src/io/DumpWriter.cpp

/*
 * Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#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

namespace oopse {

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

    Globals* simParams = info->getSimParams();
    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) 
    : 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();
    
#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();
    sprintf(buffer, "        Time: %.10g\n", time);
    os << buffer;

    Mat3x3d hmat;
    hmat = s->getHmat();
    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();
    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
    os << buffer;

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

    if (worldRank == masterNode) {      
      os << "  <Snapshot>\n";   
      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
      os << buffer;     
      os << "    <StuntDoubles>\n";
        
      int nProc;
      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
      for (int i = 1; i < nProc; ++i) {

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

        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();
      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();
    vel = integrableObject->getVel();           
    sprintf(tempBuffer, "%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g", 
            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();
      ji = integrableObject->getJ();
      sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g",
              q[0], q[1], q[2], q[3],
              ji[0], ji[1], ji[2]);
      line += tempBuffer;
    }

    if (needForceVector_) {
      type += "ft";
      Vector3d frc;
      Vector3d trq;
      frc = integrableObject->getFrc();
      trq = integrableObject->getTrq();
              
      sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g",
              frc[0], frc[1], frc[2],
              trq[0], trq[1], trq[2]);
      line += tempBuffer;
    }
        
    sprintf(tempBuffer, "%d\t%s\t%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) << "<OOPSE version=4>" << std::endl;
    (*newOStream) << "  <MetaData>" << std::endl;
    (*newOStream) << info_->getRawMetaData();
    (*newOStream) << "  </MetaData>" << std::endl;
    return newOStream;
  }

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

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

}//end namespace oopse
Revision:	1024
Committed:	Wed Aug 30 18:42:29 2006 UTC (19 years, 2 months ago) by tim
File size:	11857 byte(s)
Log Message:	Massive changes preparing for release of OOPSE-4: The main difference is that the new MD file format (.md, .dump, .eor) now contains meta-data information along with the configuration information.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "io/DumpWriter.hpp"
43			#include "primitives/Molecule.hpp"
44			#include "utils/simError.h"
45	tim	376	#include "io/basic_teebuf.hpp"
46	tim	615	#include "io/gzstream.hpp"
47			#include "io/Globals.hpp"
48
49	gezelter	2	#ifdef IS_MPI
50			#include <mpi.h>
51	gezelter	246	#endif //is_mpi
52	gezelter	2
53	gezelter	246	namespace oopse {
54	gezelter	2
55	gezelter	507	DumpWriter::DumpWriter(SimInfo* info)
56			: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
57	tim	615
58			Globals* simParams = info->getSimParams();
59			needCompression_ = simParams->getCompressDumpFile();
60	chrisfen	726	needForceVector_ = simParams->getOutputForceVector();
61	chuckv	791	createDumpFile_ = true;
62	tim	619	#ifdef HAVE_LIBZ
63	tim	615	if (needCompression_) {
64	tim	1024	filename_ += ".gz";
65			eorFilename_ += ".gz";
66	tim	615	}
67	tim	619	#endif
68	tim	615
69	tim	376	#ifdef IS_MPI
70
71	tim	1024	if (worldRank == 0) {
72	tim	376	#endif // is_mpi
73	chuckv	791
74	tim	1024	dumpFile_ = createOStream(filename_);
75	tim	615
76	tim	1024	if (!dumpFile_) {
77			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
78			filename_.c_str());
79			painCave.isFatal = 1;
80			simError();
81			}
82	tim	376
83			#ifdef IS_MPI
84
85	tim	1024	}
86	tim	376
87			#endif // is_mpi
88
89	tim	1024	}
90	tim	376
91
92	gezelter	507	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
93			: info_(info), filename_(filename){
94	tim	615
95			Globals* simParams = info->getSimParams();
96			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
97
98			needCompression_ = simParams->getCompressDumpFile();
99	chrisfen	726	needForceVector_ = simParams->getOutputForceVector();
100	chuckv	791	createDumpFile_ = true;
101	tim	619	#ifdef HAVE_LIBZ
102	tim	615	if (needCompression_) {
103	tim	1024	filename_ += ".gz";
104			eorFilename_ += ".gz";
105	tim	615	}
106	tim	619	#endif
107	tim	615
108	gezelter	246	#ifdef IS_MPI
109	gezelter	2
110	tim	1024	if (worldRank == 0) {
111	gezelter	246	#endif // is_mpi
112	gezelter	2
113	chuckv	791
114	tim	1024	dumpFile_ = createOStream(filename_);
115	tim	615
116	tim	1024	if (!dumpFile_) {
117			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
118			filename_.c_str());
119			painCave.isFatal = 1;
120			simError();
121			}
122	gezelter	2
123			#ifdef IS_MPI
124
125	tim	1024	}
126	gezelter	2
127			#endif // is_mpi
128	gezelter	246
129	tim	1024	}
130	chuckv	791
131			DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
132	tim	1024	: info_(info), filename_(filename){
133	chuckv	791
134			Globals* simParams = info->getSimParams();
135			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
136
137			needCompression_ = simParams->getCompressDumpFile();
138			needForceVector_ = simParams->getOutputForceVector();
139
140			#ifdef HAVE_LIBZ
141			if (needCompression_) {
142			filename_ += ".gz";
143			eorFilename_ += ".gz";
144			}
145			#endif
146
147			#ifdef IS_MPI
148
149			if (worldRank == 0) {
150			#endif // is_mpi
151
152			createDumpFile_ = writeDumpFile;
153			if (createDumpFile_) {
154			dumpFile_ = createOStream(filename_);
155
156			if (!dumpFile_) {
157			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
158			filename_.c_str());
159			painCave.isFatal = 1;
160			simError();
161			}
162			}
163			#ifdef IS_MPI
164
165			}
166	tim	1024
167	chuckv	791
168			#endif // is_mpi
169
170			}
171	gezelter	2
172	gezelter	507	DumpWriter::~DumpWriter() {
173	gezelter	2
174			#ifdef IS_MPI
175	gezelter	246
176			if (worldRank == 0) {
177	gezelter	2	#endif // is_mpi
178	chuckv	791	if (createDumpFile_){
179	tim	1024	writeClosing(*dumpFile_);
180	chuckv	791	delete dumpFile_;
181			}
182	gezelter	2	#ifdef IS_MPI
183	gezelter	246
184			}
185
186	gezelter	2	#endif // is_mpi
187	gezelter	246
188	gezelter	507	}
189	gezelter	2
190	tim	1024	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
191	gezelter	2
192	tim	1024	char buffer[1024];
193
194			os << " <FrameData>\n";
195
196			RealType currentTime = s->getTime();
197			sprintf(buffer, " Time: %.10g\n", time);
198			os << buffer;
199
200	gezelter	246	Mat3x3d hmat;
201			hmat = s->getHmat();
202	tim	1024	sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
203			hmat(0, 0), hmat(1, 0), hmat(2, 0),
204			hmat(0, 1), hmat(1, 1), hmat(2, 1),
205			hmat(0, 2), hmat(1, 2), hmat(2, 2));
206			os << buffer;
207	gezelter	2
208	tim	1024	RealType chi = s->getChi();
209			RealType integralOfChiDt = s->getIntegralOfChiDt();
210			sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
211			os << buffer;
212	gezelter	246
213	tim	1024	Mat3x3d eta;
214			eta = s->getEta();
215			sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
216			eta(0, 0), eta(1, 0), eta(2, 0),
217			eta(0, 1), eta(1, 1), eta(2, 1),
218			eta(0, 2), eta(1, 2), eta(2, 2));
219			os << buffer;
220	gezelter	246
221	tim	1024	os << " </FrameData>\n";
222	gezelter	507	}
223	gezelter	2
224	gezelter	507	void DumpWriter::writeFrame(std::ostream& os) {
225	gezelter	246
226	tim	1024	#ifdef IS_MPI
227			MPI_Status istatus;
228			#endif
229	gezelter	246
230			Molecule* mol;
231			StuntDouble* integrableObject;
232			SimInfo::MoleculeIterator mi;
233			Molecule::IntegrableObjectIterator ii;
234	gezelter	2
235	gezelter	246	#ifndef IS_MPI
236	tim	1024	os << " <Snapshot>\n";
237	gezelter	2
238	tim	1024	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
239	gezelter	2
240	tim	1024	os << " <StuntDoubles>\n";
241	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
242	gezelter	2
243	gezelter	507	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
244	tim	1024	integrableObject = mol->nextIntegrableObject(ii)) {
245			os << prepareDumpLine(integrableObject);
246	gezelter	2
247	tim	1024	}
248			}
249			os << " </StuntDoubles>\n";
250	gezelter	2
251	tim	1024	os << " </Snapshot>\n";
252	gezelter	2
253	tim	1024	os.flush();
254			#else
255			//every node prepares the dump lines for integrable objects belong to itself
256			std::string buffer;
257			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
258
259			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
260			integrableObject = mol->nextIntegrableObject(ii)) {
261			buffer += prepareDumpLine(integrableObject);
262	gezelter	507	}
263	gezelter	2	}
264	tim	1024
265	gezelter	246	const int masterNode = 0;
266	gezelter	2
267	tim	1024	if (worldRank == masterNode) {
268			os << " <Snapshot>\n";
269			writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
270			os << buffer;
271			os << " <StuntDoubles>\n";
272
273			int nProc;
274	gezelter	507	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
275	tim	1024	for (int i = 1; i < nProc; ++i) {
276	gezelter	2
277	tim	1024	// receive the length of the string buffer that was
278			// prepared by processor i
279	gezelter	2
280	tim	1024	int recvLength;
281			MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
282			char* recvBuffer = new char[recvLength];
283			if (recvBuffer == NULL) {
284
285			} else {
286			MPI_Recv(&recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
287			os << recvBuffer;
288			delete recvBuffer;
289			}
290	chrisfen	721
291	tim	1024	}
292			os << " </StuntDoubles>\n";
293
294			os << " </Snapshot>\n";
295	gezelter	507	os.flush();
296	gezelter	246	} else {
297	tim	1024	int sendBufferLength = buffer.size();
298			MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
299			MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
300			}
301	gezelter	2
302	tim	1024	#endif // is_mpi
303	gezelter	2
304	tim	1024	}
305	gezelter	2
306	tim	1024	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
307
308			int index = integrableObject->getGlobalIntegrableObjectIndex();
309			std::string type("pv");
310			std::string line;
311			char tempBuffer[4096];
312	gezelter	2
313	tim	1024	Vector3d pos;
314			Vector3d vel;
315			pos = integrableObject->getPos();
316			vel = integrableObject->getVel();
317			sprintf(tempBuffer, "%18.10g\t%18.10g\t%18.10g\t%14.10g\t%14.10g\t%14.10g",
318			pos[0], pos[1], pos[2],
319			vel[0], vel[1], vel[2]);
320			line += tempBuffer;
321	gezelter	2
322	tim	1024	if (integrableObject->isDirectional()) {
323			type += "qj";
324			Quat4d q;
325			Vector3d ji;
326			q = integrableObject->getQ();
327			ji = integrableObject->getJ();
328			sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g",
329			q[0], q[1], q[2], q[3],
330			ji[0], ji[1], ji[2]);
331			line += tempBuffer;
332			}
333	gezelter	2
334	tim	1024	if (needForceVector_) {
335			type += "ft";
336			Vector3d frc;
337			Vector3d trq;
338			frc = integrableObject->getFrc();
339			trq = integrableObject->getTrq();
340
341			sprintf(tempBuffer, "\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g\t%14.10g",
342			frc[0], frc[1], frc[2],
343			trq[0], trq[1], trq[2]);
344			line += tempBuffer;
345	gezelter	246	}
346	tim	1024
347			sprintf(tempBuffer, "%d\t%s\t%s\n", index, type.c_str(), line.c_str());
348			return std::string(tempBuffer);
349	gezelter	507	}
350	gezelter	2
351	gezelter	507	void DumpWriter::writeDump() {
352	tim	615	writeFrame(*dumpFile_);
353	gezelter	507	}
354	tim	376
355	gezelter	507	void DumpWriter::writeEor() {
356	tim	615	std::ostream* eorStream;
357	tim	376
358			#ifdef IS_MPI
359			if (worldRank == 0) {
360			#endif // is_mpi
361
362	tim	615	eorStream = createOStream(eorFilename_);
363	tim	376
364			#ifdef IS_MPI
365			}
366			#endif // is_mpi
367
368	tim	615	writeFrame(*eorStream);
369
370			#ifdef IS_MPI
371			if (worldRank == 0) {
372			#endif // is_mpi
373	tim	1024	writeClosing(*eorStream);
374			delete eorStream;
375	tim	615	#ifdef IS_MPI
376			}
377			#endif // is_mpi
378
379	gezelter	507	}
380	tim	376
381
382	gezelter	507	void DumpWriter::writeDumpAndEor() {
383	tim	376	std::vector<std::streambuf*> buffers;
384	tim	615	std::ostream* eorStream;
385	tim	376	#ifdef IS_MPI
386			if (worldRank == 0) {
387			#endif // is_mpi
388
389	tim	615	buffers.push_back(dumpFile_->rdbuf());
390	tim	376
391	tim	615	eorStream = createOStream(eorFilename_);
392	tim	376
393	tim	615	buffers.push_back(eorStream->rdbuf());
394	tim	376
395			#ifdef IS_MPI
396			}
397			#endif // is_mpi
398
399			TeeBuf tbuf(buffers.begin(), buffers.end());
400			std::ostream os(&tbuf);
401
402			writeFrame(os);
403	tim	615
404			#ifdef IS_MPI
405			if (worldRank == 0) {
406			#endif // is_mpi
407	tim	1024	writeClosing(*eorStream);
408			delete eorStream;
409	tim	615	#ifdef IS_MPI
410			}
411			#endif // is_mpi
412	tim	376
413	gezelter	507	}
414	tim	376
415	tim	1024	std::ostream* DumpWriter::createOStream(const std::string& filename) {
416	tim	619
417	tim	615	std::ostream* newOStream;
418	tim	619	#ifdef HAVE_LIBZ
419	tim	615	if (needCompression_) {
420	tim	1024	newOStream = new ogzstream(filename.c_str());
421	tim	615	} else {
422	tim	1024	newOStream = new std::ofstream(filename.c_str());
423	tim	615	}
424	tim	619	#else
425			newOStream = new std::ofstream(filename.c_str());
426			#endif
427	tim	1024	//write out MetaData first
428			(*newOStream) << "<OOPSE version=4>" << std::endl;
429			(*newOStream) << " <MetaData>" << std::endl;
430			(*newOStream) << info_->getRawMetaData();
431			(*newOStream) << " </MetaData>" << std::endl;
432	tim	615	return newOStream;
433	tim	1024	}
434	tim	376
435	tim	1024	void DumpWriter::writeClosing(std::ostream& os) {
436
437			os << "</OOPSE>\n";
438			os.flush();
439			}
440
441	gezelter	246	}//end namespace oopse