From 71cae9c71c4be5c1de9fe264be9f5df446aabbb5 Mon Sep 17 00:00:00 2001
From: Ian Bell <ian.bell@nist.gov>
Date: Wed, 6 Jul 2022 15:16:24 -0400
Subject: [PATCH] Work on docs
Add cubics info, auto-execute, getting started
---
doc/source/algorithms/critical_curves.ipynb | 38 ++++++++
doc/source/algorithms/index.rst | 8 +-
doc/source/conf.py | 8 ++
doc/source/derivs/derivs.ipynb | 35 +++++--
doc/source/getting_started/index.rst | 12 +++
doc/source/index.rst | 3 +-
doc/source/models/CPA.ipynb | 43 +++++++++
doc/source/models/PCSAFT.ipynb | 43 +++++++++
doc/source/models/cubics.ipynb | 80 +++++++++++++++-
doc/source/models/index.rst | 2 +
doc/source/models/multifluid.ipynb | 100 +++++++++++++++++---
11 files changed, 344 insertions(+), 28 deletions(-)
create mode 100644 doc/source/algorithms/critical_curves.ipynb
create mode 100644 doc/source/getting_started/index.rst
create mode 100644 doc/source/models/CPA.ipynb
create mode 100644 doc/source/models/PCSAFT.ipynb
diff --git a/doc/source/algorithms/critical_curves.ipynb b/doc/source/algorithms/critical_curves.ipynb
new file mode 100644
index 0000000..c90ede6
--- /dev/null
+++ b/doc/source/algorithms/critical_curves.ipynb
@@ -0,0 +1,38 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "8218498b",
+ "metadata": {},
+ "source": [
+ "# Critical curves\n",
+ "\n",
+ "A pure fluid has a single vapor-liquid critical point, but mixtures are different:\n",
+ "\n",
+ "* They may have multiple (or zero!) critical points for given mixture composition\n",
+ "* The critical curves may not emanate from the pure fluid endpoints"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.10.4"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/doc/source/algorithms/index.rst b/doc/source/algorithms/index.rst
index 57169ed..13225b9 100644
--- a/doc/source/algorithms/index.rst
+++ b/doc/source/algorithms/index.rst
@@ -5,4 +5,10 @@ Algorithms
:maxdepth: 2
:caption: Contents:
- VLE
\ No newline at end of file
+ VLE
+ critical_curves
+
+Information
+-----------
+
+The algorithms are written in a very generic way; they take an instance of a thermodynamic model, and the necessary derivatives are calculated from this model with automatic differentiation (or similar). In that way, implementing a model is all that is required to enable its use in the calculation of critical curves or to trace the phase equilibria. Determining the starting values, on the other hand, may require model-specific assistance, for instance with superancillary equations.
\ No newline at end of file
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 5449eb1..debde9b 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -4,6 +4,8 @@
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
+import os, subprocess
+
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
@@ -25,6 +27,12 @@ author = 'Ian Bell'
import teqp
release = teqp.__version__
+# -- Exeucute all notebooks --------------------------------------------------
+
+for path, dirs, files in os.walk('.'):
+ for file in files:
+ if file.endswith('.ipynb'):
+ subprocess.check_output(f'jupyter nbconvert --ExecutePreprocessor.allow_errors=True --to notebook --output {file} --execute {file}', cwd=path)
# -- General configuration ---------------------------------------------------
diff --git a/doc/source/derivs/derivs.ipynb b/doc/source/derivs/derivs.ipynb
index 7af50d8..aa39bc3 100644
--- a/doc/source/derivs/derivs.ipynb
+++ b/doc/source/derivs/derivs.ipynb
@@ -10,9 +10,16 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": 1,
"id": "ca35cc29",
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:39:50.124207Z",
+ "iopub.status.busy": "2022-07-06T18:39:50.124207Z",
+ "iopub.status.idle": "2022-07-06T18:39:50.261696Z",
+ "shell.execute_reply": "2022-07-06T18:39:50.261181Z"
+ }
+ },
"outputs": [],
"source": [
"import teqp\n",
@@ -21,9 +28,16 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 2,
"id": "8d254c40",
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:39:50.264736Z",
+ "iopub.status.busy": "2022-07-06T18:39:50.264736Z",
+ "iopub.status.idle": "2022-07-06T18:39:50.277541Z",
+ "shell.execute_reply": "2022-07-06T18:39:50.276780Z"
+ }
+ },
"outputs": [],
"source": [
"Tc_K = [300]\n",
@@ -34,9 +48,16 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 3,
"id": "49ee3453",
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:39:50.280537Z",
+ "iopub.status.busy": "2022-07-06T18:39:50.280537Z",
+ "iopub.status.idle": "2022-07-06T18:39:50.292555Z",
+ "shell.execute_reply": "2022-07-06T18:39:50.292555Z"
+ }
+ },
"outputs": [
{
"data": {
@@ -44,7 +65,7 @@
"-0.06836660379313926"
]
},
- "execution_count": 8,
+ "execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
diff --git a/doc/source/getting_started/index.rst b/doc/source/getting_started/index.rst
new file mode 100644
index 0000000..e573440
--- /dev/null
+++ b/doc/source/getting_started/index.rst
@@ -0,0 +1,12 @@
+Getting Started
+===============
+
+teqp is a C++-based library with wrappers. The documentation is based on the Python wrapper because it can be readily integrated with the documentation tools and can be auto-generated at documentation build time.
+
+The library can (for Python) be installed with:
+
+.. code::
+
+ pip install teqp
+
+as the binary wheels for all major platforms are provided on pypi.
\ No newline at end of file
diff --git a/doc/source/index.rst b/doc/source/index.rst
index d321ead..9cbb358 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -5,8 +5,9 @@ Welcome to teqp's documentation!
:maxdepth: 2
:caption: Contents:
- derivs/index
+ getting_started/index
models/index
+ derivs/index
algorithms/index
Indices and tables
diff --git a/doc/source/models/CPA.ipynb b/doc/source/models/CPA.ipynb
new file mode 100644
index 0000000..2a597f2
--- /dev/null
+++ b/doc/source/models/CPA.ipynb
@@ -0,0 +1,43 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "df447d16",
+ "metadata": {},
+ "source": [
+ "# Cubic EOS\n",
+ "\n",
+ "Something about cubic EOS"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "9a884dab",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.10.4"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/doc/source/models/PCSAFT.ipynb b/doc/source/models/PCSAFT.ipynb
new file mode 100644
index 0000000..2a597f2
--- /dev/null
+++ b/doc/source/models/PCSAFT.ipynb
@@ -0,0 +1,43 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "df447d16",
+ "metadata": {},
+ "source": [
+ "# Cubic EOS\n",
+ "\n",
+ "Something about cubic EOS"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "9a884dab",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.10.4"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/doc/source/models/cubics.ipynb b/doc/source/models/cubics.ipynb
index 2a597f2..1b1ba08 100644
--- a/doc/source/models/cubics.ipynb
+++ b/doc/source/models/cubics.ipynb
@@ -5,18 +5,90 @@
"id": "df447d16",
"metadata": {},
"source": [
- "# Cubic EOS\n",
+ "# General cubics\n",
"\n",
- "Something about cubic EOS"
+ "The reduced residual Helmholtz energy for the main cubic EOS (van der Waals, Peng-Robinson, and Soave-Redlich-Kwong) can be written in a common form:\n",
+ "\n",
+ "$$ \\begin{equation}\n",
+ "\\label{eq:alphar_from_psi}\n",
+ "\\alpha^r = \\psi^{(-)} - \\dfrac{\\tau a_m}{RT_r } \\psi^{(+)}.\n",
+ "\\end{equation}$$\n",
+ "\n",
+ "$$ \\begin{eqnarray}\n",
+ "\\psi^{(-)} &=& \\int_0^\\delta\\dfrac{b_m\\rho_r }{1-b_m\\delta\\rho_r }{\\rm d}\\delta \\label{eq:psiminusintegral}\\\\\n",
+ " &=&-\\ln(1-b_m\\rho ). \\label{eq:psiminusresult}\n",
+ "\\end{eqnarray} $$\n",
+ "\n",
+ "$$ \\begin{eqnarray}\n",
+ "\\psi^{(+)} &=& \\int_0^\\delta \\dfrac{\\rho_r}{\\left(1+\\Delta_1 b_m\\delta\\rho_r \\right)\\left(1+\\Delta_2 b_m\\delta\\rho_r \\right)} {\\rm d}\\delta \\label{eq:psiplusintegral}\\\\\n",
+ " &=& \\dfrac{\\ln\\left(\\dfrac{\\Delta_1 b_m\\rho+1}{\\Delta_2b_m\\rho+1}\\right)}{b_m(\\Delta_1-\\Delta_2)}\\label{eq:psiplusresult}\n",
+ "\\end{eqnarray} $$\n",
+ "\n",
+ "with the constants given by:\n",
+ "\n",
+ "* vdW: $\\Delta_1=0$, $\\Delta_2=0$\n",
+ "* SRK: $\\Delta_1=1$, $\\Delta_2=0$\n",
+ "* PR: $\\Delta_1=1+\\sqrt{2}$, $\\Delta_2=1-\\sqrt{2}$\n",
+ "\n",
+ "The quantities $a_m$ and $b_m$ are described (with exact solutions for the numerical coefficients) for each of these EOS in https://pubs.acs.org/doi/abs/10.1021/acs.iecr.1c00847.\n",
+ "\n",
+ "The models in teqp are instantiated based on knowledge of the critical temperature, pressure, and acentric factor. Thereafter all quantities are obtained from derivatives of $\\alpha^r$."
]
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 4,
"id": "9a884dab",
"metadata": {},
"outputs": [],
- "source": []
+ "source": [
+ "import teqp\n",
+ "\n",
+ "# Values taken from http://dx.doi.org/10.6028/jres.121.011\n",
+ "Tc_K = [ 190.564, 154.581, 150.687 ]\n",
+ "pc_Pa = [ 4599200, 5042800, 4863000 ]\n",
+ "acentric = [ 0.011, 0.022, -0.002 ]\n",
+ "\n",
+ "# Instantiate Peng-Robinson model\n",
+ "modelPR = teqp.canonical_PR(Tc_K, pc_Pa, acentric)\n",
+ "\n",
+ "# Instantiate Soave-Redlich-Kwong model\n",
+ "modelSRK = teqp.canonical_SRK(Tc_K, pc_Pa, acentric)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "615c7830",
+ "metadata": {},
+ "source": [
+ "## Adjusting k_ij\n",
+ "\n",
+ "Fine-tuned values of $k_{ij}$ can be provided when instantiating the model, for Peng-Robinson and SRK. A complete matrix of all the $k_{ij}$ values must be provided. This allows for asymmetric mixing models in which $k_{ij}\\neq k_{ji}$."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "id": "a8c87890",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "<teqp.teqp.GenericCubic at 0x20b222799b0>"
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "k_12 = 0.01\n",
+ "kmat = [[0,k_12,0],[k_12,0,0],[0,0,0]]\n",
+ "teqp.canonical_PR(Tc_K, pc_Pa, acentric, kmat)\n",
+ "teqp.canonical_SRK(Tc_K, pc_Pa, acentric, kmat)"
+ ]
}
],
"metadata": {
diff --git a/doc/source/models/index.rst b/doc/source/models/index.rst
index 3556777..30b3ec5 100644
--- a/doc/source/models/index.rst
+++ b/doc/source/models/index.rst
@@ -7,3 +7,5 @@ Models
cubics
multifluid
+ CPA
+ PCSAFT
diff --git a/doc/source/models/multifluid.ipynb b/doc/source/models/multifluid.ipynb
index 82d80bc..7603722 100644
--- a/doc/source/models/multifluid.ipynb
+++ b/doc/source/models/multifluid.ipynb
@@ -12,12 +12,19 @@
{
"cell_type": "code",
"execution_count": 1,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:06.606089Z",
+ "iopub.status.busy": "2022-07-06T18:40:06.605465Z",
+ "iopub.status.idle": "2022-07-06T18:40:07.147629Z",
+ "shell.execute_reply": "2022-07-06T18:40:07.146669Z"
+ }
+ },
"outputs": [
{
"data": {
"text/plain": [
- "'0.8.1'"
+ "'0.9.2'"
]
},
"execution_count": 1,
@@ -43,13 +50,20 @@
{
"cell_type": "code",
"execution_count": 2,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:07.163785Z",
+ "iopub.status.busy": "2022-07-06T18:40:07.163785Z",
+ "iopub.status.idle": "2022-07-06T18:40:17.280030Z",
+ "shell.execute_reply": "2022-07-06T18:40:17.278333Z"
+ }
+ },
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "13.4 ms ± 158 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n"
+ "12.9 ms ± 4.32 ms per loop (mean ± std. dev. of 7 runs, 100 loops each)\n"
]
}
],
@@ -62,13 +76,20 @@
{
"cell_type": "code",
"execution_count": 3,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:17.286031Z",
+ "iopub.status.busy": "2022-07-06T18:40:17.285350Z",
+ "iopub.status.idle": "2022-07-06T18:40:27.300085Z",
+ "shell.execute_reply": "2022-07-06T18:40:27.299050Z"
+ }
+ },
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "121 ms ± 3.07 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+ "120 ms ± 19.9 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
]
}
],
@@ -89,13 +110,20 @@
{
"cell_type": "code",
"execution_count": 4,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:27.307115Z",
+ "iopub.status.busy": "2022-07-06T18:40:27.307115Z",
+ "iopub.status.idle": "2022-07-06T18:40:34.876155Z",
+ "shell.execute_reply": "2022-07-06T18:40:34.875146Z"
+ }
+ },
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "105 ms ± 968 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
+ "85.4 ms ± 12.3 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)\n"
]
}
],
@@ -110,13 +138,20 @@
{
"cell_type": "code",
"execution_count": 5,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:34.879157Z",
+ "iopub.status.busy": "2022-07-06T18:40:34.879157Z",
+ "iopub.status.idle": "2022-07-06T18:40:42.930387Z",
+ "shell.execute_reply": "2022-07-06T18:40:42.930079Z"
+ }
+ },
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
- "14.1 ms ± 1.12 ms per loop (mean ± std. dev. of 7 runs, 100 loops each)\n"
+ "9.9 ms ± 164 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)\n"
]
}
],
@@ -138,7 +173,14 @@
{
"cell_type": "code",
"execution_count": 6,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:42.932720Z",
+ "iopub.status.busy": "2022-07-06T18:40:42.932720Z",
+ "iopub.status.idle": "2022-07-06T18:40:42.946939Z",
+ "shell.execute_reply": "2022-07-06T18:40:42.945927Z"
+ }
+ },
"outputs": [],
"source": [
"# And you can also load the JSON that teqp is loading for the pure fluids\n",
@@ -155,7 +197,14 @@
{
"cell_type": "code",
"execution_count": 7,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:42.949975Z",
+ "iopub.status.busy": "2022-07-06T18:40:42.948972Z",
+ "iopub.status.idle": "2022-07-06T18:40:42.962308Z",
+ "shell.execute_reply": "2022-07-06T18:40:42.961547Z"
+ }
+ },
"outputs": [],
"source": [
"# Load the default JSON for the binary interaction parameters\n",
@@ -165,7 +214,14 @@
{
"cell_type": "code",
"execution_count": 8,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:42.965595Z",
+ "iopub.status.busy": "2022-07-06T18:40:42.964944Z",
+ "iopub.status.idle": "2022-07-06T18:40:42.978409Z",
+ "shell.execute_reply": "2022-07-06T18:40:42.977232Z"
+ }
+ },
"outputs": [
{
"data": {
@@ -197,7 +253,14 @@
{
"cell_type": "code",
"execution_count": 9,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:42.981288Z",
+ "iopub.status.busy": "2022-07-06T18:40:42.981288Z",
+ "iopub.status.idle": "2022-07-06T18:40:42.993879Z",
+ "shell.execute_reply": "2022-07-06T18:40:42.993281Z"
+ }
+ },
"outputs": [
{
"data": {
@@ -229,7 +292,14 @@
{
"cell_type": "code",
"execution_count": 10,
- "metadata": {},
+ "metadata": {
+ "execution": {
+ "iopub.execute_input": "2022-07-06T18:40:42.996338Z",
+ "iopub.status.busy": "2022-07-06T18:40:42.996338Z",
+ "iopub.status.idle": "2022-07-06T18:40:43.423368Z",
+ "shell.execute_reply": "2022-07-06T18:40:43.422895Z"
+ }
+ },
"outputs": [
{
"ename": "ValueError",
--
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