Merge pull request #97 from MobleyLab/post_edits

Merge in Samarjeet's updated figure and code

Author: davidlmobley

paper/basic_training.pdf

@@ -35,7 +35,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%% ARTICLE SETUP
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\title{Best Practices for Foundations in Molecular Simulations [Article V1.0] v\versionnumber}
+\title{Best Practices for Foundations in Molecular Simulations [Article v\versionnumber]}
 
 \author[1]{Efrem Braun}
 \author[2]{Justin Gilmer}
@@ -1077,8 +1077,9 @@ \subsubsection{ Ewald Summation}
 
 \begin{figure}[h]
 \centering
-\includegraphics[width=\linewidth]{decay_comparison.pdf}
-    \caption{Comparison of decay of the original $r^{-1}$ term for Coulomb interactions (blue,*), the resulting direct-space term after Gaussian screening (black,-) and the $r^{-6}$ in van der Waals term (red, -.).  }
+\includegraphics[width=\linewidth]{py_decay_comparison.pdf}
+    \caption{Comparison of decay of the original $r^{-1}$ term for Coulomb interactions (blue,*), the resulting direct-space term after Gaussian screening (black,-) and the $r^{-6}$ in van der Waals term (red, -.). 
+    Note: The value on the vertical axis has been scaled to allow easy visualization of the relative decay of each term. }
 \label{decay}
 \end{figure}
 

paper/basic_training.tex

@@ -0,0 +1,21 @@
+import numpy as np
+from scipy import special as spc
+import matplotlib.pyplot as plt
+
+r = np.linspace(1.0, 3.0, 30)
+print(r)
+
+y = 1./r
+ylj = np.power(y, 6)
+print(ylj)
+e = spc.erfc(r) / r
+e = e /e[0]
+
+fig = plt.figure()
+plt.plot(r, y, 'b*', r, ylj, 'r--', r, e, 'k-')
+plt.title("Comparison of 1/r, erfc(r) and 1/r^6")
+plt.legend(['1/r', '1/r^6', 'erfc(r)/r'])
+plt.xlabel('distance (r)')
+plt.ylabel('Function value ')
+plt.show()
+fig.savefig("py_decay_comparison.pdf", bbox_inches='tight')

paper/decay_comparison.pdf

@@ -0,0 +1,19 @@
+x=1.0:0.1:3.5;
+
+y = 1./x;
+h=figure
+plot(x,y,'b*')
+hold on;
+ylj=1./(x.^6);
+plot(x,ylj,'r-.')
+plot(x,erfc(x),'k-');
+hold off
+xlabel('distance')
+ylabel('function value')
+title('Comparison of 1/r, erfc(r) and 1/(r^6)')
+
+set(h,'Units','Inches');
+pos = get(h,'Position');
+set(h,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)])
+
+print(h,'decay_comparison.pdf','-dpdf')