From 6145d52034bac5a189608c0912ad76ada49bec9a Mon Sep 17 00:00:00 2001 From: Philipp Ruessmann Date: Wed, 1 Dec 2021 10:12:23 +0000 Subject: [PATCH 1/2] Remove parsed files from retrieved folder that have a dedicated output node This uses the retrieve_temporary list and the corresponding changes to the parser --- aiida_spirit/calculations.py | 13 ++++-- aiida_spirit/parsers.py | 86 ++++++++++++++++++++++++------------ 2 files changed, 67 insertions(+), 32 deletions(-) diff --git a/aiida_spirit/calculations.py b/aiida_spirit/calculations.py index 6fe6d3d..8f0a49e 100644 --- a/aiida_spirit/calculations.py +++ b/aiida_spirit/calculations.py @@ -184,7 +184,11 @@ def prepare_for_submission(self, folder): # this should be a list of the filenames we expect when spirit ran # i.e. the files we specify here will be copied back to the file repository + # note that the retlist_tmp contains only files which are only needed in parsing + # but are then not kept in the file repository (e.g. magnetization arrays which are + # stored as numy arrays instead of also keeping the raw text files) retlist = _RETLIST.copy() + retlist_tmp = [] if 'pinning' in self.inputs: # also retreive the pinning file retlist += ['pinning.txt'] @@ -194,17 +198,18 @@ def prepare_for_submission(self, folder): run_opts = self.inputs.run_options.get_dict() if run_opts['simulation_method'].upper() == 'LLG': - retlist += ['spirit_Image-00_Energy-archive.txt', - 'spirit_Image-00_Spins-final.ovf', - 'spirit_Image-00_Spins-initial.ovf'] + retlist_tmp += ['spirit_Image-00_Energy-archive.txt', + 'spirit_Image-00_Spins-final.ovf', + 'spirit_Image-00_Spins-initial.ovf'] elif run_opts['simulation_method'].upper() == 'MC': - retlist += ['output_mc.txt'] + retlist_tmp += ['output_mc.txt'] # from the input we can specify additional files that should be retrieved if 'add_to_retrieved' in self.inputs: retlist += self.inputs.add_to_retrieved.get_list() calcinfo.retrieve_list = retlist + calcinfo.retrieve_temporary_list = retlist_tmp return calcinfo diff --git a/aiida_spirit/parsers.py b/aiida_spirit/parsers.py index abff620..165542e 100644 --- a/aiida_spirit/parsers.py +++ b/aiida_spirit/parsers.py @@ -4,6 +4,7 @@ Register parsers via the "aiida.parsers" entry point in setup.json. """ +import pathlib import numpy as np from aiida.engine import ExitCode from aiida.parsers.parser import Parser @@ -54,6 +55,14 @@ def parse(self, **kwargs): # parse information from output file (number of iterations, convergence info, ...) retrieved_dict = self.parse_retrieved() + # parse files in temporary folder + # these files are not kept in the file repository but become numy arrays and are stored as ArrayData output nodes + retrieved_temporary_folder = kwargs.get('retrieved_temporary_folder', + None) + if retrieved_temporary_folder is not None: + retrieved_dict = self.parse_temporary_retrieved( + retrieved_dict, retrieved_temporary_folder) + for key, value in retrieved_dict.items(): self.out(key, value) @@ -70,17 +79,27 @@ def parse(self, **kwargs): return ExitCode(0) - def _retrieve_if_found(self, filename, *args, **kwargs): - """Retrieves a file and loads it with `np.loadtxt`. + def _parse_if_found(self, filename, *args, folder=None, **kwargs): + """Parses a file and loads it with `np.loadtxt`. The `*args` and `**kwargs` are passed to `np.loadtxt`. If the file is not found it returns None.""" - retrieved = self.retrieved - if filename in retrieved.list_object_names(): - with retrieved.open(filename, 'r') as _f: - return np.loadtxt(_f, *args, **kwargs) + if folder is None: + folder = self.retrieved + if filename in folder.list_object_names(): + with folder.open(filename, 'r') as _f: + return np.loadtxt(_f, *args, **kwargs) + else: + return self._file_not_found(filename) else: - self.logger.info('{} not found!'.format(filename)) - return None + filenames = [f.name for f in folder.glob('*')] + if filename in filenames: + with (folder / filename).open('r') as _f: + return np.loadtxt(_f, *args, **kwargs) + else: + return self._file_not_found(filename) + + def _file_not_found(self, filename): + self.logger.info('{} not found!'.format(filename)) def parse_retrieved(self): # pylint: disable=too-many-locals """Parse the output from the retrieved and create aiida nodes""" @@ -96,26 +115,45 @@ def parse_retrieved(self): # pylint: disable=too-many-locals output_node = Dict(dict=out_dict) # parse output files + self.logger.info('Parsing atom types') + atyp = self._parse_if_found(_ATOM_TYPES) + + # Write dictionary of retrieved quantities + _retrieved_dict = {'output_parameters': output_node} + + # collect arrays in ArrayData + if atyp is not None: + atypes = ArrayData() + atypes.set_array('atom_types', atyp) + atypes.extras['description'] = { + 'atom_types': 'list of atom types for all positions', + } + _retrieved_dict.update({'atom_types': atypes}) + + return _retrieved_dict + + def parse_temporary_retrieved(self, _retrieved_dict, + retrieved_temporary_folder): + """Parse files that are defined in the retrieve_temporary_list""" + retrieved_temporary_folder = pathlib.Path(retrieved_temporary_folder) + self.logger.info('Parsing energy archive') - energ = self._retrieve_if_found('spirit_Image-00_Energy-archive.txt', - skiprows=1) + energ = self._parse_if_found('spirit_Image-00_Energy-archive.txt', + folder=retrieved_temporary_folder, + skiprows=1) self.logger.info('Parsing initial magnetization') - m_init = self._retrieve_if_found('spirit_Image-00_Spins-initial.ovf') + m_init = self._parse_if_found('spirit_Image-00_Spins-initial.ovf', + folder=retrieved_temporary_folder) self.logger.info('Parsing final magnetization') - m_final = self._retrieve_if_found('spirit_Image-00_Spins-final.ovf') - - self.logger.info('Parsing atom types') - atyp = self._retrieve_if_found(_ATOM_TYPES) + m_final = self._parse_if_found('spirit_Image-00_Spins-final.ovf', + folder=retrieved_temporary_folder) self.logger.info('Parsing MC output') - out_mc = self._retrieve_if_found('output_mc.txt') + out_mc = self._parse_if_found('output_mc.txt', + folder=retrieved_temporary_folder) - # Write dictionary of retrieved quantities - _retrieved_dict = {'output_parameters': output_node} - - # collect arrays in ArrayData if m_init is not None and m_final is not None: mag = ArrayData() mag.set_array( @@ -136,14 +174,6 @@ def parse_retrieved(self): # pylint: disable=too-many-locals } _retrieved_dict.update({'energies': energies}) - if atyp is not None: - atypes = ArrayData() - atypes.set_array('atom_types', atyp) - atypes.extras['description'] = { - 'atom_types': 'list of atom types for all positions', - } - _retrieved_dict.update({'atom_types': atypes}) - # Only add mc if it is found if out_mc is not None: output_mc = ArrayData() From c992fb42bf33d0d026671c7df23e02ff15f41f32 Mon Sep 17 00:00:00 2001 From: Philipp Ruessmann Date: Wed, 1 Dec 2021 10:17:18 +0000 Subject: [PATCH 2/2] Bumb version number to v0.2.0 --- aiida_spirit/__init__.py | 2 +- setup.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/aiida_spirit/__init__.py b/aiida_spirit/__init__.py index e065f3c..d8bee6a 100644 --- a/aiida_spirit/__init__.py +++ b/aiida_spirit/__init__.py @@ -5,4 +5,4 @@ AiiDA plugin for the spirit code """ -__version__ = '0.1.0' +__version__ = '0.2.0' diff --git a/setup.json b/setup.json index e05a024..455d33c 100644 --- a/setup.json +++ b/setup.json @@ -12,7 +12,7 @@ "Natural Language :: English", "Framework :: AiiDA" ], - "version": "0.1.0", + "version": "0.2.0", "entry_points": { "aiida.calculations": [ "spirit = aiida_spirit.calculations:SpiritCalculation"