From c0a152ed56d8f98687e0188382153cf23ba49a97 Mon Sep 17 00:00:00 2001
From: Alvin Noe Ladines <ladinesalvinnoe@gmail.com>
Date: Thu, 3 Sep 2020 20:36:50 +0200
Subject: [PATCH] Switched to use nomad metainfo
---
elasticparser/__init__.py | 19 +-
elasticparser/__main__.py | 21 +
elasticparser/elastic_parser.py | 177 ++
.../elastic_parser_input_exciting.py | 80 -
elasticparser/elastic_parser_input_wien2k.py | 138 --
elasticparser/elastic_properties.py | 417 +++++
elasticparser/parser_elastic.py | 1453 -----------------
7 files changed, 633 insertions(+), 1672 deletions(-)
create mode 100644 elasticparser/__main__.py
create mode 100644 elasticparser/elastic_parser.py
delete mode 100644 elasticparser/elastic_parser_input_exciting.py
delete mode 100644 elasticparser/elastic_parser_input_wien2k.py
create mode 100644 elasticparser/elastic_properties.py
delete mode 100644 elasticparser/parser_elastic.py
diff --git a/elasticparser/__init__.py b/elasticparser/__init__.py
index 9b38a23..018dcdb 100644
--- a/elasticparser/__init__.py
+++ b/elasticparser/__init__.py
@@ -12,4 +12,21 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from elasticparser.parser_elastic import ElasticParser
+from .metainfo import m_env
+from nomad.parsing.parser import FairdiParser
+from elasticparser.elastic_parser import ElasticParserInterface
+
+
+class ElasticParser(FairdiParser):
+ def __init__(self):
+ super().__init__(
+ name='parsers/elastic', code_name='elastic', code_homepage='http://exciting-code.org/elastic',
+ mainfile_contents_re=r'\s*Order of elastic constants\s*=\s*[0-9]+\s*',
+ mainfile_name_re=(r'.*/INFO_ElaStic'))
+
+ def parse(self, filepath, archive, logger=None):
+ self._metainfo_env = m_env
+
+ parser = ElasticParserInterface(filepath, archive, logger)
+
+ parser.parse()
diff --git a/elasticparser/__main__.py b/elasticparser/__main__.py
new file mode 100644
index 0000000..47bbf8d
--- /dev/null
+++ b/elasticparser/__main__.py
@@ -0,0 +1,21 @@
+# Copyright 2016-2018 Markus Scheidgen
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import sys
+import json
+
+from elasticparser import ElasticParser
+
+if __name__ == "__main__":
+ archive = ElasticParser.main(sys.argv[1])
+ json.dump(archive.m_to_dict(), sys.stdout, indent=2)
\ No newline at end of file
diff --git a/elasticparser/elastic_parser.py b/elasticparser/elastic_parser.py
new file mode 100644
index 0000000..81a71a6
--- /dev/null
+++ b/elasticparser/elastic_parser.py
@@ -0,0 +1,177 @@
+import os
+import numpy as np
+import logging
+
+from nomadcore.unit_conversion import unit_conversion
+from nomad.datamodel.metainfo.public import section_run, section_system,\
+ section_single_configuration_calculation, section_method, section_calculation_to_calculation_refs,\
+ Workflow, Elastic
+
+from elasticparser.metainfo.elastic import x_elastic_section_strain_diagrams,\
+ x_elastic_section_fitting_parameters
+
+from elasticparser.elastic_properties import ElasticProperties
+
+a_to_m = unit_conversion.convert_unit_function('angstrom', 'meter')
+ha_to_J = unit_conversion.convert_unit(1, 'hartree', 'J')
+giga = 10 ** 9
+
+
+class ElasticParserInterface:
+ def __init__(self, filepath, archive, logger=None):
+ self.filepath = os.path.abspath(filepath)
+ self.archive = archive
+ self.logger = logger if logger is not None else logging
+ self.properties = ElasticProperties(self.filepath)
+
+ def parse_strain(self):
+ sec_scc = self.archive.section_run[-1].section_single_configuration_calculation[-1]
+ method = self.properties.info['calculation_method'].lower()
+
+ if method == 'energy':
+ strain, energy = self.properties.get_strain_energy()
+ n_strains = self.properties.info['n_strains']
+
+ sec_strain_diagram = sec_scc.m_create(x_elastic_section_strain_diagrams)
+ sec_strain_diagram.x_elastic_strain_diagram_type = 'energy'
+ sec_strain_diagram.x_elastic_strain_diagram_number_of_eta = len(strain[0])
+ sec_strain_diagram.x_elastic_strain_diagram_eta_values = strain
+ sec_strain_diagram.x_elastic_strain_diagram_values = np.array(energy) * ha_to_J
+
+ poly_fit_2 = int((n_strains - 1) / 2)
+
+ poly_fit = {
+ '2nd': poly_fit_2, '3rd': poly_fit_2 - 1, '4th': poly_fit_2 - 1,
+ '5th': poly_fit_2 - 2, '6th': poly_fit_2 - 2, '7th': poly_fit_2 - 3}
+
+ energy_fit = self.properties.get_energy_fit()
+ for diagram_type in ['cross-validation', 'd2e']:
+ for fit_order in energy_fit[diagram_type][0].keys():
+ sec_strain_diagram = sec_scc.m_create(x_elastic_section_strain_diagrams)
+ sec_strain_diagram.x_elastic_strain_diagram_type = diagram_type
+ sec_strain_diagram.x_elastic_strain_diagram_polynomial_fit_order = int(fit_order[:-2])
+ sec_strain_diagram.x_elastic_strain_diagram_number_of_eta = poly_fit.get(fit_order, None)
+ sec_strain_diagram.x_elastic_strain_diagram_eta_values = energy_fit[diagram_type][0][fit_order]
+ convert = giga if diagram_type == 'd2e' else ha_to_J
+ sec_strain_diagram.x_elastic_strain_diagram_values = np.array(energy_fit[diagram_type][1][fit_order]) * convert
+
+ elif method == 'stress':
+ strain, stress = self.properties.get_strain_stress()
+ for diagram_type in ['Lagrangian-stress', 'Physical-stress']:
+ strain_i = strain[diagram_type]
+ stress_i = np.transpose(np.array(stress[diagram_type]), axes=(2, 0, 1))
+ if not strain_i:
+ continue
+
+ for si in range(6):
+ sec_strain_diagram = sec_scc.m_create(x_elastic_section_strain_diagrams)
+ sec_strain_diagram.x_elastic_strain_diagram_type = diagram_type
+ sec_strain_diagram.x_elastic_strain_diagram_stress_Voigt_component = si + 1
+ sec_strain_diagram.x_elastic_strain_diagram_number_of_eta = len(strain_i[0])
+ sec_strain_diagram.x_elastic_strain_diagram_eta_values = strain_i
+ sec_strain_diagram.x_elastic_strain_diagram_values = stress_i[si]
+
+ stress_fit = self.properties.get_stress_fit()
+ for diagram_type in ['cross-validation', 'dtn']:
+ for si in range(6):
+ for fit_order in stress_fit[diagram_type][si][0].keys():
+ sec_strain_diagram = sec_scc.m_create(x_elastic_section_strain_diagrams)
+ sec_strain_diagram.x_elastic_strain_diagram_type = diagram_type
+ sec_strain_diagram.x_elastic_strain_diagram_stress_Voigt_component = si + 1
+ sec_strain_diagram.x_elastic_strain_diagram_polynomial_fit_order = int(fit_order[:-2])
+ sec_strain_diagram.x_elastic_strain_diagram_number_of_eta = poly_fit.get(fit_order, None)
+ sec_strain_diagram.x_elastic_strain_diagram_eta_values = stress_fit[diagram_type][si][0][fit_order]
+ convert = giga if diagram_type == 'dtn' else ha_to_J
+ sec_strain_diagram.x_elastic_strain_diagram_values = np.array(stress_fit[diagram_type][si][1][fit_order]) * convert
+
+ def parse_elastic_constant(self):
+ sec_scc = self.archive.section_run[-1].section_single_configuration_calculation[-1]
+
+ order = self.properties.info['order']
+
+ if order == 2:
+ matrices, moduli, eigenvalues = self.properties.get_elastic_constants_order2()
+
+ sec_scc.x_elastic_2nd_order_constants_notation_matrix = matrices['voigt']
+ sec_scc.x_elastic_2nd_order_constants_matrix = matrices['elastic_constant'] * giga
+ sec_scc.x_elastic_2nd_order_constants_compliance_matrix = matrices['compliance'] / giga
+
+ sec_scc.x_elastic_Voigt_bulk_modulus = moduli.get('B_V', moduli.get('K_V')) * giga
+ sec_scc.x_elastic_Voigt_shear_modulus = moduli['G_V'] * giga
+
+ sec_scc.x_elastic_Reuss_bulk_modulus = moduli.get('B_R', moduli.get('K_R')) * giga
+ sec_scc.x_elastic_Reuss_shear_modulus = moduli['G_R'] * giga
+
+ sec_scc.x_elastic_Hill_bulk_modulus = moduli.get('B_H', moduli.get('K_H')) * giga
+ sec_scc.x_elastic_Hill_shear_modulus = moduli['G_H'] * giga
+
+ sec_scc.x_elastic_Voigt_Young_modulus = moduli['E_V'] * giga
+ sec_scc.x_elastic_Voigt_Poisson_ratio = moduli['nu_V']
+ sec_scc.x_elastic_Reuss_Young_modulus = moduli['E_R'] * giga
+ sec_scc.x_elastic_Reuss_Poisson_ratio = moduli['nu_R']
+ sec_scc.x_elastic_Hill_Young_modulus = moduli['E_H'] * giga
+ sec_scc.x_elastic_Hill_Poisson_ratio = moduli['nu_H']
+
+ sec_scc.x_elastic_eigenvalues = eigenvalues * giga
+
+ elif order == 3:
+ elastic_constant = self.properties.get_elastic_constants_order3()
+
+ sec_scc.x_elastic_3rd_order_constants_matrix = elastic_constant
+
+ def parse(self):
+
+ sec_run = self.archive.m_create(section_run)
+
+ sec_run.program_name = 'elastic'
+ sec_run.program_version = '1.0'
+
+ sec_system = sec_run.m_create(section_system)
+
+ symbols, positions, cell = self.properties.get_structure_info()
+ volume = self.properties.info['equilibrium_volume']
+ volume = a_to_m(a_to_m(a_to_m(volume)))
+
+ sec_system.atom_labels = symbols
+ sec_system.atom_positions = a_to_m(positions)
+ sec_system.simulation_cell = a_to_m(cell)
+ sec_system.configuration_periodic_dimensions = [True, True, True]
+ sec_system.x_elastic_space_group_number = self.properties.info['space_group_number']
+ sec_system.x_elastic_unit_cell_volume = volume
+
+ sec_method = sec_run.m_create(section_method)
+ sec_method.x_elastic_elastic_constant_order = self.properties.info['order']
+ sec_method.x_elastic_calculation_method = self.properties.info['calculation_method']
+ sec_method.x_elastic_code = self.properties.info['code_name']
+ sec_method.x_elastic_max_lagrangian_strain = self.properties.info['max_strain']
+ sec_method.x_elastic_number_of_distorted_structures = self.properties.info['n_strains']
+
+ deformation_types = self.properties.get_deformation_types()
+ sec_method.x_elastic_deformation_types = deformation_types
+ sec_method.x_elastic_number_of_deformations = len(self.properties.deformation_dirs)
+
+ references = self.properties.get_references_to_calculations()
+ sec_scc = sec_run.m_create(section_single_configuration_calculation)
+ for reference in references:
+ sec_calc_ref = sec_scc.m_create(section_calculation_to_calculation_refs)
+ sec_calc_ref.calculation_to_calculation_external_url = reference
+ sec_calc_ref.calculation_to_calculation_kind = 'source_calculation'
+
+ fit_input = self.properties.get_input()
+ sec_fit_par = sec_method.m_create(x_elastic_section_fitting_parameters)
+ sec_fit_par.x_elastic_fitting_parameters_eta = fit_input[0]
+ sec_fit_par.x_elastic_fitting_parameters_polynomial_order = fit_input[1]
+
+ self.parse_strain()
+
+ self.parse_elastic_constant()
+
+ sec_scc.single_configuration_to_calculation_method_ref = sec_method
+ sec_scc.single_configuration_calculation_to_system_ref = sec_system
+
+ sec_workflow = self.archive.m_create(Workflow)
+ sec_workflow.workflow_type = 'elastic'
+ sec_elastic = sec_workflow.m_create(Elastic)
+ sec_elastic.calculation_method = self.properties.info['calculation_method']
+ sec_elastic.elastic_constants_order = self.properties.info['order']
+ sec_elastic.strain_maximum = self.properties.info['max_strain']
diff --git a/elasticparser/elastic_parser_input_exciting.py b/elasticparser/elastic_parser_input_exciting.py
deleted file mode 100644
index 6ba57f6..0000000
--- a/elasticparser/elastic_parser_input_exciting.py
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 2017-2018 Lorenzo Pardini
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import xml.sax
-import logging
-import numpy as np
-from nomadcore.unit_conversion.unit_conversion import convert_unit_function
-from nomadcore.unit_conversion.unit_conversion import convert_unit
-from nomadcore.unit_conversion import unit_conversion
-
-class InputHandler(xml.sax.handler.ContentHandler):
-
- def __init__(self, backend):
- self.backend = backend
- self.inputSectionGIndex = -1
- self.basevect = []
- self.latticeDummy = ''
- self.CurrentData = ''
- self.atomCoor = []
- self.atomCoorDummy = []
- self.speciesfileDummy = ''
- self.speciesfile = []
- self.scale = 1.0
- self.cell = []
- self.cellDummy = []
-
- def endDocument(self):
- bohr_to_m = convert_unit(1, "bohr", "m")
- for i in range(0,len(self.cellDummy)):
- for j in range(0,3):
- self.cell[i].append(float(self.cellDummy[i][j])*self.scale*bohr_to_m)
- self.backend.addValue("lattice_vectors", self.cell)
- self.backend.addValue('atom_positions',self.atomCoor)
- for i in range(0,len(self.atomCoor)):
- self.speciesfile.append(self.speciesfileDummy)
- self.backend.addValue("atom_labels", self.speciesfile)
- def startElement(self, name, attrs):
- self.CurrentData = name
- if name == "crystal":
- try:
- self.scale = float(attrs.getValue('scale'))
- except:
- self.scale = 1.0
- elif name == 'species':
- self.speciesfileDummy = attrs.getValue('speciesfile')[:-4]
- elif name == 'atom':
- self.atomCoorDummy = attrs.getValue('coord').split()
- for j in range(0,3):
- self.atomCoorDummy[j]=float(self.atomCoorDummy[j])
- self.atomCoor.append(self.atomCoorDummy)
- else:
- pass
-
- def endElement(self, name):
- pass
-
- def characters(self, content):
- if self.CurrentData == 'basevect':
- self.latticeDummy = content
- lattice = self.latticeDummy.split()
- if lattice != []:
- self.cellDummy.append(lattice)
- self.cell.append([])
- else:
- pass
-
-def parseInput(inF, backend):
- handler = InputHandler(backend)
- xml.sax.parse(inF, handler)
diff --git a/elasticparser/elastic_parser_input_wien2k.py b/elasticparser/elastic_parser_input_wien2k.py
deleted file mode 100644
index 107fa8f..0000000
--- a/elasticparser/elastic_parser_input_wien2k.py
+++ /dev/null
@@ -1,138 +0,0 @@
-from builtins import object
-from nomadcore.simple_parser import mainFunction, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json, logging
-import numpy as np
-import ase.geometry
-
-
-################################################################
-# This is the subparser for the main WIEN2k input file (.struct)
-################################################################
-
-# Copyright 2016-2018 Daria M. Tomecka, Fawzi Mohamed
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-__author__ = "Daria M. Tomecka"
-__maintainer__ = "Daria M. Tomecka"
-__email__ = "tomeckadm@gmail.com;"
-__date__ = "15/05/2017"
-
-########### Modified for elastic by Lorenzo Pardini ##################
-
-class Wien2kStructContext(object):
- """context for wien2k struct parser"""
-
- def __init__(self):
- self.parser = None
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- pass
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- # allows to reset values if the same superContext is used to parse different files
- self.initialize_values()
-
- def onClose_section_system(self, backend, gIndex, section):
- # unit_cell
- unit_cell_params = []
- for i in ['a', 'b', 'c']:
- uci = section['x_elastic_wien2k_unit_cell_param_' + i]
- #if uci is not None:
- unit_cell_params.append(uci[0])
- for i in ['alfa', 'beta', 'gamma']:
- uci = section['x_elastic_wien2k_angle_between_unit_axis_' + i]
- # if uci is not None:
- unit_cell_params.append(uci[0])
-
- unit_cell = ase.geometry.cellpar_to_cell(unit_cell_params)
- backend.addArrayValues('lattice_vectors', unit_cell)
-# backend.addArrayValues("configuration_periodic_dimensions", np.ones(3, dtype=bool))
-
- equiv_atoms = section["x_elastic_wien2k_section_equiv_atoms"]
- #logging.error("section: %s", section)
- labels = []
- pos = []
-
- for eqAtoms in equiv_atoms:
- label = eqAtoms["x_elastic_wien2k_atom_name"][0]
- x = eqAtoms["x_elastic_wien2k_atom_pos_x"]
- y = eqAtoms["x_elastic_wien2k_atom_pos_y"]
- z = eqAtoms["x_elastic_wien2k_atom_pos_z"]
- #logging.error("equiv_atoms: %s x %s y %s z %s",eqAtoms, x, y, z)
- if len(x) != len(y) or len(x) != len(z):
- raise Exception("incorrect parsing, different number of x,y,z components")
- groupPos = [[x[i],y[i],z[i]] for i in range(len(x))]
- nAt = len(groupPos)
- labels += [label for i in range(nAt)]
- pos += groupPos
- backend.addValue("atom_labels", labels)
-
- backend.addArrayValues('atom_positions', np.asarray(pos))
-
-
-
-# description of the input
-def buildStructureMatchers():
- return SM(
- name = 'root',
- weak = True,
- startReStr = "",
- sections = ["section_run", "section_system"],
- subMatchers = [
- SM(name = 'systemName',
- startReStr = r"(?P<x_elastic_wien2k_system_nameIn>.*)"),
- SM(r"\w+\s*LATTICE,NONEQUIV\.ATOMS.\s*(?P<x_elastic_wien2k_nonequiv_atoms>[0-9]+)"),
- SM(r"(?P<x_elastic_wien2k_calc_mode>.*)"),
- # SM(r"\s*(?P<x_wien2k_unit_cell_param_a>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)\s*(?P<x_wien2k_unit_cell_param_b>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)\s*(?P<x_wien2k_unit_cell_param_c>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)\s*(?P<x_wien2k_angle_between_unit_axis_alfa>[-+0-9.eEdD]{9})\s*(?P<x_wien2k_angle_between_unit_axis_beta>[-+0-9.eEdD]{9})\s*(?P<x_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)"),
- SM(r"\s*(?P<x_elastic_wien2k_unit_cell_param_a__angstrom>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_elastic_wien2k_unit_cell_param_b__angstrom>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_elastic_wien2k_unit_cell_param_c__angstrom>[-+0-9]*\.\d{0,6}){0,10}\s*(?P<x_elastic_wien2k_angle_between_unit_axis_alfa>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_elastic_wien2k_angle_between_unit_axis_beta>[-+]?[0-9]*\.\d{0,6}){0,10}\s*(?P<x_elastic_wien2k_angle_between_unit_axis_gamma>[-+]?[0-9]*\.\d*)"),
- SM(r"\s*ATOM\s*[-0-9]+:\s*X=(?P<x_elastic_wien2k_atom_pos_x__angstrom>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)\s*Y=(?P<x_elastic_wien2k_atom_pos_y__angstrom>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)\s*Z=(?P<x_elastic_wien2k_atom_pos_z__angstrom>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)",
- repeats=True,
- sections=["x_elastic_wien2k_section_equiv_atoms"],
- subMatchers=[
- SM(r"\s*[-0-9]+:\s*X=(?P<x_elastic_wien2k_atom_pos_x__angstrom>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)\s*Y=(?P<x_elastic_wien2k_atom_pos_y__angstrom>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)\s*Z=(?P<x_elastic_wien2k_atom_pos_z__angstrom>[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)",
- repeats=True
- ),
- # SM(r"\s*(?P<atom>.{10})\s*NPT=\s*(?P<NPT>[0-9]+)\s*R0=(?P<r0>[0-9.]+)\s*RMT=\s*(?P<rmt>[0-9.]+)\s*Z:\s*(?P<z>[0-9.]+)",)
- SM(r"\s*(?P<x_elastic_wien2k_atom_name>^.+)\s*NPT=\s*(?P<x_elastic_wien2k_NPT>[0-9]+)\s*R0=(?P<x_elastic_wien2k_R0>[0-9.]+)\s*RMT=\s*(?P<x_elastic_wien2k_RMT>[0-9.]+)\s*Z:\s*(?P<x_elastic_wien2k_atomic_number_Z>[0-9.]+)",)
- ]
- )
- ])
-
-def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
- """Sets the caching level for the metadata.
-
- Args:
- metaInfoEnv: metadata which is an object of the class InfoKindEnv in nomadcore.local_meta_info.py.
- CachingLvl: Sets the CachingLevel for the sections k_band, run, and single_configuration_calculation.
- This allows to run the parser without opening new sections.
-
- Returns:
- Dictionary with metaname as key and caching level as value.
- """
- # manually adjust caching of metadata
- cachingLevelForMetaName = {
- 'section_run': CachingLvl,
- 'section_system': CachingLvl
- }
- cachingLevelForMetaName["x_elastic_wien2k_system_nameIn"] = CachingLevel.ForwardAndCache
- cachingLevelForMetaName["x_elastic_wien2k_section_equiv_atoms"] = CachingLevel.ForwardAndCache
- cachingLevelForMetaName["atom_labels"] = CachingLevel.ForwardAndCache
- return cachingLevelForMetaName
-
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
diff --git a/elasticparser/elastic_properties.py b/elasticparser/elastic_properties.py
new file mode 100644
index 0000000..214fb12
--- /dev/null
+++ b/elasticparser/elastic_properties.py
@@ -0,0 +1,417 @@
+import os
+import numpy as np
+from ase import Atoms
+
+from nomad.parsing.text_parser import Quantity, UnstructuredTextFileParser
+
+
+class ElasticProperties:
+ def __init__(self, mainfile):
+ self._mainfile = mainfile
+ self.maindir = os.path.dirname(mainfile)
+ self._deform_dirs = None
+ self._deform_dir_prefix = 'Dst'
+ self._info = None
+
+ @property
+ def mainfile(self):
+ return self._mainfile
+
+ @mainfile.setter
+ def mainfile(self, val):
+ self._info = None
+ self._deform_dirs = None
+ self._mainfile = val
+
+ @property
+ def info(self):
+ if self._info is None:
+
+ quantities = [
+ Quantity('order', r'\s*Order of elastic constants\s*=\s*([0-9]+)'),
+ Quantity('calculation_method', r'\s*Method of calculation\s*=\s*([-a-zA-Z]+)\s*'),
+ Quantity('code_name', r'\s*DFT code name\s*=\s*([-a-zA-Z]+)'),
+ Quantity('space_group_number', r'\s*Space-group number\s*=\s*([0-9]+)'),
+ Quantity('equilibrium_volume', r'\s*Volume of equilibrium unit cell\s*=\s*([-0-9.]+)\s*\[a.u\^3\]'),
+ Quantity('max_strain', r'\s*Maximum Lagrangian strain\s*=\s*([0-9.]+)'),
+ Quantity('n_strains', r'\s*Number of distorted structures\s*=\s*([0-9]+)')
+ ]
+
+ parser = UnstructuredTextFileParser(self.mainfile, quantities)
+
+ self._info = {}
+ for key, val in parser.items():
+ self._info[key] = val[0]
+
+ return self._info
+
+ @property
+ def deformation_dirs(self):
+ if self._deform_dirs is None:
+ dirs = os.listdir(self.maindir)
+ self._deform_dirs = [
+ os.path.join(self.maindir, d) for d in dirs if d.startswith(self._deform_dir_prefix)]
+
+ return self._deform_dirs
+
+ def get_references_to_calculations(self):
+ def output_file(dirname):
+ code = self.info['code_name'].lower()
+ if code == 'exciting':
+ return os.path.join(dirname, 'INFO.OUT')
+ elif code == 'wien':
+ return os.path.join(dirname, '%s_Converged.scf' % os.path.basename(dirname))
+ elif code == 'quantum':
+ return os.path.join(dirname, '%s.out' % os.path.basename(dirname))
+ else:
+ return None
+
+ references = []
+ for deform_dir in self.deformation_dirs:
+ sub_dirs = os.listdir(deform_dir)
+ for sub_dir in sub_dirs:
+ calc_dir = os.path.join(deform_dir, sub_dir)
+ out_file = output_file(calc_dir)
+ if out_file is not None and os.path.isfile(out_file):
+ references.append(out_file)
+
+ return references
+
+ def get_structure_info(self):
+ path = os.path.join(self.maindir, 'sgroup.out')
+ if not os.path.isfile(path):
+ return
+
+ def get_sym_pos(val):
+ val = val.strip().replace('\n', '').split()
+ sym = []
+ pos = []
+ for i in range(0, len(val), 4):
+ sym.append(val[i + 3].strip())
+ pos.append([float(val[j]) for j in range(i, i + 3)])
+ sym_pos = dict(symbols=sym, positions=pos)
+ return sym_pos
+
+ quantities = [
+ Quantity('cellpar', r'a\s*b\s*c\n([\d\.\s]+)\n\s*alpha\s*beta\s*gamma\n([\d\.\s]+)\n+'),
+ Quantity('sym_pos', r'Atom positions:\n\n([\s\d\.A-Za-z]+)\n\n', str_operation=get_sym_pos)
+ ]
+
+ parser = UnstructuredTextFileParser(path, quantities)
+
+ cellpar = list(parser['cellpar'])[0]
+ sym_pos = list(parser['sym_pos'])[0]
+
+ sym = list(sym_pos['symbols'])
+ pos = list(sym_pos['positions'])
+
+ structure = Atoms(cell=cellpar, scaled_positions=pos, symbols=sym, pbc=True)
+
+ return sym, structure.get_positions(), list(structure.get_cell())
+
+ def get_strain_energy(self):
+ strains, energies = [], []
+
+ for deform_dir in self.deformation_dirs:
+ filenames = [d for d in os.listdir(deform_dir) if d.endswith('Energy.dat')]
+ if not filenames:
+ continue
+
+ path = os.path.join(deform_dir, filenames[-1])
+ data = np.loadtxt(path).T
+ strains.append(data[0])
+ energies.append(data[1])
+
+ return strains, energies
+
+ def get_strain_stress(self):
+ strains = {'Lagrangian-stress': [], 'Physical-stress': []}
+ stresses = {'Lagrangian-stress': [], 'Physical-stress': []}
+
+ for deform_dir in self.deformation_dirs:
+ filenames = [d for d in os.listdir(deform_dir) if d.endswith('stress.dat')]
+
+ for filename in filenames:
+ path = os.path.join(deform_dir, filename)
+ if not os.path.isfile(path):
+ continue
+
+ with open(path) as f:
+ lines = f.readlines()
+
+ strain, stress = [], []
+ for line in lines:
+ val = line.strip().split()
+ if not val[0].strip().replace('.', '').isdecimal():
+ continue
+
+ strain.append(float(val[0]))
+ stress.append([float(v) for v in val[1:7]])
+
+ stype = filename.rstrip('.dat').split('_')[-1]
+ strains[stype].append(strain)
+ stresses[stype].append(stress)
+
+ return strains, stresses
+
+ def get_deformation_types(self):
+ path = os.path.join(self.maindir, 'Distorted_Parameters')
+ if not os.path.isfile(path):
+ return
+
+ quantities = [
+ Quantity(
+ 'deformation', r'Lagrangian strain\s*=\s*\(([eta\s\d\.,]+)\)',
+ str_operation=lambda x: x.replace(',', '').split(), dtype=str)]
+ parser = UnstructuredTextFileParser(path, quantities)
+
+ deformation_types = [list(d) for d in list(parser['deformation'])]
+
+ return deformation_types
+
+ def _get_fit(self, path_dir, file_ext):
+ path_dir = os.path.join(self.maindir, path_dir)
+
+ if not os.path.isdir(path_dir):
+ return
+
+ paths = [p for p in os.listdir(path_dir) if p.endswith(file_ext)]
+ paths.sort()
+
+ if not paths:
+ return
+
+ eta = {'2nd': [], '3rd': [], '4th': [], '5th': [], '6th': [], '7th': []}
+ val = {'2nd': [], '3rd': [], '4th': [], '5th': [], '6th': [], '7th': []}
+
+ def split_eta_val(val):
+ val = val.strip().split()
+ return [val[0::2], val[1::2]]
+
+ quantities = [
+ Quantity(
+ order, r'%s order fit.\n([\d.\s\ne\-\+]+)\n' % order, str_operation=split_eta_val)
+ for order in eta.keys()
+ ]
+
+ parser = UnstructuredTextFileParser(os.path.join(path_dir, paths[0]), quantities)
+
+ for path in paths:
+ parser.mainfile = os.path.join(path_dir, path)
+ for key in eta.keys():
+ if parser[key] is not None:
+ eta[key].append(list(parser[key][0][0]))
+ val[key].append(list(parser[key][0][1]))
+
+ eta = {key: val for key, val in eta.items() if val}
+ val = {key: val for key, val in val.items() if val}
+
+ return eta, val
+
+ def get_energy_fit(self):
+ energy_fit = dict()
+
+ for file_ext in ['d2E.dat', 'd3E.dat', 'ddE.dat']:
+ result = self._get_fit('Energy-vs-Strain', file_ext)
+ if result is None:
+ continue
+
+ energy_fit['d2e'] = result
+
+ result = self._get_fit('Energy-vs-Strain', 'CVe.dat')
+ if result is not None:
+ energy_fit['cross-validation'] = result
+
+ return energy_fit
+
+ def get_stress_fit(self):
+ stress_fit = dict()
+ stress_fit['dtn'] = [[]] * 6
+ stress_fit['cross-validation'] = [[]] * 6
+
+ for strain_index in range(1, 7):
+ result = self._get_fit('Stress-vs-Strain', '%d_dS.dat' % strain_index)
+ if result is not None:
+ stress_fit['dtn'][strain_index - 1] = result
+
+ result = self._get_fit('Stress-vs-Strain', '%d_CVe.dat' % strain_index)
+ if result is not None:
+ stress_fit['cross-validation'][strain_index - 1] = result
+
+ return stress_fit
+
+ def get_input(self):
+ paths = os.listdir(self.maindir)
+ path = None
+ for p in paths:
+ if 'ElaStic_' in p and p.endswith('.in'):
+ path = p
+ break
+
+ if path is None:
+ return
+
+ calc_method = self.info['calculation_method']
+
+ eta_ec = []
+ fit_ec = []
+
+ def _is_number(var):
+ try:
+ float(var)
+ return True
+ except Exception:
+ return False
+
+ path = os.path.join(self.maindir, path)
+
+ with open(path) as f:
+ while True:
+ line = f.readline()
+ if not line:
+ break
+
+ if calc_method.lower() == 'energy':
+ _, eta, fit = line.strip().split()
+ eta_ec.append(float(eta))
+ fit_ec.append(int(fit))
+
+ elif calc_method.lower() == 'stress':
+ val = line.strip().split()
+ if not _is_number(val[0]):
+ eta_ec.append([float(val[i + 1]) for i in range(6)])
+ else:
+ fit_ec.append([int(val[i]) for i in range(6)])
+
+ else:
+ pass
+
+ return eta_ec, fit_ec
+
+ def get_elastic_constants_order2(self):
+ path = os.path.join(self.maindir, 'ElaStic_2nd.out')
+
+ def reshape(val):
+ return np.array(val.split()).reshape((6, 6))
+
+ quantities = [
+ Quantity(
+ 'voigt', r'Symmetry of the second-order elastic constant matrix in Voigt notation.\s*[\s\S]+\n\n([C\d\s\n]+)\n',
+ str_operation=reshape, dtype=str),
+ Quantity(
+ 'elastic_constant', r'Elastic constant \(stiffness\) matrix in GPa:\s*\n\n([\-\d\.\s\n]+)\n',
+ str_operation=reshape, dtype=float),
+ Quantity(
+ 'compliance', r'Elastic compliance matrix in 1/GPa:\s*\n\n([\-\d\.\s\n]+)\n',
+ str_operation=reshape, dtype=float)]
+
+ modulus_names = [
+ 'B_V', 'K_V', 'G_V', 'B_R', 'K_R', 'G_R', 'B_H', 'K_H', 'G_H', 'E_V',
+ 'nu_V', 'E_R', 'nu_R', 'E_H', 'nu_H', 'AVR']
+
+ quantities += [
+ Quantity(name, r'%s\s*=\s*([-+\d+\.]+)\s*' % name) for name in modulus_names]
+
+ quantities += [
+ Quantity(
+ 'eigenvalues', r'Eigenvalues of elastic constant \(stiffness\) matrix:\s*\n+([\-\d\.\n\s]+)\n')]
+
+ parser = UnstructuredTextFileParser(path, quantities)
+
+ matrices = dict(
+ voigt=list(parser['voigt'])[0], elastic_constant=list(parser['elastic_constant'])[0],
+ compliance=list(parser['compliance'])[0])
+
+ moduli = dict()
+ for name in modulus_names:
+ if parser[name] is not None:
+ moduli[name] = parser[name][0]
+
+ eigenvalues = list(parser['eigenvalues'])[0]
+
+ return matrices, moduli, eigenvalues
+
+ def get_elastic_constants_order3(self):
+ path = os.path.join(self.maindir, 'ElaStic_3rd.out')
+ elastic_constant = []
+
+ def arrange_matrix(val):
+ val = val.strip().split('\n')
+ matrix = [v.strip().split() for v in val if v.strip()]
+ matrix = np.array(matrix).reshape((12, 18))
+ arranged = []
+ for i in range(2):
+ for j in range(3):
+ arranged.append(
+ matrix[i * 6: (i + 1) * 6, j * 6: (j + 1) * 6].tolist())
+ return arranged
+
+ def get_cijk(val):
+ val = val.replace('=', '').replace('GPa', '')
+ cijk = dict()
+ for v in val.split('\n'):
+ v = v.split()
+ if len(v) == 2:
+ cijk[v[0].strip()] = float(v[1])
+ return cijk
+
+ space_group_number = self.info['space_group_number']
+
+ quantities = [
+ Quantity(
+ 'elastic_constant', r'\%\s*\n([\s0-6A-L]*)[\n\s\%1-6\-ij]*([\s0-6A-L]*)\n',
+ str_operation=arrange_matrix, dtype=str),
+ Quantity(
+ 'cijk', r'(C\d{3}\s*=\s*[C1-6\s=\n\-\.0-9GPa]*)\n\n', str_operation=get_cijk)
+ ]
+
+ parsers = UnstructuredTextFileParser(path, quantities)
+
+ elastic_constant_str = list(parsers['elastic_constant'])[0]
+
+ cijk = list(parsers['cijk'])[0]
+
+ # formulas for the coefficients
+ coeff_A = cijk.get('C111', 0) + cijk.get('C112', 0) - cijk.get('C222', 0)
+ coeff_B = -(cijk.get('C115', 0) + 3 * cijk.get('C125', 0)) / 2
+ coeff_C = (cijk.get('C114', 0) + 3 * cijk.get('C124', 0)) / 2
+ coeff_D = -(2 * cijk.get('C111', 0) + cijk.get('C112', 0) - 3 * cijk.get('C222', 0)) / 4
+ coeff_E = -cijk.get('C114', 0) - 2 * cijk.get('C124', 0)
+ coeff_F = -cijk.get('C115', 0) - 2 * cijk.get('C125', 0)
+ coeff_G = -(cijk.get('C115', 0) - cijk.get('C125', 0)) / 2
+ coeff_H = (cijk.get('C114', 0) - cijk.get('C124', 0)) / 2
+ coeff_I = (2 * cijk.get('C111', 0) - cijk.get('C112', 0) - cijk.get('C222', 0)) / 4
+ coeff_J = (cijk.get('C113', 0) - cijk.get('C123', 0)) / 2
+ coeff_K = -(cijk.get('C144', 0) - cijk.get('C155', 0)) / 2
+
+ if space_group_number <= 148: # rhombohedral II
+ coefficients = dict(
+ A=coeff_A, B=coeff_B, C=coeff_C, D=coeff_D, E=coeff_E, F=coeff_F, G=coeff_G,
+ H=coeff_H, I=coeff_I, J=coeff_J, K=coeff_K)
+ elif space_group_number <= 167: # rhombohedral I
+ coefficients = dict(
+ A=coeff_A, B=coeff_C, C=coeff_D, D=coeff_E, E=coeff_H, F=coeff_I, G=coeff_J,
+ H=coeff_K)
+ elif space_group_number <= 176: # hexagonal II
+ coefficients = dict(
+ A=coeff_A, B=coeff_D, C=coeff_I, D=coeff_J, E=coeff_K)
+ elif space_group_number <= 194: # hexagonal I
+ coefficients = dict(
+ A=coeff_A, B=coeff_D, C=coeff_I, D=coeff_J, E=coeff_K)
+ else:
+ coefficients = dict()
+
+ # assign values to the elastic constant matrix from the independent ec and coefficients
+ elastic_constant = np.zeros((6, 6, 6))
+ for i in range(6):
+ for j in range(6):
+ for k in range(6):
+ val = elastic_constant_str[i][j][k]
+ if val == '0':
+ elastic_constant[i][j][k] = 0
+ elif val.isdigit():
+ elastic_constant[i][j][k] = cijk['C%s' % val]
+ else:
+ elastic_constant[i][j][k] = coefficients.get(val, 0)
+
+ return elastic_constant
diff --git a/elasticparser/parser_elastic.py b/elasticparser/parser_elastic.py
deleted file mode 100644
index 168f1ca..0000000
--- a/elasticparser/parser_elastic.py
+++ /dev/null
@@ -1,1453 +0,0 @@
-# Copyright 2017-2018 Lorenzo Pardini
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-from builtins import object
-import numpy as np
-from nomadcore.unit_conversion.unit_conversion import convert_unit
-from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
-from nomadcore.simple_parser import SimpleMatcher as SM
-from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-from nomadcore.unit_conversion import unit_conversion
-import os, sys, json
-import logging
-import elasticparser.elastic_parser_input_exciting as elastic_parser_input_exciting
-import elasticparser.elastic_parser_input_wien2k as elastic_parser_input_wien2k
-from ase import Atoms
-#from pathlib import Path
-
-def is_number(s):
- try:
- float(s)
- return True
- except ValueError:
- return False
-
-class SampleContext(object):
-
- def __init__(self):
-# self.mainFileUri = sys.argv[1] #exciting !!!!!!LOCAL HOME!!!!!!!! OKOKOKOK
- self.mainFileUri = sys.argv[2] #exciting !!! FOR NOMAD URI nmd:// or sbt -> zip file!!!!!!!! OKOKKOOK
- self.parser = None
- self.mainFilePath = None
- self.mainFile = None
- self.etaEC = []
- self.fitEC = []
- self.SGN = 0
- self.secMethodIndex = None
- self.secSystemIndex = None
- self.sim_cell = []
-
- def initialize_values(self):
- """allows to reset values if the same superContext is used to parse different files"""
- self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
-
- def onOpen_section_system(self, backend, gIndex, section):
- self.secSystemIndex = gIndex
-
- def startedParsing(self, path, parser):
- """called when parsing starts"""
- self.parser = parser
- self.initialize_values()
-
- def onOpen_section_method(self, backend, gIndex, section):
- if self.secMethodIndex is None:
- self.secMethodIndex = gIndex
-
- def onClose_section_run(self, backend, gIndex, section):
- backend.addValue('program_name', 'elastic')
- backend.addValue('program_version', '1.0')
-
- def onClose_section_system(self, backend, gIndex, section):
- backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
- self.SGN = int(section["x_elastic_space_group_number"][0])
- mainFile = self.parser.fIn.fIn.name
- dirPath = os.path.dirname(mainFile) #####exciting sbt -> zip file#### YES ?????????? sure???? check first OKOKOKKO
- self.mainFile = self.parser.fIn.name
- self.mainFilePath = self.mainFile[0:-12]
-# dirPath = self.mainFileUri[0:-12] #####exciting LOCAL HOME or from NOMAD URI nmd:// ####### YES OKOKOKOK
- for files in os.listdir(dirPath):
- if files[-3:] == "xml":
- inputFile = files
- os.chdir(self.mainFilePath)
- with open(inputFile) as f:
- elastic_parser_input_exciting.parseInput(f, backend)
- elif files[-6:] == "struct":
- inputFile = files
- os.chdir(self.mainFilePath)
- structSuperContext = elastic_parser_input_wien2k.Wien2kStructContext()
- structParser = AncillaryParser(
- fileDescription = elastic_parser_input_wien2k.buildStructureMatchers(),
- parser = self.parser,
- cachingLevelForMetaName = elastic_parser_input_wien2k.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
- superContext = structSuperContext)
-
- # ESPRESSO INPUT FILE TO BE ADDED
-
- with open(inputFile) as fIn:
- structParser.parseFile(fIn)
-
- elif files[-3:] == ".in": ##### so far it works only for Rostam's calculations
- if files != "ElaStic_2nd.in":
- inputFile = files
- atom_labels = []
- posX = []
- posY = []
- posZ = []
- coord = []
- lattice = []
- check = False
- os.chdir(self.mainFilePath)
- with open(inputFile) as g:
- fromB = unit_conversion.convert_unit_function("bohr", "m")
- while 1:
- s = g.readline()
- if not s: break
- s = s.strip()
- s = s.split()
- if s[0] == "ibrav": ####### Rostam's: ibrav always 0
- ibrav = s[2]
- elif s[0] == "celldm(1)":
- alat = float(s[2])
- elif len(s) == 4:
- atom_labels.append(s[0])
- posX.append(float(s[1]))
- posY.append(float(s[2]))
- posZ.append(float(s[3]))
- elif len(s) == 3 and s[1] != "=":
- if is_number(s[0]):
- lattice.append([fromB(alat*float(s[0])),fromB(alat*float(s[1])),fromB(alat*float(s[2]))])
- else:
- pass
-
- for i in range(len(atom_labels)):
- coord.append([posX[i],posY[i],posZ[i]])
- cell = [[lattice[0][0],lattice[0][1],lattice[0][2]],
- [lattice[1][0],lattice[1][1],lattice[1][2]],
- [lattice[2][0],lattice[2][1],lattice[2][2]]]
- self.sim_cell = cell
- atoms = Atoms(atom_labels, coord, cell=[(1, 0, 0),(0, 1, 0),(0, 0, 1)])
- atoms.set_cell(self.sim_cell, scale_atoms=True)
- coord = atoms.get_positions()
- backend.addArrayValues('atom_positions', np.asarray(coord))
- backend.addArrayValues('atom_labels', np.asarray(atom_labels))
- backend.addValue("simulation_cell", cell)
-
- def onClose_section_method(self, backend, gIndex, section):
- ha_per_joule = convert_unit(1, "hartree", "J")
- giga = 10**9
- elCode = section['x_elastic_code']
- elasticGIndex = backend.openSection("section_single_configuration_calculation")
- self.mainFilePath = self.mainFileUri[0:-12]
- questa = os.getcwd()
- mdr = float(section['x_elastic_max_lagrangian_strain'][0])
- ordr = int(section['x_elastic_elastic_constant_order'][0])
- nds = int(section['x_elastic_number_of_distorted_structures'][0])
- meth = section['x_elastic_calculation_method'][0]
- polFit2 = (nds-1)/2
- polFit4 = polFit2 - 1
- polFit6 = polFit2 - 2
- polFit2Cross = polFit2 - 1
- polFit4Cross = polFit4 - 1
- polFit6Cross = polFit6 - 1
- polFit1 = (nds-1)/2
- polFit3 = polFit1 - 1
- polFit5 = polFit1 - 2
- polFit1Cross = polFit1 - 1
- polFit3Cross = polFit3 - 1
- polFit5Cross = polFit5 - 1
- ext_uri = []
-
- i = 1
- while 1:
- if (i<10):
- Dstn = 'Dst0'+ str(i)
- if (os.path.exists(Dstn) == True):
- i += 1
- else:
- break
- else:
- Dstn = 'Dst' + str(i)
- if (os.path.exists(Dstn) == True):
- i += 1
- else:
- break
-
- defNum = i - 1
- ECs = defNum
-
- for j in range(1, ECs+1):
- for i in range(1,nds+1):
- if (j<10):
- if (i<10):
- if elCode[0] == 'exciting':
- ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_0' + str(i) + '/INFO.OUT')
- elif elCode[0] == 'WIEN':
- ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_0' + str(i) + '/Dst0'+ str(j) + '_0' + str(i) + '_Converged.scf')
- elif elCode[0] == 'QUANTUM':
- ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_0' + str(i) + '/Dst0'+ str(j) + '_0' + str(i) + '.out')
- else:
- if elCode[0] == 'exciting':
- ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_' + str(i) + '/INFO.OUT')
- elif elCode[0] == 'WIEN':
- ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_' + str(i) + '/Dst0' + str(j) + '_' + str(i) + '_Converged.scf')
- elif elCode[0] == 'QUANTUM':
- ext_uri.append(self.mainFilePath + 'Dst0' + str(j) + '/Dst0' + str(j) + '_' + str(i) + '/Dst0' + str(j) + '_' + str(i) + '.out')
- else:
- if (i<10):
- if elCode[0] == 'exciting':
- ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_0' + str(i) + '/INFO.OUT')
- elif elCode[0] == 'WIEN':
- ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_0' + str(i) + '/Dst' + str(j) + '_0' + str(i) + '_Converged.scf')
- elif elCode[0] == 'QUANTUM':
- ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_0' + str(i) + '/Dst' + str(j) + '_0' + str(i) + '.out')
- else:
- if elCode[0] == 'exciting':
- ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_' + str(i) + '/INFO.OUT')
- elif elCode[0] == 'WIEN':
- ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_' + str(i) +'/Dst' + str(j) + '_' + str(i) + '_Converged.scf')
- elif elCode[0] == 'QUANTUM':
- ext_uri.append(self.mainFilePath + 'Dst' + str(j) + '/Dst' + str(j) + '_' + str(i) +'/Dst' + str(j) + '_' + str(i) + '.out')
- for ref in ext_uri:
- refGindex = backend.openSection("section_calculation_to_calculation_refs")
- backend.addValue("calculation_to_calculation_external_url", ref)
- backend.addValue("calculation_to_calculation_kind", "source_calculation")
- backend.closeSection("section_calculation_to_calculation_refs", refGindex)
-
- energy = []
- eta = []
- LagrStress = []
- LagrStress_dummy = []
- physStress = []
- physStress_dummy = []
- for j in range(1, ECs+1):
- if (j<10):
- Dstn = 'Dst0'+ str(j)
- eta.append([])
- energy.append([])
- LagrStress_dummy.append([])
- physStress_dummy.append([])
- else:
- Dstn = 'Dst' + str(j)
- eta.append([])
- energy.append([])
- LagrStress_dummy.append([])
- physStress_dummy.append([])
-
- os.chdir(Dstn)
- cur_dir = os.getcwd()
-
- if elCode[0] == 'exciting':
- try:
- f = open(Dstn+'-Energy.dat', 'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- dummy_eta, dummy_energy = s.split()
- eta[-1].append(float(dummy_eta))
- energy[-1].append(float(dummy_energy)*ha_per_joule)
- os.chdir('../')
- except:
- pass
- try:
- f = open(Dstn+'_Energy.dat', 'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- dummy_eta, dummy_energy = s.split()
- eta[-1].append(float(dummy_eta))
- energy[-1].append(float(dummy_energy)*ha_per_joule)
- os.chdir('../')
- except:
- pass
-
- elif elCode[0] == 'WIEN':
- f = open(Dstn+'_Energy.dat', 'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- dummy_eta, dummy_energy = s.split()
- eta[-1].append(float(dummy_eta))
- energy[-1].append(float(dummy_energy)*ha_per_joule)
- os.chdir('../')
-
- elif (elCode[0] == 'QUANTUM' or elCode[0] == 'Quantum') and meth == 'Energy':
- f = open(Dstn+'_Energy.dat', 'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- dummy_eta, dummy_energy = s.split()
- eta[-1].append(float(dummy_eta))
- energy[-1].append(float(dummy_energy)*ha_per_joule)
- os.chdir('../')
-
- elif elCode[0] == 'QUANTUM' and meth == 'Stress':
- f = open(Dstn+'_Lagrangian-stress.dat', 'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- s = s.split()
- if is_number(s[0]):
- dummy_eta = s[0]
- dummy_LS1 = s[1]
- dummy_LS2 = s[2]
- dummy_LS3 = s[3]
- dummy_LS4 = s[4]
- dummy_LS5 = s[5]
- dummy_LS6 = s[6]
- eta[-1].append(float(dummy_eta))
- LagrStress_dummy[-1].append([float(dummy_LS1),float(dummy_LS2),float(dummy_LS3),float(dummy_LS4),float(dummy_LS5),float(dummy_LS6)])
-
- g = open(Dstn+'_Physical-stress.dat', 'r')
- while 1:
- s = g.readline()
- if not s: break
- s = s.strip()
- s = s.split()
- if is_number(s[0]):
- dummy_PS1 = s[1]
- dummy_PS2 = s[2]
- dummy_PS3 = s[3]
- dummy_PS4 = s[4]
- dummy_PS5 = s[5]
- dummy_PS6 = s[6]
- physStress_dummy[-1].append([float(dummy_PS1),float(dummy_PS2),float(dummy_PS3),float(dummy_PS4),float(dummy_PS5),float(dummy_PS6)])
- os.chdir('../')
-
- else:
- os.chdir('../')
-
- defTyp = []
-
- f = open('Distorted_Parameters','r')
-
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if 'Lagrangian' in s:
- defTyp.append([])
- s = s.split("(")
- s = s[-1].split(")")
- s = s[0].split(",")
- for i in range(0,6):
- s[i] = s[i].strip()
- defTyp[-1].append(s[i])
-
- f.close()
- prova = os.listdir('.')
- if 'Energy-vs-Strain' in prova:
- os.chdir('Energy-vs-Strain')
-
- d2e6_val = []
- d2e4_val = []
- d2e2_val = []
- d2e6_eta = []
- d2e4_eta = []
- d2e2_eta = []
- d2e_val_tot = []
- d2e_eta_tot = []
-
- for i in range(1, ECs+1):
- d2e_val_tot.append([])
- d2e_eta_tot.append([])
- if (i<10):
- if ordr == 2:
- Dstna = 'Dst0'+ str(i) + '_d2E.dat'
- Dstnb = 'Dst0'+ str(i) + '_ddE.dat'
- elif ordr == 3:
- Dstna = 'Dst0'+ str(i) + '_d3E.dat'
-# Dstnb = 'Dst0'+ str(i) + '-d3E.dat'
- try:
- f = open (Dstna,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- d2e_val_tot[-1].append([])
- d2e_eta_tot[-1].append([])
- elif len(s) >= 30:
- d2e_eta, d2e_values = s.split()
- d2e_val_tot[-1][-1].append(float(d2e_values)*giga)
- d2e_eta_tot[-1][-1].append(float(d2e_eta))
- f.close()
- except:
- pass
- try:
- f = open (Dstnb,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- d2e_val_tot[-1].append([])
- d2e_eta_tot[-1].append([])
- elif len(s) >= 30:
- d2e_eta, d2e_values = s.split()
- d2e_val_tot[-1][-1].append(float(d2e_values)*giga)
- d2e_eta_tot[-1][-1].append(float(d2e_eta))
- f.close()
- except:
- pass
- else:
- if ordr == 2:
- Dstna = 'Dst' + str(i) + '_d2E.dat'
- Dstnb = 'Dst' + str(i) + '_ddE.dat'
- elif ordr == 3:
- Dstna = 'Dst'+ str(i) + '_d3E.dat'
- try:
- f = open (Dstna,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- d2e_val_tot[-1].append([])
- d2e_eta_tot[-1].append([])
- elif len(s) >= 30:
- d2e_eta, d2e_values = s.split()
- d2e_val_tot[-1][-1].append(float(d2e_values)*giga)
- d2e_eta_tot[-1][-1].append(float(d2e_eta))
- f.close()
- except:
- pass
- try:
- f = open (Dstnb,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- d2e_val_tot[-1].append([])
- d2e_eta_tot[-1].append([])
- elif len(s) >= 30:
- d2e_eta, d2e_values = s.split()
- d2e_val_tot[-1][-1].append(float(d2e_values)*giga)
- d2e_eta_tot[-1][-1].append(float(d2e_eta))
- f.close()
- except:
- pass
-
- d2e6_val.append(d2e_val_tot[i-1][0])
- d2e4_val.append(d2e_val_tot[i-1][1])
- d2e2_val.append(d2e_val_tot[i-1][2])
- d2e6_eta.append(d2e_eta_tot[i-1][0])
- d2e4_eta.append(d2e_eta_tot[i-1][1])
- d2e2_eta.append(d2e_eta_tot[i-1][2])
- CrossVal6_val = []
- CrossVal4_val = []
- CrossVal2_val = []
- CrossVal_val_tot = []
-
- CrossVal6_eta = []
- CrossVal4_eta = []
- CrossVal2_eta = []
- CrossVal_eta_tot = []
-
- for i in range(1, ECs+1):
- CrossVal_val_tot.append([])
- CrossVal_eta_tot.append([])
- if (i<10):
- DstnCV = 'Dst0'+ str(i) + '_CVe.dat'
- f = open (DstnCV,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- CrossVal_val_tot[-1].append([])
- CrossVal_eta_tot[-1].append([])
- elif len(s) >= 20 and s.split()[0] != '#':
- CrossVal_eta, CrossVal_values = s.split()
- CrossVal_val_tot[-1][-1].append(float(CrossVal_values)*ha_per_joule)
- CrossVal_eta_tot[-1][-1].append(float(CrossVal_eta))
- f.close()
- else:
- DstnCV = 'Dst' + str(i) + '_CVe.dat'
- f = open (Dstn,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- CrossVal_val_tot[-1].append([])
- CrossVal_eta_tot[-1].append([])
- elif len(s) >= 20 and s.split()[0] != '#':
- CrossVal_eta, CrossVal_values = s.split()
- CrossVal_val_tot[-1][-1].append(float(CrossVal_values)*ha_per_joule)
- CrossVal_eta_tot[-1][-1].append(float(CrossVal_eta))
- f.close()
- CrossVal6_val.append(CrossVal_val_tot[i-1][0])
- CrossVal4_val.append(CrossVal_val_tot[i-1][1])
- CrossVal2_val.append(CrossVal_val_tot[i-1][2])
- CrossVal6_eta.append(CrossVal_eta_tot[i-1][0])
- CrossVal4_eta.append(CrossVal_eta_tot[i-1][1])
- CrossVal2_eta.append(CrossVal_eta_tot[i-1][2])
-
- os.chdir('../')
-
- elif 'Stress-vs-Strain' in prova:
-
- os.chdir('Stress-vs-Strain')
-
- dS5_val = [[],[],[],[],[],[]]
- dS3_val = [[],[],[],[],[],[]]
- dS1_val = [[],[],[],[],[],[]]
- dS5_eta = [[],[],[],[],[],[]]
- dS3_eta = [[],[],[],[],[],[]]
- dS1_eta = [[],[],[],[],[],[]]
- dS_val_tot = [[],[],[],[],[],[]]
- dS_eta_tot = [[],[],[],[],[],[]]
- string = []
- stringCV = []
-
- for i in range(6):
- string.append('Dstn'+str(i+1))
- stringCV.append('DstnCV'+str(i+1))
-
- for Dstn in string:
- j = string.index(Dstn)
- for i in range(1, ECs+1):
- dS_val_tot[string.index(Dstn)].append([])
- dS_eta_tot[string.index(Dstn)].append([])
- if (i<10):
- Dstn = 'Dst0'+ str(i) + '_LS' + str(string.index(Dstn)+1) + '_dS.dat'
- f = open (Dstn,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- dS_val_tot[j][-1].append([])
- dS_eta_tot[j][-1].append([])
- elif len(s) >= 30:
- dS_eta, dS_values = s.split()
- dS_val_tot[j][-1][-1].append(float(dS_values)*giga)
- dS_eta_tot[j][-1][-1].append(float(dS_eta))
- f.close()
- else:
- Dstn = 'Dst'+ str(i) + '_LS' + str(string.index(Dstn)+1) + '_dS.dat'
- f = open (Dstn,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- dS_val_tot[j][-1].append([])
- dS_eta_tot[j][-1].append([])
- elif len(s) >= 30:
- dS_eta, dS_values = s.split()
- dS_val_tot[j][-1][-1].append(float(dS_values)*giga)
- dS_eta_tot[j][-1][-1].append(float(dS_eta))
- f.close()
-
- dS5_val[j].append(dS_val_tot[j][i-1][0])
- dS3_val[j].append(dS_val_tot[j][i-1][1])
- dS1_val[j].append(dS_val_tot[j][i-1][2])
- dS5_eta[j].append(dS_eta_tot[j][i-1][0])
- dS3_eta[j].append(dS_eta_tot[j][i-1][1])
- dS1_eta[j].append(dS_eta_tot[j][i-1][2])
-
- CrossVal5_val = [[],[],[],[],[],[]]
- CrossVal3_val = [[],[],[],[],[],[]]
- CrossVal1_val = [[],[],[],[],[],[]]
- CrossVal_val_tot = [[],[],[],[],[],[]]
-
- CrossVal5_eta = [[],[],[],[],[],[]]
- CrossVal3_eta = [[],[],[],[],[],[]]
- CrossVal1_eta = [[],[],[],[],[],[]]
- CrossVal_eta_tot = [[],[],[],[],[],[]]
-
- for DstnCV in stringCV:
- j = stringCV.index(DstnCV)
- for i in range(1, ECs+1):
- CrossVal_val_tot[stringCV.index(DstnCV)].append([])
- CrossVal_eta_tot[stringCV.index(DstnCV)].append([])
- if (i<10):
- DstnCV = 'Dst0'+ str(i) + '_LS' + str(stringCV.index(DstnCV)+1) + '_CVe.dat'
- f = open (DstnCV,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- CrossVal_val_tot[j][-1].append([])
- CrossVal_eta_tot[j][-1].append([])
- elif len(s) >= 20 and s.split()[0] != '#':
- CrossVal_eta, CrossVal_values = s.split()
- CrossVal_val_tot[j][-1][-1].append(float(CrossVal_values)*ha_per_joule)
- CrossVal_eta_tot[j][-1][-1].append(float(CrossVal_eta))
- f.close()
- else:
- DstnCV = 'Dst'+ str(i) + '_LS' + str(stringCV.index(DstnCV)+1) + '_CVe.dat'
- f = open (DstnCV,'r')
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- if "order" in s.split():
- CrossVal_val_tot[j][-1].append([])
- CrossVal_eta_tot[j][-1].append([])
- elif len(s) >= 20 and s.split()[0] != '#':
- CrossVal_eta, CrossVal_values = s.split()
- CrossVal_val_tot[j][-1][-1].append(float(CrossVal_values)*ha_per_joule)
- CrossVal_eta_tot[j][-1][-1].append(float(CrossVal_eta))
- f.close()
- CrossVal5_val[j].append(CrossVal_val_tot[j][i-1][0])
- CrossVal3_val[j].append(CrossVal_val_tot[j][i-1][1])
- CrossVal1_val[j].append(CrossVal_val_tot[j][i-1][2])
- CrossVal5_eta[j].append(CrossVal_eta_tot[j][i-1][0])
- CrossVal3_eta[j].append(CrossVal_eta_tot[j][i-1][1])
- CrossVal1_eta[j].append(CrossVal_eta_tot[j][i-1][2])
- os.chdir('../')
-
- else:
- pass
-
- if ordr == 2:
- f = open ('ElaStic_'+str(ordr)+'nd.in','r')
- elif ordr == 3:
- f = open ('ElaStic_'+str(ordr)+'rd.in','r')
-
- EC_eigen = []
-
- if meth == 'Energy':
- for i in range(1, ECs+1):
- s = f.readline()
- s = s.strip()
- dummy, etaEC_dummy, fitEC_dummy = s.split()
- self.etaEC.append(float(etaEC_dummy))
- self.fitEC.append(int(fitEC_dummy))
-
- elif meth == 'Stress':
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- s = s.split()
- if not is_number(s[0]):
- self.etaEC.append([])
- for i in range(6): self.etaEC[-1].append(float(s[i+1]))
- else:
- self.fitEC.append([])
- for i in range(6): self.fitEC[-1].append(int(s[i]))
- else:
- pass
-
- f.close()
-
- if ordr == 2:
- f = open ('ElaStic_'+str(ordr)+'nd.out','r')
-
- allMat = [[],[],[],[],[],[]]
- voigtMat = [[],[],[],[],[],[]]
- ECMat = [[],[],[],[],[],[]]
- complMat = [[],[],[],[],[],[]]
-
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- s = s.split()
- if len(s) == 1:
- try: float(s[0])
- except ValueError:
- continue
- else:
- EC_eigen.append(float(s[0])*giga)
- elif "B_V" in s:
- B_V = float(s[5])*giga
- elif "K_V" in s:
- B_V = float(s[5])*giga
- elif "G_V" in s:
- G_V = float(s[5])*giga
- elif "B_R" in s:
- B_R = float(s[5])*giga
- elif "K_R" in s:
- B_R = float(s[5])*giga
- elif "G_R" in s:
- G_R = float(s[5])*giga
- elif "B_H" in s:
- B_H = float(s[5])*giga
- elif "K_H" in s:
- B_H = float(s[5])*giga
- elif "G_H" in s:
- G_H = float(s[5])*giga
- elif "E_V" in s:
- E_V = float(s[5])*giga
- elif "nu_V" in s:
- nu_V = float(s[5])
- elif "E_R" in s:
- E_R = float(s[5])*giga
- elif "nu_R" in s:
- nu_R = float(s[5])
- elif "E_H" in s:
- E_H = float(s[5])*giga
- elif "nu_H" in s:
- nu_H = float(s[5])
- elif len(s) == 6 and s[0] != "Elastic" and s[0] != "Eigenvalues":
- for i in range(0,6):
- allMat[i].append(s[i])
- elif "AVR" in s:
- AVR = float(s[6])
-
- f.close()
-
- for i in range(0,6):
- voigtMat[i] = allMat[i][0:6]
- ECMat[i] = allMat[i][6:12]
- complMat[i] = allMat[i][12:18]
-
- for i in range(0,6):
- for j in range(0,6):
- voigtMat[i][j] = voigtMat[j][i]
- ECMat[i][j] = float(ECMat[j][i])*giga
- complMat[i][j] = float(complMat[j][i])/giga
-
- if meth == 'Energy':
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "energy")
- backend.addValue("x_elastic_strain_diagram_number_of_eta", len(eta[0]))
- backend.addValue("x_elastic_strain_diagram_eta_values", eta)
- backend.addValue("x_elastic_strain_diagram_values", energy)
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "cross-validation")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 2)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit2Cross)
- backend.addValue("x_elastic_strain_diagram_eta_values", CrossVal2_eta)
- backend.addValue("x_elastic_strain_diagram_values", CrossVal2_val)
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "cross-validation")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 4)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit4Cross)
- backend.addValue("x_elastic_strain_diagram_eta_values", CrossVal4_eta)
- backend.addValue("x_elastic_strain_diagram_values", CrossVal4_val)
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "cross-validation")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 6)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit6Cross)
- backend.addValue("x_elastic_strain_diagram_eta_values", CrossVal6_eta)
- backend.addValue("x_elastic_strain_diagram_values", CrossVal6_val)
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "d2e")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 2)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit2)
- backend.addValue("x_elastic_strain_diagram_eta_values", d2e2_eta)
- backend.addValue("x_elastic_strain_diagram_values", d2e2_val)
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "d2e")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 4)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit4)
- backend.addValue("x_elastic_strain_diagram_eta_values", d2e4_eta)
- backend.addValue("x_elastic_strain_diagram_values", d2e4_val)
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "d2e")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 6)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit6)
- backend.addValue("x_elastic_strain_diagram_eta_values", d2e6_eta)
- backend.addValue("x_elastic_strain_diagram_values", d2e6_val)
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elif meth == 'Stress':
- for k in range(6):
- LagrStress.append([])
- physStress.append([])
- for j in range(len(LagrStress_dummy)):
- LagrStress[-1].append([])
- physStress[-1].append([])
- for i in range(len(LagrStress_dummy[j])):
- LagrStress[k][j].append(LagrStress_dummy[j][i][k])
- physStress[k][j].append(physStress_dummy[j][i][k])
-
- for i in range(0,6):
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "Lagrangian-stress")
- backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
- backend.addValue("x_elastic_strain_diagram_number_of_eta", len(eta[0]))
- backend.addValue("x_elastic_strain_diagram_eta_values", eta)
- backend.addValue("x_elastic_strain_diagram_values", LagrStress[i])
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "Physical-stress")
- backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
- backend.addValue("x_elastic_strain_diagram_number_of_eta", len(eta[0]))
- backend.addValue("x_elastic_strain_diagram_eta_values", eta)
- backend.addValue("x_elastic_strain_diagram_values", physStress[i])
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "cross-validation")
- backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 1)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit1Cross)
- backend.addValue("x_elastic_strain_diagram_eta_values", CrossVal1_eta[i])
- backend.addValue("x_elastic_strain_diagram_values", CrossVal1_val[i])
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "cross-validation")
- backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 3)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit3Cross)
- backend.addValue("x_elastic_strain_diagram_eta_values", CrossVal3_eta[i])
- backend.addValue("x_elastic_strain_diagram_values", CrossVal3_val[i])
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "cross-validation")
- backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 5)
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit5Cross)
- backend.addValue("x_elastic_strain_diagram_eta_values", CrossVal5_eta[i])
- backend.addValue("x_elastic_strain_diagram_values", CrossVal5_val[i])
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "dtn")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 1)
- backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit1)
- backend.addValue("x_elastic_strain_diagram_eta_values", dS1_eta[i])
- backend.addValue("x_elastic_strain_diagram_values", dS1_val[i])
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "dtn")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 3)
- backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit3)
- backend.addValue("x_elastic_strain_diagram_eta_values", dS3_eta[i])
- backend.addValue("x_elastic_strain_diagram_values", dS3_val[i])
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "dtn")
- backend.addValue("x_elastic_strain_diagram_polynomial_fit_order", 5)
- backend.addValue("x_elastic_strain_diagram_stress_Voigt_component", int(i+1))
- backend.addValue("x_elastic_strain_diagram_number_of_eta", polFit5)
- backend.addValue("x_elastic_strain_diagram_eta_values", dS5_eta[i])
- backend.addValue("x_elastic_strain_diagram_values", dS5_val[i])
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
-
- else:
- pass
-
- backend.addValue('x_elastic_2nd_order_constants_notation_matrix',voigtMat)
- backend.addValue('x_elastic_2nd_order_constants_matrix',ECMat)
- backend.addValue('x_elastic_2nd_order_constants_compliance_matrix',complMat)
- backend.addValue('x_elastic_Voigt_bulk_modulus',B_V)
- backend.addValue('x_elastic_Voigt_shear_modulus',G_V)
- backend.addValue('x_elastic_Reuss_bulk_modulus',B_R)
- backend.addValue('x_elastic_Reuss_shear_modulus',G_R)
- backend.addValue('x_elastic_Hill_bulk_modulus',B_H)
- backend.addValue('x_elastic_Hill_shear_modulus',G_H)
- backend.addValue('x_elastic_Voigt_Young_modulus',E_V)
- backend.addValue('x_elastic_Voigt_Poisson_ratio',nu_V)
- backend.addValue('x_elastic_Reuss_Young_modulus',E_R)
- backend.addValue('x_elastic_Reuss_Poisson_ratio',nu_R)
- backend.addValue('x_elastic_Hill_Young_modulus',E_H)
- backend.addValue('x_elastic_Hill_Poisson_ratio',nu_H)
- backend.addValue('x_elastic_eigenvalues',EC_eigen)
- backend.closeSection("section_single_configuration_calculation", elasticGIndex)
- backend.addValue("x_elastic_deformation_types", defTyp)
- backend.addValue("x_elastic_number_of_deformations", defNum)
- if meth == "Energy":
- elasticPIndex = backend.openSection("x_elastic_section_fitting_parameters")
- backend.addValue("x_elastic_fitting_parameters_eta", self.etaEC)
- backend.addValue("x_elastic_fitting_parameters_polynomial_order", self.fitEC)
- backend.closeSection("x_elastic_section_fitting_parameters", elasticPIndex)
- else:
- pass
-
- elif ordr == 3:
- f = open ('ElaStic_'+str(ordr)+'rd.out','r')
-
- ECmat = []
- for i in range(0,6):
- ECmat.append([])
- for j in range(0,6):
- ECmat[i].append([])
- for k in range(0,6):
- ECmat[i][j].append([])
- ECmat[i][j][k] = int(0)
-
- while 1:
- s = f.readline()
- if not s: break
- s = s.strip()
- s = s.split()
- if len(s) == 4:
- if s[0] == 'C111':
- C111 = float(s[2])
- elif s[0] == 'C112':
- C112 = float(s[2])
- elif s[0] == 'C123':
- C123 = float(s[2])
- elif s[0] == 'C144':
- C144 = float(s[2])
- elif s[0] == 'C155':
- C155 = float(s[2])
- elif s[0] == 'C456':
- C456 = float(s[2])
- elif s[0] == 'C113':
- C113 = float(s[2])
- elif s[0] == 'C166':
- C166 = float(s[2])
- elif s[0] == 'C133':
- C133 = float(s[2])
- elif s[0] == 'C222':
- C222 = float(s[2])
- elif s[0] == 'C333':
- C333 = float(s[2])
- elif s[0] == 'C344':
- C344 = float(s[2])
- elif s[0] == 'C116':
- C116 = float(s[2])
- elif s[0] == 'C145':
- C145 = float(s[2])
- elif s[0] == 'C114':
- C114 = float(s[2])
- elif s[0] == 'C124':
- C124 = float(s[2])
- elif s[0] == 'C134':
- C134 = float(s[2])
- elif s[0] == 'C444':
- C444 = float(s[2])
-
-
- if(149 <= self.SGN and self.SGN <= 167): # Rhombohedral I
- LC = 'RI'
- ECs= 14
-
- A = C111-C222+C112
- B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
- C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
- D = float(1/2)*(C113-C123)
- E = float(1/2)*(C155-C144)
- F = float(1/2)*(C114+float(3)*C124)
- G =-C114-float(2)*C124
- H = float(1/2)*(C114-C124)
-
- ECmat[0][0][0] = C111
- ECmat[0][0][1] = C112
- ECmat[0][0][2] = C113
- ECmat[0][0][3] = C114
- ECmat[0][1][0] = C112
- ECmat[0][1][1] = A
- ECmat[0][1][2] = C123
- ECmat[0][1][3] = C124
- ECmat[0][2][0] = C113
- ECmat[0][2][1] = C123
- ECmat[0][2][2] = C133
- ECmat[0][2][3] = C134
- ECmat[0][3][0] = C114
- ECmat[0][3][1] = C124
- ECmat[0][3][2] = C134
- ECmat[0][3][3] = C144
- ECmat[0][4][4] = C155
- ECmat[0][4][5] = F
- ECmat[0][5][4] = F
- ECmat[0][5][5] = B
-
- ECmat[1][0][0] = C112
- ECmat[1][0][1] = A
- ECmat[1][0][2] = C123
- ECmat[1][0][3] = C124
- ECmat[1][1][0] = A
- ECmat[1][1][1] = C222
- ECmat[1][1][2] = C113
- ECmat[1][1][3] = G
- ECmat[1][2][0] = C123
- ECmat[1][2][1] = C113
- ECmat[1][2][2] = C133
- ECmat[1][2][3] = -C134
- ECmat[1][3][0] = C124
- ECmat[1][3][1] = G
- ECmat[1][3][2] = -C134
- ECmat[1][3][3] = C155
- ECmat[1][4][4] = C144
- ECmat[1][4][5] = H
- ECmat[1][5][4] = H
- ECmat[1][5][5] = C
-
- ECmat[2][0][0] = C113
- ECmat[2][0][1] = C123
- ECmat[2][0][2] = C133
- ECmat[2][0][3] = C134
- ECmat[2][1][0] = C123
- ECmat[2][1][1] = C113
- ECmat[2][1][2] = C133
- ECmat[2][1][3] = -C134
- ECmat[2][2][0] = C133
- ECmat[2][2][1] = C133
- ECmat[2][2][2] = C133
- ECmat[2][3][0] = C134
- ECmat[2][3][1] = -C134
- ECmat[2][3][3] = C344
- ECmat[2][4][4] = C344
- ECmat[2][4][5] = C134
- ECmat[2][5][4] = C134
- ECmat[2][5][5] = D
-
- ECmat[3][0][0] = C114
- ECmat[3][0][1] = C124
- ECmat[3][0][2] = C134
- ECmat[3][0][3] = C144
- ECmat[3][1][0] = C12
- ECmat[3][1][1] = G
- ECmat[3][1][2] = -C134
- ECmat[3][1][3] = C155
- ECmat[3][2][0] = C134
- ECmat[3][2][1] = -C134
- ECmat[3][2][3] = C344
- ECmat[3][3][0] = C144
- ECmat[3][3][1] = C155
- ECmat[3][3][2] = C344
- ECmat[3][3][3] = C444
- ECmat[3][4][4] = -C444
- ECmat[3][4][5] = E
- ECmat[3][5][4] = E
- ECmat[3][5][5] = C124
-
- ECmat[4][0][4] = C155
- ECmat[4][0][5] = F
- ECmat[4][1][4] = C144
- ECmat[4][1][5] = H
- ECmat[4][2][4] = C344
- ECmat[4][2][5] = C134
- ECmat[4][3][5] = E
- ECmat[4][4][0] = C155
- ECmat[4][4][1] = C144
- ECmat[4][4][2] = C344
- ECmat[4][5][0] = F
- ECmat[4][5][1] = H
- ECmat[4][5][2] = C134
- ECmat[4][5][3] = E
-
- ECmat[5][0][4] = F
- ECmat[5][0][5] = B
- ECmat[5][1][4] = H
- ECmat[5][1][5] = C
- ECmat[5][2][4] = C134
- ECmat[5][2][5] = D
- ECmat[5][3][4] = E
- ECmat[5][3][5] = C124
- ECmat[5][4][0] = F
- ECmat[5][4][1] = H
- ECmat[5][4][2] = C134
- ECmat[5][4][3] = E
- ECmat[5][5][0] = B
- ECmat[5][5][1] = C
- ECmat[5][5][2] = D
- ECmat[5][5][3] = C124
-
-
- elif(168 <= self.SGN and self.SGN <= 176): # Hexagonal II
- LC = 'HII'
- ECs= 12
-
- A = C111-C222+C112
- B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
- C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
- D = float(1/2)*(C113-C123)
- E = float(1/2)*(C155-C144)
-
- ECmat[0][0][0] = C111
- ECmat[0][0][1] = C112
- ECmat[0][0][2] = C113
- ECmat[0][0][5] = C116
- ECmat[0][1][0] = C112
- ECmat[0][1][1] = A
- ECmat[0][1][2] = C123
- ECmat[0][1][5] = -C116
- ECmat[0][2][0] = C113
- ECmat[0][2][1] = C123
- ECmat[0][2][2] = C133
- ECmat[0][3][3] = C144
- ECmat[0][3][4] = C145
- ECmat[0][4][3] = C145
- ECmat[0][4][4] = C155
- ECmat[0][5][0] = C116
- ECmat[0][5][1] = -C116
- ECmat[0][5][5] = B
-
- ECmat[1][0][0] = C112
- ECmat[1][0][1] = A
- ECmat[1][0][2] = C123
- ECmat[1][1][0] = A
- ECmat[1][1][1] = A222
- ECmat[1][1][2] = C113
- ECmat[1][1][5] = C116
- ECmat[1][2][0] = C123
- ECmat[1][2][1] = C113
- ECmat[1][2][2] = C133
- ECmat[1][3][3] = C155
- ECmat[1][3][4] = -C145
- ECmat[1][4][3] = -C145
- ECmat[1][4][4] = C144
- ECmat[1][5][1] = C116
- ECmat[1][5][5] = C
-
- ECmat[2][0][0] = C113
- ECmat[2][0][1] = C123
- ECmat[2][0][2] = C133
- ECmat[2][1][0] = C123
- ECmat[2][1][1] = C113
- ECmat[2][1][2] = C133
- ECmat[2][2][0] = C133
- ECmat[2][2][1] = C133
- ECmat[2][2][2] = C133
- ECmat[2][3][3] = C344
- ECmat[2][4][4] = C344
- ECmat[2][5][5] = D
-
- ECmat[3][0][3] = C144
- ECmat[3][1][3] = C155
- ECmat[3][2][3] = C344
- ECmat[3][3][0] = C144
- ECmat[3][3][1] = C155
- ECmat[3][3][2] = C344
- ECmat[3][3][5] = C145
- ECmat[3][4][5] = E
- ECmat[3][5][3] = C145
- ECmat[3][5][4] = E
-
- ECmat[4][0][3] = C155
- ECmat[4][1][3] = C144
- ECmat[4][2][3] = C344
- ECmat[4][3][5] = E
- ECmat[4][4][0] = C155
- ECmat[4][4][1] = C144
- ECmat[4][4][2] = C344
- ECmat[4][4][5] = -C145
- ECmat[4][5][3] = E
- ECmat[4][5][4] = -C145
-
- ECmat[5][0][5] = B
- ECmat[5][1][5] = C
- ECmat[5][2][5] = D
- ECmat[5][3][4] = E
- ECmat[5][4][3] = E
- ECmat[5][5][0] = B
- ECmat[5][5][1] = C
- ECmat[5][5][2] = D
- ECmat[5][5][5] = -C116
-
- elif(177 <= self.SGN and self.SGN <= 194): # Hexagonal I
- LC = 'HI'
- ECs= 10
-
- A = C111-C222+C112
- B = float(3/4)*C222-float(1/2)*C111-float(1/4)*C112
- C = float(1/2)*C111-float(1/4)*C222-float(1/4)*C112
- D = float(1/2)*(C113-C123)
- E = float(1/2)*(C155-C144)
-
- ECmat[0][0][0] = C111
- ECmat[0][0][1] = C112
- ECmat[0][0][2] = C113
- ECmat[0][1][0] = C112
- ECmat[0][1][1] = A
- ECmat[0][1][2] = C123
- ECmat[0][2][0] = C113
- ECmat[0][2][1] = C123
- ECmat[0][2][2] = C133
- ECmat[0][3][3] = C144
- ECmat[0][4][4] = C155
- ECmat[0][5][5] = B
-
- ECmat[1][0][0] = C112
- ECmat[1][0][1] = A
- ECmat[1][0][2] = C123
- ECmat[1][1][0] = A
- ECmat[1][1][1] = C222
- ECmat[1][1][2] = C113
- ECmat[1][2][0] = C123
- ECmat[1][2][1] = C113
- ECmat[1][2][2] = C133
- ECmat[1][3][3] = C155
- ECmat[1][4][4] = C144
- ECmat[1][5][5] = C
-
- ECmat[2][0][0] = C113
- ECmat[2][0][1] = C123
- ECmat[2][0][2] = C133
- ECmat[2][1][0] = C123
- ECmat[2][1][1] = C113
- ECmat[2][1][2] = C133
- ECmat[2][2][0] = C133
- ECmat[2][2][1] = C133
- ECmat[2][2][2] = C133
- ECmat[2][3][3] = C344
- ECmat[2][4][4] = C344
- ECmat[2][5][5] = D
-
- ECmat[3][0][3] = C144
- ECmat[3][1][3] = C155
- ECmat[3][2][3] = C344
- ECmat[3][3][0] = C144
- ECmat[3][3][1] = C155
- ECmat[3][3][2] = C344
- ECmat[3][4][5] = E
- ECmat[3][5][4] = E
-
- ECmat[4][0][4] = C155
- ECmat[4][1][4] = C144
- ECmat[4][2][4] = C344
- ECmat[4][3][5] = E
- ECmat[4][4][0] = C155
- ECmat[4][4][1] = C144
- ECmat[4][4][2] = C344
- ECmat[4][5][3] = E
-
- ECmat[5][0][5] = B
- ECmat[5][1][5] = C
- ECmat[5][2][5] = D
- ECmat[5][3][4] = E
- ECmat[5][4][3] = E
- ECmat[5][5][0] = B
- ECmat[5][5][1] = C
- ECmat[5][5][2] = D
-
- elif(195 <= self.SGN and self.SGN <= 206): # Cubic II
- LC = 'CII'
- ECs= 8
-
- ECmat[0][0][0] = C111
- ECmat[0][0][1] = C112
- ECmat[0][0][2] = C113
- ECmat[0][1][0] = C112
- ECmat[0][1][1] = C113
- ECmat[0][1][2] = C123
- ECmat[0][2][0] = C113
- ECmat[0][2][1] = C123
- ECmat[0][2][2] = C112
- ECmat[0][3][3] = C144
- ECmat[0][4][4] = C155
- ECmat[0][5][5] = C166
-
- ECmat[1][0][0] = C112
- ECmat[1][0][1] = C112
- ECmat[1][0][2] = C113
- ECmat[1][1][0] = C112
- ECmat[1][1][1] = C111
- ECmat[1][1][2] = C112
- ECmat[1][2][0] = C123
- ECmat[1][2][1] = C112
- ECmat[1][2][2] = C113
- ECmat[1][3][3] = C166
- ECmat[1][4][4] = C144
- ECmat[1][5][5] = C155
-
- ECmat[2][0][0] = C112
- ECmat[2][0][1] = C123
- ECmat[2][0][2] = C112
- ECmat[2][1][0] = C123
- ECmat[2][1][1] = C112
- ECmat[2][1][2] = C112
- ECmat[2][2][0] = C112
- ECmat[2][2][1] = C112
- ECmat[2][2][2] = C111
- ECmat[2][3][3] = C155
- ECmat[2][4][4] = C166
- ECmat[2][5][5] = C144
-
- ECmat[3][0][3] = C144
- ECmat[3][1][3] = C155
- ECmat[3][2][3] = C155
- ECmat[3][3][0] = C144
- ECmat[3][3][1] = C155
- ECmat[3][3][2] = C155
- ECmat[3][4][5] = C456
- ECmat[3][5][4] = C456
-
- ECmat[4][0][3] = C155
- ECmat[4][1][3] = C144
- ECmat[4][2][3] = C155
- ECmat[4][3][5] = C456
- ECmat[4][4][0] = C155
- ECmat[4][4][1] = C144
- ECmat[4][4][2] = C155
- ECmat[4][5][3] = C456
-
- ECmat[5][0][5] = C155
- ECmat[5][1][5] = C155
- ECmat[5][2][5] = C144
- ECmat[5][3][4] = C456
- ECmat[5][4][3] = C456
- ECmat[5][5][0] = C155
- ECmat[5][5][1] = C155
- ECmat[5][5][2] = C144
-
- elif(207 <= self.SGN and self.SGN <= 230): # Cubic I
- LC = 'CI'
- ECs= 6
-
- ECmat[0][0][0] = C111
- ECmat[0][0][1] = C112
- ECmat[0][0][2] = C112
- ECmat[0][1][0] = C112
- ECmat[0][1][1] = C112
- ECmat[0][1][2] = C113
- ECmat[0][2][0] = C112
- ECmat[0][2][1] = C123
- ECmat[0][2][2] = C112
- ECmat[0][3][3] = C144
- ECmat[0][4][4] = C155
- ECmat[0][5][5] = C155
-
- ECmat[1][0][0] = C112
- ECmat[1][0][1] = C112
- ECmat[1][0][2] = C123
- ECmat[1][1][0] = C112
- ECmat[1][1][1] = C111
- ECmat[1][1][2] = C112
- ECmat[1][2][0] = C123
- ECmat[1][2][1] = C112
- ECmat[1][2][2] = C112
- ECmat[1][3][3] = C155
- ECmat[1][4][4] = C144
- ECmat[1][5][5] = C155
-
- ECmat[2][0][0] = C112
- ECmat[2][0][1] = C123
- ECmat[2][0][2] = C112
- ECmat[2][1][0] = C123
- ECmat[2][1][1] = C112
- ECmat[2][1][2] = C112
- ECmat[2][2][0] = C112
- ECmat[2][2][1] = C112
- ECmat[2][2][2] = C111
- ECmat[2][3][3] = C155
- ECmat[2][4][4] = C155
- ECmat[2][5][5] = C144
-
- ECmat[3][0][3] = C144
- ECmat[3][1][3] = C155
- ECmat[3][2][3] = C155
- ECmat[3][3][0] = C144
- ECmat[3][3][1] = C155
- ECmat[3][3][2] = C155
- ECmat[3][4][5] = C456
- ECmat[3][5][4] = C456
-
- ECmat[4][0][3] = C155
- ECmat[4][1][3] = C144
- ECmat[4][2][3] = C155
- ECmat[4][3][5] = C456
- ECmat[4][4][0] = C155
- ECmat[4][4][1] = C144
- ECmat[4][4][2] = C155
- ECmat[4][5][3] = C456
-
- ECmat[5][0][5] = C155
- ECmat[5][1][5] = C155
- ECmat[5][2][5] = C144
- ECmat[5][3][4] = C456
- ECmat[5][4][3] = C456
- ECmat[5][5][0] = C155
- ECmat[5][5][1] = C155
- ECmat[5][5][2] = C144
-
- elasticSIndex = backend.openSection("x_elastic_section_strain_diagrams")
- backend.addValue("x_elastic_strain_diagram_type", "energy")
- backend.addValue("x_elastic_strain_diagram_number_of_eta", len(eta))
- backend.addValue("x_elastic_strain_diagram_eta_values", eta)
- backend.addValue("x_elastic_strain_diagram_values", energy)
- backend.closeSection("x_elastic_section_strain_diagrams", elasticSIndex)
- backend.addValue('x_elastic_3rd_order_constants_matrix',ECmat)
- backend.closeSection("section_single_configuration_calculation", elasticGIndex)
- backend.addValue("x_elastic_deformation_types", defTyp)
- backend.addValue("x_elastic_number_of_deformations", defNum)
- if meth == "Energy":
- elasticPIndex = backend.openSection("x_elastic_section_fitting_parameters")
- backend.addValue("x_elastic_fitting_parameters_eta", self.etaEC)
- backend.addValue("x_elastic_fitting_parameters_polynomial_order", self.fitEC)
- backend.closeSection("x_elastic_section_fitting_parameters", elasticPIndex)
- else:
- pass
-
- def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
-# logging.error("BASE onClose_section_single_configuration_calculation")
- backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
- backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemIndex)
-
-mainFileDescription = \
- SM(name = 'root',
- weak = False,
- startReStr = "",
- subMatchers = [
- SM(name = 'input',
- startReStr = r"\s*Order of elastic constants\s*=\s*(?P<x_elastic_elastic_constant_order>[0-9]+)",
- repeats = False,
- required = False,
- forwardMatch = False,
- sections = ['section_run', 'section_method'],
- subMatchers = [
- SM(r"\s*Method of calculation\s*=\s*(?P<x_elastic_calculation_method>[-a-zA-Z]+)"),
- SM(r"\s*DFT code name\s*=\s*(?P<x_elastic_code>[-a-zA-Z]+)"),
- SM(name = 'system',
- startReStr = r"\s*Space-group number\s*=\s*(?P<x_elastic_space_group_number>[0-9]+)",
- sections = ['section_system'],
- subMatchers = [
- SM(r"\s*Volume of equilibrium unit cell\s*=\s*(?P<x_elastic_unit_cell_volume__bohr3>[-0-9.]+)\s*\[a.u\^3\]")
- ]),
- SM(r"\s*Maximum Lagrangian strain\s*=\s*(?P<x_elastic_max_lagrangian_strain>[0-9.]+)"),
- SM(r"\s*Number of distorted structures\s*=\s*(?P<x_elastic_number_of_distorted_structures>[0-9]+)")
- ] )
- ])
-
-
-parserInfo = {
- "name": "elastic_parser",
- "version": "1.0"
-}
-
-
-class ElasticParser():
- """ A proper class envolop for running this parser from within python. """
- def __init__(self, backend, **kwargs):
- self.backend_factory = backend
-
- def parse(self, mainfile):
- from unittest.mock import patch
- logging.info('elastic parser started')
- logging.getLogger('nomadcore').setLevel(logging.WARNING)
- backend = self.backend_factory("elastic.nomadmetainfo.json")
- with patch.object(sys, 'argv', ['<exe>', '--uri', 'nmd://uri', mainfile]):
- mainFunction(
- mainFileDescription,
- None,
- parserInfo,
- superContext=SampleContext(),
- superBackend=backend)
-
- return backend
--
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