From d7a88c0e1701fc3056fdc46055135c85116684ce Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 31 May 2023 09:02:03 +0000 Subject: [PATCH 01/32] `HpCalculation`: add more exit codes Two exit codes are added, for which a possible handler can be implemented in the future. --- .../calculations/hp.py | 4 +++ src/aiida_quantumespresso_hp/parsers/hp.py | 26 ++++++++++++++++--- .../parsers/parse_raw/hp.py | 2 ++ .../hp/failed_incompatible_fft_grid/aiida.out | 7 +++++ .../hp/failed_missing_chi_matrices/aiida.out | 7 +++++ tests/parsers/test_hp.py | 2 ++ 6 files changed, 44 insertions(+), 4 deletions(-) create mode 100644 tests/parsers/fixtures/hp/failed_incompatible_fft_grid/aiida.out create mode 100644 tests/parsers/fixtures/hp/failed_missing_chi_matrices/aiida.out diff --git a/src/aiida_quantumespresso_hp/calculations/hp.py b/src/aiida_quantumespresso_hp/calculations/hp.py index f4b49aa..b2fd397 100644 --- a/src/aiida_quantumespresso_hp/calculations/hp.py +++ b/src/aiida_quantumespresso_hp/calculations/hp.py @@ -191,6 +191,10 @@ def define(cls, spec): message='The electronic minimization cycle did not reach self-consistency.') spec.exit_code(462, 'ERROR_COMPUTING_CHOLESKY', message='The code failed during the cholesky factorization.') + spec.exit_code(490, 'ERROR_MISSING_CHI_MATRICES', + message='The code failed to reconstruct the full chi matrix as some chi matrices were missing') + spec.exit_code(495, 'ERROR_INCOMPATIBLE_FFT_GRID', + message='The code failed due to incompatibility between the FFT grid and the parallelization options.') @classproperty def filename_output_hubbard_chi(cls): # pylint: disable=no-self-argument diff --git a/src/aiida_quantumespresso_hp/parsers/hp.py b/src/aiida_quantumespresso_hp/parsers/hp.py index 35ed8db..1c039f2 100644 --- a/src/aiida_quantumespresso_hp/parsers/hp.py +++ b/src/aiida_quantumespresso_hp/parsers/hp.py @@ -15,16 +15,24 @@ class HpParser(Parser): def parse(self, **kwargs): """Parse the contents of the output files retrieved in the `FolderData`.""" + self.exit_code_stdout = None # pylint: disable=attribute-defined-outside-init + try: self.retrieved except exceptions.NotExistent: return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER # The stdout is always parsed by default. - exit_code = self.parse_stdout() + logs = self.parse_stdout() + + # Check for specific known problems that can cause a pre-mature termination of the calculation + exit_code = self.validate_premature_exit(logs) if exit_code: return exit_code + if self.exit_code_stdout: + return self.exit_code_stdout + # If it only initialized, then we do NOT parse the `{prefix}.Hubbard_parameters.dat`` # and the {prefix}.chi.dat files. # This check is needed since the `hp.x` routine will print the `{prefix}.Hubbard_parameters.dat` @@ -88,7 +96,7 @@ def parse_stdout(self): Parse the output parameters from the output of a Hp calculation written to standard out. - :return: optional exit code in case of an error + :return: log messages """ from .parse_raw.hp import parse_raw_output @@ -109,14 +117,24 @@ def parse_stdout(self): else: self.out('parameters', orm.Dict(parsed_data)) + # If the stdout was incomplete, most likely the job was interrupted before it could cleanly finish, so the + # output files are most likely corrupt and cannot be restarted from + if 'ERROR_OUTPUT_STDOUT_INCOMPLETE' in logs['error']: + self.exit_code_stdout = self.exit_codes.ERROR_OUTPUT_STDOUT_INCOMPLETE # pylint: disable=attribute-defined-outside-init + + return logs + + def validate_premature_exit(self, logs): + """Analyze problems that will cause a pre-mature termination of the calculation, controlled or not.""" for exit_status in [ + 'ERROR_OUT_OF_WALLTIME', 'ERROR_INVALID_NAMELIST', 'ERROR_INCORRECT_ORDER_ATOMIC_POSITIONS', 'ERROR_MISSING_PERTURBATION_FILE', 'ERROR_CONVERGENCE_NOT_REACHED', - 'ERROR_OUT_OF_WALLTIME', 'ERROR_COMPUTING_CHOLESKY', - 'ERROR_OUTPUT_STDOUT_INCOMPLETE', + 'ERROR_MISSING_CHI_MATRICES', + 'ERROR_INCOMPATIBLE_FFT_GRID', ]: if exit_status in logs['error']: return self.exit_codes.get(exit_status) diff --git a/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py b/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py index 6b4f101..3bf862c 100644 --- a/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py +++ b/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py @@ -84,6 +84,8 @@ def detect_important_message(logs, line): 'Maximum CPU time exceeded': 'ERROR_OUT_OF_WALLTIME', 'reading inputhp namelist': 'ERROR_INVALID_NAMELIST', 'problems computing cholesky': 'ERROR_COMPUTING_CHOLESKY', + 'Reconstruction problem: some chi were not found': 'ERROR_MISSING_CHI_MATRICES', + 'incompatible FFT grid': 'ERROR_INCOMPATIBLE_FFT_GRID', REG_ERROR_CONVERGENCE_NOT_REACHED: 'ERROR_CONVERGENCE_NOT_REACHED', ERROR_POSITIONS: 'ERROR_INCORRECT_ORDER_ATOMIC_POSITIONS' }, diff --git a/tests/parsers/fixtures/hp/failed_incompatible_fft_grid/aiida.out b/tests/parsers/fixtures/hp/failed_incompatible_fft_grid/aiida.out new file mode 100644 index 0000000..b8baff4 --- /dev/null +++ b/tests/parsers/fixtures/hp/failed_incompatible_fft_grid/aiida.out @@ -0,0 +1,7 @@ + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + Error in routine scale_sym_ops (3): + incompatible FFT grid + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + stopping ... diff --git a/tests/parsers/fixtures/hp/failed_missing_chi_matrices/aiida.out b/tests/parsers/fixtures/hp/failed_missing_chi_matrices/aiida.out new file mode 100644 index 0000000..12ae124 --- /dev/null +++ b/tests/parsers/fixtures/hp/failed_missing_chi_matrices/aiida.out @@ -0,0 +1,7 @@ + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + Error in routine reconstruct_full_chi (1): + Reconstruction problem: some chi were not found + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + stopping ... diff --git a/tests/parsers/test_hp.py b/tests/parsers/test_hp.py index 14d174b..159bd9f 100644 --- a/tests/parsers/test_hp.py +++ b/tests/parsers/test_hp.py @@ -225,6 +225,8 @@ def test_hp_failed_invalid_namelist(aiida_localhost, generate_calc_job_node, gen ('failed_out_of_walltime', HpCalculation.exit_codes.ERROR_OUT_OF_WALLTIME.status), ('failed_stdout_incomplete', HpCalculation.exit_codes.ERROR_OUTPUT_STDOUT_INCOMPLETE.status), ('failed_computing_cholesky', HpCalculation.exit_codes.ERROR_COMPUTING_CHOLESKY.status), + ('failed_missing_chi_matrices', HpCalculation.exit_codes.ERROR_MISSING_CHI_MATRICES.status), + ('failed_incompatible_fft_grid', HpCalculation.exit_codes.ERROR_INCOMPATIBLE_FFT_GRID.status), )) def test_failed_calculation( generate_calc_job_node, From 5b20e18eb7e5615e775df79de002a916c6da703c Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 31 May 2023 13:31:35 +0000 Subject: [PATCH 02/32] Workflows: add the `skip_relax_iterations` logic We implement the logic to skip a certain number of relax iterations. For these iterations the check on convergence is also skipped. Some fixes are also added. --- .../functions/structure_relabel_kinds.py | 2 +- .../workflows/hubbard.py | 192 ++++++++---------- .../workflows/protocols/hubbard.yaml | 1 - tests/workflows/protocols/test_hubbard.py | 2 +- .../protocols/test_hubbard/test_default.yml | 1 - tests/workflows/test_hubbard.py | 76 +++++-- 6 files changed, 146 insertions(+), 128 deletions(-) diff --git a/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py b/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py index 176c81e..0c547e6 100644 --- a/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py +++ b/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py @@ -13,7 +13,7 @@ def structure_relabel_kinds( hubbard_structure: HubbardStructureData, hubbard: Dict, - magnetization: Dict | None = None, + magnetization: dict | None = None, ) -> Dict: """Create a clone of the given structure but with new kinds, based on the new hubbard sites. diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index cdacca4..c4ab9ff 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -44,6 +44,12 @@ def get_separated_parameters( return onsites, intersites +def validate_positive(value, _): + """Validate that the value is positive.""" + if value.value < 0: + return 'the value must be positive.' + + def validate_inputs(inputs, _): """Validate the entire inputs.""" parameters = AttributeDict(inputs).scf.pw.parameters.get_dict() @@ -100,74 +106,36 @@ class SelfConsistentHubbardWorkChain(WorkChain, ProtocolMixin): @classmethod def define(cls, spec): """Define the specifications of the process.""" + # yapf: disable super().define(spec) - - spec.input('hubbard_structure', valid_type=HubbardStructureData) - spec.input( - 'tolerance_onsite', - valid_type=orm.Float, - default=lambda: orm.Float(0.1), - help=( - 'Tolerance value for self-consistent calculation of Hubbard U. ' - 'In case of DFT+U+V calculation, it refers to the diagonal elements (i.e. on-site).' - ) - ) - spec.input( - 'tolerance_intersite', - valid_type=orm.Float, - default=lambda: orm.Float(0.01), - help=( - 'Tolerance value for self-consistent DFT+U+V calculation. ' - 'It refers to the only off-diagonal elements V.' - ) - ) - spec.input( - 'skip_first_relax', - valid_type=orm.Bool, - default=lambda: orm.Bool(False), - help='If True, skip the first relaxation' - ) - spec.input( - 'relax_frequency', - valid_type=orm.Int, - required=False, - help='Integer value referring to the number of iterations to wait before performing the `relax` step.' - ) - spec.expose_inputs( - PwRelaxWorkChain, - namespace='relax', - exclude=( - 'clean_workdir', - 'structure', - ), - namespace_options={ - 'required': False, - 'populate_defaults': False, - 'help': 'Inputs for the `PwRelaxWorkChain` that, when defined, will iteratively relax the structure.' - } - ) - spec.expose_inputs(PwBaseWorkChain, namespace='scf', exclude=( - 'clean_workdir', - 'pw.structure', - )) - spec.expose_inputs( - HpWorkChain, - namespace='hubbard', - exclude=( - 'clean_workdir', - 'hp.parent_scf', - 'hp.parent_hp', - 'hp.hubbard_structure', - ) - ) - spec.input('max_iterations', valid_type=orm.Int, default=lambda: orm.Int(10)) - spec.input('meta_convergence', valid_type=orm.Bool, default=lambda: orm.Bool(False)) - spec.input( - 'clean_workdir', - valid_type=orm.Bool, - default=lambda: orm.Bool(True), - help='If `True`, work directories of all called calculation will be cleaned at the end of execution.' - ) + spec.input('hubbard_structure', valid_type=HubbardStructureData, + help=('The HubbardStructureData containing the initialized parameters for triggering ' + 'the Hubbard atoms which the `hp.x` code will perturbe.')) + spec.input('tolerance_onsite', valid_type=orm.Float, default=lambda: orm.Float(0.1), + help=('Tolerance value for self-consistent calculation of Hubbard U. ' + 'In case of DFT+U+V calculation, it refers to the diagonal elements (i.e. on-site).')) + spec.input('tolerance_intersite', valid_type=orm.Float, default=lambda: orm.Float(0.01), + help=('Tolerance value for self-consistent DFT+U+V calculation. ' + 'It refers to the only off-diagonal elements V.')) + spec.input('skip_relax_iterations', valid_type=orm.Int, required=False, validator=validate_positive, + help=('The number of iterations for skipping the `relax` ' + 'step without performing check on parameters convergence.')) + spec.input('relax_frequency', valid_type=orm.Int, required=False, validator=validate_positive, + help='Integer value referring to the number of iterations to wait before performing the `relax` step.') + spec.expose_inputs(PwRelaxWorkChain, namespace='relax', + exclude=('clean_workdir', 'structure', 'base_final_scf'), + namespace_options={'required': False, 'populate_defaults': False, + 'help': 'Inputs for the `PwRelaxWorkChain` that, when defined, will iteratively relax the structure.'}) + spec.expose_inputs(PwBaseWorkChain, namespace='scf', + exclude=('clean_workdir','pw.structure')) + spec.expose_inputs(HpWorkChain, namespace='hubbard', + exclude=('clean_workdir', 'hp.parent_scf', 'hp.parent_hp', 'hp.hubbard_structure')) + spec.input('max_iterations', valid_type=orm.Int, default=lambda: orm.Int(10), + help='Maximum number of iterations of the (relax-)scf-hp cycle.') + spec.input('meta_convergence', valid_type=orm.Bool, default=lambda: orm.Bool(False), + help='Whether performing the self-consistent cycle. If False, it will stop at the first iteration.') + spec.input('clean_workdir', valid_type=orm.Bool, default=lambda: orm.Bool(True), + help='If `True`, work directories of all called calculation will be cleaned at the end of execution.') spec.inputs.validator = validate_inputs spec.inputs['hubbard']['hp'].validator = None @@ -188,44 +156,30 @@ def define(cls, spec): ), cls.run_hp, cls.inspect_hp, - if_(cls.should_check_convergence)(cls.check_convergence,), + if_(cls.should_check_convergence)( + cls.check_convergence, + ), ), cls.run_results, ) - spec.output( - 'hubbard_structure', - valid_type=HubbardStructureData, - required=False, - help='The Hubbard structure containing the structure and associated Hubbard parameters.' - ) - - spec.exit_code( - 330, - 'ERROR_FAILED_TO_DETERMINE_PSEUDO_POTENTIAL', - message='Failed to determine the correct pseudo potential after the structure changed its kind names.' - ) - spec.exit_code( - 401, 'ERROR_SUB_PROCESS_FAILED_RECON', message='The reconnaissance PwBaseWorkChain sub process failed' - ) - spec.exit_code( - 402, - 'ERROR_SUB_PROCESS_FAILED_RELAX', - message='The PwRelaxWorkChain sub process failed in iteration {iteration}' - ) - spec.exit_code( - 403, - 'ERROR_SUB_PROCESS_FAILED_SCF', - message='The scf PwBaseWorkChain sub process failed in iteration {iteration}' - ) - spec.exit_code( - 404, 'ERROR_SUB_PROCESS_FAILED_HP', message='The HpWorkChain sub process failed in iteration {iteration}' - ) - spec.exit_code( - 405, 'ERROR_NON_INTEGER_TOT_MAGNETIZATION', + spec.output('hubbard_structure', valid_type=HubbardStructureData, required=False, + help='The Hubbard structure containing the structure and associated Hubbard parameters.') + + spec.exit_code(330, 'ERROR_FAILED_TO_DETERMINE_PSEUDO_POTENTIAL', + message='Failed to determine the correct pseudo potential after the structure changed its kind names.') + spec.exit_code(401, 'ERROR_SUB_PROCESS_FAILED_RECON', + message='The reconnaissance PwBaseWorkChain sub process failed') + spec.exit_code(402, 'ERROR_SUB_PROCESS_FAILED_RELAX', + message='The PwRelaxWorkChain sub process failed in iteration {iteration}') + spec.exit_code(403, 'ERROR_SUB_PROCESS_FAILED_SCF', + message='The scf PwBaseWorkChain sub process failed in iteration {iteration}') + spec.exit_code(404, 'ERROR_SUB_PROCESS_FAILED_HP', + message='The HpWorkChain sub process failed in iteration {iteration}') + spec.exit_code(405, 'ERROR_NON_INTEGER_TOT_MAGNETIZATION', message='The scf PwBaseWorkChain sub process in iteration {iteration}'\ - 'returned a non integer total magnetization (threshold exceeded).' - ) + 'returned a non integer total magnetization (threshold exceeded).') + # yapf: enable @classmethod def get_protocol_filepath(cls): @@ -289,12 +243,13 @@ def get_builder_from_protocol( if 'relax_frequency' in inputs: builder.relax_frequency = orm.Int(inputs['relax_frequency']) + if 'skip_relax_iterations' in inputs: + builder.skip_relax_iterations = orm.Int(inputs['skip_relax_iterations']) builder.hubbard_structure = hubbard_structure builder.relax = relax builder.scf = scf builder.hubbard = hubbard - builder.skip_first_relax = orm.Bool(inputs['skip_first_relax']) builder.tolerance_onsite = orm.Float(inputs['tolerance_onsite']) builder.tolerance_intersite = orm.Float(inputs['tolerance_intersite']) builder.max_iterations = orm.Int(inputs['max_iterations']) @@ -312,7 +267,9 @@ def setup(self): self.ctx.is_insulator = None self.ctx.is_magnetic = False self.ctx.iteration = 0 - self.ctx.skip_first_relax = self.inputs.skip_first_relax.value + self.ctx.skip_relax_iterations = 0 + if 'skip_relax_iterations' in self.inputs: + self.ctx.skip_relax_iterations = self.inputs.skip_relax_iterations.value self.ctx.relax_frequency = 1 if 'relax_frequency' in self.inputs: self.ctx.relax_frequency = self.inputs.relax_frequency.value @@ -342,23 +299,35 @@ def should_run_relax(self): if 'relax' not in self.inputs: return False - if self.ctx.skip_first_relax: - self.ctx.skip_first_relax = False # only the first one will be skipped - self.report('`skip_first_relax` is set to `True`. Skipping first relaxation.') + if self.ctx.iteration <= self.ctx.skip_relax_iterations: + self.report(( + f'`skip_relax_iterations` is set to {self.ctx.skip_relax_iterations}. ' + f'Skipping relaxation for iteration {self.ctx.iteration}.' + )) return False if self.ctx.iteration % self.ctx.relax_frequency != 0: self.report(( f'`relax_frequency` is set to {self.ctx.relax_frequency}. ' - f'Skipping relaxation for iteration {self.ctx.iteration }.' + f'Skipping relaxation for iteration {self.ctx.iteration}.' )) return False - return 'relax' in self.inputs + return True def should_check_convergence(self): """Return whether to check the convergence of Hubbard parameters.""" - return self.inputs.meta_convergence.value + if not self.inputs.meta_convergence.value: + return False + + if self.ctx.iteration <= self.ctx.skip_relax_iterations: + self.report(( + f'`skip_relax_iterations` is set to {self.ctx.skip_relax_iterations}. ' + f'Skipping convergence check for iteration {self.ctx.iteration}.' + )) + return False + + return True def should_run_iteration(self): """Return whether a new process should be run.""" @@ -601,10 +570,11 @@ def inspect_hp(self): self.report(f'hp.x in iteration {self.ctx.iteration} failed with exit status {workchain.exit_status}') return self.exit_codes.ERROR_SUB_PROCESS_FAILED_HP.format(iteration=self.ctx.iteration) - if not self.inputs.meta_convergence: + if not self.should_check_convergence(): self.ctx.current_hubbard_structure = workchain.outputs.hubbard_structure - self.report('meta convergence is switched off, so not checking convergence of Hubbard parameters.') - self.ctx.is_converged = True + if not self.inputs.meta_convergence: + self.report('meta convergence is switched off, so not checking convergence of Hubbard parameters.') + self.ctx.is_converged = True def check_convergence(self): """Check the convergence of the Hubbard parameters.""" diff --git a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml index b4aa3ad..cb32044 100644 --- a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml +++ b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml @@ -4,7 +4,6 @@ default_inputs: meta_convergence: True tolerance_onsite: 0.1 tolerance_intersite: 0.01 - skip_first_relax: False scf: kpoints_distance: 0.4 diff --git a/tests/workflows/protocols/test_hubbard.py b/tests/workflows/protocols/test_hubbard.py index 9da437b..37d0f21 100644 --- a/tests/workflows/protocols/test_hubbard.py +++ b/tests/workflows/protocols/test_hubbard.py @@ -39,7 +39,7 @@ def test_default(fixture_code, data_regression, generate_hubbard_structure, seri 'tolerance_intersite': 1 }, { - 'skip_first_relax': True + 'skip_relax_iterations': 2 }, { 'relax_frequency': 3 diff --git a/tests/workflows/protocols/test_hubbard/test_default.yml b/tests/workflows/protocols/test_hubbard/test_default.yml index 275708d..ee18383 100644 --- a/tests/workflows/protocols/test_hubbard/test_default.yml +++ b/tests/workflows/protocols/test_hubbard/test_default.yml @@ -92,6 +92,5 @@ scf: Co: Co Li: Li O: O -skip_first_relax: false tolerance_intersite: 0.01 tolerance_onsite: 0.1 diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index 41482d4..e235613 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -115,6 +115,20 @@ def test_validate_inputs_invalid_inputs(generate_workchain_hubbard, generate_inp generate_workchain_hubbard(inputs=inputs) +@pytest.mark.parametrize('parameters', ('skip_relax_iterations', 'relax_frequency')) +@pytest.mark.usefixtures('aiida_profile') +def test_validate_invalid_positve_input(generate_workchain_hubbard, generate_inputs_hubbard, parameters): + """Test `SelfConsistentHubbardWorkChain` for invalid positive inputs.""" + from aiida.orm import Int + + inputs = AttributeDict(generate_inputs_hubbard()) + inputs.update({parameters: Int(-1)}) + + match = 'the value must be positive.' + with pytest.raises(ValueError, match=match): + generate_workchain_hubbard(inputs=inputs) + + @pytest.mark.usefixtures('aiida_profile') def test_setup(generate_workchain_hubbard, generate_inputs_hubbard): """Test `SelfConsistentHubbardWorkChain.setup`.""" @@ -124,12 +138,12 @@ def test_setup(generate_workchain_hubbard, generate_inputs_hubbard): assert process.ctx.iteration == 0 assert process.ctx.relax_frequency == 1 + assert process.ctx.skip_relax_iterations == 0 assert process.ctx.current_hubbard_structure == inputs['hubbard_structure'] assert process.ctx.current_magnetic_moments is None - assert process.ctx.is_converged is False + assert not process.ctx.is_converged assert process.ctx.is_insulator is None assert not process.ctx.is_magnetic - assert not process.ctx.skip_first_relax assert not process.should_check_convergence() @@ -162,19 +176,55 @@ def test_magnetic_setup(generate_workchain_hubbard, generate_inputs_hubbard): @pytest.mark.usefixtures('aiida_profile') -def test_skip_first_relax(generate_workchain_hubbard, generate_inputs_hubbard): - """Test `SelfConsistentHubbardWorkChain` when skipping only the first relax.""" - from aiida.orm import Bool +def test_skip_relax_iterations(generate_workchain_hubbard, generate_inputs_hubbard, generate_hp_workchain_node): + """Test `SelfConsistentHubbardWorkChain` when skipping the first relax iterations.""" + from aiida.orm import Bool, Int inputs = generate_inputs_hubbard() - inputs['skip_first_relax'] = Bool(True) + inputs['skip_relax_iterations'] = Int(1) + inputs['meta_convergence'] = Bool(True) process = generate_workchain_hubbard(inputs=inputs) - process.setup() + # 1 + process.update_iteration() + assert process.ctx.skip_relax_iterations == 1 + assert process.ctx.iteration == 1 + assert not process.should_run_relax() + assert not process.should_check_convergence() + process.ctx.workchains_hp = [generate_hp_workchain_node()] + process.inspect_hp() + assert process.ctx.current_hubbard_structure == process.ctx.workchains_hp[-1].outputs.hubbard_structure + # 2 + process.update_iteration() + assert process.should_run_relax() + assert process.should_check_convergence() + # 3 + process.update_iteration() + assert process.should_run_relax() + assert process.should_check_convergence() - assert not process.should_run_relax() # skip only first one - assert process.should_run_relax() # the second one not - assert process.should_run_relax() # and the third neither! + inputs['skip_relax_iterations'] = Int(2) + process = generate_workchain_hubbard(inputs=inputs) + process.setup() + # 1 + process.update_iteration() + assert process.ctx.skip_relax_iterations == 2 + assert not process.should_run_relax() + assert not process.should_check_convergence() + process.ctx.workchains_hp = [generate_hp_workchain_node()] + process.inspect_hp() + assert process.ctx.current_hubbard_structure == process.ctx.workchains_hp[-1].outputs.hubbard_structure + # 2 + process.update_iteration() + assert not process.should_run_relax() + assert not process.should_check_convergence() + process.ctx.workchains_hp.append(generate_hp_workchain_node()) + process.inspect_hp() + assert process.ctx.current_hubbard_structure == process.ctx.workchains_hp[-1].outputs.hubbard_structure + # 3 + process.update_iteration() + assert process.should_run_relax() + assert process.should_check_convergence() @pytest.mark.usefixtures('aiida_profile') @@ -185,10 +235,9 @@ def test_relax_frequency(generate_workchain_hubbard, generate_inputs_hubbard): inputs = generate_inputs_hubbard() inputs['relax_frequency'] = Int(3) process = generate_workchain_hubbard(inputs=inputs) - process.setup() - process.update_iteration() # it updates first in the while of the outline + process.update_iteration() assert not process.should_run_relax() # skip process.update_iteration() assert not process.should_run_relax() # skip @@ -205,7 +254,8 @@ def test_should_check_convergence(generate_workchain_hubbard, generate_inputs_hu inputs = generate_inputs_hubbard() inputs['meta_convergence'] = Bool(True) process = generate_workchain_hubbard(inputs=inputs) - + process.setup() + process.update_iteration() assert process.should_check_convergence() From 9bf0ac5ec42585b894da3b02494e5fb1e23bac36 Mon Sep 17 00:00:00 2001 From: bastonero Date: Tue, 6 Jun 2023 09:22:37 +0000 Subject: [PATCH 03/32] `Parser`: fix typo in the q point regex matching --- .../parsers/parse_raw/hp.py | 2 +- .../aiida.in | 13 + .../aiida.out | 234 ++++++++++++++++++ tests/parsers/test_hp.py | 34 +++ ...p_initialization_only_mesh_more_points.yml | 4 + 5 files changed, 286 insertions(+), 1 deletion(-) create mode 100644 tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.in create mode 100644 tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.out create mode 100644 tests/parsers/test_hp/test_hp_initialization_only_mesh_more_points.yml diff --git a/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py b/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py index 6b4f101..b291af2 100644 --- a/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py +++ b/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py @@ -31,7 +31,7 @@ def parse_raw_output(stdout): detect_important_message(logs, line) # A calculation that will only perturb a single atom will only print one line - match = re.search(r'.*The grid of q-points.*\s+([0-9])+\s+q-points.*', line) + match = re.search(r'.*The grid of q-points.*\s+([0-9]+)+\s+q-points.*', line) if match: parsed_data['number_of_qpoints'] = int(match.group(1)) diff --git a/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.in b/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.in new file mode 100644 index 0000000..bd64f89 --- /dev/null +++ b/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.in @@ -0,0 +1,13 @@ +&INPUTHP + conv_thr_chi = 1.0000000000d-06 + determine_q_mesh_only = .true. + find_atpert = 3 + iverbosity = 2 + max_seconds = 3.4200000000d+03 + nq1 = 4 + nq2 = 4 + nq3 = 4 + outdir = 'out' + perturb_only_atom(13) = .true. + prefix = 'aiida' +/ diff --git a/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.out b/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.out new file mode 100644 index 0000000..a5b4b02 --- /dev/null +++ b/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.out @@ -0,0 +1,234 @@ + Program HP v.7.2 starts on 5Jun2023 at 13:54:28 + + This program is part of the open-source Quantum ESPRESSO suite + for quantum simulation of materials; please cite + "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); + "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017); + "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020); + URL http://www.quantum-espresso.org", + in publications or presentations arising from this work. More details at + http://www.quantum-espresso.org/quote + + Parallel version (MPI), running on 48 processors + + MPI processes distributed on 1 nodes + K-points division: npool = 16 + R & G space division: proc/nbgrp/npool/nimage = 3 + 24962 MiB available memory on the printing compute node when the environment starts + + + =---------------------------------------------------------------------------= + + Calculation of Hubbard parameters using the HP code based on DFPT + + Please cite the following papers when using this program: + + - HP code : Comput. Phys. Commun. 279, 108455 (2022). + + - Theory : Phys. Rev. B 98, 085127 (2018) and + + Phys. Rev. B 103, 045141 (2021). + + =-----------------------------------------------------------------------------= + + Reading xml data from directory: + + out/aiida.save/ + + IMPORTANT: XC functional enforced from input : + Exchange-correlation= PBESOL + ( 1 4 10 8 0 0 0) + Any further DFT definition will be discarded + Please, verify this is what you really want + + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 905 905 271 30463 30463 5034 + Max 906 906 271 30465 30465 5035 + Sum 2717 2717 813 91393 91393 15103 + + Using Slab Decomposition + + + Check: negative core charge= -0.000036 + Reading collected, re-writing distributed wavefunctions + + + bravais-lattice index = 0 + lattice parameter (alat) = 12.3672 (a.u.) + unit-cell volume = 1453.9300 (a.u.)^3 + number of atoms/cell = 16 + number of atomic types = 2 + kinetic-energy cut-off = 60.00 (Ry) + charge density cut-off = 240.00 (Ry) + conv. thresh. for NSCF = 1.0E-11 + conv. thresh. for chi = 1.0E-06 + Input Hubbard parameters (in eV): + V ( 1, 1) = 5.0000 + V ( 1, 229) = 0.0000 + V ( 1, 230) = 0.0000 + V ( 2, 2) = 5.0000 + V ( 2, 6) = 0.0000 + V ( 2, 405) = 0.0000 + V ( 3, 3) = 5.0000 + V ( 4, 4) = 5.0000 + V ( 5, 5) = 0.0000 + V ( 5, 34) = 0.0000 + V ( 5, 209) = 0.0000 + V ( 6, 2) = 0.0000 + V ( 6, 6) = 0.0000 + V ( 6, 209) = 0.0000 + V ( 7, 7) = 0.0000 + V ( 8, 8) = 0.0000 + V ( 9, 9) = 0.0000 + V ( 10, 10) = 0.0000 + V ( 11, 11) = 0.0000 + V ( 12, 12) = 0.0000 + V ( 13, 13) = 0.0000 + V ( 14, 14) = 0.0000 + V ( 15, 15) = 0.0000 + V ( 16, 16) = 0.0000 + + celldm(1) = 12.36723 celldm(2) = 0.00000 celldm(3) = 0.00000 + celldm(4) = 0.00000 celldm(5) = 0.00000 celldm(6) = 0.00000 + + crystal axes: (cart. coord. in units of alat) + a(1) = ( 0.5609 0.5784 0.5924 ) + a(2) = ( 0.5609 -0.5784 -0.5924 ) + a(3) = ( -0.5609 0.5784 -0.5924 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( 0.8915 0.8645 0.0000 ) + b(2) = ( 0.8915 0.0000 -0.8440 ) + b(3) = ( 0.0000 0.8645 -0.8440 ) + + Atoms inside the unit cell (Cartesian axes): + site n. atom mass positions (alat units) + 1 W 183.8400 tau( 1) = ( -0.28043 0.57835 -0.55568 ) + 2 W 183.8400 tau( 2) = ( 0.84128 0.00000 -0.03673 ) + 3 W 183.8400 tau( 3) = ( 0.28043 0.00000 -0.55450 ) + 4 W 183.8400 tau( 4) = ( 0.28043 0.57835 -0.03791 ) + 5 O 15.9994 tau( 5) = ( 0.00000 0.00000 0.00000 ) + 6 O 15.9994 tau( 6) = ( 0.56086 0.00000 0.00000 ) + 7 O 15.9994 tau( 7) = ( 0.56086 0.57835 0.00000 ) + 8 O 15.9994 tau( 8) = ( 0.00000 0.57835 0.00000 ) + 9 O 15.9994 tau( 9) = ( 0.28043 0.28397 0.03317 ) + 10 O 15.9994 tau( 10) = ( 0.28043 0.29438 -0.62558 ) + 11 O 15.9994 tau( 11) = ( -0.28043 0.29438 -0.55923 ) + 12 O 15.9994 tau( 12) = ( 0.84128 0.28397 -0.03317 ) + 13 O 15.9994 tau( 13) = ( 0.28043 0.00000 -0.87440 ) + 14 O 15.9994 tau( 14) = ( 0.28043 0.57835 0.28199 ) + 15 O 15.9994 tau( 15) = ( 0.28043 0.00000 -0.26540 ) + 16 O 15.9994 tau( 16) = ( 0.28043 0.57835 -0.32701 ) + + Atom which will be perturbed: + + 13 O 15.9994 tau(13) = ( 0.28043 0.00000 -0.87440 ) + + Reading xml data from directory: + + out/aiida.save/ + + IMPORTANT: XC functional enforced from input : + Exchange-correlation= PBESOL + ( 1 4 10 8 0 0 0) + Any further DFT definition will be discarded + Please, verify this is what you really want + + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 905 905 271 30463 30463 5034 + Max 906 906 271 30465 30465 5035 + Sum 2717 2717 813 91393 91393 15103 + + Using Slab Decomposition + + + Check: negative core charge= -0.000036 + Reading collected, re-writing distributed wavefunctions + + ===================================================================== + + PERTURBED ATOM # 13 + + site n. atom mass positions (alat units) + 13 O 15.9994 tau(13) = ( 0.28043 0.00000 -0.87440 ) + + ===================================================================== + + The perturbed atom has a type which is not unique! + Changing the type of the perturbed atom and recomputing the symmetries... + The number of symmetries is reduced : + nsym = 4 nsym_PWscf = 8 + Changing the type of the perturbed atom back to its original type... + + + The grid of q-points ( 4, 4, 4) ( 18 q-points ) : + N xq(1) xq(2) xq(3) wq + 1 0.000000000 0.000000000 0.000000000 0.015625000 + 2 0.000000000 0.216131358 -0.211002628 0.062500000 + 3 0.000000000 -0.432262716 0.422005257 0.031250000 + 4 0.222873502 0.000000000 -0.211002628 0.062500000 + 5 0.222873502 0.216131358 -0.422005257 0.125000000 + 6 0.222873502 -0.432262716 0.211002628 0.125000000 + 7 0.222873502 -0.216131358 0.000000000 0.062500000 + 8 -0.445747005 0.000000000 0.422005257 0.031250000 + 9 -0.445747005 0.216131358 0.211002628 0.125000000 + 10 -0.445747005 -0.432262716 0.844010513 0.031250000 + 11 0.445747005 0.432262716 -0.422005257 0.031250000 + 12 0.445747005 0.000000000 0.000000000 0.031250000 + 13 -0.222873502 -0.216131358 0.844010513 0.062500000 + 14 -0.222873502 0.000000000 0.633007885 0.062500000 + 15 0.000000000 0.432262716 0.000000000 0.031250000 + 16 0.000000000 -0.216131358 0.633007885 0.062500000 + 17 0.000000000 0.000000000 0.422005257 0.031250000 + 18 -0.891494009 -0.864525432 0.844010513 0.015625000 + + PRINTING TIMING FROM PWSCF ROUTINES: + + + Called by init_run: + + Called by electrons: + v_of_rho : 0.17s CPU 0.21s WALL ( 2 calls) + v_h : 0.01s CPU 0.01s WALL ( 2 calls) + v_xc : 0.17s CPU 0.20s WALL ( 2 calls) + + Called by c_bands: + + Called by sum_band: + + Called by *egterg: + + Called by h_psi: + + General routines + fft : 0.09s CPU 0.16s WALL ( 22 calls) + davcio : 0.00s CPU 0.02s WALL ( 6 calls) + + Parallel routines + + Hubbard U routines + alloc_neigh : 0.33s CPU 0.34s WALL ( 2 calls) + + init_vloc : 0.37s CPU 0.37s WALL ( 2 calls) + init_us_1 : 0.02s CPU 0.03s WALL ( 2 calls) + + PRINTING TIMING FROM HP ROUTINES: + + + PRINTING TIMING FROM LR MODULE: + + + HP : 2.09s CPU 3.79s WALL + + + This run was terminated on: 13:54:32 5Jun2023 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/tests/parsers/test_hp.py b/tests/parsers/test_hp.py index 14d174b..bca62b5 100644 --- a/tests/parsers/test_hp.py +++ b/tests/parsers/test_hp.py @@ -204,6 +204,40 @@ def test_hp_initialization_only_mesh( }) +def test_hp_initialization_only_mesh_more_points( + aiida_localhost, generate_calc_job_node, generate_parser, generate_inputs_mesh_only, data_regression, tmpdir +): + """Test an initialization only `hp.x` calculation with intersites with more points.""" + name = 'initialization_only_mesh_more_points' + entry_point_calc_job = 'quantumespresso.hp' + entry_point_parser = 'quantumespresso.hp' + + # QE generates the ``HUBBARD.dat``, but with empty values, thus we make sure the parser + # does not recognize it as a final calculation and it does not crash as a consequence. + attributes = {'retrieve_temporary_list': ['HUBBARD.dat']} + node = generate_calc_job_node( + entry_point_calc_job, + aiida_localhost, + test_name=name, + inputs=generate_inputs_mesh_only, + attributes=attributes, + retrieve_temporary=(tmpdir, ['HUBBARD.dat']) + ) + parser = generate_parser(entry_point_parser) + results, calcfunction = parser.parse_from_node(node, store_provenance=False, retrieved_temporary_folder=tmpdir) + + assert calcfunction.is_finished, calcfunction.exception + assert calcfunction.is_finished_ok, calcfunction.exit_message + assert 'parameters' in results + assert 'hubbard' not in results + assert 'hubbard_chi' not in results + assert 'hubbard_matrices' not in results + assert 'hubbard_structure' not in results + data_regression.check({ + 'parameters': results['parameters'].get_dict(), + }) + + def test_hp_failed_invalid_namelist(aiida_localhost, generate_calc_job_node, generate_parser, generate_inputs_default): """Test an `hp.x` calculation that fails because of an invalid namelist.""" name = 'failed_invalid_namelist' diff --git a/tests/parsers/test_hp/test_hp_initialization_only_mesh_more_points.yml b/tests/parsers/test_hp/test_hp_initialization_only_mesh_more_points.yml new file mode 100644 index 0000000..0194b68 --- /dev/null +++ b/tests/parsers/test_hp/test_hp_initialization_only_mesh_more_points.yml @@ -0,0 +1,4 @@ +parameters: + hubbard_sites: + '13': O + number_of_qpoints: 18 From 481a45512bcb8ac76dc16feb02d2eef4f68078a8 Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 31 May 2023 09:02:03 +0000 Subject: [PATCH 04/32] `HpCalculation`: add more exit codes Two exit codes are added, for which a possible handler can be implemented in the future. --- .../calculations/hp.py | 4 +++ src/aiida_quantumespresso_hp/parsers/hp.py | 26 ++++++++++++++++--- .../parsers/parse_raw/hp.py | 2 ++ .../hp/failed_incompatible_fft_grid/aiida.out | 7 +++++ .../hp/failed_missing_chi_matrices/aiida.out | 7 +++++ tests/parsers/test_hp.py | 2 ++ 6 files changed, 44 insertions(+), 4 deletions(-) create mode 100644 tests/parsers/fixtures/hp/failed_incompatible_fft_grid/aiida.out create mode 100644 tests/parsers/fixtures/hp/failed_missing_chi_matrices/aiida.out diff --git a/src/aiida_quantumespresso_hp/calculations/hp.py b/src/aiida_quantumespresso_hp/calculations/hp.py index f4b49aa..b2fd397 100644 --- a/src/aiida_quantumespresso_hp/calculations/hp.py +++ b/src/aiida_quantumespresso_hp/calculations/hp.py @@ -191,6 +191,10 @@ def define(cls, spec): message='The electronic minimization cycle did not reach self-consistency.') spec.exit_code(462, 'ERROR_COMPUTING_CHOLESKY', message='The code failed during the cholesky factorization.') + spec.exit_code(490, 'ERROR_MISSING_CHI_MATRICES', + message='The code failed to reconstruct the full chi matrix as some chi matrices were missing') + spec.exit_code(495, 'ERROR_INCOMPATIBLE_FFT_GRID', + message='The code failed due to incompatibility between the FFT grid and the parallelization options.') @classproperty def filename_output_hubbard_chi(cls): # pylint: disable=no-self-argument diff --git a/src/aiida_quantumespresso_hp/parsers/hp.py b/src/aiida_quantumespresso_hp/parsers/hp.py index 35ed8db..1c039f2 100644 --- a/src/aiida_quantumespresso_hp/parsers/hp.py +++ b/src/aiida_quantumespresso_hp/parsers/hp.py @@ -15,16 +15,24 @@ class HpParser(Parser): def parse(self, **kwargs): """Parse the contents of the output files retrieved in the `FolderData`.""" + self.exit_code_stdout = None # pylint: disable=attribute-defined-outside-init + try: self.retrieved except exceptions.NotExistent: return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER # The stdout is always parsed by default. - exit_code = self.parse_stdout() + logs = self.parse_stdout() + + # Check for specific known problems that can cause a pre-mature termination of the calculation + exit_code = self.validate_premature_exit(logs) if exit_code: return exit_code + if self.exit_code_stdout: + return self.exit_code_stdout + # If it only initialized, then we do NOT parse the `{prefix}.Hubbard_parameters.dat`` # and the {prefix}.chi.dat files. # This check is needed since the `hp.x` routine will print the `{prefix}.Hubbard_parameters.dat` @@ -88,7 +96,7 @@ def parse_stdout(self): Parse the output parameters from the output of a Hp calculation written to standard out. - :return: optional exit code in case of an error + :return: log messages """ from .parse_raw.hp import parse_raw_output @@ -109,14 +117,24 @@ def parse_stdout(self): else: self.out('parameters', orm.Dict(parsed_data)) + # If the stdout was incomplete, most likely the job was interrupted before it could cleanly finish, so the + # output files are most likely corrupt and cannot be restarted from + if 'ERROR_OUTPUT_STDOUT_INCOMPLETE' in logs['error']: + self.exit_code_stdout = self.exit_codes.ERROR_OUTPUT_STDOUT_INCOMPLETE # pylint: disable=attribute-defined-outside-init + + return logs + + def validate_premature_exit(self, logs): + """Analyze problems that will cause a pre-mature termination of the calculation, controlled or not.""" for exit_status in [ + 'ERROR_OUT_OF_WALLTIME', 'ERROR_INVALID_NAMELIST', 'ERROR_INCORRECT_ORDER_ATOMIC_POSITIONS', 'ERROR_MISSING_PERTURBATION_FILE', 'ERROR_CONVERGENCE_NOT_REACHED', - 'ERROR_OUT_OF_WALLTIME', 'ERROR_COMPUTING_CHOLESKY', - 'ERROR_OUTPUT_STDOUT_INCOMPLETE', + 'ERROR_MISSING_CHI_MATRICES', + 'ERROR_INCOMPATIBLE_FFT_GRID', ]: if exit_status in logs['error']: return self.exit_codes.get(exit_status) diff --git a/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py b/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py index b291af2..d26ddad 100644 --- a/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py +++ b/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py @@ -84,6 +84,8 @@ def detect_important_message(logs, line): 'Maximum CPU time exceeded': 'ERROR_OUT_OF_WALLTIME', 'reading inputhp namelist': 'ERROR_INVALID_NAMELIST', 'problems computing cholesky': 'ERROR_COMPUTING_CHOLESKY', + 'Reconstruction problem: some chi were not found': 'ERROR_MISSING_CHI_MATRICES', + 'incompatible FFT grid': 'ERROR_INCOMPATIBLE_FFT_GRID', REG_ERROR_CONVERGENCE_NOT_REACHED: 'ERROR_CONVERGENCE_NOT_REACHED', ERROR_POSITIONS: 'ERROR_INCORRECT_ORDER_ATOMIC_POSITIONS' }, diff --git a/tests/parsers/fixtures/hp/failed_incompatible_fft_grid/aiida.out b/tests/parsers/fixtures/hp/failed_incompatible_fft_grid/aiida.out new file mode 100644 index 0000000..b8baff4 --- /dev/null +++ b/tests/parsers/fixtures/hp/failed_incompatible_fft_grid/aiida.out @@ -0,0 +1,7 @@ + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + Error in routine scale_sym_ops (3): + incompatible FFT grid + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + stopping ... diff --git a/tests/parsers/fixtures/hp/failed_missing_chi_matrices/aiida.out b/tests/parsers/fixtures/hp/failed_missing_chi_matrices/aiida.out new file mode 100644 index 0000000..12ae124 --- /dev/null +++ b/tests/parsers/fixtures/hp/failed_missing_chi_matrices/aiida.out @@ -0,0 +1,7 @@ + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + Error in routine reconstruct_full_chi (1): + Reconstruction problem: some chi were not found + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + stopping ... diff --git a/tests/parsers/test_hp.py b/tests/parsers/test_hp.py index bca62b5..55648e6 100644 --- a/tests/parsers/test_hp.py +++ b/tests/parsers/test_hp.py @@ -259,6 +259,8 @@ def test_hp_failed_invalid_namelist(aiida_localhost, generate_calc_job_node, gen ('failed_out_of_walltime', HpCalculation.exit_codes.ERROR_OUT_OF_WALLTIME.status), ('failed_stdout_incomplete', HpCalculation.exit_codes.ERROR_OUTPUT_STDOUT_INCOMPLETE.status), ('failed_computing_cholesky', HpCalculation.exit_codes.ERROR_COMPUTING_CHOLESKY.status), + ('failed_missing_chi_matrices', HpCalculation.exit_codes.ERROR_MISSING_CHI_MATRICES.status), + ('failed_incompatible_fft_grid', HpCalculation.exit_codes.ERROR_INCOMPATIBLE_FFT_GRID.status), )) def test_failed_calculation( generate_calc_job_node, From 043feceddad2e07c9af46c60f60ffa702e3434fa Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 31 May 2023 07:57:30 +0000 Subject: [PATCH 05/32] Workflows: change logic for relabeling +V case The `hp.x` and `pw.x` code can distinguish hubbard values for atoms with the same names, thus relabeling is not performed for the intersite case. Alghough, this is not the case when utilizing only onsite U. --- .../workflows/hubbard.py | 21 +++++++++-------- tests/workflows/test_hubbard.py | 23 +++++++++++-------- 2 files changed, 26 insertions(+), 18 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index 7ea2506..f298304 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -608,6 +608,8 @@ def inspect_hp(self): def check_convergence(self): """Check the convergence of the Hubbard parameters.""" + from aiida_quantumespresso.utils.hubbard import is_intersite_hubbard + workchain = self.ctx.workchains_hp[-1] # We store in memory the parameters before relabelling to make the comparison easier. @@ -624,15 +626,16 @@ def check_convergence(self): # We check if new types were created, in which case we relabel the `HubbardStructureData` self.ctx.current_hubbard_structure = workchain.outputs.hubbard_structure - for site in workchain.outputs.hubbard.dict.sites: - if not site['type'] == site['new_type']: - self.report('new types have been detected: relabeling the structure and starting new iteration.') - result = structure_relabel_kinds( - self.ctx.current_hubbard_structure, workchain.outputs.hubbard, self.ctx.current_magnetic_moments - ) - self.ctx.current_hubbard_structure = result['hubbard_structure'] - if self.ctx.current_magnetic_moments is not None: - self.ctx.current_magnetic_moments = result['starting_magnetization'] + if not is_intersite_hubbard(workchain.outputs.hubbard_structure.hubbard): + for site in workchain.outputs.hubbard.dict.sites: + if not site['type'] == site['new_type']: + self.report('new types have been detected: relabeling the structure and starting new iteration.') + result = structure_relabel_kinds( + self.ctx.current_hubbard_structure, workchain.outputs.hubbard, self.ctx.current_magnetic_moments + ) + self.ctx.current_hubbard_structure = result['hubbard_structure'] + if self.ctx.current_magnetic_moments is not None: + self.ctx.current_magnetic_moments = result['starting_magnetization'] break if not len(ref_params) == len(new_params): diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index 41482d4..feda8fe 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -329,8 +329,6 @@ def test_not_converged_check_convergence( process.setup() - # Mocking current (i.e. "old") and "new" HubbardStructureData, - # containing different Hubbard parameters process.ctx.current_hubbard_structure = generate_hubbard_structure() process.ctx.workchains_hp = [generate_hp_workchain_node(u_value=5.0)] @@ -354,19 +352,26 @@ def test_relabel_check_convergence( process.setup() - # Mocking current (i.e. "old") and "new" HubbardStructureData, - # containing different Hubbard parameters - process.ctx.current_hubbard_structure = generate_hubbard_structure() - process.ctx.workchains_hp = [generate_hp_workchain_node(relabel=True, u_value=100)] - + current_hubbard_structure = generate_hubbard_structure(u_value=1, only_u=True) + process.ctx.current_hubbard_structure = current_hubbard_structure + process.ctx.workchains_hp = [generate_hp_workchain_node(relabel=True, u_value=100, only_u=True)] process.check_convergence() assert not process.ctx.is_converged + assert process.ctx.current_hubbard_structure.get_kind_names() != current_hubbard_structure.get_kind_names() - process.ctx.current_hubbard_structure = generate_hubbard_structure(u_value=99.99) - process.ctx.workchains_hp = [generate_hp_workchain_node(relabel=True, u_value=100)] + current_hubbard_structure = generate_hubbard_structure(u_value=99.99, only_u=True) + process.ctx.current_hubbard_structure = current_hubbard_structure + process.ctx.workchains_hp = [generate_hp_workchain_node(relabel=True, u_value=100, only_u=True)] + process.check_convergence() + assert process.ctx.is_converged + assert process.ctx.current_hubbard_structure.get_kind_names() != current_hubbard_structure.get_kind_names() + current_hubbard_structure = generate_hubbard_structure(u_value=99.99) + process.ctx.current_hubbard_structure = current_hubbard_structure + process.ctx.workchains_hp = [generate_hp_workchain_node(relabel=True, u_value=100)] process.check_convergence() assert process.ctx.is_converged + assert process.ctx.current_hubbard_structure.get_kind_names() == current_hubbard_structure.get_kind_names() @pytest.mark.usefixtures('aiida_profile') From 9db7cedc5b6f39c128e2b2ac3ec2bc5c39a86f15 Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 31 May 2023 13:31:35 +0000 Subject: [PATCH 06/32] Workflows: add the `skip_relax_iterations` logic We implement the logic to skip a certain number of relax iterations. For these iterations the check on convergence is also skipped. Some fixes are also added. --- .../functions/structure_relabel_kinds.py | 2 +- .../workflows/hubbard.py | 192 ++++++++---------- .../workflows/protocols/hubbard.yaml | 1 - tests/workflows/protocols/test_hubbard.py | 2 +- .../protocols/test_hubbard/test_default.yml | 1 - tests/workflows/test_hubbard.py | 76 +++++-- 6 files changed, 146 insertions(+), 128 deletions(-) diff --git a/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py b/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py index 176c81e..0c547e6 100644 --- a/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py +++ b/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py @@ -13,7 +13,7 @@ def structure_relabel_kinds( hubbard_structure: HubbardStructureData, hubbard: Dict, - magnetization: Dict | None = None, + magnetization: dict | None = None, ) -> Dict: """Create a clone of the given structure but with new kinds, based on the new hubbard sites. diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index f298304..60123a8 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -44,6 +44,12 @@ def get_separated_parameters( return onsites, intersites +def validate_positive(value, _): + """Validate that the value is positive.""" + if value.value < 0: + return 'the value must be positive.' + + def validate_inputs(inputs, _): """Validate the entire inputs.""" parameters = AttributeDict(inputs).scf.pw.parameters.get_dict() @@ -100,74 +106,36 @@ class SelfConsistentHubbardWorkChain(WorkChain, ProtocolMixin): @classmethod def define(cls, spec): """Define the specifications of the process.""" + # yapf: disable super().define(spec) - - spec.input('hubbard_structure', valid_type=HubbardStructureData) - spec.input( - 'tolerance_onsite', - valid_type=orm.Float, - default=lambda: orm.Float(0.1), - help=( - 'Tolerance value for self-consistent calculation of Hubbard U. ' - 'In case of DFT+U+V calculation, it refers to the diagonal elements (i.e. on-site).' - ) - ) - spec.input( - 'tolerance_intersite', - valid_type=orm.Float, - default=lambda: orm.Float(0.01), - help=( - 'Tolerance value for self-consistent DFT+U+V calculation. ' - 'It refers to the only off-diagonal elements V.' - ) - ) - spec.input( - 'skip_first_relax', - valid_type=orm.Bool, - default=lambda: orm.Bool(False), - help='If True, skip the first relaxation' - ) - spec.input( - 'relax_frequency', - valid_type=orm.Int, - required=False, - help='Integer value referring to the number of iterations to wait before performing the `relax` step.' - ) - spec.expose_inputs( - PwRelaxWorkChain, - namespace='relax', - exclude=( - 'clean_workdir', - 'structure', - ), - namespace_options={ - 'required': False, - 'populate_defaults': False, - 'help': 'Inputs for the `PwRelaxWorkChain` that, when defined, will iteratively relax the structure.' - } - ) - spec.expose_inputs(PwBaseWorkChain, namespace='scf', exclude=( - 'clean_workdir', - 'pw.structure', - )) - spec.expose_inputs( - HpWorkChain, - namespace='hubbard', - exclude=( - 'clean_workdir', - 'hp.parent_scf', - 'hp.parent_hp', - 'hp.hubbard_structure', - ) - ) - spec.input('max_iterations', valid_type=orm.Int, default=lambda: orm.Int(10)) - spec.input('meta_convergence', valid_type=orm.Bool, default=lambda: orm.Bool(False)) - spec.input( - 'clean_workdir', - valid_type=orm.Bool, - default=lambda: orm.Bool(True), - help='If `True`, work directories of all called calculation will be cleaned at the end of execution.' - ) + spec.input('hubbard_structure', valid_type=HubbardStructureData, + help=('The HubbardStructureData containing the initialized parameters for triggering ' + 'the Hubbard atoms which the `hp.x` code will perturbe.')) + spec.input('tolerance_onsite', valid_type=orm.Float, default=lambda: orm.Float(0.1), + help=('Tolerance value for self-consistent calculation of Hubbard U. ' + 'In case of DFT+U+V calculation, it refers to the diagonal elements (i.e. on-site).')) + spec.input('tolerance_intersite', valid_type=orm.Float, default=lambda: orm.Float(0.01), + help=('Tolerance value for self-consistent DFT+U+V calculation. ' + 'It refers to the only off-diagonal elements V.')) + spec.input('skip_relax_iterations', valid_type=orm.Int, required=False, validator=validate_positive, + help=('The number of iterations for skipping the `relax` ' + 'step without performing check on parameters convergence.')) + spec.input('relax_frequency', valid_type=orm.Int, required=False, validator=validate_positive, + help='Integer value referring to the number of iterations to wait before performing the `relax` step.') + spec.expose_inputs(PwRelaxWorkChain, namespace='relax', + exclude=('clean_workdir', 'structure', 'base_final_scf'), + namespace_options={'required': False, 'populate_defaults': False, + 'help': 'Inputs for the `PwRelaxWorkChain` that, when defined, will iteratively relax the structure.'}) + spec.expose_inputs(PwBaseWorkChain, namespace='scf', + exclude=('clean_workdir','pw.structure')) + spec.expose_inputs(HpWorkChain, namespace='hubbard', + exclude=('clean_workdir', 'hp.parent_scf', 'hp.parent_hp', 'hp.hubbard_structure')) + spec.input('max_iterations', valid_type=orm.Int, default=lambda: orm.Int(10), + help='Maximum number of iterations of the (relax-)scf-hp cycle.') + spec.input('meta_convergence', valid_type=orm.Bool, default=lambda: orm.Bool(False), + help='Whether performing the self-consistent cycle. If False, it will stop at the first iteration.') + spec.input('clean_workdir', valid_type=orm.Bool, default=lambda: orm.Bool(True), + help='If `True`, work directories of all called calculation will be cleaned at the end of execution.') spec.inputs.validator = validate_inputs spec.inputs['hubbard']['hp'].validator = None @@ -188,44 +156,30 @@ def define(cls, spec): ), cls.run_hp, cls.inspect_hp, - if_(cls.should_check_convergence)(cls.check_convergence,), + if_(cls.should_check_convergence)( + cls.check_convergence, + ), ), cls.run_results, ) - spec.output( - 'hubbard_structure', - valid_type=HubbardStructureData, - required=False, - help='The Hubbard structure containing the structure and associated Hubbard parameters.' - ) - - spec.exit_code( - 330, - 'ERROR_FAILED_TO_DETERMINE_PSEUDO_POTENTIAL', - message='Failed to determine the correct pseudo potential after the structure changed its kind names.' - ) - spec.exit_code( - 401, 'ERROR_SUB_PROCESS_FAILED_RECON', message='The reconnaissance PwBaseWorkChain sub process failed' - ) - spec.exit_code( - 402, - 'ERROR_SUB_PROCESS_FAILED_RELAX', - message='The PwRelaxWorkChain sub process failed in iteration {iteration}' - ) - spec.exit_code( - 403, - 'ERROR_SUB_PROCESS_FAILED_SCF', - message='The scf PwBaseWorkChain sub process failed in iteration {iteration}' - ) - spec.exit_code( - 404, 'ERROR_SUB_PROCESS_FAILED_HP', message='The HpWorkChain sub process failed in iteration {iteration}' - ) - spec.exit_code( - 405, 'ERROR_NON_INTEGER_TOT_MAGNETIZATION', + spec.output('hubbard_structure', valid_type=HubbardStructureData, required=False, + help='The Hubbard structure containing the structure and associated Hubbard parameters.') + + spec.exit_code(330, 'ERROR_FAILED_TO_DETERMINE_PSEUDO_POTENTIAL', + message='Failed to determine the correct pseudo potential after the structure changed its kind names.') + spec.exit_code(401, 'ERROR_SUB_PROCESS_FAILED_RECON', + message='The reconnaissance PwBaseWorkChain sub process failed') + spec.exit_code(402, 'ERROR_SUB_PROCESS_FAILED_RELAX', + message='The PwRelaxWorkChain sub process failed in iteration {iteration}') + spec.exit_code(403, 'ERROR_SUB_PROCESS_FAILED_SCF', + message='The scf PwBaseWorkChain sub process failed in iteration {iteration}') + spec.exit_code(404, 'ERROR_SUB_PROCESS_FAILED_HP', + message='The HpWorkChain sub process failed in iteration {iteration}') + spec.exit_code(405, 'ERROR_NON_INTEGER_TOT_MAGNETIZATION', message='The scf PwBaseWorkChain sub process in iteration {iteration}'\ - 'returned a non integer total magnetization (threshold exceeded).' - ) + 'returned a non integer total magnetization (threshold exceeded).') + # yapf: enable @classmethod def get_protocol_filepath(cls): @@ -289,12 +243,13 @@ def get_builder_from_protocol( if 'relax_frequency' in inputs: builder.relax_frequency = orm.Int(inputs['relax_frequency']) + if 'skip_relax_iterations' in inputs: + builder.skip_relax_iterations = orm.Int(inputs['skip_relax_iterations']) builder.hubbard_structure = hubbard_structure builder.relax = relax builder.scf = scf builder.hubbard = hubbard - builder.skip_first_relax = orm.Bool(inputs['skip_first_relax']) builder.tolerance_onsite = orm.Float(inputs['tolerance_onsite']) builder.tolerance_intersite = orm.Float(inputs['tolerance_intersite']) builder.max_iterations = orm.Int(inputs['max_iterations']) @@ -312,7 +267,9 @@ def setup(self): self.ctx.is_insulator = None self.ctx.is_magnetic = False self.ctx.iteration = 0 - self.ctx.skip_first_relax = self.inputs.skip_first_relax.value + self.ctx.skip_relax_iterations = 0 + if 'skip_relax_iterations' in self.inputs: + self.ctx.skip_relax_iterations = self.inputs.skip_relax_iterations.value self.ctx.relax_frequency = 1 if 'relax_frequency' in self.inputs: self.ctx.relax_frequency = self.inputs.relax_frequency.value @@ -342,23 +299,35 @@ def should_run_relax(self): if 'relax' not in self.inputs: return False - if self.ctx.skip_first_relax: - self.ctx.skip_first_relax = False # only the first one will be skipped - self.report('`skip_first_relax` is set to `True`. Skipping first relaxation.') + if self.ctx.iteration <= self.ctx.skip_relax_iterations: + self.report(( + f'`skip_relax_iterations` is set to {self.ctx.skip_relax_iterations}. ' + f'Skipping relaxation for iteration {self.ctx.iteration}.' + )) return False if self.ctx.iteration % self.ctx.relax_frequency != 0: self.report(( f'`relax_frequency` is set to {self.ctx.relax_frequency}. ' - f'Skipping relaxation for iteration {self.ctx.iteration }.' + f'Skipping relaxation for iteration {self.ctx.iteration}.' )) return False - return 'relax' in self.inputs + return True def should_check_convergence(self): """Return whether to check the convergence of Hubbard parameters.""" - return self.inputs.meta_convergence.value + if not self.inputs.meta_convergence.value: + return False + + if self.ctx.iteration <= self.ctx.skip_relax_iterations: + self.report(( + f'`skip_relax_iterations` is set to {self.ctx.skip_relax_iterations}. ' + f'Skipping convergence check for iteration {self.ctx.iteration}.' + )) + return False + + return True def should_run_iteration(self): """Return whether a new process should be run.""" @@ -601,10 +570,11 @@ def inspect_hp(self): self.report(f'hp.x in iteration {self.ctx.iteration} failed with exit status {workchain.exit_status}') return self.exit_codes.ERROR_SUB_PROCESS_FAILED_HP.format(iteration=self.ctx.iteration) - if not self.inputs.meta_convergence: + if not self.should_check_convergence(): self.ctx.current_hubbard_structure = workchain.outputs.hubbard_structure - self.report('meta convergence is switched off, so not checking convergence of Hubbard parameters.') - self.ctx.is_converged = True + if not self.inputs.meta_convergence: + self.report('meta convergence is switched off, so not checking convergence of Hubbard parameters.') + self.ctx.is_converged = True def check_convergence(self): """Check the convergence of the Hubbard parameters.""" diff --git a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml index b4aa3ad..cb32044 100644 --- a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml +++ b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml @@ -4,7 +4,6 @@ default_inputs: meta_convergence: True tolerance_onsite: 0.1 tolerance_intersite: 0.01 - skip_first_relax: False scf: kpoints_distance: 0.4 diff --git a/tests/workflows/protocols/test_hubbard.py b/tests/workflows/protocols/test_hubbard.py index 9da437b..37d0f21 100644 --- a/tests/workflows/protocols/test_hubbard.py +++ b/tests/workflows/protocols/test_hubbard.py @@ -39,7 +39,7 @@ def test_default(fixture_code, data_regression, generate_hubbard_structure, seri 'tolerance_intersite': 1 }, { - 'skip_first_relax': True + 'skip_relax_iterations': 2 }, { 'relax_frequency': 3 diff --git a/tests/workflows/protocols/test_hubbard/test_default.yml b/tests/workflows/protocols/test_hubbard/test_default.yml index 275708d..ee18383 100644 --- a/tests/workflows/protocols/test_hubbard/test_default.yml +++ b/tests/workflows/protocols/test_hubbard/test_default.yml @@ -92,6 +92,5 @@ scf: Co: Co Li: Li O: O -skip_first_relax: false tolerance_intersite: 0.01 tolerance_onsite: 0.1 diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index feda8fe..11b5152 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -115,6 +115,20 @@ def test_validate_inputs_invalid_inputs(generate_workchain_hubbard, generate_inp generate_workchain_hubbard(inputs=inputs) +@pytest.mark.parametrize('parameters', ('skip_relax_iterations', 'relax_frequency')) +@pytest.mark.usefixtures('aiida_profile') +def test_validate_invalid_positve_input(generate_workchain_hubbard, generate_inputs_hubbard, parameters): + """Test `SelfConsistentHubbardWorkChain` for invalid positive inputs.""" + from aiida.orm import Int + + inputs = AttributeDict(generate_inputs_hubbard()) + inputs.update({parameters: Int(-1)}) + + match = 'the value must be positive.' + with pytest.raises(ValueError, match=match): + generate_workchain_hubbard(inputs=inputs) + + @pytest.mark.usefixtures('aiida_profile') def test_setup(generate_workchain_hubbard, generate_inputs_hubbard): """Test `SelfConsistentHubbardWorkChain.setup`.""" @@ -124,12 +138,12 @@ def test_setup(generate_workchain_hubbard, generate_inputs_hubbard): assert process.ctx.iteration == 0 assert process.ctx.relax_frequency == 1 + assert process.ctx.skip_relax_iterations == 0 assert process.ctx.current_hubbard_structure == inputs['hubbard_structure'] assert process.ctx.current_magnetic_moments is None - assert process.ctx.is_converged is False + assert not process.ctx.is_converged assert process.ctx.is_insulator is None assert not process.ctx.is_magnetic - assert not process.ctx.skip_first_relax assert not process.should_check_convergence() @@ -162,19 +176,55 @@ def test_magnetic_setup(generate_workchain_hubbard, generate_inputs_hubbard): @pytest.mark.usefixtures('aiida_profile') -def test_skip_first_relax(generate_workchain_hubbard, generate_inputs_hubbard): - """Test `SelfConsistentHubbardWorkChain` when skipping only the first relax.""" - from aiida.orm import Bool +def test_skip_relax_iterations(generate_workchain_hubbard, generate_inputs_hubbard, generate_hp_workchain_node): + """Test `SelfConsistentHubbardWorkChain` when skipping the first relax iterations.""" + from aiida.orm import Bool, Int inputs = generate_inputs_hubbard() - inputs['skip_first_relax'] = Bool(True) + inputs['skip_relax_iterations'] = Int(1) + inputs['meta_convergence'] = Bool(True) process = generate_workchain_hubbard(inputs=inputs) - process.setup() + # 1 + process.update_iteration() + assert process.ctx.skip_relax_iterations == 1 + assert process.ctx.iteration == 1 + assert not process.should_run_relax() + assert not process.should_check_convergence() + process.ctx.workchains_hp = [generate_hp_workchain_node()] + process.inspect_hp() + assert process.ctx.current_hubbard_structure == process.ctx.workchains_hp[-1].outputs.hubbard_structure + # 2 + process.update_iteration() + assert process.should_run_relax() + assert process.should_check_convergence() + # 3 + process.update_iteration() + assert process.should_run_relax() + assert process.should_check_convergence() - assert not process.should_run_relax() # skip only first one - assert process.should_run_relax() # the second one not - assert process.should_run_relax() # and the third neither! + inputs['skip_relax_iterations'] = Int(2) + process = generate_workchain_hubbard(inputs=inputs) + process.setup() + # 1 + process.update_iteration() + assert process.ctx.skip_relax_iterations == 2 + assert not process.should_run_relax() + assert not process.should_check_convergence() + process.ctx.workchains_hp = [generate_hp_workchain_node()] + process.inspect_hp() + assert process.ctx.current_hubbard_structure == process.ctx.workchains_hp[-1].outputs.hubbard_structure + # 2 + process.update_iteration() + assert not process.should_run_relax() + assert not process.should_check_convergence() + process.ctx.workchains_hp.append(generate_hp_workchain_node()) + process.inspect_hp() + assert process.ctx.current_hubbard_structure == process.ctx.workchains_hp[-1].outputs.hubbard_structure + # 3 + process.update_iteration() + assert process.should_run_relax() + assert process.should_check_convergence() @pytest.mark.usefixtures('aiida_profile') @@ -185,10 +235,9 @@ def test_relax_frequency(generate_workchain_hubbard, generate_inputs_hubbard): inputs = generate_inputs_hubbard() inputs['relax_frequency'] = Int(3) process = generate_workchain_hubbard(inputs=inputs) - process.setup() - process.update_iteration() # it updates first in the while of the outline + process.update_iteration() assert not process.should_run_relax() # skip process.update_iteration() assert not process.should_run_relax() # skip @@ -205,7 +254,8 @@ def test_should_check_convergence(generate_workchain_hubbard, generate_inputs_hu inputs = generate_inputs_hubbard() inputs['meta_convergence'] = Bool(True) process = generate_workchain_hubbard(inputs=inputs) - + process.setup() + process.update_iteration() assert process.should_check_convergence() From 63e018d478815dd3590686091f6ece47b7caf589 Mon Sep 17 00:00:00 2001 From: bastonero Date: Thu, 1 Jun 2023 11:49:54 +0000 Subject: [PATCH 07/32] Fix `break` wrong indent --- src/aiida_quantumespresso_hp/workflows/hubbard.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index 60123a8..533beb7 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -606,7 +606,7 @@ def check_convergence(self): self.ctx.current_hubbard_structure = result['hubbard_structure'] if self.ctx.current_magnetic_moments is not None: self.ctx.current_magnetic_moments = result['starting_magnetization'] - break + break if not len(ref_params) == len(new_params): self.report('The new and old Hubbard parameters have different lenghts. Assuming to be at the first cycle.') From cf50ce6ce321d9590184807a26eba0683545a6fc Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 5 Jul 2023 16:07:07 +0000 Subject: [PATCH 08/32] Feat: clean the workdirs at each iteration Modify the `SelfConsistentHubbardWorkChain` to clean the work directories at each iteration instead of cleaning everything at the end, eventually saving lots of storage space, which may be crucial for large scale calculations or for users with few space. --- .../workflows/hubbard.py | 21 ++++++++++++------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index 7ea2506..529c982 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -172,6 +172,7 @@ def define(cls, spec): spec.inputs.validator = validate_inputs spec.inputs['hubbard']['hp'].validator = None + # yapf: disable spec.outline( cls.setup, while_(cls.should_run_iteration)( @@ -188,10 +189,16 @@ def define(cls, spec): ), cls.run_hp, cls.inspect_hp, - if_(cls.should_check_convergence)(cls.check_convergence,), + if_(cls.should_check_convergence)( + cls.check_convergence, + ), + if_(cls.should_clean_workdir)( + cls.clean_iteration, + ) ), cls.run_results, ) + # yapf: enable spec.output( 'hubbard_structure', @@ -673,14 +680,12 @@ def run_results(self): self.report(f'Hubbard parameters self-consistently converged in {self.ctx.iteration} iterations') self.out('hubbard_structure', self.ctx.current_hubbard_structure) - def on_terminated(self): - """Clean the working directories of all child calculations if `clean_workdir=True` in the inputs.""" - super().on_terminated() - - if self.inputs.clean_workdir.value is False: - self.report('remote folders will not be cleaned') - return + def should_clean_workdir(self): + """Whether to clean the work directories at each iteration.""" + return self.inputs.clean_workdir.value + def clean_iteration(self): + """Clean all work directiories of the current iteration.""" cleaned_calcs = [] for called_descendant in self.node.called_descendants: From e196fb3cef6113e57c1a23230f1f7b85f19e11f3 Mon Sep 17 00:00:00 2001 From: bastonero Date: Tue, 14 Nov 2023 16:20:49 +0000 Subject: [PATCH 09/32] Address some python warning on typing --- .../calculations/functions/structure_relabel_kinds.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py b/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py index 0c547e6..176c81e 100644 --- a/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py +++ b/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py @@ -13,7 +13,7 @@ def structure_relabel_kinds( hubbard_structure: HubbardStructureData, hubbard: Dict, - magnetization: dict | None = None, + magnetization: Dict | None = None, ) -> Dict: """Create a clone of the given structure but with new kinds, based on the new hubbard sites. From 800072b7f1d66944345e282d08fdecc0d8f1a31b Mon Sep 17 00:00:00 2001 From: bastonero Date: Mon, 27 Nov 2023 17:24:53 +0000 Subject: [PATCH 10/32] `Feature`: add radial analysis during cycle Some structures may have onsite atoms of the same specie but with different nearest neighbours (e.g. Fe3O4). The hp.x code can handle this only specifying a maximum radius, within which one can find the nearest neighbours. As such radius may change during relaxation of the atomic structure, an analysis is introduced to define at each iteration such maximum radius. --- .../workflows/hubbard.py | 19 +++++++++++++++- .../workflows/protocols/hubbard.yaml | 4 ++++ tests/conftest.py | 2 +- .../protocols/test_hubbard/test_default.yml | 4 ++++ tests/workflows/test_hubbard.py | 22 +++++++++++++++++++ 5 files changed, 49 insertions(+), 2 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index 05a3dc6..0789695 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -120,6 +120,8 @@ def define(cls, spec): spec.input('skip_relax_iterations', valid_type=orm.Int, required=False, validator=validate_positive, help=('The number of iterations for skipping the `relax` ' 'step without performing check on parameters convergence.')) + spec.input('radial_analysis', valid_type=orm.Dict, required=False, + help='If specified, it performs a nearest neighbour analysis and feed the radius to hp.x') spec.input('relax_frequency', valid_type=orm.Int, required=False, validator=validate_positive, help='Integer value referring to the number of iterations to wait before performing the `relax` step.') spec.expose_inputs(PwRelaxWorkChain, namespace='relax', @@ -255,6 +257,7 @@ def get_builder_from_protocol( builder.hubbard = hubbard builder.tolerance_onsite = orm.Float(inputs['tolerance_onsite']) builder.tolerance_intersite = orm.Float(inputs['tolerance_intersite']) + builder.radial_analysis = orm.Dict(inputs['radial_analysis']) builder.max_iterations = orm.Int(inputs['max_iterations']) builder.meta_convergence = orm.Bool(inputs['meta_convergence']) builder.clean_workdir = orm.Bool(inputs['clean_workdir']) @@ -550,6 +553,20 @@ def run_hp(self): workchain = self.ctx.workchains_scf[-1] inputs = AttributeDict(self.exposed_inputs(HpWorkChain, namespace='hubbard')) + + if 'radial_analysis' in self.inputs: + from qe_tools import CONSTANTS + + kwargs = self.inputs.radial_analysis.get_dict() + hubbard_utils = HubbardUtils(self.ctx.current_hubbard_structure) + radius = hubbard_utils.get_intersites_radius(**kwargs) # in Angstrom + + parameters = inputs.hp.parameters.get_dict() + parameters['INPUTHP'].pop('num_neigh', None) + parameters['INPUTHP']['rmax'] = radius / CONSTANTS.bohr_to_ang + + inputs.hp.parameters = orm.Dict(parameters) + inputs.clean_workdir = self.inputs.clean_workdir inputs.hp.parent_scf = workchain.outputs.remote_folder inputs.hp.hubbard_structure = self.ctx.current_hubbard_structure @@ -558,7 +575,7 @@ def run_hp(self): running = self.submit(HpWorkChain, **inputs) self.report(f'launching HpWorkChain<{running.pk}> iteration #{self.ctx.iteration}') - return ToContext(workchains_hp=append_(running)) + self.to_context(**{'workchains_hp': append_(running)}) def inspect_hp(self): """Analyze the last completed HpWorkChain. diff --git a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml index cb32044..9c39c49 100644 --- a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml +++ b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml @@ -4,6 +4,10 @@ default_inputs: meta_convergence: True tolerance_onsite: 0.1 tolerance_intersite: 0.01 + radial_analysis: + radius_max: 10.0 # in Angstrom + thr: 0.01 + nn_finder: 'crystal' scf: kpoints_distance: 0.4 diff --git a/tests/conftest.py b/tests/conftest.py index 31950db..a64a69e 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -58,7 +58,7 @@ def _fixture_code(entry_point_name): try: return load_code(label=label) - except exceptions.NotExistent: + except (exceptions.NotExistent, exceptions.MultipleObjectsError): return InstalledCode( label=label, computer=fixture_localhost, diff --git a/tests/workflows/protocols/test_hubbard/test_default.yml b/tests/workflows/protocols/test_hubbard/test_default.yml index ee18383..59bad83 100644 --- a/tests/workflows/protocols/test_hubbard/test_default.yml +++ b/tests/workflows/protocols/test_hubbard/test_default.yml @@ -19,6 +19,10 @@ hubbard: hubbard_structure: CoLiO2 max_iterations: 10 meta_convergence: true +radial_analysis: + nn_finder: 'crystal' + radius_max: 10.0 + thr: 0.01 relax: base: kpoints_distance: 0.15 diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index 11b5152..13dc817 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -247,6 +247,28 @@ def test_relax_frequency(generate_workchain_hubbard, generate_inputs_hubbard): assert not process.should_run_relax() # skip +@pytest.mark.usefixtures('aiida_profile') +def test_radial_analysis( + generate_workchain_hubbard, + generate_inputs_hubbard, + generate_scf_workchain_node, +): + """Test `SelfConsistentHubbardWorkChain` outline when radial analysis is activated. + + We want to make sure `rmax` is in `hp.parameters`. + """ + inputs = generate_inputs_hubbard() + inputs['radial_analysis'] = Dict({}) # no need to specify inputs, it will use the defaults + process = generate_workchain_hubbard(inputs=inputs) + + process.setup() + process.ctx.workchains_scf = [generate_scf_workchain_node(remote_folder=True)] + process.run_hp() + + # parameters = process.ctx['workchains_hp'][-1].inputs['hp']['parameters'].get_dict() + # assert 'rmax' in parameters + + @pytest.mark.usefixtures('aiida_profile') def test_should_check_convergence(generate_workchain_hubbard, generate_inputs_hubbard): """Test `SelfConsistentHubbardWorkChain.should_check_convergence`.""" From 4e28e25caf85918e759b079e027a608c521410bc Mon Sep 17 00:00:00 2001 From: bastonero Date: Mon, 27 Nov 2023 17:32:52 +0000 Subject: [PATCH 11/32] Fix overrides test --- tests/workflows/protocols/test_hubbard/test_default.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/workflows/protocols/test_hubbard/test_default.yml b/tests/workflows/protocols/test_hubbard/test_default.yml index 59bad83..f2297fe 100644 --- a/tests/workflows/protocols/test_hubbard/test_default.yml +++ b/tests/workflows/protocols/test_hubbard/test_default.yml @@ -20,7 +20,7 @@ hubbard_structure: CoLiO2 max_iterations: 10 meta_convergence: true radial_analysis: - nn_finder: 'crystal' + nn_finder: crystal radius_max: 10.0 thr: 0.01 relax: @@ -34,6 +34,7 @@ relax: max_wallclock_seconds: 43200 resources: num_machines: 1 + num_mpiprocs_per_machine: 1 withmpi: true parameters: CELL: @@ -73,6 +74,7 @@ scf: max_wallclock_seconds: 43200 resources: num_machines: 1 + num_mpiprocs_per_machine: 1 withmpi: true parameters: CONTROL: From 7aa81fde43803e74eba53a3322c76d2cd2874f1d Mon Sep 17 00:00:00 2001 From: bastonero Date: Tue, 5 Dec 2023 15:28:20 +0000 Subject: [PATCH 12/32] Fix bug in regex for perturbed atoms --- src/aiida_quantumespresso_hp/utils/general.py | 2 +- tests/utils/test_general.py | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/src/aiida_quantumespresso_hp/utils/general.py b/src/aiida_quantumespresso_hp/utils/general.py index 3566bac..99c9fd0 100644 --- a/src/aiida_quantumespresso_hp/utils/general.py +++ b/src/aiida_quantumespresso_hp/utils/general.py @@ -28,7 +28,7 @@ def is_perturb_only_atom(parameters: dict) -> int | None: match = None # making sure that if the dictionary is empty we don't raise an `UnboundLocalError` for key in parameters.keys(): - match = re.search(r'perturb_only_atom.*([0-9]).*', key) + match = re.search(r'perturb_only_atom.*?(\d+).*', key) if match: if not parameters[key]: # also the key must be `True` match = None # making sure to have `None` diff --git a/tests/utils/test_general.py b/tests/utils/test_general.py index 031947f..c7e3567 100644 --- a/tests/utils/test_general.py +++ b/tests/utils/test_general.py @@ -26,5 +26,8 @@ def test_is_perturb_only_atom(): parameters = {'perturb_only_atom(1)': True} assert is_perturb_only_atom(parameters) == 1 + parameters = {'perturb_only_atom(20)': True} + assert is_perturb_only_atom(parameters) == 20 + parameters = {'perturb_only_atom(1)': False} assert is_perturb_only_atom(parameters) is None From f9f949f2b4e7ded061d59d1d92d90c078ca4bac0 Mon Sep 17 00:00:00 2001 From: bastonero Date: Tue, 5 Dec 2023 15:29:07 +0000 Subject: [PATCH 13/32] Fix bug in the hubbard outline --- src/aiida_quantumespresso_hp/workflows/hubbard.py | 7 ++++--- .../workflows/protocols/hubbard.yaml | 2 +- tests/workflows/test_hubbard.py | 7 +++++-- 3 files changed, 10 insertions(+), 6 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index 0789695..a62c3fb 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -158,9 +158,7 @@ def define(cls, spec): ), cls.run_hp, cls.inspect_hp, - if_(cls.should_check_convergence)( - cls.check_convergence, - ), + cls.check_convergence, if_(cls.should_clean_workdir)( cls.clean_iteration, ) @@ -628,6 +626,9 @@ def check_convergence(self): self.ctx.current_magnetic_moments = result['starting_magnetization'] break + if not self.should_check_convergence(): + return + if not len(ref_params) == len(new_params): self.report('The new and old Hubbard parameters have different lenghts. Assuming to be at the first cycle.') return diff --git a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml index 9c39c49..2459162 100644 --- a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml +++ b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml @@ -6,7 +6,7 @@ default_inputs: tolerance_intersite: 0.01 radial_analysis: radius_max: 10.0 # in Angstrom - thr: 0.01 + thr: 0.1 nn_finder: 'crystal' scf: kpoints_distance: 0.4 diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index 13dc817..b320329 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -257,6 +257,8 @@ def test_radial_analysis( We want to make sure `rmax` is in `hp.parameters`. """ + from aiida.orm import load_node + inputs = generate_inputs_hubbard() inputs['radial_analysis'] = Dict({}) # no need to specify inputs, it will use the defaults process = generate_workchain_hubbard(inputs=inputs) @@ -265,8 +267,9 @@ def test_radial_analysis( process.ctx.workchains_scf = [generate_scf_workchain_node(remote_folder=True)] process.run_hp() - # parameters = process.ctx['workchains_hp'][-1].inputs['hp']['parameters'].get_dict() - # assert 'rmax' in parameters + node = load_node(process.ctx['workchains_hp'][-1].pk) + parameters = node.inputs['hp']['parameters'].get_dict() + assert 'rmax' in parameters['INPUTHP'] @pytest.mark.usefixtures('aiida_profile') From 5bc0efc01d2c05ad16ce1717fd7a3a163ff60a59 Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 6 Dec 2023 11:51:14 +0000 Subject: [PATCH 14/32] Fix bug in the hubbard outline --- src/aiida_quantumespresso_hp/workflows/hubbard.py | 7 ++++--- .../workflows/protocols/hubbard.yaml | 2 +- tests/workflows/test_hubbard.py | 7 +++++-- 3 files changed, 10 insertions(+), 6 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index 0789695..a62c3fb 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -158,9 +158,7 @@ def define(cls, spec): ), cls.run_hp, cls.inspect_hp, - if_(cls.should_check_convergence)( - cls.check_convergence, - ), + cls.check_convergence, if_(cls.should_clean_workdir)( cls.clean_iteration, ) @@ -628,6 +626,9 @@ def check_convergence(self): self.ctx.current_magnetic_moments = result['starting_magnetization'] break + if not self.should_check_convergence(): + return + if not len(ref_params) == len(new_params): self.report('The new and old Hubbard parameters have different lenghts. Assuming to be at the first cycle.') return diff --git a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml index 9c39c49..2459162 100644 --- a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml +++ b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml @@ -6,7 +6,7 @@ default_inputs: tolerance_intersite: 0.01 radial_analysis: radius_max: 10.0 # in Angstrom - thr: 0.01 + thr: 0.1 nn_finder: 'crystal' scf: kpoints_distance: 0.4 diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index 13dc817..b320329 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -257,6 +257,8 @@ def test_radial_analysis( We want to make sure `rmax` is in `hp.parameters`. """ + from aiida.orm import load_node + inputs = generate_inputs_hubbard() inputs['radial_analysis'] = Dict({}) # no need to specify inputs, it will use the defaults process = generate_workchain_hubbard(inputs=inputs) @@ -265,8 +267,9 @@ def test_radial_analysis( process.ctx.workchains_scf = [generate_scf_workchain_node(remote_folder=True)] process.run_hp() - # parameters = process.ctx['workchains_hp'][-1].inputs['hp']['parameters'].get_dict() - # assert 'rmax' in parameters + node = load_node(process.ctx['workchains_hp'][-1].pk) + parameters = node.inputs['hp']['parameters'].get_dict() + assert 'rmax' in parameters['INPUTHP'] @pytest.mark.usefixtures('aiida_profile') From 5aa1ebffb5b7e2ff000b8f1eced5ef98d7513a5c Mon Sep 17 00:00:00 2001 From: Timo Reents Date: Wed, 6 Dec 2023 15:00:16 +0100 Subject: [PATCH 15/32] Fix convergence error handler to prevent exceeding niter_max of 500 --- src/aiida_quantumespresso_hp/workflows/hp/base.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hp/base.py b/src/aiida_quantumespresso_hp/workflows/hp/base.py index 17d35f7..daf16cf 100644 --- a/src/aiida_quantumespresso_hp/workflows/hp/base.py +++ b/src/aiida_quantumespresso_hp/workflows/hp/base.py @@ -233,7 +233,8 @@ def handle_convergence_not_reached(self, _): changes.append(f'set `{parameter}` to {parameters[parameter]}') if 'niter_max' in parameters: - parameters['niter_max'] *= self.defaults.delta_factor_niter_max + # QE has a hard-coded limit of 500 + parameters['niter_max'] = min(parameters['niter_max'] * self.defaults.delta_factor_niter_max, 500) else: parameters['niter_max'] = 200 From 1e1cd96ac20b003ff55281c8f9803c9ecb2ccd95 Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 6 Dec 2023 20:30:53 +0000 Subject: [PATCH 16/32] Fix exit status when convergence is not met Fixes #55 Exit status 0 was given when at the last iteration no self-consistency (of Hubbard parameters) was reached. This is misleading, and a new exit code is added to highlitght better this condition. --- src/aiida_quantumespresso_hp/workflows/hubbard.py | 10 +++++++++- tests/workflows/test_hubbard.py | 7 +++++++ 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index e29539e..33d974b 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -182,6 +182,9 @@ def define(cls, spec): spec.exit_code(405, 'ERROR_NON_INTEGER_TOT_MAGNETIZATION', message='The scf PwBaseWorkChain sub process in iteration {iteration}'\ 'returned a non integer total magnetization (threshold exceeded).') + + spec.exit_code(601, 'ERROR_NO_CONVERGENCE_AT_LAST_ITERATION', + message='The Hubbard parameters did not converge at the last iteration #{iteration}') # yapf: enable @classmethod @@ -646,9 +649,14 @@ def check_convergence(self): def run_results(self): """Attach the final converged Hubbard U parameters and the corresponding structure.""" - self.report(f'Hubbard parameters self-consistently converged in {self.ctx.iteration} iterations') self.out('hubbard_structure', self.ctx.current_hubbard_structure) + if self.ctx.is_converged: + self.report(f'Hubbard parameters self-consistently converged in {self.ctx.iteration} iterations') + else: + self.report(f'Hubbard parameters did not converged at the last iteration #{self.ctx.iteration}.') + return self.exit_codes.ERROR_NO_CONVERGENCE_AT_LAST_ITERATION.format(iteration=self.ctx.iteration) + def should_clean_workdir(self): """Whether to clean the work directories at each iteration.""" return self.inputs.clean_workdir.value diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index 11b5152..0e3dcdc 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -374,6 +374,8 @@ def test_not_converged_check_convergence( generate_workchain_hubbard, generate_hp_workchain_node, generate_inputs_hubbard, generate_hubbard_structure ): """Test when `SelfConsistentHubbardWorkChain.check_convergence` is not at convergence.""" + from aiida_quantumespresso_hp.workflows.hubbard import SelfConsistentHubbardWorkChain as WorkChain + inputs = generate_inputs_hubbard() process = generate_workchain_hubbard(inputs=inputs) @@ -391,6 +393,11 @@ def test_not_converged_check_convergence( process.check_convergence() assert not process.ctx.is_converged + result = process.run_results() + assert 'hubbard_structure' in process.outputs + assert process.outputs['hubbard_structure'] == process.ctx.workchains_hp[-1].outputs['hubbard_structure'] + assert result == WorkChain.exit_codes.ERROR_NO_CONVERGENCE_AT_LAST_ITERATION.format(iteration=process.ctx.iteration) + @pytest.mark.usefixtures('aiida_profile') def test_relabel_check_convergence( From 14bc1fc9b6fb58cc174572d341adc119c90b9dd2 Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 6 Dec 2023 22:33:08 +0000 Subject: [PATCH 17/32] Fix exit code name --- src/aiida_quantumespresso_hp/workflows/hubbard.py | 4 ++-- tests/workflows/test_hubbard.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index 33d974b..2118163 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -183,7 +183,7 @@ def define(cls, spec): message='The scf PwBaseWorkChain sub process in iteration {iteration}'\ 'returned a non integer total magnetization (threshold exceeded).') - spec.exit_code(601, 'ERROR_NO_CONVERGENCE_AT_LAST_ITERATION', + spec.exit_code(601, 'ERROR_CONVERGENCE_NOT_REACHED', message='The Hubbard parameters did not converge at the last iteration #{iteration}') # yapf: enable @@ -655,7 +655,7 @@ def run_results(self): self.report(f'Hubbard parameters self-consistently converged in {self.ctx.iteration} iterations') else: self.report(f'Hubbard parameters did not converged at the last iteration #{self.ctx.iteration}.') - return self.exit_codes.ERROR_NO_CONVERGENCE_AT_LAST_ITERATION.format(iteration=self.ctx.iteration) + return self.exit_codes.ERROR_CONVERGENCE_NOT_REACHED.format(iteration=self.ctx.iteration) def should_clean_workdir(self): """Whether to clean the work directories at each iteration.""" diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index 0e3dcdc..2a06584 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -396,7 +396,7 @@ def test_not_converged_check_convergence( result = process.run_results() assert 'hubbard_structure' in process.outputs assert process.outputs['hubbard_structure'] == process.ctx.workchains_hp[-1].outputs['hubbard_structure'] - assert result == WorkChain.exit_codes.ERROR_NO_CONVERGENCE_AT_LAST_ITERATION.format(iteration=process.ctx.iteration) + assert result == WorkChain.exit_codes.ERROR_CONVERGENCE_NOT_REACHED.format(iteration=process.ctx.iteration) @pytest.mark.usefixtures('aiida_profile') From 6263392a3a9dcb11baacc58b68e9326f3f5f3f3e Mon Sep 17 00:00:00 2001 From: Timo Reents Date: Thu, 7 Dec 2023 14:39:29 +0100 Subject: [PATCH 18/32] Simplify `convergence_not_reached` handler Adapt the `convergence_not_reached` handler so that it only adjusts `alpha_mix`. `niter_max` is moved to the protocol. --- src/aiida_quantumespresso_hp/workflows/hp/base.py | 12 ++---------- .../workflows/protocols/hp/base.yaml | 3 +++ tests/workflows/hp/test_base.py | 8 +++----- 3 files changed, 8 insertions(+), 15 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hp/base.py b/src/aiida_quantumespresso_hp/workflows/hp/base.py index daf16cf..67eda47 100644 --- a/src/aiida_quantumespresso_hp/workflows/hp/base.py +++ b/src/aiida_quantumespresso_hp/workflows/hp/base.py @@ -210,10 +210,10 @@ def handle_computing_cholesky(self, _): @process_handler(priority=410, exit_codes=HpCalculation.exit_codes.ERROR_CONVERGENCE_NOT_REACHED) def handle_convergence_not_reached(self, _): - """Handle `ERROR_CONVERGENCE_NOT_REACHED`: decrease `alpha_mix`, increase `niter_max`, and restart. + """Handle `ERROR_CONVERGENCE_NOT_REACHED`: decrease `alpha_mix` and restart. Since `hp.x` does not support restarting from incomplete calculations, the entire calculation will have to be - restarted from scratch. By increasing the `niter_max` and decreasing `alpha_mix` there is a chance that the next + restarted from scratch. By decreasing `alpha_mix` there is a chance that the next run will converge. If these keys are present in the input parameters, they will be scaled by a default factor, otherwise, a hardcoded default value will be set that is lower/higher than that of the code's default. """ @@ -232,14 +232,6 @@ def handle_convergence_not_reached(self, _): parameters[parameter] = 0.20 changes.append(f'set `{parameter}` to {parameters[parameter]}') - if 'niter_max' in parameters: - # QE has a hard-coded limit of 500 - parameters['niter_max'] = min(parameters['niter_max'] * self.defaults.delta_factor_niter_max, 500) - else: - parameters['niter_max'] = 200 - - changes.append(f"changed `niter_max` to {parameters['niter_max']}") - if changes: self.report(f"convergence not reached: {', '.join(changes)}") else: diff --git a/src/aiida_quantumespresso_hp/workflows/protocols/hp/base.yaml b/src/aiida_quantumespresso_hp/workflows/protocols/hp/base.yaml index 0e2a402..3e6c846 100644 --- a/src/aiida_quantumespresso_hp/workflows/protocols/hp/base.yaml +++ b/src/aiida_quantumespresso_hp/workflows/protocols/hp/base.yaml @@ -11,6 +11,9 @@ default_inputs: parameters: INPUTHP: conv_thr_chi: 5.e-6 + niter_max: 200 + nmix: 8 + alpha_mix(1): 0.4 qpoints: - 2 - 2 diff --git a/tests/workflows/hp/test_base.py b/tests/workflows/hp/test_base.py index 729d2fc..4701951 100644 --- a/tests/workflows/hp/test_base.py +++ b/tests/workflows/hp/test_base.py @@ -96,11 +96,9 @@ def test_handle_unrecoverable_failure(generate_workchain_hp): @pytest.mark.parametrize( ('inputs', 'expected'), ( - ({}, {'alpha_mix(1)': 0.2, 'niter_max': 200}), - ({'niter_max': 5}, {'alpha_mix(1)': 0.2, 'niter_max': 10}), - ({'alpha_mix(5)': 0.5}, {'alpha_mix(5)': 0.25, 'niter_max': 200}), - ({'alpha_mix(5)': 0.5, 'alpha_mix(10)': 0.4}, {'alpha_mix(5)': 0.25, 'alpha_mix(10)': 0.2, 'niter_max': 200}), - ({'niter_max': 1, 'alpha_mix(2)': 0.3}, {'niter_max': 2, 'alpha_mix(2)': 0.15}), + ({}, {'alpha_mix(1)': 0.2}), + ({'alpha_mix(5)': 0.5}, {'alpha_mix(5)': 0.25}), + ({'alpha_mix(5)': 0.5, 'alpha_mix(10)': 0.4}, {'alpha_mix(5)': 0.25, 'alpha_mix(10)': 0.2}), ), ) # yapf: disable def test_handle_convergence_not_reached(generate_workchain_hp, generate_inputs_hp, inputs, expected): From 9aac7e8bfd082a3b8bdc900daad1a70506397b78 Mon Sep 17 00:00:00 2001 From: Timo Reents Date: Thu, 7 Dec 2023 16:51:19 +0100 Subject: [PATCH 19/32] Fix tests. --- tests/workflows/protocols/hp/test_base/test_default.yml | 3 +++ tests/workflows/protocols/hp/test_main/test_default.yml | 3 +++ tests/workflows/protocols/test_hubbard/test_default.yml | 5 +++++ 3 files changed, 11 insertions(+) diff --git a/tests/workflows/protocols/hp/test_base/test_default.yml b/tests/workflows/protocols/hp/test_base/test_default.yml index 75c8b3b..f6f7742 100644 --- a/tests/workflows/protocols/hp/test_base/test_default.yml +++ b/tests/workflows/protocols/hp/test_base/test_default.yml @@ -9,7 +9,10 @@ hp: withmpi: true parameters: INPUTHP: + alpha_mix(1): 0.4 conv_thr_chi: 5.0e-06 + niter_max: 200 + nmix: 8 qpoints: - - 2 - 2 diff --git a/tests/workflows/protocols/hp/test_main/test_default.yml b/tests/workflows/protocols/hp/test_main/test_default.yml index 6b15aa1..8b3d0a1 100644 --- a/tests/workflows/protocols/hp/test_main/test_default.yml +++ b/tests/workflows/protocols/hp/test_main/test_default.yml @@ -9,7 +9,10 @@ hp: withmpi: true parameters: INPUTHP: + alpha_mix(1): 0.4 conv_thr_chi: 5.0e-06 + niter_max: 200 + nmix: 8 settings: parent_folder_symlink: true parallelize_atoms: true diff --git a/tests/workflows/protocols/test_hubbard/test_default.yml b/tests/workflows/protocols/test_hubbard/test_default.yml index ee18383..010c091 100644 --- a/tests/workflows/protocols/test_hubbard/test_default.yml +++ b/tests/workflows/protocols/test_hubbard/test_default.yml @@ -10,7 +10,10 @@ hubbard: withmpi: true parameters: INPUTHP: + alpha_mix(1): 0.4 conv_thr_chi: 5.0e-06 + niter_max: 200 + nmix: 8 settings: parent_folder_symlink: true parallelize_atoms: true @@ -30,6 +33,7 @@ relax: max_wallclock_seconds: 43200 resources: num_machines: 1 + num_mpiprocs_per_machine: 1 withmpi: true parameters: CELL: @@ -69,6 +73,7 @@ scf: max_wallclock_seconds: 43200 resources: num_machines: 1 + num_mpiprocs_per_machine: 1 withmpi: true parameters: CONTROL: From 7427431d69ed89117e8669438343a887fd4d4fec Mon Sep 17 00:00:00 2001 From: bastonero Date: Fri, 22 Dec 2023 23:32:56 +0000 Subject: [PATCH 20/32] Some fixes to protocol --- .../workflows/protocols/hubbard.yaml | 8 +++++-- tests/conftest.py | 3 +++ .../protocols/test_hubbard/test_default.yml | 4 ++++ tests/workflows/test_hubbard.py | 23 ++++++++----------- 4 files changed, 22 insertions(+), 16 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml index 2459162..d477234 100644 --- a/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml +++ b/src/aiida_quantumespresso_hp/workflows/protocols/hubbard.yaml @@ -5,9 +5,13 @@ default_inputs: tolerance_onsite: 0.1 tolerance_intersite: 0.01 radial_analysis: - radius_max: 10.0 # in Angstrom - thr: 0.1 nn_finder: 'crystal' + nn_inputs: + distance_cutoffs: null # in Angstrom + x_diff_weight: 0 + porous_adjustment: False + radius_max: 10.0 # in Angstrom + thr: 0.01 # in Angstrom scf: kpoints_distance: 0.4 diff --git a/tests/conftest.py b/tests/conftest.py index a64a69e..3f0065a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -494,6 +494,8 @@ def generate_inputs_hubbard(generate_inputs_pw, generate_inputs_hp, generate_hub def _generate_inputs_hubbard(hubbard_structure=None): """Generate default inputs for a `SelfConsistentHubbardWorkChain.""" + from aiida.orm import Bool + hubbard_structure = hubbard_structure or generate_hubbard_structure() inputs_pw = generate_inputs_pw(structure=hubbard_structure) inputs_relax = generate_inputs_pw(structure=hubbard_structure) @@ -508,6 +510,7 @@ def _generate_inputs_hubbard(hubbard_structure=None): inputs_hp.pop('parent_scf') inputs = { + 'meta_convergence': Bool(True), 'hubbard_structure': hubbard_structure, 'relax': { 'base': { diff --git a/tests/workflows/protocols/test_hubbard/test_default.yml b/tests/workflows/protocols/test_hubbard/test_default.yml index ad4e55b..0e87e89 100644 --- a/tests/workflows/protocols/test_hubbard/test_default.yml +++ b/tests/workflows/protocols/test_hubbard/test_default.yml @@ -24,6 +24,10 @@ max_iterations: 10 meta_convergence: true radial_analysis: nn_finder: crystal + nn_inputs: + distance_cutoffs: null + porous_adjustment: false + x_diff_weight: 0 radius_max: 10.0 thr: 0.01 relax: diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index aa72296..98b67f4 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -2,7 +2,7 @@ # pylint: disable=no-member,redefined-outer-name """Tests for the `SelfConsistentHubbardWorkChain` class.""" from aiida.common import AttributeDict -from aiida.orm import Dict +from aiida.orm import Bool, Dict, Int, load_node from plumpy import ProcessState import pytest @@ -119,8 +119,6 @@ def test_validate_inputs_invalid_inputs(generate_workchain_hubbard, generate_inp @pytest.mark.usefixtures('aiida_profile') def test_validate_invalid_positve_input(generate_workchain_hubbard, generate_inputs_hubbard, parameters): """Test `SelfConsistentHubbardWorkChain` for invalid positive inputs.""" - from aiida.orm import Int - inputs = AttributeDict(generate_inputs_hubbard()) inputs.update({parameters: Int(-1)}) @@ -178,8 +176,6 @@ def test_magnetic_setup(generate_workchain_hubbard, generate_inputs_hubbard): @pytest.mark.usefixtures('aiida_profile') def test_skip_relax_iterations(generate_workchain_hubbard, generate_inputs_hubbard, generate_hp_workchain_node): """Test `SelfConsistentHubbardWorkChain` when skipping the first relax iterations.""" - from aiida.orm import Bool, Int - inputs = generate_inputs_hubbard() inputs['skip_relax_iterations'] = Int(1) inputs['meta_convergence'] = Bool(True) @@ -230,8 +226,6 @@ def test_skip_relax_iterations(generate_workchain_hubbard, generate_inputs_hubba @pytest.mark.usefixtures('aiida_profile') def test_relax_frequency(generate_workchain_hubbard, generate_inputs_hubbard): """Test `SelfConsistentHubbardWorkChain` when `relax_frequency` is different from 1.""" - from aiida.orm import Int - inputs = generate_inputs_hubbard() inputs['relax_frequency'] = Int(3) process = generate_workchain_hubbard(inputs=inputs) @@ -257,8 +251,6 @@ def test_radial_analysis( We want to make sure `rmax` is in `hp.parameters`. """ - from aiida.orm import load_node - inputs = generate_inputs_hubbard() inputs['radial_analysis'] = Dict({}) # no need to specify inputs, it will use the defaults process = generate_workchain_hubbard(inputs=inputs) @@ -275,7 +267,6 @@ def test_radial_analysis( @pytest.mark.usefixtures('aiida_profile') def test_should_check_convergence(generate_workchain_hubbard, generate_inputs_hubbard): """Test `SelfConsistentHubbardWorkChain.should_check_convergence`.""" - from aiida.orm import Bool inputs = generate_inputs_hubbard() inputs['meta_convergence'] = Bool(True) process = generate_workchain_hubbard(inputs=inputs) @@ -292,12 +283,12 @@ def test_outline_without_metaconvergence( We want to make sure the `outputs.hubbard_structure` is the last computed. """ - from aiida.orm import Bool inputs = generate_inputs_hubbard() inputs['meta_convergence'] = Bool(False) process = generate_workchain_hubbard(inputs=inputs) process.setup() + process.update_iteration() process.ctx.workchains_hp = [generate_hp_workchain_node()] assert process.inspect_hp() is None @@ -313,12 +304,12 @@ def test_outline( generate_workchain_hubbard, generate_inputs_hubbard, generate_scf_workchain_node, generate_hp_workchain_node ): """Test `SelfConsistentHubbardWorkChain` outline.""" - from aiida.orm import Bool inputs = generate_inputs_hubbard() inputs['meta_convergence'] = Bool(True) process = generate_workchain_hubbard(inputs=inputs) process.setup() + process.update_iteration() process.run_relax() # assert 'workchains_relax' in process.ctx @@ -347,6 +338,7 @@ def test_outline( process.ctx.workchains_hp = [generate_hp_workchain_node()] assert process.inspect_hp() is None + assert process.should_check_convergence() process.check_convergence() assert process.ctx.is_converged @@ -358,9 +350,7 @@ def test_outline( @pytest.mark.usefixtures('aiida_profile') def test_should_run_relax(generate_workchain_hubbard, generate_inputs_hubbard): """Test `SelfConsistentHubbardWorkChain.should_run_relax` method.""" - from aiida.orm import Bool inputs = generate_inputs_hubbard() - inputs['meta_convergence'] = Bool(True) inputs.pop('relax') process = generate_workchain_hubbard(inputs=inputs) @@ -378,6 +368,7 @@ def test_converged_check_convergence( process = generate_workchain_hubbard(inputs=inputs) process.setup() + process.update_iteration() # Mocking current (i.e. "old") and "new" HubbardStructureData, # containing different Hubbard parameters @@ -433,11 +424,13 @@ def test_relabel_check_convergence( process = generate_workchain_hubbard(inputs=inputs) process.setup() + process.update_iteration() current_hubbard_structure = generate_hubbard_structure(u_value=1, only_u=True) process.ctx.current_hubbard_structure = current_hubbard_structure process.ctx.workchains_hp = [generate_hp_workchain_node(relabel=True, u_value=100, only_u=True)] process.check_convergence() + assert process.should_check_convergence() assert not process.ctx.is_converged assert process.ctx.current_hubbard_structure.get_kind_names() != current_hubbard_structure.get_kind_names() @@ -445,6 +438,7 @@ def test_relabel_check_convergence( process.ctx.current_hubbard_structure = current_hubbard_structure process.ctx.workchains_hp = [generate_hp_workchain_node(relabel=True, u_value=100, only_u=True)] process.check_convergence() + assert process.should_check_convergence() assert process.ctx.is_converged assert process.ctx.current_hubbard_structure.get_kind_names() != current_hubbard_structure.get_kind_names() @@ -452,6 +446,7 @@ def test_relabel_check_convergence( process.ctx.current_hubbard_structure = current_hubbard_structure process.ctx.workchains_hp = [generate_hp_workchain_node(relabel=True, u_value=100)] process.check_convergence() + assert process.should_check_convergence() assert process.ctx.is_converged assert process.ctx.current_hubbard_structure.get_kind_names() == current_hubbard_structure.get_kind_names() From a3cad5508ee8b61129e940db2101ef4aeedf9a9a Mon Sep 17 00:00:00 2001 From: bastonero Date: Tue, 13 Feb 2024 13:22:07 +0000 Subject: [PATCH 21/32] HpParser: fix q-points/atoms output test case The current raw output parser would miss some corner cases, when lots of q-points are generated and the number has no more any space left from the parenthesis. The solution is to use a more general regex search. As a sanity check, also the perturbed atom number sites regex search is changed correspondingly. --- src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py | 4 ++-- .../hp/initialization_only_mesh_more_points/aiida.out | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py b/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py index 5041839..96b5a4e 100644 --- a/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py +++ b/src/aiida_quantumespresso_hp/parsers/parse_raw/hp.py @@ -31,13 +31,13 @@ def parse_raw_output(stdout): detect_important_message(logs, line) # A calculation that will only perturb a single atom will only print one line - match = re.search(r'.*The grid of q-points.*\s+([0-9]+)+\s+q-points.*', line) + match = re.search(r'.*The grid of q-points.*?(\d+)+\s+q-points.*', line) if match: parsed_data['number_of_qpoints'] = int(match.group(1)) # Determine the atomic sites that will be perturbed, or that the calculation expects # to have been calculated when post-processing the final matrices - match = re.search(r'.*List of\s+([0-9]+)\s+atoms which will be perturbed.*', line) + match = re.search(r'.*List of.*?(\d+)\s+atoms which will be perturbed.*', line) if match: hubbard_sites = {} number_of_perturbed_atoms = int(match.group(1)) diff --git a/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.out b/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.out index a5b4b02..dc3e095 100644 --- a/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.out +++ b/tests/parsers/fixtures/hp/initialization_only_mesh_more_points/aiida.out @@ -167,7 +167,7 @@ Changing the type of the perturbed atom back to its original type... - The grid of q-points ( 4, 4, 4) ( 18 q-points ) : + The grid of q-points ( 4, 4, 4) (18 q-points ) : N xq(1) xq(2) xq(3) wq 1 0.000000000 0.000000000 0.000000000 0.015625000 2 0.000000000 0.216131358 -0.211002628 0.062500000 From 392a772abe71eccabb0836f0d0c07dd9821f66fc Mon Sep 17 00:00:00 2001 From: bastonero Date: Fri, 19 Apr 2024 10:54:39 +0000 Subject: [PATCH 22/32] Fix logic compatibility with `main` --- src/aiida_quantumespresso_hp/workflows/hubbard.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index bb13deb..b4cf257 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -158,10 +158,12 @@ def define(cls, spec): ), cls.run_hp, cls.inspect_hp, - cls.check_convergence, + if_(cls.should_check_convergence)( + cls.check_convergence, + ), if_(cls.should_clean_workdir)( cls.clean_iteration, - ) + ), ), cls.run_results, ) @@ -414,7 +416,7 @@ def get_pseudos(self) -> dict: for kind in self.ctx.current_hubbard_structure.kinds: for key, pseudo in pseudos.items(): symbol = re.sub(r'\d', '', key) - if re.match(fr'{kind.symbol}[0-9]*', symbol): + if re.match(fr'{kind.symbol}*.', symbol): results[kind.name] = pseudo break else: @@ -634,8 +636,8 @@ def check_convergence(self): self.ctx.current_hubbard_structure = workchain.outputs.hubbard_structure self.relabel_hubbard_structure(workchain) - if not self.should_check_convergence(): - return + # if not self.should_check_convergence(): + # return if not len(ref_params) == len(new_params): self.report('The new and old Hubbard parameters have different lenghts. Assuming to be at the first cycle.') From 2c512766dee2858091683288167a21fa75e7738b Mon Sep 17 00:00:00 2001 From: bastonero Date: Fri, 19 Apr 2024 11:20:05 +0000 Subject: [PATCH 23/32] Add exit code for relabelling failure Fixes #66 The relabel function might not work if the spin configuration changes and the kinds cannot be determined uniquely by the parsed configuration from the hp.x post-processing. For this reason, we catch the error and exit smoothly with a new exit code if this would happen. --- .../functions/structure_relabel_kinds.py | 5 ++++- src/aiida_quantumespresso_hp/workflows/hubbard.py | 13 ++++++++++--- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py b/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py index 0c547e6..d175d5e 100644 --- a/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py +++ b/src/aiida_quantumespresso_hp/calculations/functions/structure_relabel_kinds.py @@ -64,7 +64,10 @@ def structure_relabel_kinds( new_magnetization[kind_name] = old_magnetization[site['kind']] site = sites[index] - relabeled.append_atom(position=site.position, symbols=symbol, name=kind_name) + try: + relabeled.append_atom(position=site.position, symbols=symbol, name=kind_name) + except ValueError as exc: + raise ValueError('cannot distinguish kinds with the given Hubbard input configuration') from exc # Now add the non-Hubbard sites for site in sites[len(relabeled.sites):]: diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index d517163..d7c13f4 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -171,6 +171,9 @@ def define(cls, spec): spec.exit_code(330, 'ERROR_FAILED_TO_DETERMINE_PSEUDO_POTENTIAL', message='Failed to determine the correct pseudo potential after the structure changed its kind names.') + spec.exit_code(340, 'ERROR_RELABELLING_KINDS', + message='Failed to determine the kind names during the relabelling.') + spec.exit_code(401, 'ERROR_SUB_PROCESS_FAILED_RECON', message='The reconnaissance PwBaseWorkChain sub process failed') spec.exit_code(402, 'ERROR_SUB_PROCESS_FAILED_RELAX', @@ -428,9 +431,13 @@ def relabel_hubbard_structure(self, workchain) -> None: if not is_intersite_hubbard(workchain.outputs.hubbard_structure.hubbard): for site in workchain.outputs.hubbard.dict.sites: if not site['type'] == site['new_type']: - result = structure_relabel_kinds( - self.ctx.current_hubbard_structure, workchain.outputs.hubbard, self.ctx.current_magnetic_moments - ) + try: + result = structure_relabel_kinds( + self.ctx.current_hubbard_structure, workchain.outputs.hubbard, + self.ctx.current_magnetic_moments + ) + except ValueError: + return self.exit_codes.ERROR_RELABELLING_KINDS self.ctx.current_hubbard_structure = result['hubbard_structure'] if self.ctx.current_magnetic_moments is not None: self.ctx.current_magnetic_moments = result['starting_magnetization'] From 3671a3c6963052ca4fbb0f9a6ffd7ca8c8ac27c0 Mon Sep 17 00:00:00 2001 From: bastonero Date: Mon, 22 Apr 2024 13:41:56 +0000 Subject: [PATCH 24/32] Fix the convergence check in self-consistent workflow The convergence check on parameters had a bug in the logic. That logic would work for 1 Hubbard atom only, and that's the reason why this passed unseen in the tests. The fix is rather simple, and the new tests are tested again a case which made the old tests to make. --- src/aiida_quantumespresso_hp/workflows/hubbard.py | 4 ++-- tests/conftest.py | 4 +++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index d517163..8e346e6 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -634,7 +634,7 @@ def check_convergence(self): new = np.array(new_onsites, dtype='object') diff = np.abs(old[:, 4] - new[:, 4]) - if (diff > self.inputs.tolerance_onsite).all(): + if (diff > self.inputs.tolerance_onsite).any(): check_onsites = False self.report(f'Hubbard onsites parameters are not converged. Max difference is {diff.max()}.') @@ -644,7 +644,7 @@ def check_convergence(self): new = np.array(new_intersites, dtype='object') diff = np.abs(old[:, 4] - new[:, 4]) - if (diff > self.inputs.tolerance_intersite).all(): + if (diff > self.inputs.tolerance_intersite).any(): check_onsites = False self.report(f'Hubbard intersites parameters are not converged. Max difference is {diff.max()}.') diff --git a/tests/conftest.py b/tests/conftest.py index 84a2943..2bce368 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -377,7 +377,7 @@ def _generate_structure(structure_id=None): def generate_hubbard_structure(generate_structure): """Return a `HubbardStructureData` representing bulk silicon.""" - def _generate_hubbard_structure(only_u=False, u_value=1e-5, v_value=1e-5): + def _generate_hubbard_structure(only_u=False, u_value=1e-5, v_value=1e-5, u_o_value=1e-5): """Return a `StructureData` representing bulk silicon.""" from aiida_quantumespresso.data.hubbard_structure import HubbardStructureData @@ -386,8 +386,10 @@ def _generate_hubbard_structure(only_u=False, u_value=1e-5, v_value=1e-5): if only_u: hubbard_structure.initialize_onsites_hubbard('Co', '3d', u_value) + hubbard_structure.initialize_onsites_hubbard('O', '2p', u_o_value) else: hubbard_structure.initialize_onsites_hubbard('Co', '3d', u_value) + hubbard_structure.initialize_onsites_hubbard('O', '2p', u_o_value) hubbard_structure.initialize_intersites_hubbard('Co', '3d', 'O', '2p', v_value) return hubbard_structure From 2fe8e72c1423d33a2e8f4d87d3f30d2ccb3fe7d8 Mon Sep 17 00:00:00 2001 From: bastonero Date: Tue, 23 Apr 2024 16:30:05 +0000 Subject: [PATCH 25/32] Fix the convergence check in self-consistent workflow The convergence check on parameters had a bug in the logic. That logic would work for 1 Hubbard atom only, and that's the reason why this passed unseen in the tests. The fix is rather simple, and the new tests are tested again a case which made the old tests to make. --- src/aiida_quantumespresso_hp/workflows/hubbard.py | 4 ++-- tests/conftest.py | 5 ++++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index d517163..8e346e6 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -634,7 +634,7 @@ def check_convergence(self): new = np.array(new_onsites, dtype='object') diff = np.abs(old[:, 4] - new[:, 4]) - if (diff > self.inputs.tolerance_onsite).all(): + if (diff > self.inputs.tolerance_onsite).any(): check_onsites = False self.report(f'Hubbard onsites parameters are not converged. Max difference is {diff.max()}.') @@ -644,7 +644,7 @@ def check_convergence(self): new = np.array(new_intersites, dtype='object') diff = np.abs(old[:, 4] - new[:, 4]) - if (diff > self.inputs.tolerance_intersite).all(): + if (diff > self.inputs.tolerance_intersite).any(): check_onsites = False self.report(f'Hubbard intersites parameters are not converged. Max difference is {diff.max()}.') diff --git a/tests/conftest.py b/tests/conftest.py index 84a2943..187de05 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -377,7 +377,7 @@ def _generate_structure(structure_id=None): def generate_hubbard_structure(generate_structure): """Return a `HubbardStructureData` representing bulk silicon.""" - def _generate_hubbard_structure(only_u=False, u_value=1e-5, v_value=1e-5): + def _generate_hubbard_structure(only_u=False, u_value=1e-5, v_value=1e-5, u_o_value=1e-5): """Return a `StructureData` representing bulk silicon.""" from aiida_quantumespresso.data.hubbard_structure import HubbardStructureData @@ -386,9 +386,12 @@ def _generate_hubbard_structure(only_u=False, u_value=1e-5, v_value=1e-5): if only_u: hubbard_structure.initialize_onsites_hubbard('Co', '3d', u_value) + hubbard_structure.initialize_onsites_hubbard('O', '2p', u_o_value) else: hubbard_structure.initialize_onsites_hubbard('Co', '3d', u_value) + hubbard_structure.initialize_onsites_hubbard('O', '2p', u_o_value) hubbard_structure.initialize_intersites_hubbard('Co', '3d', 'O', '2p', v_value) + hubbard_structure.initialize_intersites_hubbard('O', '2p', 'Co', '3d', u_o_value) return hubbard_structure From 996ce6407e02e2c007ec287eebf33efd2a519e22 Mon Sep 17 00:00:00 2001 From: bastonero Date: Tue, 7 May 2024 13:52:06 +0000 Subject: [PATCH 26/32] Fix symbol matching pattern --- .../workflows/hubbard.py | 23 +++++++++++++++---- tests/workflows/test_hubbard.py | 14 ++++++----- 2 files changed, 26 insertions(+), 11 deletions(-) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index a42e449..10b3d2f 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -419,7 +419,7 @@ def get_pseudos(self) -> dict: for kind in self.ctx.current_hubbard_structure.kinds: for key, pseudo in pseudos.items(): symbol = re.sub(r'\d', '', key) - if re.match(fr'{kind.symbol}*.', symbol): + if re.match(fr'{kind.symbol}[0-9]*', symbol): results[kind.name] = pseudo break else: @@ -562,12 +562,25 @@ def recon_scf(self): bands = workchain.outputs.output_band parameters = workchain.outputs.output_parameters.get_dict() - # number_electrons = parameters['number_of_electrons'] - # is_insulator, _ = find_bandgap(bands, number_electrons=number_electrons) + fermi_energy = parameters['fermi_energy'] - is_insulator, _ = find_bandgap(bands, fermi_energy=fermi_energy) + number_electrons = parameters['number_of_electrons'] + + # Due to uncertainty in the prediction of the fermi energy, we try + # both options of this function. If one of the two give an insulating + # state as a result, we then set fixed occupation as it is likely that + # hp.x would crash otherwise. + is_insulator_1, _ = find_bandgap(bands, fermi_energy=fermi_energy) + + # I am not sure, but I think for some materials, e.g. having anti-ferromagnetic + # ordering, the following function would crash for some reason, possibly due + # to the format of the BandsData. To double check if actually needed. + try: + is_insulator_2, _ = find_bandgap(bands, number_electrons=number_electrons) + except: # pylint: disable=bare-except + is_insulator_2 = False - if is_insulator: + if is_insulator_1 or is_insulator_2: self.report('after relaxation, system is determined to be an insulator') self.ctx.is_insulator = True else: diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index fb66a5b..84c780e 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -36,10 +36,14 @@ def _generate_scf_workchain_node(exit_status=0, relax=False, remote_folder=False node.set_process_state(ProcessState.FINISHED) node.set_exit_status(exit_status) - parameters = Dict(dict={ - 'number_of_bands': 1, - 'total_magnetization': 1, - }).store() + parameters = Dict( + dict={ + 'number_of_bands': 1, + 'number_of_electrons': 1, + 'fermi_energy': 0, + 'total_magnetization': 1, + } + ).store() parameters.base.links.add_incoming(node, link_type=LinkType.RETURN, link_label='output_parameters') if relax: @@ -228,8 +232,6 @@ def test_skip_relax_iterations_relabeling( generate_workchain_hubbard, generate_inputs_hubbard, generate_hp_workchain_node, generate_hubbard_structure ): """Test `SelfConsistentHubbardWorkChain` when skipping the first relax iterations and relabeling is needed.""" - from aiida.orm import Bool, Int - inputs = generate_inputs_hubbard() inputs['skip_relax_iterations'] = Int(1) inputs['meta_convergence'] = Bool(True) From 729fc02d457f618c2e3ed7de58ccf8d697de114d Mon Sep 17 00:00:00 2001 From: bastonero Date: Wed, 2 Oct 2024 08:50:38 +0000 Subject: [PATCH 27/32] Change nearest-neighbour analysis and parser The self-consistent workflow now checks the maximum number of neighbours and defines the hp inputs so to print all the possible intersites couples. The parser is then instructed to only keep the interactions that were defined in the initial HubbardStructureData. This is useful in case the actual first neighbours are different then the activated intersite interactions, thus a screening of the HUBBARD.dat file cannot be avoided. This methodology allows for having a more consistent definition and parsing of the nearest neighbours using Voronoi tessellation. --- pyproject.toml | 2 +- src/aiida_quantumespresso_hp/parsers/hp.py | 33 +- .../workflows/hubbard.py | 13 +- tests/fixtures/structures/MnCoS.cif | 28 + .../hp/voronoi_hubbard_structure/HUBBARD.dat | 24 + .../aiida.Hubbard_parameters.dat | 5073 +++++++++++++++++ .../voronoi_hubbard_structure/aiida.chi.dat | 5 + .../hp/voronoi_hubbard_structure/aiida.in | 9 + .../hp/voronoi_hubbard_structure/aiida.out | 323 ++ tests/parsers/test_hp.py | 82 + ...st_hp_voronoi_hubbard_structure_False_.yml | 179 + ...est_hp_voronoi_hubbard_structure_True_.yml | 259 + .../protocols/test_hubbard/test_default.yml | 2 - tests/workflows/test_hubbard.py | 5 +- 14 files changed, 6022 insertions(+), 15 deletions(-) create mode 100644 tests/fixtures/structures/MnCoS.cif create mode 100644 tests/parsers/fixtures/hp/voronoi_hubbard_structure/HUBBARD.dat create mode 100644 tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.Hubbard_parameters.dat create mode 100644 tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.chi.dat create mode 100644 tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.in create mode 100644 tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.out create mode 100644 tests/parsers/test_hp/test_hp_voronoi_hubbard_structure_False_.yml create mode 100644 tests/parsers/test_hp/test_hp_voronoi_hubbard_structure_True_.yml diff --git a/pyproject.toml b/pyproject.toml index 47ad3fc..f54350f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ keywords = ['aiida', 'workflows'] requires-python = '>=3.8' dependencies = [ 'aiida-core~=2.2', - 'aiida-quantumespresso~=4.3', + 'aiida-quantumespresso@git+https://github.com/bastonero/aiida-quantumespresso.git@feat/voronoi', ] [project.urls] diff --git a/src/aiida_quantumespresso_hp/parsers/hp.py b/src/aiida_quantumespresso_hp/parsers/hp.py index 74bb691..3028d2a 100644 --- a/src/aiida_quantumespresso_hp/parsers/hp.py +++ b/src/aiida_quantumespresso_hp/parsers/hp.py @@ -5,7 +5,7 @@ from aiida import orm from aiida.common import exceptions from aiida.parsers import Parser -import numpy +import numpy as np from aiida_quantumespresso_hp.calculations.hp import HpCalculation @@ -114,8 +114,8 @@ def parse_stdout(self): parsed_data, logs = parse_raw_output(stdout) except Exception: # pylint: disable=broad-except return self.exit_codes.ERROR_OUTPUT_STDOUT_PARSE - else: - self.out('parameters', orm.Dict(parsed_data)) + + self.out('parameters', orm.Dict(parsed_data)) # If the stdout was incomplete, most likely the job was interrupted before it could cleanly finish, so the # output files are most likely corrupt and cannot be restarted from @@ -202,17 +202,38 @@ def parse_hubbard_dat(self, folder_path): :return: optional exit code in case of an error """ + from aiida_quantumespresso.common.hubbard import Hubbard from aiida_quantumespresso.utils.hubbard import HubbardUtils filename = HpCalculation.filename_output_hubbard_dat filepath = os.path.join(folder_path, filename) hubbard_structure = self.node.inputs.hubbard_structure.clone() + + intersites = None + if 'settings' in self.node.inputs: + if 'radial_analysis' in self.node.inputs.settings.get_dict(): + kwargs = self.node.inputs.settings.dict.radial_analysis + intersites = HubbardUtils(hubbard_structure).get_intersites_list(**kwargs) + hubbard_structure.clear_hubbard_parameters() hubbard_utils = HubbardUtils(hubbard_structure) hubbard_utils.parse_hubbard_dat(filepath=filepath) - self.out('hubbard_structure', hubbard_utils.hubbard_structure) + if intersites is None: + self.out('hubbard_structure', hubbard_utils.hubbard_structure) + else: + hubbard_list = np.array(hubbard_utils.hubbard_structure.hubbard.to_list(), dtype='object') + parsed_intersites = hubbard_list[:, [0, 2, 5]].tolist() + selected_indices = [] + + for i, intersite in enumerate(parsed_intersites): + if intersite in intersites: + selected_indices.append(i) + + hubbard = Hubbard.from_list(hubbard_list[selected_indices]) + hubbard_structure.hubbard = hubbard + self.out('hubbard_structure', hubbard_structure) def get_hubbard_structure(self): """Set in output an ``HubbardStructureData`` with standard Hubbard U formulation.""" @@ -264,7 +285,7 @@ def parse_chi_content(self, handle): for matrix_name in ('chi0', 'chi'): matrix_block = blocks[matrix_name] matrix_data = data[matrix_block[0]:matrix_block[1]] - matrix = numpy.array(self.parse_hubbard_matrix(matrix_data)) + matrix = np.array(self.parse_hubbard_matrix(matrix_data)) result[matrix_name] = matrix return result @@ -377,4 +398,4 @@ def parse_hubbard_matrix(data): if row: matrix.append(row) - return numpy.array(matrix) + return np.array(matrix) diff --git a/src/aiida_quantumespresso_hp/workflows/hubbard.py b/src/aiida_quantumespresso_hp/workflows/hubbard.py index 10b3d2f..aaf2bd2 100644 --- a/src/aiida_quantumespresso_hp/workflows/hubbard.py +++ b/src/aiida_quantumespresso_hp/workflows/hubbard.py @@ -594,17 +594,20 @@ def run_hp(self): inputs = AttributeDict(self.exposed_inputs(HpWorkChain, namespace='hubbard')) if 'radial_analysis' in self.inputs: - from qe_tools import CONSTANTS - kwargs = self.inputs.radial_analysis.get_dict() hubbard_utils = HubbardUtils(self.ctx.current_hubbard_structure) - radius = hubbard_utils.get_intersites_radius(**kwargs) # in Angstrom + num_neigh = hubbard_utils.get_max_number_of_neighbours(**kwargs) parameters = inputs.hp.parameters.get_dict() - parameters['INPUTHP'].pop('num_neigh', None) - parameters['INPUTHP']['rmax'] = radius / CONSTANTS.bohr_to_ang + parameters['INPUTHP']['num_neigh'] = num_neigh + + settings = {'radial_analysis': self.inputs.radial_analysis.get_dict()} + if 'settings' in inputs.hp: + settings = inputs.hp.settings.get_dict() + settings['radial_analysis'] = self.inputs.radial_analysis.get_dict() inputs.hp.parameters = orm.Dict(parameters) + inputs.hp.settings = orm.Dict(settings) inputs.clean_workdir = self.inputs.clean_workdir inputs.hp.parent_scf = workchain.outputs.remote_folder diff --git a/tests/fixtures/structures/MnCoS.cif b/tests/fixtures/structures/MnCoS.cif new file mode 100644 index 0000000..2d2b5c4 --- /dev/null +++ b/tests/fixtures/structures/MnCoS.cif @@ -0,0 +1,28 @@ +data_image0 +_chemical_formula_structural MnCoS +_chemical_formula_sum "Mn1 Co1 S1" +_cell_length_a 4.02254 +_cell_length_b 4.02254 +_cell_length_c 4.02254 +_cell_angle_alpha 60 +_cell_angle_beta 60 +_cell_angle_gamma 60 + +_space_group_name_H-M_alt "P 1" +_space_group_IT_number 1 + +loop_ + _space_group_symop_operation_xyz + 'x, y, z' + +loop_ + _atom_site_type_symbol + _atom_site_label + _atom_site_symmetry_multiplicity + _atom_site_fract_x + _atom_site_fract_y + _atom_site_fract_z + _atom_site_occupancy + Mn Mn1 1.0 0.00000 0.00000 0.00000 1.0000 + Co Co1 1.0 0.75000 0.75000 0.75000 1.0000 + S S1 1.0 0.50000 0.50000 0.50000 1.0000 diff --git a/tests/parsers/fixtures/hp/voronoi_hubbard_structure/HUBBARD.dat b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/HUBBARD.dat new file mode 100644 index 0000000..7b250a8 --- /dev/null +++ b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/HUBBARD.dat @@ -0,0 +1,24 @@ +# Copy this data in the pw.x input file for DFT+Hubbard calculations +HUBBARD {ortho-atomic} +V Mn-3d Mn-3d 1 1 5.3443 +V Mn-3d Co-3d 1 14 0.4967 +V Mn-3d Co-3d 1 8 0.4967 +V Mn-3d Co-3d 1 5 0.4967 +V Mn-3d Co-3d 1 32 0.4967 +V Mn-3d S-3p 1 42 0.0256 +V Mn-3d S-3p 1 36 0.0256 +V Mn-3d S-3p 1 18 0.0256 +V Mn-3d S-3p 1 33 0.0256 +V Mn-3d S-3p 1 15 0.0256 +V Mn-3d S-3p 1 9 0.0256 +V Co-3d Co-3d 2 2 6.6772 +V Co-3d Mn-3d 2 79 0.4967 +V Co-3d S-3p 2 45 0.1165 +V Co-3d S-3p 2 69 0.1165 +V Co-3d S-3p 2 51 0.1165 +V Co-3d Mn-3d 2 76 0.4967 +V Co-3d Mn-3d 2 70 0.4967 +V Co-3d Mn-3d 2 52 0.4967 +V Co-3d S-3p 2 3 0.1165 +V Co-3d Co-3d 2 17 0.0948 +V Co-3d Co-3d 2 44 0.0948 diff --git a/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.Hubbard_parameters.dat b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.Hubbard_parameters.dat new file mode 100644 index 0000000..d60b755 --- /dev/null +++ b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.Hubbard_parameters.dat @@ -0,0 +1,5073 @@ + + =-------------------------------------------------------------------------------= + + Hubbard U parameters: + + site n. type label spin new_type new_label manifold Hubbard U (eV) + 1 2 Mn 1 2 Mn 3d 5.3443 + 2 1 Co 1 1 Co 3d 6.6772 + 3 3 S 0 3 S 3p 3.1641 + + =-------------------------------------------------------------------------------= + + + Hubbard V parameters: + (adapted for a supercell 3x3x3) + + Atom 1 Atom 2 Distance (Bohr) Hubbard V (eV) + + 1 Mn 1 Mn 0.000000 5.3443 + 1 Mn 14 Co 4.451418 0.4967 + 1 Mn 8 Co 4.451418 0.4967 + 1 Mn 5 Co 4.451418 0.4967 + 1 Mn 32 Co 4.451418 0.4967 + 1 Mn 42 S 5.140055 0.0256 + 1 Mn 36 S 5.140055 0.0256 + 1 Mn 18 S 5.140055 0.0256 + 1 Mn 33 S 5.140055 0.0256 + 1 Mn 15 S 5.140055 0.0256 + 1 Mn 9 S 5.140055 0.0256 + 1 Mn 43 Mn 7.269136 -0.0439 + 1 Mn 25 Mn 7.269136 -0.0439 + 1 Mn 16 Mn 7.269136 -0.0439 + 1 Mn 67 Mn 7.269136 -0.0439 + 1 Mn 64 Mn 7.269136 -0.0439 + 1 Mn 49 Mn 7.269136 -0.0439 + 1 Mn 46 Mn 7.269136 -0.0439 + 1 Mn 40 Mn 7.269136 -0.0439 + 1 Mn 34 Mn 7.269136 -0.0439 + 1 Mn 58 Mn 7.269136 -0.0439 + 1 Mn 37 Mn 7.269136 -0.0439 + 1 Mn 19 Mn 7.269136 -0.0439 + 1 Mn 41 Co 8.523817 -0.0257 + 1 Mn 35 Co 8.523817 -0.0257 + 1 Mn 17 Co 8.523817 -0.0257 + 1 Mn 57 S 8.902837 -0.0431 + 1 Mn 24 S 8.902837 -0.0407 + 1 Mn 12 S 8.902837 -0.0407 + 1 Mn 6 S 8.902837 -0.0407 + 1 Mn 3 S 8.902837 -0.0407 + 1 Mn 55 Mn 10.280110 -0.1085 + 1 Mn 22 Mn 10.280110 -0.1085 + 1 Mn 10 Mn 10.280110 -0.1085 + 1 Mn 73 Mn 10.280110 -0.1085 + 1 Mn 61 Mn 10.280110 -0.1085 + 1 Mn 28 Mn 10.280110 -0.1085 + 1 Mn 56 Co 11.202490 -0.0784 + 1 Mn 23 Co 11.202490 -0.0784 + 1 Mn 11 Co 11.202490 -0.0784 + 1 Mn 66 S 11.493513 -0.0641 + 1 Mn 60 S 11.493513 -0.0641 + 1 Mn 48 S 11.493513 -0.0641 + 1 Mn 39 S 11.493513 -0.0641 + 1 Mn 27 S 11.493513 -0.0641 + 1 Mn 21 S 11.493513 -0.0641 + 1 Mn 76 Mn 12.590512 -0.1215 + 1 Mn 70 Mn 12.590512 -0.1215 + 1 Mn 52 Mn 12.590512 -0.1215 + 1 Mn 31 Mn 12.590512 -0.1215 + 1 Mn 13 Mn 12.590512 -0.1215 + 1 Mn 7 Mn 12.590512 -0.1215 + 1 Mn 2 Co 13.354255 -0.1035 + 1 Mn 45 S 15.420165 -0.0443 + + 2 Co 2 Co 0.000000 6.6772 + 2 Co 79 Mn 4.451418 0.4967 + 2 Co 45 S 4.451418 0.1165 + 2 Co 69 S 4.451418 0.1165 + 2 Co 51 S 4.451418 0.1165 + 2 Co 76 Mn 4.451418 0.4967 + 2 Co 70 Mn 4.451418 0.4967 + 2 Co 52 Mn 4.451418 0.4967 + 2 Co 3 S 4.451418 0.1165 + 2 Co 17 Co 7.269136 0.0948 + 2 Co 44 Co 7.269136 0.0948 + 2 Co 65 Co 7.269136 0.0948 + 2 Co 47 Co 7.269136 0.0948 + 2 Co 41 Co 7.269136 0.0948 + 2 Co 26 Co 7.269136 0.0948 + 2 Co 68 Co 7.269136 0.0948 + 2 Co 50 Co 7.269136 0.0948 + 2 Co 35 Co 7.269136 0.0948 + 2 Co 59 Co 7.269136 0.0948 + 2 Co 38 Co 7.269136 0.0948 + 2 Co 20 Co 7.269136 0.0948 + 2 Co 54 S 8.523817 -0.0531 + 2 Co 39 S 8.523817 -0.0531 + 2 Co 21 S 8.523817 -0.0531 + 2 Co 78 S 8.523817 -0.0531 + 2 Co 66 S 8.523817 -0.0531 + 2 Co 60 S 8.523817 -0.0531 + 2 Co 49 Mn 8.523817 -0.0257 + 2 Co 75 S 8.523817 -0.0531 + 2 Co 72 S 8.523817 -0.0531 + 2 Co 63 S 8.523817 -0.0531 + 2 Co 48 S 8.523817 -0.0531 + 2 Co 30 S 8.523817 -0.0531 + 2 Co 27 S 8.523817 -0.0531 + 2 Co 67 Mn 8.523817 -0.0257 + 2 Co 43 Mn 8.523817 -0.0257 + 2 Co 56 Co 10.280110 -0.0591 + 2 Co 23 Co 10.280110 -0.0591 + 2 Co 11 Co 10.280110 -0.0591 + 2 Co 74 Co 10.280110 -0.0591 + 2 Co 62 Co 10.280110 -0.0591 + 2 Co 29 Co 10.280110 -0.0591 + 2 Co 61 Mn 11.202490 -0.0784 + 2 Co 28 Mn 11.202490 -0.0784 + 2 Co 36 S 11.202490 -0.0722 + 2 Co 18 S 11.202490 -0.0722 + 2 Co 73 Mn 11.202490 -0.0784 + 2 Co 42 S 11.202490 -0.0722 + 2 Co 77 Co 12.590512 -0.0565 + 2 Co 14 Co 12.590512 -0.0565 + 2 Co 71 Co 12.590512 -0.0565 + 2 Co 53 Co 12.590512 -0.0565 + 2 Co 32 Co 12.590512 -0.0565 + 2 Co 8 Co 12.590512 -0.0565 + 2 Co 81 S 13.354255 -0.0478 + 2 Co 12 S 13.354255 -0.0525 + 2 Co 57 S 13.354255 -0.0478 + 2 Co 24 S 13.354255 -0.0478 + 2 Co 1 Mn 13.354255 -0.1035 + + 3 S 3 S 0.000000 3.1641 + 3 S 41 Co 4.451418 0.1165 + 3 S 35 Co 4.451418 0.1165 + 3 S 17 Co 4.451418 0.1165 + 3 S 2 Co 4.451418 0.1165 + 3 S 76 Mn 5.140055 0.0256 + 3 S 70 Mn 5.140055 0.0256 + 3 S 67 Mn 5.140055 0.0256 + 3 S 52 Mn 5.140055 0.0256 + 3 S 49 Mn 5.140055 0.0256 + 3 S 43 Mn 5.140055 0.0256 + 3 S 66 S 7.269136 -0.0568 + 3 S 60 S 7.269136 -0.0568 + 3 S 48 S 7.269136 -0.0568 + 3 S 42 S 7.269136 -0.0568 + 3 S 39 S 7.269136 -0.0568 + 3 S 21 S 7.269136 -0.0568 + 3 S 18 S 7.269136 -0.0568 + 3 S 69 S 7.269136 -0.0568 + 3 S 51 S 7.269136 -0.0568 + 3 S 45 S 7.269136 -0.0568 + 3 S 36 S 7.269136 -0.0568 + 3 S 27 S 7.269136 -0.0568 + 3 S 65 Co 8.523817 -0.0531 + 3 S 59 Co 8.523817 -0.0531 + 3 S 56 Co 8.523817 -0.0531 + 3 S 38 Co 8.523817 -0.0531 + 3 S 26 Co 8.523817 -0.0531 + 3 S 14 Co 8.523817 -0.0531 + 3 S 32 Co 8.523817 -0.0531 + 3 S 20 Co 8.523817 -0.0531 + 3 S 11 Co 8.523817 -0.0531 + 3 S 47 Co 8.523817 -0.0531 + 3 S 23 Co 8.523817 -0.0531 + 3 S 8 Co 8.523817 -0.0531 + 3 S 79 Mn 8.902837 -0.0431 + 3 S 73 Mn 8.902837 -0.0431 + 3 S 61 Mn 8.902837 -0.0407 + 3 S 28 Mn 8.902837 -0.0407 + 3 S 1 Mn 8.902837 -0.0407 + 3 S 75 S 10.280110 -0.0117 + 3 S 63 S 10.280110 -0.0117 + 3 S 30 S 10.280110 -0.0117 + 3 S 57 S 10.280110 -0.0117 + 3 S 24 S 10.280110 -0.0117 + 3 S 12 S 10.280110 -0.0117 + 3 S 50 Co 11.202490 -0.0722 + 3 S 68 Co 11.202490 -0.0722 + 3 S 44 Co 11.202490 -0.0722 + 3 S 64 Mn 11.493513 -0.0641 + 3 S 58 Mn 11.493513 -0.0641 + 3 S 46 Mn 11.493513 -0.0641 + 3 S 37 Mn 11.493513 -0.0641 + 3 S 25 Mn 11.493513 -0.0641 + 3 S 19 Mn 11.493513 -0.0641 + 3 S 78 S 12.590512 -0.0149 + 3 S 15 S 12.590512 -0.0149 + 3 S 72 S 12.590512 -0.0149 + 3 S 54 S 12.590512 -0.0149 + 3 S 33 S 12.590512 -0.0149 + 3 S 9 S 12.590512 -0.0149 + 3 S 74 Co 13.354255 -0.0478 + 3 S 62 Co 13.354255 -0.0478 + 3 S 29 Co 13.354255 -0.0478 + 3 S 5 Co 13.354255 -0.0478 + 3 S 16 Mn 15.420165 -0.0443 + + + =-------------------------------------------------------------------= + + 6 nearest neighbors of every atom are written to HUBBARD.dat + + chi0 matrix : + -0.349013 0.021811 -0.001012 0.005204 0.021283 -0.001012 0.005204 0.021283 + 0.002361 0.005204 0.021283 -0.001012 0.007641 0.021811 0.000506 0.005204 + 0.021283 0.000506 0.005204 0.021283 0.002361 0.005204 0.021283 0.000506 + 0.007641 -0.095742 0.002361 0.005204 0.021283 -0.001012 0.007641 0.021811 + 0.000506 0.005204 0.021283 0.000506 0.007641 0.021811 0.000506 0.007641 + 0.021811 0.000542 0.006119 0.028618 0.000506 0.005204 0.021283 0.000506 + 0.006119 0.028618 0.000506 0.006119 0.028618 -0.001012 0.005204 0.021283 + 0.002361 0.005204 0.021283 0.000506 0.007641 -0.095742 0.002361 0.005204 + 0.021283 0.000506 0.006119 0.028618 0.000506 0.006119 0.028618 -0.001012 + 0.007641 -0.095742 0.002361 0.006119 0.028618 -0.001012 0.007641 -0.095742 + -0.001012 + + 0.021811 -1.971126 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b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.chi.dat new file mode 100644 index 0000000..04d4379 --- /dev/null +++ b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.chi.dat @@ -0,0 +1,5 @@ + chi0 : + -0.270847692461309 + + chi : + -0.086463439940486 diff --git a/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.in b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.in new file mode 100644 index 0000000..8648ec6 --- /dev/null +++ b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.in @@ -0,0 +1,9 @@ +&INPUTHP + conv_thr_chi = 1.0000000000d-06 + iverbosity = 2 + nq1 = 1 + nq2 = 1 + nq3 = 1 + outdir = 'out' + prefix = 'aiida' +/ diff --git a/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.out b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.out new file mode 100644 index 0000000..bfe7be4 --- /dev/null +++ b/tests/parsers/fixtures/hp/voronoi_hubbard_structure/aiida.out @@ -0,0 +1,323 @@ + + Program HP v.7.2 starts on 20May2024 at 22: 5:43 + + This program is part of the open-source Quantum ESPRESSO suite + for quantum simulation of materials; please cite + "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); + "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017); + "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020); + URL http://www.quantum-espresso.org", + in publications or presentations arising from this work. More details at + http://www.quantum-espresso.org/quote + + Parallel version (MPI), running on 32 processors + + MPI processes distributed on 1 nodes + R & G space division: proc/nbgrp/npool/nimage = 32 + 507506 MiB available memory on the printing compute node when the environment starts + + + =---------------------------------------------------------------------------= + + Calculation of Hubbard parameters using the HP code based on DFPT + + Please cite the following papers when using this program: + + - HP code : Comput. Phys. Commun. 279, 108455 (2022). + + - Theory : Phys. Rev. B 98, 085127 (2018) and + + Phys. Rev. B 103, 045141 (2021). + + =-----------------------------------------------------------------------------= + + Reading xml data from directory: + + out/aiida.save/ + + IMPORTANT: XC functional enforced from input : + Exchange-correlation= PBESOL + ( 1 4 10 8 0 0 0) + Any further DFT definition will be discarded + Please, verify this is what you really want + + + Parallelization info + -------------------- + sticks: dense smooth PW G-vecs: dense smooth PW + Min 88 29 8 3117 599 96 + Max 89 30 9 3122 601 99 + Sum 2839 955 283 99845 19195 3143 + + Using Pencil Decomposition + + + Check: negative core charge= -0.000013 + + negative rho (up, down): 0.000E+00 6.244E-05 + Reading collected, re-writing distributed wavefunctions + + + bravais-lattice index = 0 + lattice parameter (alat) = 7.2691 (a.u.) + unit-cell volume = 271.6022 (a.u.)^3 + number of atoms/cell = 3 + number of atomic types = 3 + kinetic-energy cut-off = 65.00 (Ry) + charge density cut-off = 780.00 (Ry) + conv. thresh. for NSCF = 1.0E-11 + conv. thresh. for chi = 1.0E-06 + Input Hubbard parameters (in eV): + V ( 1, 1) = 4.5000 + V ( 1, 9) = 0.0000 + V ( 1, 15) = 0.0000 + V ( 1, 18) = 0.0000 + V ( 1, 33) = 0.0000 + V ( 1, 36) = 0.0000 + V ( 1, 42) = 0.0000 + V ( 2, 2) = 5.5000 + V ( 2, 3) = 0.0000 + V ( 2, 45) = 0.0000 + V ( 2, 51) = 0.0000 + V ( 2, 69) = 0.0000 + V ( 3, 2) = 0.0000 + V ( 3, 3) = 0.0000 + V ( 3, 17) = 0.0000 + V ( 3, 35) = 0.0000 + V ( 3, 41) = 0.0000 + V ( 3, 43) = 0.0000 + V ( 3, 49) = 0.0000 + V ( 3, 52) = 0.0000 + V ( 3, 67) = 0.0000 + V ( 3, 70) = 0.0000 + V ( 3, 76) = 0.0000 + + celldm(1) = 7.26914 celldm(2) = 0.00000 celldm(3) = 0.00000 + celldm(4) = 0.00000 celldm(5) = 0.00000 celldm(6) = 0.00000 + + crystal axes: (cart. coord. in units of alat) + a(1) = ( 0.0000 0.7071 0.7071 ) + a(2) = ( 0.7071 0.0000 0.7071 ) + a(3) = ( 0.7071 0.7071 0.0000 ) + + reciprocal axes: (cart. coord. in units 2 pi/alat) + b(1) = ( -0.7071 0.7071 0.7071 ) + b(2) = ( 0.7071 -0.7071 0.7071 ) + b(3) = ( 0.7071 0.7071 -0.7071 ) + + Atoms inside the unit cell (Cartesian axes): + site n. atom mass positions (alat units) + 1 Mn 54.9380 tau( 1) = ( 0.00000 0.00000 0.00000 ) + 2 Co 58.9332 tau( 2) = ( 1.06066 1.06066 1.06066 ) + 3 S 32.0650 tau( 3) = ( 0.70711 0.70711 0.70711 ) + + List of 3 atoms which will be perturbed (one at a time): + + 1 Mn 54.9380 tau( 1) = ( 0.00000 0.00000 0.00000 ) + 2 Co 58.9332 tau( 2) = ( 1.06066 1.06066 1.06066 ) + 3 S 32.0650 tau( 3) = ( 0.70711 0.70711 0.70711 ) + + ===================================================================== + + PERTURBED ATOM # 1 + + site n. atom mass positions (alat units) + 1 Mn 54.9380 tau( 1) = ( 0.00000 0.00000 0.00000 ) + + ===================================================================== + + The perturbed atom has a type which is unique! + + + The grid of q-points ( 3, 3, 3) ( 4 q-points ) : + N xq(1) xq(2) xq(3) wq + 1 0.000000000 0.000000000 0.000000000 0.037037037 + 2 0.235702260 0.235702260 -0.235702260 0.296296296 + 3 0.471404521 -0.000000000 0.000000000 0.222222222 + 4 -0.000000000 -0.471404521 0.471404521 0.444444444 + + + =-------------------------------------------------------------= + + Calculation for q # 1 = ( 0.0000000 0.0000000 0.0000000 ) + + =-------------------------------------------------------------= + + WRITING LINEAR-RESPONSE SUMMARY: + +# ... +# Many lines of code deleted +# ... + + =--------------------------------------------= + CONVERGENCE HAS BEEN REACHED + =--------------------------------------------= + + Computing the sum over q of the response occupation matrices... + + q # 1 = 0.000000000 0.000000000 0.000000000 + + Number of q in the star = 1 + List of q in the star: + 1 0.000000000 0.000000000 0.000000000 + + q # 2 = 0.235702260 0.235702260 -0.235702260 + + Number of q in the star = 4 + List of q in the star: + 1 0.235702260 0.235702260 -0.235702260 + 2 -0.235702260 -0.235702260 -0.235702260 + 3 -0.235702260 0.235702260 0.235702260 + 4 0.235702260 -0.235702260 0.235702260 + In addition there is the -q list: + 1 -0.235702260 -0.235702260 0.235702260 + 2 0.235702260 0.235702260 0.235702260 + 3 0.235702260 -0.235702260 -0.235702260 + 4 -0.235702260 0.235702260 -0.235702260 + + q # 3 = 0.471404521 -0.000000000 0.000000000 + + Number of q in the star = 6 + List of q in the star: + 1 0.471404521 -0.000000000 0.000000000 + 2 -0.000000000 0.471404521 0.000000000 + 3 -0.471404521 0.000000000 -0.000000000 + 4 0.000000000 -0.000000000 0.471404521 + 5 0.000000000 -0.471404521 -0.000000000 + 6 -0.000000000 0.000000000 -0.471404521 + + q # 4 = -0.000000000 -0.471404521 0.471404521 + + Number of q in the star = 12 + List of q in the star: + 1 0.000000000 -0.471404521 0.471404521 + 2 -0.000000000 0.471404521 -0.471404521 + 3 -0.471404521 0.000000000 0.471404521 + 4 0.000000000 0.471404521 0.471404521 + 5 0.471404521 -0.471404521 0.000000000 + 6 0.471404521 -0.000000000 -0.471404521 + 7 0.471404521 -0.000000000 0.471404521 + 8 -0.471404521 0.000000000 -0.471404521 + 9 -0.000000000 -0.471404521 -0.471404521 + 10 -0.471404521 -0.471404521 -0.000000000 + 11 -0.471404521 0.471404521 -0.000000000 + 12 0.471404521 0.471404521 0.000000000 + + Post-processing calculation of Hubbard parameters ... + + + PRINTING TIMING FROM PWSCF ROUTINES: + + init_run : 2.30s CPU 2.40s WALL ( 9 calls) + electrons : 264.09s CPU 271.26s WALL ( 9 calls) + + Called by init_run: + wfcinit : 1.25s CPU 1.29s WALL ( 9 calls) + wfcinit:atom : 0.09s CPU 0.10s WALL ( 3084 calls) + wfcinit:wfcr : 14.80s CPU 15.36s WALL ( 3084 calls) + potinit : 0.15s CPU 0.16s WALL ( 9 calls) + hinit0 : 0.53s CPU 0.56s WALL ( 9 calls) + + Called by electrons: + c_bands : 264.04s CPU 271.21s WALL ( 9 calls) + v_of_rho : 0.16s CPU 0.17s WALL ( 12 calls) + v_h : 0.01s CPU 0.01s WALL ( 12 calls) + v_xc : 0.15s CPU 0.16s WALL ( 12 calls) + newd : 0.23s CPU 0.26s WALL ( 12 calls) + + Called by c_bands: + init_us_2 : 1.36s CPU 1.45s WALL ( 40224 calls) + init_us_2:cp : 1.31s CPU 1.40s WALL ( 40224 calls) + cegterg : 248.04s CPU 254.61s WALL ( 3216 calls) + + Called by sum_band: + + Called by *egterg: + cdiaghg : 128.75s CPU 130.69s WALL ( 47508 calls) + cegterg:over : 19.47s CPU 20.38s WALL ( 44424 calls) + cegterg:upda : 8.60s CPU 8.68s WALL ( 44424 calls) + cegterg:last : 5.51s CPU 5.55s WALL ( 11382 calls) + cdiaghg:chol : 6.52s CPU 6.76s WALL ( 47508 calls) + cdiaghg:inve : 1.29s CPU 1.34s WALL ( 47508 calls) + cdiaghg:para : 9.47s CPU 9.69s WALL ( 95016 calls) + h_psi : 1066.62s CPU 1114.68s WALL ( 951981 calls) + s_psi : 23.45s CPU 24.50s WALL ( 1888644 calls) + g_psi : 0.25s CPU 0.25s WALL ( 44424 calls) + + Called by h_psi: + h_psi:calbec : 38.49s CPU 40.30s WALL ( 951981 calls) + vloc_psi : 894.15s CPU 934.45s WALL ( 951981 calls) + add_vuspsi : 13.68s CPU 14.36s WALL ( 951981 calls) + vhpsi : 114.61s CPU 119.71s WALL ( 951981 calls) + + General routines + calbec : 98.10s CPU 102.70s WALL ( 2871501 calls) + fft : 1.71s CPU 1.77s WALL ( 6285 calls) + ffts : 0.22s CPU 0.22s WALL ( 2704 calls) + fftw : 876.21s CPU 917.20s WALL (24358006 calls) + interpolate : 0.27s CPU 0.29s WALL ( 844 calls) + davcio : 7.39s CPU 8.55s WALL ( 1186711 calls) + + Parallel routines + fft_scatt_xy : 90.01s CPU 94.29s WALL (24366995 calls) + fft_scatt_yz : 579.47s CPU 607.09s WALL (24366995 calls) + + Hubbard U routines + alloc_neigh : 0.00s CPU 0.00s WALL ( 3 calls) + vhpsi : 114.61s CPU 119.71s WALL ( 951981 calls) + + init_vloc : 0.12s CPU 0.12s WALL ( 12 calls) + init_us_1 : 0.41s CPU 0.47s WALL ( 12 calls) + newd : 0.23s CPU 0.26s WALL ( 12 calls) + add_vuspsi : 13.68s CPU 14.36s WALL ( 951981 calls) + + PRINTING TIMING FROM HP ROUTINES: + + hp_setup_q : 0.61s CPU 0.68s WALL ( 12 calls) + hp_init_q : 1.45s CPU 1.54s WALL ( 12 calls) + hp_solve_lin : 1284.03s CPU 1344.51s WALL ( 12 calls) + hp_dvpsi_per : 0.07s CPU 0.12s WALL ( 1638 calls) + hp_dnsq : 2.79s CPU 3.48s WALL ( 199 calls) + hp_symdnsq : 0.01s CPU 0.02s WALL ( 199 calls) + hp_dnstot_su : 0.00s CPU 0.00s WALL ( 3 calls) + hp_rotate_dn : 0.00s CPU 0.00s WALL ( 114 calls) + hp_calc_chi : 0.00s CPU 0.00s WALL ( 3 calls) + hp_postproc : 0.01s CPU 0.01s WALL ( 1 calls) + ef_shift : 0.03s CPU 0.03s WALL ( 34 calls) + hp_run_nscf : 280.95s CPU 289.29s WALL ( 9 calls) + hp_postproc : 0.01s CPU 0.01s WALL ( 1 calls) + hp_psymdvscf : 13.17s CPU 13.94s WALL ( 199 calls) + + PRINTING TIMING FROM LR MODULE: + + sth_kernel : 1254.93s CPU 1313.03s WALL ( 199 calls) + apply_dpot_b : 42.48s CPU 45.56s WALL ( 27504 calls) + ortho : 5.11s CPU 5.36s WALL ( 29142 calls) + cgsolve : 1150.99s CPU 1202.38s WALL ( 29142 calls) + ch_psi : 1078.33s CPU 1126.88s WALL ( 901257 calls) + incdrhoscf : 48.08s CPU 50.93s WALL ( 29142 calls) + 0.00s GPU ( 29142 calls) + localdos : 0.23s CPU 0.23s WALL ( 3 calls) + dv_of_drho : 2.15s CPU 2.20s WALL ( 199 calls) + mix_pot : 0.80s CPU 1.53s WALL ( 199 calls) + setup_dgc : 0.47s CPU 0.52s WALL ( 12 calls) + setup_dmuxc : 0.13s CPU 0.14s WALL ( 12 calls) + setup_nbnd_o : 0.00s CPU 0.00s WALL ( 12 calls) + lr_orthoUwfc : 1.30s CPU 1.37s WALL ( 12 calls) + cft_wave : 40.45s CPU 43.37s WALL ( 1067748 calls) + + USPP ROUTINES: + + newdq : 4.38s CPU 4.40s WALL ( 199 calls) + adddvscf : 2.94s CPU 3.10s WALL ( 27504 calls) + addusdbec : 2.10s CPU 2.20s WALL ( 29142 calls) + addusldos : 0.05s CPU 0.05s WALL ( 3 calls) + + HP : 26m 8.62s CPU 27m17.87s WALL + + + This run was terminated on: 22:33: 0 20May2024 + +=------------------------------------------------------------------------------= + JOB DONE. +=------------------------------------------------------------------------------= diff --git a/tests/parsers/test_hp.py b/tests/parsers/test_hp.py index 759fef1..dc1f13c 100644 --- a/tests/parsers/test_hp.py +++ b/tests/parsers/test_hp.py @@ -40,6 +40,50 @@ def generate_inputs_mesh_only(): return AttributeDict({'parameters': orm.Dict(parameters)}) +@pytest.fixture +def generate_inputs_voronoi(filepath_tests): + """Return inputs that the parser will expect when nearest-neighbours analysis is active.""" + + def _generate_inputs_voronoi(all_neihbours=False): + """Return inputs that the parser will expect when nearest-neighbours analysis is active.""" + import os + + from aiida_quantumespresso.utils.hubbard import initialize_hubbard_parameters + from ase.io import read + path = os.path.join(filepath_tests, 'fixtures', 'structures', 'MnCoS.cif') + atoms = read(path) + pairs = { + 'Mn': ['3d', 5.0, 1e-8, { + 'S': '3p' + }], + 'Co': ['3d', 5.0, 1e-8, { + 'S': '3p' + }], + } + if all_neihbours: + pairs = { + 'Mn': ['3d', 5.0, 1e-8, { + 'S': '3p', + 'Co': '3d' + }], + 'Co': ['3d', 5.0, 1e-8, { + 'S': '3p', + 'Mn': '3d' + }], + } + structure = orm.StructureData(ase=atoms) + hubbard_structure = initialize_hubbard_parameters(structure=structure, pairs=pairs) + parameters = {'INPUTHP': {'num_neigh': 10}} + settings = {'radial_analysis': {}} + return AttributeDict({ + 'parameters': orm.Dict(parameters), + 'settings': orm.Dict(settings), + 'hubbard_structure': hubbard_structure, + }) + + return _generate_inputs_voronoi + + def test_hp_default( aiida_localhost, generate_calc_job_node, generate_parser, generate_inputs_default, data_regression, tmpdir ): @@ -112,6 +156,44 @@ def test_hp_default_hubbard_structure( }) +@pytest.mark.parametrize('all_neihbours', (True, False)) +def test_hp_voronoi_hubbard_structure( + aiida_localhost, generate_calc_job_node, generate_parser, generate_inputs_voronoi, data_regression, tmpdir, + all_neihbours +): + """Test a `hp.x` calculation with nearest-neihbour analysis.""" + name = 'voronoi_hubbard_structure' + entry_point_calc_job = 'quantumespresso.hp' + entry_point_parser = 'quantumespresso.hp' + + attributes = {'retrieve_temporary_list': ['HUBBARD.dat']} + node = generate_calc_job_node( + entry_point_calc_job, + aiida_localhost, + test_name=name, + inputs=generate_inputs_voronoi(all_neihbours), + attributes=attributes, + retrieve_temporary=(tmpdir, ['HUBBARD.dat']) + ) + parser = generate_parser(entry_point_parser) + results, calcfunction = parser.parse_from_node(node, store_provenance=False, retrieved_temporary_folder=tmpdir) + + assert calcfunction.is_finished, calcfunction.exception + assert calcfunction.is_finished_ok, calcfunction.exit_message + assert 'parameters' in results + assert 'hubbard' in results + assert 'hubbard_chi' in results + assert 'hubbard_structure' in results + assert 'hubbard_matrices' in results + data_regression.check({ + 'parameters': results['parameters'].get_dict(), + 'hubbard': results['hubbard'].get_dict(), + 'hubbard_chi': results['hubbard_chi'].base.attributes.all, + 'hubbard_matrices': results['hubbard_matrices'].base.attributes.all, + 'hubbard_data': results['hubbard_structure'].hubbard.dict(), + }) + + def test_hp_initialization_only( aiida_localhost, generate_calc_job_node, generate_parser, generate_inputs_init_only, data_regression ): diff --git a/tests/parsers/test_hp/test_hp_voronoi_hubbard_structure_False_.yml b/tests/parsers/test_hp/test_hp_voronoi_hubbard_structure_False_.yml new file mode 100644 index 0000000..b5beb9d --- /dev/null +++ b/tests/parsers/test_hp/test_hp_voronoi_hubbard_structure_False_.yml @@ -0,0 +1,179 @@ +hubbard: + sites: + - index: 0 + kind: Mn + manifold: 3d + new_kind: Mn + new_type: 2 + spin: 1 + type: 2 + value: 5.3443 + - index: 1 + kind: Co + manifold: 3d + new_kind: Co + new_type: 1 + spin: 1 + type: 1 + value: 6.6772 + - index: 2 + kind: S + manifold: 3p + new_kind: S + new_type: 3 + spin: 0 + type: 3 + value: 3.1641 +hubbard_chi: + array|chi: + - 1 + - 1 + array|chi0: + - 1 + - 1 +hubbard_data: + formulation: dudarev + parameters: + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 0 + neighbour_manifold: 3d + translation: + - 0 + - 0 + - 0 + value: 5.3443 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - 0 + - -1 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - -1 + - 0 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - -1 + - 0 + - 0 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - -1 + - -1 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - -1 + - 0 + - -1 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - -1 + - -1 + - 0 + value: 0.0256 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 1 + neighbour_manifold: 3d + translation: + - 0 + - 0 + - 0 + value: 6.6772 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - 0 + - 1 + value: 0.1165 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 1 + - 0 + - 0 + value: 0.1165 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - 1 + - 0 + value: 0.1165 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - 0 + - 0 + value: 0.1165 + projectors: ortho-atomic +hubbard_matrices: + array|chi: + - 81 + - 81 + array|chi0: + - 81 + - 81 + array|chi0_inv: + - 81 + - 81 + array|chi_inv: + - 81 + - 81 + array|hubbard: + - 81 + - 81 +parameters: + hubbard_sites: + '1': Mn + '2': Co + '3': S + number_of_qpoints: 4 diff --git a/tests/parsers/test_hp/test_hp_voronoi_hubbard_structure_True_.yml b/tests/parsers/test_hp/test_hp_voronoi_hubbard_structure_True_.yml new file mode 100644 index 0000000..9fee15f --- /dev/null +++ b/tests/parsers/test_hp/test_hp_voronoi_hubbard_structure_True_.yml @@ -0,0 +1,259 @@ +hubbard: + sites: + - index: 0 + kind: Mn + manifold: 3d + new_kind: Mn + new_type: 2 + spin: 1 + type: 2 + value: 5.3443 + - index: 1 + kind: Co + manifold: 3d + new_kind: Co + new_type: 1 + spin: 1 + type: 1 + value: 6.6772 + - index: 2 + kind: S + manifold: 3p + new_kind: S + new_type: 3 + spin: 0 + type: 3 + value: 3.1641 +hubbard_chi: + array|chi: + - 1 + - 1 + array|chi0: + - 1 + - 1 +hubbard_data: + formulation: dudarev + parameters: + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 0 + neighbour_manifold: 3d + translation: + - 0 + - 0 + - 0 + value: 5.3443 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 1 + neighbour_manifold: 3d + translation: + - -1 + - 0 + - -1 + value: 0.4967 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 1 + neighbour_manifold: 3d + translation: + - -1 + - -1 + - 0 + value: 0.4967 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 1 + neighbour_manifold: 3d + translation: + - -1 + - -1 + - -1 + value: 0.4967 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 1 + neighbour_manifold: 3d + translation: + - 0 + - -1 + - -1 + value: 0.4967 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - 0 + - -1 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - -1 + - 0 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - -1 + - 0 + - 0 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - -1 + - -1 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - -1 + - 0 + - -1 + value: 0.0256 + - atom_index: 0 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - -1 + - -1 + - 0 + value: 0.0256 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 1 + neighbour_manifold: 3d + translation: + - 0 + - 0 + - 0 + value: 6.6772 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 0 + neighbour_manifold: 3d + translation: + - 1 + - 1 + - 1 + value: 0.4967 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - 0 + - 1 + value: 0.1165 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 1 + - 0 + - 0 + value: 0.1165 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - 1 + - 0 + value: 0.1165 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 0 + neighbour_manifold: 3d + translation: + - 1 + - 1 + - 0 + value: 0.4967 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 0 + neighbour_manifold: 3d + translation: + - 1 + - 0 + - 1 + value: 0.4967 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 0 + neighbour_manifold: 3d + translation: + - 0 + - 1 + - 1 + value: 0.4967 + - atom_index: 1 + atom_manifold: 3d + hubbard_type: V + neighbour_index: 2 + neighbour_manifold: 3p + translation: + - 0 + - 0 + - 0 + value: 0.1165 + projectors: ortho-atomic +hubbard_matrices: + array|chi: + - 81 + - 81 + array|chi0: + - 81 + - 81 + array|chi0_inv: + - 81 + - 81 + array|chi_inv: + - 81 + - 81 + array|hubbard: + - 81 + - 81 +parameters: + hubbard_sites: + '1': Mn + '2': Co + '3': S + number_of_qpoints: 4 diff --git a/tests/workflows/protocols/test_hubbard/test_default.yml b/tests/workflows/protocols/test_hubbard/test_default.yml index 70720dd..0e87e89 100644 --- a/tests/workflows/protocols/test_hubbard/test_default.yml +++ b/tests/workflows/protocols/test_hubbard/test_default.yml @@ -34,7 +34,6 @@ relax: base: kpoints_distance: 0.15 kpoints_force_parity: false - max_iterations: 5 pw: code: test.quantumespresso.pw@localhost metadata: @@ -75,7 +74,6 @@ relax: scf: kpoints_distance: 0.4 kpoints_force_parity: false - max_iterations: 5 pw: code: test.quantumespresso.pw@localhost metadata: diff --git a/tests/workflows/test_hubbard.py b/tests/workflows/test_hubbard.py index 84c780e..e84e1c3 100644 --- a/tests/workflows/test_hubbard.py +++ b/tests/workflows/test_hubbard.py @@ -298,7 +298,10 @@ def test_radial_analysis( node = load_node(process.ctx['workchains_hp'][-1].pk) parameters = node.inputs['hp']['parameters'].get_dict() - assert 'rmax' in parameters['INPUTHP'] + settings = node.inputs['hp']['settings'].get_dict() + + assert 'num_neigh' in parameters['INPUTHP'] + assert 'radial_analysis' in settings @pytest.mark.usefixtures('aiida_profile') From 5bb9e1b8a1b1f1fbf32d475439826704236d9dcc Mon Sep 17 00:00:00 2001 From: bastonero Date: Thu, 23 Jan 2025 14:53:12 +0000 Subject: [PATCH 28/32] Update dependencies --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f54350f..c583adf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,8 +26,8 @@ classifiers = [ keywords = ['aiida', 'workflows'] requires-python = '>=3.8' dependencies = [ - 'aiida-core~=2.2', - 'aiida-quantumespresso@git+https://github.com/bastonero/aiida-quantumespresso.git@feat/voronoi', + 'aiida-core>=2.3.0', + 'aiida-quantumespresso>=4.8.0', ] [project.urls] From 8291e350c086e61797ded2d71a701ad1e2ada994 Mon Sep 17 00:00:00 2001 From: bastonero Date: Thu, 23 Jan 2025 14:57:50 +0000 Subject: [PATCH 29/32] Update python version and ci --- .github/workflows/ci.yml | 4 ++-- pyproject.toml | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index afab926..231984b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -23,7 +23,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v2 with: - python-version: '3.8' + python-version: '3.9' - name: Install python dependencies run: pip install -e .[pre-commit,tests] @@ -40,7 +40,7 @@ jobs: strategy: matrix: - python-version: ['3.8', '3.9'] + python-version: ['3.9'] services: rabbitmq: diff --git a/pyproject.toml b/pyproject.toml index c583adf..5422b51 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,6 @@ classifiers = [ 'Operating System :: POSIX :: Linux', 'Operating System :: MacOS :: MacOS X', 'Programming Language :: Python', - 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', 'Programming Language :: Python :: 3.11', From 250c6de114a1e91f61669ccd18bbfc23d224ee83 Mon Sep 17 00:00:00 2001 From: bastonero Date: Thu, 23 Jan 2025 15:05:01 +0000 Subject: [PATCH 30/32] Fix pre-commit --- docs/source/conf.py | 4 ++-- src/aiida_quantumespresso_hp/calculations/hp.py | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index fa3702d..e11e70e 100755 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -17,14 +17,14 @@ # Load the dummy profile even if we are running locally, this way the documentation will succeed even if the current # default profile of the AiiDA installation does not use a Django backend. -from aiida.manage.configuration import load_documentation_profile +from aiida.manage.configuration import Profile, load_profile # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. import aiida_quantumespresso_hp -load_documentation_profile() +load_profile(Profile('docs', {'process_control': {}, 'storage': {}})) # -- Project information ----------------------------------------------------- diff --git a/src/aiida_quantumespresso_hp/calculations/hp.py b/src/aiida_quantumespresso_hp/calculations/hp.py index e5b9258..53836a8 100644 --- a/src/aiida_quantumespresso_hp/calculations/hp.py +++ b/src/aiida_quantumespresso_hp/calculations/hp.py @@ -211,17 +211,17 @@ def filename_output_hubbard(cls): # pylint: disable=no-self-argument return f'{cls.prefix}.Hubbard_parameters.dat' @classproperty - def filename_input_hubbard_parameters(cls): # pylint: disable=no-self-argument,invalid-name, no-self-use + def filename_input_hubbard_parameters(cls): # pylint: disable=no-self-argument,invalid-name """Return the relative input filename for Hubbard parameters, for QuantumESPRESSO version below 7.1.""" return 'parameters.in' @classproperty - def filename_output_hubbard_dat(cls): # pylint: disable=no-self-argument,invalid-name, no-self-use + def filename_output_hubbard_dat(cls): # pylint: disable=no-self-argument,invalid-name """Return the relative input filename for generalised Hubbard parameters, for QuantumESPRESSO v.7.2 onwards.""" return 'HUBBARD.dat' @classproperty - def dirname_output(cls): # pylint: disable=no-self-argument, no-self-use + def dirname_output(cls): # pylint: disable=no-self-argument """Return the relative directory name that contains raw output data.""" return 'out' From 2e5bbf8e77f4f2063f7e305e3b15dd238b06e2d8 Mon Sep 17 00:00:00 2001 From: bastonero Date: Thu, 23 Jan 2025 15:11:45 +0000 Subject: [PATCH 31/32] Fix tests --- tests/workflows/protocols/test_hubbard/test_default.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/workflows/protocols/test_hubbard/test_default.yml b/tests/workflows/protocols/test_hubbard/test_default.yml index 0e87e89..70720dd 100644 --- a/tests/workflows/protocols/test_hubbard/test_default.yml +++ b/tests/workflows/protocols/test_hubbard/test_default.yml @@ -34,6 +34,7 @@ relax: base: kpoints_distance: 0.15 kpoints_force_parity: false + max_iterations: 5 pw: code: test.quantumespresso.pw@localhost metadata: @@ -74,6 +75,7 @@ relax: scf: kpoints_distance: 0.4 kpoints_force_parity: false + max_iterations: 5 pw: code: test.quantumespresso.pw@localhost metadata: From 2cb4a8265fef8ea260652681abb3d9cc78bae4c8 Mon Sep 17 00:00:00 2001 From: bastonero Date: Thu, 23 Jan 2025 15:23:17 +0000 Subject: [PATCH 32/32] Update pylint deps --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5422b51..71244cc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,7 +48,7 @@ docs = [ ] pre-commit = [ 'pre-commit~=2.17', - 'pylint~=2.12.2', + 'pylint~=2.17.2', 'pylint-aiida~=0.1.1', 'toml' ]