musica 0.11.1.2__cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl → 0.11.1.4__cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl

musica/CMakeLists.txt

@@ -1,47 +1,42 @@
-pybind11_add_module(_musica
-  binding.cpp
-  musica.cpp
-  mechanism_configuration.cpp
-)
+################################################################################
+# Python Extension Modules
+
+#include(setup_muisca_target)
+
+# Define the list of Python extension module targets
+set(PY_MODULES _musica)
 
-target_link_libraries(_musica
-  PRIVATE
-    musica::musica
+set(
+  MUSICA_PYTHON_SOURCES 
+    binding_common.cpp
+    cuda.cpp 
+    mechanism_configuration.cpp 
+    musica.cpp 
+
+    ${MUSICA_SOURCES}
 )
 
-include(silence_warnings)
-silence_warnings(_musica)
-
-if (APPLE)
-  # set the rpath for the shared library
-  set_target_properties(_musica PROPERTIES
-    INSTALL_RPATH "@loader_path"
-    BUILD_WITH_INSTALL_RPATH TRUE
-  )
-elseif(UNIX)
-  set(CUDA_RPATH
-    "$ORIGIN/../../nvidia/cublas/lib"
-    "$ORIGIN/../../nvidia/cuda_runtime/lib"
-  )
-
-  message(STATUS "Adding RPATH for python site packages libs at ${CUDA_RPATH}")
-
-  set_target_properties(_musica PROPERTIES
-    INSTALL_RPATH "$ORIGIN;${CUDA_RPATH}"
-    BUILD_WITH_INSTALL_RPATH TRUE
-  )
+pybind11_add_module(_musica cpu_binding.cpp ${MUSICA_PYTHON_SOURCES})
+musica_setup_target(_musica MODE CPU)
+
+if (NOT ${MUSICA_GPU_TYPE} STREQUAL "None")
+  pybind11_add_module(_musica_gpu gpu_binding.cpp ${MUSICA_PYTHON_SOURCES}) 
+  musica_setup_target(_musica_gpu MODE GPU)
+  list(APPEND PY_MODULES _musica_gpu)
 endif()
 
-if(WIN32)
-  # makefiles on windows don't need the config directory
-  if (${CMAKE_GENERATOR} MATCHES "MinGW Makefiles")
-      set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}")
-  else()
-  # but visual studio does
-      set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}/$<CONFIG>")
+foreach(lib ${PY_MODULES})
+  if (APPLE)
+    set_target_properties(${lib} PROPERTIES
+      INSTALL_RPATH "@loader_path"
+      BUILD_WITH_INSTALL_RPATH TRUE
+    )
+  elseif(UNIX)
+    set_target_properties(${lib} PROPERTIES
+      INSTALL_RPATH "$ORIGIN"
+      BUILD_WITH_INSTALL_RPATH TRUE
+    )
   endif()
-else()
-  set(PYTHON_MODULE_PATH "${CMAKE_CURRENT_BINARY_DIR}")
-endif()
 
-install(TARGETS _musica yaml-cpp musica LIBRARY DESTINATION .)
+  install(TARGETS ${lib} LIBRARY DESTINATION musica)
+endforeach()

musica/__init__.py

@@ -1,3 +1,51 @@
-from _musica import *
-from .types import *
-from .mechanism_configuration import *
+import importlib.util
+
+
+def _safe_find_spec(name):
+    try:
+        return importlib.util.find_spec(name)
+    except ModuleNotFoundError:
+        return None
+
+
+def _gpu_deps_installed():
+    return (
+        _safe_find_spec("nvidia.cublas") is not None or
+        _safe_find_spec("nvidia_cuda_runtime") is not None or
+        _safe_find_spec("nvidia-cublas-cu12") is not None or
+        _safe_find_spec("nvidia-cuda-runtime-cu12") is not None
+    )
+
+
+if _gpu_deps_installed():
+    from . import _musica_gpu as _backend
+else:
+    from . import _musica as _backend
+
+# Helper to re-export names from a module
+def _export_all(module, names, globals_):
+    for name in names:
+        globals_[name] = getattr(module, name)
+
+
+_core_names = [
+    "_Conditions", "_SolverType", "_Solver", "_State", "_create_solver",
+    "_create_solver_from_mechanism", "_create_state", "_micm_solve", "_vector_size",
+    "_species_ordering", "_user_defined_rate_parameters_ordering",
+]
+_mechanism_names = [
+    "_ReactionType", "_Species", "_Phase", "_ReactionComponent", "_Arrhenius",
+    "_CondensedPhaseArrhenius", "_Troe", "_Branched", "_Tunneling", "_Surface",
+    "_Photolysis", "_CondensedPhasePhotolysis", "_Emission", "_FirstOrderLoss",
+    "_AqueousEquilibrium", "_WetDeposition", "_HenrysLaw", "_SimpolPhaseTransfer",
+    "_UserDefined", "_Reactions", "_ReactionsIterator", "_Mechanism", "_Version", "_Parser"
+]
+
+# this allows us to use the same symbols in both the GPU and CPU versionspp
+_export_all(_backend._core, _core_names, globals())
+_export_all(_backend._mechanism_configuration, _mechanism_names, globals())
+
+__all__ = _core_names + _mechanism_names
+
+from .types import MICM, SolverType, State, Conditions
+from ._version import version as __version__

musica/_version.py

@@ -1 +1 @@
-version = "0.11.1.2"
+version = "0.11.1.4"

musica/binding_common.cpp

@@ -0,0 +1,16 @@
+#include "binding_common.hpp"
+
+void bind_cuda(py::module_ &);
+void bind_musica(py::module_ &);
+
+void bind_mechanism_configuration(py::module_ &);
+
+void bind_all(py::module_ &m) {
+    py::module_ core = m.def_submodule("_core", "Wrapper classes for MUSICA C library structs and functions");
+    py::module_ mechanism_configuration = m.def_submodule("_mechanism_configuration", "Wrapper classes for Mechanism Configuration library structs and functions");
+
+    bind_cuda(core);
+    bind_musica(core);
+
+    bind_mechanism_configuration(mechanism_configuration);
+}

musica/binding_common.hpp

@@ -0,0 +1,7 @@
+#pragma once
+
+#include <pybind11/pybind11.h>
+
+namespace py = pybind11;
+
+void bind_all(py::module_ &m);

musica/cpu_binding.cpp

@@ -0,0 +1,10 @@
+// Copyright (C) 2023-2025 University Corporation for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
+
+#include <pybind11/pybind11.h>
+#include "binding_common.hpp"
+
+PYBIND11_MODULE(_musica, m)
+{
+  bind_all(m);
+}

musica/cuda.cpp

@@ -0,0 +1,12 @@
+// Copyright (C) 2023-2025 University Corporation for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
+#include <musica/micm/cuda_availability.hpp>
+
+#include <pybind11/pybind11.h>
+
+namespace py = pybind11;
+
+void bind_cuda(py::module_ &cuda)
+{
+  cuda.def("_is_cuda_available", &musica::IsCudaAvailable, "Check if CUDA is available");
+}

musica/cuda.py

@@ -0,0 +1,10 @@
+from . import _backend
+
+def is_cuda_available() -> bool:
+    """
+    Check if CUDA is available.
+
+    Returns:
+        bool: True if CUDA is available, False otherwise.
+    """
+    return _backend._core._is_cuda_available()

musica/gpu_binding.cpp

@@ -0,0 +1,10 @@
+// Copyright (C) 2023-2025 University Corporation for Atmospheric Research
+// SPDX-License-Identifier: Apache-2.0
+
+#include <pybind11/pybind11.h>
+#include "binding_common.hpp"
+
+PYBIND11_MODULE(_musica_gpu, m)
+{
+  bind_all(m);
+}

musica/mechanism_configuration.py

@@ -4,7 +4,7 @@
 # This file is part of the musica Python package.
 # For more information, see the LICENSE file in the top-level directory of this distribution.
 from typing import Optional, Any, Dict, List, Union, Tuple
-from _musica._mechanism_configuration import (
+from musica import (
     _ReactionType,
     _Species,
     _Phase,

musica/musica.cpp

@@ -211,4 +211,4 @@ void bind_musica(py::module_ &core)
         }, state->state_variant_);
       },
       "Print the state to stdout with the current time");
-}
+}

musica/test/test_analytical.py

@@ -3,7 +3,7 @@ import numpy as np
 import musica
 import random
 import musica.mechanism_configuration as mc
-from _musica._core import _is_cuda_available
+from musica.cuda import is_cuda_available
 
 
 def TestSingleGridCell(solver, state, time_step, places=5):
@@ -118,6 +118,7 @@ def TestMultipleGridCell(solver, state, num_grid_cells, time_step, places=5):
         rate_constants["USER.reaction 2"].append(
             0.002 + random.uniform(-0.0001, 0.0001))
 
+
     state.set_conditions(temperatures, pressures)  # Air density should be calculated in the state
     state.set_concentrations(concentrations)
     state.set_user_defined_rate_parameters(rate_constants)
@@ -127,6 +128,7 @@ def TestMultipleGridCell(solver, state, num_grid_cells, time_step, places=5):
     initial_temperatures = state.get_conditions()["temperature"]
     initial_pressures = state.get_conditions()["pressure"]
     initial_air_density = state.get_conditions()["air_density"]
+
     for i in range(num_grid_cells):
         assert np.isclose(initial_concentrations["A"][i], concentrations["A"][i], atol=1e-13)
         assert np.isclose(initial_concentrations["B"][i], concentrations["B"][i], atol=1e-13)
@@ -242,7 +244,7 @@ def GetMechanism():
 
 def test_single_grid_cell_standard_rosenbrock():
     solver = musica.MICM(
-        config_path="configs/analytical",
+        config_path="configs/v0/analytical",
         solver_type=musica.SolverType.rosenbrock_standard_order)
     state = solver.create_state()
     TestSingleGridCell(solver, state, 200.0, 5)
@@ -251,16 +253,16 @@ def test_single_grid_cell_standard_rosenbrock():
 def test_multiple_grid_cells_standard_rosenbrock():
     for i in range(1, 11):
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.rosenbrock_standard_order)
         state = solver.create_state(i)
         TestMultipleGridCell(solver, state, i, 200.0, 5)
 
 
 def test_cuda_rosenbrock():
-    if _is_cuda_available():
+    if is_cuda_available():
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.cuda_rosenbrock)
         state = solver.create_state()
         TestSingleGridCell(solver, state, 200.0, 5)
@@ -270,7 +272,7 @@ def test_cuda_rosenbrock():
 
 def test_single_grid_cell_backward_euler():
     solver = musica.MICM(
-        config_path="configs/analytical",
+        config_path="configs/v0/analytical",
         solver_type=musica.SolverType.backward_euler_standard_order)
     state = solver.create_state()
     TestSingleGridCell(solver, state, 10.0, places=2)
@@ -279,7 +281,7 @@ def test_single_grid_cell_backward_euler():
 def test_multiple_grid_cells_backward_euler():
     for i in range(1, 11):
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.backward_euler_standard_order)
         state = solver.create_state(i)
         TestMultipleGridCell(solver, state, i, 10.0, places=2)
@@ -287,7 +289,7 @@ def test_multiple_grid_cells_backward_euler():
 
 def test_single_grid_cell_rosenbrock():
     solver = musica.MICM(
-        config_path="configs/analytical",
+        config_path="configs/v0/analytical",
         solver_type=musica.SolverType.rosenbrock)
     state = solver.create_state()
     TestSingleGridCell(solver, state, 200.0, 5)
@@ -296,7 +298,7 @@ def test_single_grid_cell_rosenbrock():
 def test_multiple_grid_cells_rosenbrock():
     for i in range(1, 11):
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.rosenbrock)
         state = solver.create_state(i)
         TestMultipleGridCell(solver, state, i, 200.0, 5)
@@ -304,7 +306,7 @@ def test_multiple_grid_cells_rosenbrock():
 
 def test_single_grid_cell_backward_euler_standard_order():
     solver = musica.MICM(
-        config_path="configs/analytical",
+        config_path="configs/v0/analytical",
         solver_type=musica.SolverType.backward_euler_standard_order)
     state = solver.create_state()
     TestSingleGridCell(solver, state, 10.0, places=2)
@@ -313,7 +315,7 @@ def test_single_grid_cell_backward_euler_standard_order():
 def test_multiple_grid_cells_backward_euler_standard_order():
     for i in range(1, 11):
         solver = musica.MICM(
-            config_path="configs/analytical",
+            config_path="configs/v0/analytical",
             solver_type=musica.SolverType.backward_euler_standard_order)
         state = solver.create_state(i)
         TestMultipleGridCell(solver, state, i, 10.0, places=2)

musica/test/test_chapman.py

@@ -3,9 +3,25 @@ import musica
 import musica.mechanism_configuration as mc
 
 
-def test_solve_with_config_path():
+def test_solve_with_config_path_v0():
     solver = musica.MICM(
-        config_path="configs/chapman",
+        config_path="configs/v0/chapman",
+        solver_type=musica.SolverType.rosenbrock_standard_order,
+    )
+    TestSolve(solver)
+
+
+def test_solve_with_config_path_v1_json():
+    solver = musica.MICM(
+        config_path="configs/v1/chapman/config.json",
+        solver_type=musica.SolverType.rosenbrock_standard_order,
+    )
+    TestSolve(solver)
+
+
+def test_solve_with_config_path_v1_yaml():
+    solver = musica.MICM(
+        config_path="configs/v1/chapman/config.yaml",
         solver_type=musica.SolverType.rosenbrock_standard_order,
     )
     TestSolve(solver)

musica/test/test_parser.py

@@ -1,6 +1,6 @@
 import pytest
 from musica.mechanism_configuration import *
-from _musica._mechanism_configuration import _ReactionType
+from musica import _ReactionType
 
 
 def validate_species(species):
@@ -400,7 +400,7 @@ def test_parsed_full_v1_configuration():
     parser = Parser()
     extensions = [".yaml", ".json"]
     for extension in extensions:
-        path = f"musica/test/examples/v1/full_configuration{extension}"
+        path = f"musica/test/examples/v1/full_configuration/full_configuration{extension}"
         mechanism = parser.parse(path)
         validate_full_v1_mechanism(mechanism)
 

musica/tools/prepare_build_environment_linux.sh

@@ -11,7 +11,7 @@ sed -i s/^mirrorlist=http/#mirrorlist=http/g /etc/yum.repos.d/*.repo
 sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
 sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*
 
-yum install -y zip tree
+yum install -y zip tree wget
 
 # Use CIBW_ARCHS or CIBW_ARCH if set, else fallback to uname -m
 if [ -n "$CIBW_ARCHS" ]; then
@@ -32,10 +32,12 @@ if [ "$target_arch" = "x86_64" ]; then
   sed -i s/^#.*baseurl=http/baseurl=http/g /etc/yum.repos.d/*.repo
   sed -i s/^mirrorlist=http/#mirrorlist=http/g /etc/yum.repos.d/*.repo
   yum install --setopt=obsoletes=0 -y \
-      cuda-nvcc-12-2-12.2.140-1 \
-      cuda-cudart-devel-12-2-12.2.140-1 \
-      libcurand-devel-12-2-10.3.3.141-1 \
-      libcublas-devel-12-2-12.2.5.6-1 \
-      libnccl-devel-2.19.3-1+cuda12.2
+      cuda-nvcc-12-2 \
+      cuda-cudart-devel-12-2 \
+      libcurand-devel-12-2 \
+      libcublas-devel-12-2 
   ln -s cuda-12.2 /usr/local/cuda
+
+  # list the installed CUDA packages
+  tree -L 4 /usr/local/cuda-12.2
 fi

musica/tools/repair_wheel_gpu.sh

@@ -7,21 +7,31 @@ for whl in "$2"/*.whl; do
   tmpdir=$(mktemp -d)
   unzip -q "$whl" -d "$tmpdir"
   tree "$tmpdir"
-  echo "Before patchelf:"
-  readelf -d "$tmpdir"/_musica*.so
-  # Use patchelf to fix the rpath and library dependencies
-  patchelf --remove-rpath "$tmpdir"/_musica*.so
-  patchelf --set-rpath "\$ORIGIN:\$ORIGIN/../../nvidia/cublas/lib:\$ORIGIN/../../nvidia/cuda_runtime/lib" --force-rpath "$tmpdir"/_musica*.so
-  # these may need to be periodically updated
-  patchelf --replace-needed libcudart-b5a066d7.so.12.2.140 libcudart.so.12 "$tmpdir"/_musica*.so
-  patchelf --replace-needed libcublas-e779a79d.so.12.2.5.6 libcublas.so.12 "$tmpdir"/_musica*.so
-  patchelf --replace-needed libcublasLt-fbfbc8a1.so.12.2.5.6 libcublasLt.so.12 "$tmpdir"/_musica*.so
-  # Remove bundled CUDA libraries
-  rm -f "$tmpdir"/musica.libs/libcudart-*.so*
-  rm -f "$tmpdir"/musica.libs/libcublas-*.so*
-  rm -f "$tmpdir"/musica.libs/libcublasLt-*.so*
-  echo "After patchelf:"
-  readelf -d "$tmpdir"/_musica*.so
+
+  so_files=("$tmpdir"/musica/_musica_gpu*.so)
+
+  if [[ -f "${so_files[0]}" ]]; then
+      so_path="${so_files[0]}"
+      ls $so_path
+      echo "Before patchelf:"
+      readelf -d $so_path
+      # Use patchelf to fix the rpath and library dependencies
+      patchelf --remove-rpath $so_path
+      patchelf --set-rpath "\$ORIGIN:\$ORIGIN/../nvidia/cublas/lib:\$ORIGIN/../nvidia/cuda_runtime/lib" --force-rpath $so_path
+      # these may need to be periodically updated
+      patchelf --replace-needed libcudart-b5a066d7.so.12.2.140 libcudart.so.12 $so_path
+      patchelf --replace-needed libcublas-e779a79d.so.12.2.5.6 libcublas.so.12 $so_path
+      patchelf --replace-needed libcublasLt-fbfbc8a1.so.12.2.5.6 libcublasLt.so.12 $so_path
+      # Remove bundled CUDA libraries
+      rm -f "$tmpdir"/musica.libs/libcudart-*.so*
+      rm -f "$tmpdir"/musica.libs/libcublas-*.so*
+      rm -f "$tmpdir"/musica.libs/libcublasLt-*.so*
+      echo "After patchelf:"
+      readelf -d $so_path
+  else
+    echo "No GPU .so file found, skipping patchelf steps"
+  fi
+
   # Repack the wheel with correct structure
   (cd "$tmpdir" && zip -qr "${whl%.whl}.patched.whl" .)
   rm -rf "$tmpdir"

musica/types.py

@@ -3,10 +3,10 @@
 #
 # This file is part of the musica Python package.
 # For more information, see the LICENSE file in the top-level directory of this distribution.
-from typing import Optional, Any, Dict, List, Union, Tuple
+from typing import Optional, Dict, List, Union, Tuple
 from os import PathLike
 import math
-from _musica._core import (
+from musica import (
     _Conditions,
     _SolverType,
     _Solver,
@@ -172,6 +172,7 @@ class State():
                     state.user_defined_rate_parameters[i_param * param_stride + i_cell * cell_stride] = value[k]
                     k += 1
 
+
     def set_conditions(self,
                        temperatures: Union[Union[float, int], List[Union[float, int]]],
                        pressures: Union[Union[float, int], List[Union[float, int]]],
@@ -358,5 +359,5 @@ class MICM():
         if not isinstance(time_step, (int, float)):
             raise TypeError("time_step must be an int or float.")
         states = state.get_internal_states()
-        for _, _state in enumerate(states):
+        for _state in states:
             _micm_solve(self.__solver, _state, time_step)

{musica-0.11.1.2.dist-info → musica-0.11.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: musica
-Version: 0.11.1.2
+Version: 0.11.1.4
 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>
@@ -240,7 +240,110 @@ At present the project encompasses these components
 - [MICM](https://github.com/NCAR/micm)
     - Model Independent Chemical Module
 
-## Available grids
+# Installation
+MUSICA is installable via pip for Python or CMake for C++. 
+
+## Pip
+```
+pip install musica
+```
+## CMake
+```
+$ git clone https://github.com/NCAR/musica.git
+$ cd musica
+$ mkdir build
+$ cd build
+$ ccmake ..
+$ make
+$ 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.
+```
+# --- Import Musica ---
+import musica
+import musica.mechanism_configuration as mc
+
+# --- 1. Define the chemical system of interest ---
+A = mc.Species(name="A")
+B = mc.Species(name="B")
+C = mc.Species(name="C")
+species = [A, B, C]
+gas = mc.Phase(name="gas", species=species)
+
+# --- 2. Define a mechanism of interest ---
+# Through Musica, several different mechanisms can be explored to define reaction rates. Here, we use the Arrhenius equation as a simple example.
+
+r1 = mc.Arrhenius(name="A->B", A=4.0e-3, C=50, reactants=[A], products=[B], gas_phase=gas)
+r2 = mc.Arrhenius(name="B->C", A=1.2e-4, B=2.5, C=75, D=50, E=0.5, reactants=[B], products=[C], gas_phase=gas)
+
+mechanism = mc.Mechanism(name="musica_example", species=species, phases=[gas], reactions=[r1, r2])
+
+# --- 3. Create MICM solver ---
+# A solver must be initialized with either a configuration file or a mechanism:
+
+solver = musica.MICM(mechanism=mechanism, solver_type=musica.SolverType.rosenbrock_standard_order)
+
+# --- 4. Define environmental conditions ---
+temperature=300.0
+pressure=101000.0
+
+# --- 5. Create and initialize State ---
+# In the model, conditions represent the starting environment for the reactions and are assigned by modifying the state.
+
+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
+sim_length = 20  # total simulation time
+
+# --- (Optional) 7. Save initial state (t=0) for output visualization ---
+initial_row = {"time.s": 0.0, "ENV.temperature.K": temperature, "ENV.pressure.Pa": pressure, "ENV.air number density.mol m-3": state.get_conditions()['air_density'][0]}
+initial_row.update({f"CONC.{k}.mol m-3": v[0] for k, v in state.get_concentrations().items()})
+
+# --- 8. Solve through time loop only ---
+# The following loop simply solves the model per each time step:
+
+curr_time = time_step
+while curr_time <= sim_length:
+    solver.solve(state, time_step)
+    concentrations = state.get_concentrations()
+    curr_time += time_step
+
+# --- 9. Solve and create DataFrame ---
+# It is likely more useful to solve at each time step and store the associated data:
+import pandas as pd
+
+output_data = [] # prepare to store output per time step
+output_data.append(initial_row) # save t=0 data
+
+curr_time = time_step
+while curr_time <= sim_length:
+    solver.solve(state, time_step)
+    row = {
+        "time.s": curr_time,
+        "ENV.temperature.K": state.get_conditions()['temperature'][0],
+        "ENV.pressure.Pa": state.get_conditions()['pressure'][0],
+        "ENV.air number density.mol m-3": state.get_conditions()['air_density'][0]
+    }
+    row.update({f"CONC.{k}.mol m-3": v[0] for k, v in state.get_concentrations().items()})
+    output_data.append(row)
+    curr_time += time_step
+
+df = pd.DataFrame(output_data)
+print(df)
+
+# --- 10. Visualize Specific Results ---
+import matplotlib.pyplot as plt
+
+df.plot(x='time.s', y=['CONC.A.mol m-3', 'CONC.B.mol m-3', 'CONC.C.mol m-3'], title='Concentration over time', ylabel='Concentration (mol m-3)', xlabel='Time (s)')
+plt.show()
+```
+# Available grids
 
 Pre-made grids for use in MUSICA are available [here](https://wiki.ucar.edu/display/MUSICA/Available+Grids).
 
@@ -282,7 +385,25 @@ Specifying a specific version of `tuv-x` by has, but using the official reposito
 ### Python build
 Musica has python bindings. If you want to install the python package, you may `pip install musica`.
 
-To build the package locally,
+#### 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 .

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{musica-0.11.1.2.dist-info → musica-0.11.1.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.11.3
+Generator: scikit-build-core 0.11.4
 Root-Is-Purelib: false
 Tag: cp312-cp312-manylinux_2_17_i686
 Tag: cp312-cp312-manylinux2014_i686

musica/binding.cpp

@@ -1,19 +0,0 @@
-// Copyright (C) 2023-2025 University Corporation for Atmospheric Research
-// SPDX-License-Identifier: Apache-2.0
-
-#include <pybind11/pybind11.h>
-
-namespace py = pybind11;
-
-void bind_musica(py::module_ &);
-void bind_mechanism_configuration(py::module_ &);
-
-// Wraps micm.cpp
-PYBIND11_MODULE(_musica, m)
-{
-  py::module_ core = m.def_submodule("_core", "Wrapper classes for MUSICA C library structs and functions");
-  py::module_ mechanism_configuration = m.def_submodule("_mechanism_configuration", "Wrapper classes for Mechanism Configuration library structs and functions");
-
-  bind_musica(core);
-  bind_mechanism_configuration(mechanism_configuration);
-}

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