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_Atoms_h
      23             : #define __PLUMED_core_Atoms_h
      24             : 
      25             : #include "tools/TypesafePtr.h"
      26             : #include "tools/Communicator.h"
      27             : #include "tools/Tensor.h"
      28             : #include "tools/Units.h"
      29             : #include "tools/Exception.h"
      30             : #include "tools/AtomNumber.h"
      31             : #include "tools/ForwardDecl.h"
      32             : #include <vector>
      33             : #include <set>
      34             : #include <map>
      35             : #include <string>
      36             : #include <memory>
      37             : 
      38             : namespace PLMD {
      39             : 
      40             : class MDAtomsBase;
      41             : class PlumedMain;
      42             : class ActionAtomistic;
      43             : class ActionWithVirtualAtom;
      44             : class Pbc;
      45             : 
      46             : /// Class containing atom related quantities from the MD code.
      47             : /// IT IS STILL UNDOCUMENTED. IT PROBABLY NEEDS A STRONG CLEANUP
      48             : class Atoms
      49             : {
      50             :   friend class ActionAtomistic;
      51             :   friend class ActionWithVirtualAtom;
      52             :   int natoms;
      53             :   std::set<AtomNumber> unique;
      54             :   std::vector<unsigned> uniq_index;
      55             : /// Map global indexes to local indexes
      56             : /// E.g. g2l[i] is the position of atom i in the array passed from the MD engine.
      57             : /// Called "global to local" since originally it was used to map global indexes to local
      58             : /// ones used in domain decomposition. However, it is now also used for the NAMD-like
      59             : /// interface, where only a small number of atoms is passed to plumed.
      60             :   std::vector<int> g2l;
      61             :   std::vector<Vector> positions;
      62             :   std::vector<Vector> forces;
      63             :   std::vector<double> masses;
      64             :   std::vector<double> charges;
      65             :   std::vector<ActionWithVirtualAtom*> virtualAtomsActions;
      66             :   Tensor box;
      67             :   ForwardDecl<Pbc> pbc_fwd;
      68             :   Pbc&   pbc=*pbc_fwd;
      69             :   Tensor virial;
      70             : // this is the energy set by each processor:
      71             :   double md_energy;
      72             : // this is the summed energy:
      73             :   double energy;
      74             : 
      75             :   bool   dataCanBeSet;
      76             :   bool   collectEnergy;
      77             :   bool   energyHasBeenSet;
      78             :   unsigned positionsHaveBeenSet;
      79             :   bool massesHaveBeenSet;
      80             :   bool chargesHaveBeenSet;
      81             :   bool boxHasBeenSet;
      82             :   unsigned forcesHaveBeenSet;
      83             :   bool virialHasBeenSet;
      84             :   bool massAndChargeOK;
      85             :   unsigned shuffledAtoms;
      86             : 
      87             :   std::map<std::string,std::vector<AtomNumber> > groups;
      88             : 
      89             :   void resizeVectors(unsigned);
      90             : 
      91             :   std::vector<int> fullList;
      92             : 
      93             :   std::unique_ptr<MDAtomsBase> mdatoms;
      94             : 
      95             :   PlumedMain & plumed;
      96             : 
      97             :   Units MDUnits;
      98             :   Units units;
      99             : 
     100             :   bool naturalUnits;
     101             :   bool MDnaturalUnits;
     102             : 
     103             :   double timestep;
     104             :   double forceOnEnergy;
     105             : 
     106             : /// if set to true, all the forces in the global array are zeroes
     107             : /// at every step. It should not be necessary in general, but it is
     108             : /// for actions accessing to modifyGlobalForce() (e.g. FIT_TO_TEMPLATE).
     109             :   bool zeroallforces;
     110             : 
     111             :   double kbT;
     112             : 
     113             :   std::vector<ActionAtomistic*> actions;
     114             :   std::vector<int>    gatindex;
     115             : 
     116             :   bool asyncSent;
     117             :   bool atomsNeeded;
     118             : 
     119             :   class DomainDecomposition:
     120             :     public Communicator
     121             :   {
     122             :   public:
     123             :     bool on;
     124             :     bool async;
     125             : 
     126             :     std::vector<Communicator::Request> mpi_request_positions;
     127             :     std::vector<Communicator::Request> mpi_request_index;
     128             : 
     129             :     std::vector<double> positionsToBeSent;
     130             :     std::vector<double> positionsToBeReceived;
     131             :     std::vector<int>    indexToBeSent;
     132             :     std::vector<int>    indexToBeReceived;
     133      161297 :     operator bool() const {return on;}
     134      404395 :     DomainDecomposition():
     135      404395 :       on(false), async(false)
     136      404395 :     {}
     137             :     void enable(Communicator& c);
     138             :   };
     139             : 
     140             :   DomainDecomposition dd;
     141             :   long int ddStep;  //last step in which dd happened
     142             : 
     143             :   void share(const std::set<AtomNumber>&);
     144             : 
     145             : public:
     146             : 
     147             :   explicit Atoms(PlumedMain&plumed);
     148             :   ~Atoms();
     149             : 
     150             :   void init();
     151             : 
     152             :   void share();
     153             :   void shareAll();
     154             :   void wait();
     155             :   void updateForces();
     156             : 
     157             :   void setRealPrecision(int);
     158             :   int  getRealPrecision()const;
     159             : 
     160             :   void setTimeStep(const TypesafePtr &);
     161             :   double getTimeStep()const;
     162             : 
     163             :   void setKbT(const TypesafePtr &);
     164             :   double getKbT()const;
     165             : 
     166             :   void setNatoms(int);
     167             :   int getNatoms()const;
     168             :   int getNVirtualAtoms()const;
     169             : 
     170             :   const long int& getDdStep()const;
     171             :   const std::vector<int>& getGatindex()const;
     172             :   const Pbc& getPbc()const;
     173             :   void getLocalMasses(std::vector<double>&);
     174             :   void getLocalPositions(std::vector<Vector>&);
     175             :   void getLocalForces(std::vector<Vector>&);
     176             :   void getLocalMDForces(std::vector<Vector>&);
     177             :   const Tensor& getVirial()const;
     178             : 
     179        3989 :   void setCollectEnergy(bool b) { collectEnergy=b; }
     180             : 
     181             :   void setDomainDecomposition(Communicator&);
     182             :   void setAtomsGatindex(const TypesafePtr &,bool);
     183             :   void setAtomsContiguous(int);
     184             :   void setAtomsNlocal(int);
     185             : 
     186             :   void startStep();
     187             :   void setEnergy(const TypesafePtr &);
     188             :   void setBox(const TypesafePtr &);
     189             :   void setVirial(const TypesafePtr &);
     190             :   void setPositions(const TypesafePtr &);
     191             :   void setPositions(const TypesafePtr &,int);
     192             :   void setForces(const TypesafePtr &);
     193             :   void setForces(const TypesafePtr &,int);
     194             :   void setMasses(const TypesafePtr &);
     195             :   void setCharges(const TypesafePtr &);
     196             :   bool chargesWereSet() const ;
     197             :   bool boxWasSet() const ;
     198             : 
     199             :   void MD2double(const TypesafePtr & m,double&d)const;
     200             :   void double2MD(const double&d,const TypesafePtr & m)const;
     201             : 
     202             :   void createFullList(const TypesafePtr &);
     203             :   void getFullList(const TypesafePtr &);
     204             :   void clearFullList();
     205             : 
     206             :   void add(ActionAtomistic*);
     207             :   void remove(ActionAtomistic*);
     208             : 
     209        3989 :   double getEnergy()const {plumed_assert(collectEnergy && energyHasBeenSet); return energy;}
     210             : 
     211          96 :   bool isEnergyNeeded()const {return collectEnergy;}
     212             : 
     213          45 :   void setMDEnergyUnits(double d) {MDUnits.setEnergy(d);}
     214         718 :   void setMDLengthUnits(double d) {MDUnits.setLength(d);}
     215           6 :   void setMDTimeUnits(double d) {MDUnits.setTime(d);}
     216         718 :   void setMDChargeUnits(double d) {MDUnits.setCharge(d);}
     217         718 :   void setMDMassUnits(double d) {MDUnits.setMass(d);}
     218             :   const Units& getMDUnits() {return MDUnits;}
     219          19 :   void setUnits(const Units&u) {units=u;}
     220             :   const Units& getUnits() {return units;}
     221             :   void updateUnits();
     222             : 
     223             :   AtomNumber addVirtualAtom(ActionWithVirtualAtom*);
     224             :   void removeVirtualAtom(ActionWithVirtualAtom*);
     225             :   ActionWithVirtualAtom* getVirtualAtomsAction(AtomNumber)const;
     226             :   bool isVirtualAtom(AtomNumber)const;
     227             :   void insertGroup(const std::string&name,const std::vector<AtomNumber>&a);
     228             :   void removeGroup(const std::string&name);
     229             :   void writeBinary(std::ostream&)const;
     230             :   void readBinary(std::istream&);
     231             :   double getKBoltzmann()const;
     232             :   double getMDKBoltzmann()const;
     233             :   bool usingNaturalUnits()const;
     234          19 :   void setNaturalUnits(bool n) {naturalUnits=n;}
     235           0 :   void setMDNaturalUnits(bool n) {MDnaturalUnits=n;}
     236             : 
     237             :   void setExtraCV(const std::string &name,const TypesafePtr & p);
     238             :   void setExtraCVForce(const std::string &name,const TypesafePtr & p);
     239             :   double getExtraCV(const std::string &name);
     240             :   void updateExtraCVForce(const std::string &name,double f);
     241             : };
     242             : 
     243             : inline
     244             : int Atoms::getNatoms()const {
     245      795366 :   return natoms;
     246             : }
     247             : 
     248             : inline
     249             : int Atoms::getNVirtualAtoms()const {
     250          10 :   return virtualAtomsActions.size();
     251             : }
     252             : 
     253             : inline
     254             : const long int& Atoms::getDdStep()const {
     255             :   return ddStep;
     256             : }
     257             : 
     258             : inline
     259             : const std::vector<int>& Atoms::getGatindex()const {
     260           9 :   return gatindex;
     261             : }
     262             : 
     263             : inline
     264             : const Pbc& Atoms::getPbc()const {
     265         900 :   return pbc;
     266             : }
     267             : 
     268             : inline
     269             : bool Atoms::isVirtualAtom(AtomNumber i)const {
     270     1178139 :   return i.index()>=(unsigned) getNatoms();
     271             : }
     272             : 
     273             : inline
     274             : ActionWithVirtualAtom* Atoms::getVirtualAtomsAction(AtomNumber i)const {
     275        7230 :   return virtualAtomsActions[i.index()-getNatoms()];
     276             : }
     277             : 
     278             : inline
     279             : bool Atoms::usingNaturalUnits() const {
     280        2440 :   return naturalUnits || MDnaturalUnits;
     281             : }
     282             : 
     283             : inline
     284             : bool Atoms::chargesWereSet() const {
     285      168223 :   return chargesHaveBeenSet;
     286             : }
     287             : 
     288             : inline
     289             : bool Atoms::boxWasSet() const {
     290             :   return boxHasBeenSet;
     291             : }
     292             : 
     293             : inline
     294             : const Tensor& Atoms::getVirial()const {
     295         450 :   return virial;
     296             : }
     297             : 
     298             : 
     299             : }
     300             : #endif