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dbacchet committed 783930a

moved python code in a subfolder
working on the report

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docs/sm_final_report/sm_final_report.aux

-\relax 
-\select@language{english}
-\@writefile{toc}{\select@language{english}}
-\@writefile{lof}{\select@language{english}}
-\@writefile{lot}{\select@language{english}}
-\@writefile{toc}{\contentsline {section}{\numberline {1}Problem}{1}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Grancanonical Ensemble}{2}}
-\newlabel{math:grand_partition}{{2}{2}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.1.1}Grand Potential}{2}}
-\@writefile{toc}{\contentsline {paragraph}{Definition}{2}}
-\newlabel{math:grand_potential}{{4}{2}}
-\citation{chandler1987introduction}
-\citation{chandler1987introduction}
-\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}The Lattice-gas Model}{3}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Assumptions}{3}}
-\citation{wiki:hcp}
-\@writefile{toc}{\contentsline {section}{\numberline {2}Formalism}{4}}
-\@writefile{toc}{\contentsline {section}{\numberline {3}Introduction}{4}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}First Subsection}{4}}
-\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.1}First Sub-subsection}{4}}
-\citation{DeOliveira1978687}
-\citation{*}
-\bibstyle{plain}
-\bibdata{sm_final_report}
-\@writefile{toc}{\contentsline {paragraph}{First Paragraph}{5}}
-\newlabel{eq_first_sum}{{9}{5}}
-\newlabel{eq_1}{{10}{5}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Playing with figures}{5}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {3.3}Playing with tables}{5}}
-\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces This is a floating figure, with default (proposed) options\relax }}{6}}
-\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces  my second test table, just numeric with no frills\relax }}{6}}
-\newlabel{table:fifth_test_table}{{1}{6}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces This is the same floating figure, but centered\relax }}{6}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces And again a floating figure, but with imposed width\relax }}{7}}
-\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
-\newlabel{fig:sub1}{{4a}{7}}
-\newlabel{sub@fig:sub1}{{a}{7}}
-\newlabel{fig:sub2}{{4b}{7}}
-\newlabel{sub@fig:sub2}{{b}{7}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces A figure with two subfigures\relax }}{7}}
-\newlabel{fig:test}{{4}{7}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces first test table\relax }}{7}}
-\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces my second test table, just numeric with no frills\relax }}{7}}
-\newlabel{table:second_test_table}{{6}{7}}
+\relax 
+\select@language{english}
+\@writefile{toc}{\select@language{english}}
+\@writefile{lof}{\select@language{english}}
+\@writefile{lot}{\select@language{english}}
+\citation{chandler1987introduction}
+\@writefile{toc}{\contentsline {section}{\numberline {1}Problem}{2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.1}Grand Canonical Ensemble}{2}}
+\newlabel{math:grand_potential}{{3}{2}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {1.1.1}Grand Potential}{2}}
+\citation{chandler1987introduction}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.2}The Lattice-gas Model}{3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {1.3}Assumptions}{3}}
+\citation{wiki:hcp}
+\newlabel{math:ebner_v}{{8}{4}}
+\newlabel{math:ebner_v_e}{{9}{4}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Formalism}{4}}
+\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces  Distances from a reference lattice site $i_{ref}$ at layer $n$ and the sites at layer $n'$. \relax }}{5}}
+\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
+\newlabel{fig:hcp_layers}{{1}{5}}
+\citation{DeOliveira1978687}
+\newlabel{math:omega}{{18}{6}}
+\newlabel{math:domega}{{20}{6}}
+\newlabel{math:yn}{{21}{6}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}Algorithm}{7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}HCP class}{7}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Thread Pool}{7}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Thread pool structure.\relax }}{8}}
+\newlabel{fig:threadpool}{{2}{8}}
+\@writefile{toc}{\contentsline {section}{\numberline {4}Introduction}{9}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}First Subsection}{9}}
+\@writefile{toc}{\contentsline {subsubsection}{\numberline {4.1.1}First Sub-subsection}{9}}
+\@writefile{toc}{\contentsline {paragraph}{First Paragraph}{9}}
+\newlabel{eq_first_sum}{{26}{9}}
+\newlabel{eq_1}{{27}{9}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Playing with figures}{10}}
+\newlabel{fig:sub1}{{3a}{10}}
+\newlabel{sub@fig:sub1}{{a}{10}}
+\newlabel{fig:sub2}{{3b}{10}}
+\newlabel{sub@fig:sub2}{{b}{10}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces A figure with two subfigures\relax }}{10}}
+\newlabel{fig:test}{{3}{10}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.3}Playing with tables}{10}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces first test table\relax }}{10}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces my second test table, just numeric with no frills\relax }}{10}}
+\newlabel{table:second_test_table}{{5}{10}}
+\citation{DeOliveira1978687}
+\citation{*}
+\bibstyle{plain}
+\bibdata{sm_final_report}
+\bibcite{chandler1987introduction}{1}
+\bibcite{PhysRevA.22.2776}{2}
+\bibcite{DeOliveira1978687}{3}
+\bibcite{wiki:hcp}{4}
+\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces  my second test table, just numeric with no frills\relax }}{11}}
+\newlabel{table:fifth_test_table}{{1}{11}}

docs/sm_final_report/sm_final_report.pdf

Binary file modified.

docs/sm_final_report/sm_final_report.tex

 \usepackage{subcaption}
 \usepackage[english]{babel}
 \usepackage[utf8]{inputenc}
-
+\usepackage{courier}
+\usepackage{color}
+	\definecolor{codegray}{rgb}{0.4,0.4,0.4}
+\usepackage{listings}
+	\lstset{language=C++,                    
+			basicstyle=\ttfamily\footnotesize,
+			commentstyle=\color{codegray},
+  			keywordstyle=\color{blue},
+  			stringstyle=\color{red},
+			keepspaces=true,
+  			tabsize=4,
+		   }
 
 \title{Gas adsorption on a weakly attractive substrate}
 \author{Davide Bacchet}
 \begin{equation}
   \mathcal{Z} = \sum_N \sum_{\sigma_j} e^{-\beta (E_{\sigma_j}^{(N)}-\mu N)}
 \end{equation}
-
+
+and the corresponding grand potential is:
 \begin{equation}
     \label{math:grand_potential}
   \Omega = - \ln(\mathcal{Z}) / \beta
 \end{equation}
 where $f(ni,n'i') = v(r_{ni,n'i'})/\epsilon$.
 
-\begin{figure}[hbt]
+\begin{figure}[tb]
   \centering
   \includegraphics[width=0.6\textwidth]{images/hcp_layers.png}
   \caption{\label{fig:hcp_layers} Distances from a reference lattice site $i_{ref}$ at layer $n$ and the sites at layer $n'$. }
 \begin{equation}
   \frac{d\Omega}{d\rho_n} = 0
 \end{equation}
-that, forgetting the scaling $N/\beta$ in (\ref{math:omega}), gives:
+that, neglecting the scaling $N/\beta$ in (\ref{math:omega}), gives:
 \begin{equation}
     \label{math:domega}
   \ln{\left(\frac{1-\rho_n}{\rho_n}\right)} + \beta \epsilon \sum_{n'}{f(n-n') \rho_{n'}} - \beta (V_n-\mu) = 0     \quad   \forall n
 
 \subsection{Thread Pool}
 thread pool implementation
+
+
+
+\begin{lstlisting}
+// HCP lattice, with a set of N layers (A-B-A-B-...);
+// each layer is a square with side L=2Ni+1
+class HCP
+{
+public:
+    HCP(int N, int Ni, const Point &offset=Point(0.0,0.0,0.0));
+    virtual ~HCP();
+    // retrieve points
+    Point&       point(unsigned int layer, unsigned int index);
+	// lattice data
+    unsigned int num_layers(void);
+    unsigned int num_layer_points(void);
+    unsigned int side_len(void);
+    Point        offset(void);
+
+	(...)
+};
+\end{lstlisting}
+
+the potentials are implemented by a pure interface class
+ 
+\begin{lstlisting}
+// Pure interface class for the potentials used in the lattice gas models
+class Potentials
+{
+protected:
+    Potentials() {}
+    virtual ~Potentials() {}
+public:
+    // interparticle potential
+    virtual double f_pot(int n, int n1) = 0;
+    // substrate potential
+    virtual double f_sub(int n) = 0;
+};
+
+// specific implementations
+class DeOliveiraPotentials: public Potentials  {...}
+class EbnerPotentials:      public Potentials  {...}
+\end{lstlisting}
+
+and the main class
+
+\begin{lstlisting}
+// Ebner (generic) approach for solving film formations on a substrate.
+class Ebner
+{
+public:
+    // create an instance using de oliveira potentials
+    Ebner(int N, double C=4.20, double D=7.85);
+    // create an instance using Lennard-Jones potentials
+    Ebner(int N, double sigma, ... , bool long_dist=true);
+    virtual ~Ebner();
+	// set the T* value
+    void set_Tstar(double val);
+    // find m0 by iteration
+    double find_m0(double gamma, unsigned int max_itx=100);
+    // calc state energy
+    double calc_energy(double gamma, double beta, std::vector<double> ro);
+    // calc the coverage. Also return the corresponding energy
+    double calc_theta(double gamma, int samples, int max_itx, double *final_energy=NULL);
+	(...)
+};
+\end{lstlisting}
+
+all functions have been made reentrant, to allow a safe concurrent execution by many threads.
+
+The multithread approach is based on a thread pool
 \begin{figure}[hbt]
   \centering
   \includegraphics[width=0.6\textwidth]{images/thread_pool.png}
-  \caption{And again a floating figure, but with imposed width}
+  \caption{\label{fig:threadpool}Thread pool structure.}
 \end{figure}
 
+the thread pool is filled with jobs to be executed; these jobs are placed in a shared queue, and a set of worker threads continuously execute jobs, until the queue is empty.
+This approach allows the performances to scale (almost) linearly with the number of CPU cores.
 
+Each job consists on a function and its supporting data, that have been implemented as in the following fragment.
 
+\begin{lstlisting}
+// support struct for the thread job
+struct SampleData
+{
+    Ebner      *ebner;         ///< simulation class
+    double      gamma;         ///< mu/epsilon
+    double      final_energy;  ///< [out] final energy
+    double      final_theta;   ///< [out] final layer coverage
+};
 
+/// find the layer coverage using the ebner model
+void ebner_find_theta(void *data)
+{
+    SampleData *sd = (SampleData*)data;
+    // calc
+    double energy = 0.0;
+    double theta = sd->ebner->calc_theta(sd->gamma,300,250,&energy);
+    // set data
+    sd->final_theta = theta;
+    sd->final_energy = energy;
+}
+\end{lstlisting}
+
+The function \texttt{ebner\_find\_theta()}, being composed only by reentrant functions and working on local data, is thread-safe.
 
 
 

docs/sm_final_report/sm_final_report.toc

-\select@language {english}
-\contentsline {section}{\numberline {1}Problem}{1}
-\contentsline {subsection}{\numberline {1.1}Grancanonical Ensemble}{2}
-\contentsline {subsubsection}{\numberline {1.1.1}Grand Potential}{2}
-\contentsline {paragraph}{Definition}{2}
-\contentsline {subsection}{\numberline {1.2}The Lattice-gas Model}{3}
-\contentsline {subsection}{\numberline {1.3}Assumptions}{3}
-\contentsline {section}{\numberline {2}Formalism}{4}
-\contentsline {section}{\numberline {3}Introduction}{4}
-\contentsline {subsection}{\numberline {3.1}First Subsection}{4}
-\contentsline {subsubsection}{\numberline {3.1.1}First Sub-subsection}{4}
-\contentsline {paragraph}{First Paragraph}{5}
-\contentsline {subsection}{\numberline {3.2}Playing with figures}{5}
-\contentsline {subsection}{\numberline {3.3}Playing with tables}{5}
+\select@language {english}
+\contentsline {section}{\numberline {1}Problem}{2}
+\contentsline {subsection}{\numberline {1.1}Grand Canonical Ensemble}{2}
+\contentsline {subsubsection}{\numberline {1.1.1}Grand Potential}{2}
+\contentsline {subsection}{\numberline {1.2}The Lattice-gas Model}{3}
+\contentsline {subsection}{\numberline {1.3}Assumptions}{3}
+\contentsline {section}{\numberline {2}Formalism}{4}
+\contentsline {section}{\numberline {3}Algorithm}{7}
+\contentsline {subsection}{\numberline {3.1}HCP class}{7}
+\contentsline {subsection}{\numberline {3.2}Thread Pool}{7}
+\contentsline {section}{\numberline {4}Introduction}{9}
+\contentsline {subsection}{\numberline {4.1}First Subsection}{9}
+\contentsline {subsubsection}{\numberline {4.1.1}First Sub-subsection}{9}
+\contentsline {paragraph}{First Paragraph}{9}
+\contentsline {subsection}{\numberline {4.2}Playing with figures}{10}
+\contentsline {subsection}{\numberline {4.3}Playing with tables}{10}

src/lg_adsorption/de_oliveira.py

-# test functions for lattice-gas model adsorption using De Oliveira approach
-import os, sys
-from math import tanh, log, exp
-
-import random
-random.seed(20110912)
-
-a = 6
-b = 3
-C = 4.20
-D = 7.85
-
-def fv(j):
-	if j==1:
-		return D
-	return C/(j*j*j)
-
-
-def test1():
-	"""repeated iteration for solving the m_inf equation"""
-	T = 0.6
-	x = 1.5	# ro/ro0
-	def free_energy(r):
-		e = 0.0
-		return e
-	def fun(m):
-		mo = tanh(0.5*log(x)+m/T)
-		return mo
-	m = -1.0
-	for k in range(-10,10):
-		m = float(k)/10.0
-		# print(m)
-		for i in range(0,100):
-			m = fun(m)
-			# print(m)
-		print(float(k)/10.0, m)
-		# print('------')
-
-
-def find_m_inf(T, gamma, itx=100):
-	"""repeated iteration for solving the m_inf equation, starting from T and gamma"""
-	# a = 6
-	# b = 3
-	# C = 4.20
-	# D = 7.85
-	# T = 0.45
-	# gamma = -1.0 
-	def fun(m):
-		mo = tanh(2*gamma/T/(a+2*b) +m/T)
-		return mo
-	sol = []
-	for k in range(-1,2):
-		m = float(k)
-		# print(m)
-		for i in range(0,itx):
-			m = fun(m)
-			# print(m)
-		# print(float(k), m)
-		sol.append(m)
-	return min(sol)
-
-
-def test2():
-	for ii in range(0,10):
-		T = 1+ii*0.1
-		mm = find_m_inf(T,-0.5)
-		print(mm)
-
-	
-def calc_free_energy(beta, ro, N, mu):
-	etot = 0.0
-	# layer 1 does not have other particles below (using b/2 in c2 calc) !!
-	c1 = (ro[1]*log(ro[1]) + (1-ro[1])*log(1-ro[1]))/beta
-	c2 = 0.5*a*ro[1]*ro[1] + 0.5*b*ro[1]*ro[2]
-	c3 = (mu+fv(1))*ro[1]
-	etot = etot + c1-c2-c3
-	# sys.stdout.write('(%6.3f %6.3f %6.3f) --> %f\n' % (c1,c2,c3,etot))
-	# other layers
-	for j in range(2,N+1):
-		# print j, ro[j]
-		c1 = (ro[j]*log(ro[j]) + (1-ro[j])*log(1-ro[j]))/beta
-		# c2 = 0.5*a*ro[j]*ro[j] + b*ro[j]*ro[j+1]	# de oliveira formulation (POSSIBLY WRONG!!!)
-		c2 = 0.5*a*ro[j]*ro[j] + 0.5*b*ro[j]*ro[j+1] + 0.5*b*ro[j]*ro[j-1]
-		c3 = (mu+fv(j))*ro[j]
-		etot = etot + c1-c2-c3
-		# sys.stdout.write('(%6.3f %6.3f %6.3f) --> %f\n' % (c1,c2,c3,etot))
-	return etot
-
-
-def test3():
-	T = 0.45 #0.60
-	gamma = -0.04
-	beta = 4/(T*(a+2*b))
-	mu = gamma-0.5*a-b
-	# mu = 0
-	N = 30
-
-	ro = [0.01 for i in range(0,N+2)]
-	E = calc_free_energy(beta, ro, N, mu)
-	print E
-	for i in range(1,N):
-		ro[i] = 0.99
-		E = calc_free_energy(beta, ro, N, mu)
-		print E
-
-
-def test3b():
-	T = 0.45 #0.60
-	gamma = -0.1
-	beta = 4/(T*(a+2*b))
-	mu = gamma-0.5*a-b
-	# mu = 0
-	N = 20
-
-	ro = [0.0001, 0.999999, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.98, 0.82, 0.10, 0.01]
-	E = calc_free_energy(beta, ro, N, mu)
-	print E
-
-
-def _vec_to_string(v):
-		out = '['
-		for i in range(0,len(v)):
-			out = out + ' ' + '%4.2f' %(v[i])
-		out = out + ']'
-		return out
-
-def calc_theta(T, gamma):
-	m_inf = find_m_inf(T,gamma)
-	# print('m_inf = %f' %(m_inf))
-	ro_inf = (m_inf+1)/2.0
-	# array of m_j
-	N = 20
-	m = [-1.0 for i in range (0,N+2)]
-	m[N+1] = m_inf
-	E_min = 1e8
-	theta_min = 1e8
-	for tt in range(0,300):
-		for i in range(1,N+1):
-			m[i] = random.random()*2-1.0
-			# m[i] = -0.5 - 0.5*random.random()
-		def calc_mj(m):
-			mo = m[:]
-			# print mo
-			for j in range(1,len(m)-1):
-			# for j in range(3,4):
-				mo[j] = tanh(2/(T*(a+2*b))*(gamma+fv(j) + 0.5*(a*m[j]+b*m[j-1]+b*m[j+1])))
-			return mo
-
-		for k in range(0,250):
-			m = calc_mj(m)
-			# print _vec_to_string(m)
-		# print m
-
-		def calc_ro(m):
-			ro = m[:]
-			for i in range(0,len(ro)):
-				ro[i] = (m[i]+1.0)/2.0
-			return ro
-		ro = calc_ro(m)
-		# print _vec_to_string(ro)		
-		# calc theta
-		ro_inf = ro[N+1]
-		theta = 0.0
-		for j in range(1,N+1):
-			theta = theta + (ro[j]-ro_inf)
-		# print theta
-		# calc associated free energy
-		E = calc_free_energy(4/(T*(a+2*b)), ro, N, gamma-0.5*a-b)
-		# print E, theta
-		# return
-		if E<E_min:
-			E_min = E
-			theta_min = theta
-	# print('min theta: ', theta_min)
-	return theta_min, E_min
-
-
-def test4():
-	# theta, energy = calc_theta(0.60,-0.3)
-	# print theta
-	T = 0.45 #0.60
-	gamma = -0.04
-	gamma = -0.1
-	gamma = -0.5083913005530134
-	theta, energy = calc_theta(T,gamma)
-	print(gamma,theta)
-
-
-
-def calc_isotherm_layers():
-	# theta, energy = calc_theta(0.60,-0.3)
-	# print theta
-	T = 0.45
-	T = 0.60
-	gamma = -0.3
-	beta = 4/(T*(a+2*b))
-	
-	St = 1000
-	outfile = open("de_oliveira_out_T"+str(T)+".txt","w")
-	for i in range(0,St+1):
-		x = 0.01 + (0.99-0.01)*float(i)/St
-		gamma = log(x)/beta
-		# x = exp(beta*gamma)
-		theta, energy = calc_theta(T,gamma)
-		print(x,gamma,theta, energy)
-		outfile.write("%f %f %f %f\n" %(x,gamma,theta,energy))
-	outfile.close()
-
-
-if __name__ == '__main__':
-	# test1()
-	# test2()
-	# test3()
-	# test3b()
-	# test4()
-	calc_isotherm_layers()

src/lg_adsorption/de_oliveira_energy_comparison_045.png

Removed
Old image

src/lg_adsorption/de_oliveira_out_045_1000_orig.txt

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-0.010980 0.051572
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-0.012940 0.063237
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-0.016860 0.090266
-0.017840 0.098034
-0.018820 0.106326
-0.019800 0.115231
-0.020780 0.124862
-0.021760 0.135372
-0.022740 0.146970
-0.023720 0.159958
-0.024700 0.174801
-0.025680 0.192278
-0.026660 0.213880
-0.027640 0.773565
-0.028620 0.798085
-0.029600 0.816083
-0.030580 0.830334
-0.031560 0.842108
-0.032540 0.852109
-0.033520 0.860771
-0.034500 0.868387
-0.035480 0.875161
-0.036460 0.881244
-0.037440 0.886748
-0.038420 0.891764
-0.039400 0.896360
-0.040380 0.900592
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-0.043320 0.911531
-0.044300 0.914699
-0.045280 0.917669
-0.046260 0.920462
-0.047240 0.923094
-0.048220 0.925581
-0.049200 0.927934
-0.050180 0.930167
-0.051160 0.932288
-0.052140 0.934308
-0.053120 0.936233
-0.054100 0.938071
-0.055080 0.939829
-0.056060 0.941512
-0.057040 0.943126
-0.058020 0.944675
-0.059000 0.946164
-0.059980 0.947597
-0.060960 0.948976
-0.061940 0.950306
-0.062920 0.951590
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