Adding ENVIRON namelists #703
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| # -*- coding: utf-8 -*- | ||
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| from aiida import orm | ||
| from aiida.engine import run, submit | ||
| import numpy as np | ||
| from ase import Atoms | ||
| from ase import units | ||
| """ | ||
| Calculation that recreates the environ calculation of | ||
| CO on Pt(111) with a unit charge | ||
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| More details about the solvation models and potential corrections | ||
| can be found here: | ||
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| O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136,064102 (2012). | ||
| I. Dabo et al. Phys.Rev. B 77, 115139 (2008) | ||
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| This system is taken directly from Example04 in the | ||
| examples folder from Environ | ||
| """ | ||
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| def runner(code, structure): | ||
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| ## Base calculation for testing | ||
| PwBaseWorkChain = WorkflowFactory('quantumespresso.pw.base') | ||
| builder = PwBaseWorkChain.get_builder() | ||
| builder.pw.structure = structure | ||
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| builder.metadata.label = 'Single point environ' | ||
| builder.metadata.description = 'Testing calculation with environ for Pt(111) + CO' | ||
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| KpointsData = DataFactory('array.kpoints') | ||
| kpoints = KpointsData() | ||
| kpoints.set_kpoints_mesh([1, 1, 1]) # Not physical just a test | ||
| builder.kpoints = kpoints | ||
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| family = load_group('SSSP/1.1/PBE/efficiency') | ||
| builder.pw.pseudos = family.get_pseudos(structure=structure) | ||
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| calculation = { | ||
| 'CONTROL': { | ||
| 'calculation': 'scf', | ||
| 'tprnfor': True, | ||
| }, | ||
| 'SYSTEM': { | ||
| 'ecutwfc': 35, | ||
| 'ecutrho': 280, | ||
| 'occupations': 'smearing', | ||
| 'smearing': 'cold', | ||
| 'degauss': 0.03, | ||
| 'tot_charge': 1, | ||
| }, | ||
| 'ELECTRONS': { | ||
| 'conv_thr': 5e-9, | ||
| 'electron_maxstep': 200, | ||
| 'mixing_beta': 0.2, | ||
| 'mixing_ndim': 15, | ||
| 'diagonalization': 'david', | ||
| }, | ||
| } | ||
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| environ_calculation = { | ||
| 'ENVIRON': { | ||
| 'verbose': 0, | ||
| 'environ_thr': 1.0, | ||
| 'environ_type': 'input', | ||
| 'env_static_permittivity': 1, | ||
| 'env_surface_tension': 0.0, | ||
| 'env_pressure': 0.0, | ||
| 'env_electrostatic': True, | ||
| }, | ||
| 'BOUNDARY': { | ||
| 'solvent_mode': 'full', | ||
| }, | ||
| 'ELECTROSTATIC': { | ||
| 'pbc_correction': 'parabolic', | ||
| 'pbc_dim': 2, | ||
| 'pbc_axis': 3, | ||
| 'tol': 5e-13, | ||
| } | ||
| } | ||
| # these are the main cube files that could potentially be parsed | ||
| # if the verbosity is set to 2 or higher | ||
| # environ_calculation['additional_retrieve_list'] = ['epsilon.cube', \ | ||
| # 'vreference.cube', 'velectrostatic.cube', 'vsoftcavity.cube', \ | ||
| # 'electrons.cube', 'charges.cube', 'smeared_ions.cube'] | ||
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| builder.pw.parameters = orm.Dict(dict=calculation) | ||
| builder.pw.settings = orm.Dict(dict=environ_calculation) | ||
| builder.pw.metadata.options.resources = {'num_machines': 1} | ||
| builder.pw.metadata.options.max_wallclock_seconds = 5 * 60 | ||
| builder.pw.code = code | ||
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| calculation = submit(builder) | ||
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| if __name__ == '__main__': | ||
| code = load_code('insert-code-here') | ||
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| StructureData = DataFactory('structure') | ||
| # these are the original coordinates for the Pt-CO system | ||
| positions = [ | ||
| [5.335084148, 4.646723426, 12.901029877], | ||
| [5.335009643, 4.619623254, 15.079854269], | ||
| [8.061327071, 0.098057998, 8.992142901], | ||
| [2.608989366, 0.098058283, 8.992140585], | ||
| [0.000036609, 4.720846294, 8.968756935], | ||
| [5.335159557, 4.721612729, 9.380196435], | ||
| [0.000041121, 7.802951963, 4.604626508], | ||
| [5.335161233, 7.697749113, 4.753489408], | ||
| [2.697860636, 3.152173889, 4.688412329], | ||
| [7.972463687, 3.152174491, 4.688415209], | ||
| ] | ||
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| ## setting up the system with ASE | ||
| ## notice the units that are being used | ||
| atoms = Atoms('COPt8') | ||
| atoms.set_positions(np.array(positions) * units.Bohr) | ||
| atoms.set_pbc([True, True, True]) | ||
| a = 10.6881 * units.Bohr | ||
| b = 0.866025 * a * units.Bohr | ||
| c = 3.95422 * a * units.Bohr | ||
| atoms.set_cell([a, b, c]) | ||
| structure = StructureData(ase=atoms) | ||
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| runner(code=code, structure=structure) |
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@@ -73,7 +73,7 @@ def test_pw_ibrav( | |
| calc_info = generate_calc_job(fixture_sandbox, entry_point_name, inputs) | ||
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| cmdline_params = ['-in', 'aiida.in'] | ||
| local_copy_list = [(upf.uuid, upf.filename, './pseudo/Si.upf')] | ||
| retrieve_list = ['aiida.out', './out/aiida.save/data-file-schema.xml', './out/aiida.save/data-file.xml'] | ||
| retrieve_temporary_list = [['./out/aiida.save/K*[0-9]/eigenval*.xml', '.', 2]] | ||
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@@ -250,3 +250,37 @@ def test_pw_parallelization_duplicate_cmdline_flag(fixture_sandbox, generate_cal | |
| with pytest.raises(InputValidationError) as exc: | ||
| generate_calc_job(fixture_sandbox, entry_point_name, inputs) | ||
| assert 'Conflicting' in str(exc.value) | ||
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| def test_environ_namelists(fixture_sandbox, generate_calc_job, generate_inputs_pw, file_regression): | ||
| """Test that Environ does not change the contents of the pw file created.""" | ||
| entry_point_name = 'quantumespresso.pw' | ||
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| inputs = generate_inputs_pw() | ||
| inputs['settings'] = orm.Dict( | ||
| dict={ | ||
| 'ENVIRON': { | ||
| 'electrolyte_linearized': True, | ||
| 'environ_type': 'input', | ||
| }, | ||
| 'BOUNDARY': { | ||
| 'solvent_mode': 'electronic', | ||
| 'electrolyte_mode': 'electronic', | ||
| }, | ||
| 'ELECTROSTATIC': { | ||
| 'pbc_correction': 'parabolic', | ||
| } | ||
| }, | ||
| ) | ||
| generate_calc_job(fixture_sandbox, entry_point_name, inputs) | ||
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There was a problem hiding this comment. This test is not actually yet testing that the namelists are (properly) generates. The The There was a problem hiding this comment. Hi @sphuber - thanks a lot for the comments! I have a few questions about how these tests work. I have added in Regarding the parser, I modeled the Environ test after the There was a problem hiding this comment. If you just add the
No, it doesn't run the calculation. I set up the framework for these parser tests that it simply mocks an already completed calculation with outputs taking from the test directory. Each test has its own folder that corresponds to the name of the test. So all you have to do is add a folder for your test with the output files of a run you did manually with the environ module enabled. There was a problem hiding this comment. Thanks a lot! So I think I understand now how the tests for the calculations work (and have updated the latest commit with the right files). The same thing seems to work for the parser, but I am not sure I am testing this properly. All inputs to Environ would be passed through the settings, so I am not sure if this information is included in the yml that is generated. |
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| with fixture_sandbox.open('aiida.in') as handle: | ||
| input_written = handle.read() | ||
| with fixture_sandbox.open('environ.in') as handle: | ||
| environ_written = handle.read() | ||
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| # Checks on the files written to the sandbox folder as raw input | ||
| assert sorted(fixture_sandbox.get_content_list()) == sorted(['aiida.in', 'pseudo', 'out', 'environ.in']) | ||
| # Check the aiida.in files are written correctly | ||
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| file_regression.check(input_written, encoding='utf-8', extension='.aiida.in') | ||
| file_regression.check(environ_written, encoding='utf-8', extension='.environ.in') | ||
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| &CONTROL | ||
| calculation = 'scf' | ||
| outdir = './out/' | ||
| prefix = 'aiida' | ||
| pseudo_dir = './pseudo/' | ||
| verbosity = 'high' | ||
| / | ||
| &SYSTEM | ||
| ecutrho = 2.4000000000d+02 | ||
| ecutwfc = 3.0000000000d+01 | ||
| ibrav = 0 | ||
| nat = 2 | ||
| ntyp = 1 | ||
| / | ||
| &ELECTRONS | ||
| / | ||
| ATOMIC_SPECIES | ||
| Si 28.0855 Si.upf | ||
| ATOMIC_POSITIONS angstrom | ||
| Si 0.0000000000 0.0000000000 0.0000000000 | ||
| Si 1.3575000000 1.3575000000 1.3575000000 | ||
| K_POINTS automatic | ||
| 2 2 2 0 0 0 | ||
| CELL_PARAMETERS angstrom | ||
| 2.7150000000 2.7150000000 0.0000000000 | ||
| 2.7150000000 0.0000000000 2.7150000000 | ||
| 0.0000000000 2.7150000000 2.7150000000 |
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| &ENVIRON | ||
| electrolyte_linearized = .true. | ||
| environ_type = 'input' | ||
| / | ||
| &BOUNDARY | ||
| electrolyte_mode = 'electronic' | ||
| solvent_mode = 'electronic' | ||
| / | ||
| &ELECTROSTATIC | ||
| pbc_correction = 'parabolic' | ||
| / |
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Note that using mutable objects (as a
dictis) for function defaults is dangerous. The reason is that the default can actually change if it is mutated. Rather, you should definesettings=Noneand then in the function body you callsettings = settings or {}which will assign the empty dict if it isNone.There was a problem hiding this comment.
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I see, that makes sense, good to know - thanks!