IpplParticleBase.hpp

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/***************************************************************************
 *
 * The IPPL Framework
 *
 * This program was prepared by PSI.
 * All rights in the program are reserved by PSI.
 * Neither PSI nor the author(s)
 * makes any warranty, express or implied, or assumes any liability or
 * responsibility for the use of this software
 *
 * Visit www.amas.web.psi for more details
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 ***************************************************************************/
 
#include "Particle/IpplParticleBase.h"
#include "Particle/ParticleLayout.h"
#include "Particle/ParticleAttrib.h"
#include "Message/Message.h"
#include "Message/Communicate.h"
#include "Utility/Inform.h"
#include "Utility/PAssert.h"
#include "Utility/IpplInfo.h"
#include "Utility/IpplStats.h"
#include "Utility/IpplException.h"
#include <algorithm>
 
// For a IpplParticleBase that was created with the default constructor,
// initialize performs the same actions as are done in the non-default
// constructor.  If this object has already been initialized, it is
// an error.  For initialize, you must supply a layout instance.
template<class PLayout>
void IpplParticleBase<PLayout>::initialize(PLayout *layout) {
 
  // make sure we have not already been initialized, and that we have
  // been given a good layout
  PAssert(Layout == 0);
  PAssert(layout != 0);
 
  // save the layout, and perform setup tasks
  Layout = layout;
  setup();
}
 
 
// set up this new object:  add attributes and check in to the layout
template<class PLayout>
void IpplParticleBase<PLayout>::setup() {
 
  TotalNum = 0;
  LocalNum = 0;
  DestroyNum = 0;
  GhostNum = 0;
 
  // shift ID back so that first ID retrieved is myNode
  NextID = Ippl::Comm->myNode() - Ippl::Comm->getNodes();
 
  // Create position R and index ID attributes for the particles,
  // and add them to our list of attributes.
  addAttribute(R);
  addAttribute(ID);
 
  // set pointer for base class AbstractParticle
  this->R_p  = &R;
  this->ID_p = &ID;
  
  // indicate we have created a new IpplParticleBase object
  INCIPPLSTAT(incIpplParticleBases);
}
 
 
// Return a boolean value indicating if we are on a processor which can
// be used for single-node particle creation and initialization
 
template<class PLayout>
bool IpplParticleBase<PLayout>::singleInitNode() const {
    return (Ippl::Comm->myNode() == 0);
}
 
// Return a new unique ID value for use by new particles.
// The ID number = (i * numprocs) + myproc, i = 0, 1, 2, ...
template<class PLayout>
unsigned IpplParticleBase<PLayout>::getNextID() {
 
 
 
  return (NextID += Ippl::Comm->getNodes());
}
 
// Reset the particle ID's to be globally consecutive, 0 thru TotalNum.
template <class PLayout>
void IpplParticleBase<PLayout>::resetID(void) {
 
 
 
  unsigned int nodes = Ippl::getNodes();
  unsigned int myNode = Ippl::myNode();
  size_t localNum = this->getLocalNum();
  size_t ip;
  int master = 0;
  if (myNode == (unsigned int) master) {
    // Node 0 can immediately set its ID's to 0 thru LocalNum-1
    for (ip=0; ip<localNum; ++ip)
      this->ID[ip] = ip;
    // if there is only one processor, we are done
    if (nodes == 1) return;
    // parallel case: must find out how many particles each processor has
    // Node 0 gathers this information into an array
    size_t *lp;
    lp = new size_t[nodes];
    lp[0] = localNum;  // enter our own number of particles
    // get next message tag and receive messages
    int tag1 = Ippl::Comm->next_tag(P_RESET_ID_TAG,P_LAYOUT_CYCLE);
    Message* msg1;
    for (ip=1; ip<nodes; ++ip) {
      int rnode = COMM_ANY_NODE;
      msg1 = Ippl::Comm->receive_block(rnode,tag1);
      PAssert(msg1);
      msg1->get(lp[rnode]);
      delete msg1;
    }
    // now we should have all the localnum values.
    // figure out starting ID for each processor and send back
    size_t current, sum = 0;
    for (ip=0; ip<nodes; ++ip) {
      current = lp[ip];
      lp[ip] = sum;
      sum += current;
    }
    // send initial ID values back out
    int tag2 = Ippl::Comm->next_tag(P_RESET_ID_TAG,P_LAYOUT_CYCLE);
    for (ip=1; ip<nodes; ++ip) {
      Message* msg2 = new Message;
      msg2->put(lp[ip]);
      bool success = Ippl::Comm->send(msg2,ip,tag2);
      if (success == false) {
              throw IpplException (
                      "IpplParticleBase<PLayout>::resetID()",
                      "sending initial ID values failed.");
      }
    }
    // we are done
    return;
  }
  else {
    // first send number of local particles to Node 0
    int tag1 = Ippl::Comm->next_tag(P_RESET_ID_TAG,P_LAYOUT_CYCLE);
    Message* msg1 = new Message;
    msg1->put(localNum);
    bool success = Ippl::Comm->send(msg1,master,tag1);
    if (success == false) {
            throw IpplException (
                    "IpplParticleBase<PLayout>::resetID()",
                    "sending initial ID values failed.");
    }
    // now receive back our initial ID number
    size_t initialID = 0;
    int tag2 = Ippl::Comm->next_tag(P_RESET_ID_TAG,P_LAYOUT_CYCLE);
    Message* msg2 = Ippl::Comm->receive_block(master,tag2);
    PAssert(msg2);
    msg2->get(initialID);
    delete msg2;
    // now reset our particle ID's using this initial value
    for (ip=0; ip<localNum; ++ip)
      this->ID[ip] = ip + initialID;
    // we are done
    return;
  }
}
 
 
// put the data for M particles starting from local index I in a Message
template<class PLayout>
size_t
IpplParticleBase<PLayout>::putMessage(Message& msg, size_t M, size_t I) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // put into message the number of items in the message
  msg.put(M);
 
  // go through all the attributes and put their data in the message
  if (M > 0) {
    // this routine should only be called for local particles; call
    // ghostPutMessage to put in particles which might be ghost particles
    PAssert_LT(I, R.size());
    PAssert_LE(I + M, R.size());
 
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; abeg++ )
      (*abeg)->putMessage(msg, M, I);
  }
 
  return M;
}
 
 
// put the data for a list of particles in a Message
template<class PLayout>
size_t
IpplParticleBase<PLayout>::putMessage(Message& msg,
                                  const std::vector<size_t>& putList)
{
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  std::vector<size_t>::size_type M = putList.size();
  msg.put(M);
 
  // go through all the attributes and put their data in the message
  if (M > 0) {
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; ++abeg )
      (*abeg)->putMessage(msg, putList);
  }
 
  return M;
}
 
template<class PLayout>
size_t
IpplParticleBase<PLayout>::putMessage(Message& msg, size_t I) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // put into message the number of items in the message
 
  // go through all the attributes and put their data in the message
 
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; abeg++ )
      (*abeg)->putMessage(msg, 1, I);
 
 return 1;
}
 
template<class PLayout>
Format* IpplParticleBase<PLayout>::getFormat()
{
        //create dummy particle so we can obtain the format
    bool wasempty = false;
    if(this->getLocalNum()==0)
    {
                this->create(1);
                wasempty = true;
        }
 
        //obtain the format
    Message *msg = new Message;
    this->putMessage(*msg, (size_t) 0);
    Format *format = new Format(msg);
    delete msg;
 
        //remove the dummy particle again
    if (wasempty)
        this->destroy(1, 0, true);
 
    return format;
}
 
template<class PLayout>
size_t
IpplParticleBase<PLayout>::writeMsgBuffer(MsgBuffer *&msgbuf, const std::vector<size_t> &list)
{
    msgbuf = new MsgBuffer(this->getFormat(), list.size());
 
    for (unsigned int i = 0;i<list.size();++i)
    {
        Message msg;
        this->putMessage(msg, list[i]);
        msgbuf->add(&msg);
    }
    return list.size();
}
 
template<class PLayout>
template<class O>
size_t
IpplParticleBase<PLayout>::writeMsgBufferWithOffsets(MsgBuffer *&msgbuf, const std::vector<size_t> &list, const std::vector<O> &offset)
 {
     msgbuf = new MsgBuffer(this->getFormat(), list.size());
     typename PLayout::SingleParticlePos_t oldpos;
     for (unsigned int i = 0;i<list.size();++i)
         {
             oldpos = R[list[i]];
             for(int d = 0;d<Dim;++d)
                 {
                     R[list[i]][d] += offset[i][d];
                 }
 
             Message msg;
             this->putMessage(msg, list[i]);
             msgbuf->add(&msg);
 
             R[list[i]] = oldpos;
         }
     return list.size();
 }
 
template<class PLayout>
size_t
IpplParticleBase<PLayout>::readMsgBuffer(MsgBuffer *msgbuf)
{
        size_t added = 0;
        Message *msg = msgbuf->get();
    while (msg != 0)
    {
                added += this->getSingleMessage(*msg);
        delete msg;
        msg = msgbuf->get();
    }
    return added;
}
 
 
template<class PLayout>
size_t
IpplParticleBase<PLayout>::readGhostMsgBuffer(MsgBuffer *msgbuf, int node)
{
        size_t added = 0;
        Message *msg = msgbuf->get();
    while (msg != 0)
    {
                added += this->ghostGetSingleMessage(*msg, node);
        delete msg;
        msg = msgbuf->get();
    }
    return added;
}
 
// retrieve particles from the given message and store them
template<class PLayout>
size_t IpplParticleBase<PLayout>::getMessage(Message& msg) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // get the number of items in the message
  size_t numitems = 0;
  msg.get(numitems);
 
  // go through all the attributes and get their data from the message
  if (numitems > 0) {
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; abeg++ )
      (*abeg)->getMessage(msg, numitems);
  }
 
  return numitems;
}
 
// retrieve particles from the given message and store them
template<class PLayout>
size_t IpplParticleBase<PLayout>::getSingleMessage(Message& msg) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // get the number of items in the message
  size_t numitems=1;
 
  // go through all the attributes and get their data from the message
  if (numitems > 0) {
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; abeg++ )
      (*abeg)->getMessage(msg, numitems);
  }
 
  return numitems;
}
 
 
// retrieve particles from the given message and store them, also
// signaling we are creating the given number of particles.  Return the
// number of particles created.
template<class PLayout>
size_t IpplParticleBase<PLayout>::getMessageAndCreate(Message& msg) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // call the regular create, and add in the particles to our LocalNum
  size_t numcreate = getMessage(msg);
  LocalNum += numcreate;
  ADDIPPLSTAT(incParticlesCreated,numcreate);
  return numcreate;
}
 
 
// create M new particles on this processor
template<class PLayout>
void IpplParticleBase<PLayout>::create(size_t M) {
 
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // go through all the attributes, and allocate space for M new particles
  attrib_container_t::iterator abeg = AttribList.begin();
  attrib_container_t::iterator aend = AttribList.end();
  for ( ; abeg != aend; abeg++ )
    (*abeg)->create(M);
 
  // set the unique ID value for these new particles
  size_t i1 = LocalNum;
  size_t i2 = i1 + M;
  while (i1 < i2)
    ID[i1++] = getNextID();
 
  // remember that we're creating these new particles
  LocalNum += M;
  ADDIPPLSTAT(incParticlesCreated,M);
}
 
 
// create 1 new particle with a given ID
template<class PLayout>
void IpplParticleBase<PLayout>::createWithID(unsigned id) {
 
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // go through all the attributes, and allocate space for M new particles
  attrib_container_t::iterator abeg = AttribList.begin();
  attrib_container_t::iterator aend = AttribList.end();
  for ( ; abeg != aend; abeg++ )
    (*abeg)->create(1);
 
  const size_t M = 1;
  // set the unique ID value for these new particles
  size_t i1 = LocalNum;
  size_t i2 = i1 + M;
  while (i1 < i2)
      ID[i1++] = id;
 
  // remember that we're creating these new particles
  LocalNum += M;
   ADDIPPLSTAT(incParticlesCreated,1);
}
 
 
// create np new particles globally, equally distributed among all processors
template<class PLayout>
void IpplParticleBase<PLayout>::globalCreate(size_t np) {
 
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // Compute the number of particles local to each processor:
  unsigned nPE = IpplInfo::getNodes();
  unsigned npLocal = np/nPE;
 
  // Handle the case where np/nPE is not an integer:
  unsigned myPE = IpplInfo::myNode();
  unsigned rem = np - npLocal * nPE;
  if (myPE < rem) ++npLocal;
 
  // Now each PE calls the local IpplParticleBase::create() function to create it's
  // local number of particles:
  create(npLocal);
}
 
 
// delete M particles, starting with the Ith particle.  If the last argument
// is true, the destroy will be done immediately, otherwise the request
// will be cached.
template<class PLayout>
void IpplParticleBase<PLayout>::destroy(size_t M, size_t I, bool doNow) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  if (M > 0) {
    if (doNow) {
      // find out if we are using optimized destroy method
      bool optDestroy = getUpdateFlag(PLayout::OPTDESTROY);
      // loop over attributes and carry out the destroy request
      attrib_container_t::iterator abeg, aend = AttribList.end();
      for (abeg = AttribList.begin(); abeg != aend; ++abeg)
        (*abeg)->destroy(M,I,optDestroy);
      LocalNum -= M;
    }
    else {
      // add this group of particle indices to our list of items to destroy
      std::pair<size_t,size_t> destroyEvent(I,M);
      DestroyList.push_back(destroyEvent);
      DestroyNum += M;
    }
 
    // remember we have this many more items to destroy (or have destroyed)
    ADDIPPLSTAT(incParticlesDestroyed,M);
  }
}
 
 
// Update the particle object after a timestep.  This routine will change
// our local, total, create particle counts properly.
template<class PLayout>
void IpplParticleBase<PLayout>::update() {
 
 
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // ask the layout manager to update our atoms, etc.
  Layout->update(*this);
  INCIPPLSTAT(incParticleUpdates);
}
 
 
// Update the particle object after a timestep.  This routine will change
// our local, total, create particle counts properly.
template<class PLayout>
void IpplParticleBase<PLayout>::update(const ParticleAttrib<char>& canSwap) {
 
 
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // ask the layout manager to update our atoms, etc.
  Layout->update(*this, &canSwap);
  INCIPPLSTAT(incParticleUpdates);
}
 
 
// Actually perform the delete atoms action for all the attributes; the
// calls to destroy() only stored a list of what to do.  This actually
// does it.  This should in most cases only be called by the layout manager.
template<class PLayout>
void IpplParticleBase<PLayout>::performDestroy(bool updateLocalNum) {
 
 
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // nothing to do if destroy list is empty
  if (DestroyList.empty()) return;
 
  // before processing the list, we should make sure it is sorted
  bool isSorted = true;
  typedef std::vector< std::pair<size_t,size_t> > dlist_t;
  dlist_t::const_iterator curr = DestroyList.begin();
  const dlist_t::const_iterator last = DestroyList.end();
  dlist_t::const_iterator next = curr + 1;
  while (next != last && isSorted) {
    if (*next++ < *curr++) isSorted = false;
  }
  if (!isSorted)
    std::sort(DestroyList.begin(),DestroyList.end());
 
  // find out if we are using optimized destroy method
  bool optDestroy = getUpdateFlag(PLayout::OPTDESTROY);
 
  // loop over attributes and process destroy list
  attrib_container_t::iterator abeg, aend = AttribList.end();
  for (abeg = AttribList.begin(); abeg != aend; ++abeg)
    (*abeg)->destroy(DestroyList,optDestroy);
 
  if (updateLocalNum) {
      for (curr = DestroyList.begin(); curr != last; ++ curr) {
          LocalNum -= curr->second;
      }
  }
 
  // clear destroy list and update destroy num counter
  DestroyList.erase(DestroyList.begin(),DestroyList.end());
  DestroyNum = 0;
}
 
 
// delete M ghost particles, starting with the Ith particle.
// This is done immediately.
template<class PLayout>
void IpplParticleBase<PLayout>::ghostDestroy(size_t M, size_t I) {
 
 
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  if (M > 0) {
    // delete the data from the attribute containers
    size_t dnum = 0;
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; ++abeg )
      dnum = (*abeg)->ghostDestroy(M, I);
    GhostNum -= dnum;
  }
}
 
 
// Put the data for M particles starting from local index I in a Message.
// Return the number of particles put in the Message.  This is for building
// ghost particle interaction lists.
template<class PLayout>
size_t
IpplParticleBase<PLayout>::ghostPutMessage(Message &msg, size_t M, size_t I) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // put into message the number of items in the message
  if (I >= R.size()) {
    // we're putting in ghost particles ...
    if ((I + M) > (R.size() + GhostNum))
      M = (R.size() + GhostNum) - I;
  } else {
    // we're putting in local particles ...
    if ((I + M) > R.size())
      M = R.size() - I;
  }
  msg.put(M);
 
  // go through all the attributes and put their data in the message
  if (M > 0) {
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; abeg++ )
      (*abeg)->ghostPutMessage(msg, M, I);
  }
 
  return M;
}
 
 
// put the data for particles on a list into a Message, given list of indices
// Return the number of particles put in the Message.  This is for building
// ghost particle interaction lists.
template<class PLayout>
size_t
IpplParticleBase<PLayout>::ghostPutMessage(Message &msg,
                                       const std::vector<size_t>& pl) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  std::vector<size_t>::size_type M = pl.size();
  msg.put(M);
 
  // go through all the attributes and put their data in the message
  if (M > 0) {
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; ++abeg )
      (*abeg)->ghostPutMessage(msg, pl);
  }
 
  return M;
}
 
 
// retrieve particles from the given message and sending node and store them
template<class PLayout>
size_t
IpplParticleBase<PLayout>::ghostGetMessage(Message& msg, int /*node*/) {
 
 
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // get the number of items in the message
  size_t numitems;
  msg.get(numitems);
  GhostNum += numitems;
 
  // go through all the attributes and get their data from the message
  if (numitems > 0) {
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; abeg++ )
      (*abeg)->ghostGetMessage(msg, numitems);
  }
 
  return numitems;
}
 
template<class PLayout>
size_t
IpplParticleBase<PLayout>::ghostGetSingleMessage(Message& msg, int /*node*/) {
 
  // make sure we've been initialized
  PAssert(Layout != 0);
 
  // get the number of items in the message
  size_t numitems=1;
  GhostNum += numitems;
 
  // go through all the attributes and get their data from the message
  if (numitems > 0) {
    attrib_container_t::iterator abeg = AttribList.begin();
    attrib_container_t::iterator aend = AttribList.end();
    for ( ; abeg != aend; abeg++ )
      (*abeg)->ghostGetMessage(msg, numitems);
  }
 
  return numitems;
}
 
// Apply the given sort-list to all the attributes.  The sort-list
// may be temporarily modified, thus it must be passed by non-const ref.
template<class PLayout>
void IpplParticleBase<PLayout>::sort(SortList_t &sortlist) {
  attrib_container_t::iterator abeg = AttribList.begin();
  attrib_container_t::iterator aend = AttribList.end();
  for ( ; abeg != aend; ++abeg )
    (*abeg)->sort(sortlist);
}
 
 
// print it out
template<class PLayout>
std::ostream& operator<<(std::ostream& out, const IpplParticleBase<PLayout>& P) {
 
 
  out << "Particle object contents:";
  out << "\n  Total particles: " << P.getTotalNum();
  out << "\n  Local particles: " << P.getLocalNum();
  out << "\n  Attributes (including R and ID): " << P.numAttributes();
  out << "\n  Layout = " << P.getLayout();
  return out;
}
 
 
// print out debugging information
template<class PLayout>
void IpplParticleBase<PLayout>::printDebug(Inform& o) {
 
  o << "PBase: total = " << getTotalNum() << ", local = " << getLocalNum();
  o << ", attributes = " << AttribList.size() << endl;
  for (attrib_container_t::size_type i=0; i < AttribList.size(); ++i) {
    o << "    ";
    AttribList[i]->printDebug(o);
    o << endl;
  }
  o << "    ";
  Layout->printDebug(o);
}