Issue #12

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 ### Fixed
 
 - Fixed bug in soln2ck.py where the reaction high rate was being used instead of the reaction low rate.
+- Fixed issue #12 from git: made sure input species are included in target or retained species
 
 ## [1.1.0] - 2019-09-06
 

ignition_output.txt

@@ -0,0 +1,2 @@
+1.066764602384077554e+00
+3.055344172355624333e-02

pymars/pymars.py

@@ -111,6 +111,13 @@ def parse_inputs(input_dict):
     psr_inputs = parse_psr_inputs(model, psr_conditions, phase_name)
     flame_inputs = parse_flame_inputs(model, flame_conditions, phase_name)
 
+    # check all input species included in target or retained species
+    combined_species = target_species + safe_species
+    for case in  ignition_conditions:
+        for inputs in list(case['fuel'].keys()) + list(case['oxidizer'].keys()):
+            if inputs not in combined_species:
+                safe_species.append(inputs)
+
     return ReductionInputs(
         model=model, error=error, 
         ignition_conditions=ignition_inputs, 

pymars/tests/assets/example1_input_file.yaml

@@ -0,0 +1,45 @@
+model: gri30.cti
+# List of target species
+targets: 
+  - CH4
+  - O2
+# List of species to be always retained
+retained-species:
+  - N2
+# options: DRG, DRGEP, PFA
+method: DRG
+# Error limit, in percentage
+error: 10.0
+
+# Sensitivity analysis inputs
+# True to enable sensitivity analysis
+sensitivity-analysis: False
+# options: initial, greedy
+sensitivity-type: initial
+upper-threshold: 0.2
+
+autoignition-conditions:
+  - kind: constant volume
+    # units: atm
+    pressure: 1.0
+    # units: K
+    temperature: 1000
+    # species given in mole fractions
+    fuel: 
+      CH4: 0.5
+      H2: 0.5
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+    equivalence-ratio: 1.0
+
+  - kind: constant volume 
+    pressure: 1.0
+    temperature: 1200
+    end-time: 10.0
+    fuel: 
+      CH4: 1.0
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+    equivalence-ratio: 0.5

pymars/tests/assets/example2_input_file.yaml

@@ -0,0 +1,46 @@
+model: gri30.cti
+# List of target species
+targets: 
+  - CH4
+  - O2
+# List of species to be always retained
+retained-species:
+  - N2
+# options: DRG, DRGEP, PFA
+method: DRG
+# Error limit, in percentage
+error: 10.0
+
+# Sensitivity analysis inputs
+# True to enable sensitivity analysis
+sensitivity-analysis: False
+# options: initial, greedy
+sensitivity-type: initial
+upper-threshold: 0.2
+
+autoignition-conditions:
+  - kind: constant volume
+    # units: atm
+    pressure: 1.0
+    # units: K
+    temperature: 1000
+    # species given in mole fractions
+    fuel: 
+      CH4: 0.5
+      H2: 0.5
+      AR: 0.5
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+    equivalence-ratio: 1.0
+
+  - kind: constant volume 
+    pressure: 1.0
+    temperature: 1200
+    end-time: 10.0
+    fuel: 
+      CH4: 1.0
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+    equivalence-ratio: 0.5

pymars/tests/assets/example3_input_file.yaml

@@ -0,0 +1,46 @@
+model: gri30.cti
+# List of target species
+targets: 
+  - CH4
+  - O2
+# List of species to be always retained
+retained-species:
+  - N2
+# options: DRG, DRGEP, PFA
+method: DRG
+# Error limit, in percentage
+error: 10.0
+
+# Sensitivity analysis inputs
+# True to enable sensitivity analysis
+sensitivity-analysis: False
+# options: initial, greedy
+sensitivity-type: initial
+upper-threshold: 0.2
+
+autoignition-conditions:
+  - kind: constant volume
+    # units: atm
+    pressure: 1.0
+    # units: K
+    temperature: 1000
+    # species given in mole fractions
+    fuel: 
+      CH4: 0.5
+      H2: 0.5
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+      AR: 1.0
+    equivalence-ratio: 1.0
+
+  - kind: constant volume 
+    pressure: 1.0
+    temperature: 1200
+    end-time: 10.0
+    fuel: 
+      CH4: 1.0
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+    equivalence-ratio: 0.5

pymars/tests/assets/example4_input_file.yaml

@@ -0,0 +1,46 @@
+model: gri30.cti
+# List of target species
+targets: 
+  - CH4
+  - O2
+# List of species to be always retained
+retained-species:
+  - N2
+# options: DRG, DRGEP, PFA
+method: DRG
+# Error limit, in percentage
+error: 10.0
+
+# Sensitivity analysis inputs
+# True to enable sensitivity analysis
+sensitivity-analysis: False
+# options: initial, greedy
+sensitivity-type: initial
+upper-threshold: 0.2
+
+autoignition-conditions:
+  - kind: constant volume
+    # units: atm
+    pressure: 1.0
+    # units: K
+    temperature: 1000
+    # species given in mole fractions
+    fuel: 
+      CH4: 0.5
+      H2: 0.5
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+    equivalence-ratio: 1.0
+
+  - kind: constant volume 
+    pressure: 1.0
+    temperature: 1200
+    end-time: 10.0
+    fuel: 
+      CH4: 1.0
+      AR: 1.0
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+    equivalence-ratio: 0.5

pymars/tests/assets/example5_input_file.yaml

@@ -0,0 +1,46 @@
+model: gri30.cti
+# List of target species
+targets: 
+  - CH4
+  - O2
+# List of species to be always retained
+retained-species:
+  - N2
+# options: DRG, DRGEP, PFA
+method: DRG
+# Error limit, in percentage
+error: 10.0
+
+# Sensitivity analysis inputs
+# True to enable sensitivity analysis
+sensitivity-analysis: False
+# options: initial, greedy
+sensitivity-type: initial
+upper-threshold: 0.2
+
+autoignition-conditions:
+  - kind: constant volume
+    # units: atm
+    pressure: 1.0
+    # units: K
+    temperature: 1000
+    # species given in mole fractions
+    fuel: 
+      CH4: 0.5
+      H2: 0.5
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+    equivalence-ratio: 1.0
+
+  - kind: constant volume 
+    pressure: 1.0
+    temperature: 1200
+    end-time: 10.0
+    fuel: 
+      CH4: 1.0
+    oxidizer:
+      O2: 1.0
+      N2: 3.76
+      AR: 1.0
+    equivalence-ratio: 0.5

pymars/tests/test_pymars.py

@@ -0,0 +1,47 @@
+#tests to verify that various input species get included in retained or safe species
+
+import os
+import pkg_resources
+import ruamel_yaml as yaml
+
+from ..pymars import parse_inputs
+
+def relative_location(file):
+    file_path = os.path.join(file)
+    return pkg_resources.resource_filename(__name__, file_path)
+
+
+def test_species_check1():
+    input_file = relative_location(os.path.join('assets', 'example1_input_file.yaml'))
+    with open(input_file, 'r') as the_file:
+        input_dict = yaml.safe_load(the_file)
+    inputs = parse_inputs(input_dict)
+    assert 'H2' in inputs.safe_species
+
+def test_species_check2():
+    input_file = relative_location(os.path.join('assets', 'example2_input_file.yaml'))
+    with open(input_file, 'r') as the_file:
+        input_dict = yaml.safe_load(the_file)
+    inputs = parse_inputs(input_dict)
+    assert 'AR' in inputs.safe_species
+
+def test_species_check3():
+    input_file = relative_location(os.path.join('assets', 'example3_input_file.yaml'))
+    with open(input_file, 'r') as the_file:
+        input_dict = yaml.safe_load(the_file)
+    inputs = parse_inputs(input_dict)
+    assert 'AR' in inputs.safe_species
+
+def test_species_check4():
+    input_file = relative_location(os.path.join('assets', 'example4_input_file.yaml'))
+    with open(input_file, 'r') as the_file:
+        input_dict = yaml.safe_load(the_file)
+    inputs = parse_inputs(input_dict)
+    assert 'AR' in inputs.safe_species
+
+def test_species_check5():
+    input_file = relative_location(os.path.join('assets', 'example5_input_file.yaml'))
+    with open(input_file, 'r') as the_file:
+        input_dict = yaml.safe_load(the_file)
+    inputs = parse_inputs(input_dict)
+    assert 'AR' in inputs.safe_species