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Tue, Jun 18, 21:23

manifold.h
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
-----------------------------------------------------------------------
This file is a part of the USER-MANIFOLD package.
This package allows LAMMPS to perform MD simulations of particles
constrained on a manifold (i.e., a 2D subspace of the 3D simulation
box). It achieves this using the RATTLE constraint algorithm applied
to single-particle constraint functions g(xi,yi,zi) = 0 and their
derivative (i.e. the normal of the manifold) n = grad(g).
It is very easy to add your own manifolds to the current zoo
(we now have sphere, a dendritic spine approximation, a 2D plane (for
testing purposes) and a wave-y plane.
See the README file for more info.
Stefan Paquay, stefanpaquay@gmail.com
Applied Physics/Theory of Polymers and Soft Matter,
Eindhoven University of Technology (TU/e), The Netherlands
Thanks to Remy Kusters at TU/e for testing.
This software is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
#ifndef LMP_MANIFOLD_H
#define LMP_MANIFOLD_H
#include "pointers.h"
#include <math.h>
namespace LAMMPS_NS {
namespace user_manifold {
// Abstract base class.
class manifold : protected Pointers {
public:
manifold(class LAMMPS* lmp) : Pointers(lmp), params(NULL){ }
virtual ~manifold(){ delete[] params; }
virtual double g( const double * ) = 0;
virtual void n( const double *, double * ) = 0;
// Variant of g that computes n at the same time.
virtual double g_and_n( const double *x, double *nn )
{
this->n(x,nn);
return g(x);
}
virtual const char *id() = 0;
virtual void set_atom_id( tagint a_id ){}
virtual int nparams() = 0;
// double *get_params(){ return params; };
// Overload if any initialization depends on params:
virtual void post_param_init(){}
virtual void checkup(){} // Some diagnostics...
double *params;
};
// Some utility functions that are templated, so I implement them
// here in the header.
template< unsigned int size > inline
double infnorm( double *vect )
{
double largest = fabs( vect[0] );
for( unsigned int i = 1; i < size; ++i ){
double c = fabs( vect[i] );
largest = ( c > largest ) ? c : largest;
}
return largest;
}
inline double dot( double *a, double *b ){
return a[0]*b[0] + a[1]*b[1] + a[2]*b[2];
}
} // namespace LAMMPS_NS
}
#endif // LMP_MANIFOLD_H

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