ExoGibbs 0.2.2__tar.gz → 0.2.4__tar.gz

exogibbs-0.2.4/AGENTS.md

@@ -0,0 +1,34 @@
+# Repository Guidelines
+
+## Project Structure & Module Organization
+- Source: `src/exogibbs/` with subpackages `io/`, `equilibrium/`, `thermo/`, `optimize/`, `api/`, `presets/`, `utils/`; data files under `src/exogibbs/data/`.
+- Tests: `tests/unittests/` organized by domain (e.g., `io/`, `equilibrium/`); files named `*_test.py`.
+- Examples & docs: `examples/` and `documents/`.
+
+## Build, Test, and Development Commands
+- Install (editable): `python -m pip install -e .` (Python >= 3.9).
+- Run tests: `pytest tests/unittests` (CI exports `results/pytest.xml`).
+- Optional build: `python -m pip install build && python -m build` (ensure Git tags for correct versioning).
+
+## Coding Style & Naming Conventions
+- Language: Python with type hints where practical; 4-space indentation; keep functions short and focused.
+- Naming: modules/functions/variables `snake_case`; classes `CapWords`; constants `UPPER_SNAKE_CASE`.
+- Imports: standard lib, third-party, then local; avoid unused imports.
+
+## Testing Guidelines
+- Framework: `pytest`; keep tests deterministic (no network/GPU). Use small fixtures and cover edge cases (e.g., parsing, interpolation bounds).
+- Location/pattern: place tests under `tests/unittests/<area>/`, name `*_test.py`.
+- Run locally: `pytest tests/unittests`. Aim to maintain/raise coverage of changed code.
+
+## Commit & Pull Request Guidelines
+- Commits: concise, imperative (e.g., "thermo: fix electron parsing"); group related changes; reference issues (`#123`) when applicable.
+- PRs: include a clear description, motivation, and testing notes; link issues; add/adjust tests; update data packaging (`MANIFEST.in`) when adding files under `src/exogibbs/data/`.
+- CI: PRs to `develop`/`main` must pass the pytest workflow.
+
+## Architecture Overview (Quick)
+- `io.load_data`: loads molecule catalogs and JANAF-like tables.
+- `thermo.stoichiometry`: builds formula matrices from species names.
+- `equilibrium.gibbs`: pads tables and provides JAX-friendly interpolation of h-vectors.
+- `optimize.*`: JAX-based core, VJP, and minimization routines.
+- `api.chemistry` and `presets/`: typed containers and ready-to-use setups.
+

{exogibbs-0.2.2 → exogibbs-0.2.4}/MANIFEST.in

@@ -2,5 +2,4 @@ include src/exogibbs/data/janaf_raw_sample.txt
 include src/exogibbs/data/testdata.dat
 include src/exogibbs/data/matrix_v3.dat
 include src/exogibbs/data/molecule_names.csv
-include src/exogibbs/data/gibbs_matrices.npz
-include src/exogibbs/data/number_of_species.sample.list
+include src/exogibbs/data/gibbs_matrices.npz

{exogibbs-0.2.2/src/exogibbs.egg-info → exogibbs-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exogibbs
-Version: 0.2.2
+Version: 0.2.4
 Summary: Differentiable Thermochemical Equilibrium Solver for Exoplanet Atmospheres
 Author-email: Hajime Kawahara <divrot@gmail.com>
 Maintainer-email: Hajime Kawahara <divrot@gmail.com>
@@ -24,11 +24,36 @@ Requires-Dist: thermochem
 Dynamic: license-file
 
 # ExoGibbs
+ [![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/HajimeKawahara/exogibbs)
 
 Differentiable Thermochemical Equilibrium, powered by JAX. 
 
-The optimization scheme is based on the Lagrange multiplier, similar to NASA/CEA algorithm. 
-The terminology follows Smith and Missen. 
+The optimization scheme is based on the Lagrange multiplier, similar to [NASA/CEA algorithm](https://ntrs.nasa.gov/api/citations/19950013764/downloads/19950013764.pdf). 
+The terminology follows Smith and Missen, [Chemical Reaction Equilibrium Analysis](https://aiche.onlinelibrary.wiley.com/doi/10.1002/aic.690310127) (1983, Wiley-Interscience). 
+
+## Basic Use
+
+```python
+from exogibbs.presets.ykb4 import prepare_ykb4_setup
+from exogibbs.api.equilibrium import equilibrium_profile, EquilibriumOptions
+
+# chemical setup
+chem = prepare_ykb4_setup()
+
+# Thermodynamic conditions
+Pref = 1.0  # bar, reference pressure
+opts = EquilibriumOptions(epsilon_crit=1e-11, max_iter=1000)
+
+res = equilibrium_profile(
+    chem,
+    temperature_profile,
+    pressure_profile,
+    chem.element_vector,
+    Pref=Pref,
+    options=opts,
+)
+nk_result = res.x #mixing ratio
+```
 
 ExoGibbs is designed to plug into [ExoJAX](https://github.com/HajimeKawahara/exojax) and enable gradient-based equilibrium retrievals. 
 It is still in a very beta stage, so please use it at your own risk.

exogibbs-0.2.4/README.md

@@ -0,0 +1,34 @@
+# ExoGibbs
+ [![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/HajimeKawahara/exogibbs)
+
+Differentiable Thermochemical Equilibrium, powered by JAX. 
+
+The optimization scheme is based on the Lagrange multiplier, similar to [NASA/CEA algorithm](https://ntrs.nasa.gov/api/citations/19950013764/downloads/19950013764.pdf). 
+The terminology follows Smith and Missen, [Chemical Reaction Equilibrium Analysis](https://aiche.onlinelibrary.wiley.com/doi/10.1002/aic.690310127) (1983, Wiley-Interscience). 
+
+## Basic Use
+
+```python
+from exogibbs.presets.ykb4 import prepare_ykb4_setup
+from exogibbs.api.equilibrium import equilibrium_profile, EquilibriumOptions
+
+# chemical setup
+chem = prepare_ykb4_setup()
+
+# Thermodynamic conditions
+Pref = 1.0  # bar, reference pressure
+opts = EquilibriumOptions(epsilon_crit=1e-11, max_iter=1000)
+
+res = equilibrium_profile(
+    chem,
+    temperature_profile,
+    pressure_profile,
+    chem.element_vector,
+    Pref=Pref,
+    options=opts,
+)
+nk_result = res.x #mixing ratio
+```
+
+ExoGibbs is designed to plug into [ExoJAX](https://github.com/HajimeKawahara/exojax) and enable gradient-based equilibrium retrievals. 
+It is still in a very beta stage, so please use it at your own risk.

{exogibbs-0.2.2 → exogibbs-0.2.4}/documents/conf.py

@@ -58,7 +58,7 @@ html_theme = "sphinx_rtd_theme"
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
-html_logo = "_static/logo.png"
+html_logo = "_static/exogibbs_logo.png"
 
 # html_theme_options = {
 #    'style_nav_header_background': '#333',

exogibbs-0.2.4/documents/exogibbs/conf.py

@@ -0,0 +1,36 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'exogibbs'
+copyright = '2025, Author'
+author = 'Author'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.todo',
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+language = 'en'
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']
+
+# -- Options for todo extension ----------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/todo.html#configuration
+
+todo_include_todos = True

exogibbs-0.2.4/documents/index.rst

@@ -0,0 +1,47 @@
+.. exojax documentation master file, created by
+   sphinx-quickstart on Mon Jan 11 14:38:51 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+   
+ExoGibbs
+==================================
+
+Version 0.2
+
+|:frog:| `DeepWiki for ExoGibbs <https://deepwiki.com/HajimeKawahara/exogibbs>`_
+
+
+`ExoGibbs <https://github.com/HajimeKawahara/exogibbs>`_ provides an auto-differentiable thermalchemical equilibrium solver
+based on the Gibbs free energy minimization method, powered by `JAX <https://github.com/google/jax>`_. 
+
+
+Contents
+==================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: PRESETS:
+
+   presets/ykb4.rst
+   
+   
+.. toctree::
+   :maxdepth: 1
+   :caption: API:
+
+   exogibbs/exogibbs.rst
+
+
+
+
+License & Attribution
+---------------------
+
+Copyright 2025-, Contributors
+
+- `Hajime Kawahara <http://secondearths.sakura.ne.jp/en/index.html>`_ (@HajimeKawahara, maintainer)
+- `Yui Kawashima <https://sites.google.com/view/yuikawashima/home>`_ (@ykawashima, the reference code author we inherit, the presets ykb4 originally comes from this code.)
+-
+
+ExoGibbs is free software made available under the MIT License.
+   

exogibbs-0.2.4/documents/presets/ykb4.rst

@@ -0,0 +1,196 @@
+YKB4 Preset
+===========
+
+Overview
+--------
+The ykb4 preset bundles a ready-to-use ChemicalSetup based on JANAF-like
+Gibbs tables. It exposes a device-friendly stoichiometric matrix and a
+JAX-differentiable h(T) interpolator for equilibrium calculations.
+
+Quick Start
+-----------
+.. code-block:: python
+
+   from exogibbs.presets.ykb4 import prepare_ykb4_setup
+   from exogibbs.api.equilibrium import equilibrium
+
+   setup = prepare_ykb4_setup()
+   T, P = 1500.0, 1.0  # K, bar
+   b = setup.element_vector_reference  # or your own jnp.array([...])
+   result = equilibrium(setup, T=T, P=P, b=b)
+   print(result.x)  # mole fractions (K,)
+
+Elements
+--------
+The following elements are included in this preset (including electrons as "e-"):
+
+``C, H, He, K, N, Na, O, P, S, Ti, V, e-``
+
+The reference elemental abundances (`element_vector_ref`) are taken from Asplund, Amarsi & Grevesse (2021).
+
+Species (JANAF key)
+-------------------
+The species list corresponds to the ``JANAF`` column in ``molecule_names.csv``.
+
+.. code-block:: text
+
+   000: C1
+   001: H2
+   002: He1
+   003: K1
+   004: N2
+   005: Na1
+   006: O2
+   007: Ti1
+   008: V1
+   009: P1
+   010: S1
+   011: e1-
+   012: C1H1
+   013: C1H1N1
+   014: C1H1N1O1
+   015: C1H1O1
+   016: C1H2
+   017: C1H2O1
+   018: C1H3
+   019: C1H4
+   020: C1K1N1
+   021: C1N1
+   022: C1N1Na1
+   023: C1N1O1
+   024: C1N2(CNN)
+   025: C1N2(NCN)
+   026: C1O1
+   027: C1O2
+   028: C2
+   029: C2H1
+   030: C2H2
+   031: C2H4
+   032: C2H4O1
+   033: C2K2N2
+   034: C2N1
+   035: C2N2
+   036: C2N2Na2
+   037: C2O1
+   038: C3
+   039: C3O2
+   040: C4
+   041: C4N2
+   042: C5
+   043: H1
+   044: H1K1
+   045: H1K1O1
+   046: H1N1
+   047: H1N1O1
+   048: H1N1O2(cis)
+   049: H1N1O2(trans)
+   050: H1N1O3
+   051: H1Na1
+   052: H1Na1O1
+   053: H1O1
+   054: H1O2
+   055: H2K2O2
+   056: H2N1
+   057: H2N2
+   058: H2Na2O2
+   059: H2O1
+   060: H2O2
+   061: H3N1
+   062: H4N2
+   063: K1O1
+   064: K2
+   065: N1
+   066: N1O1
+   067: N1O2
+   068: N1O3
+   069: N2O1
+   070: N2O3
+   071: N2O4
+   072: N2O5
+   073: N3
+   074: Na1O1
+   075: Na2
+   076: O1
+   077: O3
+   078: N1V1
+   079: O1Ti1
+   080: O1V1
+   081: O2Ti1
+   082: O2V1
+   083: C1H1P1
+   084: C1O1S1
+   085: C1P1
+   086: C1S1
+   087: C1S2
+   088: H1P1
+   089: H1S1
+   090: H2O4S1
+   091: H2P1
+   092: H2S1
+   093: H3P1
+   094: K2O4S1
+   095: N1P1
+   096: N1S1
+   097: Na2O4S1
+   098: O1P1
+   099: O1S1
+   100: O1S2
+   101: O2P1
+   102: O2S1
+   103: O3S1
+   104: O6P4
+   105: O10P4
+   106: P1S1
+   107: P2
+   108: P4
+   109: P4S3
+   110: S2
+   111: S3
+   112: S4
+   113: S5
+   114: S6
+   115: S7
+   116: S8
+   117: C1+
+   118: C1-
+   119: C1H1+
+   120: C1H1O1+
+   121: C1N1+
+   122: C1N1-
+   123: C1O2-
+   124: C2-
+   125: H1+
+   126: H1-
+   127: H1K1O1+
+   128: H1Na1O1+
+   129: H1O1+
+   130: H1O1-
+   131: H2+
+   132: H2-
+   133: H3O1+
+   134: He1+
+   135: K1+
+   136: K1-
+   137: K1O1-
+   138: N1+
+   139: N1-
+   140: N1O1+
+   141: N1O2-
+   142: N2+
+   143: N2-
+   144: N2O1+
+   145: Na1+
+   146: Na1-
+   147: Na1O1-
+   148: O1+
+   149: O1-
+   150: O2+
+   151: O2-
+   152: P1+
+   153: P1-
+   154: S1+
+   155: S1-
+   156: Ti1+
+   157: Ti1-
+   158: V1+
+   159: V1-

exogibbs-0.2.4/examples/benchmark/clfac_yk.py

@@ -0,0 +1,73 @@
+"""
+Validation of Gibbs Minimization Against ykawashima's B4 code
+============================================================
+
+This example demonstrates and validates the ExoGibbs thermochemical equilibrium
+solver against the code by ykawashima when she was at B4.
+
+Updated to use the high-level API: exogibbs.api.equilibrium.equilibrium.
+"""
+from exogibbs.presets.ykb4 import prepare_ykb4_setup
+import jax.numpy as jnp
+from exogibbs.api.chemistry import ThermoState
+from exogibbs.optimize.minimize import minimize_gibbs_core
+
+from exogibbs.optimize.core import compute_ln_normalized_pressure
+
+from jax import config
+
+config.update("jax_enable_x64", True)
+
+#chemical setup
+chem = prepare_ykb4_setup()
+
+# Thermodynamic conditions
+temperature = 500.0  # K
+P = 10.0  # bar
+Pref = 1.0  # bar, reference pressure
+ln_normalized_pressure = compute_ln_normalized_pressure(P, Pref)
+
+# Initial guess for log number densities
+ln_nk = jnp.zeros(chem.formula_matrix.shape[1])  # log(n_species)
+ln_ntot = 0.0  # log(total number density)
+
+# old reference elemental abundance b from yk's sample number densities
+b_old_ref = jnp.array(
+    [
+        4.8774824e-04,
+        1.6749767e00,
+        1.6143440e-01,
+        2.5438149e-07,
+        1.3435642e-04,
+        3.9624806e-06,
+        9.7356725e-04,
+        5.7690579e-07,
+        3.0653933e-05,
+        1.6687756e-07,
+        1.9870969e-08,
+        0.0000000e00,
+    ]
+)
+# ThermoState instance
+thermo_state = ThermoState(
+    temperature=temperature,
+    ln_normalized_pressure=ln_normalized_pressure,
+    element_vector=b_old_ref,
+)
+
+# Convergence criteria
+epsilon_crit = 1e-11
+max_iter = 1000
+
+ln_nk_result, _, icount = minimize_gibbs_core(
+    thermo_state,
+    ln_nk,
+    ln_ntot,
+    chem.formula_matrix,
+    chem.hvector_func,
+    epsilon_crit=epsilon_crit,
+    max_iter=max_iter,
+)
+nk_result = jnp.exp(ln_nk_result)
+print("icount", icount) 
+#702 for clfac = 0.1, 347 for _cea_lambda

{exogibbs-0.2.2 → exogibbs-0.2.4}/examples/comparisons/comparison_with_hcosystem.py

@@ -67,10 +67,10 @@ def hvector_func(temperature):
 bH = 0.5
 bC = 0.2
 bO = 0.3
-b_element_vector = jnp.array([bH, bC, bO])  # H, C, O
+element_vector = jnp.array([bH, bC, bO])  # H, C, O
 
 # ThermoState instance
-thermo_state = ThermoState(temperature, ln_normalized_pressure, b_element_vector)
+thermo_state = ThermoState(temperature, ln_normalized_pressure, element_vector)
 
 # Convergence criteria
 epsilon_crit = 1e-11
@@ -110,8 +110,8 @@ assert jnp.abs(res) < epsilon_crit * 10.0
 from exogibbs.test.analytic_hcosystem import derivative_dlnnCO_db
 
 dlnn_db = jacrev(
-    lambda b_element_vector_in: minimize_gibbs(
-        ThermoState(temperature, ln_normalized_pressure, b_element_vector_in),
+    lambda element_vector_in: minimize_gibbs(
+        ThermoState(temperature, ln_normalized_pressure, element_vector_in),
         ln_nk,
         ln_ntot,
         formula_matrix,
@@ -119,7 +119,7 @@ dlnn_db = jacrev(
         epsilon_crit=epsilon_crit,
         max_iter=max_iter,
     )
-)(b_element_vector) # (n_species, n_elements)
+)(element_vector) # (n_species, n_elements)
 
 # analytical derivatives
 gradf = derivative_dlnnCO_db(ln_nk_result[1], bC, bH, bO, k)

{exogibbs-0.2.2 → exogibbs-0.2.4}/examples/comparisons/comparison_with_hsystem.py

@@ -61,10 +61,10 @@ def hvector_func(temperature):
 
 
 # Element abundance constraint: total H nuclei = 1.0
-b_element_vector = jnp.array([1.0])
+element_vector = jnp.array([1.0])
 
 # ThermoState instance
-thermo_state = ThermoState(temperature, ln_normalized_pressure, b_element_vector)
+thermo_state = ThermoState(temperature, ln_normalized_pressure, element_vector)
 
 # Convergence criteria
 epsilon_crit = 1e-11
@@ -116,7 +116,7 @@ dln_dT = jacrev(
         ThermoState(
             temperature_in,
             ln_normalized_pressure,
-            b_element_vector,
+            element_vector,
         ),
         ln_nk,
         ln_ntot,
@@ -152,7 +152,7 @@ dln_dlogp = jacrev(
         ThermoState(
             temperature,
             ln_normalized_pressure,
-            b_element_vector,
+            element_vector,
         ),
         ln_nk,
         ln_ntot,
@@ -193,7 +193,7 @@ ln_ntot_init = 0.0
 # Vectorize minimize_gibbs over temperature axis
 def func(T):
         return minimize_gibbs(
-            ThermoState(T, ln_normalized_pressure, b_element_vector),
+            ThermoState(T, ln_normalized_pressure, element_vector),
             ln_nk_init,
             ln_ntot_init,
             formula_matrix,
@@ -327,7 +327,7 @@ print(f"Pressure range: {Parr[0]:.3f} to {Parr[-1]:.0f} bar ({len(Parr)} points)
 # Vectorize minimize_gibbs over temperature axis
 def funcp(logpin):
         return minimize_gibbs(
-            ThermoState(temperature, logpin, b_element_vector),
+            ThermoState(temperature, logpin, element_vector),
             ln_nk_init,
             ln_ntot_init,
             formula_matrix,

{exogibbs-0.2.2 → exogibbs-0.2.4}/examples/comparisons/comparison_with_ykcode.py

@@ -11,7 +11,7 @@ Updated to use the high-level API: exogibbs.api.equilibrium.equilibrium.
 from exogibbs.presets.ykb4 import prepare_ykb4_setup
 from exogibbs.api.equilibrium import equilibrium, EquilibriumOptions
 import numpy as np
-
+import jax.numpy as jnp
 from jax import config
 
 config.update("jax_enable_x64", True)
@@ -22,9 +22,28 @@ temperature = 500.0  # K
 P = 10.0  # bar
 Pref = 1.0  # bar, reference pressure
 
-#chemical setup
+# chemical setup
 chem = prepare_ykb4_setup()
 
+# old reference elemental abundance b from yk's sample number densities
+b_old_ref = jnp.array(
+    [
+        4.8774824e-04,
+        1.6749767e00,
+        1.6143440e-01,
+        2.5438149e-07,
+        1.3435642e-04,
+        3.9624806e-06,
+        9.7356725e-04,
+        5.7690579e-07,
+        3.0653933e-05,
+        1.6687756e-07,
+        1.9870969e-08,
+        0.0000000e00,
+    ]
+)
+
+
 ##############################################################################
 # Solve equilibrium via high-level API
 # ------------------------------------
@@ -33,7 +52,7 @@ res = equilibrium(
     chem,
     T=temperature,
     P=P,
-    b=chem.b_element_vector_reference,
+    b=b_old_ref,
     Pref=Pref,
     options=opts,
 )
@@ -43,21 +62,22 @@ nk_result = res.n
 
 # load yk's results for 10 bar
 dat = np.loadtxt("../data/p10.txt", delimiter=",")
-mask = dat > 1.e-14
+mask = dat > 1.0e-14
 mask_nk_result = nk_result[mask]
 mask_dat = dat[mask]
 
-res = mask_nk_result/mask_dat - 1.0
-print(res,"diff for n>1.e-14")
+res = mask_nk_result / mask_dat - 1.0
+print(res, "diff for n>1.e-14")
 assert np.max(np.abs(res)) < 0.051
 # 8/9/2025
-#[-0.00163185 -0.00163185  0.02571018 -0.00203837 -0.05069541 -0.00163185
+# [-0.00163185 -0.00163185  0.02571018 -0.00203837 -0.05069541 -0.00163185
 # -0.00481986 -0.00420364 -0.00161074 -0.00163182 -0.00163185 -0.00163183
 # -0.00163184 -0.00163178 -0.00163185 -0.00163184]
 
 
 ind = np.arange(len(nk_result))
 import matplotlib.pyplot as plt
+
 plt.plot(ind, nk_result, "+", label="ExoGibbs")
 plt.plot(ind, dat, ".", alpha=0.5, label="yk B4 code")
 plt.xlabel("Species Index")
@@ -66,4 +86,3 @@ plt.yscale("log")
 plt.legend()
 plt.grid()
 plt.show()
-

exogibbs-0.2.4/examples/layers/layer_ykb4.py

@@ -0,0 +1,44 @@
+"""
+Validation of Gibbs Minimization for Layered Systems 
+===================================================================================
+
+This example demonstrates and validates the ExoGibbs thermochemical equilibrium for the layered system
+
+Updated to use the high-level API: exogibbs.api.equilibrium.equilibrium.
+"""
+
+from exogibbs.presets.ykb4 import prepare_ykb4_setup
+from exogibbs.api.equilibrium import equilibrium_profile, EquilibriumOptions
+import numpy as np
+import jax.numpy as jnp
+from jax import config
+
+config.update("jax_enable_x64", True)
+
+
+# Thermodynamic conditions
+Pref = 1.0  # bar, reference pressure
+Parr = jnp.logspace(-8, 2, 10)/Pref  # bar
+Tarr = 1500*Parr**0.1
+
+
+#chemical setup
+chem = prepare_ykb4_setup()
+
+##############################################################################
+# Solve equilibrium via high-level API
+# ------------------------------------
+opts = EquilibriumOptions(epsilon_crit=1e-11, max_iter=1000)
+
+res = equilibrium_profile(
+    chem,
+    Tarr,
+    Parr,
+    chem.element_vector_reference,
+    Pref=Pref,
+    options=opts,
+)
+
+##############################################################################
+nk_result = res.n
+print(nk_result)