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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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();
    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();

    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;

    if (worldRank == masterNode) {      
      os << "  <Snapshot>\n";   
      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
      os << "    <StuntDoubles>\n";
        
      os << buffer;

      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() + 1;
      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;
      }      
    }
    
    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:	1437
Committed:	Wed Apr 21 14:59:18 2010 UTC (15 years ago) by gezelter
Original Path:	*trunk/src/io/DumpWriter.cpp*
File size:	15426 byte(s)
Log Message:	Adding nan/inf detection to DumpWriter, fixing one message
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
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	1437
50	gezelter	2	#ifdef IS_MPI
51			#include <mpi.h>
52	gezelter	246	#endif //is_mpi
53	gezelter	2
54	gezelter	1437	using namespace std;
55	gezelter	1390	namespace OpenMD {
56	gezelter	2
57	gezelter	507	DumpWriter::DumpWriter(SimInfo* info)
58			: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
59	tim	615
60			Globals* simParams = info->getSimParams();
61			needCompression_ = simParams->getCompressDumpFile();
62	chrisfen	726	needForceVector_ = simParams->getOutputForceVector();
63	chuckv	791	createDumpFile_ = true;
64	tim	619	#ifdef HAVE_LIBZ
65	tim	615	if (needCompression_) {
66	tim	1024	filename_ += ".gz";
67			eorFilename_ += ".gz";
68	tim	615	}
69	tim	619	#endif
70	tim	615
71	tim	376	#ifdef IS_MPI
72
73	tim	1024	if (worldRank == 0) {
74	tim	376	#endif // is_mpi
75	chuckv	791
76	tim	1024	dumpFile_ = createOStream(filename_);
77	tim	615
78	tim	1024	if (!dumpFile_) {
79			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
80			filename_.c_str());
81			painCave.isFatal = 1;
82			simError();
83			}
84	tim	376
85			#ifdef IS_MPI
86
87	tim	1024	}
88	tim	376
89			#endif // is_mpi
90
91	tim	1024	}
92	tim	376
93
94	gezelter	507	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
95			: info_(info), filename_(filename){
96	tim	615
97			Globals* simParams = info->getSimParams();
98			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
99
100			needCompression_ = simParams->getCompressDumpFile();
101	chrisfen	726	needForceVector_ = simParams->getOutputForceVector();
102	chuckv	791	createDumpFile_ = true;
103	tim	619	#ifdef HAVE_LIBZ
104	tim	615	if (needCompression_) {
105	tim	1024	filename_ += ".gz";
106			eorFilename_ += ".gz";
107	tim	615	}
108	tim	619	#endif
109	tim	615
110	gezelter	246	#ifdef IS_MPI
111	gezelter	2
112	tim	1024	if (worldRank == 0) {
113	gezelter	246	#endif // is_mpi
114	gezelter	2
115	chuckv	791
116	tim	1024	dumpFile_ = createOStream(filename_);
117	tim	615
118	tim	1024	if (!dumpFile_) {
119			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
120			filename_.c_str());
121			painCave.isFatal = 1;
122			simError();
123			}
124	gezelter	2
125			#ifdef IS_MPI
126
127	tim	1024	}
128	gezelter	2
129			#endif // is_mpi
130	gezelter	246
131	tim	1024	}
132	chuckv	791
133			DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
134	tim	1024	: info_(info), filename_(filename){
135	chuckv	791
136			Globals* simParams = info->getSimParams();
137			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
138
139			needCompression_ = simParams->getCompressDumpFile();
140			needForceVector_ = simParams->getOutputForceVector();
141
142			#ifdef HAVE_LIBZ
143			if (needCompression_) {
144			filename_ += ".gz";
145			eorFilename_ += ".gz";
146			}
147			#endif
148
149			#ifdef IS_MPI
150
151			if (worldRank == 0) {
152			#endif // is_mpi
153
154			createDumpFile_ = writeDumpFile;
155			if (createDumpFile_) {
156			dumpFile_ = createOStream(filename_);
157
158			if (!dumpFile_) {
159			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
160			filename_.c_str());
161			painCave.isFatal = 1;
162			simError();
163			}
164			}
165			#ifdef IS_MPI
166
167			}
168	tim	1024
169	chuckv	791
170			#endif // is_mpi
171
172			}
173	gezelter	2
174	gezelter	507	DumpWriter::~DumpWriter() {
175	gezelter	2
176			#ifdef IS_MPI
177	gezelter	246
178			if (worldRank == 0) {
179	gezelter	2	#endif // is_mpi
180	chuckv	791	if (createDumpFile_){
181	tim	1024	writeClosing(*dumpFile_);
182	chuckv	791	delete dumpFile_;
183			}
184	gezelter	2	#ifdef IS_MPI
185	gezelter	246
186			}
187
188	gezelter	2	#endif // is_mpi
189	gezelter	246
190	gezelter	507	}
191	gezelter	2
192	tim	1024	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
193	gezelter	2
194	tim	1024	char buffer[1024];
195
196			os << " <FrameData>\n";
197
198			RealType currentTime = s->getTime();
199	gezelter	1437
200			if (isinf(currentTime) \|\| isnan(currentTime)) {
201			sprintf( painCave.errMsg,
202			"DumpWriter detected a numerical error writing the time");
203			painCave.isFatal = 1;
204			simError();
205			}
206
207	gezelter	1025	sprintf(buffer, " Time: %.10g\n", currentTime);
208	tim	1024	os << buffer;
209
210	gezelter	246	Mat3x3d hmat;
211			hmat = s->getHmat();
212	gezelter	1437
213			for (unsigned int i = 0; i < 3; i++) {
214			for (unsigned int j = 0; j < 3; j++) {
215			if (isinf(hmat(i,j)) \|\| isnan(hmat(i,j))) {
216			sprintf( painCave.errMsg,
217			"DumpWriter detected a numerical error writing the box");
218			painCave.isFatal = 1;
219			simError();
220			}
221			}
222			}
223
224	tim	1024	sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
225			hmat(0, 0), hmat(1, 0), hmat(2, 0),
226			hmat(0, 1), hmat(1, 1), hmat(2, 1),
227			hmat(0, 2), hmat(1, 2), hmat(2, 2));
228			os << buffer;
229	gezelter	2
230	tim	1024	RealType chi = s->getChi();
231			RealType integralOfChiDt = s->getIntegralOfChiDt();
232	gezelter	1437	if (isinf(chi) \|\| isnan(chi) \|\|
233			isinf(integralOfChiDt) \|\| isnan(integralOfChiDt)) {
234			sprintf( painCave.errMsg,
235			"DumpWriter detected a numerical error writing the thermostat");
236			painCave.isFatal = 1;
237			simError();
238			}
239	tim	1024	sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
240			os << buffer;
241	gezelter	246
242	tim	1024	Mat3x3d eta;
243			eta = s->getEta();
244	gezelter	1437
245			for (unsigned int i = 0; i < 3; i++) {
246			for (unsigned int j = 0; j < 3; j++) {
247			if (isinf(eta(i,j)) \|\| isnan(eta(i,j))) {
248			sprintf( painCave.errMsg,
249			"DumpWriter detected a numerical error writing the barostat");
250			painCave.isFatal = 1;
251			simError();
252			}
253			}
254			}
255
256	tim	1024	sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
257			eta(0, 0), eta(1, 0), eta(2, 0),
258			eta(0, 1), eta(1, 1), eta(2, 1),
259			eta(0, 2), eta(1, 2), eta(2, 2));
260			os << buffer;
261	gezelter	246
262	tim	1024	os << " </FrameData>\n";
263	gezelter	507	}
264	gezelter	2
265	gezelter	507	void DumpWriter::writeFrame(std::ostream& os) {
266	gezelter	246
267	tim	1024	#ifdef IS_MPI
268			MPI_Status istatus;
269			#endif
270	gezelter	246
271			Molecule* mol;
272			StuntDouble* integrableObject;
273			SimInfo::MoleculeIterator mi;
274			Molecule::IntegrableObjectIterator ii;
275	gezelter	2
276	gezelter	246	#ifndef IS_MPI
277	tim	1024	os << " <Snapshot>\n";
278	gezelter	1025
279	tim	1024	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
280	gezelter	2
281	tim	1024	os << " <StuntDoubles>\n";
282	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
283	gezelter	2
284	xsun	1217
285			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
286	tim	1024	integrableObject = mol->nextIntegrableObject(ii)) {
287	xsun	1217	os << prepareDumpLine(integrableObject);
288
289	tim	1024	}
290			}
291			os << " </StuntDoubles>\n";
292	xsun	1217
293	tim	1024	os << " </Snapshot>\n";
294	gezelter	2
295	tim	1024	os.flush();
296			#else
297			//every node prepares the dump lines for integrable objects belong to itself
298			std::string buffer;
299			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
300	xsun	1217
301
302	tim	1024	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
303			integrableObject = mol->nextIntegrableObject(ii)) {
304	xsun	1217	buffer += prepareDumpLine(integrableObject);
305	gezelter	507	}
306	gezelter	2	}
307	tim	1024
308	gezelter	246	const int masterNode = 0;
309	gezelter	2
310	tim	1024	if (worldRank == masterNode) {
311			os << " <Snapshot>\n";
312			writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
313			os << " <StuntDoubles>\n";
314
315	gezelter	1025	os << buffer;
316
317	tim	1024	int nProc;
318	gezelter	507	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
319	tim	1024	for (int i = 1; i < nProc; ++i) {
320	gezelter	2
321	tim	1024	// receive the length of the string buffer that was
322			// prepared by processor i
323	gezelter	2
324	tim	1024	int recvLength;
325			MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
326			char* recvBuffer = new char[recvLength];
327			if (recvBuffer == NULL) {
328			} else {
329	gezelter	1025	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
330	tim	1024	os << recvBuffer;
331	gezelter	1313	delete [] recvBuffer;
332	tim	1024	}
333			}
334			os << " </StuntDoubles>\n";
335
336			os << " </Snapshot>\n";
337	gezelter	507	os.flush();
338	gezelter	246	} else {
339	gezelter	1025	int sendBufferLength = buffer.size() + 1;
340	tim	1024	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
341	gezelter	1025	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
342	tim	1024	}
343	gezelter	2
344	tim	1024	#endif // is_mpi
345	gezelter	2
346	tim	1024	}
347	gezelter	2
348	tim	1024	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
349
350			int index = integrableObject->getGlobalIntegrableObjectIndex();
351			std::string type("pv");
352			std::string line;
353			char tempBuffer[4096];
354	gezelter	2
355	tim	1024	Vector3d pos;
356			Vector3d vel;
357			pos = integrableObject->getPos();
358	gezelter	1437
359			if (isinf(pos[0]) \|\| isnan(pos[0]) \|\|
360			isinf(pos[1]) \|\| isnan(pos[1]) \|\|
361			isinf(pos[2]) \|\| isnan(pos[2]) ) {
362			sprintf( painCave.errMsg,
363			"DumpWriter detected a numerical error writing the position"
364			" for object %d", index);
365			painCave.isFatal = 1;
366			simError();
367			}
368
369	tim	1024	vel = integrableObject->getVel();
370	gezelter	1437
371			if (isinf(vel[0]) \|\| isnan(vel[0]) \|\|
372			isinf(vel[1]) \|\| isnan(vel[1]) \|\|
373			isinf(vel[2]) \|\| isnan(vel[2]) ) {
374			sprintf( painCave.errMsg,
375			"DumpWriter detected a numerical error writing the velocity"
376			" for object %d", index);
377			painCave.isFatal = 1;
378			simError();
379			}
380
381	gezelter	1025	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
382	tim	1024	pos[0], pos[1], pos[2],
383			vel[0], vel[1], vel[2]);
384			line += tempBuffer;
385	gezelter	2
386	tim	1024	if (integrableObject->isDirectional()) {
387			type += "qj";
388			Quat4d q;
389			Vector3d ji;
390			q = integrableObject->getQ();
391	gezelter	1437
392			if (isinf(q[0]) \|\| isnan(q[0]) \|\|
393			isinf(q[1]) \|\| isnan(q[1]) \|\|
394			isinf(q[2]) \|\| isnan(q[2]) \|\|
395			isinf(q[3]) \|\| isnan(q[3]) ) {
396			sprintf( painCave.errMsg,
397			"DumpWriter detected a numerical error writing the quaternion"
398			" for object %d", index);
399			painCave.isFatal = 1;
400			simError();
401			}
402
403	tim	1024	ji = integrableObject->getJ();
404	gezelter	1437
405			if (isinf(ji[0]) \|\| isnan(ji[0]) \|\|
406			isinf(ji[1]) \|\| isnan(ji[1]) \|\|
407			isinf(ji[2]) \|\| isnan(ji[2]) ) {
408			sprintf( painCave.errMsg,
409			"DumpWriter detected a numerical error writing the angular"
410			" momentum for object %d", index);
411			painCave.isFatal = 1;
412			simError();
413			}
414
415	gezelter	1025	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
416	tim	1024	q[0], q[1], q[2], q[3],
417			ji[0], ji[1], ji[2]);
418			line += tempBuffer;
419			}
420	gezelter	2
421	tim	1024	if (needForceVector_) {
422	gezelter	1437	type += "f";
423	tim	1024	Vector3d frc;
424	gezelter	1437
425	tim	1024	frc = integrableObject->getFrc();
426	gezelter	1437
427			if (isinf(frc[0]) \|\| isnan(frc[0]) \|\|
428			isinf(frc[1]) \|\| isnan(frc[1]) \|\|
429			isinf(frc[2]) \|\| isnan(frc[2]) ) {
430			sprintf( painCave.errMsg,
431			"DumpWriter detected a numerical error writing the force"
432			" for object %d", index);
433			painCave.isFatal = 1;
434			simError();
435			}
436			sprintf(tempBuffer, " %13e %13e %13e",
437			frc[0], frc[1], frc[2]);
438	tim	1024	line += tempBuffer;
439	gezelter	1437
440			if (integrableObject->isDirectional()) {
441			type += "t";
442			Vector3d trq;
443
444			trq = integrableObject->getTrq();
445
446			if (isinf(trq[0]) \|\| isnan(trq[0]) \|\|
447			isinf(trq[1]) \|\| isnan(trq[1]) \|\|
448			isinf(trq[2]) \|\| isnan(trq[2]) ) {
449			sprintf( painCave.errMsg,
450			"DumpWriter detected a numerical error writing the torque"
451			" for object %d", index);
452			painCave.isFatal = 1;
453			simError();
454			}
455
456			sprintf(tempBuffer, " %13e %13e %13e",
457			trq[0], trq[1], trq[2]);
458			line += tempBuffer;
459			}
460	gezelter	246	}
461	gezelter	1437
462	gezelter	1025	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
463	tim	1024	return std::string(tempBuffer);
464	gezelter	507	}
465	gezelter	2
466	gezelter	507	void DumpWriter::writeDump() {
467	tim	615	writeFrame(*dumpFile_);
468	gezelter	507	}
469	tim	376
470	gezelter	507	void DumpWriter::writeEor() {
471	tim	615	std::ostream* eorStream;
472	tim	376
473			#ifdef IS_MPI
474			if (worldRank == 0) {
475			#endif // is_mpi
476
477	tim	615	eorStream = createOStream(eorFilename_);
478	tim	376
479			#ifdef IS_MPI
480			}
481			#endif // is_mpi
482
483	tim	615	writeFrame(*eorStream);
484
485			#ifdef IS_MPI
486			if (worldRank == 0) {
487			#endif // is_mpi
488	tim	1024	writeClosing(*eorStream);
489			delete eorStream;
490	tim	615	#ifdef IS_MPI
491			}
492			#endif // is_mpi
493
494	gezelter	507	}
495	tim	376
496
497	gezelter	507	void DumpWriter::writeDumpAndEor() {
498	tim	376	std::vector<std::streambuf*> buffers;
499	tim	615	std::ostream* eorStream;
500	tim	376	#ifdef IS_MPI
501			if (worldRank == 0) {
502			#endif // is_mpi
503
504	tim	615	buffers.push_back(dumpFile_->rdbuf());
505	tim	376
506	tim	615	eorStream = createOStream(eorFilename_);
507	tim	376
508	tim	615	buffers.push_back(eorStream->rdbuf());
509	tim	376
510			#ifdef IS_MPI
511			}
512			#endif // is_mpi
513
514			TeeBuf tbuf(buffers.begin(), buffers.end());
515			std::ostream os(&tbuf);
516
517			writeFrame(os);
518	tim	615
519			#ifdef IS_MPI
520			if (worldRank == 0) {
521			#endif // is_mpi
522	tim	1024	writeClosing(*eorStream);
523			delete eorStream;
524	tim	615	#ifdef IS_MPI
525			}
526			#endif // is_mpi
527	tim	376
528	gezelter	507	}
529	tim	376
530	tim	1024	std::ostream* DumpWriter::createOStream(const std::string& filename) {
531	tim	619
532	tim	615	std::ostream* newOStream;
533	tim	619	#ifdef HAVE_LIBZ
534	tim	615	if (needCompression_) {
535	tim	1024	newOStream = new ogzstream(filename.c_str());
536	tim	615	} else {
537	tim	1024	newOStream = new std::ofstream(filename.c_str());
538	tim	615	}
539	tim	619	#else
540			newOStream = new std::ofstream(filename.c_str());
541			#endif
542	tim	1024	//write out MetaData first
543	gezelter	1390	(*newOStream) << "<OpenMD version=1>" << std::endl;
544	tim	1024	(*newOStream) << " <MetaData>" << std::endl;
545			(*newOStream) << info_->getRawMetaData();
546			(*newOStream) << " </MetaData>" << std::endl;
547	tim	615	return newOStream;
548	tim	1024	}
549	tim	376
550	tim	1024	void DumpWriter::writeClosing(std::ostream& os) {
551
552	gezelter	1390	os << "</OpenMD>\n";
553	tim	1024	os.flush();
554			}
555
556	gezelter	1390	}//end namespace OpenMD