Merge commit '4ebe6417a5fce5f0994fc0c31bebf732be96a07c' as 'boost'

boost/libs/numeric/odeint/examples/molecular_dynamics.cpp

@@ -0,0 +1,160 @@
+/*
+ [auto_generated]
+ libs/numeric/odeint/examples/molecular_dynamics.cpp
+
+ [begin_description]
+ Molecular dynamics example.
+ [end_description]
+
+ Copyright 2009-2012 Karsten Ahnert
+ Copyright 2009-2012 Mario Mulansky
+
+ Distributed under the Boost Software License, Version 1.0.
+ (See accompanying file LICENSE_1_0.txt or
+ copy at http://www.boost.org/LICENSE_1_0.txt)
+ */
+
+#include <boost/numeric/odeint.hpp>
+
+#include <vector>
+#include <iostream>
+#include <random>
+
+using namespace boost::numeric::odeint;
+
+
+
+using namespace std;
+#define tab "\t"
+
+const size_t n1 = 16;
+const size_t n2 = 16;
+
+struct md_system
+{
+    static const size_t n = n1 * n2;
+    typedef std::vector< double > vector_type;
+
+    md_system( double a = 0.0 ,            // strength of harmonic oscillator
+               double gamma = 0.0   ,       // friction
+               double eps = 0.1 ,          // interaction strenght
+               double sigma = 1.0 ,            // interaction radius
+               double xmax = 150.0 , double ymax = 150.0 )
+    : m_a( a ) , m_gamma( gamma ) 
+    , m_eps( eps ) , m_sigma( sigma ) 
+    , m_xmax( xmax ) , m_ymax( ymax )
+    { }
+    
+    static void init_vector_type( vector_type &x ) { x.resize( 2 * n ); }
+    
+    void operator()( vector_type const& x , vector_type const& v , vector_type &a , double t ) const
+    {
+        for( size_t i=0 ; i<n ; ++i )
+        {
+            double diffx = x[i] - 0.5 * m_xmax , diffy = x[i+n] - 0.5 * m_ymax;
+            double r2 = diffx * diffx + diffy * diffy ;
+            double r = std::sqrt( r2 );
+            a[     i ] = - m_a * r * diffx - m_gamma * v[     i ] ;
+            a[ n + i ] = - m_a * r * diffy - m_gamma * v[ n + i ] ;
+        }
+        
+        for( size_t i=0 ; i<n ; ++i )
+        {
+            double xi = x[i] , yi = x[n+i];
+            xi = periodic_bc( xi , m_xmax );
+            yi = periodic_bc( yi , m_ymax );
+            for( size_t j=0 ; j<i ; ++j )
+            {
+                double xj = x[j] , yj = x[n+j];
+                xj = periodic_bc( xj , m_xmax );
+                yj = periodic_bc( yj , m_ymax );
+                
+                double diffx = ( xj - xi ) , diffy = ( yj - yi );
+                double r = sqrt( diffx * diffx + diffy * diffy );
+                double f = lennard_jones( r );
+                a[     i ] += diffx / r * f;
+                a[ n + i ] += diffy / r * f;
+                a[     j ] -= diffx / r * f;
+                a[ n + j ] -= diffy / r * f;
+            }
+        }
+    }
+    
+    void bc( vector_type &x )
+    {
+        for( size_t i=0 ; i<n ; ++i )
+        {
+            x[ i     ] = periodic_bc( x[ i     ] , m_xmax );
+            x[ i + n ] = periodic_bc( x[ i + n ] , m_ymax );
+        }
+    }
+    
+    inline double lennard_jones( double r ) const
+    {
+        double c = m_sigma / r;
+        double c3 = c * c * c;
+        double c6 = c3 * c3;
+        return 4.0 * m_eps * ( -12.0 * c6 * c6 / r + 6.0 * c6 / r );
+    }
+    
+    static inline double periodic_bc( double x , double xmax )
+    {
+        return ( x < 0.0 ) ? x + xmax : ( x > xmax ) ? x - xmax : x ;
+    }
+    
+    double m_a;
+    double m_gamma;
+    double m_eps ;
+    double m_sigma ;
+    double m_xmax , m_ymax;
+};
+
+
+
+
+
+int main( int argc , char *argv[] )
+{
+    const size_t n = md_system::n;
+    typedef md_system::vector_type vector_type;
+    
+    
+    std::mt19937 rng;
+    std::normal_distribution<> dist( 0.0 , 1.0 );
+    
+    vector_type x , v;
+    md_system::init_vector_type( x );
+    md_system::init_vector_type( v );
+    
+    for( size_t i=0 ; i<n1 ; ++i )
+    {
+        for( size_t j=0 ; j<n2 ; ++j )
+        {
+            x[i*n2+j  ] = 5.0 + i * 4.0 ;
+            x[i*n2+j+n] = 5.0 + j * 4.0 ;
+            v[i]   = dist( rng ) ;
+            v[i+n] = dist( rng ) ;
+        }
+    }
+    
+    velocity_verlet< vector_type > stepper;
+    const double dt = 0.025;
+    double t = 0.0;
+    md_system sys;
+    for( size_t oi=0 ; oi<100000 ; ++oi )
+    {
+        for( size_t ii=0 ; ii<100 ; ++ii,t+=dt )
+            stepper.do_step( sys , std::make_pair( std::ref( x ) , std::ref( v ) ) , t , dt );
+        sys.bc( x );
+        
+        std::cout << "set size square" << "\n";
+        std::cout << "unset key" << "\n";
+        std::cout << "p [0:" << sys.m_xmax << "][0:" << sys.m_ymax << "] '-' pt 7 ps 0.5" << "\n";
+        for( size_t i=0 ; i<n ; ++i )
+            std::cout << x[i] << " " << x[i+n] << " " << v[i] << " " << v[i+n] << "\n";
+        std::cout << "e" << std::endl;
+    }
+    
+    
+    return 0;
+}