', + 'md-maxforcetol': '0.04 eV/Ang' + }) +calc.use_parameters(parameters) + +##-----Basis--------- + +basis = ParameterData(dict={ +'pao-energy-shift': '300 meV', +'%block pao-basis-sizes': """ +Si SZP +H DZP """, +}) +calc.use_basis(basis) + +##-----k points ---------- + +kpoints = KpointsData() +# method mesh +kpoints_mesh = 1 +kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) +calc.use_kpoints(kpoints) + + +##----------settings---------- +# (the object settings is optional) +settings_dict={'test_key': 'test_value'} +settings = ParameterData(dict=settings_dict) + + + +if settings is not None: + calc.use_settings(settings) +#from aiida.orm.data.remote import RemoteData +#calc.set_outdir(remotedata) + +if submit_test: + subfolder, script_filename = calc.submit_test() + print "Test_submit for calculation (uuid='{}')".format( + calc.uuid) + print "Submit file in {}".format(os.path.join( + os.path.relpath(subfolder.abspath), + script_filename + )) +else: + calc.store_all() + print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( + calc.uuid,calc.dbnode.pk) + calc.submit() + print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( + calc.uuid,calc.dbnode.pk) + diff --git a/aiida_siesta/examples/plugins/siesta/example_restart.py b/aiida_siesta/examples/plugins/siesta/example_restart.py new file mode 100755 index 00000000..b5f7eb7b --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_restart.py @@ -0,0 +1,91 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +from __future__ import absolute_import +from __future__ import print_function + +# See LICENSE and Contributors + +# This script will restart a calculation that ended without +# scf convergence in the allotted number of iterations, or without geometry convergence. +# +# Usage: +# ./test_siesta_restart.py {--send, --dont-send} PK_of_failed_calculation + +import sys, os + +from aiida.engine import submit +from aiida.orm import load_code +from aiida.common import NotExistent +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory + +Dict = DataFactory('dict') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), file=sys.stderr) + sys.exit(1) + +try: + PK = int(sys.argv[2]) +except IndexError: + print(("The second parameter must be the PK of a calculation"), file=sys.stderr) + sys.exit(1) + + +c = load_node(PK) + +print("Restarting calculation (uuid='{}')".format(c.uuid)) +print("Is excepted?: '{}'".format(c.is_excepted)) +# +# Note that this use of 'failed' does not correspond to the process state. +# +print("Is failed?: '{}'".format(c.is_failed)) +if c.is_failed: + print("Exit code: '{}'".format(c.exit_status)) + print("'{}'".format(c.exit_message)) +print(" ") + +restart=c.get_builder_restart() + +newpar=restart.parameters.clone() +newpar.attributes["max-scf-iterations"]= 50 +restart.parameters=newpar + +if c.outputs.output_parameters.attributes["variable_geometry"]: + restart.structure=c.outputs.output_structure + +# The most important line. The presence of +# parent_calc_folder triggers the 'restart' operations +# in the plugin, such as the copy of the .DM and the +# addition of use-save-dm to the parameters + +restart.parent_calc_folder=c.outputs.remote_folder + +if submit_test: + + m=restart["metadata"] + + # An attempt to clone the 'metadata' section of the object raised this error: + # Error: AttributeError: 'ProcessBuilderNamespace' object has no attribute 'clone' + # It seems that one can simply set this attributes by hand: + + m.dry_run = True + m.store_provenance = False + print("Dry run without storing provenance. See the submit_test directory") + +else: + print("Calculation restarted") + + +submit(restart) + diff --git a/aiida_siesta/examples/plugins/siesta/example_scf_fail.py b/aiida_siesta/examples/plugins/siesta/example_scf_fail.py new file mode 100755 index 00000000..1034f188 --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_scf_fail.py @@ -0,0 +1,179 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +from __future__ import absolute_import +from __future__ import print_function + +# +# This is an example of a calculation that will end in a FINISHED +# state but with a non-zero exit code, due to lack of scf convergence +# in the allotted number of iterations. + +import sys +import os + +from aiida.engine import submit +from aiida.orm import load_code +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory + +################################################################ + +PsfData = DataFactory('siesta.psf') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') +Dict = DataFactory('dict') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'siesta4.0.1@kelvin' + +# +#------------------Code +# +code = load_code(codename) + +#--------------- Structure +# +# Bulk Silicon +# +alat = 5.430 # angstrom +cell = [ + [ + 0.5 * alat, + 0.5 * alat, + 0., + ], + [ + 0., + 0.5 * alat, + 0.5 * alat, + ], + [ + 0.5 * alat, + 0., + 0.5 * alat, + ], +] + +s = StructureData(cell=cell) +s.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), + symbols=['Si']) +s.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), + symbols=['Si']) + +#---------------------------------------------- + +options = { + "queue_name": "debug", + "max_wallclock_seconds": 1700, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} + +#-------------------------- Settings --------------------------------- +# +settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +settings = Dict(dict=settings_dict) + +#--------------------------------------------- +# Code-specific operational parameters +# +params_dict = { + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'spin-polarized': True, + 'meshcutoff': '40.000 Ry', + 'dm-numberpulay': 4, + 'dm-mixingweight': 0.3, + 'dm-tolerance': 1.e-3, + 'max-scfiterations': 3, + 'scf-must-converge': True, + 'md-typeofrun': 'cg', + 'md-numcgsteps': 0 +} + +parameters = Dict(dict=params_dict) + +# ---------------------Basis Set Info ----------------------------------- +# The basis dictionary follows the 'parameters' convention +# +basis_dict = { + 'pao-energy-shift': + '300 meV', + '%block pao-basis-sizes': + """ +Si DZP +%endblock pao-basis-sizes""", +} + +basis = Dict(dict=basis_dict) + +#------------------------------------------- +kpoints = KpointsData() + +# method mesh +kpoints_mesh = 4 +kpoints.set_kpoints_mesh([kpoints_mesh, kpoints_mesh, kpoints_mesh]) + +#------------------------------------------------ +pseudos_list = [] +raw_pseudos = [("Si.psf", 'Si')] +for fname, kinds, in raw_pseudos: + absname = os.path.realpath( + os.path.join(os.path.dirname(__file__), "data/sample-psf-family", + fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + if created: + print("Created the pseudo for {}".format(kinds)) + else: + print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + pseudos_list.append(pseudo) + +#--------------------------------------------- + +inputs = { + 'structure': s, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'kpoints': kpoints, + 'pseudos': { + 'Si': pseudos_list[0], + }, + 'metadata': { + 'options': options, + 'label': "Bulk Si short scf cycle" + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_soc_bands.py b/aiida_siesta/examples/plugins/siesta/example_soc_bands.py new file mode 100755 index 00000000..705b04fd --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_soc_bands.py @@ -0,0 +1,166 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- +from __future__ import absolute_import +from __future__ import print_function + +import os.path as op +import sys +from aiida.tools import get_explicit_kpoints_path + +#In this example we will calculate the band structure of Ge with SOC. +#Thanks to SeeK-path we can automatically generate the +#high symmetry points path where to calculate the bands. +#Alternatively, a manual list of k-points can be set. + +################################################################ + +from aiida.engine import submit +from aiida.orm import load_code +from aiida.orm import (Dict, StructureData, KpointsData) +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory + +PsfData = DataFactory('siesta.psf') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta4.0.1@kelvin' + +##-------------------Structure----------------------------------- +##Manually set the structure, all the quantities must be in Ang. +##Then, we pass through SeeK-path, to get the standardized cell, +##necessary for the automatic choice of the bands path. + +alat = 5.65 # angstrom +cell = [ + [ + 0.5 * alat, + 0.5 * alat, + 0., + ], + [ + 0., + 0.5 * alat, + 0.5 * alat, + ], + [ + 0.5 * alat, + 0., + 0.5 * alat, + ], +] + +s = StructureData(cell=cell) +s.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), + symbols=['Ge']) +s.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), + symbols=['Ge']) + +elements = list(s.get_symbols_set()) + +seekpath_parameters = Dict(dict={ + 'reference_distance': 0.02, + 'symprec': 0.0001 +}) +result = get_explicit_kpoints_path(s, **seekpath_parameters.get_dict()) +structure = result['primitive_structure'] + +code = load_code(codename) + +parameters = Dict( + dict={ + 'xc-functional': 'GGA', + 'xc-authors': 'PBE', + 'max-scfiterations': 50, + 'dm-numberpulay': 4, + 'Spin': "SO", + 'dm-mixingweight': 0.3, + 'dm-tolerance': 1.e-3, + 'electronic-temperature': '25 meV' + }) + +basis = Dict( + dict={ + 'pao-energy-shift': '300 meV', + '%block pao-basis-sizes': """ +Ge DZP +%endblock pao-basis-sizes""", + }) + +kpoints = KpointsData() +kpoints.set_kpoints_mesh([4, 4, 4]) + +##-------------------K-points for bands -------------------- +bandskpoints = KpointsData() + +##.....Making use of SeeK-path for the automatic path...... +##The choice of the distance between kpoints is in the call seekpath_parameters +##All high symmetry points included, labels already included +##This calls BandLine in siesta +bandskpoints = result['explicit_kpoints'] + +pseudos_list = [] +raw_pseudos = [("Ge.psf", 'Ge')] +for fname, kind in raw_pseudos: + absname = op.realpath( + op.join(op.dirname(__file__), "data/sample-psf-family", fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + if created: + print("\nCreated the pseudo for {}".format(kind)) + else: + print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) + pseudos_list.append(pseudo) + +options = { + "max_wallclock_seconds": 600, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 1, + } +} + +inputs = { + 'structure': structure, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'kpoints': kpoints, + 'bandskpoints': bandskpoints, + 'pseudos': { + 'Ge': pseudos_list[0], + }, + 'metadata': { + "label": "Ge band-structure with SOC", + 'options': options, + } +} + +if submit_test: + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + # subfolder, script_filename = calc.submit_test() + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + +else: + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_varcell.py b/aiida_siesta/examples/plugins/siesta/example_varcell.py new file mode 100755 index 00000000..3bb6b72e --- /dev/null +++ b/aiida_siesta/examples/plugins/siesta/example_varcell.py @@ -0,0 +1,169 @@ +#!/usr/bin/env runaiida +# -*- coding: utf-8 -*- + +__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." +__license__ = "MIT license, see LICENSE.txt file" +__version__ = "0.7.0" +__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" + +import sys +import os + +from aiida.common.example_helpers import test_and_get_code +from aiida.common.exceptions import NotExistent + +################################################################ + +PsfData = DataFactory('siesta.psf') +ParameterData = DataFactory('parameter') +KpointsData = DataFactory('array.kpoints') +StructureData = DataFactory('structure') + +try: + dontsend = sys.argv[1] + if dontsend == "--dont-send": + submit_test = True + elif dontsend == "--send": + submit_test = False + else: + raise IndexError +except IndexError: + print >> sys.stderr, ("The first parameter can only be either " + "--send or --dont-send") + sys.exit(1) + +try: + codename = sys.argv[2] +except IndexError: + codename = 'Siesta-4.0@rinaldo' + +# If True, load the pseudos from the family specified below +# Otherwise, use static files provided +auto_pseudos = True + +queue = None +settings = None + +code = test_and_get_code(codename, expected_code_type='siesta.siesta') + +alat = 5.430 # angstrom +cell = [[0.5*alat, 0.5*alat, 0.,], + [0., 0.5*alat, 0.5*alat,], + [0.5*alat, 0., 0.5*alat,], + ] + +# Si +# This was originally given in the "ScaledCartesian" format +# +s = StructureData(cell=cell) +s.append_atom(position=(0.000*alat,0.000*alat,0.000*alat),symbols=['Si']) +s.append_atom(position=(0.250*alat,0.250*alat,0.250*alat),symbols=['Si']) + + +elements = list(s.get_symbols_set()) + +if auto_pseudos: + valid_pseudo_groups = PsfData.get_psf_groups(filter_elements=elements) + + try: + #pseudo_family = sys.argv[3] + pseudo_family = 'lda-ag' + except IndexError: + print >> sys.stderr, "Error, auto_pseudos set to True. You therefore need to pass as second parameter" + print >> sys.stderr, "the pseudo family name." + print >> sys.stderr, "Valid PSF families are:" + print >> sys.stderr, "\n".join("* {}".format(i.name) for i in valid_pseudo_groups) + sys.exit(1) + + try: + PsfData.get_psf_group(pseudo_family) + except NotExistent: + print >> sys.stderr, "auto_pseudos is set to True and pseudo_family='{}',".format(pseudo_family) + print >> sys.stderr, "but no group with such a name found in the DB." + print >> sys.stderr, "Valid PSF groups are:" + print >> sys.stderr, ",".join(i.name for i in valid_pseudo_groups) + sys.exit(1) + +parameters = ParameterData(dict={ + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'max-scfiterations': 50, + 'dm-numberpulay': 4, + 'dm-mixingweight': 0.3, + 'dm-tolerance': 1.e-3, + 'solution-method': 'diagon', + 'electronic-temperature': '25 meV', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 20, + 'md-variablecell': True, + 'md-maxforcetol': '0.04 eV/Ang' + }) + +basis = ParameterData(dict={ +'pao-energy-shift': '300 meV', +'%block pao-basis-sizes': """ +Si SZP """, +}) + +kpoints = KpointsData() + +# method mesh +kpoints_mesh = 4 +kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) + +calc = code.new_calc() +calc.label = "Si bulk" +calc.description = "Test calculation with the Siesta code. Si bulk varcell" +calc.set_max_wallclock_seconds(30*60) # 30 min + +#------------ clarify this +calc.set_resources({"num_machines": 1}) + +calc.use_structure(s) +calc.use_parameters(parameters) +calc.use_basis(basis) + +if auto_pseudos: + try: + calc.use_pseudos_from_family(pseudo_family) + print "Pseudos successfully loaded from family {}".format(pseudo_family) + except NotExistent: + print ("Pseudo or pseudo family not found. You may want to load the " + "pseudo family, or set auto_pseudos to False.") + raise +else: + raw_pseudos = [("Si.psf", 'Si')] + + for fname, kinds, in raw_pseudos: + absname = os.path.realpath(os.path.join(os.path.dirname(__file__), + "data",fname)) + pseudo, created = PsfData.get_or_create(absname,use_first=True) + if created: + print "Created the pseudo for {}".format(kinds) + else: + print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) + + # Attach pseudo node to the calculation + calc.use_pseudo(pseudo,kind=kinds) + +calc.use_kpoints(kpoints) + +if settings is not None: + calc.use_settings(settings) + +if submit_test: + subfolder, script_filename = calc.submit_test() + print "Test_submit for calculation (uuid='{}')".format( + calc.uuid) + print "Submit file in {}".format(os.path.join( + os.path.relpath(subfolder.abspath), + script_filename + )) +else: + calc.store_all() + print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( + calc.uuid,calc.dbnode.pk) + calc.submit() + print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( + calc.uuid,calc.dbnode.pk) + From f5ad595908d3202ef706e1a48633abc71e1f1811 Mon Sep 17 00:00:00 2001 From: Bosoni Date: Mon, 11 Nov 2019 11:20:06 +0100 Subject: [PATCH 06/10] Fix previous commit I didn't realise that if you don't do --all, the deleted file are not added to the stage area. So new I actually delete them. --- aiida_siesta/docs/plugins/siesta.rst | 36 +- .../examples/plugins/siesta/__init__.py | 0 .../plugins/siesta/get_benchmark_info.py | 95 - .../examples/plugins/siesta/get_scalars.py | 64 - .../examples/plugins/siesta/get_status.py | 49 - .../examples/plugins/siesta/get_structures.py | 63 - .../plugins/siesta/test_bands_ge_collinear.py | 166 - .../plugins/siesta/test_bands_ge_soc.py | 166 - .../examples/plugins/siesta/test_psml.py | 193 -- .../examples/plugins/siesta/test_siesta.py | 233 -- .../plugins/siesta/test_siesta_bands_si.py | 190 -- .../plugins/siesta/test_siesta_cif_bands.py | 173 - .../plugins/siesta/test_siesta_family.py | 185 -- .../plugins/siesta/test_siesta_geom_fail.py | 144 - .../plugins/siesta/test_siesta_ldos.py | 199 -- .../plugins/siesta/test_siesta_magnetic.py | 142 - .../plugins/siesta/test_siesta_restart.py | 91 - .../plugins/siesta/test_siesta_scf_fail.py | 179 -- .../examples/plugins/siesta/test_siesta_si.py | 146 - .../plugins/siesta/test_siesta_sih.py | 276 -- .../plugins/siesta/test_siesta_varcell.py | 169 - aiida_siesta/tests/__init__.py | 0 aiida_siesta/tests/calculations/test_bands.py | 129 - .../tests/calculations/test_restart.py | 42 - .../calculations/test_serial_workfunction.py | 166 - .../calculations/test_simple_submission.py | 120 - .../test_simple_submission.py.bak | 119 - .../tests/calculations/test_submission.py | 106 - aiida_siesta/tests/conftest.py | 15 - aiida_siesta/tests/conftest.py.bak | 16 - aiida_siesta/tests/fdfdict/test_fdfdict.py | 14 - .../tests/plugin_configuration/__init__.py | 0 .../plugin_configuration/test_endpoints.py | 17 - .../test_endpoints.py.bak | 16 - aiida_siesta/tests/pseudos/C.psf | 1779 ----------- aiida_siesta/tests/pseudos/Fe.psf | 2831 ----------------- aiida_siesta/tests/pseudos/H.psf | 1527 --------- aiida_siesta/tests/pseudos/Mg.psf | 1877 ----------- aiida_siesta/tests/pseudos/O.psf | 1821 ----------- aiida_siesta/tests/pseudos/Si.psf | 1898 ----------- 40 files changed, 24 insertions(+), 15428 deletions(-) delete mode 100644 aiida_siesta/examples/plugins/siesta/__init__.py delete mode 100755 aiida_siesta/examples/plugins/siesta/get_benchmark_info.py delete mode 100755 aiida_siesta/examples/plugins/siesta/get_scalars.py delete mode 100755 aiida_siesta/examples/plugins/siesta/get_status.py delete mode 100755 aiida_siesta/examples/plugins/siesta/get_structures.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_bands_ge_collinear.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_bands_ge_soc.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_psml.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_bands_si.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_cif_bands.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_family.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_geom_fail.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_ldos.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_magnetic.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_restart.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_scf_fail.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_si.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_sih.py delete mode 100755 aiida_siesta/examples/plugins/siesta/test_siesta_varcell.py delete mode 100644 aiida_siesta/tests/__init__.py delete mode 100644 aiida_siesta/tests/calculations/test_bands.py delete mode 100644 aiida_siesta/tests/calculations/test_restart.py delete mode 100644 aiida_siesta/tests/calculations/test_serial_workfunction.py delete mode 100644 aiida_siesta/tests/calculations/test_simple_submission.py delete mode 100644 aiida_siesta/tests/calculations/test_simple_submission.py.bak delete mode 100755 aiida_siesta/tests/calculations/test_submission.py delete mode 100644 aiida_siesta/tests/conftest.py delete mode 100644 aiida_siesta/tests/conftest.py.bak delete mode 100644 aiida_siesta/tests/fdfdict/test_fdfdict.py delete mode 100644 aiida_siesta/tests/plugin_configuration/__init__.py delete mode 100644 aiida_siesta/tests/plugin_configuration/test_endpoints.py delete mode 100644 aiida_siesta/tests/plugin_configuration/test_endpoints.py.bak delete mode 100644 aiida_siesta/tests/pseudos/C.psf delete mode 100644 aiida_siesta/tests/pseudos/Fe.psf delete mode 100644 aiida_siesta/tests/pseudos/H.psf delete mode 100644 aiida_siesta/tests/pseudos/Mg.psf delete mode 100644 aiida_siesta/tests/pseudos/O.psf delete mode 100644 aiida_siesta/tests/pseudos/Si.psf diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index 948e8ba4..1e421f07 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -61,10 +61,11 @@ Inputs as internal units, the cell and atom positions must be specified in Angstrom. The :py:class:`StructureData ` can also import - ase structure or pymatgen structures. This two tools can be used to load + ase structures or pymatgen structures. This two tools can be used to load structure from files. See example in .... * **parameters**, class :py:class:`Dict `, *Mandatory* + A dictionary with scalar fdf variables and blocks, which are the basic elements of any Siesta input file. A given Siesta fdf file can be cast almost directly into this dictionary form, except that @@ -160,6 +161,7 @@ Inputs any basis specification and it will run with the default DZP. * **kpoints**, class :py:class:`KpointsData `, *Optional* + Reciprocal space points for the full sampling of the BZ during the self-consistent-field iteration. It must be given in mesh form. There is no support yet for Siesta's kgrid-cutoff keyword:: @@ -171,6 +173,7 @@ Inputs If this node is not present, only the Gamma point is used for sampling. * **bandskpoints**, class :py:class:`KpointsData `, *Optional* + Reciprocal space points for the calculation of bands. This keyword is meant to facilitate the management of kpoints exploiting the functionality @@ -206,7 +209,8 @@ Inputs .. note:: 'get_explicit_kpoints_path' make use of "SeeK-path". Please cite the `HPKOT paper`_ if you use this tool. - Warning: as explained in the `aiida documentation`_, SeekPath + + .. warning:: as explained in the `aiida documentation`_, SeekPath might modify the structure to follow particular conventions and the generated kpoints might only apply on the internally generated 'primitive_structure' and not @@ -236,16 +240,16 @@ Inputs The full list of cases can be explored looking at the example ... - If the keyword node **bandskpoints** is not present, no band structure is computed. - .. warning:: The implementation relies on the correct description of the labels in the class :py:class:`KpointsData `. Refrain from the use of 'bandskpoints.labels' in any other situation apart from the one described above. An incorrect use of the labels might result in an incorrect parsing of the bands. + If the keyword node **bandskpoints** is not present, no band structure is computed. * **settings**, class :py:class:`Dict ` , *Optional* + An optional dictionary that activates non-default operations. For a list of possible values to pass, see the section on :ref:`advanced features `. @@ -256,10 +260,12 @@ Once all the inputs above are set, the subsequent step consists in passing them calculation class and run/submit it. First, the Siesta calculation class is loaded:: + from aiida_siesta.calculations.siesta import SiestaCalculation builder = SiestaCalculation.get_builder() The inputs (defined as in the previous section) are passed to the builder:: + builder.code = code builder.structure = structure builder.parameters = parameters @@ -269,22 +275,27 @@ The inputs (defined as in the previous section) are passed to the builder:: builder.bandskpoints = bandskpoints Finally the resources for the calculation must be set, for instance:: + builder.metadata.options.resources = {'num_machines': 1} builder.metadata.options.max_wallclock_seconds = 1800 Optionally, label and description:: + builder.metadata.label = 'My generic title' builder.metadata.description 'My more detailed description' -Run the calculation for interactive run:: +To run the calculation in an interactive way:: + from aiida.engine import run results = run(builder) -where the results variable will contain a dictionary containing all the nodes that were produced as output. +Here the results variable will contain a dictionary +containing all the nodes that were produced as output. + +Another option is to submit it to the deamon:: -Or submit it to the deamon to run in backround:: from aiida.engine import run calc = submit(builder) -In this case, calc is the calculation node, and not the result dictionary. +In this case, calc is the calculation node and not the results dictionary. .. note:: In order to inspect the inputs created by AiiDA without actually running the calculation, we can perform a dry run of the submission process:: @@ -369,13 +380,14 @@ functionality should be compiled in and active in the run! * **bands**, :py:class:`BandsData ` Present only if a band calculation is requested (signaled by the - presence of a **bandskpoints** input node of class KpointsData) - Contains an array with the list of electronic energies (in eV) for every + presence of a **bandskpoints** input node of class KpointsData). + It contains an array with the list of electronic energies (in eV) for every kpoint. For spin-polarized calculations, there is an extra dimension for spin. In this class also the full list of kpoints is stored and they are in units of 1/Angstrom. Therefore a direct comparison with the Siesta output SystLabel.bands is possible only after the conversion of Angstrom to Bohr. - The bands are not rescaled by the Fermi energy. + The bands are not rescaled by the Fermi energy. Tools for the generation + of files that can be easly plot are available through ``bands.export``. No trajectories have been implemented yet. @@ -384,7 +396,7 @@ Errors Errors during the parsing stage are reported in the log of the calculation (accessible with the ``verdi process report`` command). -Moreover, they are stored in the `output_parameters` node under the key ``warnings``. +Moreover, they are stored in the **output_parameters** node under the key ``warnings``. Restarts -------- diff --git a/aiida_siesta/examples/plugins/siesta/__init__.py b/aiida_siesta/examples/plugins/siesta/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/aiida_siesta/examples/plugins/siesta/get_benchmark_info.py b/aiida_siesta/examples/plugins/siesta/get_benchmark_info.py deleted file mode 100755 index 29903658..00000000 --- a/aiida_siesta/examples/plugins/siesta/get_benchmark_info.py +++ /dev/null @@ -1,95 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function -import sys -import os - -__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved" -__license__ = "Non-Commercial, End-User Software License Agreement, see LICENSE.txt file." -__version__ = "0.7.0" -__authors__ = "The AiiDA team." - -# -# Prints benchmark info for a calculation -# - -# Used to test the parent calculation -SiestaCalc = CalculationFactory('siesta.siesta') - -try: - calc_id = sys.argv[1] -except IndexError: - print(("Must provide as parameter the calc ID"), file=sys.stderr) - sys.exit(1) - - -try: - int(calc_id) -except ValueError: - raise ValueError('Calc_id not an integer: {}'.format(calc_id)) - -calc = load_node(int(calc_id)) - -if calc.process_class==SiestaCalc: - - print("Calculation is '{0}' with exit code '{1}'".format(calc.process_state.name,calc.exit_status), file=sys.stderr) - print("Label: {}".format(calc.label), file=sys.stderr) - d=calc.outputs.output_parameters.get_dict() - - sys.stdout.write("{} ".format(int(calc_id))) - try: - no_u = d['no_u'] - nnz = d['nnz'] - print("No of orbitals: {} nnz: {}".format(no_u,nnz), file=sys.stderr) - sys.stdout.write("{} {}".format(no_u,nnz)) - except: - pass - try: - mesh = d['mesh'] - np = mesh[0]*mesh[1]*mesh[2] - print("Mesh points: {} (total {})".format(mesh,np), file=sys.stderr) - sys.stdout.write(" {} {}".format(mesh,np)) - except: - pass - try: - nodes= d['siesta:Nodes'] - print("Number of nodes {}".format(nodes), file=sys.stderr) - sys.stdout.write(" {} ".format(int(nodes))) - except: - pass - try: - code= str(calc.inputs.code.get_full_text_info()[2][1]).split()[0] - print("Code: {}".format(code), file=sys.stderr) - sys.stdout.write(" {} ".format(code)) - except: - pass - try: - computer= str(calc.computer.name).split()[0] - print("Computer: {}".format(computer), file=sys.stderr) - sys.stdout.write(" {} ".format(computer)) - except: - pass - try: - t_global = d['global_time'] - print("Total time: {}".format(t_global), file=sys.stderr) - except: - pass - - try: - t_decomp = d['timing_decomposition'] - t_solver = t_decomp['compute_DM'] - t_H = t_decomp['setup_H'] - print("Total time, solver, setup_H: {} {} {}".format(t_global,t_solver,t_H), file=sys.stderr) - sys.stdout.write(" {} {} {}\n".format(t_global,t_solver,t_H)) - except: - pass - - sys.stdout.flush() - -else: - print(("Calculation should be a Siesta calculation."), file=sys.stderr) - sys.exit(1) - - - diff --git a/aiida_siesta/examples/plugins/siesta/get_scalars.py b/aiida_siesta/examples/plugins/siesta/get_scalars.py deleted file mode 100755 index 3ab4027e..00000000 --- a/aiida_siesta/examples/plugins/siesta/get_scalars.py +++ /dev/null @@ -1,64 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function -import sys -import os - -__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved" -__license__ = "Non-Commercial, End-User Software License Agreement, see LICENSE.txt file." -__version__ = "0.7.0" -__authors__ = "The AiiDA team." - -# -# Prints energies (and spin, if available) for a calculation -# - -# Used to test the parent calculation -SiestaCalc = CalculationFactory('siesta.siesta') - -try: - calc_id = sys.argv[1] -except IndexError: - print(("Must provide as parameter the calc ID"), file=sys.stderr) - sys.exit(1) - - -try: - int(calc_id) -except ValueError: - raise ValueError('Calc_id not an integer: {}'.format(calc_id)) - -#calc = Calculation.get_subclass_from_pk(calc_id) -calc = load_node(int(calc_id)) -##### - -if calc.process_class==SiestaCalc: - print("Calculation is '{0}' with exit code '{1}'".format(calc.process_state.name,calc.exit_status)) -##?? print "Desc: {}".format(calc.description) - d=calc.outputs.output_parameters.get_dict() - - try: - print("Total (free) energy: {} {}".format(d['FreeE'],d['FreeE_units'])) - except: - pass - try: - print("Band energy: {} {}".format(d['Ebs'],d['Ebs_units'])) - except: - pass - try: - print("Fermi energy: {} {}".format(d['E_Fermi'],d['E_Fermi_units'])) - except: - pass - try: - print("Total spin: {}".format(d['stot'])) - except: - pass - - -else: - print(("Calculation should be a Siesta calculation."), file=sys.stderr) - sys.exit(1) - - - diff --git a/aiida_siesta/examples/plugins/siesta/get_status.py b/aiida_siesta/examples/plugins/siesta/get_status.py deleted file mode 100755 index 9943ba07..00000000 --- a/aiida_siesta/examples/plugins/siesta/get_status.py +++ /dev/null @@ -1,49 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function -import sys -import os - -__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved" -__license__ = "Non-Commercial, End-User Software License Agreement, see LICENSE.txt file." -__version__ = "0.7.0" -__authors__ = "The AiiDA team." - -# -# Prints warnings for a calculation -# - -# Used to test the parent calculation -from aiida_siesta.calculations.siesta import SiestaCalculation -#SiestaCalc = CalculationFactory('siesta.siesta') - -try: - calc_id = sys.argv[1] -except IndexError: - print(("Must provide as parameter the calc ID"), file=sys.stderr) - sys.exit(1) - - -try: - int(calc_id) -except ValueError: - raise ValueError('Calc_id not an integer: {}'.format(calc_id)) - -calc = load_node(int(calc_id)) - -if (calc.process_class == SiestaCalculation): - - print("Calculation is '{0}' with exit code '{1}'".format(calc.process_state.name,calc.exit_status)) - d=calc.outputs.output_parameters.get_dict() - try: - print("Warnings: {}".format(d['warnings'])) - except: - pass - -else: - print(("Calculation should be a Siesta calculation."), file=sys.stderr) - sys.exit(1) - - - diff --git a/aiida_siesta/examples/plugins/siesta/get_structures.py b/aiida_siesta/examples/plugins/siesta/get_structures.py deleted file mode 100755 index 11f2b0c3..00000000 --- a/aiida_siesta/examples/plugins/siesta/get_structures.py +++ /dev/null @@ -1,63 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function -import sys -import os - -__copyright__ = u"Copyright (c), This file is part of the AiiDA platform. For further information please visit http://www.aiida.net/. All rights reserved" -__license__ = "Non-Commercial, End-User Software License Agreement, see LICENSE.txt file." -__version__ = "0.7.0" -__authors__ = "The AiiDA team." - -# -# Prints initial and final structures for a calculation -# - -# Used to test the parent calculation -from aiida_siesta.calculations.siesta import SiestaCalculation - -try: - calc_id = sys.argv[1] -except IndexError: - print(("Must provide as parameter the calc ID"), file=sys.stderr) - sys.exit(1) - - -try: - int(calc_id) -except ValueError: - raise ValueError('Calc_id not an integer: {}'.format(calc_id)) - -#calc = Calculation.get_subclass_from_pk(calc_id) -calc = load_node(int(calc_id)) -##### - -if (calc.process_class==SiestaCalculation): - - print("Calculation status: '{}'".format(calc.process_state.name)) - - d=calc.outputs.output_parameters.get_dict() - - sin=calc.inputs.structure - print("Input structure:") - print(" Cell lengths: {}".format(sin.cell_lengths)) - print(" Cell angles: {}".format(sin.cell_angles)) - print(" Cell volume: {}".format(sin.get_cell_volume())) - - if d['variable_geometry']: - try: - sout=calc.outputs.output_structure - print("Output structure:") - print(" Cell lengths: {}".format(sout.cell_lengths)) - print(" Cell angles: {}".format(sout.cell_angles)) - print(" Cell volume: {}".format(sout.get_cell_volume())) - except: - print("Output structure not available...") - -else: - print(("Calculation should be a Siesta calculation."), file=sys.stderr) - sys.exit(1) - - - diff --git a/aiida_siesta/examples/plugins/siesta/test_bands_ge_collinear.py b/aiida_siesta/examples/plugins/siesta/test_bands_ge_collinear.py deleted file mode 100755 index a9b3c591..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_bands_ge_collinear.py +++ /dev/null @@ -1,166 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function - -import os.path as op -import sys -from aiida.tools import get_explicit_kpoints_path - -#In this example we will calculate the band structure of Ge with SOC. -#Thanks to SeeK-path we can automatically generate the -#high symmetry points path where to calculate the bands. -#Alternatively, a manual list of k-points can be set. - -################################################################ - -from aiida.engine import submit -from aiida.orm import load_code -from aiida.orm import (Dict, StructureData, KpointsData) -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -PsfData = DataFactory('siesta.psf') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta4.0.1@kelvin' - -##-------------------Structure----------------------------------- -##Manually set the structure, all the quantities must be in Ang. -##Then, we pass through SeeK-path, to get the standardized cell, -##necessary for the automatic choice of the bands path. - -alat = 5.65 # angstrom -cell = [ - [ - 0.5 * alat, - 0.5 * alat, - 0., - ], - [ - 0., - 0.5 * alat, - 0.5 * alat, - ], - [ - 0.5 * alat, - 0., - 0.5 * alat, - ], -] - -s = StructureData(cell=cell) -s.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), - symbols=['Ge']) -s.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), - symbols=['Ge']) - -elements = list(s.get_symbols_set()) - -seekpath_parameters = Dict(dict={ - 'reference_distance': 0.02, - 'symprec': 0.0001 -}) -result = get_explicit_kpoints_path(s, **seekpath_parameters.get_dict()) -structure = result['primitive_structure'] - -code = load_code(codename) - -parameters = Dict( - dict={ - 'xc-functional': 'GGA', - 'xc-authors': 'PBE', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'Spin': "collinear", - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'electronic-temperature': '25 meV' - }) - -basis = Dict( - dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': """ -Ge DZP -%endblock pao-basis-sizes""", - }) - -kpoints = KpointsData() -kpoints.set_kpoints_mesh([4, 4, 4]) - -##-------------------K-points for bands -------------------- -bandskpoints = KpointsData() - -##.....Making use of SeeK-path for the automatic path...... -##The choice of the distance between kpoints is in the call seekpath_parameters -##All high symmetry points included, labels already included -##This calls BandLine in siesta -bandskpoints = result['explicit_kpoints'] - -pseudos_list = [] -raw_pseudos = [("Ge.psf", 'Ge')] -for fname, kind in raw_pseudos: - absname = op.realpath( - op.join(op.dirname(__file__), "data/sample-psf-family", fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - if created: - print("\nCreated the pseudo for {}".format(kind)) - else: - print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) - pseudos_list.append(pseudo) - -options = { - "max_wallclock_seconds": 600, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} - -inputs = { - 'structure': structure, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'kpoints': kpoints, - 'bandskpoints': bandskpoints, - 'pseudos': { - 'Ge': pseudos_list[0], - }, - 'metadata': { - "label": "Ge band-structure with collinear spin", - 'options': options, - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_bands_ge_soc.py b/aiida_siesta/examples/plugins/siesta/test_bands_ge_soc.py deleted file mode 100755 index 705b04fd..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_bands_ge_soc.py +++ /dev/null @@ -1,166 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function - -import os.path as op -import sys -from aiida.tools import get_explicit_kpoints_path - -#In this example we will calculate the band structure of Ge with SOC. -#Thanks to SeeK-path we can automatically generate the -#high symmetry points path where to calculate the bands. -#Alternatively, a manual list of k-points can be set. - -################################################################ - -from aiida.engine import submit -from aiida.orm import load_code -from aiida.orm import (Dict, StructureData, KpointsData) -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -PsfData = DataFactory('siesta.psf') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta4.0.1@kelvin' - -##-------------------Structure----------------------------------- -##Manually set the structure, all the quantities must be in Ang. -##Then, we pass through SeeK-path, to get the standardized cell, -##necessary for the automatic choice of the bands path. - -alat = 5.65 # angstrom -cell = [ - [ - 0.5 * alat, - 0.5 * alat, - 0., - ], - [ - 0., - 0.5 * alat, - 0.5 * alat, - ], - [ - 0.5 * alat, - 0., - 0.5 * alat, - ], -] - -s = StructureData(cell=cell) -s.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), - symbols=['Ge']) -s.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), - symbols=['Ge']) - -elements = list(s.get_symbols_set()) - -seekpath_parameters = Dict(dict={ - 'reference_distance': 0.02, - 'symprec': 0.0001 -}) -result = get_explicit_kpoints_path(s, **seekpath_parameters.get_dict()) -structure = result['primitive_structure'] - -code = load_code(codename) - -parameters = Dict( - dict={ - 'xc-functional': 'GGA', - 'xc-authors': 'PBE', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'Spin': "SO", - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'electronic-temperature': '25 meV' - }) - -basis = Dict( - dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': """ -Ge DZP -%endblock pao-basis-sizes""", - }) - -kpoints = KpointsData() -kpoints.set_kpoints_mesh([4, 4, 4]) - -##-------------------K-points for bands -------------------- -bandskpoints = KpointsData() - -##.....Making use of SeeK-path for the automatic path...... -##The choice of the distance between kpoints is in the call seekpath_parameters -##All high symmetry points included, labels already included -##This calls BandLine in siesta -bandskpoints = result['explicit_kpoints'] - -pseudos_list = [] -raw_pseudos = [("Ge.psf", 'Ge')] -for fname, kind in raw_pseudos: - absname = op.realpath( - op.join(op.dirname(__file__), "data/sample-psf-family", fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - if created: - print("\nCreated the pseudo for {}".format(kind)) - else: - print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) - pseudos_list.append(pseudo) - -options = { - "max_wallclock_seconds": 600, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} - -inputs = { - 'structure': structure, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'kpoints': kpoints, - 'bandskpoints': bandskpoints, - 'pseudos': { - 'Ge': pseudos_list[0], - }, - 'metadata': { - "label": "Ge band-structure with SOC", - 'options': options, - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_psml.py b/aiida_siesta/examples/plugins/siesta/test_psml.py deleted file mode 100755 index b635f597..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_psml.py +++ /dev/null @@ -1,193 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -from __future__ import absolute_import -from __future__ import print_function - -import sys -import os - -from aiida.engine import submit -from aiida.orm import load_code -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -########################################################## -# # -# Siesta calculation on benzene molecule, first to try # -# # -########################################################## - -PsmlData = DataFactory('siesta.psml') -Dict = DataFactory('dict') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) -# -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta4.0.1@kelvin' - -# -#------------------Code and computer options --------------------------- -# -code = load_code(codename) - -options = { - "queue_name": "debug", - "max_wallclock_seconds": 1700, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} - -# -#-------------------------- Settings --------------------------------- -# -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} -settings = Dict(dict=settings_dict) -#--------------------------------------------------------------------- - -# -#-------------------------- Structure -------------------------------- -# -alat = 5.430 # angstrom -cell = [ - [ - 0.5 * alat, - 0.5 * alat, - 0., - ], - [ - 0., - 0.5 * alat, - 0.5 * alat, - ], - [ - 0.5 * alat, - 0., - 0.5 * alat, - ], -] - -s = StructureData(cell=cell) -s.append_atom( - position=(0.000 * alat, 0.000 * alat, 0.000 * alat), symbols=['Si']) -s.append_atom( - position=(0.250 * alat, 0.250 * alat, 0.250 * alat), symbols=['Si']) - -#----------------------------------------------------------------------- - -# -# ----------------------Parameters ------------------------------------- -# -# Note the use of '.' in some entries. This will be fixed below. -# Note also that some entries have ':' as separator. This is not -# allowed in Siesta, and will be fixed by the plugin itself. The -# latter case is an unfortunate historical choice. It should not -# be used in modern scripts. -# -params_dict = { - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'spin': 'SO', - 'mesh-cutoff': '200.000 Ry', - 'max-scfiterations': 1000, - 'dm-numberpulay': 5, - 'dm-mixingweight': 0.050, - 'dm-tolerance': 1.e-4, - 'dm-mixscf1': True, - 'negl-nonoverlap-int': False, - 'solution-method': 'diagon', - 'electronic-temperature': '100.000 K', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 2, - 'md-maxcgdispl': '0.200 bohr', - 'md-maxforcetol': '0.050 eV/Ang', - 'writeforces': True, - 'writecoorstep': True, - 'write-mulliken-pop': 1, -} - -parameters = Dict(dict=params_dict) -#------------------------------------------------------------------------ - -# -# ---------------------Basis Set Info ----------------------------------- -# The basis dictionary follows the 'parameters' convention -# -basis_dict = { - 'pao-basistype': 'split', - 'pao-splitnorm': 0.150, - 'pao-energyshift': '0.020 Ry' -} - -basis = Dict(dict=basis_dict) -#------------------------------------------------------------------------ - -#--------------------- Pseudopotentials --------------------------------- -# -# This exemplifies the handling of pseudos for different species -# Those sharing the same pseudo should be indicated. -# -pseudos_list = [] -raw_pseudos = [("Si.psml", 'Si')] - -for fname, kinds, in raw_pseudos: - absname = os.path.realpath( - os.path.join(os.path.dirname(__file__), "data/sample-psml-family", fname)) - pseudo, created = PsmlData.get_or_create(absname, use_first=True) - if created: - print("Created the pseudo for {}".format(kinds)) - else: - print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) - pseudos_list.append(pseudo) - -#----------------------------------------------------------------------- - -# -#--All the inputs of a Siesta calculations are listed in a dictionary-- -# -inputs = { - 'structure': s, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'pseudos': { - 'Si': pseudos_list[0] - }, - 'metadata': { - 'options': options, - 'label': "Si crystal with PSML pseudos", - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta.py b/aiida_siesta/examples/plugins/siesta/test_siesta.py deleted file mode 100755 index 02f50648..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta.py +++ /dev/null @@ -1,233 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -from __future__ import absolute_import -from __future__ import print_function - -import sys -import os - -from aiida.engine import submit -from aiida.orm import load_code -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -# Siesta calculation on benzene molecule - -PsfData = DataFactory('siesta.psf') -Dict = DataFactory('dict') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) -# -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta4.0.1@kelvin' - -# -#------------------Code and computer options --------------------------- -# -code = load_code(codename) - -options = { - "queue_name": "debug", - "max_wallclock_seconds": 1700, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} - -#TO DO: -# A Siesta executable compiled in serial mode might not work properly -# on a computer set up for MPI operation. -# This snippet can be used to check whether a code has been compiled -# with mpi support, and act accordingly -# For this to work, the user has to manually add the record in the -# database. In the verdi shell: -# -# code = load_node(code_PK) -# code.set_extra("mpi",True) -#code_mpi_enabled = False -#try: -# code_mpi_enabled = code.get_extra("mpi") -#except AttributeError: -# pass -#calc.set_withmpi(code_mpi_enabled) -#----------------------------------------------------------------------- - -# -#-------------------------- Settings --------------------------------- -# -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} -settings = Dict(dict=settings_dict) -#--------------------------------------------------------------------- - -# -#-------------------------- Structure -------------------------------- -# -alat = 15. # angstrom -cell = [ - [ - alat, - 0., - 0., - ], - [ - 0., - alat, - 0., - ], - [ - 0., - 0., - alat, - ], -] - -# Note an atom tagged (for convenience) with a different label - -s = StructureData(cell=cell) -s.append_atom(position=(0.000, 0.000, 0.468), symbols=['H']) -s.append_atom(position=(0.000, 0.000, 1.620), symbols=['C']) -s.append_atom(position=(0.000, -2.233, 1.754), symbols=['H']) -s.append_atom(position=(0.000, 2.233, 1.754), symbols=['H']) -s.append_atom(position=(0.000, -1.225, 2.327), symbols='C', name="Cred") -s.append_atom(position=(0.000, 1.225, 2.327), symbols=['C']) -s.append_atom(position=(0.000, -1.225, 3.737), symbols=['C']) -s.append_atom(position=(0.000, 1.225, 3.737), symbols=['C']) -s.append_atom(position=(0.000, -2.233, 4.311), symbols=['H']) -s.append_atom(position=(0.000, 2.233, 4.311), symbols=['H']) -s.append_atom(position=(0.000, 0.000, 4.442), symbols=['C']) -s.append_atom(position=(0.000, 0.000, 5.604), symbols=['H']) - -elements = list(s.get_symbols_set()) -#----------------------------------------------------------------------- - -# -# ----------------------Parameters ------------------------------------- -# -# Note the use of '.' in some entries. This will be fixed below. -# Note also that some entries have ':' as separator. This is not -# allowed in Siesta, and will be fixed by the plugin itself. The -# latter case is an unfortunate historical choice. It should not -# be used in modern scripts. -# -params_dict = { - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'spin-polarized': True, - 'noncollinearspin': False, - 'mesh-cutoff': '200.000 Ry', - 'max-scfiterations': 1000, - 'dm-numberpulay': 5, - 'dm-mixingweight': 0.050, - 'dm-tolerance': 1.e-4, - 'dm-mixscf1': True, - 'negl-nonoverlap-int': False, - 'solution-method': 'diagon', - 'electronic-temperature': '100.000 K', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 2, - 'md-maxcgdispl': '0.200 bohr', - 'md-maxforcetol': '0.050 eV/Ang', - 'writeforces': True, - 'writecoorstep': True, - 'write-mulliken-pop': 1, -} - -parameters = Dict(dict=params_dict) -#------------------------------------------------------------------------ - -# -# ---------------------Basis Set Info ----------------------------------- -# The basis dictionary follows the 'parameters' convention -# -basis_dict = { - 'pao-basistype': - 'split', - 'pao-splitnorm': - 0.150, - 'pao-energyshift': - '0.020 Ry', - '%block pao-basis-sizes': - """ -C SZP -Cred SZ -H SZP -%endblock pao-basis-sizes""", -} - -basis = Dict(dict=basis_dict) -#------------------------------------------------------------------------ - -#--------------------- Pseudopotentials --------------------------------- -# -# This exemplifies the handling of pseudos for different species -# Those sharing the same pseudo should be indicated. -# -pseudos_list = [] -raw_pseudos = [("C.psf", ['C', 'Cred']), ("H.psf", 'H')] - -for fname, kinds, in raw_pseudos: - absname = os.path.realpath( - os.path.join(os.path.dirname(__file__), "data/sample-psf-family", - fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - if created: - print("Created the pseudo for {}".format(kinds)) - else: - print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) - pseudos_list.append(pseudo) - -#----------------------------------------------------------------------- - -# -#--All the inputs of a Siesta calculations are listed in a dictionary-- -# -inputs = { - 'structure': s, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'pseudos': { - 'C': pseudos_list[0], - 'Cred': pseudos_list[0], - 'H': pseudos_list[1], - }, - 'metadata': { - 'options': options, - 'label': "Benzene molecule", - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") -# I could't find a way to access the actual folder (subfolder of submit_test) -# from the calculation node. So I can't print the exact location - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_bands_si.py b/aiida_siesta/examples/plugins/siesta/test_siesta_bands_si.py deleted file mode 100755 index daa4302e..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_bands_si.py +++ /dev/null @@ -1,190 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function - -import os.path as op -import sys -from aiida.tools import get_explicit_kpoints_path - -#In this example we will calculate the band structure of Si. -#Thanks to SeeK-path we can automatically generate the -#high symmetry points path where to calculate the bands. -#Alternatively, a manual list of k-points can be set. - -################################################################ - -from aiida.engine import submit -from aiida.orm import load_code -from aiida.orm import (Dict, StructureData, KpointsData) -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -PsfData = DataFactory('siesta.psf') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta4.0.1@kelvin' - -##-------------------Structure----------------------------------- -##Manually set the structure, all the quantities must be in Ang. -##Then, we pass through SeeK-path, to get the standardized cell, -##necessary for the automatic choice of the bands path. - -alat = 5.430 # angstrom -cell = [ - [ - 0.5 * alat, - 0.5 * alat, - 0., - ], - [ - 0., - 0.5 * alat, - 0.5 * alat, - ], - [ - 0.5 * alat, - 0., - 0.5 * alat, - ], -] - -s = StructureData(cell=cell) -s.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), - symbols=['Si']) -s.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), - symbols=['Si']) - -elements = list(s.get_symbols_set()) - -seekpath_parameters = Dict(dict={ - 'reference_distance': 0.02, - 'symprec': 0.0001 -}) -result = get_explicit_kpoints_path(s, **seekpath_parameters.get_dict()) -structure = result['primitive_structure'] - -code = load_code(codename) - -parameters = Dict( - dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'Solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang', - 'write-forces': True, - # 'xml-write': True - }) - -basis = Dict( - dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': """ -Si DZP -%endblock pao-basis-sizes""", - }) - -kpoints = KpointsData() -kpoints.set_kpoints_mesh([4, 4, 4]) - -##-------------------K-points for bands -------------------- -bandskpoints = KpointsData() -##Uncomment your favourite, two options: - -##1) -##.....Making use of SeeK-path for the automatic path...... -##The choice of the distance between kpoints is in the call seekpath_parameters -##All high symmetry points included, labels already included -##This calls BandLine in siesta -bandskpoints = result['explicit_kpoints'] - -##2) -##.....Only points, no labels....... -##Mandatory to set cell and pbc -##This calls BandsPoint -#kpp = [(0.500, 0.250, 0.750), (0.500, 0.500, 0.500), (0., 0., 0.)] -#bandskpoints.set_cell(structure.cell, structure.pbc) -#bandskpoints.set_kpoints(kpp) - -#Note: The option to define a path touching specific kpoints -#for instance: -#kpp = [('W', (0.500, 0.250, 0.750), 'L', (0.500, 0.500, 0.500), 40), -# ('L', (0.500, 0.500, 0.500), 'G', (0., 0., 0.), 40)] -#Now is not easy to set. I'll study more on that - -pseudos_list = [] -raw_pseudos = [("Si.psf", 'Si')] -for fname, kind in raw_pseudos: - absname = op.realpath( - op.join(op.dirname(__file__), "data/sample-psf-family", fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - if created: - print("\nCreated the pseudo for {}".format(kind)) - else: - print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) - pseudos_list.append(pseudo) - -options = { - "max_wallclock_seconds": 600, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} - -inputs = { - 'structure': structure, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'kpoints': kpoints, - 'bandskpoints': bandskpoints, - 'pseudos': { - 'Si': pseudos_list[0], - }, - 'metadata': { - "label": "TestOnSiliconBandsLines", - 'options': options, - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") -# I could't find a way to access the actual folder (subfolder of submit_test) -# from the calculation node. So I can't print the exact location - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_cif_bands.py b/aiida_siesta/examples/plugins/siesta/test_siesta_cif_bands.py deleted file mode 100755 index d89c37ea..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_cif_bands.py +++ /dev/null @@ -1,173 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -from __future__ import absolute_import -from __future__ import print_function - -import sys - -import pymatgen as mg - -from aiida.engine import submit -from aiida.orm import load_code -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida_siesta.data.psf import get_pseudos_from_structure -from aiida.plugins import DataFactory -from aiida.tools import get_explicit_kpoints_path - -# This script will send a Siesta calculation on a structure taken from -# a cif file. -# The band structure is calculated and the kpoint path is automatically -# generated using seekpath. - -PsfData = DataFactory('siesta.psf') -Dict = DataFactory('dict') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'siesta4.0.1@parsons' - -# -#------------------Code and computer options --------------------------- -# -code = load_code(codename) - -options = { - "queue_name": "debug", - "max_wallclock_seconds": 1700, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} -# -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} -settings = Dict(dict=settings_dict) -#--------------------------------------------------------------------- - -# -# Structure ----------------------------------------- -# -# Passing through SeeK-path first, to get the standardized cell. -# Necessary for the automatic choice of the bands path. -# -structure = mg.Structure.from_file("data/O2_ICSD_173933.cif", primitive=False) -s = StructureData(pymatgen_structure=structure) - -seekpath_parameters = {'reference_distance': 0.02, 'symprec': 0.0001} -result = get_explicit_kpoints_path(s, **seekpath_parameters) -newstructure = result['primitive_structure'] - -# -# Parameters --------------------------------------------------- -# -params_dict = { - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'spin-polarized': True, - 'noncollinearspin': False, - 'mesh-cutoff': '200.000 Ry', - 'max-scfiterations': 1000, - 'dm-numberpulay': 5, - 'dm-mixingweight': 0.050, - 'dm-tolerance': 1.e-4, - 'dm-mixscf1': True, - 'negl-nonoverlap-int': False, - 'solution-method': 'diagon', - 'electronic-temperature': '100.000 K', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 2, - 'md-maxcgdispl': '0.200 bohr', - 'md-maxforcetol': '0.050 eV/Ang', - 'writeforces': True, - 'writecoorstep': True, - 'write-mulliken-pop': 1 -} -# -parameters = Dict(dict=params_dict) - -#---------------------------------------------------------- -# -# Basis Set Info ------------------------------------------ -# The basis dictionary follows the 'parameters' convention -# -basis_dict = { - 'pao-basistype': 'split', - 'pao-splitnorm': 0.150, - 'pao-energyshift': '0.020 Ry', - '%block pao-basis-sizes': """ -O SZP -%endblock pao-basis-sizes""", -} -# -basis = Dict(dict=basis_dict) -#-------------------------------------------------------------- - -#--------------------- Pseudopotentials --------------------------------- -# -# FIXME: The family name is hardwired -# -pseudos_dict = get_pseudos_from_structure(s, 'sample_psf_family') -print(pseudos_dict) -#----------------------------------------------------------------------- - -# K-points for scf cycle ------------------------------------------- -kts = KpointsData() -kpoints_mesh = 4 -kts.set_kpoints_mesh([kpoints_mesh, kpoints_mesh, kpoints_mesh]) - -# -bandskpoints = KpointsData() - -# Making use of SeeK-path for the automatic path -# The choice of the distance between kpoints is in the call seekpath_parameters -# All high symmetry points included, labels already included -bandskpoints = result['explicit_kpoints'] - -# -#--All the inputs of a Siesta calculations are listed in a dictionary-- -# -inputs = { - 'structure': newstructure, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'kpoints': kts, - 'bandskpoints': bandskpoints, - 'pseudos': pseudos_dict, - 'metadata': { - 'options': options, - 'label': "O_el_cell_spin from CIF" - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_family.py b/aiida_siesta/examples/plugins/siesta/test_siesta_family.py deleted file mode 100755 index b8a8d662..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_family.py +++ /dev/null @@ -1,185 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -from __future__ import absolute_import -from __future__ import print_function - -import sys - -from aiida.engine import submit -from aiida.orm import load_code -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida_siesta.data.psf import get_pseudos_from_structure -from aiida.plugins import DataFactory - -#----------------- Example of the use of a pseudopotential family - -PsfData = DataFactory('siesta.psf') -Dict = DataFactory('dict') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) -# -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta4.0.1@kelvin' - -# -#------------------Code and computer options --------------------------- -# -code = load_code(codename) - -options = { - "queue_name": "debug", - "max_wallclock_seconds": 1700, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} -# -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} -settings = Dict(dict=settings_dict) -#--------------------------------------------------------------------- - -# -#-------------------------- Structure -------------------------------- -# -alat = 15. # angstrom -cell = [ - [ - alat, - 0., - 0., - ], - [ - 0., - alat, - 0., - ], - [ - 0., - 0., - alat, - ], -] - -# Note an atom tagged (for convenience) with a different label - -s = StructureData(cell=cell) -s.append_atom(position=(0.000, 0.000, 0.468), symbols=['H']) -s.append_atom(position=(0.000, 0.000, 1.620), symbols=['C']) -s.append_atom(position=(0.000, -2.233, 1.754), symbols=['H']) -s.append_atom(position=(0.000, 2.233, 1.754), symbols=['H']) -s.append_atom(position=(0.000, -1.225, 2.327), symbols='C', name="Cred") -s.append_atom(position=(0.000, 1.225, 2.327), symbols=['C']) -s.append_atom(position=(0.000, -1.225, 3.737), symbols=['C']) -s.append_atom(position=(0.000, 1.225, 3.737), symbols=['C']) -s.append_atom(position=(0.000, -2.233, 4.311), symbols=['H']) -s.append_atom(position=(0.000, 2.233, 4.311), symbols=['H']) -s.append_atom(position=(0.000, 0.000, 4.442), symbols=['C']) -s.append_atom(position=(0.000, 0.000, 5.604), symbols=['H']) - -#----------------------------------------------------------------------- - -# -# ----------------------Parameters ------------------------------------- -# -params_dict = { - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'spin-polarized': True, - 'noncollinearspin': False, - 'mesh-cutoff': '200.000 Ry', - 'max-scfiterations': 1000, - 'dm-numberpulay': 5, - 'dm-mixingweight': 0.050, - 'dm-tolerance': 1.e-4, - 'dm-mixscf1': True, - 'negl-nonoverlap-int': False, - 'solution-method': 'diagon', - 'electronic-temperature': '100.000 K', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 2, - 'md-maxcgdispl': '0.200 bohr', - 'md-maxforcetol': '0.050 eV/Ang', - 'writeforces': True, - 'writecoorstep': True, - 'write-mulliken-pop': 1, -} - -parameters = Dict(dict=params_dict) -#------------------------------------------------------------------------ - -# -# ---------------------Basis Set Info ----------------------------------- -# The basis dictionary follows the 'parameters' convention -# -basis_dict = { - 'pao-basistype': - 'split', - 'pao-splitnorm': - 0.150, - 'pao-energyshift': - '0.020 Ry', - '%block pao-basis-sizes': - """ -C SZP -Cred SZ -H SZP -%endblock pao-basis-sizes""", -} - -basis = Dict(dict=basis_dict) -#------------------------------------------------------------------------ - -#--------------------- Pseudopotentials --------------------------------- -# -# FIXME: The family name is hardwired -# -pseudos_dict = get_pseudos_from_structure(s, 'sample_psf_family') -print(pseudos_dict) -#----------------------------------------------------------------------- - -# -#--All the inputs of a Siesta calculations are listed in a dictionary-- -# -inputs = { - 'structure': s, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'pseudos': pseudos_dict, - 'metadata': { - 'options': options, - 'label': "Benzene molecule with pseudo family", - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_geom_fail.py b/aiida_siesta/examples/plugins/siesta/test_siesta_geom_fail.py deleted file mode 100755 index aad4d5aa..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_geom_fail.py +++ /dev/null @@ -1,144 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -from __future__ import absolute_import -from __future__ import print_function - -import sys - -from aiida.engine import submit -from aiida.orm import load_code -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida_siesta.data.psf import get_pseudos_from_structure -from aiida.plugins import DataFactory - -# Siesta calculation on Water molecule -- to fail in geom relaxation - -PsfData = DataFactory('siesta.psf') -Dict = DataFactory('dict') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) -# -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta4.0.1@kelvin' - -# -#------------------Code and computer options --------------------------- -# -code = load_code(codename) - -options = { - "queue_name": "debug", - "max_wallclock_seconds": 1700, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} -# -#-------------------------- Settings --------------------------------- -# -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} -settings = Dict(dict=settings_dict) -# -# Structure ----------------------------------------- -# -alat = 10.0 # angstrom -cell = [ - [ - alat, - 0., - 0., - ], - [ - 0., - alat, - 0., - ], - [ - 0., - 0., - alat, - ], -] - -# Water molecule -# One of the H atoms is sligthy moved - -s = StructureData(cell=cell) -s.append_atom(position=(0.000, 0.000, 0.00), symbols=['O']) -s.append_atom(position=(0.757, 0.586, 0.00), symbols=['H']) -s.append_atom(position=(-0.780, 0.600, 0.00), symbols=['H']) - -# ----------------------Parameters ------------------------------------- - -params_dict = { - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'mesh-cutoff': '100.000 Ry', - 'max-scfiterations': 30, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.1, - 'dm-tolerance': 1.e-4, - 'md-typeofrun': 'cg', - 'md-numcgsteps': 8, - 'md-maxcgdispl': '0.200 bohr', - 'md-maxforcetol': '0.020 eV/Ang', - 'geometry-must-converge': True -} - -parameters = Dict(dict=params_dict) -#------------------------------------------------------------------------ -# -# No basis set spec in this calculation (default) -# -#--------------------- Pseudopotentials --------------------------------- -# -# FIXME: The family name is hardwired -# -pseudos_dict = get_pseudos_from_structure(s, 'sample_psf_family') -#----------------------------------------------------------------------- - -# -#--All the inputs of a Siesta calculations are listed in a dictionary-- -# -inputs = { - 'structure': s, - 'parameters': parameters, - 'code': code, - 'pseudos': pseudos_dict, - 'metadata': { - 'options': options, - 'label': "Water molecule -- geom fail" - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_ldos.py b/aiida_siesta/examples/plugins/siesta/test_siesta_ldos.py deleted file mode 100755 index 97e4220a..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_ldos.py +++ /dev/null @@ -1,199 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -from __future__ import absolute_import -from __future__ import print_function - -import sys -import os - -from aiida.engine import submit -from aiida.orm import load_code -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -################################################################ - -PsfData = DataFactory('siesta.psf') -Dict = DataFactory('dict') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta-4.0@rinaldo' - -# -#------------------Code and computer options --------------------------- -# -code = load_code(codename) - -options = { - "queue_name": "debug", - "max_wallclock_seconds": 1700, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} -# -#----Settings first ----------------------------- -# -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} -settings = Dict(dict=settings_dict) -#--------------------------------------------------- - -# -# Structure ----------------------------------------- -# -alat = 15. # angstrom -cell = [ - [ - alat, - 0., - 0., - ], - [ - 0., - alat, - 0., - ], - [ - 0., - 0., - alat, - ], -] - -# Benzene molecule -# Note an atom tagged (for convenience) with a different label -# -s = StructureData(cell=cell) -s.append_atom(position=(0.000, 0.000, 0.468), symbols=['H']) -s.append_atom(position=(0.000, 0.000, 1.620), symbols=['C']) -s.append_atom(position=(0.000, -2.233, 1.754), symbols=['H']) -s.append_atom(position=(0.000, 2.233, 1.754), symbols=['H']) -s.append_atom(position=(0.000, -1.225, 2.327), symbols='C', name="Cred") -s.append_atom(position=(0.000, 1.225, 2.327), symbols=['C']) -s.append_atom(position=(0.000, -1.225, 3.737), symbols=['C']) -s.append_atom(position=(0.000, 1.225, 3.737), symbols=['C']) -s.append_atom(position=(0.000, -2.233, 4.311), symbols=['H']) -s.append_atom(position=(0.000, 2.233, 4.311), symbols=['H']) -s.append_atom(position=(0.000, 0.000, 4.442), symbols=['C']) -s.append_atom(position=(0.000, 0.000, 5.604), symbols=['H']) - -#------------------------------------------------------------- -# -# Parameters --------------------------------------------------- -# -ldos_block_content = "\n {e1} {e2} eV".format(e1=-5.0, e2=1.0) - -params_dict = { - 'xc-functional': - 'LDA', - 'xc-authors': - 'CA', - 'mesh-cutoff': - '200.000 Ry', - 'dm-numberpulay': - 5, - 'dm-mixingweight': - 0.050, - 'dm-tolerance': - 1.e-4, - 'electronic-temperature': - '100.000 K', - '%block local-density-of-states': - """ - -5.0 1.0 eV -%endblock local-density-of-states """ -} -parameters = Dict(dict=params_dict) -# -# Basis Set Info ------------------------------------------ -# The basis dictionary follows the 'parameters' convention -# -basis_dict = { - 'pao-basistype': - 'split', - 'pao-splitnorm': - 0.150, - 'pao-energyshift': - '0.020 Ry', - '%block pao-basis-sizes': - """ -C SZP -Cred SZ -H SZP -%endblock pao-basis-sizes""" -} -basis = Dict(dict=basis_dict) -#-------------------------------------------------------------- - -#--------------------- Pseudopotentials --------------------------------- -# -# This exemplifies the handling of pseudos for different species -# Those sharing the same pseudo should be indicated. -# -pseudos_list = [] -raw_pseudos = [("C.psf", ['C', 'Cred']), ("H.psf", 'H')] - -for fname, kinds, in raw_pseudos: - absname = os.path.realpath( - os.path.join(os.path.dirname(__file__), "data/sample-psf-family", - fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - if created: - print("Created the pseudo for {}".format(kinds)) - else: - print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) - pseudos_list.append(pseudo) - -#----------------------------------------------------------------------- -#--All the inputs of a Siesta calculations are listed in a dictionary-- -# -inputs = { - 'structure': s, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'pseudos': { - 'C': pseudos_list[0], - 'Cred': pseudos_list[0], - 'H': pseudos_list[1], - }, - 'metadata': { - 'options': options, - 'label': "Benzene molecule", - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_magnetic.py b/aiida_siesta/examples/plugins/siesta/test_siesta_magnetic.py deleted file mode 100755 index 412d94c2..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_magnetic.py +++ /dev/null @@ -1,142 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." -__license__ = "MIT license, see LICENSE.txt file" -__version__ = "0.7.0" -__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" - -import sys -import os - -from aiida.common.example_helpers import test_and_get_code -from aiida.common.exceptions import NotExistent - -# Calculation on Iron, collinear spin polarization applied - -################################################################ - -PsfData = DataFactory('siesta.psf') -ParameterData = DataFactory('parameter') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print >> sys.stderr, ("The first parameter can only be either " - "--send or --dont-send") - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'siesta4.0.1@parsons' - -code = test_and_get_code(codename, expected_code_type='siesta.siesta') -# -# Set up calculation object first -# -calc = code.new_calc() -calc.label = "Siesta-Fe-bulk-spin" -calc.description = "Test Siesta calculation. Fe bulk spin-polarized" - -# -# Structure ----------------------------------------- -# -# BCC -alat = 2.87 # angstrom -cell = [[alat/2, alat/2, alat/2,], - [alat/2, -alat/2, alat/2,], - [alat/2, alat/2, -alat/2,], - ] - -# -s = StructureData(cell=cell) -s.append_atom(position=(0.000,0.000,0.000),symbols=['Fe']) - -elements = list(s.get_symbols_set()) -calc.use_structure(s) -#------------------------------------------------------------- -# -# Parameters --------------------------------------------------- -# -# Note the use of '.' in some entries. This will be fixed below. -# Note also that some entries have ':' as separator. This is not -# allowed in Siesta, and will be fixed by the plugin itself. The -# latter case is an unfortunate historical choice. It should not -# be used in modern scripts. -# -params_dict= { -'xc.functional': 'GGA', -'xc.authors': 'PBE', -'spin-polarized': True, -'noncollinearspin': False, -'mesh-cutoff': '150.000 Ry', -'max-scfiterations': 40, -'dm-numberpulay': 4, -'dm-mixingweight': 0.1, -'dm-tolerance': 1.e-3, -'electronic-temperature': '300.000 K' -} -# -# Sanitize, as '.' is not kosher for the database handlers -# -params_dict = { k.replace('.','-') :v for k,v in params_dict.iteritems() } -# -parameters = ParameterData(dict=params_dict) -calc.use_parameters(parameters) -# -kpoints = KpointsData() -kpoints_mesh = 6 -kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) -calc.use_kpoints(kpoints) -# -# Pseudopotentials ---------------------------------------------- -# -# This exemplifies the handling of pseudos for different species -# Those sharing the same pseudo should be indicated. -# Families support is not yet available for this. -# -raw_pseudos = [ ("Fe.psf", 'Fe')] - -for fname, kinds, in raw_pseudos: - absname = os.path.realpath(os.path.join(os.path.dirname(__file__), - "data",fname)) - pseudo, created = PsfData.get_or_create(absname,use_first=True) - if created: - print "Created the pseudo for {}".format(kinds) - else: - print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) - - # Attach pseudo node to the calculation - calc.use_pseudo(pseudo,kind=kinds) -#------------------------------------------------------------------- - -calc.set_max_wallclock_seconds(30*60) # 30 min - -calc.set_resources({"num_machines": 1}) -#------------------ - -if submit_test: - subfolder, script_filename = calc.submit_test() - print "Test_submit for calculation (uuid='{}')".format( - calc.uuid) - print "Submit file in {}".format(os.path.join( - os.path.relpath(subfolder.abspath), - script_filename - )) -else: - calc.store_all() - print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - calc.submit() - print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_restart.py b/aiida_siesta/examples/plugins/siesta/test_siesta_restart.py deleted file mode 100755 index b5f7eb7b..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_restart.py +++ /dev/null @@ -1,91 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -from __future__ import absolute_import -from __future__ import print_function - -# See LICENSE and Contributors - -# This script will restart a calculation that ended without -# scf convergence in the allotted number of iterations, or without geometry convergence. -# -# Usage: -# ./test_siesta_restart.py {--send, --dont-send} PK_of_failed_calculation - -import sys, os - -from aiida.engine import submit -from aiida.orm import load_code -from aiida.common import NotExistent -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -Dict = DataFactory('dict') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), file=sys.stderr) - sys.exit(1) - -try: - PK = int(sys.argv[2]) -except IndexError: - print(("The second parameter must be the PK of a calculation"), file=sys.stderr) - sys.exit(1) - - -c = load_node(PK) - -print("Restarting calculation (uuid='{}')".format(c.uuid)) -print("Is excepted?: '{}'".format(c.is_excepted)) -# -# Note that this use of 'failed' does not correspond to the process state. -# -print("Is failed?: '{}'".format(c.is_failed)) -if c.is_failed: - print("Exit code: '{}'".format(c.exit_status)) - print("'{}'".format(c.exit_message)) -print(" ") - -restart=c.get_builder_restart() - -newpar=restart.parameters.clone() -newpar.attributes["max-scf-iterations"]= 50 -restart.parameters=newpar - -if c.outputs.output_parameters.attributes["variable_geometry"]: - restart.structure=c.outputs.output_structure - -# The most important line. The presence of -# parent_calc_folder triggers the 'restart' operations -# in the plugin, such as the copy of the .DM and the -# addition of use-save-dm to the parameters - -restart.parent_calc_folder=c.outputs.remote_folder - -if submit_test: - - m=restart["metadata"] - - # An attempt to clone the 'metadata' section of the object raised this error: - # Error: AttributeError: 'ProcessBuilderNamespace' object has no attribute 'clone' - # It seems that one can simply set this attributes by hand: - - m.dry_run = True - m.store_provenance = False - print("Dry run without storing provenance. See the submit_test directory") - -else: - print("Calculation restarted") - - -submit(restart) - diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_scf_fail.py b/aiida_siesta/examples/plugins/siesta/test_siesta_scf_fail.py deleted file mode 100755 index 1034f188..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_scf_fail.py +++ /dev/null @@ -1,179 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -from __future__ import absolute_import -from __future__ import print_function - -# -# This is an example of a calculation that will end in a FINISHED -# state but with a non-zero exit code, due to lack of scf convergence -# in the allotted number of iterations. - -import sys -import os - -from aiida.engine import submit -from aiida.orm import load_code -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -################################################################ - -PsfData = DataFactory('siesta.psf') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') -Dict = DataFactory('dict') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'siesta4.0.1@kelvin' - -# -#------------------Code -# -code = load_code(codename) - -#--------------- Structure -# -# Bulk Silicon -# -alat = 5.430 # angstrom -cell = [ - [ - 0.5 * alat, - 0.5 * alat, - 0., - ], - [ - 0., - 0.5 * alat, - 0.5 * alat, - ], - [ - 0.5 * alat, - 0., - 0.5 * alat, - ], -] - -s = StructureData(cell=cell) -s.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), - symbols=['Si']) -s.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), - symbols=['Si']) - -#---------------------------------------------- - -options = { - "queue_name": "debug", - "max_wallclock_seconds": 1700, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} - -#-------------------------- Settings --------------------------------- -# -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} -settings = Dict(dict=settings_dict) - -#--------------------------------------------- -# Code-specific operational parameters -# -params_dict = { - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'spin-polarized': True, - 'meshcutoff': '40.000 Ry', - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'max-scfiterations': 3, - 'scf-must-converge': True, - 'md-typeofrun': 'cg', - 'md-numcgsteps': 0 -} - -parameters = Dict(dict=params_dict) - -# ---------------------Basis Set Info ----------------------------------- -# The basis dictionary follows the 'parameters' convention -# -basis_dict = { - 'pao-energy-shift': - '300 meV', - '%block pao-basis-sizes': - """ -Si DZP -%endblock pao-basis-sizes""", -} - -basis = Dict(dict=basis_dict) - -#------------------------------------------- -kpoints = KpointsData() - -# method mesh -kpoints_mesh = 4 -kpoints.set_kpoints_mesh([kpoints_mesh, kpoints_mesh, kpoints_mesh]) - -#------------------------------------------------ -pseudos_list = [] -raw_pseudos = [("Si.psf", 'Si')] -for fname, kinds, in raw_pseudos: - absname = os.path.realpath( - os.path.join(os.path.dirname(__file__), "data/sample-psf-family", - fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - if created: - print("Created the pseudo for {}".format(kinds)) - else: - print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) - pseudos_list.append(pseudo) - -#--------------------------------------------- - -inputs = { - 'structure': s, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'kpoints': kpoints, - 'pseudos': { - 'Si': pseudos_list[0], - }, - 'metadata': { - 'options': options, - 'label': "Bulk Si short scf cycle" - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_si.py b/aiida_siesta/examples/plugins/siesta/test_siesta_si.py deleted file mode 100755 index 2f2b2155..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_si.py +++ /dev/null @@ -1,146 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function - -import os.path as op -import sys - -from aiida.engine import submit -from aiida.orm import load_code -from aiida.orm import (Dict, StructureData, KpointsData) -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -PsfData = DataFactory('siesta.psf') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print(("The first parameter can only be either " - "--send or --dont-send"), - file=sys.stderr) - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta4.0.1@kelvin' - -# Si diamond structure -alat = 5.430 # angstrom -cell = [ - [ - 0.5 * alat, - 0.5 * alat, - 0., - ], - [ - 0., - 0.5 * alat, - 0.5 * alat, - ], - [ - 0.5 * alat, - 0., - 0.5 * alat, - ], -] - -# Si -# This was originally given in the "ScaledCartesian" format -# -structure = StructureData(cell=cell) -structure.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), - symbols=['Si']) -structure.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), - symbols=['Si']) - -code = load_code(codename) - -parameters = Dict( - dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'Solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang', - 'write-forces': True, - # 'xml-write': True - }) - -basis = Dict( - dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': """ -Si DZP -%endblock pao-basis-sizes""", - }) - -kpoints = KpointsData() -kpoints.set_kpoints_mesh([4, 4, 4]) - -pseudos_list = [] -raw_pseudos = [("Si.psf", 'Si')] -for fname, kind in raw_pseudos: - absname = op.realpath( - op.join(op.dirname(__file__), "data/sample-psf-family", fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - if created: - print("\nCreated the pseudo for {}".format(kind)) - else: - print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) - pseudos_list.append(pseudo) - -options = { - "max_wallclock_seconds": 360, - "resources": { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} - -inputs = { - 'structure': structure, - 'parameters': parameters, - 'code': code, - 'basis': basis, - 'kpoints': kpoints, - 'pseudos': { - 'Si': pseudos_list[0], - }, - 'metadata': { - "label": "TestOnSiliconBulk", - 'options': options, - } -} - -if submit_test: - inputs["metadata"]["dry_run"] = True - inputs["metadata"]["store_provenance"] = False - process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() - print("Submited test for calculation (uuid='{}')".format(process.uuid)) - print("Check the folder submit_test for the result of the test") -# I could't find a way to access the actual folder (subfolder of submit_test) -# from the calculation node. So I can't print the exact location - -else: - process = submit(SiestaCalculation, **inputs) - print("Submitted calculation; ID={}".format(process.pk)) - print("For information about this calculation type: verdi process show {}". - format(process.pk)) - print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_sih.py b/aiida_siesta/examples/plugins/siesta/test_siesta_sih.py deleted file mode 100755 index 02c616fb..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_sih.py +++ /dev/null @@ -1,276 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." -__license__ = "MIT license, see LICENSE.txt file" -__version__ = "0.7.0" -__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" - -import sys -import os - -from aiida.common.example_helpers import test_and_get_code -from aiida.common.exceptions import NotExistent - -# Another molecule -# Pseudo families introduced - -################################################################ - -PsfData = DataFactory('siesta.psf') -ParameterData = DataFactory('parameter') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print >> sys.stderr, ("The first parameter can only be either " - "--send or --dont-send") - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'siesta4.0.1@parsons' - - - -queue = None -settings = None - -code = test_and_get_code(codename, expected_code_type='siesta.siesta') -## For remote codes, it is not necessary to manually set the computer, -## since it is set automatically by new_calc -#computer = code.get_remote_computer() -#calc = code.new_calc(computer=computer) - -calc = code.new_calc() -calc.label = "SiH_spin" -calc.description = "Test calculation with the Siesta code. SiH spin" -calc.set_max_wallclock_seconds(30*60) # 30 min - -#------------ clarify this -# Valid only for Slurm and PBS (using default values for the -# number_cpus_per_machine), change for SGE-like schedulers -## Otherwise, to specify a given # of cpus per machine, uncomment the following: -# calc.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 8}) -#calc.set_resources({"parallel_env": 'openmpi',"tot_num_mpiprocs": 1,"num_machines": 1,"num_cpus": 2}) -#------------ clarify this -calc.set_resources({"num_machines": 1}) - -#calc.set_custom_scheduler_commands("#SBATCH --account=ch3") - -if queue is not None: - calc.set_queue_name(queue) - - -##----Structure--- - -alat = 5.430 # angstrom -cell = [[2*alat, 0., 0.,], - [0., 2*alat, 0.,], - [0., 0., 2*alat,], - ] - -# SiH coordinates -# This was originally given in the "ScaledCartesian" format -# -s = StructureData(cell=cell) -s.append_atom(position=(0.000*alat,0.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.250*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,0.500*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.750*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,0.000*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,0.250*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,0.500*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,0.750*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,0.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,0.250*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,0.500*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,0.750*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,0.000*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,0.250*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,0.500*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,0.750*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,1.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,1.250*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,1.500*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,1.750*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,1.000*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,1.250*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,1.500*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,1.750*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,0.000*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.250*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,0.500*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.750*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,0.000*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,0.250*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,0.500*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,0.750*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,1.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,1.250*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,1.500*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,1.750*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,1.000*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,1.250*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,1.500*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,1.750*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,0.000*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,0.250*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,0.500*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,0.750*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,0.000*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,0.250*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,0.500*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,0.750*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,1.000*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,1.250*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,1.500*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,1.750*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,1.000*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,1.250*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,1.500*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,1.750*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,1.000*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,1.250*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,1.500*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,1.750*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,1.000*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,1.250*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,1.500*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,1.750*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.125*alat,1.125*alat,1.125*alat),symbols=['H']) - -elements = list(s.get_symbols_set()) - -calc.use_structure(s) - - -###-----Pseudos------ - -# If True, load the pseudos from the family specified below -# Otherwise, use static files provided -auto_pseudos = False - -if auto_pseudos: - valid_pseudo_groups = PsfData.get_psf_groups(filter_elements=elements) - - try: - pseudo_family = sys.argv[3] - except IndexError: - print >> sys.stderr, "Error, auto_pseudos set to True. You therefore need to pass as second parameter" - print >> sys.stderr, "the pseudo family name." - print >> sys.stderr, "Valid PSF families are:" - print >> sys.stderr, "\n".join("* {}".format(i.name) for i in valid_pseudo_groups) - sys.exit(1) - - try: - PsfData.get_psf_group(pseudo_family) - except NotExistent: - print >> sys.stderr, "auto_pseudos is set to True and pseudo_family='{}',".format(pseudo_family) - print >> sys.stderr, "but no group with such a name found in the DB." - print >> sys.stderr, "Valid PSF groups are:" - print >> sys.stderr, ",".join(i.name for i in valid_pseudo_groups) - sys.exit(1) - - -if auto_pseudos: - try: - calc.use_pseudos_from_family(pseudo_family) - print "Pseudos successfully loaded from family {}".format(pseudo_family) - except NotExistent: - print ("Pseudo or pseudo family not found. You may want to load the " - "pseudo family, or set auto_pseudos to False.") - raise -else: - raw_pseudos = [("Si.psf", 'Si'), - ("H.psf", 'H')] - - for fname, kinds, in raw_pseudos: - absname = os.path.realpath(os.path.join(os.path.dirname(__file__), - "data",fname)) - pseudo, created = PsfData.get_or_create(absname,use_first=True) - if created: - print "Created the pseudo for {}".format(kinds) - else: - print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) - - # Attach pseudo node to the calculation - calc.use_pseudo(pseudo,kind=kinds) - - -##-----Parameters----------- - -parameters = ParameterData(dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'spinpolarized': True, - 'meshcutoff': '40.000 Ry', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang' - }) -calc.use_parameters(parameters) - -##-----Basis--------- - -basis = ParameterData(dict={ -'pao-energy-shift': '300 meV', -'%block pao-basis-sizes': """ -Si SZP -H DZP """, -}) -calc.use_basis(basis) - -##-----k points ---------- - -kpoints = KpointsData() -# method mesh -kpoints_mesh = 1 -kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) -calc.use_kpoints(kpoints) - - -##----------settings---------- -# (the object settings is optional) -settings_dict={'test_key': 'test_value'} -settings = ParameterData(dict=settings_dict) - - - -if settings is not None: - calc.use_settings(settings) -#from aiida.orm.data.remote import RemoteData -#calc.set_outdir(remotedata) - -if submit_test: - subfolder, script_filename = calc.submit_test() - print "Test_submit for calculation (uuid='{}')".format( - calc.uuid) - print "Submit file in {}".format(os.path.join( - os.path.relpath(subfolder.abspath), - script_filename - )) -else: - calc.store_all() - print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - calc.submit() - print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - diff --git a/aiida_siesta/examples/plugins/siesta/test_siesta_varcell.py b/aiida_siesta/examples/plugins/siesta/test_siesta_varcell.py deleted file mode 100755 index 3bb6b72e..00000000 --- a/aiida_siesta/examples/plugins/siesta/test_siesta_varcell.py +++ /dev/null @@ -1,169 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- - -__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." -__license__ = "MIT license, see LICENSE.txt file" -__version__ = "0.7.0" -__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" - -import sys -import os - -from aiida.common.example_helpers import test_and_get_code -from aiida.common.exceptions import NotExistent - -################################################################ - -PsfData = DataFactory('siesta.psf') -ParameterData = DataFactory('parameter') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') - -try: - dontsend = sys.argv[1] - if dontsend == "--dont-send": - submit_test = True - elif dontsend == "--send": - submit_test = False - else: - raise IndexError -except IndexError: - print >> sys.stderr, ("The first parameter can only be either " - "--send or --dont-send") - sys.exit(1) - -try: - codename = sys.argv[2] -except IndexError: - codename = 'Siesta-4.0@rinaldo' - -# If True, load the pseudos from the family specified below -# Otherwise, use static files provided -auto_pseudos = True - -queue = None -settings = None - -code = test_and_get_code(codename, expected_code_type='siesta.siesta') - -alat = 5.430 # angstrom -cell = [[0.5*alat, 0.5*alat, 0.,], - [0., 0.5*alat, 0.5*alat,], - [0.5*alat, 0., 0.5*alat,], - ] - -# Si -# This was originally given in the "ScaledCartesian" format -# -s = StructureData(cell=cell) -s.append_atom(position=(0.000*alat,0.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.250*alat,0.250*alat),symbols=['Si']) - - -elements = list(s.get_symbols_set()) - -if auto_pseudos: - valid_pseudo_groups = PsfData.get_psf_groups(filter_elements=elements) - - try: - #pseudo_family = sys.argv[3] - pseudo_family = 'lda-ag' - except IndexError: - print >> sys.stderr, "Error, auto_pseudos set to True. You therefore need to pass as second parameter" - print >> sys.stderr, "the pseudo family name." - print >> sys.stderr, "Valid PSF families are:" - print >> sys.stderr, "\n".join("* {}".format(i.name) for i in valid_pseudo_groups) - sys.exit(1) - - try: - PsfData.get_psf_group(pseudo_family) - except NotExistent: - print >> sys.stderr, "auto_pseudos is set to True and pseudo_family='{}',".format(pseudo_family) - print >> sys.stderr, "but no group with such a name found in the DB." - print >> sys.stderr, "Valid PSF groups are:" - print >> sys.stderr, ",".join(i.name for i in valid_pseudo_groups) - sys.exit(1) - -parameters = ParameterData(dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 20, - 'md-variablecell': True, - 'md-maxforcetol': '0.04 eV/Ang' - }) - -basis = ParameterData(dict={ -'pao-energy-shift': '300 meV', -'%block pao-basis-sizes': """ -Si SZP """, -}) - -kpoints = KpointsData() - -# method mesh -kpoints_mesh = 4 -kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) - -calc = code.new_calc() -calc.label = "Si bulk" -calc.description = "Test calculation with the Siesta code. Si bulk varcell" -calc.set_max_wallclock_seconds(30*60) # 30 min - -#------------ clarify this -calc.set_resources({"num_machines": 1}) - -calc.use_structure(s) -calc.use_parameters(parameters) -calc.use_basis(basis) - -if auto_pseudos: - try: - calc.use_pseudos_from_family(pseudo_family) - print "Pseudos successfully loaded from family {}".format(pseudo_family) - except NotExistent: - print ("Pseudo or pseudo family not found. You may want to load the " - "pseudo family, or set auto_pseudos to False.") - raise -else: - raw_pseudos = [("Si.psf", 'Si')] - - for fname, kinds, in raw_pseudos: - absname = os.path.realpath(os.path.join(os.path.dirname(__file__), - "data",fname)) - pseudo, created = PsfData.get_or_create(absname,use_first=True) - if created: - print "Created the pseudo for {}".format(kinds) - else: - print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) - - # Attach pseudo node to the calculation - calc.use_pseudo(pseudo,kind=kinds) - -calc.use_kpoints(kpoints) - -if settings is not None: - calc.use_settings(settings) - -if submit_test: - subfolder, script_filename = calc.submit_test() - print "Test_submit for calculation (uuid='{}')".format( - calc.uuid) - print "Submit file in {}".format(os.path.join( - os.path.relpath(subfolder.abspath), - script_filename - )) -else: - calc.store_all() - print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - calc.submit() - print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - diff --git a/aiida_siesta/tests/__init__.py b/aiida_siesta/tests/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/aiida_siesta/tests/calculations/test_bands.py b/aiida_siesta/tests/calculations/test_bands.py deleted file mode 100644 index 9326e608..00000000 --- a/aiida_siesta/tests/calculations/test_bands.py +++ /dev/null @@ -1,129 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function -import os.path as op -import sys -from aiida.orm import load_code -import numpy as np - - -def create_FCC_structure(alat): - lvecs = np.array([1.0, - 1.0, - 1.0,]) * alat - - cell = np.array([[0.0, 0.5, 0.5,], - [0.5, 0.0, 0.5,], - [0.5, 0.5, 0.0,],]) - - return np.multiply(cell, lvecs) - - -#def test_bands(siesta_develop): -"""Test workfunction runs and outputs results in serial mode.""" -from aiida.orm import Code, Dict, StructureData,KpointsData -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory -from aiida.tools import get_explicit_kpoints_path - -PsfData = DataFactory('siesta.psf') - -# codename = 'siesta@develop' -# code = Code.get_from_string(codename) -#code = siesta_develop['siesta_code'] -code = load_code("Siesta4.0.1@kelvin") -options = { - "max_wallclock_seconds" : 360, - "resources" : { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } -} - -# Define MgO structure -alat = 4.117 # MgO lattice constant, Angstroms -cell = create_FCC_structure(alat) # Creating MgO FCC-cell -structure = StructureData(cell=cell) # Creating structure from cell -# Placing basis atoms -structure.append_atom( - position=(0.000 * alat, 0.000 * alat, 0.000 * alat), symbols=['Mg']) -structure.append_atom( - position=(0.500 * alat, 0.500 * alat, 0.500 * alat), symbols=['O']) - -seekpath_parameters = Dict(dict={'reference_distance': 0.02,'symprec': 0.0001}) -result=get_explicit_kpoints_path(structure, **seekpath_parameters.get_dict()) -newstructure = result['primitive_structure'] - -# Pseudopotentials -# from aiida_siesta.data.psf import get_pseudos_from_structure -# inputs.pseudo = get_pseudos_from_structure(structure, "test_psf_family") -raw_pseudos = [ - ("Mg.psf", 'Mg'), - ("O.psf", 'O'), -] - -pseudos_list = [] -for fname, kind in raw_pseudos: - absname = op.realpath(op.join(op.dirname(__file__), '..', 'pseudos', fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - - if created: - print("\nCreated the pseudo for {}".format(kind)) - else: - print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) - # Attach pseudo node to the calculation - pseudos_list.append(pseudo) - -# K-points mesh -kpoints_mesh = KpointsData() -kpoints_mesh.set_kpoints_mesh([6, 6, 6], [0.5, 0.5, 0.5]) - -# Bands' k-points -bandskpoints = KpointsData() -bandskpoints=result['explicit_kpoints'] - -#bandskpoints.set_cell(structure.cell, structure.pbc) -#bandskpoints.set_kpoints_path([ -# ('K', 'G', 39), -# ('G', 'X', 37), -# ('X', 'W', 19), -# ('W', 'L', 27), -# ('L', 'G', 32), -#]) - -# Calculation parameters -parameters = Dict( - dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'spin-polarized': False, - 'meshcutoff': '200 Ry', - 'max-scfiterations': 50, -# 'xml-write': True, - }) - -# Create and run Siesta calculation process -from aiida.engine import run - -inputs = { - 'structure': newstructure, - 'parameters': parameters, - 'code': code, - # 'basis': basis, - 'kpoints': kpoints_mesh, - 'bandskpoints' : bandskpoints, - 'pseudos': { - 'Mg': pseudos_list[0], - 'O': pseudos_list[1], - }, - 'metadata': { - "dry_run": True, - "store_provenance": False, - 'options': options, - } -} - -#result = run(SiestaCalculation, **inputs) -run(SiestaCalculation, **inputs) -#assert result['bands_array'] is not None diff --git a/aiida_siesta/tests/calculations/test_restart.py b/aiida_siesta/tests/calculations/test_restart.py deleted file mode 100644 index d15a558a..00000000 --- a/aiida_siesta/tests/calculations/test_restart.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function - -import os.path as op - -from aiida.engine import run - -#Loading calculation we want to restart (old_calc) -g=load_node(375) - -#Set up the a new calculation with all -#the inputs of the old one (we use the builder) -restart=g.get_builder_restart() - -#The inputs of old_calc attched to restart are -#already stored!!! Can't modify them straight away -#If you want to change something you make a clone -#and reassign it to the builder. -#Here we change dm-tollerance for example -newpar=restart.parameters.clone() -newpar.attributes["dm-tolerance"]=0.00001 -restart.parameters=newpar - - -#We need to take care here of passing the -#output geometry of old_calc to the new calculation -if g.outputs.output_parameters.attributes["variable_geometry"]: - restart.structure=g.outputs.output_structure - -#The most important line. The presence of -#parent_calc_folder triggers the real restart -#meaning the copy of the .DM and the -#addition of use-saved-dm to the parameters -restart.parent_calc_folder=g.outputs.remote_folder - - -restart.metadata.dry_run=True -restart.metadata.store_provenance=False -run(restart) - diff --git a/aiida_siesta/tests/calculations/test_serial_workfunction.py b/aiida_siesta/tests/calculations/test_serial_workfunction.py deleted file mode 100644 index 42079d97..00000000 --- a/aiida_siesta/tests/calculations/test_serial_workfunction.py +++ /dev/null @@ -1,166 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -import os -import sys - -import numpy as np - - -def test_serial_workfunction(siesta_develop): - """Test workfunction runs and outputs results in serial mode.""" - from aiida.common.example_helpers import test_and_get_code - from aiida.orm import Code, DataFactory - from aiida.orm.data.base import Float, Str - from aiida.orm.implementation.general.calculation.work import WorkCalculation - from aiida.orm.querybuilder import QueryBuilder - from aiida.work.process_registry import ProcessRegistry - from aiida.work.run import run - from aiida.work.workfunction import workfunction as wf - from aiida_siesta.calculations.siesta import SiestaCalculation - - PsfData = DataFactory('siesta.psf') - StructureData = DataFactory('structure') - ParameterData = DataFactory('parameter') - KpointsData = DataFactory('array.kpoints') - - # codename = 'siesta@develop' - scale_facs = (0.96, 0.98, 1.0, 1.02, 1.04) - labels = ["c1", "c2", "c3", "c4", "c5"] - - @wf - def create_structure(): - """ Si diamond structure """ - alat = 5.430 # angstrom - cell = np.array([[0.5, 0.5, 0.,], - [0., 0.5, 0.5,], - [0.5, 0., 0.5,],]) * alat - structure = StructureData(cell=cell) - structure.append_atom( - position=(0.000 * alat, 0.000 * alat, 0.000 * alat), - symbols=['Si']) - structure.append_atom( - position=(0.250 * alat, 0.250 * alat, 0.250 * alat), - symbols=['Si']) - - return structure - - @wf - def rescale(structure, scale): - """ - Workfunction to rescale a structure - :param structure: An AiiDA structure to rescale - :param scale: The scale factor (for the lattice constant) - :return: The rescaled structure - """ - the_ase = structure.get_ase() - new_ase = the_ase.copy() - new_ase.set_cell(the_ase.get_cell() * float(scale), scale_atoms=True) - new_structure = DataFactory("structure")(ase=new_ase) - - return new_structure - - @wf - def create_rescaled(scale): - """ - Workfunction to create and immediately rescale - a crystal structure of a given element. - """ - s0 = create_structure() - return rescale(s0, scale) - - def geninputs(structure): - inputs = SiestaCalculation.process().get_inputs_template() - inputs.structure = structure - inputs.code = siesta_develop['siesta_code'] - inputs._options.resources = { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } - inputs._options.max_wallclock_seconds = 30 * 60 - - KpointsData = DataFactory("array.kpoints") - kpoints = KpointsData() - kpoints_mesh = 4 - kpoints.set_kpoints_mesh([kpoints_mesh, kpoints_mesh, kpoints_mesh]) - inputs.kpoints = kpoints - - # Calculation parameters - parameters_dict = { - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'Solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang', - 'xml-write': True, - } - ParameterData = DataFactory("parameter") - inputs.parameters = ParameterData(dict=parameters_dict) - - # Pseudopotentials - raw_pseudos = [("Si.psf", 'Si')] - pseudo_dict = {} - for fname, kind in raw_pseudos: - absname = os.path.realpath( - os.path.join(os.path.dirname(__file__), '..', 'pseudos', fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - - if created: - print "Created the pseudo for {}".format(kind) - else: - print "Using the pseudo for {} from DB: {}".format(kind, pseudo.pk) - # Attach pseudo node to the calculation - pseudo_dict[kind] = pseudo - - inputs.pseudo = pseudo_dict - - # Basis set - inputs.basis = ParameterData(dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': 'Si DZP', - }) - - return inputs - - def get_info(calc_results, struct): - return (struct.get_cell_volume(), - calc_results['output_parameters'].dict.FreeE, - calc_results['output_parameters'].dict.FreeE_units, ) - - @wf - def run_wf(): - # print "Workfunction node identifiers: {}".format(ProcessRegistry().current_calc_node) - wcalc_uuid = ProcessRegistry().current_calc_node.uuid - print "Workfunction node: {}".format(wcalc_uuid) - #Instantiate a JobCalc process and create basic structure - JobCalc = SiestaCalculation.process() - s0 = create_structure() - calcs = {} - for label, factor in zip(labels, scale_facs): - s = rescale(s0, Float(factor)) - inputs = geninputs(s) - print "Running a scf for Si with scale factor {}".format(factor) - result = run(JobCalc, **inputs) - calcs[label] = get_info(result, s) - - eos = [] - for label in labels: - eos.append(calcs[label]) - - retdict = {'result': ParameterData(dict={'eos_data': eos})} - - return retdict - - res = run_wf() - eos_data = res['result'].get_attr('eos_data') - assert eos_data is not None - assert len(eos_data) == 5 - assert "{0:.4f}".format(eos_data[0][0]) == "35.4122" - assert "{0:.2f}".format(eos_data[4][1]) == "-215.08" - assert eos_data[3][2] == "eV" diff --git a/aiida_siesta/tests/calculations/test_simple_submission.py b/aiida_siesta/tests/calculations/test_simple_submission.py deleted file mode 100644 index 32f76212..00000000 --- a/aiida_siesta/tests/calculations/test_simple_submission.py +++ /dev/null @@ -1,120 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function -import os.path as op - - -def test_simple_submission(siesta_develop): - """Test that single calculation is submitted.""" - from aiida.plugins import DataFactory - - PsfData = DataFactory('siesta.psf') - StructureData = DataFactory('structure') - Dict = DataFactory('dict') - KpointsData = DataFactory('array.kpoints') - - code = siesta_develop['siesta_code'] - assert code is not None - - # Si diamond structure - alat = 5.430 # angstrom - cell = [ - [ - 0.5 * alat, - 0.5 * alat, - 0., - ], - [ - 0., - 0.5 * alat, - 0.5 * alat, - ], - [ - 0.5 * alat, - 0., - 0.5 * alat, - ], - ] - - # Si - # This was originally given in the "ScaledCartesian" format - # - s = StructureData(cell=cell) - s.append_atom( - position=(0.000 * alat, 0.000 * alat, 0.000 * alat), symbols=['Si']) - s.append_atom( - position=(0.250 * alat, 0.250 * alat, 0.250 * alat), symbols=['Si']) - - parameters = Dict(dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'Solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang', - 'xml-write': True - }) - - basis = Dict(dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': 'Si DZP', - }) - - kpoints = KpointsData() - kpoints.set_kpoints_mesh([4, 4, 4]) - - calc = code.new_calc( - max_wallclock_seconds=3600, - resources={ - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - }) - - calc.label = "Si bulk" - calc.description = "Test calculation with the Siesta code. Si bulk" - - # Use raw pseudos for this example: - raw_pseudos = [("Si.psf", 'Si')] - - calc.use_structure(s) - calc.use_code(code) - calc.use_parameters(parameters) - calc.use_basis(basis) - calc.use_kpoints(kpoints) - - # Pseudo business - # - # TODO: understand how to work with pseudo families - # calc.use_pseudos_from_family(pseudo_family) - # - for fname, kind in raw_pseudos: - absname = op.realpath(op.join(op.dirname(__file__), "..", "pseudos", fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - - if created: - print("\nCreated the pseudo for {}".format(kind)) - else: - print("\nUsing the pseudo for {} from DB: {}".format( - kind, pseudo.pk)) - - # Attach pseudo node to the calculation - calc.use_pseudo(pseudo, kind=kind) - - calc.store_all() - print("created calculation with PK={}".format(calc.pk)) - subfolder, script_filename = calc.submit_test() - print("Test_submit for calculation (uuid='{}')".format(calc.uuid)) - - assert op.isfile(op.join(op.relpath(subfolder.abspath), script_filename)) - print("Submit file in {}".format( - op.join(op.relpath(subfolder.abspath), script_filename))) - - assert op.isfile(op.join(op.relpath(subfolder.abspath), 'aiida.fdf')) - assert op.isfile(op.join(op.relpath(subfolder.abspath), 'Si.psf')) diff --git a/aiida_siesta/tests/calculations/test_simple_submission.py.bak b/aiida_siesta/tests/calculations/test_simple_submission.py.bak deleted file mode 100644 index ce6b5535..00000000 --- a/aiida_siesta/tests/calculations/test_simple_submission.py.bak +++ /dev/null @@ -1,119 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -import os.path as op - - -def test_simple_submission(siesta_develop): - """Test that single calculation is submitted.""" - from aiida.orm import DataFactory - from aiida.common.example_helpers import test_and_get_code - - PsfData = DataFactory('siesta.psf') - StructureData = DataFactory('structure') - ParameterData = DataFactory('parameter') - KpointsData = DataFactory('array.kpoints') - - code = siesta_develop['siesta_code'] - assert code is not None - - # Si diamond structure - alat = 5.430 # angstrom - cell = [ - [ - 0.5 * alat, - 0.5 * alat, - 0., - ], - [ - 0., - 0.5 * alat, - 0.5 * alat, - ], - [ - 0.5 * alat, - 0., - 0.5 * alat, - ], - ] - - # Si - # This was originally given in the "ScaledCartesian" format - # - s = StructureData(cell=cell) - s.append_atom( - position=(0.000 * alat, 0.000 * alat, 0.000 * alat), symbols=['Si']) - s.append_atom( - position=(0.250 * alat, 0.250 * alat, 0.250 * alat), symbols=['Si']) - - parameters = ParameterData(dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'Solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang', - 'xml-write': True - }) - - basis = ParameterData(dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': 'Si DZP', - }) - - kpoints = KpointsData() - kpoints.set_kpoints_mesh([4, 4, 4]) - - calc = code.new_calc( - max_wallclock_seconds=3600, - resources={ - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - }) - - calc.label = "Si bulk" - calc.description = "Test calculation with the Siesta code. Si bulk" - - # Use raw pseudos for this example: - raw_pseudos = [("Si.psf", 'Si')] - - calc.use_structure(s) - calc.use_code(code) - calc.use_parameters(parameters) - calc.use_basis(basis) - calc.use_kpoints(kpoints) - - # Pseudo business - # - # TODO: understand how to work with pseudo families - # calc.use_pseudos_from_family(pseudo_family) - # - for fname, kind in raw_pseudos: - absname = op.realpath(op.join(op.dirname(__file__), "..", "pseudos", fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - - if created: - print "\nCreated the pseudo for {}".format(kind) - else: - print "\nUsing the pseudo for {} from DB: {}".format( - kind, pseudo.pk) - - # Attach pseudo node to the calculation - calc.use_pseudo(pseudo, kind=kind) - - calc.store_all() - print "created calculation with PK={}".format(calc.pk) - subfolder, script_filename = calc.submit_test() - print "Test_submit for calculation (uuid='{}')".format(calc.uuid) - - assert op.isfile(op.join(op.relpath(subfolder.abspath), script_filename)) - print "Submit file in {}".format( - op.join(op.relpath(subfolder.abspath), script_filename)) - - assert op.isfile(op.join(op.relpath(subfolder.abspath), 'aiida.fdf')) - assert op.isfile(op.join(op.relpath(subfolder.abspath), 'Si.psf')) diff --git a/aiida_siesta/tests/calculations/test_submission.py b/aiida_siesta/tests/calculations/test_submission.py deleted file mode 100755 index 1c23c36c..00000000 --- a/aiida_siesta/tests/calculations/test_submission.py +++ /dev/null @@ -1,106 +0,0 @@ -#!/usr/bin/env runaiida -# -*- coding: utf-8 -*- -from __future__ import absolute_import -from __future__ import print_function - -import os.path as op - -def test_submission(siesta_develop): - - from aiida.engine import run - from aiida.orm import load_code - from aiida.orm import (Str, Code, Dict, StructureData, KpointsData) - from aiida.common import NotExistent - from aiida_siesta.calculations.siesta import SiestaCalculation - from aiida.plugins import DataFactory - - PsfData = DataFactory('siesta.psf') - - - # Si diamond structure - alat = 5.430 # angstrom - cell = [[0.5 * alat, 0.5 * alat, 0.,], - [0., 0.5 * alat, 0.5 * alat,], - [0.5 * alat, 0., 0.5 * alat,],] - - # Si - # This was originally given in the "ScaledCartesian" format - # - structure = StructureData(cell=cell) - structure.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), - symbols=['Si']) - structure.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), - symbols=['Si']) - - #code = load_code("Siesta4.0.1@kelvin") - - - code = siesta_develop['siesta_code'] - #assert code is not None - - - parameters = Dict(dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'Solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang', - 'write-forces': True, - # 'xml-write': True - }) - - basis = Dict(dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': 'Si DZP', - }) - - kpoints = KpointsData() - kpoints.set_kpoints_mesh([4, 4, 4]) - - pseudos_list = [] - raw_pseudos = [("Si.psf", 'Si')] - for fname, kind in raw_pseudos: - absname = op.realpath(op.join(op.dirname(__file__), "..", "pseudos", fname)) - pseudo, created = PsfData.get_or_create(absname, use_first=True) - if created: - print("\nCreated the pseudo for {}".format(kind)) - else: - print("\nUsing the pseudo for {} from DB: {}".format( - kind, pseudo.pk)) - pseudos_list.append(pseudo) - - - options = { - "max_wallclock_seconds" : 360, - "resources" : { - "num_machines": 1, - "num_mpiprocs_per_machine": 1, - } - } - - inputs = { - 'structure': structure, - 'parameters': parameters, - 'code': code, - # 'basis': basis, - 'kpoints': kpoints, - 'pseudos': { - 'Si': pseudos_list[0], - }, - 'metadata': { - "label":"TestOnSilicon", - "dry_run": True, - "store_provenance": False, - 'options': options, - } - } - - - run(SiestaCalculation, **inputs) diff --git a/aiida_siesta/tests/conftest.py b/aiida_siesta/tests/conftest.py deleted file mode 100644 index a41098ee..00000000 --- a/aiida_siesta/tests/conftest.py +++ /dev/null @@ -1,15 +0,0 @@ -from __future__ import absolute_import -import pytest -import configparser -from aiida.cmdline.utils import decorators - -testconfig = configparser.ConfigParser() -testconfig.read("testconfig.ini") - -@pytest.fixture(scope="session") -@decorators.with_dbenv() -def siesta_develop(): - sd = {} - from aiida.orm import Code - sd["siesta_code"] = Code.get_from_string(testconfig['codes']['siesta']) - return sd diff --git a/aiida_siesta/tests/conftest.py.bak b/aiida_siesta/tests/conftest.py.bak deleted file mode 100644 index da1177ac..00000000 --- a/aiida_siesta/tests/conftest.py.bak +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -import pytest -import configparser - -testconfig = configparser.ConfigParser() -testconfig.read("testconfig.ini") - - -@pytest.fixture(scope="session") -def siesta_develop(): - sd = {} - from aiida.orm.code import Code - sd["siesta_code"] = Code.get_from_string(testconfig['codes']['siesta']) - return sd diff --git a/aiida_siesta/tests/fdfdict/test_fdfdict.py b/aiida_siesta/tests/fdfdict/test_fdfdict.py deleted file mode 100644 index 603bc05a..00000000 --- a/aiida_siesta/tests/fdfdict/test_fdfdict.py +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - - -def test_fdfdict(): - from aiida_siesta.calculations.tkdict import FDFDict - - f = FDFDict() - - # insertion and saving - f["A-_.B"] = 1 - assert("a_b" in list(f._storage.keys())) - assert f["a_:.b"] == 1 - assert f.get_last_key("a::_b") == "A-_.B" diff --git a/aiida_siesta/tests/plugin_configuration/__init__.py b/aiida_siesta/tests/plugin_configuration/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/aiida_siesta/tests/plugin_configuration/test_endpoints.py b/aiida_siesta/tests/plugin_configuration/test_endpoints.py deleted file mode 100644 index 5f0cc0bc..00000000 --- a/aiida_siesta/tests/plugin_configuration/test_endpoints.py +++ /dev/null @@ -1,17 +0,0 @@ -from __future__ import absolute_import -def test_siesta_calculation_entry_point(siesta_develop): - from aiida.plugins import CalculationFactory - siesta_calculation = CalculationFactory('siesta.siesta') - assert siesta_calculation is not None - - -def test_siesta_parser_entry_point(siesta_develop): - from aiida.plugins import ParserFactory - siesta_parser = ParserFactory('siesta.parser') - assert siesta_parser is not None - - -def test_siesta_psf_entry_point(siesta_develop): - from aiida.plugins import DataFactory - siesta_psf = DataFactory('siesta.psf') - assert siesta_psf is not None diff --git a/aiida_siesta/tests/plugin_configuration/test_endpoints.py.bak b/aiida_siesta/tests/plugin_configuration/test_endpoints.py.bak deleted file mode 100644 index 5f601293..00000000 --- a/aiida_siesta/tests/plugin_configuration/test_endpoints.py.bak +++ /dev/null @@ -1,16 +0,0 @@ -def test_siesta_calculation_entry_point(siesta_develop): - from aiida.plugins import CalculationFactory - siesta_calculation = CalculationFactory('siesta.siesta') - assert siesta_calculation is not None - - -def test_siesta_parser_entry_point(siesta_develop): - from aiida.parsers import ParserFactory - siesta_parser = ParserFactory('siesta.parser') - assert siesta_parser is not None - - -def test_siesta_psf_entry_point(siesta_develop): - from aiida.plugins import DataFactory - siesta_psf = DataFactory('siesta.psf') - assert siesta_psf is not None diff --git a/aiida_siesta/tests/pseudos/C.psf b/aiida_siesta/tests/pseudos/C.psf deleted file mode 100644 index e072cae7..00000000 --- a/aiida_siesta/tests/pseudos/C.psf +++ /dev/null @@ -1,1779 +0,0 @@ - C ca nrl nc - ATM3 no_date Troullier-Martins - 2s 2.00 r= 1.25/2p 2.00 r= 1.25/3d 0.00 r= 1.25/4f 0.00 r= 1.25/ - 4 0 1006 0.413125362778E-03 0.125000000000E-01 4.00000000000 - Radial grid follows - 0.519647735591E-05 0.104583183504E-04 0.157863451569E-04 0.211813902904E-04 - 0.266442967376E-04 0.321759180888E-04 0.377771186712E-04 0.434487736837E-04 - 0.491917693339E-04 0.550070029765E-04 0.608953832538E-04 0.668578302370E-04 - 0.728952755706E-04 0.790086626178E-04 0.851989466078E-04 0.914670947849E-04 - 0.978140865601E-04 0.104240913664E-03 0.110748580301E-03 0.117338103307E-03 - 0.124010512309E-03 0.130766849885E-03 0.137608171725E-03 0.144535546801E-03 - 0.151550057528E-03 0.158652799939E-03 0.165844883850E-03 0.173127433041E-03 - 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0.207590830810E-52 0.431724155835E-53 0.881875547706E-54 0.176574254134E-54 - 0.346463468454E-55 0.666019574688E-56 From 7c58c7908de46ed184fa7c771bfc9b9a1ddaace3 Mon Sep 17 00:00:00 2001 From: Bosoni Date: Wed, 13 Nov 2019 16:20:56 +0100 Subject: [PATCH 07/10] All examples are now tested and referenced in docs Tested all the example to make sure they run on Siesta4.0.1 and Siesta 4.1-b3. Many examples needed big changes. Documentation has been change accordingly to reference the example. Lots of comment added to the scripts in order to make them more understandable for a person that approches aiida for the first time. Only final concern left behind is the bands parsing in the case of spin-orbit. The file shows nspin=1 and the parser works accordingly, but I'm not sure it is correct. I also don't find very usefull the example_ldos.py as aiida.LDOS is a unformatted file, so not readable. --- aiida_siesta/docs/installation.rst | 1 + aiida_siesta/docs/plugins/siesta.rst | 22 +- .../examples/plugins/siesta/example_bands.py | 70 ++-- .../plugins/siesta/example_cif_bands.py | 39 +- .../examples/plugins/siesta/example_first.py | 83 ++-- .../plugins/siesta/example_geom_fail.py | 4 +- .../examples/plugins/siesta/example_ldos.py | 23 +- .../plugins/siesta/example_magnetic_bands.py | 157 ++++---- .../plugins/siesta/example_molecule.py | 70 +--- .../plugins/siesta/example_psf_family.py | 9 +- .../examples/plugins/siesta/example_psml.py | 32 +- .../examples/plugins/siesta/example_relax.py | 367 ++++++------------ .../plugins/siesta/example_restart.py | 111 +++--- .../plugins/siesta/example_scf_fail.py | 28 +- .../plugins/siesta/example_soc_bands.py | 30 +- .../plugins/siesta/example_varcell.py | 261 ++++++------- 16 files changed, 580 insertions(+), 727 deletions(-) diff --git a/aiida_siesta/docs/installation.rst b/aiida_siesta/docs/installation.rst index b780c23e..8e9ebc6f 100644 --- a/aiida_siesta/docs/installation.rst +++ b/aiida_siesta/docs/installation.rst @@ -19,4 +19,5 @@ aiida_core python framework. :: reentry scan -r aiida + verd daemon restart diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index 1e421f07..d0dbcb1d 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -16,6 +16,8 @@ can be found in the development platform Inputs ------ +Some examples are referenced in the following list. They are located in the folder +aiida_siesta/examples/plugins/siesta. * **code**, class :py:class:`Code `, *Mandatory* @@ -62,7 +64,7 @@ Inputs The :py:class:`StructureData ` can also import ase structures or pymatgen structures. This two tools can be used to load - structure from files. See example in .... + structure from files. See example example_cif_bands.py * **parameters**, class :py:class:`Dict `, *Mandatory* @@ -116,8 +118,7 @@ Inputs Alternatively, a pseudo for every atomic species can be set with the **use_pseudos_from_family** method, if a family of pseudopotentials - has been installed. (But the family approach does not yet support - multiple species sharing the same pseudopotential.) For an example ... + has been installed. For an example see example_psf_family.py .. note:: The verdi command-line interface now supports entry points defined by external packages. We have implemented `verdi data @@ -238,7 +239,7 @@ Inputs The legacy "get_explicit_kpoints_path" shares only the name with the function in "aiida.tools", but it is very different in scope. - The full list of cases can be explored looking at the example ... + The full list of cases can be explored looking at the example example_bands.py .. warning:: The implementation relies on the correct description of the labels in the class :py:class:`KpointsData `. @@ -308,7 +309,18 @@ In this case, calc is the calculation node and not the results dictionary. launch the calculation, passing the calculation class as the first argument:: run(SiestaCalculation, structure=s, pseudos=pseudos, kpoints = kpoints, ...) -Examples in the folder ... +A large set of examples covering some standard cases are in the folder +aiida_siesta/examples/plugins/siesta. They can be run with:: + runaiida example_name.py {--send, --dont-send} + +The parameter --dont-send will activate the "dry run" option. In that case a test +folder (submit_test) will be created, containing all the files that aiida +generates automatically. The parameter --send will submit the example to +the daemon. +One of the two parameter needs to be present to run the script. Optionally, +a second argument containing the name of the code (code@computer) to use +can be passed to the script. Alternatively the name of the code can be changed +inside the script. Outputs ------- diff --git a/aiida_siesta/examples/plugins/siesta/example_bands.py b/aiida_siesta/examples/plugins/siesta/example_bands.py index daa4302e..b9454518 100755 --- a/aiida_siesta/examples/plugins/siesta/example_bands.py +++ b/aiida_siesta/examples/plugins/siesta/example_bands.py @@ -2,10 +2,8 @@ # -*- coding: utf-8 -*- from __future__ import absolute_import from __future__ import print_function - import os.path as op import sys -from aiida.tools import get_explicit_kpoints_path #In this example we will calculate the band structure of Si. #Thanks to SeeK-path we can automatically generate the @@ -14,13 +12,14 @@ ################################################################ + from aiida.engine import submit from aiida.orm import load_code from aiida.orm import (Dict, StructureData, KpointsData) from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory +from aiida_siesta.data.psf import PsfData +from aiida.tools import get_explicit_kpoints_path -PsfData = DataFactory('siesta.psf') try: dontsend = sys.argv[1] @@ -41,11 +40,13 @@ except IndexError: codename = 'Siesta4.0.1@kelvin' +#The code +code = load_code(codename) + ##-------------------Structure----------------------------------- ##Manually set the structure, all the quantities must be in Ang. ##Then, we pass through SeeK-path, to get the standardized cell, ##necessary for the automatic choice of the bands path. - alat = 5.430 # angstrom cell = [ [ @@ -80,8 +81,7 @@ result = get_explicit_kpoints_path(s, **seekpath_parameters.get_dict()) structure = result['primitive_structure'] -code = load_code(codename) - +#The parameters parameters = Dict( dict={ 'xc-functional': 'LDA', @@ -92,64 +92,66 @@ 'dm-tolerance': 1.e-3, 'Solution-method': 'diagon', 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang', 'write-forces': True, - # 'xml-write': True }) -basis = Dict( - dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': """ +#The basis +basis = Dict(dict={ +'pao-energy-shift': '300 meV', +'%block pao-basis-sizes': """ Si DZP %endblock pao-basis-sizes""", }) +#The kpoints mesh kpoints = KpointsData() kpoints.set_kpoints_mesh([4, 4, 4]) ##-------------------K-points for bands -------------------- bandskpoints = KpointsData() -##Uncomment your favourite, two options: - +##Uncomment your favourite, three options: ##1) ##.....Making use of SeeK-path for the automatic path...... ##The choice of the distance between kpoints is in the call seekpath_parameters ##All high symmetry points included, labels already included ##This calls BandLine in siesta bandskpoints = result['explicit_kpoints'] - ##2) -##.....Only points, no labels....... -##Mandatory to set cell and pbc +##.................Only discrete points............. +##Mandatory to set cell and pbc. Do not set labels! ##This calls BandsPoint #kpp = [(0.500, 0.250, 0.750), (0.500, 0.500, 0.500), (0., 0., 0.)] #bandskpoints.set_cell(structure.cell, structure.pbc) #bandskpoints.set_kpoints(kpp) - -#Note: The option to define a path touching specific kpoints -#for instance: +##3) +##...The option to define a path touching specific kpoints... +##It make use of a legacy function. Mandatory to set cell and pbc +#from aiida.tools.data.array.kpoints.legacy import get_explicit_kpoints_path as legacy_path #kpp = [('W', (0.500, 0.250, 0.750), 'L', (0.500, 0.500, 0.500), 40), # ('L', (0.500, 0.500, 0.500), 'G', (0., 0., 0.), 40)] -#Now is not easy to set. I'll study more on that +#tmp=legacy_path(kpp) +#bandskpoints.set_cell(structure.cell, structure.pbc) +#bandskpoints.set_kpoints(tmp[3]) +#bandskpoints.labels=tmp[4] -pseudos_list = [] -raw_pseudos = [("Si.psf", 'Si')] -for fname, kind in raw_pseudos: +#The pseudopotentials +pseudos_dict = {} +raw_pseudos = [("Si.psf", ['Si'])] +for fname, kinds in raw_pseudos: absname = op.realpath( op.join(op.dirname(__file__), "data/sample-psf-family", fname)) pseudo, created = PsfData.get_or_create(absname, use_first=True) if created: - print("\nCreated the pseudo for {}".format(kind)) + print("\nCreated the pseudo for {}".format(kinds)) else: - print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) - pseudos_list.append(pseudo) + print("\nUsing the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + for j in kinds: + pseudos_dict[j]=pseudo +#Resources options = { "max_wallclock_seconds": 600, +# "withmpi" : True, "resources": { "num_machines": 1, "num_mpiprocs_per_machine": 1, @@ -163,11 +165,9 @@ 'basis': basis, 'kpoints': kpoints, 'bandskpoints': bandskpoints, - 'pseudos': { - 'Si': pseudos_list[0], - }, + 'pseudos': pseudos_dict, 'metadata': { - "label": "TestOnSiliconBandsLines", + "label": "TestOnSiliconBands", 'options': options, } } diff --git a/aiida_siesta/examples/plugins/siesta/example_cif_bands.py b/aiida_siesta/examples/plugins/siesta/example_cif_bands.py index d89c37ea..21dc1921 100755 --- a/aiida_siesta/examples/plugins/siesta/example_cif_bands.py +++ b/aiida_siesta/examples/plugins/siesta/example_cif_bands.py @@ -3,10 +3,9 @@ from __future__ import absolute_import from __future__ import print_function - import sys - import pymatgen as mg +import ase.io from aiida.engine import submit from aiida.orm import load_code @@ -19,6 +18,8 @@ # a cif file. # The band structure is calculated and the kpoint path is automatically # generated using seekpath. +# The pseudopotential is taken from a family, please refer to 00_README +# and example_psf_family.py for better understanding PsfData = DataFactory('siesta.psf') Dict = DataFactory('dict') @@ -42,11 +43,9 @@ try: codename = sys.argv[2] except IndexError: - codename = 'siesta4.0.1@parsons' + codename = 'Siesta4.0.1@kelvin' -# #------------------Code and computer options --------------------------- -# code = load_code(codename) options = { @@ -58,56 +57,41 @@ } } # -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} -settings = Dict(dict=settings_dict) +#settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +#settings = Dict(dict=settings_dict) #--------------------------------------------------------------------- -# # Structure ----------------------------------------- -# -# Passing through SeeK-path first, to get the standardized cell. +# Two choices for importing the .cif, pymatgen or ase. Then +# passing through SeeK-path to get the standardized cell. # Necessary for the automatic choice of the bands path. -# structure = mg.Structure.from_file("data/O2_ICSD_173933.cif", primitive=False) s = StructureData(pymatgen_structure=structure) +#structure =ase.io.read("data/O2_ICSD_173933.cif") +#s = StructureData(ase=structure) seekpath_parameters = {'reference_distance': 0.02, 'symprec': 0.0001} result = get_explicit_kpoints_path(s, **seekpath_parameters) newstructure = result['primitive_structure'] -# # Parameters --------------------------------------------------- -# params_dict = { 'xc-functional': 'LDA', 'xc-authors': 'CA', - 'spin-polarized': True, - 'noncollinearspin': False, 'mesh-cutoff': '200.000 Ry', 'max-scfiterations': 1000, 'dm-numberpulay': 5, 'dm-mixingweight': 0.050, 'dm-tolerance': 1.e-4, 'dm-mixscf1': True, - 'negl-nonoverlap-int': False, 'solution-method': 'diagon', 'electronic-temperature': '100.000 K', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 2, - 'md-maxcgdispl': '0.200 bohr', - 'md-maxforcetol': '0.050 eV/Ang', 'writeforces': True, - 'writecoorstep': True, - 'write-mulliken-pop': 1 } # parameters = Dict(dict=params_dict) -#---------------------------------------------------------- -# # Basis Set Info ------------------------------------------ -# The basis dictionary follows the 'parameters' convention -# basis_dict = { 'pao-basistype': 'split', 'pao-splitnorm': 0.150, @@ -118,7 +102,6 @@ } # basis = Dict(dict=basis_dict) -#-------------------------------------------------------------- #--------------------- Pseudopotentials --------------------------------- # @@ -154,7 +137,7 @@ 'pseudos': pseudos_dict, 'metadata': { 'options': options, - 'label': "O_el_cell_spin from CIF" + 'label': "O_el_cell_from_CIF" } } diff --git a/aiida_siesta/examples/plugins/siesta/example_first.py b/aiida_siesta/examples/plugins/siesta/example_first.py index 2f2b2155..ed605f99 100755 --- a/aiida_siesta/examples/plugins/siesta/example_first.py +++ b/aiida_siesta/examples/plugins/siesta/example_first.py @@ -1,18 +1,28 @@ #!/usr/bin/env runaiida # -*- coding: utf-8 -*- + +#Not required by AiiDA from __future__ import absolute_import from __future__ import print_function - import os.path as op import sys +#AiiDA classes and functions from aiida.engine import submit from aiida.orm import load_code from aiida.orm import (Dict, StructureData, KpointsData) from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory +from aiida_siesta.data.psf import PsfData -PsfData = DataFactory('siesta.psf') +##In alternative, Data and Calculation factories could be loaded. +##They containing all the data and calculation plugins: +#from aiida.plugins import DataFactory +#from aiida.plugins import CalculationFactory +# +#SiestaCalculation = CalculationFactory('siesta.siesta') +#PsfData = DataFactory('siesta.psf') +#StructureData = DataFactory('structure') +#... try: dontsend = sys.argv[1] @@ -33,7 +43,10 @@ except IndexError: codename = 'Siesta4.0.1@kelvin' -# Si diamond structure +#The code +code = load_code(codename) + +#The structure. Si diamond structure alat = 5.430 # angstrom cell = [ [ @@ -52,18 +65,15 @@ 0.5 * alat, ], ] - -# Si -# This was originally given in the "ScaledCartesian" format -# +#The atom positions were originally given in the "ScaledCartesian" format +#but standard for aiida structures is Cartesian in Angstrom structure = StructureData(cell=cell) structure.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), symbols=['Si']) structure.append_atom(position=(0.250 * alat, 0.250 * alat, 0.250 * alat), symbols=['Si']) -code = load_code(codename) - +#The parameters parameters = Dict( dict={ 'xc-functional': 'LDA', @@ -74,54 +84,55 @@ 'dm-tolerance': 1.e-3, 'Solution-method': 'diagon', 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang', 'write-forces': True, - # 'xml-write': True }) -basis = Dict( - dict={ - 'pao-energy-shift': '300 meV', - '%block pao-basis-sizes': """ +#The basis set +basis = Dict(dict={ +'pao-energy-shift': '300 meV', +'%block pao-basis-sizes': """ Si DZP %endblock pao-basis-sizes""", }) +#The kpoints kpoints = KpointsData() kpoints.set_kpoints_mesh([4, 4, 4]) -pseudos_list = [] -raw_pseudos = [("Si.psf", 'Si')] -for fname, kind in raw_pseudos: +#The pseudopotentials +pseudos_dict = {} +raw_pseudos = [("Si.psf", ['Si'])] +for fname, kinds in raw_pseudos: absname = op.realpath( op.join(op.dirname(__file__), "data/sample-psf-family", fname)) pseudo, created = PsfData.get_or_create(absname, use_first=True) if created: - print("\nCreated the pseudo for {}".format(kind)) + print("\nCreated the pseudo for {}".format(kinds)) else: - print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) - pseudos_list.append(pseudo) + print("\nUsing the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + for j in kinds: + pseudos_dict[j]=pseudo +#Resources options = { "max_wallclock_seconds": 360, + 'withmpi': True, "resources": { "num_machines": 1, - "num_mpiprocs_per_machine": 1, + "num_mpiprocs_per_machine": 2, } } + +#The submission +#All the inputs of a Siesta calculations are listed in a dictionary inputs = { 'structure': structure, 'parameters': parameters, 'code': code, 'basis': basis, 'kpoints': kpoints, - 'pseudos': { - 'Si': pseudos_list[0], - }, + 'pseudos': pseudos_dict, 'metadata': { "label": "TestOnSiliconBulk", 'options': options, @@ -132,11 +143,8 @@ inputs["metadata"]["dry_run"] = True inputs["metadata"]["store_provenance"] = False process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() print("Submited test for calculation (uuid='{}')".format(process.uuid)) print("Check the folder submit_test for the result of the test") -# I could't find a way to access the actual folder (subfolder of submit_test) -# from the calculation node. So I can't print the exact location else: process = submit(SiestaCalculation, **inputs) @@ -144,3 +152,14 @@ print("For information about this calculation type: verdi process show {}". format(process.pk)) print("For a list of running processes type: verdi process list") + +##An alternative is be to use the builder +#build=SiestaCalculation.get_builder() +#build.code=code +#build.structure=structure +#build.pseudos=pseudos_dict +#... +#build.metadata.options.resources = {'num_machines': 1 "num_mpiprocs_per_machine": 1} +#process = submit(builder) + + diff --git a/aiida_siesta/examples/plugins/siesta/example_geom_fail.py b/aiida_siesta/examples/plugins/siesta/example_geom_fail.py index aad4d5aa..72874e3f 100755 --- a/aiida_siesta/examples/plugins/siesta/example_geom_fail.py +++ b/aiida_siesta/examples/plugins/siesta/example_geom_fail.py @@ -44,7 +44,7 @@ code = load_code(codename) options = { - "queue_name": "debug", +# "queue_name": "debug", "max_wallclock_seconds": 1700, "resources": { "num_machines": 1, @@ -97,7 +97,7 @@ 'dm-mixingweight': 0.1, 'dm-tolerance': 1.e-4, 'md-typeofrun': 'cg', - 'md-numcgsteps': 8, + 'md-numcgsteps': 7, 'md-maxcgdispl': '0.200 bohr', 'md-maxforcetol': '0.020 eV/Ang', 'geometry-must-converge': True diff --git a/aiida_siesta/examples/plugins/siesta/example_ldos.py b/aiida_siesta/examples/plugins/siesta/example_ldos.py index 97e4220a..55298db4 100755 --- a/aiida_siesta/examples/plugins/siesta/example_ldos.py +++ b/aiida_siesta/examples/plugins/siesta/example_ldos.py @@ -12,6 +12,8 @@ from aiida_siesta.calculations.siesta import SiestaCalculation from aiida.plugins import DataFactory +# There is no parsing for the ldos, but the file .LDOS can be +# retrieved using the "settings" feature. ################################################################ PsfData = DataFactory('siesta.psf') @@ -36,7 +38,7 @@ try: codename = sys.argv[2] except IndexError: - codename = 'Siesta-4.0@rinaldo' + codename = 'Siesta4.0.1@kelvin' # #------------------Code and computer options --------------------------- @@ -44,7 +46,7 @@ code = load_code(codename) options = { - "queue_name": "debug", +# "queue_name": "debug", "max_wallclock_seconds": 1700, "resources": { "num_machines": 1, @@ -54,7 +56,7 @@ # #----Settings first ----------------------------- # -settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.EIG']} +settings_dict = {'additional_retrieve_list': ['aiida.BONDS', 'aiida.LDOS']} settings = Dict(dict=settings_dict) #--------------------------------------------------- @@ -150,8 +152,8 @@ # This exemplifies the handling of pseudos for different species # Those sharing the same pseudo should be indicated. # -pseudos_list = [] -raw_pseudos = [("C.psf", ['C', 'Cred']), ("H.psf", 'H')] +pseudos_dict = {} +raw_pseudos = [("C.psf", ['C', 'Cred']), ("H.psf", ['H'])] for fname, kinds, in raw_pseudos: absname = os.path.realpath( @@ -162,21 +164,20 @@ print("Created the pseudo for {}".format(kinds)) else: print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) - pseudos_list.append(pseudo) + for j in kinds: + pseudos_dict[j]=pseudo + #----------------------------------------------------------------------- #--All the inputs of a Siesta calculations are listed in a dictionary-- # inputs = { + 'settings' : settings, 'structure': s, 'parameters': parameters, 'code': code, 'basis': basis, - 'pseudos': { - 'C': pseudos_list[0], - 'Cred': pseudos_list[0], - 'H': pseudos_list[1], - }, + 'pseudos': pseudos_dict, 'metadata': { 'options': options, 'label': "Benzene molecule", diff --git a/aiida_siesta/examples/plugins/siesta/example_magnetic_bands.py b/aiida_siesta/examples/plugins/siesta/example_magnetic_bands.py index 412d94c2..c9e66e32 100755 --- a/aiida_siesta/examples/plugins/siesta/example_magnetic_bands.py +++ b/aiida_siesta/examples/plugins/siesta/example_magnetic_bands.py @@ -1,23 +1,23 @@ #!/usr/bin/env runaiida # -*- coding: utf-8 -*- -__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." -__license__ = "MIT license, see LICENSE.txt file" -__version__ = "0.7.0" -__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" - +from __future__ import absolute_import +from __future__ import print_function import sys import os -from aiida.common.example_helpers import test_and_get_code -from aiida.common.exceptions import NotExistent +from aiida.engine import submit +from aiida.orm import load_code +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.plugins import DataFactory +from aiida.tools import get_explicit_kpoints_path # Calculation on Iron, collinear spin polarization applied ################################################################ PsfData = DataFactory('siesta.psf') -ParameterData = DataFactory('parameter') +Dict = DataFactory('dict') KpointsData = DataFactory('array.kpoints') StructureData = DataFactory('structure') @@ -37,15 +37,22 @@ try: codename = sys.argv[2] except IndexError: - codename = 'siesta4.0.1@parsons' + codename = 'Siesta4.0.1@kelvin' -code = test_and_get_code(codename, expected_code_type='siesta.siesta') # -# Set up calculation object first +#------------------Code and computer options --------------------------- # -calc = code.new_calc() -calc.label = "Siesta-Fe-bulk-spin" -calc.description = "Test Siesta calculation. Fe bulk spin-polarized" +code = load_code(codename) + +options = { +# "queue_name": "debug", + "max_wallclock_seconds": 1700, + 'withmpi': True, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 2, + } +} # # Structure ----------------------------------------- @@ -60,83 +67,103 @@ # s = StructureData(cell=cell) s.append_atom(position=(0.000,0.000,0.000),symbols=['Fe']) - +seekpath_parameters = {'reference_distance': 0.04, 'symprec': 0.0001} +result = get_explicit_kpoints_path(s, **seekpath_parameters) elements = list(s.get_symbols_set()) -calc.use_structure(s) -#------------------------------------------------------------- -# -# Parameters --------------------------------------------------- -# -# Note the use of '.' in some entries. This will be fixed below. -# Note also that some entries have ':' as separator. This is not -# allowed in Siesta, and will be fixed by the plugin itself. The -# latter case is an unfortunate historical choice. It should not -# be used in modern scripts. -# +newstructure = result['primitive_structure'] + + +# The parameters params_dict= { -'xc.functional': 'GGA', -'xc.authors': 'PBE', +'xc-functional': 'GGA', +'xc-authors': 'PBE', 'spin-polarized': True, 'noncollinearspin': False, -'mesh-cutoff': '150.000 Ry', +'mesh-cutoff': '100.000 Ry', 'max-scfiterations': 40, 'dm-numberpulay': 4, 'dm-mixingweight': 0.1, 'dm-tolerance': 1.e-3, 'electronic-temperature': '300.000 K' } +parameters = Dict(dict=params_dict) + +# The basis +basis_dict = { + 'pao-basistype': 'split', + 'pao-splitnorm': 0.150, + 'pao-energyshift': '0.020 Ry', + '%block pao-basis-sizes': """ +Fe SZP +%endblock pao-basis-sizes""", +} # -# Sanitize, as '.' is not kosher for the database handlers -# -params_dict = { k.replace('.','-') :v for k,v in params_dict.iteritems() } -# -parameters = ParameterData(dict=params_dict) -calc.use_parameters(parameters) -# +basis = Dict(dict=basis_dict) + + +# K ponts mesh kpoints = KpointsData() kpoints_mesh = 6 kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) -calc.use_kpoints(kpoints) + +# K points for bands +bandskpoints = KpointsData() +# Making use of SeeK-path for the automatic path +# The choice of the distance between kpoints is in the call seekpath_parameters +# All high symmetry points included, labels already included +bandskpoints = result['explicit_kpoints'] + # # Pseudopotentials ---------------------------------------------- # # This exemplifies the handling of pseudos for different species # Those sharing the same pseudo should be indicated. -# Families support is not yet available for this. # -raw_pseudos = [ ("Fe.psf", 'Fe')] +pseudos_dict = {} +raw_pseudos = [("Fe.psf", ['Fe'])] for fname, kinds, in raw_pseudos: - absname = os.path.realpath(os.path.join(os.path.dirname(__file__), - "data",fname)) - pseudo, created = PsfData.get_or_create(absname,use_first=True) + absname = os.path.realpath( + os.path.join(os.path.dirname(__file__), "data/sample-psf-family", + fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) if created: - print "Created the pseudo for {}".format(kinds) + print("Created the pseudo for {}".format(kinds)) else: - print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) - - # Attach pseudo node to the calculation - calc.use_pseudo(pseudo,kind=kinds) -#------------------------------------------------------------------- - -calc.set_max_wallclock_seconds(30*60) # 30 min + print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + for j in kinds: + pseudos_dict[j]=pseudo -calc.set_resources({"num_machines": 1}) -#------------------ +# +#--All the inputs of a Siesta calculations are listed in a dictionary-- +# +inputs = { + 'structure': newstructure, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'pseudos' : pseudos_dict, + 'kpoints' : kpoints, + 'bandskpoints' : bandskpoints, + 'metadata': { + 'options': options, + 'label': "BCC iron", + } +} if submit_test: - subfolder, script_filename = calc.submit_test() - print "Test_submit for calculation (uuid='{}')".format( - calc.uuid) - print "Submit file in {}".format(os.path.join( - os.path.relpath(subfolder.abspath), - script_filename - )) + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + else: - calc.store_all() - print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - calc.submit() - print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") + + diff --git a/aiida_siesta/examples/plugins/siesta/example_molecule.py b/aiida_siesta/examples/plugins/siesta/example_molecule.py index 02f50648..ea1901b9 100755 --- a/aiida_siesta/examples/plugins/siesta/example_molecule.py +++ b/aiida_siesta/examples/plugins/siesta/example_molecule.py @@ -3,7 +3,6 @@ from __future__ import absolute_import from __future__ import print_function - import sys import os @@ -46,30 +45,13 @@ options = { "queue_name": "debug", "max_wallclock_seconds": 1700, +# 'withmpi': True, "resources": { "num_machines": 1, "num_mpiprocs_per_machine": 1, } } -#TO DO: -# A Siesta executable compiled in serial mode might not work properly -# on a computer set up for MPI operation. -# This snippet can be used to check whether a code has been compiled -# with mpi support, and act accordingly -# For this to work, the user has to manually add the record in the -# database. In the verdi shell: -# -# code = load_node(code_PK) -# code.set_extra("mpi",True) -#code_mpi_enabled = False -#try: -# code_mpi_enabled = code.get_extra("mpi") -#except AttributeError: -# pass -#calc.set_withmpi(code_mpi_enabled) -#----------------------------------------------------------------------- - # #-------------------------- Settings --------------------------------- # @@ -100,7 +82,6 @@ ] # Note an atom tagged (for convenience) with a different label - s = StructureData(cell=cell) s.append_atom(position=(0.000, 0.000, 0.468), symbols=['H']) s.append_atom(position=(0.000, 0.000, 1.620), symbols=['C']) @@ -121,33 +102,21 @@ # # ----------------------Parameters ------------------------------------- # -# Note the use of '.' in some entries. This will be fixed below. -# Note also that some entries have ':' as separator. This is not -# allowed in Siesta, and will be fixed by the plugin itself. The -# latter case is an unfortunate historical choice. It should not -# be used in modern scripts. -# +# Note the use of '.' is not allowed. +# Note also that ':' as separator is not allowed in Siesta. +# '-' is the suggested choice. params_dict = { 'xc-functional': 'LDA', 'xc-authors': 'CA', - 'spin-polarized': True, - 'noncollinearspin': False, 'mesh-cutoff': '200.000 Ry', 'max-scfiterations': 1000, 'dm-numberpulay': 5, 'dm-mixingweight': 0.050, 'dm-tolerance': 1.e-4, 'dm-mixscf1': True, - 'negl-nonoverlap-int': False, 'solution-method': 'diagon', 'electronic-temperature': '100.000 K', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 2, - 'md-maxcgdispl': '0.200 bohr', - 'md-maxforcetol': '0.050 eV/Ang', 'writeforces': True, - 'writecoorstep': True, - 'write-mulliken-pop': 1, } parameters = Dict(dict=params_dict) @@ -158,13 +127,13 @@ # The basis dictionary follows the 'parameters' convention # basis_dict = { - 'pao-basistype': - 'split', - 'pao-splitnorm': - 0.150, - 'pao-energyshift': - '0.020 Ry', - '%block pao-basis-sizes': +'pao-basistype': +'split', +'pao-splitnorm': + 0.150, +'pao-energyshift': +'0.020 Ry', +'%block pao-basis-sizes': """ C SZP Cred SZ @@ -180,8 +149,8 @@ # This exemplifies the handling of pseudos for different species # Those sharing the same pseudo should be indicated. # -pseudos_list = [] -raw_pseudos = [("C.psf", ['C', 'Cred']), ("H.psf", 'H')] +pseudos_dict = {} +raw_pseudos = [("C.psf", ['C', 'Cred']), ("H.psf", ['H'])] for fname, kinds, in raw_pseudos: absname = os.path.realpath( @@ -192,7 +161,9 @@ print("Created the pseudo for {}".format(kinds)) else: print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) - pseudos_list.append(pseudo) + for j in kinds: + pseudos_dict[j]=pseudo + #----------------------------------------------------------------------- @@ -204,11 +175,7 @@ 'parameters': parameters, 'code': code, 'basis': basis, - 'pseudos': { - 'C': pseudos_list[0], - 'Cred': pseudos_list[0], - 'H': pseudos_list[1], - }, + 'pseudos' : pseudos_dict, 'metadata': { 'options': options, 'label': "Benzene molecule", @@ -219,11 +186,8 @@ inputs["metadata"]["dry_run"] = True inputs["metadata"]["store_provenance"] = False process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() print("Submited test for calculation (uuid='{}')".format(process.uuid)) print("Check the folder submit_test for the result of the test") -# I could't find a way to access the actual folder (subfolder of submit_test) -# from the calculation node. So I can't print the exact location else: process = submit(SiestaCalculation, **inputs) diff --git a/aiida_siesta/examples/plugins/siesta/example_psf_family.py b/aiida_siesta/examples/plugins/siesta/example_psf_family.py index b8a8d662..fb53d59c 100755 --- a/aiida_siesta/examples/plugins/siesta/example_psf_family.py +++ b/aiida_siesta/examples/plugins/siesta/example_psf_family.py @@ -13,6 +13,7 @@ from aiida.plugins import DataFactory #----------------- Example of the use of a pseudopotential family +# Read 00_README to learn how to set up a family PsfData = DataFactory('siesta.psf') Dict = DataFactory('dict') @@ -102,8 +103,6 @@ params_dict = { 'xc-functional': 'LDA', 'xc-authors': 'CA', - 'spin-polarized': True, - 'noncollinearspin': False, 'mesh-cutoff': '200.000 Ry', 'max-scfiterations': 1000, 'dm-numberpulay': 5, @@ -113,13 +112,7 @@ 'negl-nonoverlap-int': False, 'solution-method': 'diagon', 'electronic-temperature': '100.000 K', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 2, - 'md-maxcgdispl': '0.200 bohr', - 'md-maxforcetol': '0.050 eV/Ang', 'writeforces': True, - 'writecoorstep': True, - 'write-mulliken-pop': 1, } parameters = Dict(dict=params_dict) diff --git a/aiida_siesta/examples/plugins/siesta/example_psml.py b/aiida_siesta/examples/plugins/siesta/example_psml.py index b635f597..9bcf7129 100755 --- a/aiida_siesta/examples/plugins/siesta/example_psml.py +++ b/aiida_siesta/examples/plugins/siesta/example_psml.py @@ -5,17 +5,15 @@ from __future__ import print_function import sys -import os +import os.path as op from aiida.engine import submit from aiida.orm import load_code from aiida_siesta.calculations.siesta import SiestaCalculation from aiida.plugins import DataFactory -########################################################## -# # -# Siesta calculation on benzene molecule, first to try # -# # +# Version of siesta supporting psml files is needed to run +# this example ########################################################## PsmlData = DataFactory('siesta.psml') @@ -145,18 +143,19 @@ # This exemplifies the handling of pseudos for different species # Those sharing the same pseudo should be indicated. # -pseudos_list = [] -raw_pseudos = [("Si.psml", 'Si')] - -for fname, kinds, in raw_pseudos: - absname = os.path.realpath( - os.path.join(os.path.dirname(__file__), "data/sample-psml-family", fname)) +pseudos_dict = {} +raw_pseudos = [("Si.psml", ['Si'])] +for fname, kinds in raw_pseudos: + absname = op.realpath( + op.join(op.dirname(__file__), "data/sample-psml-family", fname)) pseudo, created = PsmlData.get_or_create(absname, use_first=True) if created: - print("Created the pseudo for {}".format(kinds)) + print("\nCreated the pseudo for {}".format(kinds)) else: - print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) - pseudos_list.append(pseudo) + print("\nUsing the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + for j in kinds: + pseudos_dict[j]=pseudo + #----------------------------------------------------------------------- @@ -168,9 +167,7 @@ 'parameters': parameters, 'code': code, 'basis': basis, - 'pseudos': { - 'Si': pseudos_list[0] - }, + 'pseudos': pseudos_dict, 'metadata': { 'options': options, 'label': "Si crystal with PSML pseudos", @@ -181,7 +178,6 @@ inputs["metadata"]["dry_run"] = True inputs["metadata"]["store_provenance"] = False process = submit(SiestaCalculation, **inputs) - # subfolder, script_filename = calc.submit_test() print("Submited test for calculation (uuid='{}')".format(process.uuid)) print("Check the folder submit_test for the result of the test") diff --git a/aiida_siesta/examples/plugins/siesta/example_relax.py b/aiida_siesta/examples/plugins/siesta/example_relax.py index 02c616fb..ba6cc058 100755 --- a/aiida_siesta/examples/plugins/siesta/example_relax.py +++ b/aiida_siesta/examples/plugins/siesta/example_relax.py @@ -1,26 +1,16 @@ #!/usr/bin/env runaiida # -*- coding: utf-8 -*- -__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." -__license__ = "MIT license, see LICENSE.txt file" -__version__ = "0.7.0" -__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" - +from __future__ import absolute_import +from __future__ import print_function +import os.path as op import sys -import os - -from aiida.common.example_helpers import test_and_get_code -from aiida.common.exceptions import NotExistent - -# Another molecule -# Pseudo families introduced -################################################################ - -PsfData = DataFactory('siesta.psf') -ParameterData = DataFactory('parameter') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') +from aiida.engine import submit +from aiida.orm import load_code +from aiida.orm import (Dict, StructureData, KpointsData) +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida_siesta.data.psf import PsfData try: dontsend = sys.argv[1] @@ -31,246 +21,127 @@ else: raise IndexError except IndexError: - print >> sys.stderr, ("The first parameter can only be either " - "--send or --dont-send") + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) sys.exit(1) try: codename = sys.argv[2] except IndexError: - codename = 'siesta4.0.1@parsons' - - - -queue = None -settings = None - -code = test_and_get_code(codename, expected_code_type='siesta.siesta') -## For remote codes, it is not necessary to manually set the computer, -## since it is set automatically by new_calc -#computer = code.get_remote_computer() -#calc = code.new_calc(computer=computer) - -calc = code.new_calc() -calc.label = "SiH_spin" -calc.description = "Test calculation with the Siesta code. SiH spin" -calc.set_max_wallclock_seconds(30*60) # 30 min - -#------------ clarify this -# Valid only for Slurm and PBS (using default values for the -# number_cpus_per_machine), change for SGE-like schedulers -## Otherwise, to specify a given # of cpus per machine, uncomment the following: -# calc.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 8}) -#calc.set_resources({"parallel_env": 'openmpi',"tot_num_mpiprocs": 1,"num_machines": 1,"num_cpus": 2}) -#------------ clarify this -calc.set_resources({"num_machines": 1}) - -#calc.set_custom_scheduler_commands("#SBATCH --account=ch3") - -if queue is not None: - calc.set_queue_name(queue) - - -##----Structure--- - -alat = 5.430 # angstrom -cell = [[2*alat, 0., 0.,], - [0., 2*alat, 0.,], - [0., 0., 2*alat,], - ] - -# SiH coordinates -# This was originally given in the "ScaledCartesian" format -# -s = StructureData(cell=cell) -s.append_atom(position=(0.000*alat,0.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.250*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,0.500*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.750*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,0.000*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,0.250*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,0.500*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,0.750*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,0.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,0.250*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,0.500*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,0.750*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,0.000*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,0.250*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,0.500*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,0.750*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,1.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,1.250*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,1.500*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,1.750*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,1.000*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,1.250*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,1.500*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,1.750*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,0.000*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.250*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,0.500*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.750*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,0.000*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,0.250*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,0.500*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,0.750*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,1.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,1.250*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,1.500*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,1.750*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,1.000*alat,0.500*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,1.250*alat,0.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,1.500*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,1.750*alat,0.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,0.000*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,0.250*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,0.500*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,0.750*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,0.000*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,0.250*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,0.500*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,0.750*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,1.000*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,1.250*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(0.000*alat,1.500*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,1.750*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,1.000*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,1.250*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(0.500*alat,1.500*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(0.750*alat,1.750*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,1.000*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,1.250*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.000*alat,1.500*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(1.250*alat,1.750*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,1.000*alat,1.500*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,1.250*alat,1.750*alat),symbols=['Si']) -s.append_atom(position=(1.500*alat,1.500*alat,1.000*alat),symbols=['Si']) -s.append_atom(position=(1.750*alat,1.750*alat,1.250*alat),symbols=['Si']) -s.append_atom(position=(1.125*alat,1.125*alat,1.125*alat),symbols=['H']) - -elements = list(s.get_symbols_set()) - -calc.use_structure(s) - - -###-----Pseudos------ - -# If True, load the pseudos from the family specified below -# Otherwise, use static files provided -auto_pseudos = False - -if auto_pseudos: - valid_pseudo_groups = PsfData.get_psf_groups(filter_elements=elements) - - try: - pseudo_family = sys.argv[3] - except IndexError: - print >> sys.stderr, "Error, auto_pseudos set to True. You therefore need to pass as second parameter" - print >> sys.stderr, "the pseudo family name." - print >> sys.stderr, "Valid PSF families are:" - print >> sys.stderr, "\n".join("* {}".format(i.name) for i in valid_pseudo_groups) - sys.exit(1) - - try: - PsfData.get_psf_group(pseudo_family) - except NotExistent: - print >> sys.stderr, "auto_pseudos is set to True and pseudo_family='{}',".format(pseudo_family) - print >> sys.stderr, "but no group with such a name found in the DB." - print >> sys.stderr, "Valid PSF groups are:" - print >> sys.stderr, ",".join(i.name for i in valid_pseudo_groups) - sys.exit(1) - - -if auto_pseudos: - try: - calc.use_pseudos_from_family(pseudo_family) - print "Pseudos successfully loaded from family {}".format(pseudo_family) - except NotExistent: - print ("Pseudo or pseudo family not found. You may want to load the " - "pseudo family, or set auto_pseudos to False.") - raise -else: - raw_pseudos = [("Si.psf", 'Si'), - ("H.psf", 'H')] - - for fname, kinds, in raw_pseudos: - absname = os.path.realpath(os.path.join(os.path.dirname(__file__), - "data",fname)) - pseudo, created = PsfData.get_or_create(absname,use_first=True) - if created: - print "Created the pseudo for {}".format(kinds) - else: - print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) - - # Attach pseudo node to the calculation - calc.use_pseudo(pseudo,kind=kinds) - - -##-----Parameters----------- - -parameters = ParameterData(dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'spinpolarized': True, - 'meshcutoff': '40.000 Ry', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 3, - 'md-maxcgdispl': '0.1 Ang', - 'md-maxforcetol': '0.04 eV/Ang' - }) -calc.use_parameters(parameters) - -##-----Basis--------- - -basis = ParameterData(dict={ + codename = 'Siesta4.0.1@kelvin' + +#The code +code = load_code(codename) + +#The structure. Si diamond structure +alat = 5.430 # angstrom +cell = [ + [ + 0.5 * alat, + 0.5 * alat, + 0., + ], + [ + 0., + 0.5 * alat, + 0.5 * alat, + ], + [ + 0.5 * alat, + 0., + 0.5 * alat, + ], +] +#The atom positions were originally given in the "ScaledCartesian" format +#but standard for aiida structures is Cartesian in Angstrom +structure = StructureData(cell=cell) +structure.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), + symbols=['Si']) +structure.append_atom(position=(0.260 * alat, 0.250 * alat, 0.250 * alat), + symbols=['Si']) + +#The parameters +parameters = Dict( + dict={ + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'max-scfiterations': 50, + 'dm-numberpulay': 4, + 'dm-mixingweight': 0.3, + 'dm-tolerance': 1.e-3, + 'Solution-method': 'diagon', + 'electronic-temperature': '25 meV', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 10, + 'md-maxcgdispl': '0.1 Ang', + 'md-maxforcetol': '0.04 eV/Ang', + 'write-forces': True, + }) + +#The basis set +basis = Dict(dict={ 'pao-energy-shift': '300 meV', '%block pao-basis-sizes': """ -Si SZP -H DZP """, -}) -calc.use_basis(basis) - -##-----k points ---------- +Si DZP +%endblock pao-basis-sizes""", + }) +#The kpoints kpoints = KpointsData() -# method mesh -kpoints_mesh = 1 -kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) -calc.use_kpoints(kpoints) - - -##----------settings---------- -# (the object settings is optional) -settings_dict={'test_key': 'test_value'} -settings = ParameterData(dict=settings_dict) - - - -if settings is not None: - calc.use_settings(settings) -#from aiida.orm.data.remote import RemoteData -#calc.set_outdir(remotedata) +kpoints.set_kpoints_mesh([4, 4, 4]) + +#The pseudopotentials +pseudos_dict = {} +raw_pseudos = [("Si.psf", ['Si'])] +for fname, kinds in raw_pseudos: + absname = op.realpath( + op.join(op.dirname(__file__), "data/sample-psf-family", fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + if created: + print("\nCreated the pseudo for {}".format(kinds)) + else: + print("\nUsing the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + for j in kinds: + pseudos_dict[j]=pseudo + +#Resources +options = { + "max_wallclock_seconds": 360, + 'withmpi': True, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 2, + } +} + + +#The submission +#All the inputs of a Siesta calculations are listed in a dictionary +inputs = { + 'structure': structure, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'kpoints': kpoints, + 'pseudos': pseudos_dict, + 'metadata': { + "label": "TestOnSiliconBulk", + 'options': options, + } +} if submit_test: - subfolder, script_filename = calc.submit_test() - print "Test_submit for calculation (uuid='{}')".format( - calc.uuid) - print "Submit file in {}".format(os.path.join( - os.path.relpath(subfolder.abspath), - script_filename - )) + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + else: - calc.store_all() - print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - calc.submit() - print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_restart.py b/aiida_siesta/examples/plugins/siesta/example_restart.py index b5f7eb7b..22535de2 100755 --- a/aiida_siesta/examples/plugins/siesta/example_restart.py +++ b/aiida_siesta/examples/plugins/siesta/example_restart.py @@ -1,26 +1,18 @@ #!/usr/bin/env runaiida # -*- coding: utf-8 -*- - from __future__ import absolute_import from __future__ import print_function -# See LICENSE and Contributors +import os.path as op +import sys +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida.engine import submit -# This script will restart a calculation that ended without -# scf convergence in the allotted number of iterations, or without geometry convergence. -# +# Script to restart a calculation, for instance the one obtained with +# example_scf_fail.py or example_geom_fail.py # Usage: -# ./test_siesta_restart.py {--send, --dont-send} PK_of_failed_calculation - -import sys, os +# ./example_restart.py {--send, --dont-send} PK_of_calculation_to_restart -from aiida.engine import submit -from aiida.orm import load_code -from aiida.common import NotExistent -from aiida_siesta.calculations.siesta import SiestaCalculation -from aiida.plugins import DataFactory - -Dict = DataFactory('dict') try: dontsend = sys.argv[1] @@ -32,60 +24,71 @@ raise IndexError except IndexError: print(("The first parameter can only be either " - "--send or --dont-send"), file=sys.stderr) + "--send or --dont-send"), + file=sys.stderr) sys.exit(1) try: - PK = int(sys.argv[2]) -except IndexError: - print(("The second parameter must be the PK of a calculation"), file=sys.stderr) + pke = sys.argv[2] + pk = int(pke) +except: + print(("The second parameter is the pk of the calculation " + "you want to restart, integer, mandatory!"), + file=sys.stderr) sys.exit(1) - -c = load_node(PK) +#Loading calculation we want to restart (old_cal), +#must be second parameter passed to the script +try: + g=load_node(pk) + if (g.process_class == SiestaCalculation): + print(("Restarting calculation {}").format(pk)) + else: + raise +except: + print(("PK you passed is not a valid PK. " + "Allowed are CalcJobNode with .process_class == SiestaCalculation")) + sys.exit(1) -print("Restarting calculation (uuid='{}')".format(c.uuid)) -print("Is excepted?: '{}'".format(c.is_excepted)) -# -# Note that this use of 'failed' does not correspond to the process state. -# -print("Is failed?: '{}'".format(c.is_failed)) -if c.is_failed: - print("Exit code: '{}'".format(c.exit_status)) - print("'{}'".format(c.exit_message)) -print(" ") -restart=c.get_builder_restart() +#Set up the a new calculation with all +#the inputs of the old one (we use the builder) +restart=g.get_builder_restart() +#The inputs of old_calc attched to restart are +#already stored!!! You can not modify them straight away +#If you want to change something you make a clone +#and reassign it to the builder. +#Here we change max-scfiterations for example newpar=restart.parameters.clone() -newpar.attributes["max-scf-iterations"]= 50 +newpar.attributes["max-scfiterations"]=32 +##In case of geometry fail, change th number of md steps: +#newpar.attributes["md-numcgsteps"]=20 restart.parameters=newpar -if c.outputs.output_parameters.attributes["variable_geometry"]: - restart.structure=c.outputs.output_structure -# The most important line. The presence of -# parent_calc_folder triggers the 'restart' operations -# in the plugin, such as the copy of the .DM and the -# addition of use-save-dm to the parameters +#We need to take care here of passing the +#output geometry of old_calc to the new calculation +if g.outputs.output_parameters.attributes["variable_geometry"]: + restart.structure=g.outputs.output_structure -restart.parent_calc_folder=c.outputs.remote_folder +#The most important line. The presence of +#parent_calc_folder triggers the real restart +#meaning the copy of the .DM and the +#addition of dm-use-saved-dm to the parameters +restart.parent_calc_folder=g.outputs.remote_folder if submit_test: - - m=restart["metadata"] - - # An attempt to clone the 'metadata' section of the object raised this error: - # Error: AttributeError: 'ProcessBuilderNamespace' object has no attribute 'clone' - # It seems that one can simply set this attributes by hand: - - m.dry_run = True - m.store_provenance = False - print("Dry run without storing provenance. See the submit_test directory") + restart.metadata.dry_run=True + restart.metadata.store_provenance=False + process = submit(restart) + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") else: - print("Calculation restarted") - - -submit(restart) + process = submit(restart) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") diff --git a/aiida_siesta/examples/plugins/siesta/example_scf_fail.py b/aiida_siesta/examples/plugins/siesta/example_scf_fail.py index 1034f188..4147f7bf 100755 --- a/aiida_siesta/examples/plugins/siesta/example_scf_fail.py +++ b/aiida_siesta/examples/plugins/siesta/example_scf_fail.py @@ -10,7 +10,7 @@ # in the allotted number of iterations. import sys -import os +import os.path as op from aiida.engine import submit from aiida.orm import load_code @@ -41,7 +41,7 @@ try: codename = sys.argv[2] except IndexError: - codename = 'siesta4.0.1@kelvin' + codename = 'Siesta4.0.1@kelvin' # #------------------Code @@ -80,7 +80,7 @@ #---------------------------------------------- options = { - "queue_name": "debug", +# "queue_name": "debug", "max_wallclock_seconds": 1700, "resources": { "num_machines": 1, @@ -134,18 +134,18 @@ kpoints.set_kpoints_mesh([kpoints_mesh, kpoints_mesh, kpoints_mesh]) #------------------------------------------------ -pseudos_list = [] -raw_pseudos = [("Si.psf", 'Si')] -for fname, kinds, in raw_pseudos: - absname = os.path.realpath( - os.path.join(os.path.dirname(__file__), "data/sample-psf-family", - fname)) +pseudos_dict = {} +raw_pseudos = [("Si.psf", ['Si'])] +for fname, kinds in raw_pseudos: + absname = op.realpath( + op.join(op.dirname(__file__), "data/sample-psf-family", fname)) pseudo, created = PsfData.get_or_create(absname, use_first=True) if created: - print("Created the pseudo for {}".format(kinds)) + print("\nCreated the pseudo for {}".format(kinds)) else: - print("Using the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) - pseudos_list.append(pseudo) + print("\nUsing the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + for j in kinds: + pseudos_dict[j]=pseudo #--------------------------------------------- @@ -155,9 +155,7 @@ 'code': code, 'basis': basis, 'kpoints': kpoints, - 'pseudos': { - 'Si': pseudos_list[0], - }, + 'pseudos': pseudos_dict, 'metadata': { 'options': options, 'label': "Bulk Si short scf cycle" diff --git a/aiida_siesta/examples/plugins/siesta/example_soc_bands.py b/aiida_siesta/examples/plugins/siesta/example_soc_bands.py index 705b04fd..bd8eef31 100755 --- a/aiida_siesta/examples/plugins/siesta/example_soc_bands.py +++ b/aiida_siesta/examples/plugins/siesta/example_soc_bands.py @@ -39,7 +39,7 @@ try: codename = sys.argv[2] except IndexError: - codename = 'Siesta4.0.1@kelvin' + codename = 'Siesta4.1-b3@kelvin' ##-------------------Structure----------------------------------- ##Manually set the structure, all the quantities must be in Ang. @@ -114,23 +114,31 @@ ##This calls BandLine in siesta bandskpoints = result['explicit_kpoints'] -pseudos_list = [] -raw_pseudos = [("Ge.psf", 'Ge')] -for fname, kind in raw_pseudos: + +# Pseudopotentials +pseudos_dict = {} +raw_pseudos = [("Ge.psf", ['Ge'])] +for fname, kinds in raw_pseudos: absname = op.realpath( op.join(op.dirname(__file__), "data/sample-psf-family", fname)) pseudo, created = PsfData.get_or_create(absname, use_first=True) if created: - print("\nCreated the pseudo for {}".format(kind)) + print("\nCreated the pseudo for {}".format(kinds)) else: - print("\nUsing the pseudo for {} from DB: {}".format(kind, pseudo.pk)) - pseudos_list.append(pseudo) + print("\nUsing the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + for j in kinds: + pseudos_dict[j]=pseudo + + options = { - "max_wallclock_seconds": 600, +# "queue_name": "DevQ", +# 'account' : "tcphy107c", + "max_wallclock_seconds": 1200, + "withmpi" : True, "resources": { "num_machines": 1, - "num_mpiprocs_per_machine": 1, + "num_mpiprocs_per_machine": 2, } } @@ -141,9 +149,7 @@ 'basis': basis, 'kpoints': kpoints, 'bandskpoints': bandskpoints, - 'pseudos': { - 'Ge': pseudos_list[0], - }, + 'pseudos': pseudos_dict, 'metadata': { "label": "Ge band-structure with SOC", 'options': options, diff --git a/aiida_siesta/examples/plugins/siesta/example_varcell.py b/aiida_siesta/examples/plugins/siesta/example_varcell.py index 3bb6b72e..63ec1016 100755 --- a/aiida_siesta/examples/plugins/siesta/example_varcell.py +++ b/aiida_siesta/examples/plugins/siesta/example_varcell.py @@ -1,23 +1,16 @@ #!/usr/bin/env runaiida # -*- coding: utf-8 -*- -__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved." -__license__ = "MIT license, see LICENSE.txt file" -__version__ = "0.7.0" -__contributors__ = "Andrea Cepellotti, Victor Garcia-Suarez, Alberto Garcia" - +from __future__ import absolute_import +from __future__ import print_function +import os.path as op import sys -import os - -from aiida.common.example_helpers import test_and_get_code -from aiida.common.exceptions import NotExistent - -################################################################ -PsfData = DataFactory('siesta.psf') -ParameterData = DataFactory('parameter') -KpointsData = DataFactory('array.kpoints') -StructureData = DataFactory('structure') +from aiida.engine import submit +from aiida.orm import load_code +from aiida.orm import (Dict, StructureData, KpointsData) +from aiida_siesta.calculations.siesta import SiestaCalculation +from aiida_siesta.data.psf import PsfData try: dontsend = sys.argv[1] @@ -28,142 +21,128 @@ else: raise IndexError except IndexError: - print >> sys.stderr, ("The first parameter can only be either " - "--send or --dont-send") + print(("The first parameter can only be either " + "--send or --dont-send"), + file=sys.stderr) sys.exit(1) try: codename = sys.argv[2] except IndexError: - codename = 'Siesta-4.0@rinaldo' - -# If True, load the pseudos from the family specified below -# Otherwise, use static files provided -auto_pseudos = True - -queue = None -settings = None - -code = test_and_get_code(codename, expected_code_type='siesta.siesta') - -alat = 5.430 # angstrom -cell = [[0.5*alat, 0.5*alat, 0.,], - [0., 0.5*alat, 0.5*alat,], - [0.5*alat, 0., 0.5*alat,], - ] - -# Si -# This was originally given in the "ScaledCartesian" format -# -s = StructureData(cell=cell) -s.append_atom(position=(0.000*alat,0.000*alat,0.000*alat),symbols=['Si']) -s.append_atom(position=(0.250*alat,0.250*alat,0.250*alat),symbols=['Si']) - - -elements = list(s.get_symbols_set()) - -if auto_pseudos: - valid_pseudo_groups = PsfData.get_psf_groups(filter_elements=elements) - - try: - #pseudo_family = sys.argv[3] - pseudo_family = 'lda-ag' - except IndexError: - print >> sys.stderr, "Error, auto_pseudos set to True. You therefore need to pass as second parameter" - print >> sys.stderr, "the pseudo family name." - print >> sys.stderr, "Valid PSF families are:" - print >> sys.stderr, "\n".join("* {}".format(i.name) for i in valid_pseudo_groups) - sys.exit(1) - - try: - PsfData.get_psf_group(pseudo_family) - except NotExistent: - print >> sys.stderr, "auto_pseudos is set to True and pseudo_family='{}',".format(pseudo_family) - print >> sys.stderr, "but no group with such a name found in the DB." - print >> sys.stderr, "Valid PSF groups are:" - print >> sys.stderr, ",".join(i.name for i in valid_pseudo_groups) - sys.exit(1) - -parameters = ParameterData(dict={ - 'xc-functional': 'LDA', - 'xc-authors': 'CA', - 'max-scfiterations': 50, - 'dm-numberpulay': 4, - 'dm-mixingweight': 0.3, - 'dm-tolerance': 1.e-3, - 'solution-method': 'diagon', - 'electronic-temperature': '25 meV', - 'md-typeofrun': 'cg', - 'md-numcgsteps': 20, - 'md-variablecell': True, - 'md-maxforcetol': '0.04 eV/Ang' - }) - -basis = ParameterData(dict={ + codename = 'Siesta4.0.1@kelvin' + +#The code +code = load_code(codename) + +#The structure. Si diamond structure +alat = 5.430 # angstrom +cell = [ + [ + 0.5 * alat, + 0.5 * alat, + 0., + ], + [ + 0., + 0.5 * alat, + 0.5 * alat, + ], + [ + 0.5 * alat, + 0., + 0.5 * alat, + ], +] +#The atom positions were originally given in the "ScaledCartesian" format +#but standard for aiida structures is Cartesian in Angstrom +structure = StructureData(cell=cell) +structure.append_atom(position=(0.000 * alat, 0.000 * alat, 0.000 * alat), + symbols=['Si']) +structure.append_atom(position=(0.260 * alat, 0.250 * alat, 0.250 * alat), + symbols=['Si']) + +#The parameters +parameters = Dict( + dict={ + 'xc-functional': 'LDA', + 'xc-authors': 'CA', + 'max-scfiterations': 50, + 'dm-numberpulay': 4, + 'dm-mixingweight': 0.3, + 'dm-tolerance': 1.e-3, + 'Solution-method': 'diagon', + 'electronic-temperature': '25 meV', + 'md-typeofrun': 'cg', + 'md-numcgsteps': 16, + 'md-maxcgdispl': '0.1 Ang', + 'md-maxforcetol': '0.04 eV/Ang', + 'md-variablecell': True, + 'write-forces': True, + }) + +#The basis set +basis = Dict(dict={ 'pao-energy-shift': '300 meV', '%block pao-basis-sizes': """ -Si SZP """, -}) +Si DZP +%endblock pao-basis-sizes""", + }) +#The kpoints kpoints = KpointsData() - -# method mesh -kpoints_mesh = 4 -kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) - -calc = code.new_calc() -calc.label = "Si bulk" -calc.description = "Test calculation with the Siesta code. Si bulk varcell" -calc.set_max_wallclock_seconds(30*60) # 30 min - -#------------ clarify this -calc.set_resources({"num_machines": 1}) - -calc.use_structure(s) -calc.use_parameters(parameters) -calc.use_basis(basis) - -if auto_pseudos: - try: - calc.use_pseudos_from_family(pseudo_family) - print "Pseudos successfully loaded from family {}".format(pseudo_family) - except NotExistent: - print ("Pseudo or pseudo family not found. You may want to load the " - "pseudo family, or set auto_pseudos to False.") - raise -else: - raw_pseudos = [("Si.psf", 'Si')] - - for fname, kinds, in raw_pseudos: - absname = os.path.realpath(os.path.join(os.path.dirname(__file__), - "data",fname)) - pseudo, created = PsfData.get_or_create(absname,use_first=True) - if created: - print "Created the pseudo for {}".format(kinds) - else: - print "Using the pseudo for {} from DB: {}".format(kinds,pseudo.pk) - - # Attach pseudo node to the calculation - calc.use_pseudo(pseudo,kind=kinds) - -calc.use_kpoints(kpoints) - -if settings is not None: - calc.use_settings(settings) +kpoints.set_kpoints_mesh([4, 4, 4]) + +#The pseudopotentials +pseudos_dict = {} +raw_pseudos = [("Si.psf", ['Si'])] +for fname, kinds in raw_pseudos: + absname = op.realpath( + op.join(op.dirname(__file__), "data/sample-psf-family", fname)) + pseudo, created = PsfData.get_or_create(absname, use_first=True) + if created: + print("\nCreated the pseudo for {}".format(kinds)) + else: + print("\nUsing the pseudo for {} from DB: {}".format(kinds, pseudo.pk)) + for j in kinds: + pseudos_dict[j]=pseudo + +#Resources +options = { + "max_wallclock_seconds": 360, + 'withmpi': True, + "resources": { + "num_machines": 1, + "num_mpiprocs_per_machine": 2, + } +} + + +#The submission +#All the inputs of a Siesta calculations are listed in a dictionary +inputs = { + 'structure': structure, + 'parameters': parameters, + 'code': code, + 'basis': basis, + 'kpoints': kpoints, + 'pseudos': pseudos_dict, + 'metadata': { + "label": "TestOnSiliconBulk", + 'options': options, + } +} if submit_test: - subfolder, script_filename = calc.submit_test() - print "Test_submit for calculation (uuid='{}')".format( - calc.uuid) - print "Submit file in {}".format(os.path.join( - os.path.relpath(subfolder.abspath), - script_filename - )) + inputs["metadata"]["dry_run"] = True + inputs["metadata"]["store_provenance"] = False + process = submit(SiestaCalculation, **inputs) + print("Submited test for calculation (uuid='{}')".format(process.uuid)) + print("Check the folder submit_test for the result of the test") + else: - calc.store_all() - print "created calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) - calc.submit() - print "submitted calculation; calc=Calculation(uuid='{}') # ID={}".format( - calc.uuid,calc.dbnode.pk) + process = submit(SiestaCalculation, **inputs) + print("Submitted calculation; ID={}".format(process.pk)) + print("For information about this calculation type: verdi process show {}". + format(process.pk)) + print("For a list of running processes type: verdi process list") From 219f435a2252bf80bf6ee5ee0992dcb9328b1c5a Mon Sep 17 00:00:00 2001 From: Bosoni Date: Wed, 13 Nov 2019 17:25:44 +0100 Subject: [PATCH 08/10] Added restart documentation In the previous commit I forgot to modify the documentation regarding the restart part --- aiida_siesta/docs/plugins/siesta.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index d0dbcb1d..892c0628 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -414,8 +414,7 @@ Restarts -------- A restarting capability is implemented through the optional input -**parent_calc_folder**, :py:class:`RemoteData ` - +**parent_calc_folder**, :py:class:`RemoteData `, which represents the remote scratch folder for a previous calculation. The density-matrix file is copied from the old calculation scratch @@ -425,7 +424,7 @@ This approach enables continuation of runs which have failed due to lack of time or insufficient convergence in the allotted number of steps. -Examples are in ... +An informative example is example_restart.py in the folder aiida_siesta/examples/plugins/siesta. .. _siesta-advanced-features: @@ -467,6 +466,8 @@ those files as a list as follows:: 'additional_retrieve_list': ['aiida.EIG', 'aiida.ORB_INDX'], } +See for example example_ldos.py in aiida_siesta/examples/plugins/siesta. + .. _aiida guidelines: https://aiida-core.readthedocs.io/en/latest/get_started/computers.html .. _HPKOT paper: http://dx.doi.org/10.1016/j.commatsci.2016.10.015 .. _aiida documentation: https://aiida.readthedocs.io/projects/aiida-core/en/latest/apidoc/aiida.tools.html#aiida.tools.get_explicit_kpoints_path From cc41c3f9c99303f145545e9e5c5461d9a7bc8ff7 Mon Sep 17 00:00:00 2001 From: Bosoni Date: Fri, 15 Nov 2019 14:33:35 +0100 Subject: [PATCH 09/10] Introducing changes after Alberto's comments Few changes in the documentation following Alberto's suggestions --- aiida_siesta/docs/installation.rst | 4 +-- aiida_siesta/docs/plugins/siesta.rst | 51 ++++++++++++++-------------- 2 files changed, 28 insertions(+), 27 deletions(-) diff --git a/aiida_siesta/docs/installation.rst b/aiida_siesta/docs/installation.rst index 8e9ebc6f..0559aa48 100644 --- a/aiida_siesta/docs/installation.rst +++ b/aiida_siesta/docs/installation.rst @@ -14,10 +14,10 @@ directory: As a pre-requisite, this will install an appropriate version of the aiida_core python framework. -.. important:: Next, do not forget to run the following command +.. important:: Next, do not forget to run the following commands :: reentry scan -r aiida - verd daemon restart + verdi daemon restart diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index 892c0628..e97e284b 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -63,7 +63,7 @@ aiida_siesta/examples/plugins/siesta. as internal units, the cell and atom positions must be specified in Angstrom. The :py:class:`StructureData ` can also import - ase structures or pymatgen structures. This two tools can be used to load + ase structures or pymatgen structures. These two tools can be used to load structure from files. See example example_cif_bands.py * **parameters**, class :py:class:`Dict `, *Mandatory* @@ -108,7 +108,7 @@ aiida_siesta/examples/plugins/siesta. import os from aiida_siesta.data.psf import PsfData - pseudo_file_to_species_map = [ ("C.psf", ['C', 'Cred']),("H.psf", 'H')] + pseudo_file_to_species_map = [ ("C.psf", ['C', 'Cred']),("H.psf", ['H'])] pseudos_dict = {} for fname, kinds, in pseudo_file_to_species_map: absname = os.path.realpath(os.path.join("path/to/file",fname)) @@ -118,7 +118,7 @@ aiida_siesta/examples/plugins/siesta. Alternatively, a pseudo for every atomic species can be set with the **use_pseudos_from_family** method, if a family of pseudopotentials - has been installed. For an example see example_psf_family.py + has been installed. For an example see example_psf_family.py .. note:: The verdi command-line interface now supports entry points defined by external packages. We have implemented `verdi data @@ -142,12 +142,9 @@ aiida_siesta/examples/plugins/siesta. from aiida.orm import Dict basis_dict = { - 'pao-basistype': - 'split', - 'pao-splitnorm': - 0.150, - 'pao-energyshift': - '0.020 Ry', + 'pao-basistype':'split', + 'pao-splitnorm': 0.150, + 'pao-energyshift': '0.020 Ry', '%block pao-basis-sizes': """ C SZP @@ -159,7 +156,8 @@ aiida_siesta/examples/plugins/siesta. basis = Dict(dict=basis_dict) In case no basis is set, the Siesta calculation will not include - any basis specification and it will run with the default DZP. + any basis specification and it will run with the default Basis: DZP + plus (many) other defaults. * **kpoints**, class :py:class:`KpointsData `, *Optional* @@ -168,8 +166,9 @@ aiida_siesta/examples/plugins/siesta. yet for Siesta's kgrid-cutoff keyword:: from aiida.orm import KpointsData kpoints=KpointsData() - kpoints_mesh = 5 - kpoints.set_kpoints_mesh([kpoints_mesh,kpoints_mesh,kpoints_mesh]) + kp_mesh = 5 + mesh_displ = 0.5 #optional + kpoints.set_kpoints_mesh([kp_mesh,kp_mesh,kp_mesh],[mesh_displ,mesh_displ,mesh_displ]) If this node is not present, only the Gamma point is used for sampling. @@ -191,7 +190,7 @@ aiida_siesta/examples/plugins/siesta. bandskpoints.set_cell(structure.cell, structure.pbc) kpp = [(0.500, 0.250, 0.750), (0.500, 0.500, 0.500), (0., 0., 0.)] bandskpoints.set_kpoints(kpp) - In this case the Siesta input will present the BandPoints block. + In this case the Siesta input will use the BandPoints block. Alternatively (recommended) the high-symmetry path associated to the structure under investigation can be @@ -292,9 +291,9 @@ To run the calculation in an interactive way:: Here the results variable will contain a dictionary containing all the nodes that were produced as output. -Another option is to submit it to the deamon:: +Another option is to submit it to the daemon:: - from aiida.engine import run + from aiida.engine import submit calc = submit(builder) In this case, calc is the calculation node and not the results dictionary. @@ -308,30 +307,32 @@ In this case, calc is the calculation node and not the results dictionary. is not mandatory. The inputs can be provided as keywords argument when you launch the calculation, passing the calculation class as the first argument:: run(SiestaCalculation, structure=s, pseudos=pseudos, kpoints = kpoints, ...) + same syntax for the command ``submit``. A large set of examples covering some standard cases are in the folder aiida_siesta/examples/plugins/siesta. They can be run with:: - runaiida example_name.py {--send, --dont-send} + runaiida example_name.py {--send, --dont-send} code@computer The parameter --dont-send will activate the "dry run" option. In that case a test folder (submit_test) will be created, containing all the files that aiida generates automatically. The parameter --send will submit the example to -the daemon. -One of the two parameter needs to be present to run the script. Optionally, -a second argument containing the name of the code (code@computer) to use -can be passed to the script. Alternatively the name of the code can be changed -inside the script. +the daemon. One of the two options needs to be present to run the script. +The second argument contains the name of the code (code@computer) to use +in the calculation. It must be a previously set up code, corresponding to +a siesta executable. Outputs ------- There are several output nodes that can be created by the plugin, according to the calculation details. All output nodes can be -accessed with the ``calculation.out`` method. +accessed with the ``calculation.outuputs`` method. -The output parser takes advantage of the structured output available -in Siesta as a Chemical Markup Language (CML) file. The CML-writer -functionality should be compiled in and active in the run! +.. The output parser takes advantage of the structured output available +.. in Siesta as a Chemical Markup Language (CML) file. The CML-writer +.. functionality should be compiled in Siesta. AiiDA then takes care automitically +.. to include the right keywords in the siesta.fdf in order to prodeuce the +.. CML file. * **output_parameters** :py:class:`Dict ` From b351049e0dab2b92a08d60de501e8316ee6b55fc Mon Sep 17 00:00:00 2001 From: Bosoni Date: Mon, 18 Nov 2019 15:03:48 +0100 Subject: [PATCH 10/10] More info on SeeK-path and typo fixing Added few lines on the Node regarding SeeK-path. --- aiida_siesta/docs/plugins/siesta.rst | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/aiida_siesta/docs/plugins/siesta.rst b/aiida_siesta/docs/plugins/siesta.rst index e97e284b..1300b5b1 100644 --- a/aiida_siesta/docs/plugins/siesta.rst +++ b/aiida_siesta/docs/plugins/siesta.rst @@ -208,9 +208,14 @@ aiida_siesta/examples/plugins/siesta. calculation. .. note:: 'get_explicit_kpoints_path' make use of "SeeK-path". - Please cite the `HPKOT paper`_ if you use this tool. - - .. warning:: as explained in the `aiida documentation`_, SeekPath + Please cite the `HPKOT paper`_ if you use this tool. "SeeK-path" + is a external utility, not a requirement for aiida-core, therefore + it is not available by default. It can be easily installed using + ``pip install seekpath``. "SeeK-path" allows to + determine canonical unit cells and k-point information in an easy + way. For more general information, refer to the `SeeK-path documentation`_. + + .. warning:: as explained in the `aiida documentation`_, "SeeK-path" might modify the structure to follow particular conventions and the generated kpoints might only apply on the internally generated 'primitive_structure' and not @@ -326,13 +331,8 @@ Outputs There are several output nodes that can be created by the plugin, according to the calculation details. All output nodes can be -accessed with the ``calculation.outuputs`` method. +accessed with the ``calculation.outputs`` method. -.. The output parser takes advantage of the structured output available -.. in Siesta as a Chemical Markup Language (CML) file. The CML-writer -.. functionality should be compiled in Siesta. AiiDA then takes care automitically -.. to include the right keywords in the siesta.fdf in order to prodeuce the -.. CML file. * **output_parameters** :py:class:`Dict ` @@ -469,6 +469,7 @@ those files as a list as follows:: See for example example_ldos.py in aiida_siesta/examples/plugins/siesta. +.. _SeeK-path documentation: https://seekpath.readthedocs.io/en/latest/ .. _aiida guidelines: https://aiida-core.readthedocs.io/en/latest/get_started/computers.html .. _HPKOT paper: http://dx.doi.org/10.1016/j.commatsci.2016.10.015 .. _aiida documentation: https://aiida.readthedocs.io/projects/aiida-core/en/latest/apidoc/aiida.tools.html#aiida.tools.get_explicit_kpoints_path