Collision cross sections - figures.ipynb

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    "## <font color='blue'>Collision cross sections of monosaccharides </font> \n",
    "\n",
    "### Title: The remarkable influence of structure, partial charges and basis sets on subsequent evaluation of collision cross sections of monosaccharides \n",
    "### Authors: Lukasz G. Migas, Christopher J. Gray, Sabine L. Flitsch and Perdita E. Barran\n",
    "### DOI: - not available yet\n",
    "\n",
    "#### Here we show the collision cross sections (CCS) for each charge scheme (Mulliken, APT, MK, CHelpG, HLY and NPA) computed using MOBCAL (in nitrogen buffer gas) with partial charges computed combination of functionals (HF, B3LYP and M05) and basis sets (STO-3G, 3-21G, 6-31G, 6-31+G and 6-31G*). \n",
    "\n",
    "### Interactive tools:\n",
    "#### <font color='green'>Hover</font>  - hover over any data point and it will bring detailed information about partial atomic charge, standard error, atom ID\n",
    "#### <font color='green'>Zoom</font> - drag on the plot to zoom on specific region of interest\n",
    "#### <font color='green'>Legend</font> - click on legend marker to select/deselect datasets "
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    "# Pre-sets\n",
    "colorSets=['#000080','#FF0080','#008000', '#FF8000', '#8009FF']\n",
    "\n",
    "ylabelsHF=['HF/STO-3G','HF/3-21G','HF/6-31G','HF/6-31+G','HF/6-31G*']\n",
    "ylabelsErrHF=['HF/STO-3G/Error','HF/3-21G/Error','HF/6-31G/Error','HF/6-31+G/Error','HF/6-31G*/Error']\n",
    "ylabelsB3LYP=['B3LYP/STO-3G','B3LYP/3-21G','B3LYP/6-31G','B3LYP/6-31+G','B3LYP/6-31G*']\n",
    "ylabelsErrB3LYP=['B3LYP/STO-3G/Error','B3LYP/3-21G/Error','B3LYP/6-31G/Error','B3LYP/6-31+G/Error','B3LYP/6-31G*/Error']\n",
    "ylabelsM05=['M05/STO-3G','M05/3-21G','M05/6-31G','M05/6-31+G','M05/6-31G*']\n",
    "ylabelsErrM05=['M05/STO-3G/Error','M05/3-21G/Error','M05/6-31G/Error','M05/6-31+G/Error','M05/6-31G*/Error']\n",
    "\n",
    "xticksLabels = [\"αGlc(1)\",\"αGlc(2)\",\"αGlc(3)\",\"αGlc(4)\",\"αGlc(5)\",\"αGlc(6)\",\"αGlc(7)\",\"αGlc(8)\",\"αGlc(9)\",\"αGlc(10)\",\n",
    "                \"βGlc(1)\",\"βGlc(2)\",\"βGlc(3)\",\"βGlc(4)\",\"βGlc(5)\",\"βGlc(6)\",\"βGlc(7)\",\"βGlc(8)\",\"βGlc(9)\",\"βGlc(10)\"]"
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   "source": [
    "# Collision cross sections - Mulliken charge scheme - Nitrogen buffer gas"
   ]
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     "metadata": {},
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   ],
   "source": [
    "# Import data\n",
    "title = \"Mulliken\"\n",
    "data = pd.read_csv(title+\"-N2.csv\", delimiter=',')\n",
    "# Extract data from the table\n",
    "xticks=data['Name']\n",
    "xdata=data['Point']\n",
    "################################ HF ################################\n",
    "hoverHF = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_HF = [hoverHF,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "t = figure(tools=TOOLS_HF, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"a) \"+title+\" - HF\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsHF)):\n",
    "    legendKey=[ylabelsHF[i]]\n",
    "    ydata = (data[ylabelsHF[i]])\n",
    "    ydataErr=(data[ylabelsErrHF[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    t.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    t.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "t.grid.grid_line_alpha=0.7\n",
    "t.title.text_font_size = '12pt'\n",
    "t.legend.click_policy = \"hide\"\n",
    "t.legend.background_fill_color = '#DCDCDC'\n",
    "t.legend.location = \"bottom_center\"\n",
    "t.legend.orientation = \"horizontal\"\n",
    "t.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "t.grid[0].ticker.num_minor_ticks = 0\n",
    "t.yaxis.major_label_text_font_size = \"12pt\"\n",
    "t.yaxis.major_label_text_font_style = 'bold'\n",
    "t.yaxis.axis_label = \"CCS (Å²)\"\n",
    "t.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "t.yaxis.axis_label_text_font_style = 'bold'\n",
    "t.xaxis.major_label_text_font_size = \"12pt\"\n",
    "t.xaxis.major_label_orientation = np.pi/4\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.major_label_text_font_style = 'bold'\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ B3LYP ################################\n",
    "hoverB3LYP = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_B3LYP = [hoverB3LYP,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "p = figure(tools=TOOLS_B3LYP, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"b) \"+title+\" - B3LYP\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsB3LYP)):\n",
    "    legendKey=[ylabelsB3LYP[i]]\n",
    "    ydata = (data[ylabelsB3LYP[i]])\n",
    "    ydataErr=(data[ylabelsErrB3LYP[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    p.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    p.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "p.grid.grid_line_alpha=0.7\n",
    "p.title.text_font_size = '12pt'\n",
    "p.legend.click_policy = \"hide\"\n",
    "p.legend.background_fill_color = '#DCDCDC'\n",
    "p.legend.location = \"bottom_center\"\n",
    "p.legend.orientation = \"horizontal\"\n",
    "p.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "p.grid[0].ticker.num_minor_ticks = 0\n",
    "p.yaxis.major_label_text_font_size = \"12pt\"\n",
    "p.yaxis.major_label_text_font_style = 'bold'\n",
    "p.yaxis.axis_label = \"CCS (Å²)\"\n",
    "p.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "p.yaxis.axis_label_text_font_style = 'bold'\n",
    "p.xaxis.major_label_text_font_size = \"12pt\"\n",
    "p.xaxis.major_label_orientation = np.pi/4\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.major_label_text_font_style = 'bold'\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ M05 ################################\n",
    "hoverM05 = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_M05 = [hoverM05,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "r = figure(tools=TOOLS_M05, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"c) \"+title+\" - M05\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsM05)):\n",
    "    legendKey=[ylabelsM05[i]]\n",
    "    ydata = (data[ylabelsM05[i]])\n",
    "    ydataErr=(data[ylabelsErrM05[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    r.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    r.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "r.grid.grid_line_alpha=0.7\n",
    "r.title.text_font_size = '12pt'\n",
    "r.legend.click_policy = \"hide\"\n",
    "r.legend.background_fill_color = '#DCDCDC'\n",
    "r.legend.location = \"bottom_center\"\n",
    "r.legend.orientation = \"horizontal\"\n",
    "r.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "r.grid[0].ticker.num_minor_ticks = 0\n",
    "r.yaxis.major_label_text_font_size = \"12pt\"\n",
    "r.yaxis.major_label_text_font_style = 'bold'\n",
    "r.yaxis.axis_label = \"CCS (Å²)\"\n",
    "r.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "r.yaxis.axis_label_text_font_style = 'bold'\n",
    "r.xaxis.major_label_text_font_size = \"12pt\"\n",
    "r.xaxis.major_label_orientation = np.pi/4\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.major_label_text_font_style = 'bold'\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "show(column(t,p,r))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Rotationally averaged collision cross sections calculated using the Trajectory Method with partial charges calculated using HF (a), B3LYP (b) or M05 (c) functional with several basis sets: STO-3G (<font color='#000080'>blue</font>), 3-21G (<font color='#FF0080'>magenta</font>), 6-31G (<font color='#008000'>green</font>), 6-31+G (<font color='#FF8000'>orange</font>) and 6-31G* (<font color='#8009FF'>purple</font>) for Mulliken charge scheme. Error bars on each data point represent the standard deviation from Trajectory Method calculation, typically less than 0.5 %, and always less than 1 %."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "# Collision cross sections - Atomic Polar Tensors (APT) charge scheme - Nitrogen buffer gas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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   "source": [
    "# Import data\n",
    "title = \"APT\"\n",
    "data = pd.read_csv(title+\"-N2.csv\", delimiter=',')\n",
    "# Extract data from the table\n",
    "xticks=data['Name']\n",
    "xdata=data['Point']\n",
    "################################ HF ################################\n",
    "hoverHF = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_HF = [hoverHF,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "t = figure(tools=TOOLS_HF, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"a) \"+title+\" - HF\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsHF)):\n",
    "    legendKey=[ylabelsHF[i]]\n",
    "    ydata = (data[ylabelsHF[i]])\n",
    "    ydataErr=(data[ylabelsErrHF[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    t.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    t.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "t.grid.grid_line_alpha=0.7\n",
    "t.title.text_font_size = '12pt'\n",
    "t.legend.click_policy = \"hide\"\n",
    "t.legend.background_fill_color = '#DCDCDC'\n",
    "t.legend.location = \"bottom_center\"\n",
    "t.legend.orientation = \"horizontal\"\n",
    "t.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "t.grid[0].ticker.num_minor_ticks = 0\n",
    "t.yaxis.major_label_text_font_size = \"12pt\"\n",
    "t.yaxis.major_label_text_font_style = 'bold'\n",
    "t.yaxis.axis_label = \"CCS (Å²)\"\n",
    "t.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "t.yaxis.axis_label_text_font_style = 'bold'\n",
    "t.xaxis.major_label_text_font_size = \"12pt\"\n",
    "t.xaxis.major_label_orientation = np.pi/4\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.major_label_text_font_style = 'bold'\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ B3LYP ################################\n",
    "hoverB3LYP = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_B3LYP = [hoverB3LYP,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "p = figure(tools=TOOLS_B3LYP, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"b) \"+title+\" - B3LYP\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsB3LYP)):\n",
    "    legendKey=[ylabelsB3LYP[i]]\n",
    "    ydata = (data[ylabelsB3LYP[i]])\n",
    "    ydataErr=(data[ylabelsErrB3LYP[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    p.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    p.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "p.grid.grid_line_alpha=0.7\n",
    "p.title.text_font_size = '12pt'\n",
    "p.legend.click_policy = \"hide\"\n",
    "p.legend.background_fill_color = '#DCDCDC'\n",
    "p.legend.location = \"bottom_center\"\n",
    "p.legend.orientation = \"horizontal\"\n",
    "p.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "p.grid[0].ticker.num_minor_ticks = 0\n",
    "p.yaxis.major_label_text_font_size = \"12pt\"\n",
    "p.yaxis.major_label_text_font_style = 'bold'\n",
    "p.yaxis.axis_label = \"CCS (Å²)\"\n",
    "p.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "p.yaxis.axis_label_text_font_style = 'bold'\n",
    "p.xaxis.major_label_text_font_size = \"12pt\"\n",
    "p.xaxis.major_label_orientation = np.pi/4\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.major_label_text_font_style = 'bold'\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ M05 ################################\n",
    "hoverM05 = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_M05 = [hoverM05,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "r = figure(tools=TOOLS_M05, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"c### Rotationally averaged collision cross sections calculated using the Trajectory Method with partial charges calculated using HF (a), B3LYP (b) or M05 (c) functional with several basis sets: STO-3G (<font color='#000080'>blue</font>), 3-21G (<font color='#FF0080'>magenta</font>), 6-31G (<font color='#008000'>green</font>), 6-31+G (<font color='#FF8000'>orange</font>) and 6-31G* (<font color='#8009FF'>purple</font>) for Mulliken charge scheme. Error bars on each data point represent the standard deviation from Trajectory Method calculation, typically less than 0.5 %, and always less than 1 %.) \"+title+\" - M05\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsM05)):\n",
    "    legendKey=[ylabelsM05[i]]\n",
    "    ydata = (data[ylabelsM05[i]])\n",
    "    ydataErr=(data[ylabelsErrM05[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    r.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    r.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "r.grid.grid_line_alpha=0.7\n",
    "r.title.text_font_size = '12pt'\n",
    "r.legend.click_policy = \"hide\"\n",
    "r.legend.background_fill_color = '#DCDCDC'\n",
    "r.legend.location = \"bottom_center\"\n",
    "r.legend.orientation = \"horizontal\"\n",
    "r.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "r.grid[0].ticker.num_minor_ticks = 0\n",
    "r.yaxis.major_label_text_font_size = \"12pt\"\n",
    "r.yaxis.major_label_text_font_style = 'bold'\n",
    "r.yaxis.axis_label = \"CCS (Å²)\"\n",
    "r.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "r.yaxis.axis_label_text_font_style = 'bold'\n",
    "r.xaxis.major_label_text_font_size = \"12pt\"\n",
    "r.xaxis.major_label_orientation = np.pi/4\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.major_label_text_font_style = 'bold'\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "show(column(t,p,r))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Rotationally averaged collision cross sections calculated using the Trajectory Method with partial charges calculated using HF (a), B3LYP (b) or M05 (c) functional with several basis sets: STO-3G (<font color='#000080'>blue</font>), 3-21G (<font color='#FF0080'>magenta</font>), 6-31G (<font color='#008000'>green</font>), 6-31+G (<font color='#FF8000'>orange</font>) and 6-31G* (<font color='#8009FF'>purple</font>) for APT charge scheme. Error bars on each data point represent the standard deviation from Trajectory Method calculation, typically less than 0.5 %, and always less than 1 %."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "# Collision cross sections - Merz-Singh-Kollman (MK) charge scheme - Nitrogen buffer gas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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   "source": [
    "# Import data\n",
    "title = \"MK\"\n",
    "data = pd.read_csv(title+\"-N2.csv\", delimiter=',')\n",
    "# Extract data from the table\n",
    "xticks=data['Name']\n",
    "xdata=data['Point']\n",
    "################################ HF ################################\n",
    "hoverHF = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_HF = [hoverHF,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "t = figure(tools=TOOLS_HF, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"a) \"+title+\" - HF\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsHF)):\n",
    "    legendKey=[ylabelsHF[i]]\n",
    "    ydata = (data[ylabelsHF[i]])\n",
    "    ydataErr=(data[ylabelsErrHF[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    t.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    t.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "t.grid.grid_line_alpha=0.7\n",
    "t.title.text_font_size = '12pt'\n",
    "t.legend.click_policy = \"hide\"\n",
    "t.legend.background_fill_color = '#DCDCDC'\n",
    "t.legend.location = \"bottom_center\"\n",
    "t.legend.orientation = \"horizontal\"\n",
    "t.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "t.grid[0].ticker.num_minor_ticks = 0\n",
    "t.yaxis.major_label_text_font_size = \"12pt\"\n",
    "t.yaxis.major_label_text_font_style = 'bold'\n",
    "t.yaxis.axis_label = \"CCS (Å²)\"\n",
    "t.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "t.yaxis.axis_label_text_font_style = 'bold'\n",
    "t.xaxis.major_label_text_font_size = \"12pt\"\n",
    "t.xaxis.major_label_orientation = np.pi/4\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.major_label_text_font_style = 'bold'\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ B3LYP ################################\n",
    "hoverB3LYP = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_B3LYP = [hoverB3LYP,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "p = figure(tools=TOOLS_B3LYP, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"b) \"+title+\" - B3LYP\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsB3LYP)):\n",
    "    legendKey=[ylabelsB3LYP[i]]\n",
    "    ydata = (data[ylabelsB3LYP[i]])\n",
    "    ydataErr=(data[ylabelsErrB3LYP[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    p.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    p.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "p.grid.grid_line_alpha=0.7\n",
    "p.title.text_font_size = '12pt'\n",
    "p.legend.click_policy = \"hide\"\n",
    "p.legend.background_fill_color = '#DCDCDC'\n",
    "p.legend.location = \"bottom_center\"\n",
    "p.legend.orientation = \"horizontal\"\n",
    "p.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "p.grid[0].ticker.num_minor_ticks = 0\n",
    "p.yaxis.major_label_text_font_size = \"12pt\"\n",
    "p.yaxis.major_label_text_font_style = 'bold'\n",
    "p.yaxis.axis_label = \"CCS (Å²)\"\n",
    "p.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "p.yaxis.axis_label_text_font_style = 'bold'\n",
    "p.xaxis.major_label_text_font_size = \"12pt\"\n",
    "p.xaxis.major_label_orientation = np.pi/4\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.major_label_text_font_style = 'bold'\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ M05 ################################\n",
    "hoverM05 = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_M05 = [hoverM05,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "r = figure(tools=TOOLS_M05, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"c) \"+title+\" - M05\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsM05)):\n",
    "    legendKey=[ylabelsM05[i]]\n",
    "    ydata = (data[ylabelsM05[i]])\n",
    "    ydataErr=(data[ylabelsErrM05[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    r.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    r.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "r.grid.grid_line_alpha=0.7\n",
    "r.title.text_font_size = '12pt'\n",
    "r.legend.click_policy = \"hide\"\n",
    "r.legend.background_fill_color = '#DCDCDC'\n",
    "r.legend.location = \"bottom_center\"\n",
    "r.legend.orientation = \"horizontal\"\n",
    "r.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "r.grid[0].ticker.num_minor_ticks = 0\n",
    "r.yaxis.major_label_text_font_size = \"12pt\"\n",
    "r.yaxis.major_label_text_font_style = 'bold'\n",
    "r.yaxis.axis_label = \"CCS (Å²)\"\n",
    "r.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "r.yaxis.axis_label_text_font_style = 'bold'\n",
    "r.xaxis.major_label_text_font_size = \"12pt\"\n",
    "r.xaxis.major_label_orientation = np.pi/4\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.major_label_text_font_style = 'bold'\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "show(column(t,p,r))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Rotationally averaged collision cross sections calculated using the Trajectory Method with partial charges calculated using HF (a), B3LYP (b) or M05 (c) functional with several basis sets: STO-3G (<font color='#000080'>blue</font>), 3-21G (<font color='#FF0080'>magenta</font>), 6-31G (<font color='#008000'>green</font>), 6-31+G (<font color='#FF8000'>orange</font>) and 6-31G* (<font color='#8009FF'>purple</font>) for MK charge scheme. Error bars on each data point represent the standard deviation from Trajectory Method calculation, typically less than 0.5 %, and always less than 1 %."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "# Collision cross sections - CHelpG charge scheme - Nitrogen buffer gas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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       "  \n",
       "    function display_loaded() {\n",
       "      if (window.Bokeh !== undefined) {\n",
       "        var el = document.getElementById(\"b808f87d-1e65-42cf-ba60-fcb25024ddd3\");\n",
       "        el.textContent = \"BokehJS \" + Bokeh.version + \" successfully loaded.\";\n",
       "      } else if (Date.now() < window._bokeh_timeout) {\n",
       "        setTimeout(display_loaded, 100)\n",
       "      }\n",
       "    }\n",
       "  \n",
       "    function run_callbacks() {\n",
       "      try {\n",
       "        window._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n",
       "      }\n",
       "      finally {\n",
       "        delete window._bokeh_onload_callbacks\n",
       "      }\n",
       "      console.info(\"Bokeh: all callbacks have finished\");\n",
       "    }\n",
       "  \n",
       "    function load_libs(js_urls, callback) {\n",
       "      window._bokeh_onload_callbacks.push(callback);\n",
       "      if (window._bokeh_is_loading > 0) {\n",
       "        console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
       "        return null;\n",
       "      }\n",
       "      if (js_urls == null || js_urls.length === 0) {\n",
       "        run_callbacks();\n",
       "        return null;\n",
       "      }\n",
       "      console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
       "      window._bokeh_is_loading = js_urls.length;\n",
       "      for (var i = 0; i < js_urls.length; i++) {\n",
       "        var url = js_urls[i];\n",
       "        var s = document.createElement('script');\n",
       "        s.src = url;\n",
       "        s.async = false;\n",
       "        s.onreadystatechange = s.onload = function() {\n",
       "          window._bokeh_is_loading--;\n",
       "          if (window._bokeh_is_loading === 0) {\n",
       "            console.log(\"Bokeh: all BokehJS libraries loaded\");\n",
       "            run_callbacks()\n",
       "          }\n",
       "        };\n",
       "        s.onerror = function() {\n",
       "          console.warn(\"failed to load library \" + url);\n",
       "        };\n",
       "        console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
       "        document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
       "      }\n",
       "    };var element = document.getElementById(\"b808f87d-1e65-42cf-ba60-fcb25024ddd3\");\n",
       "    if (element == null) {\n",
       "      console.log(\"Bokeh: ERROR: autoload.js configured with elementid 'b808f87d-1e65-42cf-ba60-fcb25024ddd3' but no matching script tag was found. \")\n",
       "      return false;\n",
       "    }\n",
       "  \n",
       "    var js_urls = [];\n",
       "  \n",
       "    var inline_js = [\n",
       "      function(Bokeh) {\n",
       "        (function() {\n",
       "          var fn = function() {\n",
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   var labels = {1: 'aGlc(1)', 2: 'aGlc(2)', 3: 'aGlc(3)', 4: 'aGlc(4)', 5: 'aGlc(5)', 6: 'aGlc(6)', 7: 'aGlc(7)', 8: 'aGlc(8)', 9: 'aGlc(9)', 10: 'aGlc(10)', 11: 'bGlc(1)', 12: 'bGlc(2)', 13: 'bGlc(3)', 14: 'bGlc(4)', 15: 'bGlc(5)', 16: 'bGlc(6)', 17: 'bGlc(7)', 18: 'bGlc(8)', 19: 'bGlc(9)', 20: 'bGlc(10)'};\\n    return labels[tick];\\n\"},\"id\":\"f146a33e-bc02-419a-96d2-d9fef43ba667\",\"type\":\"FuncTickFormatter\"},{\"attributes\":{\"fill_color\":{\"value\":\"#008000\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"9e280c4a-afcd-4ff7-966c-a87be91b8b10\",\"type\":\"Square\"},{\"attributes\":{\"callback\":null,\"end\":150,\"start\":115},\"id\":\"6b49a325-d2b3-444a-922a-9d3fa8e410dc\",\"type\":\"Range1d\"},{\"attributes\":{\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"line_width\":{\"value\":5},\"x0\":{\"field\":\"x\"},\"x1\":{\"field\":\"x\"},\"y0\":{\"field\":\"yLow\"},\"y1\":{\"field\":\"yHigh\"}},\"id\":\"b5124c6b-6cd1-4bd1-b151-8511b4fc5b12\",\"type\":\"Segment\"},{\"attributes\":{\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"line_width\":{\"value\":5},\"x0\":{\"field\":\"x\"},\"x1\":{\"field\":\"x\"},\"y0\":{\"field\":\"yLow\"},\"y1\":{\"field\":\"yHigh\"}},\"id\":\"13140c1e-82df-4e3c-901e-c681ea45b271\",\"type\":\"Segment\"},{\"attributes\":{},\"id\":\"74d5c4a1-a905-49d9-9c93-41273a45c139\",\"type\":\"BasicTicker\"},{\"attributes\":{\"bottom_units\":\"screen\",\"fill_alpha\":{\"value\":0.5},\"fill_color\":{\"value\":\"lightgrey\"},\"left_units\":\"screen\",\"level\":\"overlay\",\"line_alpha\":{\"value\":1.0},\"line_color\":{\"value\":\"black\"},\"line_dash\":[4,4],\"line_width\":{\"value\":2},\"plot\":null,\"render_mode\":\"css\",\"right_units\":\"screen\",\"top_units\":\"screen\"},\"id\":\"58f69477-ad9a-4741-b869-458f9edde757\",\"type\":\"BoxAnnotation\"},{\"attributes\":{\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1f77b4\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"bc8e42d6-76e3-44b2-9a69-91e7609811cb\",\"type\":\"Square\"},{\"attributes\":{\"data_source\":{\"id\":\"80a2c25c-be89-4f15-a5e1-30422c7c9d2d\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"8b0b11cc-f81a-4d0f-8027-89b19a118cf6\",\"type\":\"Square\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"ed3f0320-a401-44e6-b38f-a427a0a7b9f7\",\"type\":\"Square\"},\"selection_glyph\":null},\"id\":\"c249473e-7b0b-4d48-8a9b-a3c8828a8cc0\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"data_source\":{\"id\":\"1a66f676-16f7-467e-8ea8-13c02c735f2f\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"e94be3da-97bd-40c8-a176-dfd6a38de0ad\",\"type\":\"Segment\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"1c2b5fb5-3e3d-49b5-bafc-859481070a73\",\"type\":\"Segment\"},\"selection_glyph\":null},\"id\":\"cf8ae4e6-413a-42b9-8b34-0ebf71b51585\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"label\":{\"value\":\"M05/3-21G\"},\"renderers\":[{\"id\":\"5bf2b8b0-4d39-42ac-a7fc-0576b7506276\",\"type\":\"GlyphRenderer\"},{\"id\":\"a0c90d1b-3e28-4b83-bcf3-32541aed69a1\",\"type\":\"GlyphRenderer\"}]},\"id\":\"dc333775-a170-4ae3-9917-88335267698b\",\"type\":\"LegendItem\"},{\"attributes\":{\"plot\":{\"id\":\"5e7cf9d3-8a1b-4b1f-8835-28c34c7f4d9d\",\"subtype\":\"Figure\",\"type\":\"Plot\"}},\"id\":\"c9dce6d9-c622-4233-be1d-a8787b8354ca\",\"type\":\"SaveTool\"},{\"attributes\":{\"data_source\":{\"id\":\"87ff27cd-d2e1-46bf-8e73-e0c6d26969fc\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"2732e3ff-5654-4000-9b25-f03cff28f53f\",\"type\":\"Square\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"92c9c06b-7dfd-45da-8869-89addb1c2dd5\",\"type\":\"Square\"},\"selection_glyph\":null},\"id\":\"3f318f2b-4709-4bb5-a149-5636c49df234\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1f77b4\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"ed3f0320-a401-44e6-b38f-a427a0a7b9f7\",\"type\":\"Square\"},{\"attributes\":{\"data_source\":{\"id\":\"dd4f3dd1-92ee-40a3-b82c-cce8e35e50ef\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"617fa774-b1f4-407a-80f0-d63b27770c5f\",\"type\":\"Segment\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"fb1df077-e419-48c6-8815-68ea25bf1fab\",\"type\":\"Segment\"},\"selection_glyph\":null},\"id\":\"94924285-122f-4b15-9f79-d8fafebfa513\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"line_width\":{\"value\":5},\"x0\":{\"field\":\"x\"},\"x1\":{\"field\":\"x\"},\"y0\":{\"field\":\"yLow\"},\"y1\":{\"field\":\"yHigh\"}},\"id\":\"12548be3-ab22-4a8d-b9ef-0ec960edd6c8\",\"type\":\"Segment\"},{\"attributes\":{\"code\":\"\\n 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       "            var render_items = [{\"docid\":\"06fd0723-81cd-4678-a2f5-ee7f97843277\",\"elementid\":\"b808f87d-1e65-42cf-ba60-fcb25024ddd3\",\"modelid\":\"2aac0b35-c71f-42f3-ae88-09334670be73\"}];\n",
       "            \n",
       "            Bokeh.embed.embed_items(docs_json, render_items);\n",
       "          };\n",
       "          if (document.readyState != \"loading\") fn();\n",
       "          else document.addEventListener(\"DOMContentLoaded\", fn);\n",
       "        })();\n",
       "      },\n",
       "      function(Bokeh) {\n",
       "      }\n",
       "    ];\n",
       "  \n",
       "    function run_inline_js() {\n",
       "      \n",
       "      if ((window.Bokeh !== undefined) || (force === true)) {\n",
       "        for (var i = 0; i < inline_js.length; i++) {\n",
       "          inline_js[i](window.Bokeh);\n",
       "        }if (force === true) {\n",
       "          display_loaded();\n",
       "        }} else if (Date.now() < window._bokeh_timeout) {\n",
       "        setTimeout(run_inline_js, 100);\n",
       "      } else if (!window._bokeh_failed_load) {\n",
       "        console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "        window._bokeh_failed_load = true;\n",
       "      } else if (force !== true) {\n",
       "        var cell = $(document.getElementById(\"b808f87d-1e65-42cf-ba60-fcb25024ddd3\")).parents('.cell').data().cell;\n",
       "        cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
       "      }\n",
       "  \n",
       "    }\n",
       "  \n",
       "    if (window._bokeh_is_loading === 0) {\n",
       "      console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "      run_inline_js();\n",
       "    } else {\n",
       "      load_libs(js_urls, function() {\n",
       "        console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "        run_inline_js();\n",
       "      });\n",
       "    }\n",
       "  }(this));\n",
       "</script>"
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     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Import data\n",
    "title = \"CHelpG\"\n",
    "data = pd.read_csv(title+\"-N2.csv\", delimiter=',')\n",
    "# Extract data from the table\n",
    "xticks=data['Name']\n",
    "xdata=data['Point']\n",
    "################################ HF ################################\n",
    "hoverHF = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_HF = [hoverHF,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "t = figure(tools=TOOLS_HF, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"a) \"+title+\" - HF\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsHF)):\n",
    "    legendKey=[ylabelsHF[i]]\n",
    "    ydata = (data[ylabelsHF[i]])\n",
    "    ydataErr=(data[ylabelsErrHF[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    t.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    t.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "t.grid.grid_line_alpha=0.7\n",
    "t.title.text_font_size = '12pt'\n",
    "t.legend.click_policy = \"hide\"\n",
    "t.legend.background_fill_color = '#DCDCDC'\n",
    "t.legend.location = \"bottom_center\"\n",
    "t.legend.orientation = \"horizontal\"\n",
    "t.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "t.grid[0].ticker.num_minor_ticks = 0\n",
    "t.yaxis.major_label_text_font_size = \"12pt\"\n",
    "t.yaxis.major_label_text_font_style = 'bold'\n",
    "t.yaxis.axis_label = \"CCS (Å²)\"\n",
    "t.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "t.yaxis.axis_label_text_font_style = 'bold'\n",
    "t.xaxis.major_label_text_font_size = \"12pt\"\n",
    "t.xaxis.major_label_orientation = np.pi/4\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.major_label_text_font_style = 'bold'\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ B3LYP ################################\n",
    "hoverB3LYP = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_B3LYP = [hoverB3LYP,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "p = figure(tools=TOOLS_B3LYP, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"b) \"+title+\" - B3LYP\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsB3LYP)):\n",
    "    legendKey=[ylabelsB3LYP[i]]\n",
    "    ydata = (data[ylabelsB3LYP[i]])\n",
    "    ydataErr=(data[ylabelsErrB3LYP[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    p.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    p.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "p.grid.grid_line_alpha=0.7\n",
    "p.title.text_font_size = '12pt'\n",
    "p.legend.click_policy = \"hide\"\n",
    "p.legend.background_fill_color = '#DCDCDC'\n",
    "p.legend.location = \"bottom_center\"\n",
    "p.legend.orientation = \"horizontal\"\n",
    "p.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "p.grid[0].ticker.num_minor_ticks = 0\n",
    "p.yaxis.major_label_text_font_size = \"12pt\"\n",
    "p.yaxis.major_label_text_font_style = 'bold'\n",
    "p.yaxis.axis_label = \"CCS (Å²)\"\n",
    "p.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "p.yaxis.axis_label_text_font_style = 'bold'\n",
    "p.xaxis.major_label_text_font_size = \"12pt\"\n",
    "p.xaxis.major_label_orientation = np.pi/4\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.major_label_text_font_style = 'bold'\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ M05 ################################\n",
    "hoverM05 = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_M05 = [hoverM05,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "r = figure(tools=TOOLS_M05, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"c) \"+title+\" - M05\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsM05)):\n",
    "    legendKey=[ylabelsM05[i]]\n",
    "    ydata = (data[ylabelsM05[i]])\n",
    "    ydataErr=(data[ylabelsErrM05[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    r.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    r.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "r.grid.grid_line_alpha=0.7\n",
    "r.title.text_font_size = '12pt'\n",
    "r.legend.click_policy = \"hide\"\n",
    "r.legend.background_fill_color = '#DCDCDC'\n",
    "r.legend.location = \"bottom_center\"\n",
    "r.legend.orientation = \"horizontal\"\n",
    "r.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "r.grid[0].ticker.num_minor_ticks = 0\n",
    "r.yaxis.major_label_text_font_size = \"12pt\"\n",
    "r.yaxis.major_label_text_font_style = 'bold'\n",
    "r.yaxis.axis_label = \"CCS (Å²)\"\n",
    "r.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "r.yaxis.axis_label_text_font_style = 'bold'\n",
    "r.xaxis.major_label_text_font_size = \"12pt\"\n",
    "r.xaxis.major_label_orientation = np.pi/4\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.major_label_text_font_style = 'bold'\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "show(column(t,p,r))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Rotationally averaged collision cross sections calculated using the Trajectory Method with partial charges calculated using HF (a), B3LYP (b) or M05 (c) functional with several basis sets: STO-3G (<font color='#000080'>blue</font>), 3-21G (<font color='#FF0080'>magenta</font>), 6-31G (<font color='#008000'>green</font>), 6-31+G (<font color='#FF8000'>orange</font>) and 6-31G* (<font color='#8009FF'>purple</font>) for CHelpG charge scheme. Error bars on each data point represent the standard deviation from Trajectory Method calculation, typically less than 0.5 %, and always less than 1 %."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "# Collision cross sections - HLY charge scheme - Nitrogen buffer gas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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M05\",\"text_font_size\":{\"value\":\"12pt\"}},\"id\":\"d1b9ec17-7b82-47b0-b264-e986b485af13\",\"type\":\"Title\"},{\"attributes\":{\"label\":{\"value\":\"HF/STO-3G\"},\"renderers\":[{\"id\":\"de373edc-4878-4aee-9e4e-f3e1da338c3a\",\"type\":\"GlyphRenderer\"},{\"id\":\"3736407a-463f-4bfd-b7cc-aca5561112a6\",\"type\":\"GlyphRenderer\"}]},\"id\":\"a690bf59-1418-41cf-b2c1-745c5039a8c2\",\"type\":\"LegendItem\"},{\"attributes\":{\"line_color\":{\"value\":\"#8009FF\"},\"line_width\":{\"value\":5},\"x0\":{\"field\":\"x\"},\"x1\":{\"field\":\"x\"},\"y0\":{\"field\":\"yLow\"},\"y1\":{\"field\":\"yHigh\"}},\"id\":\"c7fc9695-fed2-4169-abcf-3581d600b750\",\"type\":\"Segment\"},{\"attributes\":{\"line_color\":{\"value\":\"#8009FF\"},\"line_width\":{\"value\":5},\"x0\":{\"field\":\"x\"},\"x1\":{\"field\":\"x\"},\"y0\":{\"field\":\"yLow\"},\"y1\":{\"field\":\"yHigh\"}},\"id\":\"18d8d9df-8562-4de4-92be-bde6a9ed4562\",\"type\":\"Segment\"},{\"attributes\":{\"callback\":null,\"end\":20.5,\"start\":0.5},\"id\":\"8acdb8c4-8533-4e0d-aca6-3b67de9e753f\",\"type\":\"Range1d\"},{\"attributes\":{\"plot\":{\"id\":\"063265c4-b42e-41e5-a957-f82b6b3ad200\",\"subtype\":\"Figure\",\"type\":\"Plot\"}},\"id\":\"51cc108d-7d05-4a2f-a9c8-40f57efa9e78\",\"type\":\"SaveTool\"},{\"attributes\":{\"line_color\":{\"value\":\"#FF0080\"},\"line_width\":{\"value\":5},\"x0\":{\"field\":\"x\"},\"x1\":{\"field\":\"x\"},\"y0\":{\"field\":\"yLow\"},\"y1\":{\"field\":\"yHigh\"}},\"id\":\"eeb3a7c3-ce29-46d2-92d8-37f5f6de27dc\",\"type\":\"Segment\"},{\"attributes\":{\"fill_color\":{\"value\":\"#FF0080\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"90e9831c-2640-462f-9419-f939db45901c\",\"type\":\"Square\"},{\"attributes\":{\"label\":{\"value\":\"M05/3-21G\"},\"renderers\":[{\"id\":\"1af4bda4-ebce-4f8e-afe7-5ffe7209e72b\",\"type\":\"GlyphRenderer\"},{\"id\":\"3ac2c51b-ea99-4166-a324-cd200f05a25c\",\"type\":\"GlyphRenderer\"}]},\"id\":\"f55a33f0-9cc6-4eae-8951-d8c2e6a78c0f\",\"type\":\"LegendItem\"},{\"attributes\":{\"label\":{\"value\":\"M05/6-31G\"},\"renderers\":[{\"id\":\"12d39d87-250b-4c39-8362-f36584e91ffe\",\"type\":\"GlyphRenderer\"},{\"id\":\"4fc97a8a-f993-4d8d-a93b-838c9ec7c065\",\"type\":\"GlyphRenderer\"}]},\"id\":\"678f32a1-7101-4939-ae32-87f03a9542ec\",\"type\":\"LegendItem\"},{\"attributes\":{\"fill_color\":{\"value\":\"#FF0080\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"8c85e0ff-5c5a-4388-977c-810da9a81547\",\"type\":\"Square\"},{\"attributes\":{\"label\":{\"value\":\"B3LYP/6-31G\"},\"renderers\":[{\"id\":\"4fc23422-4731-4ec4-9881-4175bcbddcdc\",\"type\":\"GlyphRenderer\"},{\"id\":\"df927f9e-e896-4b75-940b-86ec2bcac333\",\"type\":\"GlyphRenderer\"}]},\"id\":\"adeeb7bd-3b6f-4a38-8cd1-d23b76a5c6ae\",\"type\":\"LegendItem\"},{\"attributes\":{\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1f77b4\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"c321c6a7-3673-42db-8178-467826bb77f7\",\"type\":\"Square\"},{\"attributes\":{},\"id\":\"e92741e1-ef07-4264-aa27-fe95125e9930\",\"type\":\"LinearScale\"},{\"attributes\":{\"fill_color\":{\"value\":\"#008000\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"03ee86f8-9dc6-491c-b5ae-4637f15c48b9\",\"type\":\"Square\"},{\"attributes\":{\"data_source\":{\"id\":\"275eabb4-fe5d-4eac-b8d1-a42880720063\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"9cdc7a21-c931-4c16-a077-debfb51a2130\",\"type\":\"Square\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"f6e17ed2-99ed-4cb4-b9c9-6c9e860c48cb\",\"type\":\"Square\"},\"selection_glyph\":null},\"id\":\"b932f599-abc8-49b3-bf3e-1c2c7fd718c4\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"line_color\":{\"value\":\"#000080\"},\"line_width\":{\"value\":5},\"x0\":{\"field\":\"x\"},\"x1\":{\"field\":\"x\"},\"y0\":{\"field\":\"yLow\"},\"y1\":{\"field\":\"yHigh\"}},\"id\":\"1b87a611-d5f7-46c4-a8ea-42595e8f0642\",\"type\":\"Segment\"},{\"attributes\":{\"fill_color\":{\"value\":\"#FF8000\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"d6b10833-f714-4669-a574-fbf7a5e18f3d\",\"type\":\"Square\"},{\"attributes\":{\"callback\":null,\"column_names\":[\"chargeScheme\",\"yErrPerc\",\"labels\",\"yHigh\",\"y\",\"x\",\"yLow\",\"yErr\"],\"data\":{\"chargeScheme\":[[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"],[\"B3LYP/6-31G*\"]],\"labels\":[\"\\u03b1Glc(1)\",\"\\u03b1Glc(2)\",\"\\u03b1Glc(3)\",\"\\u03b1Glc(4)\",\"\\u03b1Glc(5)\",\"\\u03b1Glc(6)\",\"\\u03b1Glc(7)\",\"\\u03b1Glc(8)\",\"\\u03b1Glc(9)\",\"\\u03b1Glc(10)\",\"\\u03b2Glc(1)\",\"\\u03b2Glc(2)\",\"\\u03b2Glc(3)\",\"\\u03b2Glc(4)\",\"\\u03b2Glc(5)\",\"\\u03b2Glc(6)\",\"\\u03b2Glc(7)\",\"\\u03b2Glc(8)\",\"\\u03b2Glc(9)\",\"\\u03b2Glc(10)\"],\"x\":[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20],\"y\":{\"__ndarray__\":\"j8L1KFxfYUAUrkfhenRhQFK4HoXraWFAUrgehevxYEDNzMzMzCRhQM3MzMzM1GBA9ihcj8LlYEBI4XoUrt9gQOxRuB6F82BAj8L1KFxnYED2KFyPwqVhQLgehetRqGFAMzMzMzN7YUAK16NwPXphQArXo3A9WmFAuB6F61EoYUCkcD0K1+NgQEjhehSuH2FAj8L1KFzvYEDhehSuR/lgQA==\",\"dtype\":\"float64\",\"shape\":[20]},\"yErr\":{\"__ndarray__\":\"iGNd3EYD3D9uNIC3QILeP3ctIR/0bOQ/uK8D54wo4z9txf6ye/LgP/FjzF1LyOM/AAAAAAAA4j+ZKhiV1AngP4qO5PIf0us/kKD4Meau4z/BOSNKe4PfP5LLf0i/feM/nRGlvcEX3j96xyk6ksvhP0w3iUFg5eQ/PSzUmuYd2z8Fo5I6AU3kPwHeAgmKH9c/2ht8YTJV6j/35GGh1jThPw==\",\"dtype\":\"float64\",\"shape\":[20]},\"yErrPerc\":{\"__ndarray__\":\"ahp3M+8n1D8DzHZkItnVP+baaKLuUt0/829uEvxD3D+SdScKoLbYPwwdSAcpYt0/iIG8mZOh2j+MugmNKcPXP2vDEMjqg+Q/j6IRKH7/3T+YuCrCUlLWP3vGxO2gmNs/3ApP4pWE1T+G/PBFVnTZPyHRIpDsGt4/nSxslHvB0z/rdWa8bQzeP9SMMJ4l4dA/IFSFlMlv4z8rQ1+puFfZPw==\",\"dtype\":\"float64\",\"shape\":[20]},\"yHigh\":{\"__ndarray__\":\"QfFjzF1tYUAubqMBvINhQH/ZPXlYfmFAArwFEhQFYUCSy39IvzVhQDGZKhiV6GBA9ihcj8L3YEBz+Q/pt+9gQHs2qz5XD2FAMLsnDwt7YECTOgFNhLVhQISezarPu2FAvAUSFD+KYUDRAN4CCYxhQEFg5dAib2FAzojS3uA1YUBHA3gLJPhgQLdif9k9K2FAqz5XW7EJYUDG3LWEfAphQA==\",\"dtype\":\"float64\",\"shape\":[20]},\"yLow\":{\"__ndarray__\":\"3ZOHhVpRYUD67evAOWVhQCWX/5B+VWFAorQ3+MLeYEAIzhlR2hNhQGkAb4EEwWBA9ihcj8LTYEAdyeU/pM9gQF1txf6y12BA7snDQq1TYEBZF7fRAJZhQOyePCzUlGFAqmBUUidsYUBDrWnecWhhQNNNYhBYRWFAorQ3+MIaYUAB3gIJis9gQNlfdk8eFGFAc0aU9gbVYED8GHPXEuhgQA==\",\"dtype\":\"float64\",\"shape\":[20]}}},\"id\":\"42de3eeb-9a57-466f-8ef5-fd6f788024be\",\"type\":\"ColumnDataSource\"},{\"attributes\":{\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1f77b4\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"3bcf09f4-69ca-4850-abc1-bbd4d38d0fdd\",\"type\":\"Square\"},{\"attributes\":{\"callback\":null,\"plot\":{\"id\":\"b04522ee-7d84-47e4-a9ae-fbaead33d64a\",\"subtype\":\"Figure\",\"type\":\"Plot\"},\"tooltips\":[[\"Index\",\"$index\"],[\"CCS (\\u00c5\\u00b2):\",\"@y \\u00c5\\u00b2\"],[\"Error (\\u00c5\\u00b2):\",\"\\u00b1@yErr{0.000} \\u00c5\\u00b2\"],[\"Error (%)\",\"\\u00b1@yErrPerc{0.000} %\"],[\"Model:\",\"@labels\"],[\"Method:\",\"@chargeScheme\"]]},\"id\":\"75fdc1bb-dc95-421c-9966-9ae46436fbb8\",\"type\":\"HoverTool\"}],\"root_ids\":[\"65e3b6e0-809d-454c-a180-add018da01aa\"]},\"title\":\"Bokeh Application\",\"version\":\"0.12.6\"}};\n",
       "            var render_items = [{\"docid\":\"70aa572e-aa3a-4f27-8059-df34f15fd003\",\"elementid\":\"d0d52d82-e373-43ad-ae07-c6a51af3d88f\",\"modelid\":\"65e3b6e0-809d-454c-a180-add018da01aa\"}];\n",
       "            \n",
       "            Bokeh.embed.embed_items(docs_json, render_items);\n",
       "          };\n",
       "          if (document.readyState != \"loading\") fn();\n",
       "          else document.addEventListener(\"DOMContentLoaded\", fn);\n",
       "        })();\n",
       "      },\n",
       "      function(Bokeh) {\n",
       "      }\n",
       "    ];\n",
       "  \n",
       "    function run_inline_js() {\n",
       "      \n",
       "      if ((window.Bokeh !== undefined) || (force === true)) {\n",
       "        for (var i = 0; i < inline_js.length; i++) {\n",
       "          inline_js[i](window.Bokeh);\n",
       "        }if (force === true) {\n",
       "          display_loaded();\n",
       "        }} else if (Date.now() < window._bokeh_timeout) {\n",
       "        setTimeout(run_inline_js, 100);\n",
       "      } else if (!window._bokeh_failed_load) {\n",
       "        console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "        window._bokeh_failed_load = true;\n",
       "      } else if (force !== true) {\n",
       "        var cell = $(document.getElementById(\"d0d52d82-e373-43ad-ae07-c6a51af3d88f\")).parents('.cell').data().cell;\n",
       "        cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
       "      }\n",
       "  \n",
       "    }\n",
       "  \n",
       "    if (window._bokeh_is_loading === 0) {\n",
       "      console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "      run_inline_js();\n",
       "    } else {\n",
       "      load_libs(js_urls, function() {\n",
       "        console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "        run_inline_js();\n",
       "      });\n",
       "    }\n",
       "  }(this));\n",
       "</script>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Import data\n",
    "title = \"HLY\"\n",
    "data = pd.read_csv(title+\"-N2.csv\", delimiter=',')\n",
    "# Extract data from the table\n",
    "xticks=data['Name']\n",
    "xdata=data['Point']\n",
    "################################ HF ################################\n",
    "hoverHF = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_HF = [hoverHF,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "t = figure(tools=TOOLS_HF, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"a) \"+title+\" - HF\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsHF)):\n",
    "    legendKey=[ylabelsHF[i]]\n",
    "    ydata = (data[ylabelsHF[i]])\n",
    "    ydataErr=(data[ylabelsErrHF[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    t.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    t.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "t.grid.grid_line_alpha=0.7\n",
    "t.title.text_font_size = '12pt'\n",
    "t.legend.click_policy = \"hide\"\n",
    "t.legend.background_fill_color = '#DCDCDC'\n",
    "t.legend.location = \"bottom_center\"\n",
    "t.legend.orientation = \"horizontal\"\n",
    "t.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "t.grid[0].ticker.num_minor_ticks = 0\n",
    "t.yaxis.major_label_text_font_size = \"12pt\"\n",
    "t.yaxis.major_label_text_font_style = 'bold'\n",
    "t.yaxis.axis_label = \"CCS (Å²)\"\n",
    "t.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "t.yaxis.axis_label_text_font_style = 'bold'\n",
    "t.xaxis.major_label_text_font_size = \"12pt\"\n",
    "t.xaxis.major_label_orientation = np.pi/4\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.major_label_text_font_style = 'bold'\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ B3LYP ################################\n",
    "hoverB3LYP = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_B3LYP = [hoverB3LYP,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "p = figure(tools=TOOLS_B3LYP, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"b) \"+title+\" - B3LYP\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsB3LYP)):\n",
    "    legendKey=[ylabelsB3LYP[i]]\n",
    "    ydata = (data[ylabelsB3LYP[i]])\n",
    "    ydataErr=(data[ylabelsErrB3LYP[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    p.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    p.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "p.grid.grid_line_alpha=0.7\n",
    "p.title.text_font_size = '12pt'\n",
    "p.legend.click_policy = \"hide\"\n",
    "p.legend.background_fill_color = '#DCDCDC'\n",
    "p.legend.location = \"bottom_center\"\n",
    "p.legend.orientation = \"horizontal\"\n",
    "p.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "p.grid[0].ticker.num_minor_ticks = 0\n",
    "p.yaxis.major_label_text_font_size = \"12pt\"\n",
    "p.yaxis.major_label_text_font_style = 'bold'\n",
    "p.yaxis.axis_label = \"CCS (Å²)\"\n",
    "p.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "p.yaxis.axis_label_text_font_style = 'bold'\n",
    "p.xaxis.major_label_text_font_size = \"12pt\"\n",
    "p.xaxis.major_label_orientation = np.pi/4\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.major_label_text_font_style = 'bold'\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ M05 ################################\n",
    "hoverM05 = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_M05 = [hoverM05,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "r = figure(tools=TOOLS_M05, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"c) \"+title+\" - M05\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsM05)):\n",
    "    legendKey=[ylabelsM05[i]]\n",
    "    ydata = (data[ylabelsM05[i]])\n",
    "    ydataErr=(data[ylabelsErrM05[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    r.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    r.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "r.grid.grid_line_alpha=0.7\n",
    "r.title.text_font_size = '12pt'\n",
    "r.legend.click_policy = \"hide\"\n",
    "r.legend.background_fill_color = '#DCDCDC'\n",
    "r.legend.location = \"bottom_center\"\n",
    "r.legend.orientation = \"horizontal\"\n",
    "r.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "r.grid[0].ticker.num_minor_ticks = 0\n",
    "r.yaxis.major_label_text_font_size = \"12pt\"\n",
    "r.yaxis.major_label_text_font_style = 'bold'\n",
    "r.yaxis.axis_label = \"CCS (Å²)\"\n",
    "r.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "r.yaxis.axis_label_text_font_style = 'bold'\n",
    "r.xaxis.major_label_text_font_size = \"12pt\"\n",
    "r.xaxis.major_label_orientation = np.pi/4\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.major_label_text_font_style = 'bold'\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "show(column(t,p,r))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Rotationally averaged collision cross sections calculated using the Trajectory Method with partial charges calculated using HF (a), B3LYP (b) or M05 (c) functional with several basis sets: STO-3G (<font color='#000080'>blue</font>), 3-21G (<font color='#FF0080'>magenta</font>), 6-31G (<font color='#008000'>green</font>), 6-31+G (<font color='#FF8000'>orange</font>) and 6-31G* (<font color='#8009FF'>purple</font>) for HLY charge scheme. Error bars on each data point represent the standard deviation from Trajectory Method calculation, typically less than 0.5 %, and always less than 1 %."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "# Collision cross sections - Natural Population Analysis (NPA) charge scheme - Nitrogen buffer gas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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M05\",\"text_font_size\":{\"value\":\"12pt\"}},\"id\":\"d0e33bee-fa26-4784-b4d9-a8127a2c6dc1\",\"type\":\"Title\"},{\"attributes\":{\"fill_color\":{\"value\":\"#000080\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"3553b186-084e-4d83-a72b-076edb09b867\",\"type\":\"Square\"},{\"attributes\":{\"label\":{\"value\":\"HF/STO-3G\"},\"renderers\":[{\"id\":\"255d5a10-fa44-4a0a-a40f-1adc08e6834c\",\"type\":\"GlyphRenderer\"},{\"id\":\"e6b30b9e-2066-4dec-a4b1-bd95e5a1560d\",\"type\":\"GlyphRenderer\"}]},\"id\":\"b5a95f6e-7150-47e9-aac4-d8b7b1669deb\",\"type\":\"LegendItem\"},{\"attributes\":{\"data_source\":{\"id\":\"a3a54725-fb29-4f07-a4bd-7b49394f2ed9\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"bf7bd657-e7b7-4fc0-91af-e9be46a531f5\",\"type\":\"Square\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"34e934c4-b213-423b-8343-67f4441d34fc\",\"type\":\"Square\"},\"selection_glyph\":null},\"id\":\"0d7a3dbf-2e2e-42b3-b581-2fb196996dc8\",\"type\":\"GlyphRenderer\"},{\"attributes\":{},\"id\":\"91585127-b41e-40b3-a687-fd6bd09042ca\",\"type\":\"BasicTicker\"},{\"attributes\":{\"data_source\":{\"id\":\"d2baba68-a9fa-40d8-ac44-ba891217f1fd\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"e7b08e3c-04e6-49ad-b6b6-3645a652ca83\",\"type\":\"Segment\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"4bc62a22-aa16-4407-92f3-8ba9c0ed1f9f\",\"type\":\"Segment\"},\"selection_glyph\":null},\"id\":\"4a72aa1a-704b-4c07-9c18-64870e100830\",\"type\":\"GlyphRenderer\"},{\"attributes\":{},\"id\":\"db22ffb1-643c-42e0-a398-cd2a461672ad\",\"type\":\"LinearScale\"},{\"attributes\":{\"data_source\":{\"id\":\"af06f501-d61f-4935-bf5a-71c1fb7a967e\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"48c173c1-0f45-48e3-951a-6646293653f0\",\"type\":\"Segment\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"48378ccf-4c40-4009-bb8a-71a9469819fd\",\"type\":\"Segment\"},\"selection_glyph\":null},\"id\":\"3b633d56-54fb-4d50-b7af-be709c81f37b\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"data_source\":{\"id\":\"81ea429c-ccf8-4650-8ba8-08daca840962\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"06a2e9d7-66d3-4bee-aac2-73fab4b1c3bb\",\"type\":\"Segment\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"202e367d-8dbb-45f0-9d0d-0a35bed93dfc\",\"type\":\"Segment\"},\"selection_glyph\":null},\"id\":\"d413b5ee-94a0-4b08-beb9-6ffd1cd591c0\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"line_color\":{\"value\":\"#000080\"},\"line_width\":{\"value\":5},\"x0\":{\"field\":\"x\"},\"x1\":{\"field\":\"x\"},\"y0\":{\"field\":\"yLow\"},\"y1\":{\"field\":\"yHigh\"}},\"id\":\"38135483-d643-478e-974b-f8290295688a\",\"type\":\"Segment\"},{\"attributes\":{\"fill_color\":{\"value\":\"#FF8000\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"e9b4df31-9bda-4834-aae6-625da366a592\",\"type\":\"Square\"},{\"attributes\":{},\"id\":\"4fd82bb5-7b2b-4771-a7e9-42971a023d7a\",\"type\":\"LinearScale\"},{\"attributes\":{\"label\":{\"value\":\"HF/6-31+G\"},\"renderers\":[{\"id\":\"b163d614-b91d-4353-9cbc-6f1caf8a4564\",\"type\":\"GlyphRenderer\"},{\"id\":\"90aa07ae-87c5-41d8-a02d-f5234a85a3d5\",\"type\":\"GlyphRenderer\"}]},\"id\":\"1ec0e923-a216-4bf8-9919-45302676a27a\",\"type\":\"LegendItem\"},{\"attributes\":{\"data_source\":{\"id\":\"504fa6cd-8cc9-4858-a6ca-e4a16c42e730\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"876b5e7b-ae4b-41f3-98fe-bcd36fe3605e\",\"type\":\"Square\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"45de0730-b79a-46d6-a688-f3a9fe3c2515\",\"type\":\"Square\"},\"selection_glyph\":null},\"id\":\"1cf4c501-e595-4420-b5a6-69eed18cb649\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"label\":{\"value\":\"M05/STO-3G\"},\"renderers\":[{\"id\":\"fdb6a84c-e4a1-42d7-b110-1c65387fe747\",\"type\":\"GlyphRenderer\"},{\"id\":\"4a72aa1a-704b-4c07-9c18-64870e100830\",\"type\":\"GlyphRenderer\"}]},\"id\":\"ea454cb3-94b2-462a-8c97-dfdd6955d937\",\"type\":\"LegendItem\"},{\"attributes\":{\"plot\":{\"id\":\"2a2acd5a-e88a-4703-a63e-09d2e83cc2d4\",\"subtype\":\"Figure\",\"type\":\"Plot\"}},\"id\":\"da05c411-9500-486b-beda-9c74a0f1096e\",\"type\":\"PanTool\"},{\"attributes\":{\"callback\":null,\"end\":20.5,\"start\":0.5},\"id\":\"63d5a5a8-95d3-4b88-94fc-190ba73504b4\",\"type\":\"Range1d\"},{\"attributes\":{\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1f77b4\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"b0895d4f-64b4-40e9-a225-1e173b8464ae\",\"type\":\"Square\"},{\"attributes\":{\"fill_color\":{\"value\":\"#FF8000\"},\"size\":{\"units\":\"screen\",\"value\":10},\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"876b5e7b-ae4b-41f3-98fe-bcd36fe3605e\",\"type\":\"Square\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       "            var render_items = [{\"docid\":\"637d1a78-e514-4aba-91e0-71f4c35bb447\",\"elementid\":\"fe0ae2d7-3d8b-41cc-829b-65ca57805a35\",\"modelid\":\"33dc2636-5d05-42f4-b78f-864238227ed2\"}];\n",
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       "      function(Bokeh) {\n",
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       "  \n",
       "    function run_inline_js() {\n",
       "      \n",
       "      if ((window.Bokeh !== undefined) || (force === true)) {\n",
       "        for (var i = 0; i < inline_js.length; i++) {\n",
       "          inline_js[i](window.Bokeh);\n",
       "        }if (force === true) {\n",
       "          display_loaded();\n",
       "        }} else if (Date.now() < window._bokeh_timeout) {\n",
       "        setTimeout(run_inline_js, 100);\n",
       "      } else if (!window._bokeh_failed_load) {\n",
       "        console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "        window._bokeh_failed_load = true;\n",
       "      } else if (force !== true) {\n",
       "        var cell = $(document.getElementById(\"fe0ae2d7-3d8b-41cc-829b-65ca57805a35\")).parents('.cell').data().cell;\n",
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       "  \n",
       "    }\n",
       "  \n",
       "    if (window._bokeh_is_loading === 0) {\n",
       "      console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "      run_inline_js();\n",
       "    } else {\n",
       "      load_libs(js_urls, function() {\n",
       "        console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n",
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     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Import data\n",
    "title = \"NPA\"\n",
    "data = pd.read_csv(title+\"-N2.csv\", delimiter=',')\n",
    "# Extract data from the table\n",
    "xticks=data['Name']\n",
    "xdata=data['Point']\n",
    "################################ HF ################################\n",
    "hoverHF = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_HF = [hoverHF,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "t = figure(tools=TOOLS_HF, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"a) \"+title+\" - HF\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsHF)):\n",
    "    legendKey=[ylabelsHF[i]]\n",
    "    ydata = (data[ylabelsHF[i]])\n",
    "    ydataErr=(data[ylabelsErrHF[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    t.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    t.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "t.grid.grid_line_alpha=0.7\n",
    "t.title.text_font_size = '12pt'\n",
    "t.legend.click_policy = \"hide\"\n",
    "t.legend.background_fill_color = '#DCDCDC'\n",
    "t.legend.location = \"bottom_center\"\n",
    "t.legend.orientation = \"horizontal\"\n",
    "t.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "t.grid[0].ticker.num_minor_ticks = 0\n",
    "t.yaxis.major_label_text_font_size = \"12pt\"\n",
    "t.yaxis.major_label_text_font_style = 'bold'\n",
    "t.yaxis.axis_label = \"CCS (Å²)\"\n",
    "t.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "t.yaxis.axis_label_text_font_style = 'bold'\n",
    "t.xaxis.major_label_text_font_size = \"12pt\"\n",
    "t.xaxis.major_label_orientation = np.pi/4\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.major_label_text_font_style = 'bold'\n",
    "t.xaxis.minor_tick_line_color = None\n",
    "t.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ B3LYP ################################\n",
    "hoverB3LYP = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_B3LYP = [hoverB3LYP,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "p = figure(tools=TOOLS_B3LYP, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"b) \"+title+\" - B3LYP\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsB3LYP)):\n",
    "    legendKey=[ylabelsB3LYP[i]]\n",
    "    ydata = (data[ylabelsB3LYP[i]])\n",
    "    ydataErr=(data[ylabelsErrB3LYP[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    p.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    p.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "p.grid.grid_line_alpha=0.7\n",
    "p.title.text_font_size = '12pt'\n",
    "p.legend.click_policy = \"hide\"\n",
    "p.legend.background_fill_color = '#DCDCDC'\n",
    "p.legend.location = \"bottom_center\"\n",
    "p.legend.orientation = \"horizontal\"\n",
    "p.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "p.grid[0].ticker.num_minor_ticks = 0\n",
    "p.yaxis.major_label_text_font_size = \"12pt\"\n",
    "p.yaxis.major_label_text_font_style = 'bold'\n",
    "p.yaxis.axis_label = \"CCS (Å²)\"\n",
    "p.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "p.yaxis.axis_label_text_font_style = 'bold'\n",
    "p.xaxis.major_label_text_font_size = \"12pt\"\n",
    "p.xaxis.major_label_orientation = np.pi/4\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.major_label_text_font_style = 'bold'\n",
    "p.xaxis.minor_tick_line_color = None\n",
    "p.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "################################ M05 ################################\n",
    "hoverM05 = HoverTool(tooltips=[(\"Index\", \"$index\"),\n",
    "                              (\"CCS (Å²):\",\"@y Å²\"),\n",
    "                              (\"Error (Å²):\", \"±@yErr{0.000} Å²\"),\n",
    "                              (\"Error (%)\",\"±@yErrPerc{0.000} %\"),\n",
    "                              (\"Model:\", \"@labels\"),\n",
    "                              (\"Method:\",\"@chargeScheme\")])\n",
    "TOOLS_M05 = [hoverM05,\"box_zoom,pan,wheel_zoom,reset,save\"]\n",
    "r = figure(tools=TOOLS_M05, plot_width=800, plot_height=300, x_range=(0.5,20.5),\n",
    "           y_range=(115,150), title=\"c) \"+title+\" - M05\", active_drag=\"box_zoom\")\n",
    "dataSource = []\n",
    "# Prepare data for plotting\n",
    "for i in range(len(ylabelsM05)):\n",
    "    legendKey=[ylabelsM05[i]]\n",
    "    ydata = (data[ylabelsM05[i]])\n",
    "    ydataErr=(data[ylabelsErrM05[i]])\n",
    "    ydataErrPerc = (ydataErr/ydata)*100\n",
    "    ydataLow = ydata-ydataErr\n",
    "    ydataHigh = ydata+ydataErr\n",
    "    source = ColumnDataSource(data=dict(x=xdata, \n",
    "                                        y=ydata, \n",
    "                                        yLow=ydataLow,\n",
    "                                        yHigh=ydataHigh,\n",
    "                                        labels=xticksLabels, \n",
    "                                        yErr=ydataErr,\n",
    "                                        yErrPerc=ydataErrPerc,\n",
    "                                        chargeScheme=([legendKey]*(len(ydata)))))\n",
    "    dataSource.append(source)\n",
    "    dataColor = colorSets[i]\n",
    "    r.square(x='x', y='y', size=10, fill_color=dataColor, color=\"black\", source=source, legend=legendKey[0])\n",
    "    r.segment(x0='x',x1='x', y0='yLow', y1='yHigh', color=dataColor, line_width=5, source=source, legend=legendKey[0])\n",
    "labelDict = {}\n",
    "for i, s in enumerate(xticks):\n",
    "    labelDict[i+1] = s\n",
    "r.grid.grid_line_alpha=0.7\n",
    "r.title.text_font_size = '12pt'\n",
    "r.legend.click_policy = \"hide\"\n",
    "r.legend.background_fill_color = '#DCDCDC'\n",
    "r.legend.location = \"bottom_center\"\n",
    "r.legend.orientation = \"horizontal\"\n",
    "r.grid[0].ticker.desired_num_ticks = len(xticks)\n",
    "r.grid[0].ticker.num_minor_ticks = 0\n",
    "r.yaxis.major_label_text_font_size = \"12pt\"\n",
    "r.yaxis.major_label_text_font_style = 'bold'\n",
    "r.yaxis.axis_label = \"CCS (Å²)\"\n",
    "r.yaxis.axis_label_text_font_size = \"14pt\"\n",
    "r.yaxis.axis_label_text_font_style = 'bold'\n",
    "r.xaxis.major_label_text_font_size = \"12pt\"\n",
    "r.xaxis.major_label_orientation = np.pi/4\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.major_label_text_font_style = 'bold'\n",
    "r.xaxis.minor_tick_line_color = None\n",
    "r.xaxis.formatter = FuncTickFormatter(code=\"\"\"\n",
    "    var labels = %s;\n",
    "    return labels[tick];\n",
    "\"\"\" % labelDict)\n",
    "\n",
    "show(column(t,p,r))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Rotationally averaged collision cross sections calculated using the Trajectory Method with partial charges calculated using HF (a), B3LYP (b) or M05 (c) functional with several basis sets: STO-3G (<font color='#000080'>blue</font>), 3-21G (<font color='#FF0080'>magenta</font>), 6-31G (<font color='#008000'>green</font>), 6-31+G (<font color='#FF8000'>orange</font>) and 6-31G* (<font color='#8009FF'>purple</font>) for NPA charge scheme. Error bars on each data point represent the standard deviation from Trajectory Method calculation, typically less than 0.5 %, and always less than 1 %."
   ]
  }
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