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 "small_vector/small_vector.h"
      28             : #include <vector>
      29             : #include <cstddef>
      30             : 
      31             : namespace PLMD {
      32             : 
      33             : //this more or less mocks c++20 span with fixed size
      34             : template < std::size_t N=3>
      35             : class MemoryView {
      36             :   double *ptr_;
      37             : public:
      38             :   MemoryView(double* p) :ptr_(p) {}
      39             :   constexpr size_t size()const {return N;}
      40             :   static constexpr size_t extent = N;
      41    77398443 :   double & operator[](size_t i) { return ptr_[i];}
      42             :   const double & operator[](size_t i) const { return ptr_[i];}
      43             : };
      44             : 
      45             : namespace helpers {
      46             : inline constexpr std::size_t dynamic_extent = -1;
      47             : }
      48             : //this more or less mocks c++23 mdspan without the fancy multi-indexed operator[]
      49             : //the idea is to take an address that you know to be strided in a certain way and
      50             : //make it avaiable to any interface (like using the data from a nunmpy.ndarray in
      51             : //a function thought for a std::vector<PLMD::Vector> )
      52             : //the N=-1 is there for mocking the run time size from the span (where a
      53             : //dynamic extent is size_t(-))
      54             : template < std::size_t N=helpers::dynamic_extent, std::size_t STRIDE=3>
      55             : class mdMemoryView {
      56             :   double *ptr_;
      57             :   size_t size_;
      58             : public:
      59      405876 :   mdMemoryView(double* p, size_t s) :ptr_(p), size_(s) {}
      60           0 :   size_t size()const {return size_;}
      61             :   static constexpr size_t extent = N;
      62             :   static constexpr size_t stride = STRIDE;
      63    77419321 :   MemoryView<STRIDE> operator[](size_t i) { return MemoryView<STRIDE>(ptr_ + i * STRIDE);}
      64             : };
      65             : 
      66             : using VectorView = mdMemoryView<helpers::dynamic_extent, 3>;
      67             : 
      68             : /*
      69             : Tool to deal with periodic boundary conditions.
      70             : 
      71             : This class is useful to apply periodic boundary conditions on interatomic
      72             : distances. It stores privately information about reduced lattice vectors
      73             : */
      74        3006 : class Pbc {
      75             : /// Type of box
      76             :   enum {unset,orthorombic,generic} type;
      77             : /// This is the maximum expected size for general boxes.
      78             : /// I found this empirically by manually modifying regtest basic/rt-make-1
      79             : /// Since it uses randomly generated boxes it should be correct.
      80             : /// In any case, this is just used as a hint for small_vector,
      81             : /// which will then switch to heap allocations if more shifts are needed
      82             :   static constexpr unsigned maxshiftsize=6;
      83             : /// Box
      84             :   Tensor box;
      85             : /// Inverse box
      86             :   Tensor invBox;
      87             : /// Reduced box.
      88             : /// This is a set of lattice vectors generating the same lattice
      89             : /// but "minimally skewed". Useful to optimize image search.
      90             :   Tensor reduced;
      91             : /// Inverse of the reduced box
      92             :   Tensor invReduced;
      93             : /// List of shifts that should be attempted.
      94             : /// Depending on the sign of the scaled coordinates representing
      95             : /// a distance vector, a different set of shifts must be tried.
      96             :   gch::small_vector<Vector,maxshiftsize> shifts[2][2][2];
      97             : /// Alternative representation for orthorombic cells.
      98             : /// Not really used, but could be used to optimize search in
      99             : /// orthorombic cells.
     100             :   Vector diag,hdiag,mdiag;
     101             : /// Build list of shifts.
     102             : /// This is expensive, and must be called only when box is
     103             : /// reset. It allows building a minimal set of shifts
     104             : /// depending on the sign of the scaled coordinates representing
     105             : /// a distance vector.
     106             :   void buildShifts(gch::small_vector<Vector,maxshiftsize> shifts[2][2][2])const;
     107             : public:
     108             : /// Constructor
     109             :   Pbc();
     110             : /// Compute modulo of (v2-v1), using or not pbc depending on bool pbc.
     111             :   double distance( const bool pbc, const Vector& v1, const Vector& v2 ) const;
     112             : /// Computes v2-v1, using minimal image convention
     113             : /// if specified, also returns the number of attempted shifts
     114             :   Vector distance(const Vector&, const Vector&,int*nshifts=nullptr)const;
     115             : /// Apply PBC to a set of positions or distance vectors
     116             :   void apply(VectorView dlist, unsigned max_index=0) const;
     117             :   void apply(std::vector<Vector>&dlist, unsigned max_index=0) const;
     118             : /// Set the lattice vectors.
     119             : /// b[i][j] is the j-th component of the i-th vector
     120             :   void setBox(const Tensor&b);
     121             : /// Returns the box
     122             :   const Tensor& getBox()const;
     123             : /// Returns the inverse matrix of box.
     124             : /// Thus: pbc.getInvBox() == inverse(pbc.getBox()).
     125             :   const Tensor& getInvBox()const;
     126             : /// Transform a vector in real space to a vector in scaled coordinates.
     127             : /// Thus:pbc.realToScaled(v) == matmul(transpose(inverse(pbc.getBox(),v)));
     128             :   Vector realToScaled(const Vector&)const;
     129             : /// Transform a vector in scaled coordinates to a vector in real space.
     130             : /// Thus:pbc.scaledToRead(v) == matmul(transpose(pbc.getBox()),v);
     131             :   Vector scaledToReal(const Vector&)const;
     132             : /// Returns true if the box vectors are orthogonal
     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       33420 :   return type!=unset;
     144             : }
     145             : 
     146             : }
     147             : 
     148             : #endif