add MBSampledReactor write input file test

Author: sevyharris

rmgpy/rmg/input.py

@@ -1828,6 +1828,15 @@ def format_initial_mole_fractions(system):
                     continue
                 f.write('        "{0!s}": ({1:g},"{2!s}"),\n'.format(spcs, conc, 'mol/m^3'))
             f.write('    },\n')
+        elif isinstance(system, MBSampledReactor):
+            f.write('mbsampledReactor(\n')
+            f.write('    temperature = ' + format_temperature(system) + '\n')
+            f.write('    pressure = ' + format_pressure(system) + '\n')
+            f.write('    initialMoleFractions={\n')
+            f.write(format_initial_mole_fractions(system))
+            f.write('    },\n')
+            f.write('    mbsamplingRate = ' + str(system.k_sampling.value_si) + ',\n')
+            f.write('    constantSpecies = ' + str([x.label for x in system.constantSpeciesList]) + ',\n')
         else:
             f.write('simpleReactor(\n')
             f.write('    temperature = ' + format_temperature(system) + '\n')

rmgpy/rmg/main.py

@@ -807,8 +807,8 @@ def execute(self, initialize=True, **kwargs):
         self.done = False
 
         # determine min and max values for T and P (don't determine P values for liquid reactors)
-        self.Tmin = min([x.Trange[0].value_si if x.Trange else x.T.value_si for x in self.reaction_systems])
-        self.Tmax = max([x.Trange[1].value_si if x.Trange else x.T.value_si for x in self.reaction_systems])
+        self.Tmin = min([x.Trange[0].value_si if hasattr(x, "Trange") and x.Trange else x.T.value_si for x in self.reaction_systems])
+        self.Tmax = max([x.Trange[1].value_si if hasattr(x, "Trange") and x.Trange else x.T.value_si for x in self.reaction_systems])
         try:
             self.Pmin = min([x.Prange[0].value_si if hasattr(x, "Prange") and x.Prange else x.P.value_si for x in self.reaction_systems])
             self.Pmax = max([x.Prange[1].value_si if hasattr(x, "Prange") and x.Prange else x.P.value_si for x in self.reaction_systems])

test/rmgpy/rmg/inputTest.py

@@ -28,7 +28,8 @@
 ###############################################################################
 
 from unittest.mock import patch
-
+import os
+import rmgpy
 import rmgpy.rmg.input as inp
 from rmgpy.rmg.main import RMG
 from rmgpy.rmg.model import CoreEdgeReactionModel
@@ -473,7 +474,7 @@ def test_write_superminimal_input(self):
         Test that we can write superminimal input file and read it back in with the same values.
         """
 
-        superminimal_input_file = '../../../examples/rmg/superminimal/input.py'
+        superminimal_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/superminimal/input.py')
         superminimal_output_file = 'temp_superminimal_input.py'
 
         rmg = RMG()
@@ -517,7 +518,7 @@ def test_write_superminimal_and_run(self):
         import os
         import shutil
 
-        superminimal_input_file = '../../../examples/rmg/superminimal/input.py'
+        superminimal_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/superminimal/input.py')
         new_run_dir = 'temp_superminimal_run'
         os.makedirs(new_run_dir, exist_ok=True)
         superminimal_output_file = os.path.join(new_run_dir, 'temp_superminimal_input.py')
@@ -538,7 +539,7 @@ def test_write_min_surf_input(self):
         Test that we can write the minimal surface input file and read it back in with the same values.
         """
 
-        min_surf_input_file = '../../../examples/rmg/minimal_surface/input.py'
+        min_surf_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/minimal_surface/input.py')
         min_surf_output_file = 'temp_min_surf_input.py'
 
         rmg = RMG()
@@ -598,7 +599,7 @@ def test_write_min_surf_and_run(self):
         import os
         import shutil
 
-        min_surf_input_file = '../../../examples/rmg/minimal_surface/input.py'
+        min_surf_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/minimal_surface/input.py')
         new_run_dir = 'temp_min_surf_run'
         os.makedirs(new_run_dir, exist_ok=True)
         min_surf_output_file = os.path.join(new_run_dir, 'temp_min_surf_input.py')
@@ -620,7 +621,7 @@ def test_write_liquid_cat_input(self):
         Test that we can write liquid catalyst input file and read it back in with the same values.
         """
 
-        liquid_cat_input_file = '../../../examples/rmg/liquid_cat/input.py'
+        liquid_cat_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/liquid_cat/input.py')
         liquid_cat_output_file = 'temp_liquid_cat_input.py'
 
         rmg = RMG()
@@ -662,7 +663,7 @@ def test_write_liquid_cat_and_run(self):
         import os
         import shutil
 
-        liquid_cat_input_file = '../../../examples/rmg/liquid_cat/input.py'
+        liquid_cat_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/liquid_cat/input.py')
         new_run_dir = 'temp_liquid_cat_run'
         os.makedirs(new_run_dir, exist_ok=True)
         liquid_cat_output_file = os.path.join(new_run_dir, 'temp_liquid_cat_input.py')
@@ -673,7 +674,7 @@ def test_write_liquid_cat_and_run(self):
 
         # run RMG with the new input file
         import subprocess
-        subprocess.run(['python', '../../../rmg.py', '-t', '00:00:01:30', liquid_cat_output_file], check=True)
+        subprocess.run(['python', os.path.join(rmgpy.settings['test_data.directory'], '../../../rmg.py'), '-t', '00:00:01:30', liquid_cat_output_file], check=True)
 
         # clean up
         shutil.rmtree(new_run_dir)
@@ -683,7 +684,7 @@ def test_write_liquid_input(self):
         Test that we can write the liquid reactor input file and read it back in with the same values.
         """
 
-        liquid_input_file = '../../../examples/rmg/liquid_phase/input.py'
+        liquid_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/liquid_phase/input.py')
         liquid_output_file = 'temp_liquid_input.py'
 
         rmg = RMG()
@@ -723,7 +724,7 @@ def test_write_liquid_and_run(self):
         import os
         import shutil
 
-        liquid_input_file = '../../../examples/rmg/liquid_phase/input.py'
+        liquid_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/liquid_phase/input.py')
         new_run_dir = 'temp_liquid_run'
         os.makedirs(new_run_dir, exist_ok=True)
         liquid_output_file = os.path.join(new_run_dir, 'temp_liquid_input.py')
@@ -734,7 +735,7 @@ def test_write_liquid_and_run(self):
 
         # run RMG with the new input file
         import subprocess
-        subprocess.run(['python', '../../../rmg.py', '-t', '00:00:01:30', liquid_output_file], check=True)
+        subprocess.run(['python', os.path.join(rmgpy.settings['test_data.directory'], '../../../rmg.py'), '-t', '00:00:01:30', liquid_output_file], check=True)
 
         # clean up
         shutil.rmtree(new_run_dir)
@@ -745,7 +746,7 @@ def test_write_constantVIdealGasReactor(self):
         Test that we can write constant volume ideal gas reactor input file and read it back in with the same values.
         """
 
-        rms_constant_V_input_file = '../../../examples/rmg/rms_constant_V/input.py'
+        rms_constant_V_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/rms_constant_V/input.py')
         rms_constant_V_output_file = 'temp_rms_constant_V_input.py'
 
         rmg = RMG()
@@ -788,7 +789,7 @@ def test_write_constantVIdealGasReactor_and_run(self):
         import os
         import shutil
 
-        constant_V_input_file = '../../../examples/rmg/rms_constant_V/input.py'
+        constant_V_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/rms_constant_V/input.py')
         new_run_dir = 'temp_constant_V_run'
         os.makedirs(new_run_dir, exist_ok=True)
         constant_V_output_file = os.path.join(new_run_dir, 'temp_constant_V_input.py')
@@ -799,7 +800,7 @@ def test_write_constantVIdealGasReactor_and_run(self):
 
         # run RMG with the new input file
         import subprocess
-        subprocess.run(['python', '../../../rmg.py', '-t', '00:00:01:30', constant_V_output_file], check=True)
+        subprocess.run(['python', os.path.join(rmgpy.settings['test_data.directory'], '../../../rmg.py'), '-t', '00:00:01:30', constant_V_output_file], check=True)
 
         # clean up
         shutil.rmtree(new_run_dir)
@@ -810,7 +811,7 @@ def test_write_constantTPdealGasReactor(self):
         Test that we can write constant TP ideal gas reactor input file and read it back in with the same values.
         """
 
-        rms_constant_TP_input_file = '../../../examples/rmg/nox_transitory_edge/input.py'
+        rms_constant_TP_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/nox_transitory_edge/input.py')
         rms_constant_TP_output_file = 'temp_constant_TP_input.py'
 
         rmg = RMG()
@@ -853,7 +854,7 @@ def test_write_constantTPIdealGasReactor_and_run(self):
         import os
         import shutil
 
-        constant_TP_input_file = '../../../examples/rmg/nox_transitory_edge/input.py'
+        constant_TP_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../examples/rmg/nox_transitory_edge/input.py')
         new_run_dir = 'temp_constant_TP_run'
         os.makedirs(new_run_dir, exist_ok=True)
         constant_TP_output_file = os.path.join(new_run_dir, 'temp_constant_TP_input.py')
@@ -875,7 +876,7 @@ def test_write_constantTVLiquidReactor(self):
         Test that we can write constant TV liquid reactor input file and read it back in with the same values.
         """
 
-        rms_constant_TV_input_file = '../../../test/regression/RMS_CSTR_liquid_oxidation/input.py'
+        rms_constant_TV_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../test/regression/RMS_CSTR_liquid_oxidation/input.py')
         rms_constant_TV_output_file = 'temp_constant_TV_liquid_input.py'
 
         rmg = RMG()
@@ -918,7 +919,7 @@ def test_write_constantTVLiquidReactor_and_run(self):
         import os
         import shutil
 
-        constant_TV_input_file = '../../../test/regression/RMS_CSTR_liquid_oxidation/input.py'
+        constant_TV_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../test/regression/RMS_CSTR_liquid_oxidation/input.py')
         new_run_dir = 'temp_constant_TV_run'
         os.makedirs(new_run_dir, exist_ok=True)
         constant_TV_output_file = os.path.join(new_run_dir, 'temp_constant_TV_input.py')
@@ -929,7 +930,49 @@ def test_write_constantTVLiquidReactor_and_run(self):
 
         # run RMG with the new input file
         import subprocess
-        subprocess.run(['python', '../../../rmg.py', '-t', '00:00:01:30', constant_TV_output_file], check=True)
+        subprocess.run(['python', os.path.join(rmgpy.settings['test_data.directory'], '../../../rmg.py'), '-t', '00:00:01:30', constant_TV_output_file], check=True)
 
         # clean up
         shutil.rmtree(new_run_dir)
+
+    def test_MBSampledReactor_write(self):
+        """
+        Test that we can write MB sampled reactor input file and read it back in with the same values.
+        Note that the MBSampledReactor is not intended to be used with a standard RMG job, so there's no point in running it as a test
+        """
+
+        mbsampled_input_file = os.path.join(rmgpy.settings['test_data.directory'], '../../../rmgpy/tools/data/sim/mbSampled/input.py')
+        mbsampled_output_file = 'temp_mbsampled_input.py'
+
+        rmg = RMG()
+        inp.read_input_file(mbsampled_input_file, rmg)
+
+        # read a bunch of values in from input file to check they are the same after writing
+        T = rmg.reaction_systems[0].T.value_si
+        P = rmg.reaction_systems[0].P.value_si
+        sampling_rate = rmg.reaction_systems[0].k_sampling.value_si
+
+        initialMoleFractions = {k.label: v for k, v in rmg.reaction_systems[0].initial_mole_fractions.items()}
+
+        for term in rmg.reaction_systems[0].termination:
+            if hasattr(term, 'time'):
+                termination_time = term.time.value_si
+
+        inp.save_input_file(mbsampled_output_file, rmg)
+        # read it back in and confirm all the values match
+        rmg1 = RMG()
+        inp.read_input_file(mbsampled_output_file, rmg1)
+        assert rmg1.reaction_systems[0].T.value_si == T
+        assert rmg1.reaction_systems[0].P.value_si == P
+        assert rmg1.reaction_systems[0].k_sampling.value_si == sampling_rate
+
+        new_initialMoleFractions = {k.label: v for k, v in rmg1.reaction_systems[0].initial_mole_fractions.items()}
+        assert pytest.approx(new_initialMoleFractions, rel=1e-4) == initialMoleFractions
+
+        for term in rmg1.reaction_systems[0].termination:
+            if hasattr(term, 'time'):
+                assert term.time.value_si == termination_time
+
+        # clean up
+        import os
+        os.remove(mbsampled_output_file)