musica 0.12.0__cp311-cp311-win32.whl → 0.12.2__cp311-cp311-win32.whl

{musica-0.12.0.dist-info → musica-0.12.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: musica
-Version: 0.12.0
+Version: 0.12.2
 Summary: MUSICA is a Python library for performing computational simulations in atmospheric chemistry.
 Author-Email: Matthew Dawsom <mattdawson@ucar.edu>, Jiwon Gim <jiwongim@ucar.edu>, David Fillmore <fillmore@ucar.edu>, Kyle Shores <kshores@ucar.edu>, Montek Thind <mthind@ucar.edu>
 Maintainer-Email: ACOM MUSICA Developers <musica-support@ucar.edu>
@@ -207,13 +207,25 @@ License:                                  Apache License
             limitations under the License.
          
 Project-URL: homepage, https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
+Requires-Python: >=3.9
 Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: xarray>=2022.3.0
+Requires-Dist: ussa1976>=v0.3.4
 Provides-Extra: test
 Requires-Dist: numpy; extra == "test"
 Requires-Dist: pytest; extra == "test"
+Requires-Dist: matplotlib; extra == "test"
 Provides-Extra: gpu
 Requires-Dist: nvidia-cublas-cu12; extra == "gpu"
 Requires-Dist: nvidia-cuda-runtime-cu12; extra == "gpu"
+Provides-Extra: tutorial
+Requires-Dist: pandas; extra == "tutorial"
+Requires-Dist: matplotlib; extra == "tutorial"
+Requires-Dist: numpy; extra == "tutorial"
+Requires-Dist: scipy; extra == "tutorial"
+Requires-Dist: seaborn; extra == "tutorial"
+Requires-Dist: dask[distributed]; extra == "tutorial"
+Requires-Dist: dask-jobqueue; extra == "tutorial"
 Description-Content-Type: text/markdown
 
 # MUSICA
@@ -228,6 +240,8 @@ Description-Content-Type: text/markdown
 [![PyPI version](https://badge.fury.io/py/musica.svg)](https://pypi.org/p/musica)
 [![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=22322&r=123)
 [![codecov](https://codecov.io/gh/NCAR/musica/branch/main/graph/badge.svg)](https://codecov.io/gh/NCAR/musica)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NCAR/musica/HEAD?filepath=tutorials)
+
 
 Multi-Scale Infrastructure for Chemistry and Aerosols
 
@@ -241,6 +255,9 @@ At present the project encompasses these core components
 - [MICM](https://github.com/NCAR/micm)
     - Model Independent Chemical Module
 
+- [CARMA](https://github.com/ESCOMP/CARMA)
+    - Community Aerosol and Radiation Model for Atmospheres (integration in development)
+
 - [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration)
     - The standardized format to describe atmospheric chemistry
 
@@ -257,6 +274,27 @@ MUSICA is installable via pip for Python or CMake for C++.
 pip install musica
 ```
 
+If you would like GPU support, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then you can specify the gpu install option for MUSICA. Note that GPU support has only been tested on linux.
+
+```
+pip install --upgrade setuptools pip wheel
+pip install nvidia-pyindex
+pip install musica[gpu]
+```
+
+To build the package locally,
+
+```
+pip install -e .
+```
+
+If you have an NVIDIA GPU and cuda installed, you can enable a build of musica with GPU support by setting the environment 
+variable `BUILD_GPU`.
+
+```
+BUILD_GPU=1 pip install -e .
+```
+
 ## CMake
 ```
 $ git clone https://github.com/NCAR/musica.git
@@ -270,7 +308,7 @@ $ make install
 
 # Using the MUSICA Python API
 MUSICA makes its chemical mechanism analysis and visualization available through a Python API. The following example works through solving a simple chemistry system. Please refer to the [official documentation](https://ncar.github.io/musica/index.html) for further tutorials and examples.
-```
+```python
 # --- Import Musica ---
 import musica
 import musica.mechanism_configuration as mc
@@ -305,7 +343,6 @@ pressure=101000.0
 state = solver.create_state()
 state.set_concentrations({"A": 1.0, "B": 3.0, "C": 5.0})
 state.set_conditions(temperature, pressure)
-initial_pressure = state.get_conditions()['air_density'][0] # store for visualization and output
 
 # --- 6. Time parameters ---
 time_step = 4  # stepping
@@ -368,7 +405,7 @@ Introduced in [Pull Request #124](https://github.com/NCAR/musica/pull/124), it i
 | Musica Dependency                                      | Repository                | Branch, Tag or Hash|
 | ------------------------------------------------------ | --------------------------|--------------------|
 | [Google Test](https://github.com/google/googletest.git)| GOOGLETEST_GIT_REPOSITORY | GOOGLETEST_GIT_TAG |
-| [MICM](https://github.com/NCAR/mcim.git)               | MICM_GIT_REPOSITORY       | MICM_GIT_TAG       | 
+| [MICM](https://github.com/NCAR/micm.git)               | MICM_GIT_REPOSITORY       | MICM_GIT_TAG       | 
 | [TUV-X](https://github.com/NCAR/tuv-x.git)             | TUVX_GIT_REPOSITORY       | TUVX_GIT_TAG       |
 | [PyBind11](https://github.com/pybind/pybind11)         | PYBIND11_GIT_REPOSITORY   | PYBIND11_GIT_TAG   |
 | [Mechanism Configuration](https://github.com/NCAR/MechanismConfiguration.git) | MECH_CONFIG_GIT_REPOSITORY | MECH_CONFIG_GIT_TAG |
@@ -388,41 +425,6 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
     $ cmake .. \
         -DTUVX_GIT_TAG=a6b2c4d8745
 
-
-### Python build
-Musica has python bindings. If you want to install the python package, you may `pip install musica`.
-
-#### PyPi
-If you only want to use the CPU components, 
-
-```
-pip install musica
-```
-
-Note that GPU support has only been tested on linux. If you have an NVIDIA GPU and would like to take 
-advantage of our GPU solver, you must first [add the NVIDIA pypi index](https://docs.nvidia.com/cuda/cuda-quick-start-guide/#pip-wheels-linux) and then install musica with our gpu option.
-
-```
-pip install --upgrade setuptools pip wheel
-pip install nvidia-pyindex
-pip install musica[gpu]
-```
-
-#### Local build
-
-Musica has python bindings. To build the package locally,
-
-```
-pip install -e .
-```
-
-If you have an NVIDIA GPU and cuda installed, you can enable a build of musica with GPU support by setting the environment 
-variable `BUILD_GPU`.
-
-```
-BUILD_GPU=1 pip install -e .
-```
-
 # Contributing
 
 We welcome contributions from the community! Please see our [Contributing Guide](CONTRIBUTING.md) for information on how to get involved.

musica-0.12.2.dist-info/RECORD

@@ -0,0 +1,70 @@
+musica/__init__.py,sha256=pSZ-H2IJ4EEYIbQDygjGwjhGySXdeifB1DzQBMJzz2g,403
+musica/_musica.cp311-win32.pyd,sha256=MYLdI-BEnJmTcBaemIuHrt8JZoN9h6udjJ-9se-LmdM,1419776
+musica/_version.py,sha256=4bzF9LMIExRVigCODQ4A-chBc4NdBm0Fk_FjBxMRo9Q,20
+musica/backend.py,sha256=Fw3-HECqsifQmvRonDTGeEZqS-KXYD09BCwBue_HwfM,1081
+musica/binding_common.cpp,sha256=qrJCfdePt-ZoIgCTrPJqSUF1Ie8Mq7b7S2_pEdpi4CE,1013
+musica/binding_common.hpp,sha256=YAcb9WnfXL7Ps-rR-iMBSwUgBQZfZZdCQQod5CTMEZA,108
+musica/carma.cpp,sha256=v6f2MF1PUGHR46vVZ544o6bEZjCTI2rWvtgL8M0oSns,43244
+musica/carma.py,sha256=FNd4pWJQJ8VJoo2LSl2aXUVSfLZFgABTSKqtTE-Cgv4,68716
+musica/CMakeLists.txt,sha256=MTZYtahh4tLpn6adVKZ9oZ9g-np7Hw8-VHiaFaA-lIM,1817
+musica/constants.py,sha256=sQqh1UVu2HRvl25qWPW0ACT8NrHe_r4Ugy-v_BiTGG4,126
+musica/cpu_binding.cpp,sha256=Cy06zLErMV0g7Ol9Fg-q2cpG-g5fb8hcBl-M-ihHLyk,236
+musica/cuda.cpp,sha256=oTG2ZnL-SiW2kx9eL4XJOQGJeIiGuy8tJ5BEoLRWL4M,358
+musica/cuda.py,sha256=ClHKnSNiU8SX0BANh5KybismYHH6mFUyC-3r8S9qARo,271
+musica/examples/__init__.py,sha256=hR0kZhoHfL9dcup7gg64HDJyIyAQqHAsip8LpuRNnI8,32
+musica/examples/carma_aluminum.py,sha256=Q2IRvU9jxuKAUZvhQkTawVfZV0UADiMvXP-R6uzjemo,3808
+musica/examples/carma_sulfate.py,sha256=MbV1oBrB6rc7yWMxbnYVr_SHlTMqd6uV21kwVhlUymY,8365
+musica/examples/examples.py,sha256=xWnFSNMYPpUhz04YtSSNsr6DoxmQoOdUtTT9GSUm3ps,5901
+musica/examples/sulfate_box_model.py,sha256=LU1kJYtCZNV_4Mi8kJl2V7YQwQuP1dv8Ba4-2vhPFbE,17110
+musica/examples/ts1_latin_hypercube.py,sha256=tLH9swPT4pvDnd7a86-xnt8PqXl4Y7bAXowsA0J7PV8,9868
+musica/gpu_binding.cpp,sha256=X0qISrKYz7Ldjn5UnqNw8oLzOY4VgyF3fUUszm-QSJI,240
+musica/main.py,sha256=gVCfeh44VL4EH7eFRR2wU_I_kANB94furojDi-0LhoE,2797
+musica/mechanism_configuration/__init__.py,sha256=odlwrCvBBnqUBi951RysExLDYqK_AfqP4nRY90MQpcc,40
+musica/mechanism_configuration/aqueous_equilibrium.py,sha256=60b017VeO9MrzYnkF47hzjQJRdD7k3M6L3S94SKqmAE,11270
+musica/mechanism_configuration/arrhenius.py,sha256=eIDPb485TzsRAvz2bYIjwI7n8ofhahUpCP5HRO-o00E,11479
+musica/mechanism_configuration/branched.py,sha256=g7IsOzaTK1hLWYn1agGzAPRhM0pIsz5fM0pOfVzDyKA,12061
+musica/mechanism_configuration/condensed_phase_arrhenius.py,sha256=bXXu1ctDYiZ4yrzTu2b28R-sstYIXZGNruyMxM31qFQ,11745
+musica/mechanism_configuration/condensed_phase_photolysis.py,sha256=S-J-e4-9TYw_tE1iLEqp1wDohJVx7Vkblc9kxWrXfBc,4203
+musica/mechanism_configuration/emission.py,sha256=GOlyzDqk4-_jDZn7poYJ3Rxo-KSTaPxEO7P_SBzS_xQ,3115
+musica/mechanism_configuration/first_order_loss.py,sha256=4dPG2YKeEHjJkc0biV8tGy3vLxY5f2PTeLFt6cRAuRM,6815
+musica/mechanism_configuration/henrys_law.py,sha256=vuLlqRFwThUJ9icvKJkEWXKvC9cj7ldTzDpWMXBJHQ4,1607
+musica/mechanism_configuration/mechanism_configuration.py,sha256=bLLSsdZAyn01VPbQeSJX8RpKWJoBkH7zjtUsCaCzXKw,10671
+musica/mechanism_configuration/phase.py,sha256=j7sPiVPxpaPeHwoo3SMhBgIuAWlXmKgBLpTjBbhZV3E,1680
+musica/mechanism_configuration/photolysis.py,sha256=7C3RDJ7_iFsfC_duyfl47VMsAS-EHhVdj4QExo5u7mU,3971
+musica/mechanism_configuration/reactions.py,sha256=1YbmKH2tL82ZmUdOvs6vNV9r_1GwtVHtiEZwdgrYSrI,2440
+musica/mechanism_configuration/simpol_phase_transfer.py,sha256=BneQwt4cfyBicxOXFarGqFNjJI9x0VaW1iReLy2h4DQ,9278
+musica/mechanism_configuration/species.py,sha256=dPsBPcc_E7yzxtojw3DiBP3JvUMSjmMsqH89h74ZMuk,5544
+musica/mechanism_configuration/surface.py,sha256=vJBW-brrcdzABeUV5DQSS4xli0KjB_K32sW0dnnxRGo,4440
+musica/mechanism_configuration/ternary_chemical_activation.py,sha256=rbhzhmbvewf2Q6hf3_4TcuMiQaoWiOpCzTzWPKXWE5A,14675
+musica/mechanism_configuration/troe.py,sha256=s3nTWbhRiJ2NiEhPH_Bjlyw-NP9eYy3EASN6WIeLfVQ,13959
+musica/mechanism_configuration/tunneling.py,sha256=LpSRmTjFoniIcS2D-qPL9HKaRSZ1YmxbjHCevm6fKHA,9628
+musica/mechanism_configuration/user_defined.py,sha256=dUuSpj4rc9XRuD8FZJ9CX4DFjvQcUCNt5Krrn0cj-_I,3980
+musica/mechanism_configuration/utils.py,sha256=dhMFrydNchhdRrfeJw35oJB8Y5oQJa6p65Z7I127P-8,356
+musica/mechanism_configuration/wet_deposition.py,sha256=cP8WL6T3FjGF01lyf1tNsJllaHQEOciCX8yZraBycIc,2306
+musica/mechanism_configuration.cpp,sha256=wwH5dDG7AuXRk4-ZZGPYwcAc_EpOwoXYdfje2hOobOE,29712
+musica/musica.cpp,sha256=CMPdG_ddcEhW5r7u-DDjqGAGM97zHd_7h6wk_o5t0Qk,8584
+musica/test/examples/v1/full_configuration/full_configuration.json,sha256=zBC3EVwIWtBy5t3FOIrqMNOsRaNRXth0kCqBps4PxCs,9902
+musica/test/examples/v1/full_configuration/full_configuration.yaml,sha256=XY6TW78rus0DyrI70NR3yvTeUIPff8_I9ErOXy2m3KE,5911
+musica/test/integration/test_analytical.py,sha256=eOPb3DtjQEodTZCpjelw1LQZM_VyhFi2TOlx1bmEtkk,14129
+musica/test/integration/test_carma.py,sha256=itPJNxSRp7FHJokYSicZFgqzBBrZ9dr1TDxawDPT9BM,7092
+musica/test/integration/test_carma_aluminum.py,sha256=F7_8xwZnKjSxgnZKdZR1tDwzwfVUiD7ZT1b_9cseE3M,368
+musica/test/integration/test_carma_sulfate.py,sha256=OWQDLQNao5vU2FAMpWDVqs8xrFhpxvRfhx8HrP6GTCs,759
+musica/test/integration/test_chapman.py,sha256=t6p0CadUy-B4OP7A-EZ9Wz52diuYs5yc9LKiFUS9T6A,3651
+musica/test/integration/test_sulfate_box_model.py,sha256=umqG0PAaCu27J3s5W_cnWJt9T_9EFox9z_JMHKNz5GI,1638
+musica/test/integration/test_tuvx.py,sha256=6MU5RrbNpX_I5VHTDUTreCGdL9c9y3voy68QurVazNI,1980
+musica/test/unit/test_parser.py,sha256=PF7GPddM4-Mbz0qjzqRvl_YSISj-VQR49MGXLfe8dDg,2667
+musica/test/unit/test_serializer.py,sha256=y6u_e2uJm9TGpn7B3x8_LobVGxIFyuKzF-WrIfP1Ewo,2527
+musica/test/unit/test_state.py,sha256=he0cEVOS7fnWRP7cOzift5abSAwEWUC-eQ6V5deTgdM,10694
+musica/test/unit/test_util_full_mechanism.py,sha256=O7nJjpIt1k-pxUNj4zBiLdSXruyhj8qfbp8Me75kPJg,25915
+musica/tools/prepare_build_environment_linux.sh,sha256=i69LuyY25KE-jFIFNuYC4_33_DGTngentBvt2Tbed9g,1017
+musica/tools/prepare_build_environment_macos.sh,sha256=Yhhd-8W6YvR79NabEqixexU6BsClNf7DH_EYYlsmeMo,41
+musica/tools/repair_wheel_gpu.sh,sha256=nQueyGNC2qWcBAicjVdAfB6JH4m_51dFOG83vVxke54,1525
+musica/tuvx.cpp,sha256=vvRi7T8TLZ-U8H7R-jrWIEmHBexXlms-0abhPGibnC8,3108
+musica/tuvx.py,sha256=6EDOULrBc2cojLgK-lNKH68YVHQyOFpBC-jkGYuaraY,6587
+musica/types.py,sha256=zTqzaflhrwQqVMtwN_5eNxkvMis_QWAo3XwcNSpWEqs,17544
+musica-0.12.2.dist-info/METADATA,sha256=FlXiev8ZTGt1gS9XbB3IKm4X5_jaDHB8dmMnUD29alg,26345
+musica-0.12.2.dist-info/WHEEL,sha256=ExBCVrfA44Kmc8Oihx6zOKFxiVWREsT3x1YP53Ru4Tk,102
+musica-0.12.2.dist-info/entry_points.txt,sha256=t9qRU9Ya63_yYMKJkTiVS5kCaW6dDDr0wuQ26lgXTH8,49
+musica-0.12.2.dist-info/licenses/AUTHORS.md,sha256=1ssAXR4WOMdfl5Or1raPu_2nxHbkwCpxfwJwzpF_cJM,2691
+musica-0.12.2.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
+musica-0.12.2.dist-info/RECORD,,

{musica-0.12.0.dist-info → musica-0.12.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.11.4
+Generator: scikit-build-core 0.11.6
 Root-Is-Purelib: false
 Tag: cp311-cp311-win32
 

musica-0.12.2.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+musica-cli = musica.main:main
+

musica/test/examples/v0/config.json

@@ -1,7 +0,0 @@
-{
-    "camp-files": [
-      "species.json",
-      "reactions.json"
-    ]
-  }
-  

musica/test/examples/v0/config.yaml

@@ -1,3 +0,0 @@
-camp-files:
-- species.yaml
-- reactions.yaml

musica/test/examples/v0/reactions.json

@@ -1,193 +0,0 @@
-{
-  "camp-data": [
-    {
-      "type": "MECHANISM",
-      "name": "music box interactive configuration",
-      "reactions": [
-        {
-          "type": "PHOTOLYSIS",
-          "scaling factor": 1,
-          "MUSICA name": "foo",
-          "reactants": {
-            "foo": {}
-          },
-          "products": {
-            "buz": {
-              "yield": 1
-            },
-            "bar": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "ARRHENIUS",
-          "A": 6e-34,
-          "Ea": 0,
-          "B": -2.4,
-          "D": 300,
-          "E": 0,
-          "reactants": {
-            "bar": {
-              "qty": 1
-            },
-            "quuz": {
-              "qty": 1
-            },
-            "M": {
-              "qty": 1
-            }
-          },
-          "products": {
-            "baz": {
-              "yield": 1
-            },
-            "M": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "TROE",
-          "k0_A": 2.5e-31,
-          "k0_B": -1.8,
-          "k0_C": 0,
-          "kinf_A": 2.2e-11,
-          "kinf_B": -0.7,
-          "kinf_C": 0,
-          "Fc": 0.6,
-          "N": 1,
-          "reactants": {
-            "bar": {
-              "qty": 1
-            },
-            "foo": {
-              "qty": 1
-            }
-          },
-          "products": {
-            "baz": {
-              "yield": 1
-            }
-          }
-        },
-        {
-          "type": "EMISSION",
-          "scaling factor": 1,
-          "MUSICA name": "buz",
-          "species": "buz"
-        },
-        {
-          "type": "FIRST_ORDER_LOSS",
-          "species": "bar",
-          "MUSICA name": "bar",
-          "scaling factor": 2.5
-        },
-        {
-          "type": "TERNARY_CHEMICAL_ACTIVATION",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "k0_A": 32.1,
-          "k0_B": -2.3,
-          "k0_C": 102.3,
-          "kinf_A": 63.4,
-          "kinf_B": -1.3,
-          "kinf_C": 908.5,
-          "Fc": 1.3,
-          "N": 32.1
-        },
-        {
-          "type": "BRANCHED",
-          "reactants": {
-            "foo" : { },
-            "quz" : { "qty" :2 }
-          },
-          "alkoxy products": {
-            "bar": { "yield": 1.0 },
-            "baz": { "yield": 3.2 }
-          },
-          "nitrate products": {
-            "quz": { "yield": 1.0 }
-          },
-          "Y" : 42.3,
-          "X" : 12.3,
-          "a0" : 1.0e-5,
-          "n" : 3
-        },
-        {
-          "type": "WENNBERG_NO_RO2",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "alkoxy products": {
-            "baz": { }
-          },
-          "nitrate products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "Y" : 2.3e8,
-          "X" : 0.32,
-          "a0" : 0.423,
-          "n" : 6
-        },
-        {
-          "type": "TUNNELING",
-          "reactants": {
-            "bar" : { },
-            "baz" : { }
-          },
-          "products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "A": 32.1,
-          "B": -2.3,
-          "C": 102.3
-        },
-        {
-          "type": "WENNBERG_TUNNELING",
-          "reactants": {
-            "bar2" : { },
-            "baz2" : { }
-          },
-          "products": {
-            "bar2": { "yield": 0.5 },
-            "foo2": { }
-          },
-          "A": 2.1,
-          "B": -1.3,
-          "C": 12.3
-        },
-        {
-          "type": "SURFACE",
-          "gas-phase reactant": "bar",
-          "gas-phase products": {
-            "bar": { "yield": 0.5 },
-            "foo": { }
-          },
-          "reaction probability": 0.5,
-          "MUSICA name": "kbar"
-        },
-        {
-          "type": "USER_DEFINED",
-          "MUSICA name": "bar",
-          "reactants": { 
-            "foo" : { "qty": 2 }
-          },
-          "products": {
-            "bar" : { }
-          }, 
-          "scaling factor": 2.5
-        }
-      ]
-    }
-  ]
-}

musica/test/examples/v0/reactions.yaml

@@ -1,142 +0,0 @@
-camp-data:
-- name: music box interactive configuration
-  reactions:
-  - MUSICA name: foo
-    products:
-      bar:
-        yield: 1
-      buz:
-        yield: 1
-    reactants:
-      foo: {}
-    scaling factor: 1
-    type: PHOTOLYSIS
-  - A: 6.0e-34
-    B: -2.4
-    D: 300
-    E: 0
-    Ea: 0
-    products:
-      M:
-        yield: 1
-      baz:
-        yield: 1
-    reactants:
-      M:
-        qty: 1
-      bar:
-        qty: 1
-      quuz:
-        qty: 1
-    type: ARRHENIUS
-  - Fc: 0.6
-    N: 1
-    k0_A: 2.5e-31
-    k0_B: -1.8
-    k0_C: 0
-    kinf_A: 2.2e-11
-    kinf_B: -0.7
-    kinf_C: 0
-    products:
-      baz:
-        yield: 1
-    reactants:
-      bar:
-        qty: 1
-      foo:
-        qty: 1
-    type: TROE
-  - MUSICA name: buz
-    scaling factor: 1
-    species: buz
-    type: EMISSION
-  - MUSICA name: bar
-    scaling factor: 2.5
-    species: bar
-    type: FIRST_ORDER_LOSS
-  - Fc: 1.3
-    N: 32.1
-    k0_A: 32.1
-    k0_B: -2.3
-    k0_C: 102.3
-    kinf_A: 63.4
-    kinf_B: -1.3
-    kinf_C: 908.5
-    products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: TERNARY_CHEMICAL_ACTIVATION
-  - X: 12.3
-    Y: 42.3
-    a0: 1.0e-05
-    alkoxy products:
-      bar:
-        yield: 1.0
-      baz:
-        yield: 3.2
-    n: 3
-    nitrate products:
-      quz:
-        yield: 1.0
-    reactants:
-      foo: {}
-      quz:
-        qty: 2
-    type: BRANCHED
-  - X: 0.32
-    Y: 230000000.0
-    a0: 0.423
-    alkoxy products:
-      baz: {}
-    n: 6
-    nitrate products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: WENNBERG_NO_RO2
-  - A: 32.1
-    B: -2.3
-    C: 102.3
-    products:
-      bar:
-        yield: 0.5
-      foo: {}
-    reactants:
-      bar: {}
-      baz: {}
-    type: TUNNELING
-  - A: 2.1
-    B: -1.3
-    C: 12.3
-    products:
-      bar2:
-        yield: 0.5
-      foo2: {}
-    reactants:
-      bar2: {}
-      baz2: {}
-    type: WENNBERG_TUNNELING
-  - MUSICA name: kbar
-    gas-phase products:
-      bar:
-        yield: 0.5
-      foo: {}
-    gas-phase reactant: bar
-    reaction probability: 0.5
-    type: SURFACE
-  - MUSICA name: bar
-    products:
-      bar: {}
-    reactants:
-      foo:
-        qty: 2
-    scaling factor: 2.5
-    type: USER_DEFINED
-  type: MECHANISM

musica/test/examples/v0/species.json

@@ -1,40 +0,0 @@
-{
-  "camp-data": [
-    {
-      "name": "foo",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "bar",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "buz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "quuz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "foo2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "bar2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "baz",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "baz2",
-      "type": "CHEM_SPEC"
-    },
-    {
-      "name": "M",
-      "type": "CHEM_SPEC"
-    }
-  ]
-}

musica/test/examples/v0/species.yaml

@@ -1,19 +0,0 @@
-camp-data:
-- name: foo
-  type: CHEM_SPEC
-- name: bar
-  type: CHEM_SPEC
-- name: buz
-  type: CHEM_SPEC
-- name: quuz
-  type: CHEM_SPEC
-- name: foo2
-  type: CHEM_SPEC
-- name: bar2
-  type: CHEM_SPEC
-- name: baz
-  type: CHEM_SPEC
-- name: baz2
-  type: CHEM_SPEC
-- name: M
-  type: CHEM_SPEC