Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2025 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_colvar_ColvarInput_h
      23             : #define __PLUMED_colvar_ColvarInput_h
      24             : 
      25             : #include <vector>
      26             : 
      27             : #include "tools/Pbc.h"
      28             : #include "tools/View.h"
      29             : #include "tools/View2D.h"
      30             : #include "tools/Vector.h"
      31             : #include "tools/Tensor.h"
      32             : #include "tools/ColvarOutput.h"
      33             : 
      34             : namespace PLMD {
      35             : 
      36             : class Colvar;
      37             : 
      38             : namespace colvar {
      39             : 
      40             : template <typename T=double>
      41             : struct ColvarInput {
      42             :   unsigned mode;
      43             :   const Pbc& pbc;
      44             :   View2D<const T,helpers::dynamic_extent,3> pos;
      45             :   View<const T> mass;
      46             :   View<const T> charges;
      47     3009232 :   ColvarInput( unsigned m,
      48             :                unsigned natoms,
      49             :                const T* p,
      50             :                const T* w,
      51             :                const T* q,
      52             :                const Pbc& box ) :
      53     3009232 :     mode(m),
      54     2724769 :     pbc(box),
      55      284463 :     pos(p,natoms),
      56             :     mass(w,natoms),
      57             :     charges(q,natoms) {
      58             :   }
      59             :   static ColvarInput createColvarInput( unsigned m, const std::vector<Vector>& p, const Colvar* colv );
      60             :   static void setBoxDerivativesNoPbc( const ColvarInput<T>& inpt, ColvarOutput<T>& out );
      61             :   /// same as setBoxDerivativesNoPbc but with no extra memory allocations
      62             :   static void setBoxDerivativesNoPbc_inplace( const ColvarInput<T>& inpt, ColvarOutput<T>& out );
      63             : };
      64             : 
      65             : template <typename T>
      66      284463 : ColvarInput<T>  ColvarInput<T>::createColvarInput( unsigned m,
      67             :     const std::vector<Vector>& p,
      68             :     const Colvar* colv ) {
      69             :   //this won't work with floating point
      70             :   return ColvarInput( m,
      71             :                       p.size(),
      72             :                       &p[0][0],
      73             :                       colv->getMasses().data(),
      74      284463 :                       colv->getCharges(true).data(),
      75      284463 :                       colv->getPbc() );
      76             : }
      77             : 
      78             : template <typename T>
      79     2813221 : void  ColvarInput<T>::setBoxDerivativesNoPbc( const ColvarInput<T>& inpt, ColvarOutput<T>& out ) {
      80             :   //Both version passes the tests, we should discuss wicht onw might be better
      81             : 
      82     2813221 :   unsigned nat=inpt.pos.size();
      83     5873157 :   for(unsigned i=0; i<out.ncomponents; ++i) {
      84     3059936 :     Tensor v;
      85             :     v.zero();
      86     9469963 :     for(unsigned j=0; j<nat; j++) {
      87     6410027 :       v-=Tensor(Vector(inpt.pos[j][0],inpt.pos[j][1],inpt.pos[j][2]),
      88    12820054 :                 out.derivs.getAtomDerivatives(i,j));
      89             :     }
      90     3059936 :     out.virial.set( i, v );
      91             :   }
      92     2813221 : }
      93             : 
      94             : template <typename T>
      95             : void  ColvarInput<T>::setBoxDerivativesNoPbc_inplace( const ColvarInput<T>& inpt, ColvarOutput<T>& out ) {
      96             :   //now with no extra allocated memory:
      97             :   unsigned nat=inpt.pos.size();
      98             :   for(unsigned i=0; i<out.ncomponents; ++i) {
      99             :     auto v = out.virial.getView(i);
     100             :     LoopUnroller<9>::_zero(v.data());
     101             :     for(unsigned j=0; j<nat; j++) {
     102             :       const auto deriv =  out.derivs.getView(i,j);
     103             :       v[0] -= inpt.pos[j][0]*deriv[0];
     104             :       v[1] -= inpt.pos[j][0]*deriv[1];
     105             :       v[2] -= inpt.pos[j][0]*deriv[2];
     106             : 
     107             :       v[3] -= inpt.pos[j][1]*deriv[0];
     108             :       v[4] -= inpt.pos[j][1]*deriv[1];
     109             :       v[5] -= inpt.pos[j][1]*deriv[2];
     110             : 
     111             :       v[6] -= inpt.pos[j][2]*deriv[0];
     112             :       v[7] -= inpt.pos[j][2]*deriv[1];
     113             :       v[8] -= inpt.pos[j][2]*deriv[2];
     114             :     }
     115             :   }
     116             : }
     117             : } // namespace colvar
     118             : } //namespace PLMD
     119             : #endif // __PLUMED_colvar_ColvarInput_h