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             : #include <limits>
      31             : 
      32             : namespace PLMD {
      33             : 
      34             : //this more or less mocks c++20 span with fixed size
      35             : template < std::size_t N=3>
      36             : class MemoryView {
      37             :   double *ptr_;
      38             : public:
      39             :   MemoryView(double* p) :ptr_(p) {}
      40             :   constexpr size_t size()const {
      41             :     return N;
      42             :   }
      43             :   static constexpr size_t extent = N;
      44             :   double & operator[](size_t i) {
      45    77398443 :     return ptr_[i];
      46             :   }
      47             :   const double & operator[](size_t i) const {
      48             :     return ptr_[i];
      49             :   }
      50             : };
      51             : 
      52             : namespace helpers {
      53             : inline constexpr std::size_t dynamic_extent = std::numeric_limits<std::size_t>::max();
      54             : }
      55             : //this more or less mocks c++23 mdspan without the fancy multi-indexed operator[]
      56             : //the idea is to take an address that you know to be strided in a certain way and
      57             : //make it avaiable to any interface (like using the data from a nunmpy.ndarray in
      58             : //a function thought for a std::vector<PLMD::Vector> )
      59             : //the N=-1 is there for mocking the run time size from the span (where a
      60             : //dynamic extent is size_t(-))
      61             : template < std::size_t N=helpers::dynamic_extent, std::size_t STRIDE=3>
      62             : class mdMemoryView {
      63             :   double *ptr_;
      64             :   size_t size_;
      65             : public:
      66      405876 :   mdMemoryView(double* p, size_t s) :ptr_(p), size_(s) {}
      67             :   size_t size()const {
      68           0 :     return size_;
      69             :   }
      70             :   static constexpr size_t extent = N;
      71             :   static constexpr size_t stride = STRIDE;
      72             :   MemoryView<STRIDE> operator[](size_t i) {
      73    77419321 :     return MemoryView<STRIDE>(ptr_ + i * STRIDE);
      74             :   }
      75             : };
      76             : 
      77             : using VectorView = mdMemoryView<helpers::dynamic_extent, 3>;
      78             : 
      79             : /*
      80             : Tool to deal with periodic boundary conditions.
      81             : 
      82             : This class is useful to apply periodic boundary conditions on interatomic
      83             : distances. It stores privately information about reduced lattice vectors
      84             : */
      85        3006 : class Pbc {
      86             : /// Type of box
      87             :   enum {unset,orthorombic,generic} type;
      88             : /// This is the maximum expected size for general boxes.
      89             : /// I found this empirically by manually modifying regtest basic/rt-make-1
      90             : /// Since it uses randomly generated boxes it should be correct.
      91             : /// In any case, this is just used as a hint for small_vector,
      92             : /// which will then switch to heap allocations if more shifts are needed
      93             :   static constexpr unsigned maxshiftsize=6;
      94             : /// Box
      95             :   Tensor box;
      96             : /// Inverse box
      97             :   Tensor invBox;
      98             : /// Reduced box.
      99             : /// This is a set of lattice vectors generating the same lattice
     100             : /// but "minimally skewed". Useful to optimize image search.
     101             :   Tensor reduced;
     102             : /// Inverse of the reduced box
     103             :   Tensor invReduced;
     104             : /// List of shifts that should be attempted.
     105             : /// Depending on the sign of the scaled coordinates representing
     106             : /// a distance vector, a different set of shifts must be tried.
     107             :   gch::small_vector<Vector,maxshiftsize> shifts[2][2][2];
     108             : /// Alternative representation for orthorombic cells.
     109             : /// Not really used, but could be used to optimize search in
     110             : /// orthorombic cells.
     111             :   Vector diag,hdiag,mdiag;
     112             : /// Build list of shifts.
     113             : /// This is expensive, and must be called only when box is
     114             : /// reset. It allows building a minimal set of shifts
     115             : /// depending on the sign of the scaled coordinates representing
     116             : /// a distance vector.
     117             :   void buildShifts(gch::small_vector<Vector,maxshiftsize> shifts[2][2][2])const;
     118             : public:
     119             : /// Constructor
     120             :   Pbc();
     121             : /// Compute modulo of (v2-v1), using or not pbc depending on bool pbc.
     122             :   double distance( const bool pbc, const Vector& v1, const Vector& v2 ) const;
     123             : /// Computes v2-v1, using minimal image convention
     124             : /// if specified, also returns the number of attempted shifts
     125             :   Vector distance(const Vector&, const Vector&,int*nshifts=nullptr)const;
     126             : /// Apply PBC to a set of positions or distance vectors
     127             :   void apply(VectorView dlist, unsigned max_index=0) const;
     128             :   void apply(std::vector<Vector>&dlist, unsigned max_index=0) const;
     129             : /// Set the lattice vectors.
     130             : /// b[i][j] is the j-th component of the i-th vector
     131             :   void setBox(const Tensor&b);
     132             : /// Returns the box
     133             :   const Tensor& getBox()const;
     134             : /// Returns the inverse matrix of box.
     135             : /// Thus: pbc.getInvBox() == inverse(pbc.getBox()).
     136             :   const Tensor& getInvBox()const;
     137             : /// Transform a vector in real space to a vector in scaled coordinates.
     138             : /// Thus:pbc.realToScaled(v) == matmul(transpose(inverse(pbc.getBox(),v)));
     139             :   Vector realToScaled(const Vector&)const;
     140             : /// Transform a vector in scaled coordinates to a vector in real space.
     141             : /// Thus:pbc.scaledToRead(v) == matmul(transpose(pbc.getBox()),v);
     142             :   Vector scaledToReal(const Vector&)const;
     143             : /// Returns true if the box vectors are orthogonal
     144             :   bool isOrthorombic()const;
     145             : /// Full search (for testing).
     146             : /// Perform a full search on vector
     147             :   void fullSearch(Vector&)const;
     148             : /// Returns true if box is set and non zero
     149             :   bool isSet()const;
     150             : };
     151             : 
     152             : inline
     153             : bool Pbc::isSet()const {
     154       33420 :   return type!=unset;
     155             : }
     156             : 
     157             : }
     158             : 
     159             : #endif