use adjacency list as the key of thermo cov dep models

Author: 12Chao

test/rmgpy/thermo/nasaTest.py

@@ -39,7 +39,6 @@
 import rmgpy.constants as constants
 from rmgpy.quantity import ScalarQuantity
 from rmgpy.thermo.nasa import NASA, NASAPolynomial
-from rmgpy.quantity import Dimensionless
 
 
 class TestNASA:
@@ -70,7 +69,7 @@ def setup_class(self):
         self.Tmax = 3000.0
         self.Tint = 650.73
         self.E0 = -782292.0  # J/mol.
-        self.thermo_coverage_dependence = {'OX':{'model':'polynomial', 'enthalpy-coefficients':[1,2,3], "entropy-coefficients":[1,2,3]}}
+        self.thermo_coverage_dependence = {'1 O u0 p2 c0 {2,D} \n 2 X u0 p0 c0 {1,D}':{'model':'polynomial', 'enthalpy-coefficients':[1,2,3], "entropy-coefficients":[1,2,3]}}
         self.comment = "C2H6"
         self.nasa = NASA(
             polynomials=[
@@ -377,7 +376,11 @@ def test_nasa_as_dict_full(self):
         assert nasa_dict["E0"]["value"] == self.E0
         assert nasa_dict["Tmin"]["value"] == self.Tmin
         assert nasa_dict["Tmax"]["value"] == self.Tmax
-        assert repr(nasa_dict["thermo_coverage_dependence"]) == "{'OX': {'model': 'polynomial', 'enthalpy-coefficients': [{'class': 'ScalarQuantity', 'value': 1.0}, {'class': 'ScalarQuantity', 'value': 2.0}, {'class': 'ScalarQuantity', 'value': 3.0}], 'entropy-coefficients': [{'class': 'ScalarQuantity', 'value': 1.0}, {'class': 'ScalarQuantity', 'value': 2.0}, {'class': 'ScalarQuantity', 'value': 3.0}]}}"
+        assert nasa_dict["thermo_coverage_dependence"].keys() == self.thermo_coverage_dependence.keys()
+        sp_name = list(self.thermo_coverage_dependence.keys())[0]
+        assert nasa_dict['thermo_coverage_dependence'][sp_name]['model'] == self.thermo_coverage_dependence[sp_name]['model']
+        assert nasa_dict['thermo_coverage_dependence'][sp_name]['enthalpy-coefficients']['object'] == self.thermo_coverage_dependence[sp_name]['enthalpy-coefficients']
+        assert nasa_dict['thermo_coverage_dependence'][sp_name]['entropy-coefficients']['object'] == self.thermo_coverage_dependence[sp_name]['entropy-coefficients']
         assert nasa_dict["comment"] == self.comment
         assert tuple(nasa_dict["polynomials"]["polynomial1"]["coeffs"]["object"]) == tuple(self.coeffs_low)
         assert tuple(nasa_dict["polynomials"]["polynomial2"]["coeffs"]["object"]) == tuple(self.coeffs_high)

test/rmgpy/thermo/thermodataTest.py

@@ -53,7 +53,7 @@ def setup_class(self):
         self.Tmin = 100.0
         self.Tmax = 3000.0
         self.E0 = -782292.0
-        self.thermo_coverage_dependence = {'OX':{'model':'polynomial', 'enthalpy-coefficients':[1,2,3], "entropy-coefficients":[1,2,3]}}
+        self.thermo_coverage_dependence = {'1 O u0 p2 c0 {2,D} \n 2 X u0 p0 c0 {1,D}':{'model':'polynomial', 'enthalpy-coefficients':[1,2,3], "entropy-coefficients":[1,2,3]}}
         self.comment = "C2H6"
         self.thermodata = ThermoData(
             Tdata=(self.Tdata, "K"),

test/rmgpy/thermo/wilhoitTest.py

@@ -58,7 +58,7 @@ def setup_class(self):
         self.Tmin = 300.0
         self.Tmax = 3000.0
         self.comment = "C2H6"
-        self.thermo_coverage_dependence = {'OX':{'model':'polynomial', 'enthalpy-coefficients':[1,2,3], "entropy-coefficients":[1,2,3]}}
+        self.thermo_coverage_dependence = {'1 O u0 p2 c0 {2,D} \n 2 X u0 p0 c0 {1,D}':{'model':'polynomial', 'enthalpy-coefficients':[1,2,3], "entropy-coefficients":[1,2,3]}}
         self.wilhoit = Wilhoit(
             Cp0=(self.Cp0 * constants.R, "J/(mol*K)"),
             CpInf=(self.CpInf * constants.R, "J/(mol*K)"),
@@ -458,16 +458,11 @@ def test_wilhoit_as_dict(self):
                 "value": 178.76114800000002,
             },
             "class": "Wilhoit",
-            'thermo_coverage_dependence': {'OX': {
-                                                   'model': 'polynomial', 
-                                                   'enthalpy-coefficients': [{'class': 'ScalarQuantity', 'value': 1.0}, 
-                                                                             {'class': 'ScalarQuantity', 'value': 2.0}, 
-                                                                             {'class': 'ScalarQuantity', 'value': 3.0}
-                                                                            ], 
-                                                   'entropy-coefficients': [{'class': 'ScalarQuantity', 'value': 1.0}, 
-                                                                            {'class': 'ScalarQuantity', 'value': 2.0}, 
-                                                                            {'class': 'ScalarQuantity', 'value': 3.0}
-                                                                            ]}}
+            'thermo_coverage_dependence': {'1 O u0 p2 c0 {2,D} \n 2 X u0 p0 c0 {1,D}': {
+                                                                                        'model': 'polynomial', 
+                                                                                        'enthalpy-coefficients': {'class': 'np_array', 'object': [1, 2, 3]}, 
+                                                                                        'entropy-coefficients': {'class': 'np_array', 'object': [1, 2, 3]}}
+                                          }
         }
 
     def test_make_wilhoit(self):
@@ -476,6 +471,6 @@ def test_make_wilhoit(self):
         """
         wilhoit_dict = self.wilhoit.as_dict()
         new_wilhoit = Wilhoit.__new__(Wilhoit)
-        class_dictionary = {"ScalarQuantity": ScalarQuantity, "Wilhoit": Wilhoit}
+        class_dictionary = {"ScalarQuantity": ScalarQuantity, "Wilhoit": Wilhoit, "np_array": np.array}
 
         new_wilhoit.make_object(wilhoit_dict, class_dictionary)