Written by Svetlana Kyas (ETH Zurich) on Mar 31th, 2022
\n", "\n", "```{attention}\n", "Always make sure you are using the [latest version of Reaktoro](https://anaconda.org/conda-forge/reaktoro). Otherwise, some new features documented on this website will not work on your machine and you may receive unintuitive errors. Follow these [update instructions](updating_reaktoro_via_conda) to get the latest version of Reaktoro!\n", "```\n", "\n", "This tutorial shows how to simulate the solubility of CO2 in water or, more simply, the **effect of the carbon dioxide released when you open the bottle of sparkling water**.\n", "\n", "||\n", "|:--:|\n", "|Opening bottle with sparkling water, Source: flavorman.com|\n", "\n", "First, we define the chemical system:" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from reaktoro import *\n", "\n", "db = SupcrtDatabase(\"supcrtbl\")\n", "\n", "# Create an aqueous phase automatically selecting all species with provided elements\n", "aqueousphase = AqueousPhase(speciate(\"H O C\"))\n", "aqueousphase.set(ActivityModelPitzer())\n", "\n", "# Create a gaseous phase\n", "gaseousphase = GaseousPhase(\"CO2(g)\")\n", "gaseousphase.set(ActivityModelPengRobinson())\n", "\n", "# Create the chemical system\n", "system = ChemicalSystem(db, aqueousphase, gaseousphase)\n", "\n", "# Create the equilibrium solver\n", "solver = EquilibriumSolver(system)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Then, we define the range of pressures using the `linspace()` function of the **numpy** library. The initial and final pressures correspond to the values in the bubble bottle before and after opening." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", "closedP = 3.79 # in bars\n", "openP = 1.01325 # in bars\n", "pressures = np.linspace(openP, closedP, num=100)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "> **Note**: A typical carbonated soft drink contains approximately 3–4 volumes (6–8 g/L) CO2. To obtain the amount of mol of CO2, we need to perform the following calculations: 8 g/L = 8 / 44.01 mol = 0.18 mol, where 44.01 g/mol is the CO2 molar mass.\n", "\n", "Next, we go through the created pressure list and collect the CO2(g) amounts obtained in the equilibrated chemical for a given pressure." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "df = pd.DataFrame(columns=[\"P\", \"amountCO2\"])\n", "\n", "for P in pressures:\n", " state = ChemicalState(system)\n", " state.setTemperature(20.0, \"celsius\")\n", " state.setPressure(P, \"bar\")\n", " state.add(\"H2O(aq)\", 0.5, \"kg\") # add ~ half a liter of water\n", " state.add(\"CO2(g)\", 0.18, \"mol\") # add calculated amount of gas\n", "\n", " res = solver.solve(state)\n", "\n", " df.loc[len(df)] = [P, float(state.speciesAmount(\"CO2(g)\"))]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "To visualize the changes in the CO2(g) amount in the bottle, we export [bokeh](https://docs.bokeh.org/en/latest/docs/gallery.html#standalone-examples) python plotting package." ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "lines_to_next_cell": 1, "tags": [ "hide_input" ] }, "outputs": [ { "data": { "text/html": [ "\n" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": "(function(root) {\n function now() {\n return new Date();\n }\n\n const force = true;\n\n if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n root._bokeh_onload_callbacks = [];\n root._bokeh_is_loading = undefined;\n }\n\nconst JS_MIME_TYPE = 'application/javascript';\n const HTML_MIME_TYPE = 'text/html';\n const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n const CLASS_NAME = 'output_bokeh rendered_html';\n\n /**\n * Render data to the DOM node\n */\n function render(props, node) {\n const script = document.createElement(\"script\");\n node.appendChild(script);\n }\n\n /**\n * Handle when an output is cleared or removed\n */\n function handleClearOutput(event, handle) {\n const cell = handle.cell;\n\n const id = cell.output_area._bokeh_element_id;\n const server_id = cell.output_area._bokeh_server_id;\n // Clean up Bokeh references\n if (id != null && id in Bokeh.index) {\n Bokeh.index[id].model.document.clear();\n delete Bokeh.index[id];\n }\n\n if (server_id !== undefined) {\n // Clean up Bokeh references\n const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n cell.notebook.kernel.execute(cmd_clean, {\n iopub: {\n output: function(msg) {\n const id = msg.content.text.trim();\n if (id in Bokeh.index) {\n Bokeh.index[id].model.document.clear();\n delete Bokeh.index[id];\n }\n }\n }\n });\n // Destroy server and session\n const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n cell.notebook.kernel.execute(cmd_destroy);\n }\n }\n\n /**\n * Handle when a new output is added\n */\n function handleAddOutput(event, handle) {\n const output_area = handle.output_area;\n const output = handle.output;\n\n // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n return\n }\n\n const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n\n if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n // store reference to embed id on output_area\n output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n }\n if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n const bk_div = document.createElement(\"div\");\n bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n const script_attrs = bk_div.children[0].attributes;\n for (let i = 0; i < script_attrs.length; i++) {\n toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n }\n // store reference to server id on output_area\n output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n }\n }\n\n function register_renderer(events, OutputArea) {\n\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n const toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[toinsert.length - 1]);\n element.append(toinsert);\n return toinsert\n }\n\n /* Handle when an output is cleared or removed */\n events.on('clear_output.CodeCell', handleClearOutput);\n events.on('delete.Cell', handleClearOutput);\n\n /* Handle when a new output is added */\n events.on('output_added.OutputArea', handleAddOutput);\n\n /**\n * Register the mime type and append_mime function with output_area\n */\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n /* Is output safe? */\n safe: true,\n /* Index of renderer in `output_area.display_order` */\n index: 0\n });\n }\n\n // register the mime type if in Jupyter Notebook environment and previously unregistered\n if (root.Jupyter !== undefined) {\n const events = require('base/js/events');\n const OutputArea = require('notebook/js/outputarea').OutputArea;\n\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n }\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"
\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"