diff --git a/src/acom_music_box/__init__.py b/src/acom_music_box/__init__.py index 890f7832..942cfb65 100644 --- a/src/acom_music_box/__init__.py +++ b/src/acom_music_box/__init__.py @@ -4,7 +4,7 @@ This package contains modules for handling various aspects of a music box, including species, products, reactants, reactions, and more. """ -__version__ = "2.2.0" +__version__ = "2.2.1" from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration from .species import Species diff --git a/src/acom_music_box/conditions.py b/src/acom_music_box/conditions.py index f5c239c8..e8a094fd 100644 --- a/src/acom_music_box/conditions.py +++ b/src/acom_music_box/conditions.py @@ -179,8 +179,13 @@ def from_config_JSON( for reaction in reaction_list.reactions: if (reaction.name is None): continue - if not any(rate.reaction.name == - reaction.name for rate in reaction_rates): + reaction_exists = False + for rate in reaction_rates: + if rate.reaction.name == reaction.name: + reaction_exists = True + break + + if not reaction_exists: reaction_rates.append(ReactionRate(reaction, 0)) return cls( @@ -217,18 +222,12 @@ def read_initial_rates_from_file(cls, file_path, reaction_list): # The second row of the CSV contains rates rates = initial_conditions[1] - for i in range(0, len(headers)): - - reaction_rate = headers[i] - - match = filter( - lambda x: x.name == reaction_rate.split('.')[1], - reaction_list.reactions) - - reaction = next(match, None) - rate = rates[i] + for reaction_rate, rate in zip(headers, rates): + type, name, *rest = reaction_rate.split('.') + for reaction in reaction_list.reactions: + if reaction.name == name and reaction.short_type() == type: + reaction_rates.append(ReactionRate(reaction, rate)) - reaction_rates.append(ReactionRate(reaction, rate)) return reaction_rates def add_species_concentration(self, species_concentration): diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py index f005757c..3eb0f922 100644 --- a/src/acom_music_box/music_box.py +++ b/src/acom_music_box/music_box.py @@ -10,6 +10,7 @@ import os import logging +logging.basicConfig(level=logging.DEBUG) logger = logging.getLogger(__name__) @@ -554,6 +555,7 @@ def solve(self, output_path=None): # outputs to file if output is present if (output_path is not None): logger.info("path_to_output = {}".format(output_path)) + os.makedirs(os.path.dirname(output_path), exist_ok=True) with open(output_path, 'w', newline='') as output: writer = csv.writer(output) writer.writerows(output_array) @@ -706,7 +708,7 @@ def order_reaction_rates(self, curr_conditions, rate_constant_ordering): if (rate.reaction.reaction_type == "PHOTOLYSIS"): key = "PHOTO." + rate.reaction.name - elif (rate.reaction.reaction_type == "LOSS"): + elif (rate.reaction.reaction_type == "FIRST_ORDER_LOSS"): key = "LOSS." + rate.reaction.name elif (rate.reaction.reaction_type == "EMISSION"): key = "EMIS." + rate.reaction.name @@ -714,7 +716,6 @@ def order_reaction_rates(self, curr_conditions, rate_constant_ordering): ordered_rate_constants = len(rate_constants.keys()) * [0.0] for key, value in rate_constants.items(): - ordered_rate_constants[rate_constant_ordering[key]] = float(value) return ordered_rate_constants diff --git a/src/acom_music_box/reaction.py b/src/acom_music_box/reaction.py index e02ed88b..003d8795 100644 --- a/src/acom_music_box/reaction.py +++ b/src/acom_music_box/reaction.py @@ -60,6 +60,24 @@ def add_product(self, product): """ self.products.append(product) + def short_type(self): + """ + Return the first letter of the reaction type. + + Returns: + str: The first letter of the reaction type. + """ + type_map = { + "EMISSION": "EMIS", + "PHOTOLYSIS": "PHOT", + "FIRST_ORDER_LOSS": "LOSS", + "BRANCHED": "BRAN", + "ARRHENIUS": "ARRH", + "TUNNELING": "TUNN", + "TROE_TERNARY": "TROE", + } + return type_map.get(self.reaction_type, "UNKNOWN") + class Branched(Reaction): diff --git a/tests/integration/input_use_cases/1/camp_data/config.json b/tests/integration/input_use_cases/1/camp_data/config.json deleted file mode 100644 index af4e8619..00000000 --- a/tests/integration/input_use_cases/1/camp_data/config.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json" - ] -} diff --git a/tests/integration/input_use_cases/1/camp_data/species.json b/tests/integration/input_use_cases/1/camp_data/species.json deleted file mode 100644 index 948aca00..00000000 --- a/tests/integration/input_use_cases/1/camp_data/species.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - } - ] -} - diff --git a/tests/integration/input_use_cases/1/config_camp.json b/tests/integration/input_use_cases/1/config_camp.json deleted file mode 100644 index 9354a6fa..00000000 --- a/tests/integration/input_use_cases/1/config_camp.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5 - }, - "chemical species" : { - "N2" : { "initial value [mol m-3]" : 3.29e1 }, - "O2" : { "initial value [mol m-3]" : 8.84e0 }, - "Ar" : { "initial value [mol m-3]" : 3.92e-1 }, - "CO2" : { "initial value [mol m-3]" : 1.69e-2 }, - "O" : { "initial value [mol m-3]" : 1.0e-5 } - }, - "environmental conditions" : { - "temperature" : { "initial value [K]" : 298.0 }, - "pressure" : { "initial value [atm]" : 1.0 } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] - } - \ No newline at end of file diff --git a/tests/integration/input_use_cases/1/expected_output.csv b/tests/integration/input_use_cases/1/expected_output.csv deleted file mode 100644 index 3f468492..00000000 --- a/tests/integration/input_use_cases/1/expected_output.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 diff --git a/tests/integration/input_use_cases/1/expected_output_camp.csv b/tests/integration/input_use_cases/1/expected_output_camp.csv deleted file mode 100644 index 2391c177..00000000 --- a/tests/integration/input_use_cases/1/expected_output_camp.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 diff --git a/tests/integration/input_use_cases/1/run_camp.sh b/tests/integration/input_use_cases/1/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/1/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/1/run_preprocessed_data.sh b/tests/integration/input_use_cases/1/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/1/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/1/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/1/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/1/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/1/run_preprocessor_camp.sh b/tests/integration/input_use_cases/1/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/1/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/2/camp_data/config.json b/tests/integration/input_use_cases/2/camp_data/config.json deleted file mode 100644 index af4e8619..00000000 --- a/tests/integration/input_use_cases/2/camp_data/config.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json" - ] -} diff --git a/tests/integration/input_use_cases/2/camp_data/species.json b/tests/integration/input_use_cases/2/camp_data/species.json deleted file mode 100644 index 948aca00..00000000 --- a/tests/integration/input_use_cases/2/camp_data/species.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - } - ] -} - diff --git a/tests/integration/input_use_cases/2/config_camp.json b/tests/integration/input_use_cases/2/config_camp.json deleted file mode 100644 index 4c301998..00000000 --- a/tests/integration/input_use_cases/2/config_camp.json +++ /dev/null @@ -1,27 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5 - }, - "initial conditions" : { - "initial.csv" : { - "properties" : { - "ENV.pressure" : { "units" : "atm" } - } - } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] - } \ No newline at end of file diff --git a/tests/integration/input_use_cases/2/expected_output.csv b/tests/integration/input_use_cases/2/expected_output.csv deleted file mode 100644 index 3f468492..00000000 --- a/tests/integration/input_use_cases/2/expected_output.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 diff --git a/tests/integration/input_use_cases/2/expected_output_camp.csv b/tests/integration/input_use_cases/2/expected_output_camp.csv deleted file mode 100644 index 2391c177..00000000 --- a/tests/integration/input_use_cases/2/expected_output_camp.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 diff --git a/tests/integration/input_use_cases/2/initial.csv b/tests/integration/input_use_cases/2/initial.csv deleted file mode 100644 index f422d6fa..00000000 --- a/tests/integration/input_use_cases/2/initial.csv +++ /dev/null @@ -1,2 +0,0 @@ -CONC.N2, CONC.O2, CONC.Ar, CONC.CO2, CONC.O, ENV.temperature, ENV.pressure -3.29e1, 8.84, 3.92e-1, 1.69e-2, 1.0e-5, 298.0, 1.0 diff --git a/tests/integration/input_use_cases/2/run_camp.sh b/tests/integration/input_use_cases/2/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/2/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/2/run_preprocessed_data.sh b/tests/integration/input_use_cases/2/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/2/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/2/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/2/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/2/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/2/run_preprocessor_camp.sh b/tests/integration/input_use_cases/2/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/2/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/3/camp_data/config.json b/tests/integration/input_use_cases/3/camp_data/config.json deleted file mode 100644 index af4e8619..00000000 --- a/tests/integration/input_use_cases/3/camp_data/config.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json" - ] -} diff --git a/tests/integration/input_use_cases/3/camp_data/species.json b/tests/integration/input_use_cases/3/camp_data/species.json deleted file mode 100644 index 948aca00..00000000 --- a/tests/integration/input_use_cases/3/camp_data/species.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - } - ] -} - diff --git a/tests/integration/input_use_cases/3/config_camp.json b/tests/integration/input_use_cases/3/config_camp.json deleted file mode 100644 index df4258de..00000000 --- a/tests/integration/input_use_cases/3/config_camp.json +++ /dev/null @@ -1,25 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5 - }, - "initial conditions" : { - "initial.csv" : { - "delimiter" : "&" - } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] - } \ No newline at end of file diff --git a/tests/integration/input_use_cases/3/expected_output.csv b/tests/integration/input_use_cases/3/expected_output.csv deleted file mode 100644 index 3f468492..00000000 --- a/tests/integration/input_use_cases/3/expected_output.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 diff --git a/tests/integration/input_use_cases/3/expected_output_camp.csv b/tests/integration/input_use_cases/3/expected_output_camp.csv deleted file mode 100644 index 2391c177..00000000 --- a/tests/integration/input_use_cases/3/expected_output_camp.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.10000000000000000818E-04, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.40894572562574022296E-64, 0.99999999999999991240E-05, 0.88399999999999998579E+01, 0.40894572562574022296E-64 diff --git a/tests/integration/input_use_cases/3/initial.csv b/tests/integration/input_use_cases/3/initial.csv deleted file mode 100644 index d53e9b6d..00000000 --- a/tests/integration/input_use_cases/3/initial.csv +++ /dev/null @@ -1,2 +0,0 @@ -CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& CONC.O& ENV.temperature& ENV.pressure.atm -3.29e1& 8.84& 3.92e-1& 1.69e-2& 1.0e-5& 298.0& 1.0 diff --git a/tests/integration/input_use_cases/3/run_camp.sh b/tests/integration/input_use_cases/3/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/3/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/3/run_preprocessed_data.sh b/tests/integration/input_use_cases/3/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/3/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/3/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/3/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/3/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/3/run_preprocessor_camp.sh b/tests/integration/input_use_cases/3/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/3/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/4/camp_data/config.json b/tests/integration/input_use_cases/4/camp_data/config.json deleted file mode 100644 index 4629149f..00000000 --- a/tests/integration/input_use_cases/4/camp_data/config.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json", - "camp_data/mechanism.json" - ] -} diff --git a/tests/integration/input_use_cases/4/camp_data/mechanism.json b/tests/integration/input_use_cases/4/camp_data/mechanism.json deleted file mode 100644 index 202f1b4f..00000000 --- a/tests/integration/input_use_cases/4/camp_data/mechanism.json +++ /dev/null @@ -1,95 +0,0 @@ -{ - "camp-data" : [ - { - "name" : "Chapman", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O2" : { } - }, - "products" : { - "O" : { "yield" : 2.0 } - }, - "MUSICA name" : "O2_1" - }, - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O3" : { } - }, - "products" : { - "O1D" : { }, - "O2" : { } - }, - "MUSICA name" : "O3_1" - }, - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O3" : { } - }, - "products" : { - "O" : { }, - "O2" : { } - }, - "MUSICA name" : "O3_2" - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O1D" : { }, - "N2" : { } - }, - "products" : { - "O" : { }, - "N2" : { } - }, - "A" : 2.15e-11, - "C" : 110.0 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O1D" : { }, - "O2" : { } - }, - "products" : { - "O" : { }, - "O2" : { } - }, - "A" : 3.3e-11, - "C" : 55.0 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O" : { }, - "O3" : { } - }, - "products" : { - "O2" : { "yield" : 2.0 } - }, - "A" : 8.0e-12, - "C" : -2060.00 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O" : { }, - "O2" : { }, - "M" : { } - }, - "products" : { - "O3" : { }, - "M" : { } - }, - "A" : 6.0e-34, - "B" : 2.4 - } - ] - } - ] -} - diff --git a/tests/integration/input_use_cases/4/camp_data/species.json b/tests/integration/input_use_cases/4/camp_data/species.json deleted file mode 100644 index 948aca00..00000000 --- a/tests/integration/input_use_cases/4/camp_data/species.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - } - ] -} - diff --git a/tests/integration/input_use_cases/4/check_output.F90 b/tests/integration/input_use_cases/4/check_output.F90 deleted file mode 100644 index 321a075d..00000000 --- a/tests/integration/input_use_cases/4/check_output.F90 +++ /dev/null @@ -1,38 +0,0 @@ -!> \file -!> Check results from an integration test - -!> Check results from an integration test -program check_output - - use test_common_output - - implicit none - - call check_results( ) - -contains - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - - !> Perform checks of an integration test output, in addition to comparison - !! with the `expected_results` file - subroutine check_results( ) - - use musica_string, only : string_t - - type(scaled_property_t) :: species(4) - - species(1)%name_ = 'CONC.O1D' - species(2)%name_ = 'CONC.O' - species(3)%name_ = 'CONC.O2' - species(3)%scale_factor_ = 2.0 - species(4)%name_ = 'CONC.O3' - species(4)%scale_factor_ = 3.0 - - call conservation_check( 'output.csv', species ) - - end subroutine check_results - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -end program check_output diff --git a/tests/integration/input_use_cases/4/config_b_camp.json b/tests/integration/input_use_cases/4/config_b_camp.json deleted file mode 100644 index b18b8162..00000000 --- a/tests/integration/input_use_cases/4/config_b_camp.json +++ /dev/null @@ -1,25 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5 - }, - "initial conditions" : { - "initial_b.csv" : { - "delimiter" : "&" - } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] -} diff --git a/tests/integration/input_use_cases/4/config_camp.json b/tests/integration/input_use_cases/4/config_camp.json deleted file mode 100644 index 3e1525fd..00000000 --- a/tests/integration/input_use_cases/4/config_camp.json +++ /dev/null @@ -1,30 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5 - }, - "initial conditions" : { - "initial.csv" : { - "delimiter" : "&" - } - }, - "photolysis" : { - "O2_1" : { "initial value [s-1]" : 1.0e-4 }, - "O3_1" : { "initial value [s-1]" : 1.0e-5 }, - "O3_2" : { "initial value [s-1]" : 1.0e-6 } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] -} diff --git a/tests/integration/input_use_cases/4/expected_output.csv b/tests/integration/input_use_cases/4/expected_output.csv deleted file mode 100644 index a65cfa40..00000000 --- a/tests/integration/input_use_cases/4/expected_output.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999981010E-01, 0.00000000000000000000E+00, 0.32899999999999955946E+02, 0.42403605420732882163E-13, 0.17071524585409238359E-07, 0.42715031950993740395E+01, 0.30456645309098955288E+01 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999981010E-01, 0.00000000000000000000E+00, 0.32899999999999955946E+02, 0.54421344000797236423E-13, 0.14768755918730700662E-07, 0.31881099143215476666E+01, 0.37679267188626965890E+01 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999981010E-01, 0.00000000000000000000E+00, 0.32899999999999955946E+02, 0.56928952609103817107E-13, 0.14234850785201633128E-07, 0.29718255185094277770E+01, 0.39121163162487428977E+01 diff --git a/tests/integration/input_use_cases/4/expected_output_camp.csv b/tests/integration/input_use_cases/4/expected_output_camp.csv deleted file mode 100644 index e527233f..00000000 --- a/tests/integration/input_use_cases/4/expected_output_camp.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.42390328776849406796E-13, 0.17073882177310531812E-07, 0.42727374526419792389E+01, 0.30448416925609786965E+01 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.54380901578799943281E-13, 0.14777200599742525137E-07, 0.31916245024107605666E+01, 0.37655836601476773140E+01 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.56891182677264652758E-13, 0.14243037143981733287E-07, 0.29750600231854549271E+01, 0.39099599798094502034E+01 diff --git a/tests/integration/input_use_cases/4/initial.csv b/tests/integration/input_use_cases/4/initial.csv deleted file mode 100644 index 2af07f8d..00000000 --- a/tests/integration/input_use_cases/4/initial.csv +++ /dev/null @@ -1,2 +0,0 @@ -CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& ENV.temperature& ENV.pressure.atm -3.29e1& 8.84& 3.92e-1& 1.69e-2& 298.0& 1.0 diff --git a/tests/integration/input_use_cases/4/initial_b.csv b/tests/integration/input_use_cases/4/initial_b.csv deleted file mode 100644 index c59bf8d4..00000000 --- a/tests/integration/input_use_cases/4/initial_b.csv +++ /dev/null @@ -1,2 +0,0 @@ -CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& ENV.temperature& ENV.pressure.atm& PHOT.O2_1& PHOT.O3_1& PHOT.O3_2 -3.29e1& 8.84& 3.92e-1& 1.69e-2& 298.0& 1.0& 1.0e-4& 1.0e-5& 1.0e-6 diff --git a/tests/integration/input_use_cases/4/run_b.sh b/tests/integration/input_use_cases/4/run_b.sh deleted file mode 100755 index 487d046b..00000000 --- a/tests/integration/input_use_cases/4/run_b.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_b.json" -comp_str="../../../../compare_results output.csv expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_b_camp.sh b/tests/integration/input_use_cases/4/run_b_camp.sh deleted file mode 100755 index e1009771..00000000 --- a/tests/integration/input_use_cases/4/run_b_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_b_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_b_preprocessed_data.sh b/tests/integration/input_use_cases/4/run_b_preprocessed_data.sh deleted file mode 100755 index 59b51dc8..00000000 --- a/tests/integration/input_use_cases/4/run_b_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config_b.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_b_preprocessed_data_camp.sh b/tests/integration/input_use_cases/4/run_b_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/4/run_b_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_b_preprocessor.sh b/tests/integration/input_use_cases/4/run_b_preprocessor.sh deleted file mode 100755 index 2b4d1bf3..00000000 --- a/tests/integration/input_use_cases/4/run_b_preprocessor.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_b.json" -exec_str2="./run_preprocessed_data.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_b_preprocessor_camp.sh b/tests/integration/input_use_cases/4/run_b_preprocessor_camp.sh deleted file mode 100755 index 1e7abf03..00000000 --- a/tests/integration/input_use_cases/4/run_b_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_b_camp.json" -exec_str2="./run_b_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_camp.sh b/tests/integration/input_use_cases/4/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/4/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_preprocessed_data.sh b/tests/integration/input_use_cases/4/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/4/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/4/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/4/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/4/run_preprocessor_camp.sh b/tests/integration/input_use_cases/4/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/4/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/5/camp_data/config.json b/tests/integration/input_use_cases/5/camp_data/config.json deleted file mode 100644 index 4629149f..00000000 --- a/tests/integration/input_use_cases/5/camp_data/config.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json", - "camp_data/mechanism.json" - ] -} diff --git a/tests/integration/input_use_cases/5/camp_data/mechanism.json b/tests/integration/input_use_cases/5/camp_data/mechanism.json deleted file mode 100644 index 2b6e6d87..00000000 --- a/tests/integration/input_use_cases/5/camp_data/mechanism.json +++ /dev/null @@ -1,26 +0,0 @@ -{ - "camp-data" : [ - { - "name" : "Chapman", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "EMISSION", - "species" : "O1D", - "MUSICA name" : "O1D" - }, - { - "type" : "EMISSION", - "species" : "O", - "MUSICA name" : "O" - }, - { - "type" : "EMISSION", - "species" : "O3", - "MUSICA name" : "O3" - } - ] - } - ] -} - diff --git a/tests/integration/input_use_cases/5/camp_data/species.json b/tests/integration/input_use_cases/5/camp_data/species.json deleted file mode 100644 index 948aca00..00000000 --- a/tests/integration/input_use_cases/5/camp_data/species.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - } - ] -} - diff --git a/tests/integration/input_use_cases/5/config_camp.json b/tests/integration/input_use_cases/5/config_camp.json deleted file mode 100644 index 4bd9d39e..00000000 --- a/tests/integration/input_use_cases/5/config_camp.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5 - }, - "initial conditions" : { - "initial.csv" : { - "delimiter" : "&" - } - }, - "evolving conditions" : { - "emissions.csv" : { } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] -} diff --git a/tests/integration/input_use_cases/5/emissions.csv b/tests/integration/input_use_cases/5/emissions.csv deleted file mode 100644 index 2553005b..00000000 --- a/tests/integration/input_use_cases/5/emissions.csv +++ /dev/null @@ -1,5 +0,0 @@ -time.hr, EMIS.O1D, EMIS.O, EMIS.O3 -0.0, 0.0, 0.0, 0.0 -0.2, 0.1, 0.05, 0.05 -1.0, 0.2, 0.1, 0.1 -1.5, 0.0, 0.0, 0.0 diff --git a/tests/integration/input_use_cases/5/expected_output.csv b/tests/integration/input_use_cases/5/expected_output.csv deleted file mode 100644 index efdcb0e2..00000000 --- a/tests/integration/input_use_cases/5/expected_output.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.28800000000000000000E+03, 0.14400000000000000000E+03, 0.88399999999999998579E+01, 0.14400000000000000000E+03 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.64800000000000000000E+03, 0.32400000000000000000E+03, 0.88399999999999998579E+01, 0.32400000000000000000E+03 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.64800000000000000000E+03, 0.32400000000000000000E+03, 0.88399999999999998579E+01, 0.32400000000000000000E+03 diff --git a/tests/integration/input_use_cases/5/expected_output_camp.csv b/tests/integration/input_use_cases/5/expected_output_camp.csv deleted file mode 100644 index d8cd312d..00000000 --- a/tests/integration/input_use_cases/5/expected_output_camp.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.28799999999999988631E+03, 0.14399999999999994316E+03, 0.88399999999999998579E+01, 0.14399999999999994316E+03 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.64799999999999977263E+03, 0.32399999999999988631E+03, 0.88399999999999998579E+01, 0.32399999999999988631E+03 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.64799999999999977263E+03, 0.32399999999999988631E+03, 0.88399999999999998579E+01, 0.32399999999999988631E+03 diff --git a/tests/integration/input_use_cases/5/initial.csv b/tests/integration/input_use_cases/5/initial.csv deleted file mode 100644 index 2af07f8d..00000000 --- a/tests/integration/input_use_cases/5/initial.csv +++ /dev/null @@ -1,2 +0,0 @@ -CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& ENV.temperature& ENV.pressure.atm -3.29e1& 8.84& 3.92e-1& 1.69e-2& 298.0& 1.0 diff --git a/tests/integration/input_use_cases/5/run_camp.sh b/tests/integration/input_use_cases/5/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/5/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/5/run_preprocessed_data.sh b/tests/integration/input_use_cases/5/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/5/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/5/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/5/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/5/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/5/run_preprocessor_camp.sh b/tests/integration/input_use_cases/5/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/5/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/6/camp_data/config.json b/tests/integration/input_use_cases/6/camp_data/config.json deleted file mode 100644 index 4629149f..00000000 --- a/tests/integration/input_use_cases/6/camp_data/config.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json", - "camp_data/mechanism.json" - ] -} diff --git a/tests/integration/input_use_cases/6/camp_data/mechanism.json b/tests/integration/input_use_cases/6/camp_data/mechanism.json deleted file mode 100644 index 7f67543b..00000000 --- a/tests/integration/input_use_cases/6/camp_data/mechanism.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "camp-data" : [ - { - "name" : "Chapman", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "EMISSION", - "species" : "O1D", - "MUSICA name" : "O1D" - }, - { - "type" : "EMISSION", - "species" : "O", - "MUSICA name" : "O" - }, - { - "type" : "EMISSION", - "species" : "O3", - "MUSICA name" : "O3" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "N2", - "MUSICA name" : "N2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "O2", - "MUSICA name" : "O2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "CO2", - "MUSICA name" : "CO2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "Ar", - "MUSICA name" : "Ar" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "H2O", - "MUSICA name" : "H2O" - } - ] - } - ] -} - diff --git a/tests/integration/input_use_cases/6/camp_data/species.json b/tests/integration/input_use_cases/6/camp_data/species.json deleted file mode 100644 index 948aca00..00000000 --- a/tests/integration/input_use_cases/6/camp_data/species.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - } - ] -} - diff --git a/tests/integration/input_use_cases/6/config_camp.json b/tests/integration/input_use_cases/6/config_camp.json deleted file mode 100644 index 429b43d6..00000000 --- a/tests/integration/input_use_cases/6/config_camp.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5 - }, - "initial conditions" : { - "initial.csv" : { - "delimiter" : "&" - } - }, - "evolving conditions" : { - "emissions.csv" : { }, - "wall_loss_rates_011519.txt" : { - "delimiter" : ";", - "time axis" : "columns", - "properties" : { - "simtime" : { - "MusicBox name" : "time", - "units" : "hr" - }, - "*" : { - "MusicBox name" : "LOSS.*", - "units" : "min-1" - } - } - } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] -} diff --git a/tests/integration/input_use_cases/6/emissions.csv b/tests/integration/input_use_cases/6/emissions.csv deleted file mode 100644 index 2553005b..00000000 --- a/tests/integration/input_use_cases/6/emissions.csv +++ /dev/null @@ -1,5 +0,0 @@ -time.hr, EMIS.O1D, EMIS.O, EMIS.O3 -0.0, 0.0, 0.0, 0.0 -0.2, 0.1, 0.05, 0.05 -1.0, 0.2, 0.1, 0.1 -1.5, 0.0, 0.0, 0.0 diff --git a/tests/integration/input_use_cases/6/expected_output.csv b/tests/integration/input_use_cases/6/expected_output.csv deleted file mode 100644 index c951c80f..00000000 --- a/tests/integration/input_use_cases/6/expected_output.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.14830364683772609413E+00, 0.82756181710989390465E-02, 0.00000000000000000000E+00, 0.16110522948470723748E+02, 0.28800000000000000000E+03, 0.14400000000000000000E+03, 0.33443985664425985860E+01, 0.14400000000000000000E+03 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.48002919875168893749E-01, 0.34052338713566354146E-02, 0.00000000000000000000E+00, 0.66291239270788988591E+01, 0.64800000000000000000E+03, 0.32400000000000000000E+03, 0.10825148257563599330E+01, 0.32400000000000000000E+03 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.27146872321263608441E-01, 0.21712729792329860633E-02, 0.00000000000000000000E+00, 0.42269160364949884823E+01, 0.64800000000000000000E+03, 0.32400000000000000000E+03, 0.61218967173461846798E+00, 0.32400000000000000000E+03 diff --git a/tests/integration/input_use_cases/6/expected_output_camp.csv b/tests/integration/input_use_cases/6/expected_output_camp.csv deleted file mode 100644 index 64d6b5da..00000000 --- a/tests/integration/input_use_cases/6/expected_output_camp.csv +++ /dev/null @@ -1,5 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.36000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.14871954069662024489E+00, 0.82881710648065615860E-02, 0.38134765806885220612E-64, 0.16134960238587897408E+02, 0.28799999999999982947E+03, 0.14399999999999991473E+03, 0.33537773973421494134E+01, 0.14399999999999991473E+03 - 0.72000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.48270812935350487782E-01, 0.34162853086090899137E-02, 0.37945031178675610780E-64, 0.66506382635052645469E+01, 0.64799999999999954525E+03, 0.32399999999999977263E+03, 0.10885560876237192485E+01, 0.32399999999999977263E+03 - 0.90000000000000000000E+04, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.27335231092851380863E-01, 0.21801660781599003017E-02, 0.37945031178675606563E-64, 0.42442286373645368158E+01, 0.64799999999999954525E+03, 0.32399999999999977263E+03, 0.61643735423674983487E+00, 0.32399999999999977263E+03 diff --git a/tests/integration/input_use_cases/6/initial.csv b/tests/integration/input_use_cases/6/initial.csv deleted file mode 100644 index 2af07f8d..00000000 --- a/tests/integration/input_use_cases/6/initial.csv +++ /dev/null @@ -1,2 +0,0 @@ -CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& ENV.temperature& ENV.pressure.atm -3.29e1& 8.84& 3.92e-1& 1.69e-2& 298.0& 1.0 diff --git a/tests/integration/input_use_cases/6/run_camp.sh b/tests/integration/input_use_cases/6/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/6/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/6/run_preprocessed_data.sh b/tests/integration/input_use_cases/6/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/6/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/6/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/6/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/6/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/6/run_preprocessor_camp.sh b/tests/integration/input_use_cases/6/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/6/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/6/wall_loss_rates_011519.txt b/tests/integration/input_use_cases/6/wall_loss_rates_011519.txt deleted file mode 100644 index fa5182fa..00000000 --- a/tests/integration/input_use_cases/6/wall_loss_rates_011519.txt +++ /dev/null @@ -1,6 +0,0 @@ -simtime; 0.0; 0.3; 0.6; 0.9; 1.2 -N2; 0.010; 0.012; 0.013; 0.014; 0.015 -O2; 0.015; 0.016; 0.017; 0.018; 0.019 -Ar; 0.015; 0.016; 0.017; 0.018; 0.019 -CO2; 0.010; 0.012; 0.013; 0.014; 0.015 -H2O; 0.010; 0.012; 0.013; 0.014; 0.015 diff --git a/tests/integration/input_use_cases/7/camp_data/config.json b/tests/integration/input_use_cases/7/camp_data/config.json deleted file mode 100644 index 4629149f..00000000 --- a/tests/integration/input_use_cases/7/camp_data/config.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json", - "camp_data/mechanism.json" - ] -} diff --git a/tests/integration/input_use_cases/7/camp_data/mechanism.json b/tests/integration/input_use_cases/7/camp_data/mechanism.json deleted file mode 100644 index bc6b69de..00000000 --- a/tests/integration/input_use_cases/7/camp_data/mechanism.json +++ /dev/null @@ -1,135 +0,0 @@ -{ - "camp-data" : [ - { - "name" : "Chapman", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O2" : { } - }, - "products" : { - "O" : { "yield" : 2.0 } - }, - "MUSICA name" : "O2_1" - }, - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O3" : { } - }, - "products" : { - "O1D" : { }, - "O2" : { } - }, - "MUSICA name" : "O3_1" - }, - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O3" : { } - }, - "products" : { - "O" : { }, - "O2" : { } - }, - "MUSICA name" : "O3_2" - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O1D" : { }, - "N2" : { } - }, - "products" : { - "O" : { }, - "N2" : { } - }, - "A" : 2.15e-11, - "C" : 110.0 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O1D" : { }, - "O2" : { } - }, - "products" : { - "O" : { }, - "O2" : { } - }, - "A" : 3.3e-11, - "C" : 55.0 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O" : { }, - "O3" : { } - }, - "products" : { - "O2" : { "yield" : 2.0 } - }, - "A" : 8.0e-12, - "C" : -2060.00 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O" : { }, - "O2" : { }, - "M" : { } - }, - "products" : { - "O3" : { }, - "M" : { } - }, - "A" : 6.0e-34, - "B" : 2.4 - }, - { - "type" : "EMISSION", - "species" : "O1D", - "MUSICA name" : "O1D" - }, - { - "type" : "EMISSION", - "species" : "O", - "MUSICA name" : "O" - }, - { - "type" : "EMISSION", - "species" : "O3", - "MUSICA name" : "O3" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "N2", - "MUSICA name" : "N2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "O2", - "MUSICA name" : "O2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "CO2", - "MUSICA name" : "CO2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "Ar", - "MUSICA name" : "Ar" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "H2O", - "MUSICA name" : "H2O" - } - ] - } - ] -} - diff --git a/tests/integration/input_use_cases/7/camp_data/species.json b/tests/integration/input_use_cases/7/camp_data/species.json deleted file mode 100644 index 948aca00..00000000 --- a/tests/integration/input_use_cases/7/camp_data/species.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - } - ] -} - diff --git a/tests/integration/input_use_cases/7/config_camp.json b/tests/integration/input_use_cases/7/config_camp.json deleted file mode 100644 index 6cd6ef43..00000000 --- a/tests/integration/input_use_cases/7/config_camp.json +++ /dev/null @@ -1,83 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5, - "simulation start" : { - "time zone" : "UTC-8", - "year" : 2020, - "month" : 6, - "day" : 10, - "hour" : 13 - } - }, - "initial conditions" : { - "initial.csv" : { - "delimiter" : "&" - } - }, - "evolving conditions" : { - "emissions.csv" : { - "properties" : { - "time.hr" : { - "shift first entry to" :{ - "time zone" : "UTC-8", - "year" : 2020, - "month" : 6, - "day" : 10, - "hour" : 13 - } - } - } - }, - "wall_loss_rates_011519.txt" : { - "delimiter" : ";", - "time axis" : "columns", - "properties" : { - "simtime" : { - "MusicBox name" : "time", - "units" : "hr", - "shift first entry to" :{ - "time zone" : "UTC-8", - "year" : 2020, - "month" : 6, - "day" : 10, - "hour" : 13 - } - }, - "*" : { - "MusicBox name" : "LOSS.*", - "units" : "min-1" - } - } - }, - "parking_lot_photo_rates.nc" : { - "time offset" : { "years" : 15 }, - "properties" : { - "*" : { "MusicBox name" : "PHOT.*" }, - "time" : { - "MusicBox name" : "time", - "shift first entry to" : { - "year" : 2020, - "month" : 1, - "day" : 1, - "time zone" : "UTC-8" - } - } - } - } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] -} diff --git a/tests/integration/input_use_cases/7/emissions.csv b/tests/integration/input_use_cases/7/emissions.csv deleted file mode 100644 index 2553005b..00000000 --- a/tests/integration/input_use_cases/7/emissions.csv +++ /dev/null @@ -1,5 +0,0 @@ -time.hr, EMIS.O1D, EMIS.O, EMIS.O3 -0.0, 0.0, 0.0, 0.0 -0.2, 0.1, 0.05, 0.05 -1.0, 0.2, 0.1, 0.1 -1.5, 0.0, 0.0, 0.0 diff --git a/tests/integration/input_use_cases/7/etc/gen_netcdf b/tests/integration/input_use_cases/7/etc/gen_netcdf deleted file mode 100755 index 537cb180..00000000 Binary files a/tests/integration/input_use_cases/7/etc/gen_netcdf and /dev/null differ diff --git a/tests/integration/input_use_cases/7/etc/parking_lot_photo_rates.c b/tests/integration/input_use_cases/7/etc/parking_lot_photo_rates.c deleted file mode 100644 index b037c455..00000000 --- a/tests/integration/input_use_cases/7/etc/parking_lot_photo_rates.c +++ /dev/null @@ -1,171 +0,0 @@ -#include -#include -#include -#include - -typedef enum {false, true} bool; - -void -check_err(const int stat, const int line, const char *file) { - if (stat != NC_NOERR) { - (void)fprintf(stderr,"line %d of %s: %s\n", line, file, nc_strerror(stat)); - fflush(stderr); - exit(1); - } -} - -int -get_month_in_days( const int months, const bool is_leap_year ) { - int days[12] = {31,28,31,30,31,30,31,31,30,31,30,31}; - if( is_leap_year ) { - days[1] = 29; - } - int ret_val = 0; - for(int m = months-1; m >= 0; --m) ret_val += days[m]; - return ret_val; -} - -double -get_time_in_seconds(const int year, const int month, const int day, - const double hours, const double minutes, const double seconds) { - int leap_years = (year-1) / 4 - (year-1) / 100 + (year-1) / 400; - bool is_leap_year = year % 4 == 0 && ( year % 100 != 0 || year % 400 == 0 ); - int days_to_year = ( ( year-1 - leap_years ) * 365 + leap_years * 366 ); - double s = (double)days_to_year * 24.0 * 60.0 * 60.0 + - ( ( ( (double)( get_month_in_days( month-1, is_leap_year ) + day-1 ) * 24.0 + - hours ) * 60.0 + minutes ) * 60.0 + seconds ); - return s; -} - -int -main() {/* create parking_lot_photo_rates.nc */ - - int stat; /* return status */ - int ncid; /* netCDF id */ - - /* dimension ids */ - int time_dim; - - /* dimension lengths */ - size_t time_len = NC_UNLIMITED; - - /* variable ids */ - int time_id; - int O3_1_id; - int O3_2_id; - int O2_1_id; - - /* rank (number of dimensions) for each variable */ -# define RANK_time 1 -# define RANK_O3_1 1 -# define RANK_O3_2 1 -# define RANK_O2_1 1 - - /* variable shapes */ - int time_dims[RANK_time]; - int O3_1_dims[RANK_O3_1]; - int O3_2_dims[RANK_O3_2]; - int O2_1_dims[RANK_O2_1]; - - /* enter define mode */ - stat = nc_create("parking_lot_photo_rates.nc", NC_CLOBBER, &ncid); - check_err(stat,__LINE__,__FILE__); - - /* define dimensions */ - stat = nc_def_dim(ncid, "time", time_len, &time_dim); - check_err(stat,__LINE__,__FILE__); - - /* define variables */ - - time_dims[0] = time_dim; - stat = nc_def_var(ncid, "time", NC_DOUBLE, RANK_time, time_dims, &time_id); - check_err(stat,__LINE__,__FILE__); - - O3_1_dims[0] = time_dim; - stat = nc_def_var(ncid, "O3_1", NC_DOUBLE, RANK_O3_1, O3_1_dims, &O3_1_id); - check_err(stat,__LINE__,__FILE__); - - O3_2_dims[0] = time_dim; - stat = nc_def_var(ncid, "O3_2", NC_DOUBLE, RANK_O3_2, O3_2_dims, &O3_2_id); - check_err(stat,__LINE__,__FILE__); - - O2_1_dims[0] = time_dim; - stat = nc_def_var(ncid, "O2_1", NC_DOUBLE, RANK_O2_1, O2_1_dims, &O2_1_id); - check_err(stat,__LINE__,__FILE__); - - /* assign per-variable attributes */ - - { - stat = nc_put_att_text(ncid, time_id, "units", 5, "hours"); - check_err(stat,__LINE__,__FILE__); - } - - { - stat = nc_put_att_text(ncid, O3_1_id, "units", 3, "s-1"); - check_err(stat,__LINE__,__FILE__); - } - - { - stat = nc_put_att_text(ncid, O3_2_id, "units", 3, "s-1"); - check_err(stat,__LINE__,__FILE__); - } - - { - stat = nc_put_att_text(ncid, O2_1_id, "units", 3, "s-1"); - check_err(stat,__LINE__,__FILE__); - } - - - /* leave define mode */ - stat = nc_enddef (ncid); - check_err(stat,__LINE__,__FILE__); - - /* assign variable data */ - double ref_time = get_time_in_seconds( 1, 1, 1, 0.0, 0.0, 0.0 ); - - /* the start date is set for 6/11 because 2020 is a leap year - * and 2005 is not */ - double data_set_start_time = get_time_in_seconds( 2005, 1, 1, 0.0-8.0, 0.0, 0.0 ) - ref_time; - double sim_time_start = get_time_in_seconds( 2005, 6, 11, 13.0-8.0, 0.0, 0.0 ) - ref_time; - double sim_time_stop = get_time_in_seconds( 2005, 6, 11, 15.0-8.0, 30.0, 0.0 ) - ref_time; - data_set_start_time /= 3600.0; - sim_time_start /= 3600.0; - sim_time_stop /= 3600.0; - double O3_1 = 1.0e-4; - double O3_2 = 2.0e-4; - double O2_1 = 3.0e-4; - double timea[1]; - double O3_1a[1]; - double O3_2a[1]; - double O2_1a[1]; - size_t start[1] = {0}; - size_t count[1] = {1}; - for(int i_hour = 0; i_hour <= 365 * 24; ++i_hour) { - timea[0] = data_set_start_time + i_hour; - if( timea[0] >= sim_time_start - 1.0e-10 && timea[0] <= sim_time_stop + 1.0e-10 ) { - O3_1a[0] = O3_1; - O3_2a[0] = O3_2; - O2_1a[0] = O2_1; - O3_1 += 1.0e-5; - O3_2 += 2.0e-5; - O2_1 += 3.0e-5; - } else { - O3_1a[0] = i_hour; - O3_2a[0] = 0.0; - O2_1a[0] = 0.0; - } - stat = nc_put_vara_double(ncid, time_id, start, count, timea ); - check_err(stat,__LINE__,__FILE__); - stat = nc_put_vara_double(ncid, O3_1_id, start, count, O3_1a ); - check_err(stat,__LINE__,__FILE__); - stat = nc_put_vara_double(ncid, O3_2_id, start, count, O3_2a ); - check_err(stat,__LINE__,__FILE__); - stat = nc_put_vara_double(ncid, O2_1_id, start, count, O2_1a ); - check_err(stat,__LINE__,__FILE__); - start[0] += 1; - } - - stat = nc_close(ncid); - check_err(stat,__LINE__,__FILE__); - return 0; -} diff --git a/tests/integration/input_use_cases/7/etc/parking_lot_photo_rates.cdl b/tests/integration/input_use_cases/7/etc/parking_lot_photo_rates.cdl deleted file mode 100644 index 4f06bfc7..00000000 --- a/tests/integration/input_use_cases/7/etc/parking_lot_photo_rates.cdl +++ /dev/null @@ -1,17 +0,0 @@ -netcdf parking_lot_photo_rates { - -dimensions: -time = unlimited; - -variables: - double time(time); - double O3_1(time); - double O3_2(time); - double O2_1(time); - - time:units = "hours"; - O3_1:units = "s-1"; - O3_2:units = "s-1"; - O2_1:units = "s-1"; - -} diff --git a/tests/integration/input_use_cases/7/expected_output.csv b/tests/integration/input_use_cases/7/expected_output.csv deleted file mode 100644 index 1c44ce72..00000000 --- a/tests/integration/input_use_cases/7/expected_output.csv +++ /dev/null @@ -1,37 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.63727390800000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000001510E+00, 0.16899999999999998357E-01, 0.00000000000000000000E+00, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.00000000000000000000E+00 - 0.63727391100000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.36367544664079271000E+00, 0.16075777274062060668E-01, 0.00000000000000000000E+00, 0.31295448066073483062E+02, 0.16268109841546828619E-12, 0.67976154626620338714E-07, 0.64312340717882685581E+01, 0.12719164596013519120E+01 - 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0.63727398600000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39735823528814689931E-01, 0.29328446950571658916E-02, 0.37947128607785954521E-64, 0.57095023945195730875E+01, 0.55406793691688845993E-11, 0.79506392908712897084E-07, 0.22799695975908906576E+03, 0.25654889006292512477E+03 - 0.63727398900000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.36139475415135159653E-01, 0.27211579712260415206E-02, 0.37942886064194041572E-64, 0.52974022043394519699E+01, 0.55294340654125418318E-11, 0.79511114110032127252E-07, 0.22046485579965286661E+03, 0.24737690757089751514E+03 - 0.63727399200000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.32863197571629525207E-01, 0.25245054264221157385E-02, 0.37939205087353324540E-64, 0.49145697354608053331E+01, 0.55244637145818247716E-11, 0.79513858789337464381E-07, 0.21301021790530782596E+03, 0.23862148177152550943E+03 - 0.63727399500000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.29884134982723933177E-01, 0.23420741626765974319E-02, 0.37939360632807407296E-64, 0.45594224823704179173E+01, 0.55232541042303990181E-11, 0.79515399003763220921E-07, 0.20570908358117856096E+03, 0.23023133577302496633E+03 - 0.63727399800000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.27174486024428585323E-01, 0.21727990661423697907E-02, 0.37938887884192820172E-64, 0.42298869394132525557E+01, 0.55240798406226083592E-11, 0.79516268204057901503E-07, 0.19860500798342317808E+03, 0.22216536940507728559E+03 diff --git a/tests/integration/input_use_cases/7/initial.csv b/tests/integration/input_use_cases/7/initial.csv deleted file mode 100644 index 2af07f8d..00000000 --- a/tests/integration/input_use_cases/7/initial.csv +++ /dev/null @@ -1,2 +0,0 @@ -CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& ENV.temperature& ENV.pressure.atm -3.29e1& 8.84& 3.92e-1& 1.69e-2& 298.0& 1.0 diff --git a/tests/integration/input_use_cases/7/parking_lot_photo_rates.nc b/tests/integration/input_use_cases/7/parking_lot_photo_rates.nc deleted file mode 100644 index fd3ba0f2..00000000 Binary files a/tests/integration/input_use_cases/7/parking_lot_photo_rates.nc and /dev/null differ diff --git a/tests/integration/input_use_cases/7/run_camp.sh b/tests/integration/input_use_cases/7/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/7/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/7/run_preprocessed_data.sh b/tests/integration/input_use_cases/7/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/7/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/7/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/7/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/7/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/7/run_preprocessor_camp.sh b/tests/integration/input_use_cases/7/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/7/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/7/wall_loss_rates_011519.txt b/tests/integration/input_use_cases/7/wall_loss_rates_011519.txt deleted file mode 100644 index fa5182fa..00000000 --- a/tests/integration/input_use_cases/7/wall_loss_rates_011519.txt +++ /dev/null @@ -1,6 +0,0 @@ -simtime; 0.0; 0.3; 0.6; 0.9; 1.2 -N2; 0.010; 0.012; 0.013; 0.014; 0.015 -O2; 0.015; 0.016; 0.017; 0.018; 0.019 -Ar; 0.015; 0.016; 0.017; 0.018; 0.019 -CO2; 0.010; 0.012; 0.013; 0.014; 0.015 -H2O; 0.010; 0.012; 0.013; 0.014; 0.015 diff --git a/tests/integration/input_use_cases/8/camp_data/config.json b/tests/integration/input_use_cases/8/camp_data/config.json deleted file mode 100644 index 4629149f..00000000 --- a/tests/integration/input_use_cases/8/camp_data/config.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json", - "camp_data/mechanism.json" - ] -} diff --git a/tests/integration/input_use_cases/8/camp_data/mechanism.json b/tests/integration/input_use_cases/8/camp_data/mechanism.json deleted file mode 100644 index d3a78ae3..00000000 --- a/tests/integration/input_use_cases/8/camp_data/mechanism.json +++ /dev/null @@ -1,66 +0,0 @@ -{ - "camp-data" : [ - { - "name" : "Chapman", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "EMISSION", - "species" : "O1D", - "MUSICA name" : "O1D" - }, - { - "type" : "EMISSION", - "species" : "O", - "MUSICA name" : "O" - }, - { - "type" : "EMISSION", - "species" : "O3", - "MUSICA name" : "O3" - }, - { - "type" : "EMISSION", - "species" : "N2", - "MUSICA name" : "N2" - }, - { - "type" : "EMISSION", - "species" : "Ar", - "MUSICA name" : "Ar" - }, - { - "type" : "EMISSION", - "species" : "O2", - "MUSICA name" : "O2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "N2", - "MUSICA name" : "N2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "O2", - "MUSICA name" : "O2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "CO2", - "MUSICA name" : "CO2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "Ar", - "MUSICA name" : "Ar" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "H2O", - "MUSICA name" : "H2O" - } - ] - } - ] -} - diff --git a/tests/integration/input_use_cases/8/camp_data/species.json b/tests/integration/input_use_cases/8/camp_data/species.json deleted file mode 100644 index 948aca00..00000000 --- a/tests/integration/input_use_cases/8/camp_data/species.json +++ /dev/null @@ -1,54 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - } - ] -} - diff --git a/tests/integration/input_use_cases/8/config_b_camp.json b/tests/integration/input_use_cases/8/config_b_camp.json deleted file mode 100644 index 4935c0dc..00000000 --- a/tests/integration/input_use_cases/8/config_b_camp.json +++ /dev/null @@ -1,52 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [s]" : 1.0, - "output time step [s]" : 10.0, - "simulation length [s]" : 50.0 - }, - "initial conditions" : { - "init_O_O1D_O3.csv" : { - "properties" : { - "CONC.O3" : { "variability" : "tethered" } - }, - "linear combinations" : { - "atomic oxygen" : { - "properties" : { - "CONC.O" : { }, - "CONC.O1D" : { } - } - } - } - } - }, - "environmental conditions" : { - "temperature" : { "initial value [K]" : 298.15 }, - "pressure" : { "initial value [atm]" : 1.0 } - }, - "evolving conditions" : { - "evo_N2_Ar_O2.csv" : { - "linear combinations" : { - "N2 Ar" : { - "properties" : { - "CONC.N2" : { }, - "CONC.Ar" : { } - } - } - } - }, - "emit_all.csv" : { } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] -} diff --git a/tests/integration/input_use_cases/8/config_camp.json b/tests/integration/input_use_cases/8/config_camp.json deleted file mode 100644 index 77c4a885..00000000 --- a/tests/integration/input_use_cases/8/config_camp.json +++ /dev/null @@ -1,95 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5, - "simulation start" : { - "time zone" : "UTC-8", - "year" : 2020, - "month" : 6, - "day" : 10, - "hour" : 13 - } - }, - "initial conditions" : { - "initial.csv" : { - "delimiter" : "&", - "properties" : { - "CONC.O3" : { "variability" : "tethered" } - }, - "linear combinations" : { - "atomic oxygen" : { - "properties" : { - "CONC.O" : { }, - "CONC.O1D" : { } - }, - "scale factor" : 1.2 - } - } - } - }, - "evolving conditions" : { - "emissions.csv" : { - "properties" : { - "time.hr" : { - "shift first entry to" :{ - "time zone" : "UTC-8", - "year" : 2020, - "month" : 6, - "day" : 10, - "hour" : 13 - } - } - } - }, - "wall_loss_rates_011519.txt" : { - "delimiter" : ";", - "time axis" : "columns", - "properties" : { - "simtime" : { - "MusicBox name" : "time", - "units" : "hr", - "shift first entry to" :{ - "time zone" : "UTC-8", - "year" : 2020, - "month" : 6, - "day" : 10, - "hour" : 13 - } - }, - "*" : { - "MusicBox name" : "LOSS.*", - "units" : "min-1" - } - } - }, - "parking_lot_photo_rates.nc" : { - "time offset" : { "years" : 15 }, - "properties" : { - "*" : { "MusicBox name" : "PHOT.*" }, - "time" : { - "MusicBox name" : "time", - "shift first entry to" : { - "year" : 2020, - "month" : 1, - "day" : 1, - "time zone" : "UTC-8" - } - } - } - } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] -} diff --git a/tests/integration/input_use_cases/8/emissions.csv b/tests/integration/input_use_cases/8/emissions.csv deleted file mode 100644 index 2553005b..00000000 --- a/tests/integration/input_use_cases/8/emissions.csv +++ /dev/null @@ -1,5 +0,0 @@ -time.hr, EMIS.O1D, EMIS.O, EMIS.O3 -0.0, 0.0, 0.0, 0.0 -0.2, 0.1, 0.05, 0.05 -1.0, 0.2, 0.1, 0.1 -1.5, 0.0, 0.0, 0.0 diff --git a/tests/integration/input_use_cases/8/emit_all.csv b/tests/integration/input_use_cases/8/emit_all.csv deleted file mode 100644 index 0f4445c6..00000000 --- a/tests/integration/input_use_cases/8/emit_all.csv +++ /dev/null @@ -1,4 +0,0 @@ -time, EMIS.O, EMIS.O1D, EMIS.O3, EMIS.N2, EMIS.Ar, EMIS.O2 -0, 1.0, 2.0, 3.0, 1.0, 2.0, 3.0 -20.0, 2.0, 1.0, 1.0, 2.0, 1.0, 1.0 -30.0, 1.0, 2.0, 3.0, 1.0, 2.0, 3.0 diff --git a/tests/integration/input_use_cases/8/evo_N2_Ar_O2.csv b/tests/integration/input_use_cases/8/evo_N2_Ar_O2.csv deleted file mode 100644 index 36a91614..00000000 --- a/tests/integration/input_use_cases/8/evo_N2_Ar_O2.csv +++ /dev/null @@ -1,4 +0,0 @@ -time, CONC.N2, CONC.Ar, CONC.O2 -0, 1.0, 2.0, 3.0 -20.0, 20.0, 10.0, 30.0 -30.0, 1.0, 2.0, 3.0 diff --git a/tests/integration/input_use_cases/8/expected_b_output.csv b/tests/integration/input_use_cases/8/expected_b_output.csv deleted file mode 100644 index 195f0f13..00000000 --- a/tests/integration/input_use_cases/8/expected_b_output.csv +++ /dev/null @@ -1,7 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.20000000000000000000E+01, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.10000000000000000000E+01, 0.20000000000000000000E+01, 0.10000000000000000000E+01, 0.30000000000000000000E+01, 0.30000000000000000000E+01 - 0.10000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.22000000000000000000E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.11000000000000000000E+02, 0.40000000000000000000E+01, 0.20000000000000000000E+01, 0.33000000000000000000E+02, 0.60000000000000000000E+01 - 0.20000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.42000000000000000000E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.21000000000000000000E+02, 0.40000000000000000000E+01, 0.20000000000000000000E+01, 0.63000000000000000000E+02, 0.60000000000000000000E+01 - 0.30000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.30000000000000000000E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.30000000000000000000E+02, 0.20019531250000000000E+01, 0.39980468750000000000E+01, 0.40000000000000000000E+02, 0.40000000000000000000E+01 - 0.40000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.21500000000000000000E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.11500000000000000000E+02, 0.39980487823486328125E+01, 0.20019512176513671875E+01, 0.33000000000000000000E+02, 0.60000000000000000000E+01 - 0.50000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.41500000000000000000E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.21500000000000000000E+02, 0.39999980945140123367E+01, 0.20000019054859876633E+01, 0.63000000000000000000E+02, 0.60000000000000000000E+01 diff --git a/tests/integration/input_use_cases/8/expected_b_output_camp.csv b/tests/integration/input_use_cases/8/expected_b_output_camp.csv deleted file mode 100644 index 799a430d..00000000 --- a/tests/integration/input_use_cases/8/expected_b_output_camp.csv +++ /dev/null @@ -1,7 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 0.00000000000000000000E+00, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.20000000000000000000E+01, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.10000000000000000000E+01, 0.20000000000000000000E+01, 0.10000000000000000000E+01, 0.30000000000000000000E+01, 0.30000000000000000000E+01 - 0.10000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.22000000000000000000E+02, 0.40873998402304409287E-64, 0.40873998402304409287E-64, 0.11000000000000000000E+02, 0.39999999999999995559E+01, 0.19999999999999997780E+01, 0.32999999999999985789E+02, 0.60000000000000000000E+01 - 0.20000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.41999999999999957367E+02, 0.40873998402304409287E-64, 0.40873998402304409287E-64, 0.20999999999999978684E+02, 0.39999999999999995559E+01, 0.19999999999999997780E+01, 0.62999999999999957367E+02, 0.60000000000000000000E+01 - 0.30000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.30000000000000014211E+02, 0.40873998402304409287E-64, 0.40873998402304409287E-64, 0.29999999999999992895E+02, 0.20019531249999995559E+01, 0.39980468750000000000E+01, 0.39999999999999992895E+02, 0.39999999999999995559E+01 - 0.40000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.21500000000000003553E+02, 0.40873998402304409287E-64, 0.40873998402304409287E-64, 0.11499999999999998224E+02, 0.39980487823486323684E+01, 0.20019512176513671875E+01, 0.32999999999999985789E+02, 0.60000000000000000000E+01 - 0.50000000000000000000E+02, 0.29814999999999997726E+03, 0.10132500000000000000E+06, 0.40873998402304408728E+02, 0.41499999999999971578E+02, 0.40873998402304409287E-64, 0.40873998402304409287E-64, 0.21499999999999971578E+02, 0.39999980945140118926E+01, 0.20000019054859876633E+01, 0.62999999999999957367E+02, 0.60000000000000000000E+01 diff --git a/tests/integration/input_use_cases/8/expected_output.csv b/tests/integration/input_use_cases/8/expected_output.csv deleted file mode 100644 index b7df049b..00000000 --- a/tests/integration/input_use_cases/8/expected_output.csv +++ /dev/null @@ -1,37 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3 - 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-# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_b.json" -comp_str="../../../../compare_results output.csv expected_b_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_b_camp.sh b/tests/integration/input_use_cases/8/run_b_camp.sh deleted file mode 100755 index 8184d7b9..00000000 --- a/tests/integration/input_use_cases/8/run_b_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_b_camp.json" -comp_str="../../../../compare_results output.csv expected_b_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_b_preprocessed_data.sh b/tests/integration/input_use_cases/8/run_b_preprocessed_data.sh deleted file mode 100755 index 73ac80e2..00000000 --- a/tests/integration/input_use_cases/8/run_b_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_b_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_b_preprocessed_data_camp.sh b/tests/integration/input_use_cases/8/run_b_preprocessed_data_camp.sh deleted file mode 100755 index 7f4a21da..00000000 --- a/tests/integration/input_use_cases/8/run_b_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_b_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_b_preprocessor.sh b/tests/integration/input_use_cases/8/run_b_preprocessor.sh deleted file mode 100755 index 054f42c5..00000000 --- a/tests/integration/input_use_cases/8/run_b_preprocessor.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_b.json" -exec_str2="./run_b_preprocessed_data.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_b_preprocessor_camp.sh b/tests/integration/input_use_cases/8/run_b_preprocessor_camp.sh deleted file mode 100755 index 1e7abf03..00000000 --- a/tests/integration/input_use_cases/8/run_b_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_b_camp.json" -exec_str2="./run_b_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_camp.sh b/tests/integration/input_use_cases/8/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/8/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_preprocessed_data.sh b/tests/integration/input_use_cases/8/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/8/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/8/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/8/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/8/run_preprocessor_camp.sh b/tests/integration/input_use_cases/8/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/8/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/integration/input_use_cases/8/wall_loss_rates_011519.txt b/tests/integration/input_use_cases/8/wall_loss_rates_011519.txt deleted file mode 100644 index fa5182fa..00000000 --- a/tests/integration/input_use_cases/8/wall_loss_rates_011519.txt +++ /dev/null @@ -1,6 +0,0 @@ -simtime; 0.0; 0.3; 0.6; 0.9; 1.2 -N2; 0.010; 0.012; 0.013; 0.014; 0.015 -O2; 0.015; 0.016; 0.017; 0.018; 0.019 -Ar; 0.015; 0.016; 0.017; 0.018; 0.019 -CO2; 0.010; 0.012; 0.013; 0.014; 0.015 -H2O; 0.010; 0.012; 0.013; 0.014; 0.015 diff --git a/tests/integration/input_use_cases/9/camp_data/config.json b/tests/integration/input_use_cases/9/camp_data/config.json deleted file mode 100644 index 4629149f..00000000 --- a/tests/integration/input_use_cases/9/camp_data/config.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "camp-files" : [ - "camp_data/species.json", - "camp_data/mechanism.json" - ] -} diff --git a/tests/integration/input_use_cases/9/camp_data/mechanism.json b/tests/integration/input_use_cases/9/camp_data/mechanism.json deleted file mode 100644 index 8149c85d..00000000 --- a/tests/integration/input_use_cases/9/camp_data/mechanism.json +++ /dev/null @@ -1,163 +0,0 @@ -{ - "camp-data" : [ - { - "name" : "Chapman", - "type" : "MECHANISM", - "reactions" : [ - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O2" : { } - }, - "products" : { - "O" : { "yield" : 2.0 } - }, - "MUSICA name" : "O2_1" - }, - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O3" : { } - }, - "products" : { - "O1D" : { }, - "O2" : { } - }, - "MUSICA name" : "O3_1" - }, - { - "type" : "PHOTOLYSIS", - "reactants" : { - "O3" : { } - }, - "products" : { - "O" : { }, - "O2" : { } - }, - "MUSICA name" : "O3_2" - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O1D" : { }, - "N2" : { } - }, - "products" : { - "O" : { }, - "N2" : { } - }, - "A" : 2.15e-11, - "C" : 110.0 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O1D" : { }, - "O2" : { } - }, - "products" : { - "O" : { }, - "O2" : { } - }, - "A" : 3.3e-11, - "C" : 55.0 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O" : { }, - "O3" : { } - }, - "products" : { - "O2" : { "yield" : 2.0 } - }, - "A" : 8.0e-12, - "C" : -2060.00 - }, - { - "type" : "ARRHENIUS", - "reactants" : { - "O" : { }, - "O2" : { }, - "M" : { } - }, - "products" : { - "O3" : { }, - "M" : { } - }, - "A" : 6.0e-34, - "B" : 2.4 - }, - { - "type" : "EMISSION", - "species" : "O1D", - "MUSICA name" : "O1D" - }, - { - "type" : "EMISSION", - "species" : "O", - "MUSICA name" : "O" - }, - { - "type" : "EMISSION", - "species" : "O3", - "MUSICA name" : "O3" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "N2", - "MUSICA name" : "N2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "O2", - "MUSICA name" : "O2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "CO2", - "MUSICA name" : "CO2" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "Ar", - "MUSICA name" : "Ar" - }, - { - "type" : "FIRST_ORDER_LOSS", - "species" : "H2O", - "MUSICA name" : "H2O" - } - ] - }, - { - "name" : "droplet phase", - "type" : "AERO_PHASE", - "species" : ["aH2O"] - }, - { - "type" : "AERO_REP_MODAL_BINNED_MASS", - "name" : "cloud", - "modes/bins" : - { - "single phase mode" : - { - "type" : "MODAL", - "phases" : [ "droplet phase" ], - "shape" : "LOG_NORMAL", - "geometric mean diameter" : 2.5e-8, - "geometric standard deviation" : 1.2 - }, - "binned aerosol" : - { - "type" : "BINNED", - "phases" : [ "droplet phase" ], - "bins" : 1, - "minimum diameter [m]" : 8.0e-9, - "maximum diameter [m]" : 1.0e-6, - "scale" : "LOG" - } - } - } - ] -} diff --git a/tests/integration/input_use_cases/9/camp_data/species.json b/tests/integration/input_use_cases/9/camp_data/species.json deleted file mode 100644 index 4cc07e3e..00000000 --- a/tests/integration/input_use_cases/9/camp_data/species.json +++ /dev/null @@ -1,61 +0,0 @@ -{ - "camp-data" : [ - { - "type" : "RELATIVE_TOLERANCE", - "value" : 1.0e-4 - }, - { - "name" : "M", - "type" : "CHEM_SPEC", - "tracer type" : "CONSTANT" - }, - { - "name" : "Ar", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "CO2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "H2O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "N2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O1D", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O2", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "O3", - "type" : "CHEM_SPEC", - "absolute tolerance" : 1.0e-12 - }, - { - "name" : "aH2O", - "type" : "CHEM_SPEC", - "phase" : "AEROSOL", - "molecular weight [kg mol-1]" : 18.02, - "density [kg m-3]" : 997 - } - ] -} - diff --git a/tests/integration/input_use_cases/9/config_camp.json b/tests/integration/input_use_cases/9/config_camp.json deleted file mode 100644 index 21c58a94..00000000 --- a/tests/integration/input_use_cases/9/config_camp.json +++ /dev/null @@ -1,32 +0,0 @@ -{ - "box model options" : { - "grid" : "box", - "chemistry time step [min]" : 5.0, - "output time step [hr]" : 1.0, - "simulation length [hr]" : 2.5, - "simulation start" : { - "time zone" : "UTC-8", - "year" : 2020, - "month" : 6, - "day" : 10, - "hour" : 13 - } - }, - "initial conditions" : { - "initial.csv" : { - "delimiter" : "&" - } - }, - "model components" : [ - { - "type" : "CAMP", - "configuration file" : "camp_data/config.json", - "override species" : { - "M" : { "mixing ratio mol mol-1" : 1.0 } - }, - "suppress output" : { - "M" : { } - } - } - ] -} diff --git a/tests/integration/input_use_cases/9/expected_output.csv b/tests/integration/input_use_cases/9/expected_output.csv deleted file mode 100644 index 278329bc..00000000 --- a/tests/integration/input_use_cases/9/expected_output.csv +++ /dev/null @@ -1,32 +0,0 @@ -time, ENV.temperature, ENV.pressure, ENV.number_density_air, CONC.Ar, CONC.CO2, CONC.H2O, CONC.N2, CONC.O1D, CONC.O, CONC.O2, CONC.O3, CONC.single phase mode.droplet phase.aH2O, CONC.binned aerosol.droplet phase.aH2O - 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0.63727397400000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.57906342992829510054E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 - 0.63727397700000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.60536590648730023545E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 - 0.63727398000000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.63166838304630528400E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 - 0.63727398300000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.65797085960531041891E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 - 0.63727398600000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.68427333616431564018E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 - 0.63727398900000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.71057581272332068873E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 - 0.63727399200000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.73687828928232582363E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 - 0.63727399500000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.76318076584133095854E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 - 0.63727399800000000000E+11, 0.29800000000000000000E+03, 0.10132500000000000000E+06, 0.40894572562574019514E+02, 0.39200000000000007061E+00, 0.16899999999999998357E-01, 0.40894572562574022296E-64, 0.32899999999999998579E+02, 0.00000000000000000000E+00, 0.00000000000000000000E+00, 0.88399999999999998579E+01, 0.78948324240033600709E-61, 0.14999999999999991118E+01, 0.50999999999999996447E+01 diff --git a/tests/integration/input_use_cases/9/initial.csv b/tests/integration/input_use_cases/9/initial.csv deleted file mode 100644 index 89b6e8a4..00000000 --- a/tests/integration/input_use_cases/9/initial.csv +++ /dev/null @@ -1,2 +0,0 @@ -CONC.N2& CONC.O2& CONC.Ar& CONC.CO2& ENV.temperature& ENV.pressure.atm&CONC.single phase mode.droplet phase.aH2O&CONC.binned aerosol.droplet phase.aH2O -3.29e1& 8.84& 3.92e-1& 1.69e-2& 298.0& 1.0& 1.5& 5.1 diff --git a/tests/integration/input_use_cases/9/run_camp.sh b/tests/integration/input_use_cases/9/run_camp.sh deleted file mode 100755 index 84594919..00000000 --- a/tests/integration/input_use_cases/9/run_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box config_camp.json" -comp_str="../../../../compare_results output.csv expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/9/run_preprocessed_data.sh b/tests/integration/input_use_cases/9/run_preprocessed_data.sh deleted file mode 100755 index c06ee85e..00000000 --- a/tests/integration/input_use_cases/9/run_preprocessed_data.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/9/run_preprocessed_data_camp.sh b/tests/integration/input_use_cases/9/run_preprocessed_data_camp.sh deleted file mode 100755 index a1062f8c..00000000 --- a/tests/integration/input_use_cases/9/run_preprocessed_data_camp.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd "${0%/*}/preprocessor_output" - -exec_str="../../../../../music_box config.json" -comp_str="../../../../../compare_results output.csv ../expected_output_camp.csv 1.0e-3 1.0e-12" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if $comp_str; then - echo PASS - exit 0 - else - echo unexpected results - echo FAIL - exit 1 - fi -fi diff --git a/tests/integration/input_use_cases/9/run_preprocessor_camp.sh b/tests/integration/input_use_cases/9/run_preprocessor_camp.sh deleted file mode 100755 index ded7c39b..00000000 --- a/tests/integration/input_use_cases/9/run_preprocessor_camp.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# exit on error -set -e -# turn on command echoing -set -v -# make sure that the current directory is the once where this script is -cd ${0%/*} - -exec_str="../../../../music_box --preprocess-only config_camp.json" -exec_str2="./run_preprocessed_data_camp.sh" - -if ! $exec_str; then - echo FAIL - exit 1 -else - if ! $exec_str2; then - echo FAIL - exit 1 - else - echo PASS - exit 0 - fi -fi diff --git a/tests/test_chapman.py b/tests/test_chapman.py index d73d0435..58e06175 100644 --- a/tests/test_chapman.py +++ b/tests/test_chapman.py @@ -55,7 +55,7 @@ def test_run(self): float(test_output_concs[i][j]), rel_tol=1e-8, abs_tol=1e-15, - ), f"Arrays differ at index ({i}, {j}) for " + ), f"Arrays differ at index ({i}, {j}) for species {concs_to_test[j]}" if __name__ == "__main__": diff --git a/tests/test_wall_loss.py b/tests/test_wall_loss.py index c93b62c7..f269054b 100644 --- a/tests/test_wall_loss.py +++ b/tests/test_wall_loss.py @@ -46,7 +46,8 @@ def test_run(self): float(model_output_concs[i][j]), float(test_output_concs[i][j]), rel_tol=1e-8, - ), f"Arrays differ at index ({i}, {j}) for " + abs_tol=1e-8, + ), f"Arrays differ at index ({i}, {j}) for species {concs_to_test[j]}" if __name__ == "__main__":