Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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 "ActionWithValue.h"
      27             : #include "tools/AtomNumber.h"
      28             : #include "tools/Vector.h"
      29             : #include "tools/Tensor.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             :   public ActionWithValue {
      43             : protected:
      44             : /// Set position of the virtual atom
      45             :   void setPosition(const Vector &);
      46             : /// Set its mass
      47             :   void setMass(double);
      48             : /// Set its charge
      49             :   void setCharge(double);
      50             : /// Request the atoms on which the calculation demands
      51             :   void requestAtoms(const std::vector<AtomNumber> & a);
      52             : /// Set the derivatives of virtual atom coordinate wrt atoms on which it dependes
      53             :   void setAtomsDerivatives(const std::vector<Tensor> &d);
      54             : /// Set the box derivatives.
      55             : /// This should be a vector of size 3. First index corresponds
      56             : /// to the components of the virtual atom.
      57             : /// Notice that this routine subtract the trivial term coming from cell deformation
      58             : /// since this term is already implicitly included. Indeed, if the vatom
      59             : /// position is a linear function of atomic coordinates it is not necessary
      60             : /// to call this function (implicit term is fine) (e.g. vatom::COM and vatom::Center).
      61             : /// On the other hand if the vatom position is a non-linear function of atomic coordinates this
      62             : /// should be called (see vatom::Ghost).
      63             :   void setBoxDerivatives(const std::vector<Tensor> &d);
      64             : /// Set box derivatives automatically.
      65             : /// It should be called after the settomsDerivatives has been used for all
      66             : /// single atoms.
      67             : /// \warning It only works for virtual atoms NOT using PBCs!
      68             : ///          This implies that all atoms used + the new virtual atom should be
      69             : ///          in the same periodic image.
      70             :   void setBoxDerivativesNoPbc();
      71             : public:
      72             : /// Return the atom id of the corresponding virtual atom
      73             :   AtomNumber getIndex()const;
      74             :   explicit ActionWithVirtualAtom(const ActionOptions&ao);
      75             :   static void registerKeywords(Keywords& keys);
      76             :   virtual unsigned getNumberOfDerivatives();
      77             :   virtual void apply();
      78     6700301 :   ActionWithVirtualAtom* castToActionWithVirtualAtom() noexcept final {
      79     6700301 :     return this;
      80             :   }
      81             : };
      82             : 
      83             : inline
      84      645611 : unsigned ActionWithVirtualAtom::getNumberOfDerivatives() {
      85      645611 :   return 3*getNumberOfAtoms()+9;
      86             : }
      87             : 
      88             : inline
      89       35094 : void ActionWithVirtualAtom::setPosition(const Vector & pos) {
      90      140376 :   for(unsigned i=0; i<3; ++i) {
      91      105282 :     getPntrToComponent(i)->set(pos[i]);
      92             :   }
      93       35094 : }
      94             : 
      95             : inline
      96       26807 : void ActionWithVirtualAtom::setMass(double m) {
      97       26807 :   getPntrToComponent(3)->set(m);
      98       26807 : }
      99             : 
     100             : inline
     101       26807 : void ActionWithVirtualAtom::setCharge(double c) {
     102       26807 :   getPntrToComponent(4)->set(c);
     103       26807 : }
     104             : 
     105             : inline
     106       35094 : void ActionWithVirtualAtom::setAtomsDerivatives(const std::vector<Tensor> &d) {
     107             :   unsigned jj=0;
     108       35094 :   Value* xval=getPntrToComponent(0);
     109       35094 :   Value* yval=getPntrToComponent(1);
     110       35094 :   Value* zval=getPntrToComponent(2);
     111      419563 :   for(unsigned j=0; j<getNumberOfAtoms(); ++j) {
     112     1537876 :     for(unsigned k=0; k<3; ++k) {
     113     1153407 :       xval->setDerivative( jj, d[j][k][0] );
     114     1153407 :       yval->setDerivative( jj, d[j][k][1] );
     115     1153407 :       zval->setDerivative( jj, d[j][k][2] );
     116             :       jj++;
     117             :     }
     118             :   }
     119       35094 : }
     120             : 
     121             : }
     122             : 
     123             : #endif