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();
    needParticlePot_ = simParams->getOutputParticlePotential();
    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:	1629
Committed:	Wed Sep 14 21:15:17 2011 UTC (13 years, 7 months ago) by gezelter
File size:	16300 byte(s)
Log Message:	Merging changes from old branch into development branch
#	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	gezelter	1629	needParticlePot_ = simParams->getOutputParticlePotential();
64	chuckv	791	createDumpFile_ = true;
65	tim	619	#ifdef HAVE_LIBZ
66	tim	615	if (needCompression_) {
67	tim	1024	filename_ += ".gz";
68			eorFilename_ += ".gz";
69	tim	615	}
70	tim	619	#endif
71	tim	615
72	tim	376	#ifdef IS_MPI
73
74	tim	1024	if (worldRank == 0) {
75	tim	376	#endif // is_mpi
76	chuckv	791
77	tim	1024	dumpFile_ = createOStream(filename_);
78	tim	615
79	tim	1024	if (!dumpFile_) {
80			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
81			filename_.c_str());
82			painCave.isFatal = 1;
83			simError();
84			}
85	tim	376
86			#ifdef IS_MPI
87
88	tim	1024	}
89	tim	376
90			#endif // is_mpi
91
92	tim	1024	}
93	tim	376
94
95	gezelter	507	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
96			: info_(info), filename_(filename){
97	tim	615
98			Globals* simParams = info->getSimParams();
99			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
100
101			needCompression_ = simParams->getCompressDumpFile();
102	chrisfen	726	needForceVector_ = simParams->getOutputForceVector();
103	chuckv	791	createDumpFile_ = true;
104	tim	619	#ifdef HAVE_LIBZ
105	tim	615	if (needCompression_) {
106	tim	1024	filename_ += ".gz";
107			eorFilename_ += ".gz";
108	tim	615	}
109	tim	619	#endif
110	tim	615
111	gezelter	246	#ifdef IS_MPI
112	gezelter	2
113	tim	1024	if (worldRank == 0) {
114	gezelter	246	#endif // is_mpi
115	gezelter	2
116	chuckv	791
117	tim	1024	dumpFile_ = createOStream(filename_);
118	tim	615
119	tim	1024	if (!dumpFile_) {
120			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
121			filename_.c_str());
122			painCave.isFatal = 1;
123			simError();
124			}
125	gezelter	2
126			#ifdef IS_MPI
127
128	tim	1024	}
129	gezelter	2
130			#endif // is_mpi
131	gezelter	246
132	tim	1024	}
133	chuckv	791
134			DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
135	tim	1024	: info_(info), filename_(filename){
136	chuckv	791
137			Globals* simParams = info->getSimParams();
138			eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
139
140			needCompression_ = simParams->getCompressDumpFile();
141			needForceVector_ = simParams->getOutputForceVector();
142	gezelter	1629	needParticlePot_ = simParams->getOutputParticlePotential();
143	chuckv	791
144			#ifdef HAVE_LIBZ
145			if (needCompression_) {
146			filename_ += ".gz";
147			eorFilename_ += ".gz";
148			}
149			#endif
150
151			#ifdef IS_MPI
152
153			if (worldRank == 0) {
154			#endif // is_mpi
155
156			createDumpFile_ = writeDumpFile;
157			if (createDumpFile_) {
158			dumpFile_ = createOStream(filename_);
159
160			if (!dumpFile_) {
161			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
162			filename_.c_str());
163			painCave.isFatal = 1;
164			simError();
165			}
166			}
167			#ifdef IS_MPI
168
169			}
170	tim	1024
171	chuckv	791
172			#endif // is_mpi
173
174			}
175	gezelter	2
176	gezelter	507	DumpWriter::~DumpWriter() {
177	gezelter	2
178			#ifdef IS_MPI
179	gezelter	246
180			if (worldRank == 0) {
181	gezelter	2	#endif // is_mpi
182	chuckv	791	if (createDumpFile_){
183	tim	1024	writeClosing(*dumpFile_);
184	chuckv	791	delete dumpFile_;
185			}
186	gezelter	2	#ifdef IS_MPI
187	gezelter	246
188			}
189
190	gezelter	2	#endif // is_mpi
191	gezelter	246
192	gezelter	507	}
193	gezelter	2
194	tim	1024	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
195	gezelter	2
196	tim	1024	char buffer[1024];
197
198			os << " <FrameData>\n";
199
200			RealType currentTime = s->getTime();
201	gezelter	1437
202			if (isinf(currentTime) \|\| isnan(currentTime)) {
203			sprintf( painCave.errMsg,
204			"DumpWriter detected a numerical error writing the time");
205			painCave.isFatal = 1;
206			simError();
207			}
208
209	gezelter	1025	sprintf(buffer, " Time: %.10g\n", currentTime);
210	tim	1024	os << buffer;
211
212	gezelter	246	Mat3x3d hmat;
213			hmat = s->getHmat();
214	gezelter	1437
215			for (unsigned int i = 0; i < 3; i++) {
216			for (unsigned int j = 0; j < 3; j++) {
217			if (isinf(hmat(i,j)) \|\| isnan(hmat(i,j))) {
218			sprintf( painCave.errMsg,
219			"DumpWriter detected a numerical error writing the box");
220			painCave.isFatal = 1;
221			simError();
222			}
223			}
224			}
225
226	tim	1024	sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
227			hmat(0, 0), hmat(1, 0), hmat(2, 0),
228			hmat(0, 1), hmat(1, 1), hmat(2, 1),
229			hmat(0, 2), hmat(1, 2), hmat(2, 2));
230			os << buffer;
231	gezelter	2
232	tim	1024	RealType chi = s->getChi();
233			RealType integralOfChiDt = s->getIntegralOfChiDt();
234	gezelter	1437	if (isinf(chi) \|\| isnan(chi) \|\|
235			isinf(integralOfChiDt) \|\| isnan(integralOfChiDt)) {
236			sprintf( painCave.errMsg,
237			"DumpWriter detected a numerical error writing the thermostat");
238			painCave.isFatal = 1;
239			simError();
240			}
241	tim	1024	sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
242			os << buffer;
243	gezelter	246
244	tim	1024	Mat3x3d eta;
245			eta = s->getEta();
246	gezelter	1437
247			for (unsigned int i = 0; i < 3; i++) {
248			for (unsigned int j = 0; j < 3; j++) {
249			if (isinf(eta(i,j)) \|\| isnan(eta(i,j))) {
250			sprintf( painCave.errMsg,
251			"DumpWriter detected a numerical error writing the barostat");
252			painCave.isFatal = 1;
253			simError();
254			}
255			}
256			}
257
258	tim	1024	sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
259			eta(0, 0), eta(1, 0), eta(2, 0),
260			eta(0, 1), eta(1, 1), eta(2, 1),
261			eta(0, 2), eta(1, 2), eta(2, 2));
262			os << buffer;
263	gezelter	246
264	tim	1024	os << " </FrameData>\n";
265	gezelter	507	}
266	gezelter	2
267	gezelter	507	void DumpWriter::writeFrame(std::ostream& os) {
268	gezelter	246
269	tim	1024	#ifdef IS_MPI
270			MPI_Status istatus;
271			#endif
272	gezelter	246
273			Molecule* mol;
274			StuntDouble* integrableObject;
275			SimInfo::MoleculeIterator mi;
276			Molecule::IntegrableObjectIterator ii;
277	gezelter	2
278	gezelter	246	#ifndef IS_MPI
279	tim	1024	os << " <Snapshot>\n";
280	gezelter	1025
281	tim	1024	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
282	gezelter	2
283	tim	1024	os << " <StuntDoubles>\n";
284	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
285	gezelter	2
286	xsun	1217
287			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
288	tim	1024	integrableObject = mol->nextIntegrableObject(ii)) {
289	xsun	1217	os << prepareDumpLine(integrableObject);
290
291	tim	1024	}
292			}
293			os << " </StuntDoubles>\n";
294	xsun	1217
295	tim	1024	os << " </Snapshot>\n";
296	gezelter	2
297	tim	1024	os.flush();
298			#else
299			//every node prepares the dump lines for integrable objects belong to itself
300			std::string buffer;
301			for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
302	xsun	1217
303
304	tim	1024	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
305			integrableObject = mol->nextIntegrableObject(ii)) {
306	xsun	1217	buffer += prepareDumpLine(integrableObject);
307	gezelter	507	}
308	gezelter	2	}
309	tim	1024
310	gezelter	246	const int masterNode = 0;
311	gezelter	1629	int nProc;
312			MPI_Comm_size(MPI_COMM_WORLD, &nProc);
313	tim	1024	if (worldRank == masterNode) {
314			os << " <Snapshot>\n";
315			writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
316			os << " <StuntDoubles>\n";
317
318	gezelter	1025	os << buffer;
319
320	tim	1024	for (int i = 1; i < nProc; ++i) {
321	gezelter	2
322	tim	1024	// receive the length of the string buffer that was
323			// prepared by processor i
324	gezelter	2
325	gezelter	1629	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
326	tim	1024	int recvLength;
327			MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
328			char* recvBuffer = new char[recvLength];
329			if (recvBuffer == NULL) {
330			} else {
331	gezelter	1025	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
332	tim	1024	os << recvBuffer;
333	gezelter	1313	delete [] recvBuffer;
334	tim	1024	}
335			}
336			os << " </StuntDoubles>\n";
337
338			os << " </Snapshot>\n";
339	gezelter	507	os.flush();
340	gezelter	246	} else {
341	gezelter	1025	int sendBufferLength = buffer.size() + 1;
342	gezelter	1629	int myturn = 0;
343			for (int i = 1; i < nProc; ++i){
344			MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
345			if (myturn == worldRank){
346			MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
347			MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
348			}
349			}
350	tim	1024	}
351	gezelter	2
352	tim	1024	#endif // is_mpi
353	gezelter	2
354	tim	1024	}
355	gezelter	2
356	tim	1024	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
357
358			int index = integrableObject->getGlobalIntegrableObjectIndex();
359			std::string type("pv");
360			std::string line;
361			char tempBuffer[4096];
362	gezelter	2
363	tim	1024	Vector3d pos;
364			Vector3d vel;
365			pos = integrableObject->getPos();
366	gezelter	1437
367			if (isinf(pos[0]) \|\| isnan(pos[0]) \|\|
368			isinf(pos[1]) \|\| isnan(pos[1]) \|\|
369			isinf(pos[2]) \|\| isnan(pos[2]) ) {
370			sprintf( painCave.errMsg,
371			"DumpWriter detected a numerical error writing the position"
372			" for object %d", index);
373			painCave.isFatal = 1;
374			simError();
375			}
376
377	tim	1024	vel = integrableObject->getVel();
378	gezelter	1437
379			if (isinf(vel[0]) \|\| isnan(vel[0]) \|\|
380			isinf(vel[1]) \|\| isnan(vel[1]) \|\|
381			isinf(vel[2]) \|\| isnan(vel[2]) ) {
382			sprintf( painCave.errMsg,
383			"DumpWriter detected a numerical error writing the velocity"
384			" for object %d", index);
385			painCave.isFatal = 1;
386			simError();
387			}
388
389	gezelter	1025	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
390	tim	1024	pos[0], pos[1], pos[2],
391			vel[0], vel[1], vel[2]);
392			line += tempBuffer;
393	gezelter	2
394	tim	1024	if (integrableObject->isDirectional()) {
395			type += "qj";
396			Quat4d q;
397			Vector3d ji;
398			q = integrableObject->getQ();
399	gezelter	1437
400			if (isinf(q[0]) \|\| isnan(q[0]) \|\|
401			isinf(q[1]) \|\| isnan(q[1]) \|\|
402			isinf(q[2]) \|\| isnan(q[2]) \|\|
403			isinf(q[3]) \|\| isnan(q[3]) ) {
404			sprintf( painCave.errMsg,
405			"DumpWriter detected a numerical error writing the quaternion"
406			" for object %d", index);
407			painCave.isFatal = 1;
408			simError();
409			}
410
411	tim	1024	ji = integrableObject->getJ();
412	gezelter	1437
413			if (isinf(ji[0]) \|\| isnan(ji[0]) \|\|
414			isinf(ji[1]) \|\| isnan(ji[1]) \|\|
415			isinf(ji[2]) \|\| isnan(ji[2]) ) {
416			sprintf( painCave.errMsg,
417			"DumpWriter detected a numerical error writing the angular"
418			" momentum for object %d", index);
419			painCave.isFatal = 1;
420			simError();
421			}
422
423	gezelter	1025	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
424	tim	1024	q[0], q[1], q[2], q[3],
425			ji[0], ji[1], ji[2]);
426			line += tempBuffer;
427			}
428	gezelter	2
429	tim	1024	if (needForceVector_) {
430	gezelter	1437	type += "f";
431	tim	1024	Vector3d frc;
432	gezelter	1437
433	tim	1024	frc = integrableObject->getFrc();
434	gezelter	1437
435			if (isinf(frc[0]) \|\| isnan(frc[0]) \|\|
436			isinf(frc[1]) \|\| isnan(frc[1]) \|\|
437			isinf(frc[2]) \|\| isnan(frc[2]) ) {
438			sprintf( painCave.errMsg,
439			"DumpWriter detected a numerical error writing the force"
440			" for object %d", index);
441			painCave.isFatal = 1;
442			simError();
443			}
444			sprintf(tempBuffer, " %13e %13e %13e",
445			frc[0], frc[1], frc[2]);
446	tim	1024	line += tempBuffer;
447	gezelter	1437
448			if (integrableObject->isDirectional()) {
449			type += "t";
450			Vector3d trq;
451
452			trq = integrableObject->getTrq();
453
454			if (isinf(trq[0]) \|\| isnan(trq[0]) \|\|
455			isinf(trq[1]) \|\| isnan(trq[1]) \|\|
456			isinf(trq[2]) \|\| isnan(trq[2]) ) {
457			sprintf( painCave.errMsg,
458			"DumpWriter detected a numerical error writing the torque"
459			" for object %d", index);
460			painCave.isFatal = 1;
461			simError();
462			}
463
464			sprintf(tempBuffer, " %13e %13e %13e",
465			trq[0], trq[1], trq[2]);
466			line += tempBuffer;
467			}
468	gezelter	246	}
469	gezelter	1629	if (needParticlePot_) {
470			type += "u";
471			RealType particlePot;
472
473			particlePot = integrableObject->getParticlePot();
474
475			if (isinf(particlePot) \|\| isnan(particlePot)) {
476			sprintf( painCave.errMsg,
477			"DumpWriter detected a numerical error writing the particle "
478			" potential for object %d", index);
479			painCave.isFatal = 1;
480			simError();
481			}
482			sprintf(tempBuffer, " %13e", particlePot);
483			line += tempBuffer;
484			}
485	gezelter	1437
486	gezelter	1025	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
487	tim	1024	return std::string(tempBuffer);
488	gezelter	507	}
489	gezelter	2
490	gezelter	507	void DumpWriter::writeDump() {
491	tim	615	writeFrame(*dumpFile_);
492	gezelter	507	}
493	tim	376
494	gezelter	507	void DumpWriter::writeEor() {
495	tim	615	std::ostream* eorStream;
496	tim	376
497			#ifdef IS_MPI
498			if (worldRank == 0) {
499			#endif // is_mpi
500
501	tim	615	eorStream = createOStream(eorFilename_);
502	tim	376
503			#ifdef IS_MPI
504			}
505			#endif // is_mpi
506
507	tim	615	writeFrame(*eorStream);
508
509			#ifdef IS_MPI
510			if (worldRank == 0) {
511			#endif // is_mpi
512	tim	1024	writeClosing(*eorStream);
513			delete eorStream;
514	tim	615	#ifdef IS_MPI
515			}
516			#endif // is_mpi
517
518	gezelter	507	}
519	tim	376
520
521	gezelter	507	void DumpWriter::writeDumpAndEor() {
522	tim	376	std::vector<std::streambuf*> buffers;
523	tim	615	std::ostream* eorStream;
524	tim	376	#ifdef IS_MPI
525			if (worldRank == 0) {
526			#endif // is_mpi
527
528	tim	615	buffers.push_back(dumpFile_->rdbuf());
529	tim	376
530	tim	615	eorStream = createOStream(eorFilename_);
531	tim	376
532	tim	615	buffers.push_back(eorStream->rdbuf());
533	tim	376
534			#ifdef IS_MPI
535			}
536			#endif // is_mpi
537
538			TeeBuf tbuf(buffers.begin(), buffers.end());
539			std::ostream os(&tbuf);
540
541			writeFrame(os);
542	tim	615
543			#ifdef IS_MPI
544			if (worldRank == 0) {
545			#endif // is_mpi
546	tim	1024	writeClosing(*eorStream);
547			delete eorStream;
548	tim	615	#ifdef IS_MPI
549			}
550			#endif // is_mpi
551	tim	376
552	gezelter	507	}
553	tim	376
554	tim	1024	std::ostream* DumpWriter::createOStream(const std::string& filename) {
555	tim	619
556	tim	615	std::ostream* newOStream;
557	tim	619	#ifdef HAVE_LIBZ
558	tim	615	if (needCompression_) {
559	tim	1024	newOStream = new ogzstream(filename.c_str());
560	tim	615	} else {
561	tim	1024	newOStream = new std::ofstream(filename.c_str());
562	tim	615	}
563	tim	619	#else
564			newOStream = new std::ofstream(filename.c_str());
565			#endif
566	tim	1024	//write out MetaData first
567	gezelter	1390	(*newOStream) << "<OpenMD version=1>" << std::endl;
568	tim	1024	(*newOStream) << " <MetaData>" << std::endl;
569			(*newOStream) << info_->getRawMetaData();
570			(*newOStream) << " </MetaData>" << std::endl;
571	tim	615	return newOStream;
572	tim	1024	}
573	tim	376
574	tim	1024	void DumpWriter::writeClosing(std::ostream& os) {
575
576	gezelter	1390	os << "</OpenMD>\n";
577	tim	1024	os.flush();
578			}
579
580	gezelter	1390	}//end namespace OpenMD