/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2011-2019 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed.org for more information.

   This file is part of plumed, version 2.

   plumed is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   plumed is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "PlumedMain.h"
#include "ActionAtomistic.h"
#include "ActionPilot.h"
#include "ActionRegister.h"
#include "ActionSet.h"
#include "ActionWithValue.h"
#include "ActionWithVirtualAtom.h"
#include "Atoms.h"
#include "CLToolMain.h"
#include "ExchangePatterns.h"
#include "GREX.h"
#include "config/Config.h"
#include "tools/Citations.h"
#include "tools/Communicator.h"
#include "tools/DLLoader.h"
#include "tools/Exception.h"
#include "tools/IFile.h"
#include "tools/Log.h"
#include "tools/OpenMP.h"
#include "tools/Tools.h"
#include "tools/Stopwatch.h"
#include "lepton/Exception.h"
#include "DataFetchingObject.h"
#include <cstdlib>
#include <cstring>
#include <set>
#include <unordered_map>
#include <exception>
#include <stdexcept>
#include <ios>
#include <new>
#include <typeinfo>
#ifdef __PLUMED_LIBCXX11
#include <system_error>
#include <future>
#include <memory>
#include <functional>
#endif


using namespace std;

namespace PLMD {

/// Small utility just used in this file to throw arbitrary exceptions
static void testThrow(const char* what) {
  auto words=Tools::getWords(what);
  plumed_assert(words.size()>0);
#define __PLUMED_THROW_NOMSG(type) if(words[0]==#type) throw type()
#define __PLUMED_THROW_MSG(type) if(words[0]==#type) throw type(what)
  __PLUMED_THROW_MSG(PLMD::ExceptionError);
  __PLUMED_THROW_MSG(PLMD::ExceptionDebug);
  __PLUMED_THROW_MSG(PLMD::Exception);
  __PLUMED_THROW_MSG(PLMD::lepton::Exception);
  __PLUMED_THROW_NOMSG(std::bad_exception);
#ifdef __PLUMED_LIBCXX11
  __PLUMED_THROW_NOMSG(std::bad_array_new_length);
#endif
  __PLUMED_THROW_NOMSG(std::bad_alloc);
#ifdef __PLUMED_LIBCXX11
  __PLUMED_THROW_NOMSG(std::bad_function_call);
  __PLUMED_THROW_NOMSG(std::bad_weak_ptr);
#endif
  __PLUMED_THROW_NOMSG(std::bad_cast);
  __PLUMED_THROW_NOMSG(std::bad_typeid);
  __PLUMED_THROW_MSG(std::underflow_error);
  __PLUMED_THROW_MSG(std::overflow_error);
  __PLUMED_THROW_MSG(std::range_error);
  __PLUMED_THROW_MSG(std::runtime_error);
  __PLUMED_THROW_MSG(std::out_of_range);
  __PLUMED_THROW_MSG(std::length_error);
  __PLUMED_THROW_MSG(std::domain_error);
  __PLUMED_THROW_MSG(std::invalid_argument);
  __PLUMED_THROW_MSG(std::logic_error);

#ifdef __PLUMED_LIBCXX11
  if(words[0]=="std::system_error") {
    plumed_assert(words.size()>2);
    int error_code;
    Tools::convert(words[2],error_code);
    if(words[1]=="std::generic_category") throw std::system_error(error_code,std::generic_category(),what);
    if(words[1]=="std::system_category") throw std::system_error(error_code,std::system_category(),what);
    if(words[1]=="std::iostream_category") throw std::system_error(error_code,std::iostream_category(),what);
    if(words[1]=="std::future_category") throw std::system_error(error_code,std::future_category(),what);
  }
#endif

  if(words[0]=="std::ios_base::failure") {
#ifdef __PLUMED_LIBCXX11
    int error_code=0;
    if(words.size()>2) Tools::convert(words[2],error_code);
    if(words.size()>1 && words[1]=="std::generic_category") throw std::ios_base::failure(what,std::error_code(error_code,std::generic_category()));
    if(words.size()>1 && words[1]=="std::system_category") throw std::ios_base::failure(what,std::error_code(error_code,std::system_category()));
    if(words.size()>1 && words[1]=="std::iostream_category") throw std::ios_base::failure(what,std::error_code(error_code,std::iostream_category()));
    if(words.size()>1 && words[1]=="std::future_category") throw std::ios_base::failure(what,std::error_code(error_code,std::future_category()));
#endif
    throw std::ios_base::failure(what);
  }

  plumed_error() << "unknown exception " << what;
}

PlumedMain::PlumedMain():
  initialized(false),
// automatically write on log in destructor
  stopwatch_fwd(log),
  step(0),
  active(false),
  mydatafetcher(DataFetchingObject::create(sizeof(double),*this)),
  endPlumed(false),
  atoms_fwd(*this),
  actionSet_fwd(*this),
  bias(0.0),
  work(0.0),
  exchangeStep(false),
  restart(false),
  doCheckPoint(false),
  stopFlag(NULL),
  stopNow(false),
  novirial(false),
  detailedTimers(false)
{
  log.link(comm);
  log.setLinePrefix("PLUMED: ");
}

// destructor needed to delete forward declarated objects
PlumedMain::~PlumedMain() {
}

/////////////////////////////////////////////////////////////
//  MAIN INTERPRETER

#define CHECK_INIT(ini,word) plumed_massert(ini,"cmd(\"" + word +"\") should be only used after plumed initialization")
#define CHECK_NOTINIT(ini,word) plumed_massert(!(ini),"cmd(\"" + word +"\") should be only used before plumed initialization")
#define CHECK_NOTNULL(val,word) plumed_massert(val,"NULL pointer received in cmd(\"" + word + "\")");


void PlumedMain::cmd(const std::string & word,void*val) {

// Enumerate all possible commands:
  enum {
#include "PlumedMainEnum.inc"
  };

// Static object (initialized once) containing the map of commands:
  const static std::unordered_map<std::string, int> word_map = {
#include "PlumedMainMap.inc"
  };

  try {

    auto ss=stopwatch.startPause();

    std::vector<std::string> words=Tools::getWords(word);
    unsigned nw=words.size();
    if(nw==0) {
      // do nothing
    } else {
      int iword=-1;
      double d;
      const auto it=word_map.find(words[0]);
      if(it!=word_map.end()) iword=it->second;
      switch(iword) {
      case cmd_setBox:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setBox(val);
        break;
      case cmd_setPositions:
        CHECK_INIT(initialized,word);
        atoms.setPositions(val);
        break;
      case cmd_setMasses:
        CHECK_INIT(initialized,word);
        atoms.setMasses(val);
        break;
      case cmd_setCharges:
        CHECK_INIT(initialized,word);
        atoms.setCharges(val);
        break;
      case cmd_setPositionsX:
        CHECK_INIT(initialized,word);
        atoms.setPositions(val,0);
        break;
      case cmd_setPositionsY:
        CHECK_INIT(initialized,word);
        atoms.setPositions(val,1);
        break;
      case cmd_setPositionsZ:
        CHECK_INIT(initialized,word);
        atoms.setPositions(val,2);
        break;
      case cmd_setVirial:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setVirial(val);
        break;
      case cmd_setEnergy:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setEnergy(val);
        break;
      case cmd_setForces:
        CHECK_INIT(initialized,word);
        atoms.setForces(val);
        break;
      case cmd_setForcesX:
        CHECK_INIT(initialized,word);
        atoms.setForces(val,0);
        break;
      case cmd_setForcesY:
        CHECK_INIT(initialized,word);
        atoms.setForces(val,1);
        break;
      case cmd_setForcesZ:
        CHECK_INIT(initialized,word);
        atoms.setForces(val,2);
        break;
      case cmd_calc:
        CHECK_INIT(initialized,word);
        calc();
        break;
      case cmd_prepareDependencies:
        CHECK_INIT(initialized,word);
        prepareDependencies();
        break;
      case cmd_shareData:
        CHECK_INIT(initialized,word);
        shareData();
        break;
      case cmd_prepareCalc:
        CHECK_INIT(initialized,word);
        prepareCalc();
        break;
      case cmd_performCalc:
        CHECK_INIT(initialized,word);
        performCalc();
        break;
      case cmd_performCalcNoUpdate:
        CHECK_INIT(initialized,word);
        performCalcNoUpdate();
        break;
      case cmd_update:
        CHECK_INIT(initialized,word);
        update();
        break;
      case cmd_setStep:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        step=(*static_cast<int*>(val));
        atoms.startStep();
        break;
      case cmd_setStepLong:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        step=(*static_cast<long int*>(val));
        atoms.startStep();
        break;
      // words used less frequently:
      case cmd_setAtomsNlocal:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setAtomsNlocal(*static_cast<int*>(val));
        break;
      case cmd_setAtomsGatindex:
        CHECK_INIT(initialized,word);
        atoms.setAtomsGatindex(static_cast<int*>(val),false);
        break;
      case cmd_setAtomsFGatindex:
        CHECK_INIT(initialized,word);
        atoms.setAtomsGatindex(static_cast<int*>(val),true);
        break;
      case cmd_setAtomsContiguous:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setAtomsContiguous(*static_cast<int*>(val));
        break;
      case cmd_createFullList:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.createFullList(static_cast<int*>(val));
        break;
      case cmd_getFullList:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.getFullList(static_cast<int**>(val));
        break;
      case cmd_clearFullList:
        CHECK_INIT(initialized,word);
        atoms.clearFullList();
        break;
      /* ADDED WITH API==6 */
      case cmd_getDataRank:
        CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
        if( nw==2 ) DataFetchingObject::get_rank( actionSet, words[1], "", static_cast<long*>(val) );
        else DataFetchingObject::get_rank( actionSet, words[1], words[2], static_cast<long*>(val) );
        break;
      /* ADDED WITH API==6 */
      case cmd_getDataShape:
        CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
        if( nw==2 ) DataFetchingObject::get_shape( actionSet, words[1], "", static_cast<long*>(val) );
        else DataFetchingObject::get_shape( actionSet, words[1], words[2], static_cast<long*>(val) );
        break;
      /* ADDED WITH API==6 */
      case cmd_setMemoryForData:
        CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
        if( nw==2 ) mydatafetcher->setData( words[1], "", val );
        else mydatafetcher->setData( words[1], words[2], val );
        break;
      /* ADDED WITH API==6 */
      case cmd_setErrorHandler:
      {
        if(val) error_handler=*static_cast<plumed_error_handler*>(val);
        else error_handler.handler=NULL;
      }
      break;
      case cmd_read:
        CHECK_INIT(initialized,word);
        if(val)readInputFile(static_cast<char*>(val));
        else   readInputFile("plumed.dat");
        break;
      case cmd_readInputLine:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        readInputLine(static_cast<char*>(val));
        break;
      case cmd_clear:
        CHECK_INIT(initialized,word);
        actionSet.clearDelete();
        break;
      case cmd_getApiVersion:
        CHECK_NOTNULL(val,word);
        *(static_cast<int*>(val))=6;
        break;
      // commands which can be used only before initialization:
      case cmd_init:
        CHECK_NOTINIT(initialized,word);
        init();
        break;
      case cmd_setRealPrecision:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setRealPrecision(*static_cast<int*>(val));
        mydatafetcher=DataFetchingObject::create(*static_cast<int*>(val),*this);
        break;
      case cmd_setMDLengthUnits:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.MD2double(val,d);
        atoms.setMDLengthUnits(d);
        break;
      case cmd_setMDChargeUnits:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.MD2double(val,d);
        atoms.setMDChargeUnits(d);
        break;
      case cmd_setMDMassUnits:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.MD2double(val,d);
        atoms.setMDMassUnits(d);
        break;
      case cmd_setMDEnergyUnits:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.MD2double(val,d);
        atoms.setMDEnergyUnits(d);
        break;
      case cmd_setMDTimeUnits:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.MD2double(val,d);
        atoms.setMDTimeUnits(d);
        break;
      case cmd_setNaturalUnits:
        // set the boltzman constant for MD in natural units (kb=1)
        // only needed in LJ codes if the MD is passing temperatures to plumed (so, not yet...)
        // use as cmd("setNaturalUnits")
        CHECK_NOTINIT(initialized,word);
        atoms.setMDNaturalUnits(true);
        break;
      case cmd_setNoVirial:
        CHECK_NOTINIT(initialized,word);
        novirial=true;
        break;
      case cmd_setPlumedDat:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        plumedDat=static_cast<char*>(val);
        break;
      case cmd_setMPIComm:
        CHECK_NOTINIT(initialized,word);
        comm.Set_comm(val);
        atoms.setDomainDecomposition(comm);
        break;
      case cmd_setMPIFComm:
        CHECK_NOTINIT(initialized,word);
        comm.Set_fcomm(val);
        atoms.setDomainDecomposition(comm);
        break;
      case cmd_setMPImultiSimComm:
        CHECK_NOTINIT(initialized,word);
        multi_sim_comm.Set_comm(val);
        break;
      case cmd_setNatoms:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setNatoms(*static_cast<int*>(val));
        break;
      case cmd_setTimestep:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setTimeStep(val);
        break;
      /* ADDED WITH API==2 */
      case cmd_setKbT:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.setKbT(val);
        break;
      /* ADDED WITH API==3 */
      case cmd_setRestart:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        if(*static_cast<int*>(val)!=0) restart=true;
        break;
      /* ADDED WITH API==4 */
      case cmd_doCheckPoint:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        doCheckPoint = false;
        if(*static_cast<int*>(val)!=0) doCheckPoint = true;
        break;
      /* ADDED WITH API==6 */
      case cmd_setNumOMPthreads:
        CHECK_NOTNULL(val,word);
        OpenMP::setNumThreads(*static_cast<int*>(val)>0?*static_cast<int*>(val):1);
        break;
      /* ADDED WITH API==6 */
      /* only used for testing */
      case cmd_throw:
        CHECK_NOTNULL(val,word);
        testThrow((const char*) val);
      /* STOP API */
      case cmd_setMDEngine:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        MDEngine=static_cast<char*>(val);
        break;
      case cmd_setLog:
        CHECK_NOTINIT(initialized,word);
        log.link(static_cast<FILE*>(val));
        break;
      case cmd_setLogFile:
        CHECK_NOTINIT(initialized,word);
        CHECK_NOTNULL(val,word);
        log.open(static_cast<char*>(val));
        break;
      // other commands that should be used after initialization:
      case cmd_setStopFlag:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        stopFlag=static_cast<int*>(val);
        break;
      case cmd_getExchangesFlag:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        exchangePatterns.getFlag((*static_cast<int*>(val)));
        break;
      case cmd_setExchangesSeed:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        exchangePatterns.setSeed((*static_cast<int*>(val)));
        break;
      case cmd_setNumberOfReplicas:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        exchangePatterns.setNofR((*static_cast<int*>(val)));
        break;
      case cmd_getExchangesList:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        exchangePatterns.getList((static_cast<int*>(val)));
        break;
      case cmd_runFinalJobs:
        CHECK_INIT(initialized,word);
        runJobsAtEndOfCalculation();
        break;
      case cmd_isEnergyNeeded:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        if(atoms.isEnergyNeeded()) *(static_cast<int*>(val))=1;
        else                       *(static_cast<int*>(val))=0;
        break;
      case cmd_getBias:
        CHECK_INIT(initialized,word);
        CHECK_NOTNULL(val,word);
        atoms.double2MD(getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy()),val);
        break;
      case cmd_checkAction:
        CHECK_NOTNULL(val,word);
        plumed_assert(nw==2);
        *(static_cast<int*>(val))=(actionRegister().check(words[1]) ? 1:0);
        break;
      case cmd_setExtraCV:
        CHECK_NOTNULL(val,word);
        plumed_assert(nw==2);
        atoms.setExtraCV(words[1],val);
        break;
      case cmd_setExtraCVForce:
        CHECK_NOTNULL(val,word);
        plumed_assert(nw==2);
        atoms.setExtraCVForce(words[1],val);
        break;
      case cmd_GREX:
        if(!grex) grex.reset(new GREX(*this));
        plumed_massert(grex,"error allocating grex");
        {
          std::string kk=words[1];
          for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
          grex->cmd(kk.c_str(),val);
        }
        break;
      case cmd_CLTool:
        CHECK_NOTINIT(initialized,word);
        if(!cltool) cltool.reset(new CLToolMain);
        {
          std::string kk=words[1];
          for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
          cltool->cmd(kk.c_str(),val);
        }
        break;
      default:
        plumed_merror("cannot interpret cmd(\"" + word + "\"). check plumed developers manual to see the available commands.");
        break;
      }
    }

  } catch (std::exception &e) {
    if(log.isOpen()) {
      log<<"\n\n################################################################################\n\n";
      log<<e.what();
      log<<"\n\n################################################################################\n\n";
      log.flush();
    }
    throw;
  }
}

////////////////////////////////////////////////////////////////////////

void PlumedMain::init() {
// check that initialization just happens once
  initialized=true;
  atoms.init();
  if(!log.isOpen()) log.link(stdout);
  log<<"PLUMED is starting\n";
  log<<"Version: "<<config::getVersionLong()<<" (git: "<<config::getVersionGit()<<") "
     <<"compiled on " <<config::getCompilationDate() << " at " << config::getCompilationTime() << "\n";
  log<<"Please cite this paper when using PLUMED ";
  log<<cite("Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)");
  log<<"\n";
  log<<"For further information see the PLUMED web page at http://www.plumed.org\n";
  log<<"Root: "<<config::getPlumedRoot()<<"\n";
  log<<"For installed feature, see "<<config::getPlumedRoot() + "/src/config/config.txt\n";
  log.printf("Molecular dynamics engine: %s\n",MDEngine.c_str());
  log.printf("Precision of reals: %d\n",atoms.getRealPrecision());
  log.printf("Running over %d %s\n",comm.Get_size(),(comm.Get_size()>1?"nodes":"node"));
  log<<"Number of threads: "<<OpenMP::getNumThreads()<<"\n";
  log<<"Cache line size: "<<OpenMP::getCachelineSize()<<"\n";
  log.printf("Number of atoms: %d\n",atoms.getNatoms());
  if(grex) log.printf("GROMACS-like replica exchange is on\n");
  log.printf("File suffix: %s\n",getSuffix().c_str());
  if(plumedDat.length()>0) {
    readInputFile(plumedDat);
    plumedDat="";
  }
  atoms.updateUnits();
  log.printf("Timestep: %f\n",atoms.getTimeStep());
  if(atoms.getKbT()>0.0)
    log.printf("KbT: %f\n",atoms.getKbT());
  else {
    log.printf("KbT has not been set by the MD engine\n");
    log.printf("It should be set by hand where needed\n");
  }
  log<<"Relevant bibliography:\n";
  log<<citations;
  log<<"Please read and cite where appropriate!\n";
  log<<"Finished setup\n";
}

void PlumedMain::readInputFile(std::string str) {
  plumed_assert(initialized);
  log.printf("FILE: %s\n",str.c_str());
  IFile ifile;
  ifile.link(*this);
  ifile.open(str);
  ifile.allowNoEOL();
  std::vector<std::string> words;
  while(Tools::getParsedLine(ifile,words) && !endPlumed) readInputWords(words);
  endPlumed=false;
  log.printf("END FILE: %s\n",str.c_str());
  log.flush();

  pilots=actionSet.select<ActionPilot*>();
}

void PlumedMain::readInputLine(const std::string & str) {
  plumed_assert(initialized);
  if(str.empty()) return;
  std::vector<std::string> words=Tools::getWords(str);
  citations.clear();
  readInputWords(words);
  if(!citations.empty()) {
    log<<"Relevant bibliography:\n";
    log<<citations;
    log<<"Please read and cite where appropriate!\n";
  }
}

void PlumedMain::readInputWords(const std::vector<std::string> & words) {
  plumed_assert(initialized);
  if(words.empty())return;
  else if(words[0]=="_SET_SUFFIX") {
    plumed_assert(words.size()==2);
    setSuffix(words[1]);
  } else {
    std::vector<std::string> interpreted(words);
    Tools::interpretLabel(interpreted);
    auto action=actionRegister().create(ActionOptions(*this,interpreted));
    if(!action) {
      std::string msg;
      msg ="ERROR\nI cannot understand line:";
      for(unsigned i=0; i<interpreted.size(); ++i) msg+=" "+interpreted[i];
      msg+="\nMaybe a missing space or a typo?";
      log << msg;
      log.flush();
      plumed_merror(msg);
    };
    action->checkRead();
    actionSet.emplace_back(std::move(action));
  };

  pilots=actionSet.select<ActionPilot*>();
}

////////////////////////////////////////////////////////////////////////

void PlumedMain::exit(int c) {
  comm.Abort(c);
}

Log& PlumedMain::getLog() {
  return log;
}

void PlumedMain::calc() {
  prepareCalc();
  performCalc();
}

void PlumedMain::prepareCalc() {
  prepareDependencies();
  shareData();
}

//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// here we have the main steps in "calc()"
// they can be called individually, but the standard thing is to
// traverse them in this order:
void PlumedMain::prepareDependencies() {

// Stopwatch is stopped when sw goes out of scope
  auto sw=stopwatch.startStop("1 Prepare dependencies");

// activate all the actions which are on step
// activation is recursive and enables also the dependencies
// before doing that, the prepare() method is called to see if there is some
// new/changed dependency (up to now, only useful for dependences on virtual atoms,
// which can be dynamically changed).

// First switch off all actions
  for(const auto & p : actionSet) {
    p->deactivate();
  }

// for optimization, an "active" flag remains false if no action at all is active
  active=mydatafetcher->activate();
  for(unsigned i=0; i<pilots.size(); ++i) {
    if(pilots[i]->onStep()) {
      pilots[i]->activate();
      active=true;
    }
  };

// also, if one of them is the total energy, tell to atoms that energy should be collected
  for(const auto & p : actionSet) {
    if(p->isActive()) {
      if(p->checkNeedsGradients()) p->setOption("GRADIENTS");
    }
  }

}

void PlumedMain::shareData() {
// atom positions are shared (but only if there is something to do)
  if(!active)return;
// Stopwatch is stopped when sw goes out of scope
  auto sw=stopwatch.startStop("2 Sharing data");
  if(atoms.getNatoms()>0) atoms.share();
}

void PlumedMain::performCalcNoUpdate() {
  waitData();
  justCalculate();
  backwardPropagate();
}

void PlumedMain::performCalc() {
  waitData();
  justCalculate();
  backwardPropagate();
  update();
  mydatafetcher->finishDataGrab();
}

void PlumedMain::waitData() {
  if(!active)return;
// Stopwatch is stopped when sw goes out of scope
  auto sw=stopwatch.startStop("3 Waiting for data");
  if(atoms.getNatoms()>0) atoms.wait();
}

void PlumedMain::justCalculate() {
  if(!active)return;
// Stopwatch is stopped when sw goes out of scope
  auto sw=stopwatch.startStop("4 Calculating (forward loop)");
  bias=0.0;
  work=0.0;

  int iaction=0;
// calculate the active actions in order (assuming *backward* dependence)
  for(const auto & pp : actionSet) {
    Action* p(pp.get());
    if(p->isActive()) {
// Stopwatch is stopped when sw goes out of scope.
// We explicitly declare a Stopwatch::Handler here to allow for conditional initialization.
      Stopwatch::Handler sw;
      if(detailedTimers) {
        std::string actionNumberLabel;
        Tools::convert(iaction,actionNumberLabel);
        const unsigned m=actionSet.size();
        unsigned k=0; unsigned n=1; while(n<m) { n*=10; k++; }
        const int pad=k-actionNumberLabel.length();
        for(int i=0; i<pad; i++) actionNumberLabel=" "+actionNumberLabel;
        sw=stopwatch.startStop("4A "+actionNumberLabel+" "+p->getLabel());
      }
      ActionWithValue*av=dynamic_cast<ActionWithValue*>(p);
      ActionAtomistic*aa=dynamic_cast<ActionAtomistic*>(p);
      {
        if(av) av->clearInputForces();
        if(av) av->clearDerivatives();
      }
      {
        if(aa) aa->clearOutputForces();
        if(aa) if(aa->isActive()) aa->retrieveAtoms();
      }
      if(p->checkNumericalDerivatives()) p->calculateNumericalDerivatives();
      else p->calculate();
      // This retrieves components called bias
      if(av) bias+=av->getOutputQuantity("bias");
      if(av) work+=av->getOutputQuantity("work");
      if(av)av->setGradientsIfNeeded();
      ActionWithVirtualAtom*avv=dynamic_cast<ActionWithVirtualAtom*>(p);
      if(avv)avv->setGradientsIfNeeded();
    }
    iaction++;
  }
}

void PlumedMain::justApply() {
  backwardPropagate();
  update();
}

void PlumedMain::backwardPropagate() {
  if(!active)return;
  int iaction=0;
// Stopwatch is stopped when sw goes out of scope
  auto sw=stopwatch.startStop("5 Applying (backward loop)");
// apply them in reverse order
  for(auto pp=actionSet.rbegin(); pp!=actionSet.rend(); ++pp) {
    const auto & p(pp->get());
    if(p->isActive()) {

// Stopwatch is stopped when sw goes out of scope.
// We explicitly declare a Stopwatch::Handler here to allow for conditional initialization.
      Stopwatch::Handler sw;
      if(detailedTimers) {
        std::string actionNumberLabel;
        Tools::convert(iaction,actionNumberLabel);
        const unsigned m=actionSet.size();
        unsigned k=0; unsigned n=1; while(n<m) { n*=10; k++; }
        const int pad=k-actionNumberLabel.length();
        for(int i=0; i<pad; i++) actionNumberLabel=" "+actionNumberLabel;
        sw=stopwatch.startStop("5A "+actionNumberLabel+" "+p->getLabel());
      }

      p->apply();
      ActionAtomistic*a=dynamic_cast<ActionAtomistic*>(p);
// still ActionAtomistic has a special treatment, since they may need to add forces on atoms
      if(a) a->applyForces();

    }
    iaction++;
  }

// Stopwatch is stopped when sw goes out of scope.
// We explicitly declare a Stopwatch::Handler here to allow for conditional initialization.
  Stopwatch::Handler sw1;
  if(detailedTimers) sw1=stopwatch.startStop("5B Update forces");
// this is updating the MD copy of the forces
  if(atoms.getNatoms()>0) atoms.updateForces();
}

void PlumedMain::update() {
  if(!active)return;

// Stopwatch is stopped when sw goes out of scope
  auto sw=stopwatch.startStop("6 Update");

// update step (for statistics, etc)
  updateFlags.push(true);
  for(const auto & p : actionSet) {
    p->beforeUpdate();
    if(p->isActive() && p->checkUpdate() && updateFlagsTop()) p->update();
  }
  while(!updateFlags.empty()) updateFlags.pop();
  if(!updateFlags.empty()) plumed_merror("non matching changes in the update flags");
// Check that no action has told the calculation to stop
  if(stopNow) {
    if(stopFlag) (*stopFlag)=1;
    else plumed_merror("your md code cannot handle plumed stop events - add a call to plumed.comm(stopFlag,stopCondition)");
  }

// flush by default every 10000 steps
// hopefully will not affect performance
// also if receive checkpointing signal
  if(step%10000==0||doCheckPoint) {
    fflush();
    log.flush();
    for(const auto & p : actionSet) p->fflush();
  }
}

void PlumedMain::load(const std::string& ss) {
  if(DLLoader::installed()) {
    std::string s=ss;
    size_t n=s.find_last_of(".");
    std::string extension="";
    std::string base=s;
    if(n!=std::string::npos && n<s.length()-1) extension=s.substr(n+1);
    if(n!=std::string::npos && n<s.length())   base=s.substr(0,n);
    if(extension=="cpp") {
// full path command, including environment setup
// this will work even if plumed is not in the execution path or if it has been
// installed with a name different from "plumed"
      std::string cmd=config::getEnvCommand()+" \""+config::getPlumedRoot()+"\"/scripts/mklib.sh "+s;
      log<<"Executing: "<<cmd;
      if(comm.Get_size()>0) log<<" (only on master node)";
      log<<"\n";
      if(comm.Get_rank()==0) system(cmd.c_str());
      comm.Barrier();
      base="./"+base;
    }
    s=base+"."+config::getSoExt();
    void *p=dlloader.load(s);
    if(!p) {
      const std::string error_msg="I cannot load library " + ss + " " + dlloader.error();
      log<<"ERROR\n";
      log<<error_msg<<"\n";
      plumed_merror(error_msg);
    }
    log<<"Loading shared library "<<s.c_str()<<"\n";
    log<<"Here is the new list of available actions\n";
    log<<actionRegister();
  } else plumed_merror("loading not enabled, please recompile with -D__PLUMED_HAS_DLOPEN");
}

double PlumedMain::getBias() const {
  return bias;
}

double PlumedMain::getWork() const {
  return work;
}

FILE* PlumedMain::fopen(const char *path, const char *mode) {
  std::string mmode(mode);
  std::string ppath(path);
  std::string suffix(getSuffix());
  std::string ppathsuf=ppath+suffix;
  FILE*fp=std::fopen(const_cast<char*>(ppathsuf.c_str()),const_cast<char*>(mmode.c_str()));
  if(!fp) fp=std::fopen(const_cast<char*>(ppath.c_str()),const_cast<char*>(mmode.c_str()));
  plumed_massert(fp,"file " + ppath + " cannot be found");
  return fp;
}

int PlumedMain::fclose(FILE*fp) {
  return std::fclose(fp);
}

std::string PlumedMain::cite(const std::string&item) {
  return citations.cite(item);
}

void PlumedMain::fflush() {
  for(const auto  & p : files) {
    p->flush();
  }
}

void PlumedMain::insertFile(FileBase&f) {
  files.insert(&f);
}

void PlumedMain::eraseFile(FileBase&f) {
  files.erase(&f);
}

void PlumedMain::stop() {
  stopNow=true;
}

void PlumedMain::runJobsAtEndOfCalculation() {
  for(const auto & p : actionSet) {
    p->runFinalJobs();
  }
}

#ifdef __PLUMED_HAS_PYTHON
// This is here to stop cppcheck throwing an error
#endif

}

//////////////////////////////////////////////////////////////////////////////////////////////////////////////////
