diff --git a/Star_explore.ipynb b/Star_explore.ipynb index 1fee2fb..3977369 100644 --- a/Star_explore.ipynb +++ b/Star_explore.ipynb @@ -25,7 +25,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -58,26 +58,1007 @@ "Initialise the 2 solar-mass Z=0.02 MESA stellar evolution model from set1.2 using the seeker method:" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Let's now see what the model looks like by making some Kippenhahn diagrams" + ] + }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "nugrid_path = /data/nugrid_apod2/\n", + "closest set is set1.2 (Z = 0.02)\n", + "closest mass is 2.0\n", + "Using old star.logsa file ...\n", + " reading ...100% \n", + "\n", + "Closing star.log tool ...\n" + ] + } + ], + "source": [ + "s=ms.star_log(mass=2,Z=0.02)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data for MESA output\n", + "\n", + "This data file is composed of two parts: s.header_attr and s.cols. \n", + "\n", + "data type | contents\n", + "------------------|---------------------\n", + "`s.header_attr` | The header section seems include some intial defaults like what are shown when you run s.header_attr.\n", + "`s.cols` | This section show different quanitities correspongding to a specific model or time. We can use these quantities to plot some figure we want.\n", + "\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Examples\n", + "Below shown is an example how to plot ratio of C12 to O16 at surface of star as function of logarithm of star_age." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'burn_min1': 50.0,\n", + " 'burn_min2': 1000.0,\n", + " 'c12_boundary_limit': 0.0001,\n", + " 'h1_boundary_limit': 0.0001,\n", + " 'he4_boundary_limit': 0.0001,\n", + " 'initial_mass': 2.0,\n", + " 'initial_z': 0.02}" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "s.header_attr" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'burn_c': 59,\n", + " 'burn_n': 60,\n", + " 'burn_o': 61,\n", + " 'center_c12': 50,\n", + " 'center_h1': 48,\n", + " 'center_he4': 49,\n", + " 'center_mu': 46,\n", + " 'center_o16': 51,\n", + " 'center_ye': 47,\n", + " 'cno': 57,\n", + " 'conv_mx1_bot': 9,\n", + " 'conv_mx1_top': 8,\n", + " 'conv_mx2_bot': 11,\n", + " 'conv_mx2_top': 10,\n", + " 'delta_mass': 4,\n", + " 'envelope_mass': 32,\n", + " 'epsnuc_M_1': 16,\n", + " 'epsnuc_M_2': 17,\n", + " 'epsnuc_M_3': 18,\n", + " 'epsnuc_M_4': 19,\n", + " 'epsnuc_M_5': 20,\n", + " 'epsnuc_M_6': 21,\n", + " 'epsnuc_M_7': 22,\n", + " 'epsnuc_M_8': 23,\n", + " 'gravity': 42,\n", + " 'h1_boundary_lgRho': 27,\n", + " 'h1_boundary_lgT': 26,\n", + " 'h1_boundary_mass': 24,\n", + " 'h1_boundary_radius': 25,\n", + " 'he4_boundary_lgRho': 31,\n", + " 'he4_boundary_lgT': 30,\n", + " 'he4_boundary_mass': 28,\n", + " 'he4_boundary_radius': 29,\n", + " 'log_L': 38,\n", + " 'log_LH': 33,\n", + " 'log_LHe': 34,\n", + " 'log_LZ': 35,\n", + " 'log_Lnuc': 36,\n", + " 'log_R': 40,\n", + " 'log_Teff': 39,\n", + " 'log_abs_mdot': 5,\n", + " 'log_center_P': 45,\n", + " 'log_center_Rho': 44,\n", + " 'log_center_T': 43,\n", + " 'log_dt': 6,\n", + " 'log_g': 41,\n", + " 'luminosity': 37,\n", + " 'model_number': 1,\n", + " 'mx1_bot': 13,\n", + " 'mx1_top': 12,\n", + " 'mx2_bot': 15,\n", + " 'mx2_top': 14,\n", + " 'num_backups': 64,\n", + " 'num_retries': 63,\n", + " 'num_zones': 7,\n", + " 'pp': 56,\n", + " 'star_age': 2,\n", + " 'star_mass': 3,\n", + " 'surface_c12': 52,\n", + " 'surface_o16': 53,\n", + " 'total_mass_h1': 54,\n", + " 'total_mass_he4': 55,\n", + " 'tri_alfa': 58,\n", + " 'v_div_csound_surf': 62}" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "s.cols" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Plot example" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "window.mpl = {};\n", + "\n", + "\n", + "mpl.get_websocket_type = function() {\n", + " if (typeof(WebSocket) !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof(MozWebSocket) !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert('Your browser does not have WebSocket support.' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", + " 'Firefox 4 and 5 are also supported but you ' +\n", + " 'have to enable WebSockets in about:config.');\n", + " };\n", + "}\n", + "\n", + "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", + " this.id = figure_id;\n", + "\n", + " this.ws = websocket;\n", + "\n", + " this.supports_binary = (this.ws.binaryType != undefined);\n", + "\n", + " if (!this.supports_binary) {\n", + " var warnings = document.getElementById(\"mpl-warnings\");\n", + " if (warnings) {\n", + " warnings.style.display = 'block';\n", + " warnings.textContent = (\n", + " \"This browser does not support binary websocket messages. \" +\n", + " \"Performance may be slow.\");\n", + " }\n", + " }\n", + "\n", + " this.imageObj = new Image();\n", + "\n", + " this.context = undefined;\n", + " this.message = undefined;\n", + " this.canvas = undefined;\n", + " this.rubberband_canvas = undefined;\n", + " this.rubberband_context = undefined;\n", + " this.format_dropdown = undefined;\n", + "\n", + " this.image_mode = 'full';\n", + "\n", + " this.root = $('
');\n", + " this._root_extra_style(this.root)\n", + " this.root.attr('style', 'display: inline-block');\n", + "\n", + " $(parent_element).append(this.root);\n", + "\n", + " this._init_header(this);\n", + " this._init_canvas(this);\n", + " this._init_toolbar(this);\n", + "\n", + " var fig = this;\n", + "\n", + " this.waiting = false;\n", + "\n", + " this.ws.onopen = function () {\n", + " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", + " fig.send_message(\"send_image_mode\", {});\n", + " if (mpl.ratio != 1) {\n", + " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", + " }\n", + " fig.send_message(\"refresh\", {});\n", + " }\n", + "\n", + " this.imageObj.onload = function() {\n", + " if (fig.image_mode == 'full') {\n", + " // Full images could contain transparency (where diff images\n", + " // almost always do), so we need to clear the canvas so that\n", + " // there is no ghosting.\n", + " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", + " }\n", + " fig.context.drawImage(fig.imageObj, 0, 0);\n", + " };\n", + "\n", + " this.imageObj.onunload = function() {\n", + " this.ws.close();\n", + " }\n", + "\n", + " this.ws.onmessage = this._make_on_message_function(this);\n", + "\n", + " this.ondownload = ondownload;\n", + "}\n", + "\n", + "mpl.figure.prototype._init_header = function() {\n", + " var titlebar = $(\n", + " '
');\n", + " var titletext = $(\n", + " '
');\n", + " titlebar.append(titletext)\n", + " this.root.append(titlebar);\n", + " this.header = titletext[0];\n", + "}\n", + "\n", + "\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._init_canvas = function() {\n", + " var fig = this;\n", + "\n", + " var canvas_div = $('
');\n", + "\n", + " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", + "\n", + " function canvas_keyboard_event(event) {\n", + " return fig.key_event(event, event['data']);\n", + " }\n", + "\n", + " canvas_div.keydown('key_press', canvas_keyboard_event);\n", + " canvas_div.keyup('key_release', canvas_keyboard_event);\n", + " this.canvas_div = canvas_div\n", + " this._canvas_extra_style(canvas_div)\n", + " this.root.append(canvas_div);\n", + "\n", + " var canvas = $('');\n", + " canvas.addClass('mpl-canvas');\n", + " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", + "\n", + " this.canvas = canvas[0];\n", + " this.context = canvas[0].getContext(\"2d\");\n", + "\n", + " var backingStore = this.context.backingStorePixelRatio ||\n", + "\tthis.context.webkitBackingStorePixelRatio ||\n", + "\tthis.context.mozBackingStorePixelRatio ||\n", + "\tthis.context.msBackingStorePixelRatio ||\n", + "\tthis.context.oBackingStorePixelRatio ||\n", + "\tthis.context.backingStorePixelRatio || 1;\n", + "\n", + " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", + "\n", + " var rubberband = $('');\n", + " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", + "\n", + " var pass_mouse_events = true;\n", + "\n", + " canvas_div.resizable({\n", + " start: function(event, ui) {\n", + " pass_mouse_events = false;\n", + " },\n", + " resize: function(event, ui) {\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " stop: function(event, ui) {\n", + " pass_mouse_events = true;\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " });\n", + "\n", + " function mouse_event_fn(event) {\n", + " if (pass_mouse_events)\n", + " return fig.mouse_event(event, event['data']);\n", + " }\n", + "\n", + " rubberband.mousedown('button_press', mouse_event_fn);\n", + " rubberband.mouseup('button_release', mouse_event_fn);\n", + " // Throttle sequential mouse events to 1 every 20ms.\n", + " rubberband.mousemove('motion_notify', mouse_event_fn);\n", + "\n", + " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", + " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", + "\n", + " canvas_div.on(\"wheel\", function (event) {\n", + " event = event.originalEvent;\n", + " event['data'] = 'scroll'\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " mouse_event_fn(event);\n", + " });\n", + "\n", + " canvas_div.append(canvas);\n", + " canvas_div.append(rubberband);\n", + "\n", + " this.rubberband = rubberband;\n", + " this.rubberband_canvas = rubberband[0];\n", + " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", + " this.rubberband_context.strokeStyle = \"#000000\";\n", + "\n", + " this._resize_canvas = function(width, height) {\n", + " // Keep the size of the canvas, canvas container, and rubber band\n", + " // canvas in synch.\n", + " canvas_div.css('width', width)\n", + " canvas_div.css('height', height)\n", + "\n", + " canvas.attr('width', width * mpl.ratio);\n", + " canvas.attr('height', height * mpl.ratio);\n", + " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", + "\n", + " rubberband.attr('width', width);\n", + " rubberband.attr('height', height);\n", + " }\n", + "\n", + " // Set the figure to an initial 600x600px, this will subsequently be updated\n", + " // upon first draw.\n", + " this._resize_canvas(600, 600);\n", + "\n", + " // Disable right mouse context menu.\n", + " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", + " return false;\n", + " });\n", + "\n", + " function set_focus () {\n", + " canvas.focus();\n", + " canvas_div.focus();\n", + " }\n", + "\n", + " window.setTimeout(set_focus, 100);\n", + "}\n", + "\n", + "mpl.figure.prototype._init_toolbar = function() {\n", + " var fig = this;\n", + "\n", + " var nav_element = $('
')\n", + " nav_element.attr('style', 'width: 100%');\n", + " this.root.append(nav_element);\n", + "\n", + " // Define a callback function for later on.\n", + " function toolbar_event(event) {\n", + " return fig.toolbar_button_onclick(event['data']);\n", + " }\n", + " function toolbar_mouse_event(event) {\n", + " return fig.toolbar_button_onmouseover(event['data']);\n", + " }\n", + "\n", + " for(var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " // put a spacer in here.\n", + " continue;\n", + " }\n", + " var button = $('