Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2019 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #ifndef __PLUMED_core_MDAtoms_h
      23             : #define __PLUMED_core_MDAtoms_h
      24             : 
      25             : #include "tools/Tensor.h"
      26             : #include "tools/Vector.h"
      27             : #include "tools/AtomNumber.h"
      28             : #include <vector>
      29             : #include <set>
      30             : #include <memory>
      31             : 
      32             : namespace PLMD {
      33             : 
      34             : class Units;
      35             : 
      36             : /**
      37             : Class containing interface to MDAtomsTyped
      38             : 
      39             : This class is used to translate from reals of the type used in MD to
      40             : plumed (doubles), and also to rearrange atoms list according to specific
      41             : ordering indexes (to deal with domain decomposition codes) and layout
      42             : (to allow passing xx[] yy[] zz[] arrays from the MD code).
      43             : 
      44             : The class is abstract, but it is possible to allocate a new pointer with
      45             : create(n), where n is the actual size of MD-reals e.g.
      46             : \verbatim
      47             :   std::unique_ptr<MDAtomsBase> mdatoms=MDAtomsBase::create(sizeof(float));
      48             : \endverbatim
      49             : */
      50        3389 : class MDAtomsBase
      51             : {
      52             : public:
      53             : /// Creates an MDAtomsTyped<T> object such that sizeof(T)==n
      54             :   static std::unique_ptr<MDAtomsBase> create(unsigned n);
      55             : /// Virtual destructor, just to allow inheritance.
      56        3389 :   virtual ~MDAtomsBase() {}
      57             : /// Get the size of MD-real
      58             :   virtual unsigned getRealPrecision()const=0;
      59             : /// Set a pointer to the mass array in the MD code
      60             :   virtual void setm(void*m)=0;
      61             : /// Set a pointer to the charge array in the MD code
      62             :   virtual void setc(void*m)=0;
      63             : /// Set a pointer to the box array (3x3) in the MD code
      64             :   virtual void setBox(void*)=0;
      65             : /// Set a pointer to the positions array in the MD code
      66             :   virtual void setp(void*p)=0;
      67             : /// Set a pointer to the virial array (3x3) in the MD code
      68             :   virtual void setVirial(void*)=0;
      69             : /// Set a pointer to the forces array in the MD code
      70             :   virtual void setf(void*f)=0;
      71             : /// Set a pointer to the position array in the MD code
      72             :   virtual void setp(void*p,int i)=0;
      73             : /// Set a pointer to the force array in the MD code
      74             :   virtual void setf(void*f,int i)=0;
      75             : /// Set internal and MD units
      76             :   virtual void setUnits(const Units& units,const Units& MDUnits)=0;
      77             : /// Convert a pointer to an MD-real to a double
      78             :   virtual void MD2double(const void*,double&)const=0;
      79             : /// Convert a double to a pointer to an MD-real
      80             :   virtual void double2MD(const double&,void*)const=0;
      81             : 
      82             :   virtual Vector getMDforces(const unsigned index)const=0;
      83             : /// Retrieve box as a plumed Tensor
      84             :   virtual void getBox(Tensor &)const=0;
      85             : /// Retrieve selected positions.
      86             : /// The operation is done in such a way that p[index[i]] is equal to the coordinates of atom i
      87             :   virtual void getPositions(const std::vector<int>&index,std::vector<Vector>&p)const=0;
      88             : /// Retrieve all atom positions from index i to index j.
      89             :   virtual void getPositions(unsigned i,unsigned j,std::vector<Vector>&p)const=0;
      90             : /// Retrieve all atom positions from atom indices and local indices.
      91             :   virtual void getPositions(const std::set<AtomNumber>&index,const std::vector<unsigned>&i,std::vector<Vector>&p)const=0;
      92             : /// Retrieve selected masses.
      93             : /// The operation is done in such a way that m[index[i]] is equal to the mass of atom i
      94             :   virtual void getMasses(const std::vector<int>&index,std::vector<double>&m)const=0;
      95             : /// Retrieve selected charges.
      96             : /// The operation is done in such a way that c[index[i]] is equal to the charge of atom i
      97             :   virtual void getCharges(const std::vector<int>&index,std::vector<double>&c)const=0;
      98             : /// Retrieve local positions.
      99             :   virtual void getLocalPositions(std::vector<Vector>&p)const=0;
     100             : /// Increment the virial by an amount v
     101             :   virtual void updateVirial(const Tensor&v)const=0;
     102             : /// Increment the force on selected atoms.
     103             : /// The operation is done in such a way that f[index[i]] is added to the force on atom i
     104             :   virtual void updateForces(const std::vector<int>&index,const std::vector<Vector>&f)=0;
     105             : /// Increment the force on selected atoms.
     106             : /// The operation is done only for local atoms used in an action
     107             :   virtual void updateForces(const std::set<AtomNumber>&index,const std::vector<unsigned>&i,const std::vector<Vector>&forces)=0;
     108             : /// Rescale all the forces, including the virial.
     109             : /// It is applied to all atoms with local index going from 0 to index.size()-1
     110             :   virtual void rescaleForces(const std::vector<int>&index,double factor)=0;
     111             : 
     112             : /// Set a pointer to an extra CV.
     113             :   virtual void setExtraCV(const std::string &name,void*p)=0;
     114             : /// Set a pointer to an extra CV force.
     115             :   virtual void setExtraCVForce(const std::string &name,void*p)=0;
     116             : /// Retrieve the value of an extra CV.
     117             :   virtual double getExtraCV(const std::string &name)=0;
     118             : /// Update the value of an extra CV force.
     119             : /// \todo check if this should also be scaled when acting on total energy
     120             :   virtual void updateExtraCVForce(const std::string &name,double f)=0;
     121             : };
     122             : 
     123             : }
     124             : 
     125             : 
     126             : #endif