From cac6ac6f665a3c3d2d72bb1bd87c813064a6b87a Mon Sep 17 00:00:00 2001 From: Paul Romano Date: Thu, 28 Jul 2016 12:35:15 -0500 Subject: [PATCH] Add VolumeCalculation object. Update settings.xml RELAX NG schema --- openmc/__init__.py | 5 +- openmc/settings.py | 204 +++++++++++++++++++++------------------ openmc/volume.py | 204 +++++++++++++++++++++++++++++++++++++++ src/relaxng/settings.rnc | 11 +++ src/relaxng/settings.rng | 62 ++++++++++++ 5 files changed, 392 insertions(+), 94 deletions(-) create mode 100644 openmc/volume.py diff --git a/openmc/__init__.py b/openmc/__init__.py index 557e13039f..026ccce114 100644 --- a/openmc/__init__.py +++ b/openmc/__init__.py @@ -6,6 +6,9 @@ from openmc.nuclide import * from openmc.macroscopic import * from openmc.material import * from openmc.plots import * +from openmc.region import * +from openmc.volume import * +from openmc.source import * from openmc.settings import * from openmc.surface import * from openmc.universe import * @@ -18,8 +21,6 @@ from openmc.cmfd import * from openmc.executor import * from openmc.statepoint import * from openmc.summary import * -from openmc.region import * -from openmc.source import * from openmc.particle_restart import * try: diff --git a/openmc/settings.py b/openmc/settings.py index b9a93bd114..918f97c7da 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -1,4 +1,4 @@ -from collections import Iterable +from collections import Iterable, MutableSequence from numbers import Real, Integral import warnings from xml.etree import ElementTree as ET @@ -7,10 +7,8 @@ import sys import numpy as np from openmc.clean_xml import clean_xml_indentation -from openmc.checkvalue import (check_type, check_length, check_value, - check_greater_than, check_less_than) -from openmc import Nuclide -from openmc.source import Source +import openmc.checkvalue as cv +from openmc import Nuclide, VolumeCalculation, Source if sys.version_info[0] >= 3: basestring = str @@ -137,6 +135,8 @@ class Settings(object): resonance cross sections. resonance_scattering : ResonanceScattering or iterable of ResonanceScattering The elastic scattering model to use for resonant isotopes + volume_calculations : VolumeCalculation or iterable of VolumeCalculation + Stochastic volume calculation specifications """ @@ -220,6 +220,8 @@ class Settings(object): self._multipole_active = None self._resonance_scattering = None + self._volume_calculations = cv.CheckedList(VolumeCalculation, + 'volume calculations') @property def run_mode(self): @@ -421,6 +423,10 @@ class Settings(object): def resonance_scattering(self): return self._resonance_scattering + @property + def volume_calculations(self): + return self._volume_calculations + @run_mode.setter def run_mode(self, run_mode): if run_mode not in ['eigenvalue', 'fixed source']: @@ -431,26 +437,26 @@ class Settings(object): @batches.setter def batches(self, batches): - check_type('batches', batches, Integral) - check_greater_than('batches', batches, 0) + cv.check_type('batches', batches, Integral) + cv.check_greater_than('batches', batches, 0) self._batches = batches @generations_per_batch.setter def generations_per_batch(self, generations_per_batch): - check_type('generations per patch', generations_per_batch, Integral) - check_greater_than('generations per batch', generations_per_batch, 0) + cv.check_type('generations per patch', generations_per_batch, Integral) + cv.check_greater_than('generations per batch', generations_per_batch, 0) self._generations_per_batch = generations_per_batch @inactive.setter def inactive(self, inactive): - check_type('inactive batches', inactive, Integral) - check_greater_than('inactive batches', inactive, 0, True) + cv.check_type('inactive batches', inactive, Integral) + cv.check_greater_than('inactive batches', inactive, 0, True) self._inactive = inactive @particles.setter def particles(self, particles): - check_type('particles', particles, Integral) - check_greater_than('particles', particles, 0) + cv.check_type('particles', particles, Integral) + cv.check_greater_than('particles', particles, 0) self._particles = particles @keff_trigger.setter @@ -484,14 +490,14 @@ class Settings(object): @energy_mode.setter def energy_mode(self, energy_mode): - check_value('energy mode', energy_mode, + cv.check_value('energy mode', energy_mode, ['continuous-energy', 'multi-group']) self._energy_mode = energy_mode @max_order.setter def max_order(self, max_order): - check_type('maximum scattering order', max_order, Integral) - check_greater_than('maximum scattering order', max_order, 0, True) + cv.check_type('maximum scattering order', max_order, Integral) + cv.check_greater_than('maximum scattering order', max_order, 0, True) self._max_order = max_order @source.setter @@ -499,7 +505,7 @@ class Settings(object): if isinstance(source, Source): self._source = [source,] else: - check_type('source distribution', source, Iterable, Source) + cv.check_type('source distribution', source, Iterable, Source) self._source = source @output.setter @@ -525,197 +531,197 @@ class Settings(object): @output_path.setter def output_path(self, output_path): - check_type('output path', output_path, basestring) + cv.check_type('output path', output_path, basestring) self._output_path = output_path @verbosity.setter def verbosity(self, verbosity): - check_type('verbosity', verbosity, Integral) - check_greater_than('verbosity', verbosity, 1, True) - check_less_than('verbosity', verbosity, 10, True) + cv.check_type('verbosity', verbosity, Integral) + cv.check_greater_than('verbosity', verbosity, 1, True) + cv.check_less_than('verbosity', verbosity, 10, True) self._verbosity = verbosity @statepoint_batches.setter def statepoint_batches(self, batches): - check_type('statepoint batches', batches, Iterable, Integral) + cv.check_type('statepoint batches', batches, Iterable, Integral) for batch in batches: - check_greater_than('statepoint batch', batch, 0) + cv.check_greater_than('statepoint batch', batch, 0) self._statepoint_batches = batches @statepoint_interval.setter def statepoint_interval(self, interval): - check_type('statepoint interval', interval, Integral) + cv.check_type('statepoint interval', interval, Integral) self._statepoint_interval = interval @sourcepoint_batches.setter def sourcepoint_batches(self, batches): - check_type('sourcepoint batches', batches, Iterable, Integral) + cv.check_type('sourcepoint batches', batches, Iterable, Integral) for batch in batches: - check_greater_than('sourcepoint batch', batch, 0) + cv.check_greater_than('sourcepoint batch', batch, 0) self._sourcepoint_batches = batches @sourcepoint_interval.setter def sourcepoint_interval(self, interval): - check_type('sourcepoint interval', interval, Integral) + cv.check_type('sourcepoint interval', interval, Integral) self._sourcepoint_interval = interval @sourcepoint_separate.setter def sourcepoint_separate(self, source_separate): - check_type('sourcepoint separate', source_separate, bool) + cv.check_type('sourcepoint separate', source_separate, bool) self._sourcepoint_separate = source_separate @sourcepoint_write.setter def sourcepoint_write(self, source_write): - check_type('sourcepoint write', source_write, bool) + cv.check_type('sourcepoint write', source_write, bool) self._sourcepoint_write = source_write @sourcepoint_overwrite.setter def sourcepoint_overwrite(self, source_overwrite): - check_type('sourcepoint overwrite', source_overwrite, bool) + cv.check_type('sourcepoint overwrite', source_overwrite, bool) self._sourcepoint_overwrite = source_overwrite @confidence_intervals.setter def confidence_intervals(self, confidence_intervals): - check_type('confidence interval', confidence_intervals, bool) + cv.check_type('confidence interval', confidence_intervals, bool) self._confidence_intervals = confidence_intervals @cross_sections.setter def cross_sections(self, cross_sections): - check_type('cross sections', cross_sections, basestring) + cv.check_type('cross sections', cross_sections, basestring) self._cross_sections = cross_sections @multipole_library.setter def multipole_library(self, multipole_library): - check_type('cross sections', multipole_library, basestring) + cv.check_type('cross sections', multipole_library, basestring) self._multipole_library = multipole_library @energy_grid.setter def energy_grid(self, energy_grid): - check_value('energy grid', energy_grid, + cv.check_value('energy grid', energy_grid, ['nuclide', 'logarithm', 'material-union']) self._energy_grid = energy_grid @ptables.setter def ptables(self, ptables): - check_type('probability tables', ptables, bool) + cv.check_type('probability tables', ptables, bool) self._ptables = ptables @run_cmfd.setter def run_cmfd(self, run_cmfd): - check_type('run_cmfd', run_cmfd, bool) + cv.check_type('run_cmfd', run_cmfd, bool) self._run_cmfd = run_cmfd @seed.setter def seed(self, seed): - check_type('random number generator seed', seed, Integral) - check_greater_than('random number generator seed', seed, 0) + cv.check_type('random number generator seed', seed, Integral) + cv.check_greater_than('random number generator seed', seed, 0) self._seed = seed @survival_biasing.setter def survival_biasing(self, survival_biasing): - check_type('survival biasing', survival_biasing, bool) + cv.check_type('survival biasing', survival_biasing, bool) self._survival_biasing = survival_biasing @weight.setter def weight(self, weight): - check_type('weight cutoff', weight, Real) - check_greater_than('weight cutoff', weight, 0.0) + cv.check_type('weight cutoff', weight, Real) + cv.check_greater_than('weight cutoff', weight, 0.0) self._weight = weight @weight_avg.setter def weight_avg(self, weight_avg): - check_type('average survival weight', weight_avg, Real) - check_greater_than('average survival weight', weight_avg, 0.0) + cv.check_type('average survival weight', weight_avg, Real) + cv.check_greater_than('average survival weight', weight_avg, 0.0) self._weight_avg = weight_avg @entropy_dimension.setter def entropy_dimension(self, dimension): - check_type('entropy mesh dimension', dimension, Iterable, Integral) - check_length('entropy mesh dimension', dimension, 3) + cv.check_type('entropy mesh dimension', dimension, Iterable, Integral) + cv.check_length('entropy mesh dimension', dimension, 3) self._entropy_dimension = dimension @entropy_lower_left.setter def entropy_lower_left(self, lower_left): - check_type('entropy mesh lower left corner', lower_left, + cv.check_type('entropy mesh lower left corner', lower_left, Iterable, Real) - check_length('entropy mesh lower left corner', lower_left, 3) + cv.check_length('entropy mesh lower left corner', lower_left, 3) self._entropy_lower_left = lower_left @entropy_upper_right.setter def entropy_upper_right(self, upper_right): - check_type('entropy mesh upper right corner', upper_right, + cv.check_type('entropy mesh upper right corner', upper_right, Iterable, Real) - check_length('entropy mesh upper right corner', upper_right, 3) + cv.check_length('entropy mesh upper right corner', upper_right, 3) self._entropy_upper_right = upper_right @trigger_active.setter def trigger_active(self, trigger_active): - check_type('trigger active', trigger_active, bool) + cv.check_type('trigger active', trigger_active, bool) self._trigger_active = trigger_active @trigger_max_batches.setter def trigger_max_batches(self, trigger_max_batches): - check_type('trigger maximum batches', trigger_max_batches, Integral) - check_greater_than('trigger maximum batches', trigger_max_batches, 0) + cv.check_type('trigger maximum batches', trigger_max_batches, Integral) + cv.check_greater_than('trigger maximum batches', trigger_max_batches, 0) self._trigger_max_batches = trigger_max_batches @trigger_batch_interval.setter def trigger_batch_interval(self, trigger_batch_interval): - check_type('trigger batch interval', trigger_batch_interval, Integral) - check_greater_than('trigger batch interval', trigger_batch_interval, 0) + cv.check_type('trigger batch interval', trigger_batch_interval, Integral) + cv.check_greater_than('trigger batch interval', trigger_batch_interval, 0) self._trigger_batch_interval = trigger_batch_interval @no_reduce.setter def no_reduce(self, no_reduce): - check_type('no reduction option', no_reduce, bool) + cv.check_type('no reduction option', no_reduce, bool) self._no_reduce = no_reduce @threads.setter def threads(self, threads): - check_type('number of threads', threads, Integral) - check_greater_than('number of threads', threads, 0) + cv.check_type('number of threads', threads, Integral) + cv.check_greater_than('number of threads', threads, 0) self._threads = threads @trace.setter def trace(self, trace): - check_type('trace', trace, Iterable, Integral) - check_length('trace', trace, 3) - check_greater_than('trace batch', trace[0], 0) - check_greater_than('trace generation', trace[1], 0) - check_greater_than('trace particle', trace[2], 0) + cv.check_type('trace', trace, Iterable, Integral) + cv.check_length('trace', trace, 3) + cv.check_greater_than('trace batch', trace[0], 0) + cv.check_greater_than('trace generation', trace[1], 0) + cv.check_greater_than('trace particle', trace[2], 0) self._trace = trace @track.setter def track(self, track): - check_type('track', track, Iterable, Integral) + cv.check_type('track', track, Iterable, Integral) if len(track) % 3 != 0: msg = 'Unable to set the track to "{0}" since its length is ' \ 'not a multiple of 3'.format(track) raise ValueError(msg) for t in zip(track[::3], track[1::3], track[2::3]): - check_greater_than('track batch', t[0], 0) - check_greater_than('track generation', t[0], 0) - check_greater_than('track particle', t[0], 0) + cv.check_greater_than('track batch', t[0], 0) + cv.check_greater_than('track generation', t[0], 0) + cv.check_greater_than('track particle', t[0], 0) self._track = track @ufs_dimension.setter def ufs_dimension(self, dimension): - check_type('UFS mesh dimension', dimension, Iterable, Integral) - check_length('UFS mesh dimension', dimension, 3) + cv.check_type('UFS mesh dimension', dimension, Iterable, Integral) + cv.check_length('UFS mesh dimension', dimension, 3) for dim in dimension: - check_greater_than('UFS mesh dimension', dim, 1, True) + cv.check_greater_than('UFS mesh dimension', dim, 1, True) self._ufs_dimension = dimension @ufs_lower_left.setter def ufs_lower_left(self, lower_left): - check_type('UFS mesh lower left corner', lower_left, Iterable, Real) - check_length('UFS mesh lower left corner', lower_left, 3) + cv.check_type('UFS mesh lower left corner', lower_left, Iterable, Real) + cv.check_length('UFS mesh lower left corner', lower_left, 3) self._ufs_lower_left = lower_left @ufs_upper_right.setter def ufs_upper_right(self, upper_right): - check_type('UFS mesh upper right corner', upper_right, Iterable, Real) - check_length('UFS mesh upper right corner', upper_right, 3) + cv.check_type('UFS mesh upper right corner', upper_right, Iterable, Real) + cv.check_length('UFS mesh upper right corner', upper_right, 3) self._ufs_upper_right = upper_right @dd_mesh_dimension.setter @@ -724,8 +730,8 @@ class Settings(object): warnings.warn('This feature is not yet implemented in a release ' 'version of openmc') - check_type('DD mesh dimension', dimension, Iterable, Integral) - check_length('DD mesh dimension', dimension, 3) + cv.check_type('DD mesh dimension', dimension, Iterable, Integral) + cv.check_length('DD mesh dimension', dimension, 3) self._dd_mesh_dimension = dimension @@ -735,8 +741,8 @@ class Settings(object): warnings.warn('This feature is not yet implemented in a release ' 'version of openmc') - check_type('DD mesh lower left corner', lower_left, Iterable, Real) - check_length('DD mesh lower left corner', lower_left, 3) + cv.check_type('DD mesh lower left corner', lower_left, Iterable, Real) + cv.check_length('DD mesh lower left corner', lower_left, 3) self._dd_mesh_lower_left = lower_left @@ -746,8 +752,8 @@ class Settings(object): warnings.warn('This feature is not yet implemented in a release ' 'version of openmc') - check_type('DD mesh upper right corner', upper_right, Iterable, Real) - check_length('DD mesh upper right corner', upper_right, 3) + cv.check_type('DD mesh upper right corner', upper_right, Iterable, Real) + cv.check_length('DD mesh upper right corner', upper_right, 3) self._dd_mesh_upper_right = upper_right @@ -757,7 +763,7 @@ class Settings(object): warnings.warn('This feature is not yet implemented in a release ' 'version of openmc') - check_type('DD nodemap', nodemap, Iterable) + cv.check_type('DD nodemap', nodemap, Iterable) nodemap = np.array(nodemap).flatten() @@ -782,7 +788,7 @@ class Settings(object): warnings.warn('This feature is not yet implemented in a release ' 'version of openmc') - check_type('DD allow leakage', allow, bool) + cv.check_type('DD allow leakage', allow, bool) self._dd_allow_leakage = allow @@ -793,25 +799,34 @@ class Settings(object): warnings.warn('This feature is not yet implemented in a release ' 'version of openmc') - check_type('DD count interactions', interactions, bool) + cv.check_type('DD count interactions', interactions, bool) self._dd_count_interactions = interactions @use_windowed_multipole.setter def use_windowed_multipole(self, active): - check_type('use_windowed_multipole', active, bool) + cv.check_type('use_windowed_multipole', active, bool) self._multipole_active = active @resonance_scattering.setter def resonance_scattering(self, res): if isinstance(res, Iterable): - check_type('resonance_scattering', res, Iterable, + cv.check_type('resonance_scattering', res, Iterable, ResonanceScattering) self._resonance_scattering = res else: - check_type('resonance_scattering', res, ResonanceScattering) + cv.check_type('resonance_scattering', res, ResonanceScattering) self._resonance_scattering = [res] + @volume_calculations.setter + def volume_calculations(self, vol_calcs): + name = 'stochastic volume calculations' + if not isinstance(vol_calcs, MutableSequence): + vol_calcs = [vol_calcs] + cv.check_type(name, vol_calcs, MutableSequence) + self._volume_calculations = cv.CheckedList(VolumeCalculation, + name, vol_calcs) + def _create_run_mode_subelement(self): if self.run_mode == 'eigenvalue': @@ -873,6 +888,10 @@ class Settings(object): for source in self.source: self._settings_file.append(source.to_xml()) + def _create_volume_calcs_subelement(self): + for calc in self.volume_calculations: + self._settings_file.append(calc.to_xml()) + def _create_output_subelement(self): if self._output is not None: element = ET.SubElement(self._settings_file, "output") @@ -1154,6 +1173,7 @@ class Settings(object): self._create_dd_subelement() self._create_use_multipole_subelement() self._create_resonance_scattering_element() + self._create_volume_calcs_subelement() # Clean the indentation in the file to be user-readable clean_xml_indentation(self._settings_file) @@ -1216,29 +1236,29 @@ class ResonanceScattering(object): @nuclide.setter def nuclide(self, nuc): - check_type('nuclide', nuc, Nuclide) + cv.check_type('nuclide', nuc, Nuclide) self._nuclide = nuc @nuclide_0K.setter def nuclide_0K(self, nuc): - check_type('nuclide_0K', nuc, Nuclide) + cv.check_type('nuclide_0K', nuc, Nuclide) self._nuclide_0K = nuc @method.setter def method(self, m): - check_value('method', m, ('ARES', 'CXS', 'DBRC', 'WCM')) + cv.check_value('method', m, ('ARES', 'CXS', 'DBRC', 'WCM')) self._method = m @E_min.setter def E_min(self, E): - check_type('E_min', E, Real) - check_greater_than('E_min', E, 0, True) + cv.check_type('E_min', E, Real) + cv.check_greater_than('E_min', E, 0, True) self._E_min = E @E_max.setter def E_max(self, E): - check_type('E_max', E, Real) - check_greater_than('E_max', E, 0, True) + cv.check_type('E_max', E, Real) + cv.check_greater_than('E_max', E, 0, True) self._E_max = E def create_xml_subelement(self, xml_element): diff --git a/openmc/volume.py b/openmc/volume.py new file mode 100644 index 0000000000..511af62ed3 --- /dev/null +++ b/openmc/volume.py @@ -0,0 +1,204 @@ +from collections import Iterable, Mapping +from numbers import Real, Integral +from xml.etree import ElementTree as ET + +import numpy as np +import pandas as pd + +from openmc import Cell, Union +import openmc.checkvalue as cv + + +class VolumeCalculation(object): + """Stochastic volume calculation specifications and results. + + Parameters + ---------- + cells : Iterable of Cell + Cells to find volumes of + samples : int + Number of samples used to generate volume estimates + lower_left : Iterable of float + Lower-left coordinates of bounding box used to sample points. If this + argument is not supplied, an attempt is made to automatically determine + a bounding box. + upper_right : Iterable of float + Upper-right coordinates of bounding box used to sample points. If this + argument is not supplied, an attempt is made to automatically determine + a bounding box. + + Attributes + ---------- + cell_ids : Iterable of int + IDs of cells to find volumes of + samples : int + Number of samples used to generate volume estimates + lower_left : Iterable of float + Lower-left coordinates of bounding box used to sample points + upper_right : Iterable of float + Upper-right coordinates of bounding box used to sample points + results : dict + Dictionary whose keys are unique IDs of cells and values are + dictionaries with calculated volumes and total number of atoms for each + nuclide present in the cell. + volumes : dict + Dictionary whose keys are unique IDs of cells and values are the + estimated volumes + atoms_dataframe : pandas.DataFrame + DataFrame showing the estimated number of atoms for each nuclide present + in each cell specified. + + """ + def __init__(self, cells, samples, lower_left=None, + upper_right=None): + self._results = None + + cv.check_type('cells', cells, Iterable, Cell) + self.cell_ids = [c.id for c in cells] + self.samples = samples + + if lower_left is not None: + self.lower_left = lower_left + if upper_right is None: + raise ValueError('Both lower-left and upper-right coordinates ' + 'should be specified') + self.upper_right = upper_right + else: + ll, ur = Union(*[c.region for c in cells]).bounding_box + if np.any(np.isinf(ll)) or np.any(np.isinf(ur)): + raise ValueError('Could not automatically determine bounding box ' + 'for stochastic volume calculation.') + else: + self.lower_left = ll + self.upper_right = ur + + @property + def cell_ids(self): + return self._cell_ids + + @property + def samples(self): + return self._samples + + @property + def lower_left(self): + return self._lower_left + + @property + def upper_right(self): + return self._upper_right + + @property + def results(self): + return self._results + + @property + def volumes(self): + return {uid: results['volume'] for uid, results in self.results.items()} + + @property + def atoms_dataframe(self): + items = [] + columns = ['Cell', 'Nuclide', 'Atoms', 'Uncertainty'] + for cell_id, results in self.results.items(): + for name, atoms in results['atoms']: + items.append((cell_id, name, atoms[0], atoms[1])) + + return pd.DataFrame.from_records(items, columns=columns) + + @cell_ids.setter + def cell_ids(self, cell_ids): + cv.check_type('cell IDs', cell_ids, Iterable, Real) + self._cell_ids = cell_ids + + @samples.setter + def samples(self, samples): + cv.check_type('number of samples', samples, Integral) + cv.check_greater_than('number of samples', samples, 0) + self._samples = samples + + @lower_left.setter + def lower_left(self, lower_left): + name = 'lower-left bounding box coordinates', + cv.check_type(name, lower_left, Iterable, Real) + cv.check_length(name, lower_left, 3) + self._lower_left = lower_left + + @upper_right.setter + def upper_right(self, upper_right): + name = 'upper-right bounding box coordinates' + cv.check_type(name, upper_right, Iterable, Real) + cv.check_length(name, upper_right, 3) + self._upper_right = upper_right + + @results.setter + def results(self, results): + cv.check_type('results', results, Mapping) + self._results = results + + @classmethod + def from_hdf5(cls, filename): + """Load stochastic volume calculation results from HDF5 file. + + Parameters + ---------- + filename : str + Path to volume.h5 file + + Returns + ------- + openmc.VolumeCalculation + Results of the stochastic volume calculation + + """ + import h5py + + with h5py.File(filename, 'r') as f: + samples = f.attrs['samples'] + lower_left = f.attrs['lower_left'] + upper_right = f.attrs['upper_right'] + + results = {} + cell_ids = [] + for obj_name in f: + if obj_name.startswith('cell_'): + cell_id = int(obj_name[5:]) + cell_ids.append(cell_id) + group = f[obj_name] + volume = tuple(group['volume'].value) + nucnames = group['nuclides'].value + atoms = group['atoms'].value + + atom_list = [] + for name_i, atoms_i in zip(nucnames, atoms): + atom_list.append((name_i.decode(), tuple(atoms_i))) + results[cell_id] = {'volume': volume, 'atoms': atom_list} + + # Instantiate some throw-away cells that are used by the constructor to + # assign IDs + cells = [Cell(uid) for uid in cell_ids] + + # Instantiate the class and assign results + vol = cls(cells, samples, lower_left, upper_right) + vol.results = results + return vol + + def to_xml(self): + """Return XML representation of the volume calculation + + Returns + ------- + element : xml.etree.ElementTree.Element + XML element containing volume calculation data + + """ + element = ET.Element("volume_calc") + cell_elem = ET.SubElement(element, "cells") + cell_elem.text = ' '.join(str(uid) for uid in self.cell_ids) + samples_elem = ET.SubElement(element, "samples") + samples_elem.text = str(self.samples) + ll_elem = ET.SubElement(element, "lower_left") + ll_elem.text = ' '.join(str(x) for x in self.lower_left) + ur_elem = ET.SubElement(element, "upper_right") + ur_elem.text = ' '.join(str(x) for x in self.upper_right) + return element diff --git a/src/relaxng/settings.rnc b/src/relaxng/settings.rnc index 46950c63fb..78a32171b9 100644 --- a/src/relaxng/settings.rnc +++ b/src/relaxng/settings.rnc @@ -142,6 +142,17 @@ element settings { element verbosity { xsd:positiveInteger }? & + element volume_calc { + (element cells { list { xsd:positiveInteger+ } } | + attribute cells { list { xsd:positiveInteger+ } }) & + (element samples { xsd:positiveInteger } | + attribute samples { xsd:positiveInteger }) & + (element lower_left { list { xsd:double+ } } | + attribute lower_left { list { xsd:double+ } }) & + (element upper_right { list { xsd:double+ } } | + attribute upper_right { list { xsd:double+ } }) + }+ & + element uniform_fs{ (element dimension { list { xsd:positiveInteger+ } } | attribute dimension { list { xsd:positiveInteger+ } }) & diff --git a/src/relaxng/settings.rng b/src/relaxng/settings.rng index 0b50f79699..64fe42239d 100644 --- a/src/relaxng/settings.rng +++ b/src/relaxng/settings.rng @@ -625,6 +625,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +