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_ActionWithVirtualAtom_h
      23             : #define __PLUMED_core_ActionWithVirtualAtom_h
      24             : 
      25             : #include "ActionAtomistic.h"
      26             : #include "tools/AtomNumber.h"
      27             : #include "tools/Vector.h"
      28             : #include "tools/Tensor.h"
      29             : #include "Atoms.h"
      30             : 
      31             : namespace PLMD {
      32             : 
      33             : /**
      34             : \ingroup INHERIT
      35             : Inherit from here if you are calculating the position of a virtual atom (eg a center of mass)
      36             : */
      37             : 
      38             : /// Class to add a single virtual atom to the system.
      39             : /// (it might be extended to add multiple virtual atoms).
      40             : class ActionWithVirtualAtom:
      41             :   public ActionAtomistic
      42             : {
      43             :   AtomNumber index;
      44             :   std::vector<Tensor> derivatives;
      45             :   std::vector<Tensor> boxDerivatives;
      46             :   std::map<AtomNumber,Tensor> gradients;
      47             :   void apply() override;
      48             : protected:
      49             : /// Set position of the virtual atom
      50             :   void setPosition(const Vector &);
      51             : /// Set its mass
      52             :   void setMass(double);
      53             : /// Set its charge
      54             :   void setCharge(double);
      55             : /// Request atoms on which the calculation depends
      56             :   void requestAtoms(const std::vector<AtomNumber> & a);
      57             : /// Set the derivatives of virtual atom coordinate wrt atoms on which it dependes
      58             :   void setAtomsDerivatives(const std::vector<Tensor> &d);
      59             : /// Set the box derivatives.
      60             : /// This should be a vector of size 3. First index corresponds
      61             : /// to the components of the virtual atom.
      62             : /// Notice that this routine subtract the trivial term coming from cell deformation
      63             : /// since this term is already implicitly included. Indeed, if the vatom
      64             : /// position is a linear function of atomic coordinates it is not necessary
      65             : /// to call this function (implicit term is fine) (e.g. vatom::COM and vatom::Center).
      66             : /// On the other hand if the vatom position is a non-linear function of atomic coordinates this
      67             : /// should be called (see vatom::Ghost).
      68             :   void setBoxDerivatives(const std::vector<Tensor> &d);
      69             : /// Set box derivatives automatically.
      70             : /// It should be called after the settomsDerivatives has been used for all
      71             : /// single atoms.
      72             : /// \warning It only works for virtual atoms NOT using PBCs!
      73             : ///          This implies that all atoms used + the new virtual atom should be
      74             : ///          in the same periodic image.
      75             :   void setBoxDerivativesNoPbc();
      76             : public:
      77             :   void setGradients();
      78             :   const std::map<AtomNumber,Tensor> & getGradients()const;
      79             : /// Return the atom id of the corresponding virtual atom
      80             :   AtomNumber getIndex()const;
      81             :   explicit ActionWithVirtualAtom(const ActionOptions&ao);
      82             :   ~ActionWithVirtualAtom();
      83             :   static void registerKeywords(Keywords& keys);
      84             :   void setGradientsIfNeeded();
      85             : };
      86             : 
      87             : inline
      88             : AtomNumber ActionWithVirtualAtom::getIndex()const {
      89         235 :   return index;
      90             : }
      91             : 
      92             : inline
      93             : void ActionWithVirtualAtom::setPosition(const Vector & pos) {
      94       14478 :   atoms.positions[index.index()]=pos;
      95             : }
      96             : 
      97             : inline
      98             : void ActionWithVirtualAtom::setMass(double m) {
      99       14478 :   atoms.masses[index.index()]=m;
     100             : }
     101             : 
     102             : inline
     103             : void ActionWithVirtualAtom::setCharge(double c) {
     104       14470 :   atoms.charges[index.index()]=c;
     105             : }
     106             : 
     107             : inline
     108             : void ActionWithVirtualAtom::setAtomsDerivatives(const std::vector<Tensor> &d) {
     109        7239 :   derivatives=d;
     110             : }
     111             : 
     112             : inline
     113             : const std::map<AtomNumber,Tensor> & ActionWithVirtualAtom::getGradients()const {
     114             :   return gradients;
     115             : }
     116             : 
     117             : }
     118             : 
     119             : #endif