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Fix Celcius Behavior #114

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Fix Celcius Behavior #114

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1cee8b9
Correctly read Celsius temperatures
jsantner Jun 14, 2018
cfdbae2
Add test with temperature in Celsius
jsantner Jun 14, 2018
2c0b278
Minor fix in arguments
jsantner Jun 14, 2018
73551ab
Only apply to celsius and fahrenheit
jsantner Jun 14, 2018
3681791
Syntax
jsantner Jun 14, 2018
f759ab1
Fix behavior in chemked.process_quantity
jsantner Jun 14, 2018
2147780
Fixing changes that were requested.
jsantner Jun 25, 2018
5c74873
raise pint.UndefinedUnitError if it can't be fixed by np.nan
jsantner Jun 25, 2018
ae14c43
Remove 'nan' handling
jsantner Jun 26, 2018
befbe89
Add test for changes in chemked.py
jsantner Jul 10, 2018
6eee6df
pint quantities must be in same unit to be compared with np.isclose
jsantner Jul 11, 2018
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7 changes: 6 additions & 1 deletion pyked/chemked.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import xml.etree.ElementTree as etree
import xml.dom.minidom as minidom
from itertools import chain
import pint

import numpy as np

Expand Down Expand Up @@ -718,7 +719,11 @@ def __init__(self, properties):
def process_quantity(self, properties):
"""Process the uncertainty information from a given quantity and return it
"""
quant = Q_(properties[0])
try:
quant = Q_(properties[0])
except pint.OffsetUnitCalculusError:
values = properties[0].split()
quant = Q_(float(values[0]), ''.join(values[1:]))
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Good catch, if there are multiple units, this will catch that.

if len(properties) > 1:
unc = properties[1]
uncertainty = unc.get('uncertainty', False)
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3 changes: 3 additions & 0 deletions pyked/tests/test_chemked.py
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Original file line number Diff line number Diff line change
Expand Up @@ -723,6 +723,9 @@ def test_temperature(self):
properties = self.load_properties('testfile_required.yaml')
d = DataPoint(properties[0])
assert np.isclose(d.temperature, Q_(1164.48, 'K'))
properties = self.load_properties('testfile_rcm3.yaml')
d = DataPoint(properties[0])
assert np.isclose(d.temperature.to('K'), Q_(297.4, 'K'))

def test_rcm_data(self):
properties = self.load_properties('testfile_rcm2.yaml')
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2 changes: 1 addition & 1 deletion pyked/tests/test_validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -363,7 +363,7 @@ def properties(self, request):

@pytest.mark.parametrize("properties", [
'testfile_st.yaml', 'testfile_st2.yaml', 'testfile_rcm.yaml', 'testfile_required.yaml',
'testfile_uncertainty.yaml', 'testfile_rcm2.yaml',
'testfile_uncertainty.yaml', 'testfile_rcm2.yaml', 'testfile_rcm3.yaml'
], indirect=['properties'])
def test_valid_yaml(self, properties):
"""Ensure ChemKED YAML is validated
Expand Down
178 changes: 178 additions & 0 deletions pyked/tests/testfile_rcm3.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,178 @@
---
file-authors:
- name: Kyle E Niemeyer
ORCID: 0000-0003-4425-7097
file-version: 0
chemked-version: 0.0.1
reference:
doi: 10.1002/kin.20180
authors:
- name: Gaurav Mittal
- name: Chih-Jen Sung
ORCID: 0000-0003-2046-8076
- name: Richard A Yetter
journal: International Journal of Chemical Kinetics
year: 2006
volume: 38
pages: 516-529
detail: Fig. 6, open circle
experiment-type: ignition delay
apparatus:
kind: rapid compression machine
institution: Case Western Reserve University
facility: CWRU RCM
datapoints:
- temperature:
- 24.25 degC
ignition-delay:
- 1.0 ms
first-stage-ignition-delay:
- 0.5 ms
- uncertainty-type: relative
uncertainty: 0.01
pressure:
- 958.0 torr
rcm-data:
compressed-pressure:
- 7.1 bar
compressed-temperature:
- 765 K
- uncertainty: 0.01
uncertainty-type: relative
compression-time:
- 38.0 ms
stroke:
- 10.0 inch
clearance:
- 2.5 cm
compression-ratio:
- 12.0
composition:
kind: mole fraction
species:
- species-name: H2
InChI: 1S/H2/h1H
amount:
- 0.12500
- species-name: O2
InChI: 1S/O2/c1-2
amount:
- 0.06250
- species-name: N2
InChI: 1S/N2/c1-2
amount:
- 0.18125
- species-name: Ar
InChI: 1S/Ar
amount:
- 0.63125
ignition-type:
target: pressure
type: d/dt max
time-histories:
- type: volume
time:
units: s
column: 0
quantity:
units: cm3
column: 1
values:
- [0.00E+000, 5.47669375000E+002]
- [1.00E-003, 5.46608789894E+002]
- [2.00E-003, 5.43427034574E+002]
- [3.00E-003, 5.38124109043E+002]
- [4.00E-003, 5.30700013298E+002]
- [5.00E-003, 5.21154747340E+002]
- [6.00E-003, 5.09488311170E+002]
- [7.00E-003, 4.95700704787E+002]
- [8.00E-003, 4.79791928191E+002]
- [9.00E-003, 4.61761981383E+002]
- [1.00E-002, 4.41610864362E+002]
- [1.10E-002, 4.20399162234E+002]
- [1.20E-002, 3.99187460106E+002]
- [1.30E-002, 3.77975757979E+002]
- [1.40E-002, 3.56764055851E+002]
- [1.50E-002, 3.35552353723E+002]
- [1.60E-002, 3.14340651596E+002]
- [1.70E-002, 2.93128949468E+002]
- [1.80E-002, 2.71917247340E+002]
- [1.90E-002, 2.50705545213E+002]
- [2.00E-002, 2.29493843085E+002]
- [2.10E-002, 2.08282140957E+002]
- [2.20E-002, 1.87070438830E+002]
- [2.30E-002, 1.65858736702E+002]
- [2.40E-002, 1.44647034574E+002]
- [2.50E-002, 1.23435332447E+002]
- [2.60E-002, 1.02223630319E+002]
- [2.70E-002, 8.10119281915E+001]
- [2.80E-002, 6.33355097518E+001]
- [2.90E-002, 5.27296586879E+001]
- [3.00E-002, 4.91943750000E+001]
- [3.10E-002, 4.97137623933E+001]
- [3.20E-002, 5.02063762048E+001]
- [3.30E-002, 5.06454851923E+001]
- [3.40E-002, 5.10218564529E+001]
- [3.50E-002, 5.13374097598E+001]
- [3.60E-002, 5.16004693977E+001]
- [3.70E-002, 5.18223244382E+001]
- [3.80E-002, 5.20148449242E+001]
- [3.90E-002, 5.21889350372E+001]
- [4.00E-002, 5.23536351113E+001]
- [4.10E-002, 5.25157124459E+001]
- [4.20E-002, 5.26796063730E+001]
- [4.30E-002, 5.28476160610E+001]
- [4.40E-002, 5.30202402028E+001]
- [4.50E-002, 5.31965961563E+001]
- [4.60E-002, 5.33748623839E+001]
- [4.70E-002, 5.35527022996E+001]
- [4.80E-002, 5.37276399831E+001]
- [4.90E-002, 5.38973687732E+001]
- [5.00E-002, 5.40599826225E+001]
- [5.10E-002, 5.42141273988E+001]
- [5.20E-002, 5.43590751578E+001]
- [5.30E-002, 5.44947289126E+001]
- [5.40E-002, 5.46215686913E+001]
- [5.50E-002, 5.47405518236E+001]
- [5.60E-002, 5.48529815402E+001]
- [5.70E-002, 5.49603582190E+001]
- [5.80E-002, 5.50642270863E+001]
- [5.90E-002, 5.51660349836E+001]
- [6.00E-002, 5.52670070646E+001]
- [6.10E-002, 5.53680520985E+001]
- [6.20E-002, 5.54697025392E+001]
- [6.30E-002, 5.55720927915E+001]
- [6.40E-002, 5.56749762728E+001]
- [6.50E-002, 5.57777790517E+001]
- [6.60E-002, 5.58796851466E+001]
- [6.70E-002, 5.59797461155E+001]
- [6.80E-002, 5.60770054561E+001]
- [6.90E-002, 5.61706266985E+001]
- [7.00E-002, 5.62600130036E+001]
- [7.10E-002, 5.63449057053E+001]
- [7.20E-002, 5.64254496625E+001]
- [7.30E-002, 5.65022146282E+001]
- [7.40E-002, 5.65761642150E+001]
- [7.50E-002, 5.66485675508E+001]
- [7.60E-002, 5.67208534842E+001]
- [7.70E-002, 5.67944133373E+001]
- [7.80E-002, 5.68703658198E+001]
- [7.90E-002, 5.69493069272E+001]
- [8.00E-002, 5.70310785669E+001]
- [8.10E-002, 5.71146023893E+001]
- [8.20E-002, 5.71978399741E+001]
- [8.30E-002, 5.72779572372E+001]
- [8.40E-002, 5.73517897984E+001]
- [8.50E-002, 5.74167271960E+001]
- [8.60E-002, 5.74721573687E+001]
- [8.70E-002, 5.75216388520E+001]
- [8.80E-002, 5.75759967785E+001]
- [8.90E-002, 5.76575701358E+001]
- [9.00E-002, 5.78058719368E+001]
- [9.10E-002, 5.80849611077E+001]
- [9.20E-002, 5.85928651155E+001]
- [9.30E-002, 5.94734357453E+001]
- [9.40E-002, 6.09310671165E+001]
- [9.50E-002, 6.32487551103E+001]
- [9.60E-002, 6.68100309742E+001]
...
6 changes: 5 additions & 1 deletion pyked/validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,11 @@ def _validate_isvalid_quantity(self, isvalid_quantity, field, value):
{'isvalid_quantity': {'type': 'bool'}, 'field': {'type': 'str'},
'value': {'type': 'list'}}
"""
quantity = Q_(value[0])
try:
quantity = Q_(value[0])
except pint.OffsetUnitCalculusError:
values = value[0].split()
quantity = Q_(float(values[0]), ''.join(values[1:]))
low_lim = 0.0 * units(property_units[field])

try:
Expand Down