Final submission by Drew and Mark

ArgonSim/.floo

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+{
+    "url": "https://floobits.com/mdttheory/ArgonSim"
+}

ArgonSim/.flooignore

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+#*
+*.o
+*.pyc
+*~
+extern/
+node_modules/
+tmp
+vendor/

ArgonSim/plot_results.py~

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+#!/usr/bin/env python
+import matplotlib as matl
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D
+import numpy as np
+import pylab as P
+
+SaveFigure = True #True will save as png instead of displaying
+numFigs = 1 #More than one will input/output multiple datafiles (use only with SaveFigure==True)
+
+for n in range(0,numFigs):
+
+  #with open("momentum"+str(n+1)+".dat") as f:
+   # data = map(float, f)
+  #print (np.mean(data))
+
+ # n, bins, patches = P.hist(data, 50, normed=1, histtype='stepfilled')
+  #P.setp(patches, 'facecolor', 'g', 'alpha', 0.75)
+
+  #y = P.normpdf( bins, 0, 1)
+ # l = P.plot(bins, y, 'k--', linewidth=1.5)
+
+ # if SaveFigure:
+ #   P.savefig('MomentumData'+str(n+1)+'.png', bbox_inches='tight')
+  #else:
+  #  P.show()
+
+  def plotaxis(large): 
+     x = np.linspace(-large, large, 100)
+     y = x*0.0
+     z = x*0.0
+     #   ax.plot(x, y, z)
+     y = np.linspace(-large, large, 100)
+     x = x*0.0
+     z = x*0.0
+     #   ax.plot(x, y, z)
+     z = np.linspace(-large, large, 100)
+     x = x*0.0
+     y = x*0.0
+     #   ax.plot(x, y, z)
+
+  f = open("data/position    "+str(n+1)+".dat")
+  i = 1
+  data = []
+  for line in f:
+    data_aux = []
+    for x in line.split():
+        data_aux.append(float(x))
+    data.append(data_aux)
+  f.close()
+  fig = plt.figure()
+  ax = fig.gca(projection='3d')
+  plotaxis(30)
+  print (len(data))
+  for point in data:
+    ax.scatter(point[0], point[1], point[2])
+
+  if SaveFigure:
+    plt.savefig('PositionData'+str(n+1)+'.png', bbox_inches='tight')
+  else:
+    plt.show()

ArgonSim/readme

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+We use a bash file to compile and run our fortran code.  cd to the src folder and type ./run.sh
+

ArgonSim/report/MDSimReport.aux

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+\relax 
+\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{1}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Initial Conditions}{1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Lennard-Jones Potential}{1}}
+\newlabel{eqn:equation1}{{1}{1}}
+\newlabel{eqn:equation2}{{2}{1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2}Position}{1}}
+\newlabel{eqn:equation3}{{3}{1}}
+\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Visual representation of base vectors (n = 4)\relax }}{1}}
+\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
+\newlabel{fig:figure1}{{1}{1}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Example of initial lattice (n = 32)\relax }}{1}}
+\newlabel{fig:figure2}{{2}{1}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3}Velocity}{2}}
+\newlabel{eqn:equation4}{{4}{2}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}Runtime}{2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Numerical Integration in Time}{2}}
+\newlabel{eqn:equation5}{{5}{2}}
+\newlabel{eqn:equation6}{{6}{2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Computational Limitations}{2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.3}Thermostat}{2}}
+\newlabel{eqn:equation7}{{7}{2}}
+\@writefile{toc}{\contentsline {section}{\numberline {4}Observations \& Measurements}{2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Energy Conservation}{3}}
+\newlabel{eqn:equation8}{{8}{3}}
+\newlabel{eqn:equation9}{{9}{3}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Energy around T=0\relax }}{3}}
+\newlabel{fig:figure3}{{3}{3}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Energy around T=1\relax }}{3}}
+\newlabel{fig:figure4}{{4}{3}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces Energy around T=5\relax }}{3}}
+\newlabel{fig:figure4}{{5}{3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Temperature}{3}}
+\newlabel{eqn:equation10}{{10}{3}}
+\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces Temperature around T=(10,5,1,0)\relax }}{4}}
+\newlabel{fig:figure5}{{6}{4}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.3}Pressure}{4}}
+\newlabel{eqn:equation11}{{11}{4}}
+\@writefile{lof}{\contentsline {figure}{\numberline {7}{\ignorespaces Pressure around T=(10,5,1,0)\relax }}{4}}
+\newlabel{fig:figure6}{{7}{4}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.4}Pair Correlation}{4}}
+\newlabel{eqn:equation12}{{12}{4}}
+\newlabel{eqn:equation13}{{13}{4}}
+\@writefile{lof}{\contentsline {figure}{\numberline {8}{\ignorespaces Pair correlation around T=0 showing the strong peaks at integer multiples of $\sigma $.\relax }}{5}}
+\newlabel{fig:figure7}{{8}{5}}
+\@writefile{lof}{\contentsline {figure}{\numberline {9}{\ignorespaces Pair correlation around T=1 showing the weaker, yet distinct, peaks at integer multiples of $\sigma $.\relax }}{5}}
+\newlabel{fig:figure8}{{9}{5}}
+\@writefile{lof}{\contentsline {figure}{\numberline {10}{\ignorespaces Pair correlation around T=10 showing a nearly random distribution.\relax }}{5}}
+\newlabel{fig:figure9}{{10}{5}}
+\@writefile{toc}{\contentsline {section}{\numberline {5}Conclusion}{5}}