SOC examples updated to use new slicing

CITATION.cff

@@ -9,7 +9,7 @@ authors:
     affiliation: "German Aerospace Center (DLR)"
     address: "Linder Höhe"
     city: Köln
-version: v1.1.2
+version: v1.1.3
 date-released: "2025-06-24"
 #identifiers:
 #  - description: This is the collection of archived snapshots of all versions of Gaspype

docs/source/conf.py

@@ -10,7 +10,7 @@ import os
 import sys
 sys.path.insert(0, os.path.abspath("../src/"))
 
-project = 'gaspype'
+project = 'Gaspype'
 copyright = '2025, Nicolas Kruse'
 author = 'Nicolas Kruse'
 

examples/soec_syngas.md

@@ -24,7 +24,7 @@ p = 1e5  # Pa
 fs = gp.fluid_system('H2, H2O, O2, CH4, CO, CO2')
 feed_fuel = gp.fluid({'H2O': 2, 'CO2': 1}, fs)
 
-o2_full_conv = np.sum(gp.elements(feed_fuel)[['C' ,'O']] * [-1/2, 1/2])
+o2_full_conv = np.sum(gp.elements(feed_fuel).get_n(['C' ,'O']) * [-1/2, 1/2])
 
 feed_air = gp.fluid({'O2': 1, 'N2': 4}) * o2_full_conv * utilization * air_dilution
 

examples/sofc_methane.md

@@ -25,7 +25,7 @@ p = 1e5  # Pa
 fs = gp.fluid_system('H2, H2O, O2, CH4, CO, CO2')
 feed_fuel = gp.fluid({'CH4': 1, 'H2O': 0.1}, fs)
 
-o2_full_conv = np.sum(gp.elements(feed_fuel)[['H', 'C' ,'O']] * [1/4, 1, -1/2])
+o2_full_conv = np.sum(gp.elements(feed_fuel).get_n(['H', 'C' ,'O']) * [1/4, 1, -1/2])
 
 feed_air = gp.fluid({'O2': 1, 'N2': 4}) * o2_full_conv * fuel_utilization / air_utilization
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "gaspype"
-version = "1.1.2"
+version = "1.1.3"
 authors = [
   { name="Nicolas Kruse", email="nicolas.kruse@dlr.de" },
 ]
@@ -18,9 +18,10 @@ dependencies = [
 ]
 
 [project.urls]
-Homepage = "https://github.com/DLR-Institute-of-Future-Fuels/gaspype"
+Homepage = "https://dlr-institute-of-future-fuels.github.io/gaspype/"
+documentation = "https://dlr-institute-of-future-fuels.github.io/gaspype/api/"
+Repository = "https://github.com/DLR-Institute-of-Future-Fuels/gaspype.git"
 Issues = "https://github.com/DLR-Institute-of-Future-Fuels/gaspype/issues"
-documentation = "https://dlr-institute-of-future-fuels.github.io/gaspype/"
 
 [build-system]
 requires = ["setuptools>=61.0", "wheel"]

src/gaspype/_main.py

@@ -7,7 +7,7 @@ from gaspype._phys_data import atomic_weights, db_reader
 import re
 import pkgutil
 from .constants import R, epsy, p0
-from .typing import FloatArray, NDFloat, Shape
+from .typing import FloatArray, NDFloat, Shape, ArrayIndices
 
 T = TypeVar('T', 'fluid', 'elements')
 
@@ -483,6 +483,28 @@ class fluid:
             assert set(species) <= set(self.fs.species), f'Species {", ".join([s for s in species if s not in self.fs.species])} is/are not part of the fluid system'
             return self.array_fractions[..., [self.fs.species.index(k) for k in species]]
 
+    def get_n(self, species: str | list[str] | None = None) -> FloatArray:
+        """Get molar amount of fluid species
+
+        Args:
+            species: A single species name, a list of species names or None for
+                returning the amount of all species
+
+        Returns:
+            Returns an array of floats with the molar amount of the species.
+            If the a single species name is provided the return float array has
+            the same dimensions as the fluid type. If a list or None is provided
+            the return array has an additional dimension for the species.
+        """
+        if not species:
+            return self.array_composition
+        elif isinstance(species, str):
+            assert species in self.fs.species, f'Species {species} is not part of the fluid system'
+            return self.array_composition[..., self.fs.species.index(species)]
+        else:
+            assert set(species) <= set(self.fs.species), f'Species {", ".join([s for s in species if s not in self.fs.species])} is/are not part of the fluid system'
+            return self.array_composition[..., [self.fs.species.index(k) for k in species]]
+
     def __add__(self, other: T) -> T:
         return array_operation(self, other, np.add)
 
@@ -510,16 +532,21 @@ class fluid:
     # def __array__(self) -> FloatArray:
     #     return self.array_composition
 
-    def __getitem__(self, key: str | int | list[str] | list[int] | slice) -> FloatArray:
+    @overload
+    def __getitem__(self, key: str) -> FloatArray:
+        pass
+
+    @overload
+    def __getitem__(self, key: ArrayIndices) -> 'fluid':
+        pass
+
+    def __getitem__(self, key: str | ArrayIndices) -> Any:
         if isinstance(key, str):
             assert key in self.fs.species, f'Species {key} is not part of the fluid system'
             return self.array_composition[..., self.fs.species.index(key)]
-        elif isinstance(key, (slice, int)):
-            return self.array_composition[..., key]
         else:
-            mset = set(self.fs.species) | set(range(len(self.fs.species)))
-            assert set(key) <= mset, f'Species {", ".join([str(s) for s in key if s not in mset])} is/are not part of the fluid system'
-            return self.array_composition[..., [self.fs.species.index(k) if isinstance(k, str) else k for k in key]]
+            key_tuple = key if isinstance(key, tuple) else (key,)
+            return fluid(self.array_composition[(*key_tuple, slice(None))], self.fs)
 
     def __iter__(self) -> Iterator[dict[str, float]]:
         assert len(self.shape) < 2, 'Cannot iterate over species with more than one dimension'
@@ -614,6 +641,28 @@ class elements:
         """
         return np.sum(self.array_elemental_composition * self.fs.array_atomic_mass, axis=-1, dtype=NDFloat)
 
+    def get_n(self, elemental_species: str | list[str] | None = None) -> FloatArray:
+        """Get molar amount of elements
+
+        Args:
+            elemental_species: A single element name, a list of element names or None for
+                returning the amount of all element
+
+        Returns:
+            Returns an array of floats with the molar amount of the elements.
+            If the a single element name is provided the return float array has
+            the same dimensions as the fluid type. If a list or None is provided
+            the return array has an additional dimension for the elements.
+        """
+        if not elemental_species:
+            return self.array_elemental_composition
+        elif isinstance(elemental_species, str):
+            assert elemental_species in self.fs.elements, f'Element {elemental_species} is not part of the fluid system'
+            return self.array_elemental_composition[..., self.fs.elements.index(elemental_species)]
+        else:
+            assert set(elemental_species) <= set(self.fs.elements), f'Elements {", ".join([s for s in elemental_species if s not in self.fs.elements])} is/are not part of the fluid system'
+            return self.array_elemental_composition[..., [self.fs.elements.index(k) for k in elemental_species]]
+
     def __add__(self, other: 'fluid | elements') -> 'elements':
         return array_operation(self, other, np.add)
 
@@ -639,16 +688,21 @@ class elements:
     def __array__(self) -> FloatArray:
         return self.array_elemental_composition
 
-    def __getitem__(self, key: str | int | list[str] | list[int] | slice) -> FloatArray:
+    @overload
+    def __getitem__(self, key: str) -> FloatArray:
+        pass
+
+    @overload
+    def __getitem__(self, key: ArrayIndices) -> 'elements':
+        pass
+
+    def __getitem__(self, key: str | ArrayIndices) -> Any:
         if isinstance(key, str):
             assert key in self.fs.elements, f'Element {key} is not part of the fluid system'
             return self.array_elemental_composition[..., self.fs.elements.index(key)]
-        elif isinstance(key, (slice, int)):
-            return self.array_elemental_composition[..., key]
         else:
-            mset = set(self.fs.elements) | set(range(len(self.fs.elements)))
-            assert set(key) <= mset, f'Elements {", ".join([str(s) for s in key if s not in mset])} is/are not part of the fluid system'
-            return self.array_elemental_composition[..., [self.fs.elements.index(k) if isinstance(k, str) else k for k in key]]
+            key_tuple = key if isinstance(key, tuple) else (key,)
+            return elements(self.array_elemental_composition[(*key_tuple, slice(None))], self.fs)
 
     def __iter__(self) -> Iterator[dict[str, float]]:
         assert len(self.shape) < 2, 'Cannot iterate over elements with more than one dimension'

src/gaspype/typing.py

@@ -1,6 +1,10 @@
 from numpy import float64
 from numpy.typing import NDArray
+from typing import Sequence
+from types import EllipsisType
 
 Shape = tuple[int, ...]
 NDFloat = float64
 FloatArray = NDArray[NDFloat]
+ArrayIndex = int | slice | None | EllipsisType | Sequence[int]
+ArrayIndices = ArrayIndex | tuple[ArrayIndex, ...]

tests/benchmark_cp.py

@@ -0,0 +1,42 @@
+import cantera as ct
+import numpy as np
+import time
+import gaspype as gp
+
+gas = ct.Solution("gri30.yaml")
+composition = {"H2": 0.3, "H2O": 0.3, "N2": 0.4}
+
+n_species = gas.n_species
+n_states = 1_000_000
+
+# Random temperatures and pressures
+temperatures = np.linspace(300.0, 2500.0, n_states)
+pressures = np.full(n_states, ct.one_atm)
+
+# Create a SolutionArray with many states at once
+states = ct.SolutionArray(gas, len(temperatures))
+
+time.sleep(0.5)
+
+# Vectorized assignment
+t0 = time.perf_counter()
+states.TPX = temperatures, pressures, composition
+cp_values = states.cp_mole
+elapsed = time.perf_counter() - t0
+
+print(f"Computed {n_states} Cp values in {elapsed:.4f} seconds (vectorized cantera)")
+print("First 5 Cp values (J/mol-K):", cp_values[:5] / 1000)
+
+
+# Vectorized fluid creation
+fluid = gp.fluid(composition)
+
+time.sleep(0.5)
+
+# Benchmark: calculate Cp for all states at once
+t0 = time.perf_counter()
+cp_values = fluid.get_cp(t=temperatures)
+elapsed = time.perf_counter() - t0
+
+print(f"Computed {n_states} Cp values in {elapsed:.4f} seconds (vectorized Gaspype)")
+print("First 5 Cp values (J/mol·K):", cp_values[:5])

tests/benchmark_cp_comp.py

@@ -0,0 +1,55 @@
+import cantera as ct
+import numpy as np
+import time
+import gaspype as gp
+
+gas = ct.Solution("gri30.yaml")
+n_species = gas.n_species
+n_states = 1_000_000
+
+# Random temperatures and pressures
+temperatures = np.linspace(300.0, 2500.0, n_states)
+pressures = np.full(n_states, ct.one_atm)
+
+# Generate random compositions for H2, H2O, N2
+rng = np.random.default_rng(seed=42)
+fractions = rng.random((n_states, 3))
+fractions /= fractions.sum(axis=1)[:, None]  # normalize
+
+# Convert to full 53-species mole fraction array
+X = np.zeros((n_states, n_species))
+X[:, gas.species_index('H2')] = fractions[:, 0]
+X[:, gas.species_index('H2O')] = fractions[:, 1]
+X[:, gas.species_index('N2')] = fractions[:, 2]
+
+# Build SolutionArray
+states = ct.SolutionArray(gas, n_states)
+
+time.sleep(0.5)
+
+# Vectorized assignment
+t0 = time.perf_counter()
+states.TPX = temperatures, pressures, X
+cp_values = states.cp_mole
+elapsed = time.perf_counter() - t0
+
+print(f"Computed {n_states} Cp values in {elapsed:.4f} seconds (vectorized cantera)")
+print("First 5 Cp values (J/mol-K):", cp_values[:5] / 1000)
+
+
+# Vectorized fluid creation
+fluid = (
+    gp.fluid({'H2': 1}) * fractions[:, 0]
+    + gp.fluid({'H2O': 1}) * fractions[:, 1]
+    + gp.fluid({'N2': 1}) * fractions[:, 2]
+)
+
+time.sleep(0.5)
+
+# Benchmark: calculate Cp for all states at once
+t0 = time.perf_counter()
+cp_values = fluid.get_cp(t=temperatures)
+elapsed = time.perf_counter() - t0
+
+print(f"Computed {n_states} Cp values in {elapsed:.4f} seconds (vectorized Gaspype)")
+print("First 5 Cp values (J/mol·K):", cp_values[:5])

tests/benchmark_equalibrium.py

@@ -0,0 +1,54 @@
+import cantera as ct
+import gaspype as gp
+import numpy as np
+import time
+from gaspype import fluid_system
+
+# -----------------------
+# Settings
+# -----------------------
+n_temps = 1000
+temps_C = np.linspace(300, 1000, n_temps)     # °C
+temperatures = temps_C + 273.15               # K
+pressure = 101325                             # Pa (1 atm)
+
+composition = {"CH4": 0.8, "H2O": 0.2}
+species_to_track = ["CH4", "H2O", "CO", "CO2", "H2", "O2"]
+
+# -----------------------
+# Cantera benchmark
+# -----------------------
+gas = ct.Solution("gri30.yaml")
+gas.TPX = temperatures[0], pressure, composition
+
+eq_cantera = np.zeros((n_temps, len(species_to_track)))
+
+time.sleep(0.5)
+t0 = time.perf_counter()
+for i, T in enumerate(temperatures):
+    gas.TP = T, pressure
+    gas.equilibrate('TP')
+    eq_cantera[i, :] = [gas.X[gas.species_index(s)] for s in species_to_track]
+elapsed_cantera = time.perf_counter() - t0
+print(f"Cantera: {elapsed_cantera:.4f} s")
+
+# -----------------------
+# Gaspype benchmark
+# -----------------------
+# Construct the fluid with composition and tracked species
+fluid = gp.fluid(composition, fs=fluid_system(species_to_track))
+
+time.sleep(0.5)
+t0 = time.perf_counter()
+eq_gaspype = gp.equilibrium(fluid, t=temperatures, p=pressure)
+elapsed_gaspype = time.perf_counter() - t0
+print(f"Gaspype: {elapsed_gaspype:.4f} s")
+
+# -----------------------
+# Compare first 5 results
+# -----------------------
+print("First 5 equilibrium compositions (mole fractions):")
+for i in range(5):
+    print(f"T = {temperatures[i]:.1f} K")
+    print("  Cantera:", eq_cantera[i])
+    print("  Gaspype :", eq_gaspype.array_composition[i])

tests/test_slicing.py

@@ -12,28 +12,28 @@ def test_str_index():
     assert el['C'].shape == (2, 3, 4)
 
 
-def test_str_list_index():
-    assert fl[['CO2', 'H2', 'CO']].shape == (2, 3, 4, 3)
-    assert el[['C', 'H', 'O']].shape == (2, 3, 4, 3)
+def test_single_axis_int_index():
+    assert fl[0].shape == (3, 4)
+    assert fl[1].shape == (3, 4)
+    assert el[1].shape == (3, 4)
+    assert el[0].shape == (3, 4)
 
 
-def test_int_list_index():
-    assert fl[[1, 2, 0, 5]].shape == (2, 3, 4, 4)
-    assert el[[1, 2, 0, 3]].shape == (2, 3, 4, 4)
+def test_single_axis_int_list():
+    assert fl[:, [0, 1]].shape == (2, 2, 4)
+    assert el[:, [0, 1]].shape == (2, 2, 4)
 
 
-def test_mixed_list_index():
-    assert el[[1, 'H', 0, 'O']].shape == (2, 3, 4, 4)
-
-
-def test_int_index():
-    assert fl[5].shape == (2, 3, 4)
-    assert el[-1].shape == (2, 3, 4)
-
-
-def test_slice_index():
-    assert fl[0:3].shape == (2, 3, 4, 3)
-    assert fl[:].shape == (2, 3, 4, 6)
-
-    assert el[0:3].shape == (2, 3, 4, 3)
-    assert el[:].shape == (2, 3, 4, 4)
+def test_multi_axis_int_index():
+    assert fl[0, 1].shape == (4,)
+    assert fl[0, 1, 2].shape == tuple()
+    assert fl[0, 2].shape == (4,)
+    assert fl[:, 2, :].shape == (2, 4)
+    assert fl[0, [1, 2]].shape == (2, 4)
+    assert fl[..., 0].shape == (2, 3)
+    assert el[0, 1].shape == (4,)
+    assert el[0, 1, 2].shape == tuple()
+    assert el[0, 2].shape == (4,)
+    assert el[:, 2, :].shape == (2, 4)
+    assert el[0, [1, 2]].shape == (2, 4)
+    assert el[..., 0].shape == (2, 3)