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             : {
      44             : protected:
      45             : /// Set position of the virtual atom
      46             :   void setPosition(const Vector &);
      47             : /// Set its mass
      48             :   void setMass(double);
      49             : /// Set its charge
      50             :   void setCharge(double);
      51             : /// Request the atoms on which the calculation demands
      52             :   void requestAtoms(const std::vector<AtomNumber> & a);
      53             : /// Set the derivatives of virtual atom coordinate wrt atoms on which it dependes
      54             :   void setAtomsDerivatives(const std::vector<Tensor> &d);
      55             : /// Set the box derivatives.
      56             : /// This should be a vector of size 3. First index corresponds
      57             : /// to the components of the virtual atom.
      58             : /// Notice that this routine subtract the trivial term coming from cell deformation
      59             : /// since this term is already implicitly included. Indeed, if the vatom
      60             : /// position is a linear function of atomic coordinates it is not necessary
      61             : /// to call this function (implicit term is fine) (e.g. vatom::COM and vatom::Center).
      62             : /// On the other hand if the vatom position is a non-linear function of atomic coordinates this
      63             : /// should be called (see vatom::Ghost).
      64             :   void setBoxDerivatives(const std::vector<Tensor> &d);
      65             : /// Set box derivatives automatically.
      66             : /// It should be called after the settomsDerivatives has been used for all
      67             : /// single atoms.
      68             : /// \warning It only works for virtual atoms NOT using PBCs!
      69             : ///          This implies that all atoms used + the new virtual atom should be
      70             : ///          in the same periodic image.
      71             :   void setBoxDerivativesNoPbc();
      72             : public:
      73             : /// Return the atom id of the corresponding virtual atom
      74             :   AtomNumber getIndex()const;
      75             :   explicit ActionWithVirtualAtom(const ActionOptions&ao);
      76             :   static void registerKeywords(Keywords& keys);
      77             :   virtual unsigned getNumberOfDerivatives();
      78             :   virtual void apply();
      79     6746861 :   ActionWithVirtualAtom* castToActionWithVirtualAtom() noexcept final { return this; }
      80             : };
      81             : 
      82             : inline
      83      645611 : unsigned ActionWithVirtualAtom::getNumberOfDerivatives() {
      84      645611 :   return 3*getNumberOfAtoms()+9;
      85             : }
      86             : 
      87             : inline
      88       35094 : void ActionWithVirtualAtom::setPosition(const Vector & pos) {
      89      140376 :   for(unsigned i=0; i<3; ++i) getPntrToComponent(i)->set(pos[i]);
      90       35094 : }
      91             : 
      92             : inline
      93       27098 : void ActionWithVirtualAtom::setMass(double m) {
      94       27098 :   getPntrToComponent(3)->set(m);
      95       27098 : }
      96             : 
      97             : inline
      98       27098 : void ActionWithVirtualAtom::setCharge(double c) {
      99       27098 :   getPntrToComponent(4)->set(c);
     100       27098 : }
     101             : 
     102             : inline
     103       35094 : void ActionWithVirtualAtom::setAtomsDerivatives(const std::vector<Tensor> &d) {
     104             :   unsigned jj=0;
     105       35094 :   Value* xval=getPntrToComponent(0);
     106       35094 :   Value* yval=getPntrToComponent(1);
     107       35094 :   Value* zval=getPntrToComponent(2);
     108      419563 :   for(unsigned j=0; j<getNumberOfAtoms(); ++j) {
     109     1537876 :     for(unsigned k=0; k<3; ++k) {
     110     1153407 :       xval->setDerivative( jj, d[j][k][0] );
     111     1153407 :       yval->setDerivative( jj, d[j][k][1] );
     112     1153407 :       zval->setDerivative( jj, d[j][k][2] );
     113             :       jj++;
     114             :     }
     115             :   }
     116       35094 : }
     117             : 
     118             : }
     119             : 
     120             : #endif