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Diffstat (limited to 'src/boost/libs/numeric/odeint/examples/molecular_dynamics.cpp')
-rw-r--r-- | src/boost/libs/numeric/odeint/examples/molecular_dynamics.cpp | 160 |
1 files changed, 160 insertions, 0 deletions
diff --git a/src/boost/libs/numeric/odeint/examples/molecular_dynamics.cpp b/src/boost/libs/numeric/odeint/examples/molecular_dynamics.cpp new file mode 100644 index 00000000..e1a82e03 --- /dev/null +++ b/src/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; +} |