diff --git a/HW3/README.md b/HW3/README.md index 494e0d5..eb93c41 100644 --- a/HW3/README.md +++ b/HW3/README.md @@ -12,7 +12,7 @@ *Disable the plotting routine for the solvers* d. Use the four solvers `falsepos.m`, `incsearch.m`, `newtraph.m` and `mod_secant.m` - to solve for the angle needed to reach h=1.72 m, with an initial speed of 1.5 m/s. + to solve for the angle needed to reach h=1.72 m, with an initial speed of 15 m/s. e. The `newtraph.m` function needs a derivative, calculate the derivative of your function with respect to theta, `dprojectile_dtheta.m`. This function should @@ -29,7 +29,7 @@ | solver | initial guess(es) | ea | number of iterations| | --- | --- | --- | --- | |falsepos | | | | - |incsearch | | | | + |bisect | | | | |newtraph | | | | |mod_secant | | | | ``` @@ -49,7 +49,7 @@ using the numerical solvers, `newtraph.m` and `mod_secant.m`, there are certain guesses that do not converge. a. Calculate the first 5 iterations for the Newton-Raphson method with an initial - guess of x_i=2. + guess of x_i=2 for f(x)=x*exp(-x^2). b. Add the results to a table in the `README.md` with: diff --git a/lecture_07/.lecture_07.md.swo b/lecture_07/.lecture_07.md.swo new file mode 100644 index 0000000..244c92b Binary files /dev/null and b/lecture_07/.lecture_07.md.swo differ diff --git a/lecture_07/.lecture_07.md.swp b/lecture_07/.lecture_07.md.swp new file mode 100644 index 0000000..0998c86 Binary files /dev/null and b/lecture_07/.lecture_07.md.swp differ diff --git "a/lecture_08/\020\267Y\001" "b/lecture_08/\020\267Y\001" new file mode 100644 index 0000000..e69de29 diff --git a/lecture_08/.ipynb_checkpoints/lecture_08-checkpoint.ipynb b/lecture_08/.ipynb_checkpoints/lecture_08-checkpoint.ipynb new file mode 100644 index 0000000..2fd6442 --- /dev/null +++ b/lecture_08/.ipynb_checkpoints/lecture_08-checkpoint.ipynb @@ -0,0 +1,6 @@ +{ + "cells": [], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/lecture_08/Auchain_model.gif b/lecture_08/Auchain_model.gif new file mode 100644 index 0000000..2f8c78c Binary files /dev/null and b/lecture_08/Auchain_model.gif differ diff --git a/lecture_08/au_chain.jpg b/lecture_08/au_chain.jpg new file mode 100644 index 0000000..492fee8 Binary files /dev/null and b/lecture_08/au_chain.jpg differ diff --git a/lecture_08/goldenratio.png b/lecture_08/goldenratio.png new file mode 100644 index 0000000..9493c8c Binary files /dev/null and b/lecture_08/goldenratio.png differ diff --git a/lecture_08/lecture_08.ipynb b/lecture_08/lecture_08.ipynb new file mode 100644 index 0000000..134ed8a --- /dev/null +++ b/lecture_08/lecture_08.ipynb @@ -0,0 +1,1941 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "%plot --format svg" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Optimization\n", + "\n", + "Many problems involve finding a minimum or maximum based on given constraints. Engineers and scientists typically use energy balance equations to find the conditions of minimum energy, but this value may never go to 0 and the actual value of energy may not be of interest. " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The Lennard-Jones potential is commonly used to model interatomic bonding. \n", + "\n", + "$E_{LJ}(x)=4\\epsilon \\left(\\left(\\frac{\\sigma}{x}\\right)^{12}-\\left(\\frac{\\sigma}{x}\\right)^{6}\\right)$\n", + "\n", + "Considering a 1-D gold chain, we can calculate the bond length, $x_{b}$, with no force applied to the chain and even for tension, F. This will allow us to calculate the nonlinear spring constant of a 1-D gold chain. \n", + "\n", + "![TEM image of Gold chain](au_chain.jpg)\n", + "\n", + "Computational Tools to Study and Predict the Long-Term Stability of Nanowires.\n", + "By Martin E. Zoloff Michoff, Patricio Vélez, Sergio A. Dassie and Ezequiel P. M. Leiva \n", + "\n", + "![Model of Gold chain, from molecular dynamics simulation](Auchain_model.gif)\n", + "\n", + "[Single atom gold chain mechanics](http://www.uam.es/personal_pdi/ciencias/agrait/)\n", + "\n", + "### First, let's find the minimum energy $\\min(E_{LJ}(x))$\n", + "\n", + "## Brute force" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "Gnuplot\n", + "Produced by GNUPLOT 5.0 patchlevel 3 \n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.08\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t2.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t6\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\n", + "\n", + "\tgnuplot_plot_1a\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_2a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "setdefaults\n", + "epsilon = 0.039; % kcal/mol\n", + "sigma = 2.934; % Angstrom\n", + "x=linspace(2.8,6,200); % bond length in Angstrom\n", + "\n", + "Ex = lennard_jones(x,sigma,epsilon);\n", + "\n", + "[Emin,imin]=min(Ex);\n", + "\n", + "plot(x,Ex,x(imin),Emin,'o')" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "ans = 3.2824\n", + "ans = 3.2985\n", + "ans = 3.3146\n" + ] + } + ], + "source": [ + "x(imin-1)\n", + "x(imin)\n", + "x(imin+1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Golden Search Algorithm\n", + "\n", + "We can't just look for a sign change for the problem (unless we can take a derivative) so we need a new approach to determine whether we have a maximum between the two bounds.\n", + "\n", + "Rather than using the midpoint of initial bounds, here the problem is more difficult. We need to compare the values of 4 function evaluations. The golden search uses the golden ratio to determine two interior points. \n", + "\n", + "![golden ratio](goldenratio.png)\n", + "\n", + "Start with bounds of 2.5 and 6 Angstrom. " + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "current_min = -0.019959\r\n" + ] + }, + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "Gnuplot\n", + "Produced by GNUPLOT 5.0 patchlevel 3 \n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.08\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t2.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t6\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\n", + "\n", + "\tgnuplot_plot_1a\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_2a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_3a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_4a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_5a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_6a\n", + "\n", + "\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "% define Au atomic potential\n", + "epsilon = 0.039; % kcal/mol\n", + "sigma = 2.934; % Angstrom\n", + "Au_x= @(x) lennard_jones(x,sigma,epsilon);\n", + "\n", + "% calculate golden ratio\n", + "phi = 1/2+sqrt(5)/2;\n", + "% set initial limits\n", + "x_l=2.8; \n", + "x_u=6; \n", + "\n", + "% Iteration #1\n", + "d=(phi-1)*(x_u-x_l);\n", + "\n", + "x1=x_l+d; % define point 1\n", + "x2=x_u-d; % define point 2\n", + "\n", + "\n", + "% evaluate Au_x(x1) and Au_x(x2)\n", + "\n", + "f1=Au_x(x1);\n", + "f2=Au_x(x2);\n", + "plot(x,Au_x(x),x_l,Au_x(x_l),'ro',x2,f2,'rs',x1,f1,'gs',x_u,Au_x(x_u),'go')\n", + "hold on;\n", + "\n", + "if f2\n", + "\n", + "Gnuplot\n", + "Produced by GNUPLOT 5.0 patchlevel 3 \n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.08\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t2.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t6\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\n", + "\n", + "\tgnuplot_plot_1a\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_2a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_3a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_4a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_5a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_6a\n", + "\n", + "\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "% Iteration #2\n", + "d=(phi-1)*(x_u-x_l);\n", + "\n", + "x1=x_l+d; % define point 1\n", + "x2=x_u-d; % define point 2\n", + "\n", + "% evaluate Au_x(x1) and Au_x(x2)\n", + "\n", + "f1=Au_x(x1);\n", + "f2=Au_x(x2);\n", + "plot(x,Au_x(x),x_l,Au_x(x_l),'ro',x2,f2,'rs',x1,f1,'gs',x_u,Au_x(x_u),'go')\n", + "hold on;\n", + "\n", + "if f2\n", + "\n", + "Gnuplot\n", + "Produced by GNUPLOT 5.0 patchlevel 3 \n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.08\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t2.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t6\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\n", + "\n", + "\tgnuplot_plot_1a\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_2a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_3a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_4a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_5a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_6a\n", + "\n", + "\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "% Iteration #3\n", + "d=(phi-1)*(x_u-x_l);\n", + "\n", + "x1=x_l+d; % define point 1\n", + "x2=x_u-d; % define point 2\n", + "\n", + "% evaluate Au_x(x1) and Au_x(x2)\n", + "\n", + "f1=Au_x(x1);\n", + "f2=Au_x(x2);\n", + "plot(x,Au_x(x),x_l,Au_x(x_l),'ro',x2,f2,'rs',x1,f1,'gs',x_u,Au_x(x_u),'go')\n", + "hold on;\n", + "\n", + "if f2\n", + "\n", + "Gnuplot\n", + "Produced by GNUPLOT 5.0 patchlevel 3 \n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.08\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t2.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t6\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\n", + "\n", + "\tgnuplot_plot_1a\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_2a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_3a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_4a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_5a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_6a\n", + "\n", + "\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "% Iteration #3\n", + "d=(phi-1)*(x_u-x_l);\n", + "\n", + "x1=x_l+d; % define point 1\n", + "x2=x_u-d; % define point 2\n", + "\n", + "% evaluate Au_x(x1) and Au_x(x2)\n", + "\n", + "f1=Au_x(x1);\n", + "f2=Au_x(x2);\n", + "plot(x,Au_x(x),x_l,Au_x(x_l),'ro',x2,f2,'rs',x1,f1,'gs',x_u,Au_x(x_u),'go')\n", + "hold on;\n", + "\n", + "if f2\n", + "\n", + "Gnuplot\n", + "Produced by GNUPLOT 5.0 patchlevel 3 \n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.08\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t2.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t6\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\n", + "\n", + "\tgnuplot_plot_1a\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_2a\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_3a\n", + "\n", + "\t \n", + "\t\n", + "\t\n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_4a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_5a\n", + "\n", + "\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "% define Au atomic potential\n", + "epsilon = 0.039; % kcal/mol\n", + "sigma = 2.934; % Angstrom\n", + "Au_x= @(x) lennard_jones(x,sigma,epsilon);\n", + "\n", + "% set initial limits\n", + "x_l=2.8; \n", + "x_u=3.5; \n", + "\n", + "% Iteration #1\n", + "x1=x_l;\n", + "x2=mean([x_l,x_u]);\n", + "x3=x_u;\n", + "\n", + "% evaluate Au_x(x1), Au_x(x2) and Au_x(x3)\n", + " \n", + "f1=Au_x(x1);\n", + "f2=Au_x(x2);\n", + "f3=Au_x(x3);\n", + "p = polyfit([x1,x2,x3],[f1,f2,f3],2);\n", + "x_fit = linspace(x1,x3,20);\n", + "y_fit = polyval(p,x_fit);\n", + "\n", + "plot(x,Au_x(x),x_fit,y_fit,[x1,x2,x3],[f1,f2,f3],'o')\n", + "hold on\n", + "if f2x2\n", + " plot(x4,f4,'*',[x1,x2],[f1,f2])\n", + " x1=x2;\n", + " f1=f2;\n", + " else\n", + " plot(x4,f4,'*',[x3,x2],[f3,f2])\n", + " x3=x2;\n", + " f3=f2;\n", + " end\n", + " x2=x4; f2=f4;\n", + "else\n", + " error('no minimum in bracket')\n", + "end\n", + "hold off" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "f3 = -0.038878\r\n" + ] + }, + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "Gnuplot\n", + "Produced by GNUPLOT 5.0 patchlevel 3 \n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.08\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t2.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t6\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\n", + "\n", + "\tgnuplot_plot_1a\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_2a\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_3a\n", + "\n", + "\t \n", + "\t\n", + "\t\n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_4a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_5a\n", + "\n", + "\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "p = polyfit([x1,x2,x3],[f1,f2,f3],2);\n", + "x_fit = linspace(x1,x3,20);\n", + "y_fit = polyval(p,x_fit);\n", + "\n", + "plot(x,Au_x(x),x_fit,y_fit,[x1,x2,x3],[f1,f2,f3],'o')\n", + "hold on\n", + "if f2x2\n", + " plot(x4,f4,'*',[x1,x2],[f1,f2])\n", + " x1=x2;\n", + " f1=f2;\n", + " else\n", + " plot(x4,f4,'*',[x3,x2],[f3,f2])\n", + " x3=x2;\n", + " f3=f2;\n", + " end\n", + " x2=x4; f2=f4;\n", + "else\n", + " error('no minimum in bracket')\n", + "end\n", + "hold off\n" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "f3 = -0.038878\r\n" + ] + }, + { + "data": { + "image/svg+xml": [ + "\n", + "\n", + "Gnuplot\n", + "Produced by GNUPLOT 5.0 patchlevel 3 \n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\t\n", + "\t \n", + "\t \n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t-0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.02\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.04\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.06\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t0.08\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t2.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t3.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t4.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t5.5\n", + "\t\n", + "\n", + "\n", + "\t\t\n", + "\t\t6\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\t\n", + "\n", + "\n", + "\tgnuplot_plot_1a\n", + "\n", + "\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_2a\n", + "\n", + "\t\n", + "\t\n", + "\tgnuplot_plot_3a\n", + "\n", + "\t \n", + "\t\n", + "\t\n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_4a\n", + "\n", + "\t \n", + "\t\n", + "\n", + "\t\n", + "\tgnuplot_plot_5a\n", + "\n", + "\t\n", + "\t\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "p = polyfit([x1,x2,x3],[f1,f2,f3],2);\n", + "x_fit = linspace(x1,x3,20);\n", + "y_fit = polyval(p,x_fit);\n", + "\n", + "plot(x,Au_x(x),x_fit,y_fit,[x1,x2,x3],[f1,f2,f3],'o')\n", + "hold on\n", + "if f2x2\n", + " plot(x4,f4,'*',[x1,x2],[f1,f2])\n", + " x1=x2;\n", + " f1=f2;\n", + " else\n", + " plot(x4,f4,'*',[x3,x2],[f3,f2])\n", + " x3=x2;\n", + " f3=f2;\n", + " end\n", + " x2=x4; f2=f4;\n", + "else\n", + " error('no minimum in bracket')\n", + "end\n", + "hold off\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Parabolic interpolation does not converge in many scenarios even though it it a bracketing method. Instead, functions like `fminbnd` in Matlab and Octave use a combination of the two (Golden Ratio and Parabolic)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Using the solutions to minimization for the nonlinear spring constant\n", + "\n", + "Now, we have two routines to find minimums of a univariate function (Golden Ratio and Parabolic). Let's use these to solve for the minimum energy given a range of applied forces to the single atom gold chain\n", + "\n", + "$E_{total}(\\Delta x) = E_{LJ}(x_{min}+\\Delta x) - F \\cdot \\Delta x$" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "xmin = 3.2933\r\n" + ] + } + ], + "source": [ + "xmin = fminbnd(Au_x,2.8,6)\n", + "\n", + "Etotal = @(dx,F) Au_x(xmin+dx)-F.*dx;\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Octave", + "language": "octave", + "name": "octave" + }, + "language_info": { + "file_extension": ".m", + "help_links": [ + { + "text": "MetaKernel Magics", + "url": "https://github.com/calysto/metakernel/blob/master/metakernel/magics/README.md" + } + ], + "mimetype": "text/x-octave", + "name": "octave", + "version": "0.19.14" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/lecture_08/lennard_jones.m b/lecture_08/lennard_jones.m new file mode 100644 index 0000000..d18a6ad --- /dev/null +++ b/lecture_08/lennard_jones.m @@ -0,0 +1,4 @@ +function E_LJ =lennard_jones(x,sigma,epsilon) + E_LJ = 4*epsilon*((sigma./x).^12-(sigma./x).^6); +end + diff --git a/lecture_08/octave-workspace b/lecture_08/octave-workspace new file mode 100644 index 0000000..f505b0a Binary files /dev/null and b/lecture_08/octave-workspace differ diff --git "a/lecture_08/\34040\001" "b/lecture_08/\34040\001" new file mode 100644 index 0000000..e69de29