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_tools_Pbc_h
      23             : #define __PLUMED_tools_Pbc_h
      24             : 
      25             : #include "Vector.h"
      26             : #include "Tensor.h"
      27             : #include "View.h"
      28             : #include "View2D.h"
      29             : #include <vector>
      30             : #include <cstddef>
      31             : #include <limits>
      32             : 
      33             : namespace PLMD {
      34             : 
      35             : template <std::size_t N=3>
      36             : using MemoryView=View<double,N>;
      37             : 
      38             : template < std::size_t N=helpers::dynamic_extent, std::size_t STRIDE=3>
      39             : using mdMemoryView = View2D<double,N,STRIDE>;
      40             : 
      41             : using VectorView = mdMemoryView<helpers::dynamic_extent, 3>;
      42             : 
      43             : /*
      44             : Tool to deal with periodic boundary conditions.
      45             : 
      46             : This class is useful to apply periodic boundary conditions on interatomic
      47             : distances. It stores privately information about reduced lattice vectors
      48             : */
      49             : class Pbc {
      50             : /// Type of box
      51             :   enum {unset,orthorombic,generic} type;
      52             : /// Maximum number of shifts to be tried for a given octant.
      53             : /// This is an exact bound: buildShifts only keeps shifts whose nonzero
      54             : /// components have the sign opposite to the octant, and with one or two
      55             : /// nonzero components (out of three) there are 3+3=6 such shifts.
      56             :   static constexpr unsigned maxshiftsize=6;
      57             : /// Box
      58             :   Tensor box;
      59             : /// Inverse box
      60             :   Tensor invBox;
      61             : /// Reduced box.
      62             : /// This is a set of lattice vectors generating the same lattice
      63             : /// but "minimally skewed". Useful to optimize image search.
      64             :   Tensor reduced;
      65             : /// Inverse of the reduced box
      66             :   Tensor invReduced;
      67             : /// List of shifts that should be attempted.
      68             : /// Depending on the sign of the scaled coordinates representing
      69             : /// a distance vector, a different set of shifts must be tried.
      70             : /// Fixed-size arrays (rather than a container with a pointer to its data)
      71             : /// are used so that a bitwise copy of the object, as done by OpenACC,
      72             : /// is also valid on the device.
      73             :   Vector shifts[2][2][2][maxshiftsize];
      74             : /// Number of valid entries in each list of shifts
      75             :   unsigned nShiftsPerOctant[2][2][2];
      76             : /// Alternative representation for orthorhombic cells.
      77             : /// Not really used, but could be used to optimize search in
      78             : /// orthorhombic cells.
      79             :   Vector diag,hdiag,mdiag;
      80             : /// Build list of shifts.
      81             : /// This is expensive, and must be called only when box is
      82             : /// reset. It allows building a minimal set of shifts
      83             : /// depending on the sign of the scaled coordinates representing
      84             : /// a distance vector.
      85             :   void buildShifts();
      86             : public:
      87             : ///Helper function for moving the class to an openacc device
      88             :   void toACCDevice()const ;
      89             : ///Helper function for cleaning the memory of the class from an openacc device
      90             :   void removeFromACCDevice() const;
      91             : /// Constructor
      92             :   Pbc();
      93             : /// Compute modulo of (v2-v1), using or not pbc depending on bool pbc.
      94             :   double distance( const bool pbc, const Vector& v1, const Vector& v2 ) const;
      95             : /// Computes v2-v1, using minimal image convention
      96             : /// if specified, also returns the number of attempted shifts
      97             : #pragma acc routine seq
      98             :   Vector distance(const Vector&, const Vector&)const;
      99             : #pragma acc routine seq
     100             :   Vector3f distance(const Vector3f&, const Vector3f&)const;
     101             : /// Computes v2-v1, using minimal image convention
     102             : /// if specified, also returns the number of attempted shifts
     103             :   Vector distance(const Vector&, const Vector&,int*nshifts)const;
     104             : /// Apply PBC to a set of positions or distance vectors
     105             : #pragma acc routine seq
     106             :   void apply(VectorView dlist, unsigned max_index=0) const;
     107             : #pragma acc routine seq
     108             :   void apply(std::vector<Vector>&dlist, unsigned max_index=0) const;
     109             : /// Set the lattice vectors.
     110             : /// b[i][j] is the j-th component of the i-th vector
     111             :   void setBox(const Tensor&b);
     112             : /// Returns the box
     113             : #pragma acc routine seq
     114             :   const Tensor& getBox()const;
     115             : /// Returns the inverse matrix of box.
     116             : /// Thus: pbc.getInvBox() == inverse(pbc.getBox()).
     117             : #pragma acc routine seq
     118             :   const Tensor& getInvBox()const;
     119             : /// Transform a vector in real space to a vector in scaled coordinates.
     120             : /// Thus:pbc.realToScaled(v) == matmul(transpose(inverse(pbc.getBox(),v)));
     121             : #pragma acc routine seq
     122             :   Vector realToScaled(const Vector&)const;
     123             : #pragma acc routine seq
     124             :   Vector3f realToScaled(const Vector3f&)const;
     125             : /// Transform a vector in scaled coordinates to a vector in real space.
     126             : /// Thus:pbc.scaledToRead(v) == matmul(transpose(pbc.getBox()),v);
     127             : #pragma acc routine seq
     128             :   Vector scaledToReal(const Vector&)const;
     129             : #pragma acc routine seq
     130             :   Vector3f scaledToReal(const Vector3f&)const;
     131             : /// Returns true if the box vectors are orthogonal
     132             : #pragma acc routine seq
     133             :   bool isOrthorombic()const;
     134             : /// Full search (for testing).
     135             : /// Perform a full search on vector
     136             :   void fullSearch(Vector&)const;
     137             : /// Returns true if box is set and non zero
     138             :   bool isSet()const;
     139             : };
     140             : 
     141             : inline
     142             : bool Pbc::isSet()const {
     143       37574 :   return type!=unset;
     144             : }
     145             : 
     146             : }
     147             : 
     148             : #endif