Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2019 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/Communicator.h"
      26             : #include "tools/Tensor.h"
      27             : #include "tools/Units.h"
      28             : #include "tools/Exception.h"
      29             : #include "tools/AtomNumber.h"
      30             : #include "tools/ForwardDecl.h"
      31             : #include <vector>
      32             : #include <set>
      33             : #include <map>
      34             : #include <string>
      35             : #include <memory>
      36             : 
      37             : namespace PLMD {
      38             : 
      39             : class MDAtomsBase;
      40             : class PlumedMain;
      41             : class ActionAtomistic;
      42             : class ActionWithVirtualAtom;
      43             : class Pbc;
      44             : 
      45             : /// Class containing atom related quantities from the MD code.
      46             : /// IT IS STILL UNDOCUMENTED. IT PROBABLY NEEDS A STRONG CLEANUP
      47             : class Atoms
      48             : {
      49             :   friend class ActionAtomistic;
      50             :   friend class ActionWithVirtualAtom;
      51             :   int natoms;
      52             :   std::set<AtomNumber> unique;
      53             :   std::vector<unsigned> uniq_index;
      54             : /// Map global indexes to local indexes
      55             : /// E.g. g2l[i] is the position of atom i in the array passed from the MD engine.
      56             : /// Called "global to local" since originally it was used to map global indexes to local
      57             : /// ones used in domain decomposition. However, it is now also used for the NAMD-like
      58             : /// interface, where only a small number of atoms is passed to plumed.
      59             :   std::vector<int> g2l;
      60             :   std::vector<Vector> positions;
      61             :   std::vector<Vector> forces;
      62             :   std::vector<double> masses;
      63             :   std::vector<double> charges;
      64             :   std::vector<ActionWithVirtualAtom*> virtualAtomsActions;
      65             :   Tensor box;
      66             :   ForwardDecl<Pbc> pbc_fwd;
      67             :   Pbc&   pbc=*pbc_fwd;
      68             :   Tensor virial;
      69             : // this is the energy set by each processor:
      70             :   double md_energy;
      71             : // this is the summed energy:
      72             :   double energy;
      73             : 
      74             :   bool   dataCanBeSet;
      75             :   bool   collectEnergy;
      76             :   bool   energyHasBeenSet;
      77             :   unsigned positionsHaveBeenSet;
      78             :   bool massesHaveBeenSet;
      79             :   bool chargesHaveBeenSet;
      80             :   bool boxHasBeenSet;
      81             :   unsigned forcesHaveBeenSet;
      82             :   bool virialHasBeenSet;
      83             :   bool massAndChargeOK;
      84             :   unsigned shuffledAtoms;
      85             : 
      86             :   std::map<std::string,std::vector<AtomNumber> > groups;
      87             : 
      88             :   void resizeVectors(unsigned);
      89             : 
      90             :   std::vector<int> fullList;
      91             : 
      92             :   std::unique_ptr<MDAtomsBase> mdatoms;
      93             : 
      94             :   PlumedMain & plumed;
      95             : 
      96             :   Units MDUnits;
      97             :   Units units;
      98             : 
      99             :   bool naturalUnits;
     100             :   bool MDnaturalUnits;
     101             : 
     102             :   double timestep;
     103             :   double forceOnEnergy;
     104             : 
     105             : /// if set to true, all the forces in the global array are zeroes
     106             : /// at every step. It should not be necessary in general, but it is
     107             : /// for actions accessing to modifyGlobalForce() (e.g. FIT_TO_TEMPLATE).
     108             :   bool zeroallforces;
     109             : 
     110             :   double kbT;
     111             : 
     112             :   std::vector<ActionAtomistic*> actions;
     113             :   std::vector<int>    gatindex;
     114             : 
     115             :   bool asyncSent;
     116             :   bool atomsNeeded;
     117             : 
     118        5452 :   class DomainDecomposition:
     119             :     public Communicator
     120             :   {
     121             :   public:
     122             :     bool on;
     123             :     bool async;
     124             : 
     125             :     std::vector<Communicator::Request> mpi_request_positions;
     126             :     std::vector<Communicator::Request> mpi_request_index;
     127             : 
     128             :     std::vector<double> positionsToBeSent;
     129             :     std::vector<double> positionsToBeReceived;
     130             :     std::vector<int>    indexToBeSent;
     131             :     std::vector<int>    indexToBeReceived;
     132      138117 :     operator bool() const {return on;}
     133        2726 :     DomainDecomposition():
     134        2726 :       on(false), async(false)
     135        2726 :     {}
     136             :     void enable(Communicator& c);
     137             :   };
     138             : 
     139             :   DomainDecomposition dd;
     140             :   long int ddStep;  //last step in which dd happened
     141             : 
     142             :   void share(const std::set<AtomNumber>&);
     143             : 
     144             : public:
     145             : 
     146             :   explicit Atoms(PlumedMain&plumed);
     147             :   ~Atoms();
     148             : 
     149             :   void init();
     150             : 
     151             :   void share();
     152             :   void shareAll();
     153             :   void wait();
     154             :   void updateForces();
     155             : 
     156             :   void setRealPrecision(int);
     157             :   int  getRealPrecision()const;
     158             : 
     159             :   void setTimeStep(void*);
     160             :   double getTimeStep()const;
     161             : 
     162             :   void setKbT(void*);
     163             :   double getKbT()const;
     164             : 
     165             :   void setNatoms(int);
     166             :   int getNatoms()const;
     167             :   int getNVirtualAtoms()const;
     168             : 
     169             :   const long int& getDdStep()const;
     170             :   const std::vector<int>& getGatindex()const;
     171             :   const Pbc& getPbc()const;
     172             :   void getLocalMasses(std::vector<double>&);
     173             :   void getLocalPositions(std::vector<Vector>&);
     174             :   void getLocalForces(std::vector<Vector>&);
     175             :   void getLocalMDForces(std::vector<Vector>&);
     176             :   const Tensor& getVirial()const;
     177             : 
     178        3787 :   void setCollectEnergy(bool b) { collectEnergy=b; }
     179             : 
     180             :   void setDomainDecomposition(Communicator&);
     181             :   void setAtomsGatindex(int*,bool);
     182             :   void setAtomsContiguous(int);
     183             :   void setAtomsNlocal(int);
     184             : 
     185             :   void startStep();
     186             :   void setEnergy(void*);
     187             :   void setBox(void*);
     188             :   void setVirial(void*);
     189             :   void setPositions(void*);
     190             :   void setPositions(void*,int);
     191             :   void setForces(void*);
     192             :   void setForces(void*,int);
     193             :   void setMasses(void*);
     194             :   void setCharges(void*);
     195             :   bool chargesWereSet() const ;
     196             :   bool boxWasSet() const ;
     197             : 
     198             :   void MD2double(const void*m,double&d)const;
     199             :   void double2MD(const double&d,void*m)const;
     200             : 
     201             :   void createFullList(int*);
     202             :   void getFullList(int**);
     203             :   void clearFullList();
     204             : 
     205             :   void add(ActionAtomistic*);
     206             :   void remove(ActionAtomistic*);
     207             : 
     208        3787 :   double getEnergy()const {plumed_assert(collectEnergy && energyHasBeenSet); return energy;}
     209             : 
     210          77 :   bool isEnergyNeeded()const {return collectEnergy;}
     211             : 
     212          42 :   void setMDEnergyUnits(double d) {MDUnits.setEnergy(d);}
     213         620 :   void setMDLengthUnits(double d) {MDUnits.setLength(d);}
     214           5 :   void setMDTimeUnits(double d) {MDUnits.setTime(d);}
     215         620 :   void setMDChargeUnits(double d) {MDUnits.setCharge(d);}
     216         620 :   void setMDMassUnits(double d) {MDUnits.setMass(d);}
     217             :   const Units& getMDUnits() {return MDUnits;}
     218          16 :   void setUnits(const Units&u) {units=u;}
     219             :   const Units& getUnits() {return units;}
     220             :   void updateUnits();
     221             : 
     222             :   AtomNumber addVirtualAtom(ActionWithVirtualAtom*);
     223             :   void removeVirtualAtom(ActionWithVirtualAtom*);
     224             :   ActionWithVirtualAtom* getVirtualAtomsAction(AtomNumber)const;
     225             :   bool isVirtualAtom(AtomNumber)const;
     226             :   void insertGroup(const std::string&name,const std::vector<AtomNumber>&a);
     227             :   void removeGroup(const std::string&name);
     228             :   void writeBinary(std::ostream&)const;
     229             :   void readBinary(std::istream&);
     230             :   double getKBoltzmann()const;
     231             :   double getMDKBoltzmann()const;
     232             :   bool usingNaturalUnits()const;
     233          16 :   void setNaturalUnits(bool n) {naturalUnits=n;}
     234           0 :   void setMDNaturalUnits(bool n) {MDnaturalUnits=n;}
     235             : 
     236             :   void setExtraCV(const std::string &name,void*p);
     237             :   void setExtraCVForce(const std::string &name,void*p);
     238             :   double getExtraCV(const std::string &name);
     239             :   void updateExtraCVForce(const std::string &name,double f);
     240             : };
     241             : 
     242             : inline
     243             : int Atoms::getNatoms()const {
     244     1469330 :   return natoms;
     245             : }
     246             : 
     247             : inline
     248             : int Atoms::getNVirtualAtoms()const {
     249           2 :   return virtualAtomsActions.size();
     250             : }
     251             : 
     252             : inline
     253             : const long int& Atoms::getDdStep()const {
     254             :   return ddStep;
     255             : }
     256             : 
     257             : inline
     258             : const std::vector<int>& Atoms::getGatindex()const {
     259             :   return gatindex;
     260             : }
     261             : 
     262             : inline
     263             : const Pbc& Atoms::getPbc()const {
     264        1350 :   return pbc;
     265             : }
     266             : 
     267             : inline
     268             : bool Atoms::isVirtualAtom(AtomNumber i)const {
     269     1129349 :   return i.index()>=(unsigned) getNatoms();
     270             : }
     271             : 
     272             : inline
     273             : ActionWithVirtualAtom* Atoms::getVirtualAtomsAction(AtomNumber i)const {
     274         500 :   return virtualAtomsActions[i.index()-getNatoms()];
     275             : }
     276             : 
     277             : inline
     278             : bool Atoms::usingNaturalUnits() const {
     279        2416 :   return naturalUnits || MDnaturalUnits;
     280             : }
     281             : 
     282             : inline
     283             : bool Atoms::chargesWereSet() const {
     284      143206 :   return chargesHaveBeenSet;
     285             : }
     286             : 
     287             : inline
     288             : bool Atoms::boxWasSet() const {
     289             :   return boxHasBeenSet;
     290             : }
     291             : 
     292             : inline
     293             : const Tensor& Atoms::getVirial()const {
     294             :   return virial;
     295             : }
     296             : 
     297             : 
     298             : }
     299             : #endif