src/io/DumpWriter.cpp

/*
 * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "io/DumpWriter.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "io/basic_teebuf.hpp"
#include "io/gzstream.hpp"
#include "io/Globals.hpp"


#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

using namespace std;
namespace OpenMD {

  DumpWriter::DumpWriter(SimInfo* info) 
    : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){

    Globals* simParams = info->getSimParams();
    needCompression_ = simParams->getCompressDumpFile();
    needForceVector_ = simParams->getOutputForceVector();
    needParticlePot_ = simParams->getOutputParticlePotential();
    cerr << "DW npp = " << needParticlePot_ << "\n";
    createDumpFile_ = true;
#ifdef HAVE_LIBZ
    if (needCompression_) {
      filename_ += ".gz";
      eorFilename_ += ".gz";
    }
#endif
    
#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi
        
      dumpFile_ = createOStream(filename_);

      if (!dumpFile_) {
        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                filename_.c_str());
        painCave.isFatal = 1;
        simError();
      }

#ifdef IS_MPI

    }

#endif // is_mpi

  }


  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) 
    : info_(info), filename_(filename){

    Globals* simParams = info->getSimParams();
    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    

    needCompression_ = simParams->getCompressDumpFile();
    needForceVector_ = simParams->getOutputForceVector();
    createDumpFile_ = true;
#ifdef HAVE_LIBZ
    if (needCompression_) {
      filename_ += ".gz";
      eorFilename_ += ".gz";
    }
#endif
    
#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

      
      dumpFile_ = createOStream(filename_);

      if (!dumpFile_) {
        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                filename_.c_str());
        painCave.isFatal = 1;
        simError();
      }

#ifdef IS_MPI

    }

#endif // is_mpi

  }
  
  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile) 
    : info_(info), filename_(filename){
    
    Globals* simParams = info->getSimParams();
    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
    
    needCompression_ = simParams->getCompressDumpFile();
    needForceVector_ = simParams->getOutputForceVector();
    needParticlePot_ = simParams->getOutputParticlePotential();
    
#ifdef HAVE_LIBZ
    if (needCompression_) {
      filename_ += ".gz";
      eorFilename_ += ".gz";
    }
#endif
    
#ifdef IS_MPI
    
    if (worldRank == 0) {
#endif // is_mpi
      
      createDumpFile_ = writeDumpFile;
      if (createDumpFile_) {
        dumpFile_ = createOStream(filename_);
      
        if (!dumpFile_) {
          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                  filename_.c_str());
          painCave.isFatal = 1;
          simError();
        }
      }
#ifdef IS_MPI
      
    }

    
#endif // is_mpi
    
  }

  DumpWriter::~DumpWriter() {

#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi
      if (createDumpFile_){
        writeClosing(*dumpFile_);
        delete dumpFile_;
      }
#ifdef IS_MPI

    }

#endif // is_mpi

  }

  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {

    char buffer[1024];

    os << "    <FrameData>\n";

    RealType currentTime = s->getTime();

    if (isinf(currentTime) || isnan(currentTime)) {      
      sprintf( painCave.errMsg,
               "DumpWriter detected a numerical error writing the time");      
      painCave.isFatal = 1;
      simError();
    }
    
    sprintf(buffer, "        Time: %.10g\n", currentTime);
    os << buffer;

    Mat3x3d hmat;
    hmat = s->getHmat();

    for (unsigned int i = 0; i < 3; i++) {
      for (unsigned int j = 0; j < 3; j++) {
        if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {      
          sprintf( painCave.errMsg,
                   "DumpWriter detected a numerical error writing the box");
          painCave.isFatal = 1;
          simError();
        }        
      }
    }
    
    sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", 
            hmat(0, 0), hmat(1, 0), hmat(2, 0), 
            hmat(0, 1), hmat(1, 1), hmat(2, 1),
            hmat(0, 2), hmat(1, 2), hmat(2, 2));
    os << buffer;

    RealType chi = s->getChi();
    RealType integralOfChiDt = s->getIntegralOfChiDt();
    if (isinf(chi) || isnan(chi) || 
        isinf(integralOfChiDt) || isnan(integralOfChiDt)) {      
      sprintf( painCave.errMsg,
               "DumpWriter detected a numerical error writing the thermostat");
      painCave.isFatal = 1;
      simError();
    }
    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
    os << buffer;

    Mat3x3d eta;
    eta = s->getEta();

    for (unsigned int i = 0; i < 3; i++) {
      for (unsigned int j = 0; j < 3; j++) {
        if (isinf(eta(i,j)) || isnan(eta(i,j))) {      
          sprintf( painCave.errMsg,
                   "DumpWriter detected a numerical error writing the barostat");
          painCave.isFatal = 1;
          simError();
        }        
      }
    }

    sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
            eta(0, 0), eta(1, 0), eta(2, 0), 
            eta(0, 1), eta(1, 1), eta(2, 1),
            eta(0, 2), eta(1, 2), eta(2, 2));
    os << buffer;

    os << "    </FrameData>\n";
  }

  void DumpWriter::writeFrame(std::ostream& os) {

#ifdef IS_MPI
    MPI_Status istatus;
#endif

    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator ii;

#ifndef IS_MPI
    os << "  <Snapshot>\n";
 
    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());

    os << "    <StuntDoubles>\n";
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {

      
      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
           integrableObject = mol->nextIntegrableObject(ii)) {  
          os << prepareDumpLine(integrableObject);
          
      }
    }    
    os << "    </StuntDoubles>\n";
    
    os << "  </Snapshot>\n";

    os.flush();
#else
    //every node prepares the dump lines for integrable objects belong to itself
    std::string buffer;
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {


      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(ii)) {  
          buffer += prepareDumpLine(integrableObject);
      }
    }
    
    const int masterNode = 0;
    int nProc;
    MPI_Comm_size(MPI_COMM_WORLD, &nProc);
    if (worldRank == masterNode) {      
      os << "  <Snapshot>\n";   
      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
      os << "    <StuntDoubles>\n";
        
      os << buffer;

      for (int i = 1; i < nProc; ++i) {

        // receive the length of the string buffer that was
        // prepared by processor i

        MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
        int recvLength;
        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
        char* recvBuffer = new char[recvLength];
        if (recvBuffer == NULL) {
        } else {
          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
          os << recvBuffer;
          delete [] recvBuffer;
        }
      } 
      os << "    </StuntDoubles>\n";
      
      os << "  </Snapshot>\n";
      os.flush();
    } else {
      int sendBufferLength = buffer.size() + 1;
      int myturn = 0;
      for (int i = 1; i < nProc; ++i){
        MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
        if (myturn == worldRank){
          MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
          MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
        }
      }
    }

#endif // is_mpi

  }

  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
        
    int index = integrableObject->getGlobalIntegrableObjectIndex();
    std::string type("pv");
    std::string line;
    char tempBuffer[4096];

    Vector3d pos;
    Vector3d vel;
    pos = integrableObject->getPos();

    if (isinf(pos[0]) || isnan(pos[0]) || 
        isinf(pos[1]) || isnan(pos[1]) || 
        isinf(pos[2]) || isnan(pos[2]) ) {      
      sprintf( painCave.errMsg,
               "DumpWriter detected a numerical error writing the position"
               " for object %d", index);      
      painCave.isFatal = 1;
      simError();
    }

    vel = integrableObject->getVel();           

    if (isinf(vel[0]) || isnan(vel[0]) || 
        isinf(vel[1]) || isnan(vel[1]) || 
        isinf(vel[2]) || isnan(vel[2]) ) {      
      sprintf( painCave.errMsg,
               "DumpWriter detected a numerical error writing the velocity"
               " for object %d", index);      
      painCave.isFatal = 1;
      simError();
    }

    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", 
            pos[0], pos[1], pos[2],
            vel[0], vel[1], vel[2]);                    
    line += tempBuffer;

    if (integrableObject->isDirectional()) {
      type += "qj";
      Quat4d q;
      Vector3d ji;
      q = integrableObject->getQ();

      if (isinf(q[0]) || isnan(q[0]) || 
          isinf(q[1]) || isnan(q[1]) || 
          isinf(q[2]) || isnan(q[2]) || 
          isinf(q[3]) || isnan(q[3]) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the quaternion"
                 " for object %d", index);      
        painCave.isFatal = 1;
        simError();
      }

      ji = integrableObject->getJ();

      if (isinf(ji[0]) || isnan(ji[0]) || 
          isinf(ji[1]) || isnan(ji[1]) || 
          isinf(ji[2]) || isnan(ji[2]) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the angular"
                 " momentum for object %d", index);      
        painCave.isFatal = 1;
        simError();
      }

      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
              q[0], q[1], q[2], q[3],
              ji[0], ji[1], ji[2]);
      line += tempBuffer;
    }

    if (needForceVector_) {
      type += "f";
      Vector3d frc;

      frc = integrableObject->getFrc();

      if (isinf(frc[0]) || isnan(frc[0]) || 
          isinf(frc[1]) || isnan(frc[1]) || 
          isinf(frc[2]) || isnan(frc[2]) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the force"
                 " for object %d", index);      
        painCave.isFatal = 1;
        simError();
      }
      sprintf(tempBuffer, " %13e %13e %13e",
              frc[0], frc[1], frc[2]);
      line += tempBuffer;
      
      if (integrableObject->isDirectional()) {
        type += "t";
        Vector3d trq;
        
        trq = integrableObject->getTrq();
        
        if (isinf(trq[0]) || isnan(trq[0]) || 
            isinf(trq[1]) || isnan(trq[1]) || 
            isinf(trq[2]) || isnan(trq[2]) ) {      
          sprintf( painCave.errMsg,
                   "DumpWriter detected a numerical error writing the torque"
                   " for object %d", index);      
          painCave.isFatal = 1;
          simError();
        }
        
        sprintf(tempBuffer, " %13e %13e %13e",
                trq[0], trq[1], trq[2]);
        line += tempBuffer;
      }      
    }
    if (needParticlePot_) {
      type += "u";
      RealType particlePot;

      particlePot = integrableObject->getParticlePot();

      if (isinf(particlePot) || isnan(particlePot)) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the particle "
                 " potential for object %d", index);      
        painCave.isFatal = 1;
        simError();
      }
      sprintf(tempBuffer, " %13e", particlePot);
      line += tempBuffer;
    }
    
    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
    return std::string(tempBuffer);
  }

  void DumpWriter::writeDump() {
    writeFrame(*dumpFile_);
  }

  void DumpWriter::writeEor() {
    std::ostream* eorStream;
    
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

      eorStream = createOStream(eorFilename_);

#ifdef IS_MPI
    }
#endif // is_mpi    

    writeFrame(*eorStream);

#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi
      writeClosing(*eorStream);
      delete eorStream;
#ifdef IS_MPI
    }
#endif // is_mpi  

  }


  void DumpWriter::writeDumpAndEor() {
    std::vector<std::streambuf*> buffers;
    std::ostream* eorStream;
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

      buffers.push_back(dumpFile_->rdbuf());

      eorStream = createOStream(eorFilename_);

      buffers.push_back(eorStream->rdbuf());
        
#ifdef IS_MPI
    }
#endif // is_mpi    

    TeeBuf tbuf(buffers.begin(), buffers.end());
    std::ostream os(&tbuf);

    writeFrame(os);

#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi
      writeClosing(*eorStream);
      delete eorStream;
#ifdef IS_MPI
    }
#endif // is_mpi  
    
  }

  std::ostream* DumpWriter::createOStream(const std::string& filename) {

    std::ostream* newOStream;
#ifdef HAVE_LIBZ 
    if (needCompression_) {
      newOStream = new ogzstream(filename.c_str());
    } else {
      newOStream = new std::ofstream(filename.c_str());
    }
#else
    newOStream = new std::ofstream(filename.c_str());
#endif
    //write out MetaData first
    (*newOStream) << "<OpenMD version=1>" << std::endl;
    (*newOStream) << "  <MetaData>" << std::endl;
    (*newOStream) << info_->getRawMetaData();
    (*newOStream) << "  </MetaData>" << std::endl;
    return newOStream;
  }

  void DumpWriter::writeClosing(std::ostream& os) {

    os << "</OpenMD>\n";
    os.flush();
  }

}//end namespace OpenMD
Revision:	1711
Committed:	Sat May 19 02:58:35 2012 UTC (12 years, 11 months ago) by gezelter
File size:	16419 byte(s)
Log Message:	Some fixes for DataStorage issues. Removed outdated zangle stuff that has been replaced by the more modern restraints.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	1390	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	gezelter	246	*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#include "io/DumpWriter.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "utils/simError.h"
46	tim	376	#include "io/basic_teebuf.hpp"
47	tim	615	#include "io/gzstream.hpp"
48			#include "io/Globals.hpp"
49
50	gezelter	1437
51	gezelter	2	#ifdef IS_MPI
52			#include <mpi.h>
53	gezelter	246	#endif //is_mpi
54	gezelter	2
55	gezelter	1437	using namespace std;
56	gezelter	1390	namespace OpenMD {
57	gezelter	2
58	gezelter	507	DumpWriter::DumpWriter(SimInfo* info)
59			: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
60	tim	615
61			Globals* simParams = info->getSimParams();
62			needCompression_ = simParams->getCompressDumpFile();
63	chrisfen	726	needForceVector_ = simParams->getOutputForceVector();
64	gezelter	1629	needParticlePot_ = simParams->getOutputParticlePotential();
65	gezelter	1711	cerr << "DW npp = " << needParticlePot_ << "\n";
66	chuckv	791	createDumpFile_ = true;
67	tim	619	#ifdef HAVE_LIBZ
68	tim	615	if (needCompression_) {
69	tim	1024	filename_ += ".gz";
70			eorFilename_ += ".gz";
71	tim	615	}
72	tim	619	#endif
73	tim	615
74	tim	376	#ifdef IS_MPI
75
76	tim	1024	if (worldRank == 0) {
77	tim	376	#endif // is_mpi
78	chuckv	791
79	tim	1024	dumpFile_ = createOStream(filename_);
80	tim	615
81	tim	1024	if (!dumpFile_) {
82			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
83			filename_.c_str());
84			painCave.isFatal = 1;
85			simError();
86			}
87	tim	376
88			#ifdef IS_MPI
89
90	tim	1024	}
91	tim	376
92			#endif // is_mpi
93
94	tim	1024	}
95	tim	376
96
97	gezelter	507	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
98			: info_(info), filename_(filename){
99	tim	615
100			Globals* simParams = info->getSimParams();
101			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
102
103			needCompression_ = simParams->getCompressDumpFile();
104	chrisfen	726	needForceVector_ = simParams->getOutputForceVector();
105	chuckv	791	createDumpFile_ = true;
106	tim	619	#ifdef HAVE_LIBZ
107	tim	615	if (needCompression_) {
108	tim	1024	filename_ += ".gz";
109			eorFilename_ += ".gz";
110	tim	615	}
111	tim	619	#endif
112	tim	615
113	gezelter	246	#ifdef IS_MPI
114	gezelter	2
115	tim	1024	if (worldRank == 0) {
116	gezelter	246	#endif // is_mpi
117	gezelter	2
118	chuckv	791
119	tim	1024	dumpFile_ = createOStream(filename_);
120	tim	615
121	tim	1024	if (!dumpFile_) {
122			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
123			filename_.c_str());
124			painCave.isFatal = 1;
125			simError();
126			}
127	gezelter	2
128			#ifdef IS_MPI
129
130	tim	1024	}
131	gezelter	2
132			#endif // is_mpi
133	gezelter	246
134	tim	1024	}
135	chuckv	791
136			DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
137	tim	1024	: info_(info), filename_(filename){
138	chuckv	791
139			Globals* simParams = info->getSimParams();
140			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
141
142			needCompression_ = simParams->getCompressDumpFile();
143			needForceVector_ = simParams->getOutputForceVector();
144	gezelter	1629	needParticlePot_ = simParams->getOutputParticlePotential();
145	chuckv	791
146			#ifdef HAVE_LIBZ
147			if (needCompression_) {
148			filename_ += ".gz";
149			eorFilename_ += ".gz";
150			}
151			#endif
152
153			#ifdef IS_MPI
154
155			if (worldRank == 0) {
156			#endif // is_mpi
157
158			createDumpFile_ = writeDumpFile;
159			if (createDumpFile_) {
160			dumpFile_ = createOStream(filename_);
161
162			if (!dumpFile_) {
163			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
164			filename_.c_str());
165			painCave.isFatal = 1;
166			simError();
167			}
168			}
169			#ifdef IS_MPI
170
171			}
172	tim	1024
173	chuckv	791
174			#endif // is_mpi
175
176			}
177	gezelter	2
178	gezelter	507	DumpWriter::~DumpWriter() {
179	gezelter	2
180			#ifdef IS_MPI
181	gezelter	246
182			if (worldRank == 0) {
183	gezelter	2	#endif // is_mpi
184	chuckv	791	if (createDumpFile_){
185	tim	1024	writeClosing(*dumpFile_);
186	chuckv	791	delete dumpFile_;
187			}
188	gezelter	2	#ifdef IS_MPI
189	gezelter	246
190			}
191
192	gezelter	2	#endif // is_mpi
193	gezelter	246
194	gezelter	507	}
195	gezelter	2
196	tim	1024	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
197	gezelter	2
198	tim	1024	char buffer[1024];
199
200			os << " <FrameData>\n";
201
202			RealType currentTime = s->getTime();
203	gezelter	1437
204			if (isinf(currentTime) \|\| isnan(currentTime)) {
205			sprintf( painCave.errMsg,
206			"DumpWriter detected a numerical error writing the time");
207			painCave.isFatal = 1;
208			simError();
209			}
210
211	gezelter	1025	sprintf(buffer, " Time: %.10g\n", currentTime);
212	tim	1024	os << buffer;
213
214	gezelter	246	Mat3x3d hmat;
215			hmat = s->getHmat();
216	gezelter	1437
217			for (unsigned int i = 0; i < 3; i++) {
218			for (unsigned int j = 0; j < 3; j++) {
219			if (isinf(hmat(i,j)) \|\| isnan(hmat(i,j))) {
220			sprintf( painCave.errMsg,
221			"DumpWriter detected a numerical error writing the box");
222			painCave.isFatal = 1;
223			simError();
224			}
225			}
226			}
227
228	tim	1024	sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
229			hmat(0, 0), hmat(1, 0), hmat(2, 0),
230			hmat(0, 1), hmat(1, 1), hmat(2, 1),
231			hmat(0, 2), hmat(1, 2), hmat(2, 2));
232			os << buffer;
233	gezelter	2
234	tim	1024	RealType chi = s->getChi();
235			RealType integralOfChiDt = s->getIntegralOfChiDt();
236	gezelter	1437	if (isinf(chi) \|\| isnan(chi) \|\|
237			isinf(integralOfChiDt) \|\| isnan(integralOfChiDt)) {
238			sprintf( painCave.errMsg,
239			"DumpWriter detected a numerical error writing the thermostat");
240			painCave.isFatal = 1;
241			simError();
242			}
243	tim	1024	sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
244			os << buffer;
245	gezelter	246
246	tim	1024	Mat3x3d eta;
247			eta = s->getEta();
248	gezelter	1437
249			for (unsigned int i = 0; i < 3; i++) {
250			for (unsigned int j = 0; j < 3; j++) {
251			if (isinf(eta(i,j)) \|\| isnan(eta(i,j))) {
252			sprintf( painCave.errMsg,
253			"DumpWriter detected a numerical error writing the barostat");
254			painCave.isFatal = 1;
255			simError();
256			}
257			}
258			}
259
260	tim	1024	sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
261			eta(0, 0), eta(1, 0), eta(2, 0),
262			eta(0, 1), eta(1, 1), eta(2, 1),
263			eta(0, 2), eta(1, 2), eta(2, 2));
264			os << buffer;
265	gezelter	246
266	tim	1024	os << " </FrameData>\n";
267	gezelter	507	}
268	gezelter	2
269	gezelter	507	void DumpWriter::writeFrame(std::ostream& os) {
270	gezelter	246
271	tim	1024	#ifdef IS_MPI
272			MPI_Status istatus;
273			#endif
274	gezelter	246
275			Molecule* mol;
276			StuntDouble* integrableObject;
277			SimInfo::MoleculeIterator mi;
278			Molecule::IntegrableObjectIterator ii;
279	gezelter	2
280	gezelter	246	#ifndef IS_MPI
281	tim	1024	os << " <Snapshot>\n";
282	gezelter	1025
283	tim	1024	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
284	gezelter	2
285	tim	1024	os << " <StuntDoubles>\n";
286	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
287	gezelter	2
288	xsun	1217
289			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
290	tim	1024	integrableObject = mol->nextIntegrableObject(ii)) {
291	xsun	1217	os << prepareDumpLine(integrableObject);
292
293	tim	1024	}
294			}
295			os << " </StuntDoubles>\n";
296	xsun	1217
297	tim	1024	os << " </Snapshot>\n";
298	gezelter	2
299	tim	1024	os.flush();
300			#else
301			//every node prepares the dump lines for integrable objects belong to itself
302			std::string buffer;
303			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
304	xsun	1217
305
306	tim	1024	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
307			integrableObject = mol->nextIntegrableObject(ii)) {
308	xsun	1217	buffer += prepareDumpLine(integrableObject);
309	gezelter	507	}
310	gezelter	2	}
311	tim	1024
312	gezelter	246	const int masterNode = 0;
313	gezelter	1629	int nProc;
314			MPI_Comm_size(MPI_COMM_WORLD, &nProc);
315	tim	1024	if (worldRank == masterNode) {
316			os << " <Snapshot>\n";
317			writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
318			os << " <StuntDoubles>\n";
319
320	gezelter	1025	os << buffer;
321
322	tim	1024	for (int i = 1; i < nProc; ++i) {
323	gezelter	2
324	tim	1024	// receive the length of the string buffer that was
325			// prepared by processor i
326	gezelter	2
327	gezelter	1629	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
328	tim	1024	int recvLength;
329			MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
330			char* recvBuffer = new char[recvLength];
331			if (recvBuffer == NULL) {
332			} else {
333	gezelter	1025	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
334	tim	1024	os << recvBuffer;
335	gezelter	1313	delete [] recvBuffer;
336	tim	1024	}
337			}
338			os << " </StuntDoubles>\n";
339
340			os << " </Snapshot>\n";
341	gezelter	507	os.flush();
342	gezelter	246	} else {
343	gezelter	1025	int sendBufferLength = buffer.size() + 1;
344	gezelter	1629	int myturn = 0;
345			for (int i = 1; i < nProc; ++i){
346			MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
347			if (myturn == worldRank){
348			MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
349			MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
350			}
351			}
352	tim	1024	}
353	gezelter	2
354	tim	1024	#endif // is_mpi
355	gezelter	2
356	tim	1024	}
357	gezelter	2
358	tim	1024	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
359
360			int index = integrableObject->getGlobalIntegrableObjectIndex();
361			std::string type("pv");
362			std::string line;
363			char tempBuffer[4096];
364	gezelter	2
365	tim	1024	Vector3d pos;
366			Vector3d vel;
367			pos = integrableObject->getPos();
368	gezelter	1437
369			if (isinf(pos[0]) \|\| isnan(pos[0]) \|\|
370			isinf(pos[1]) \|\| isnan(pos[1]) \|\|
371			isinf(pos[2]) \|\| isnan(pos[2]) ) {
372			sprintf( painCave.errMsg,
373			"DumpWriter detected a numerical error writing the position"
374			" for object %d", index);
375			painCave.isFatal = 1;
376			simError();
377			}
378
379	tim	1024	vel = integrableObject->getVel();
380	gezelter	1437
381			if (isinf(vel[0]) \|\| isnan(vel[0]) \|\|
382			isinf(vel[1]) \|\| isnan(vel[1]) \|\|
383			isinf(vel[2]) \|\| isnan(vel[2]) ) {
384			sprintf( painCave.errMsg,
385			"DumpWriter detected a numerical error writing the velocity"
386			" for object %d", index);
387			painCave.isFatal = 1;
388			simError();
389			}
390
391	gezelter	1025	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
392	tim	1024	pos[0], pos[1], pos[2],
393			vel[0], vel[1], vel[2]);
394			line += tempBuffer;
395	gezelter	2
396	tim	1024	if (integrableObject->isDirectional()) {
397			type += "qj";
398			Quat4d q;
399			Vector3d ji;
400			q = integrableObject->getQ();
401	gezelter	1437
402			if (isinf(q[0]) \|\| isnan(q[0]) \|\|
403			isinf(q[1]) \|\| isnan(q[1]) \|\|
404			isinf(q[2]) \|\| isnan(q[2]) \|\|
405			isinf(q[3]) \|\| isnan(q[3]) ) {
406			sprintf( painCave.errMsg,
407			"DumpWriter detected a numerical error writing the quaternion"
408			" for object %d", index);
409			painCave.isFatal = 1;
410			simError();
411			}
412
413	tim	1024	ji = integrableObject->getJ();
414	gezelter	1437
415			if (isinf(ji[0]) \|\| isnan(ji[0]) \|\|
416			isinf(ji[1]) \|\| isnan(ji[1]) \|\|
417			isinf(ji[2]) \|\| isnan(ji[2]) ) {
418			sprintf( painCave.errMsg,
419			"DumpWriter detected a numerical error writing the angular"
420			" momentum for object %d", index);
421			painCave.isFatal = 1;
422			simError();
423			}
424
425	gezelter	1025	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
426	tim	1024	q[0], q[1], q[2], q[3],
427			ji[0], ji[1], ji[2]);
428			line += tempBuffer;
429			}
430	gezelter	2
431	tim	1024	if (needForceVector_) {
432	gezelter	1437	type += "f";
433	tim	1024	Vector3d frc;
434	gezelter	1437
435	tim	1024	frc = integrableObject->getFrc();
436	gezelter	1437
437			if (isinf(frc[0]) \|\| isnan(frc[0]) \|\|
438			isinf(frc[1]) \|\| isnan(frc[1]) \|\|
439			isinf(frc[2]) \|\| isnan(frc[2]) ) {
440			sprintf( painCave.errMsg,
441			"DumpWriter detected a numerical error writing the force"
442			" for object %d", index);
443			painCave.isFatal = 1;
444			simError();
445			}
446			sprintf(tempBuffer, " %13e %13e %13e",
447			frc[0], frc[1], frc[2]);
448	tim	1024	line += tempBuffer;
449	gezelter	1437
450			if (integrableObject->isDirectional()) {
451			type += "t";
452			Vector3d trq;
453
454			trq = integrableObject->getTrq();
455
456			if (isinf(trq[0]) \|\| isnan(trq[0]) \|\|
457			isinf(trq[1]) \|\| isnan(trq[1]) \|\|
458			isinf(trq[2]) \|\| isnan(trq[2]) ) {
459			sprintf( painCave.errMsg,
460			"DumpWriter detected a numerical error writing the torque"
461			" for object %d", index);
462			painCave.isFatal = 1;
463			simError();
464			}
465
466			sprintf(tempBuffer, " %13e %13e %13e",
467			trq[0], trq[1], trq[2]);
468			line += tempBuffer;
469			}
470	gezelter	246	}
471	gezelter	1629	if (needParticlePot_) {
472			type += "u";
473			RealType particlePot;
474
475			particlePot = integrableObject->getParticlePot();
476
477			if (isinf(particlePot) \|\| isnan(particlePot)) {
478			sprintf( painCave.errMsg,
479			"DumpWriter detected a numerical error writing the particle "
480			" potential for object %d", index);
481			painCave.isFatal = 1;
482			simError();
483			}
484			sprintf(tempBuffer, " %13e", particlePot);
485			line += tempBuffer;
486			}
487	gezelter	1437
488	gezelter	1025	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
489	tim	1024	return std::string(tempBuffer);
490	gezelter	507	}
491	gezelter	2
492	gezelter	507	void DumpWriter::writeDump() {
493	tim	615	writeFrame(*dumpFile_);
494	gezelter	507	}
495	tim	376
496	gezelter	507	void DumpWriter::writeEor() {
497	tim	615	std::ostream* eorStream;
498	tim	376
499			#ifdef IS_MPI
500			if (worldRank == 0) {
501			#endif // is_mpi
502
503	tim	615	eorStream = createOStream(eorFilename_);
504	tim	376
505			#ifdef IS_MPI
506			}
507			#endif // is_mpi
508
509	tim	615	writeFrame(*eorStream);
510
511			#ifdef IS_MPI
512			if (worldRank == 0) {
513			#endif // is_mpi
514	tim	1024	writeClosing(*eorStream);
515			delete eorStream;
516	tim	615	#ifdef IS_MPI
517			}
518			#endif // is_mpi
519
520	gezelter	507	}
521	tim	376
522
523	gezelter	507	void DumpWriter::writeDumpAndEor() {
524	tim	376	std::vector<std::streambuf*> buffers;
525	tim	615	std::ostream* eorStream;
526	tim	376	#ifdef IS_MPI
527			if (worldRank == 0) {
528			#endif // is_mpi
529
530	tim	615	buffers.push_back(dumpFile_->rdbuf());
531	tim	376
532	tim	615	eorStream = createOStream(eorFilename_);
533	tim	376
534	tim	615	buffers.push_back(eorStream->rdbuf());
535	tim	376
536			#ifdef IS_MPI
537			}
538			#endif // is_mpi
539
540			TeeBuf tbuf(buffers.begin(), buffers.end());
541			std::ostream os(&tbuf);
542
543			writeFrame(os);
544	tim	615
545			#ifdef IS_MPI
546			if (worldRank == 0) {
547			#endif // is_mpi
548	tim	1024	writeClosing(*eorStream);
549			delete eorStream;
550	tim	615	#ifdef IS_MPI
551			}
552			#endif // is_mpi
553	tim	376
554	gezelter	507	}
555	tim	376
556	tim	1024	std::ostream* DumpWriter::createOStream(const std::string& filename) {
557	tim	619
558	tim	615	std::ostream* newOStream;
559	tim	619	#ifdef HAVE_LIBZ
560	tim	615	if (needCompression_) {
561	tim	1024	newOStream = new ogzstream(filename.c_str());
562	tim	615	} else {
563	tim	1024	newOStream = new std::ofstream(filename.c_str());
564	tim	615	}
565	tim	619	#else
566			newOStream = new std::ofstream(filename.c_str());
567			#endif
568	tim	1024	//write out MetaData first
569	gezelter	1390	(*newOStream) << "<OpenMD version=1>" << std::endl;
570	tim	1024	(*newOStream) << " <MetaData>" << std::endl;
571			(*newOStream) << info_->getRawMetaData();
572			(*newOStream) << " </MetaData>" << std::endl;
573	tim	615	return newOStream;
574	tim	1024	}
575	tim	376
576	tim	1024	void DumpWriter::writeClosing(std::ostream& os) {
577
578	gezelter	1390	os << "</OpenMD>\n";
579	tim	1024	os.flush();
580			}
581
582	gezelter	1390	}//end namespace OpenMD