ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/io/RestWriter.cpp
(Generate patch)

Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 UTC

# Line 1 | Line 1
1 < /*
2 < * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1 > /*
2 > * Copyright (c) 2009 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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
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 + *
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   */
41 <
42 < #include <algorithm>
41 >
42 >
43 > #include <string>
44 > #include <sstream>
45   #include <iostream>
44 – #include <map>
46  
46 – #include "primitives/Molecule.hpp"
47   #include "io/RestWriter.hpp"
48   #include "utils/simError.h"
49 + #include "brains/SnapshotManager.hpp"
50 + #ifdef IS_MPI
51 + #include <mpi.h>
52 + #endif
53  
54 <
55 < namespace oopse {
56 <  RestWriter::RestWriter(SimInfo* info) :
57 <  info_(info) {
54 > namespace OpenMD {
55 >  RestWriter::RestWriter(SimInfo* info, const std::string& filename,
56 >                         std::vector<Restraint*> restraints ) :
57 >    info_(info){
58 >    createRestFile_ = true;
59      
55 –    //we use master - slave mode, only master node writes to disk
56 –    outName = info_->getRestFileName();
57 –  }
58 –  
59 –  RestWriter::~RestWriter() {}
60 –  
61 –  void RestWriter::writeZangle(){
62 –    const int BUFFERSIZE = 2000;
63 –    char tempBuffer[BUFFERSIZE];
64 –    char writeLine[BUFFERSIZE];
65 –    
66 –    std::ofstream finalOut;
67 –    
68 –    Molecule* mol;
69 –    StuntDouble* integrableObject;
70 –    SimInfo::MoleculeIterator mi;
71 –    Molecule::IntegrableObjectIterator ii;
72 –    
60   #ifdef IS_MPI
61 <    if(worldRank == 0 ){
62 < #endif    
63 <      finalOut.open( outName.c_str(), std::ios::out | std::ios::trunc );
64 <      if( !finalOut ){
61 >    if(worldRank == 0){
62 > #endif
63 >  
64 >      output_ = new std::ofstream(filename.c_str());
65 >
66 >      if(!output_){
67          sprintf( painCave.errMsg,
68 <                 "Could not open \"%s\" for zAngle output.\n",
69 <                 outName );
68 >                 "Could not open %s for restraint output.\n",
69 >                 filename.c_str());
70          painCave.isFatal = 1;
71          simError();
72        }
73 +
74   #ifdef IS_MPI
75      }
76   #endif // is_mpi
77 +
78 +
79 + #ifdef IS_MPI
80 +    MPI_Status istatus;
81 + #endif
82      
83   #ifndef IS_MPI
84 <    // first we do output for the single processor version
85 <    finalOut
86 <      << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
87 <      << " : omega values at this time\n";
88 <    
89 <    for (mol = info_->beginMolecule(mi); mol != NULL;
90 <         mol = info_->nextMolecule(mi)) {
96 <      
97 <      for (integrableObject = mol->beginIntegrableObject(ii);
98 <           integrableObject != NULL;
99 <           integrableObject = mol->nextIntegrableObject(ii)) {    
84 >        
85 >    (*output_) << "#time\t";
86 >
87 >    std::vector<Restraint*>::const_iterator resti;
88 >
89 >    for(resti=restraints.begin(); resti != restraints.end(); ++resti){
90 >      if ((*resti)->getPrintRestraint()) {
91          
92 <        sprintf( tempBuffer,
93 <                 "%14.10lf\n",
103 <                 integrableObject->getZangle());
104 <        strcpy( writeLine, tempBuffer );
92 >        std::string myName = (*resti)->getRestraintName();
93 >        int myType = (*resti)->getRestraintType();
94          
95 <        finalOut << writeLine;      
95 >        (*output_) << myName << ":";
96 >        
97 >        if (myType & Restraint::rtDisplacement)
98 >          (*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
99 >        
100 >        if (myType & Restraint::rtTwist)
101 >          (*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
102 >        
103 >        if (myType & Restraint::rtSwingX)
104 >          (*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
105 >          
106 >        if (myType & Restraint::rtSwingY)
107 >          (*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
108        }
108 –      
109      }
110 +
111 +    (*output_) << "\n";
112 +    (*output_).flush();
113      
114   #else
112 –    int nproc;
113 –    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
114 –    const int masterNode = 0;
115 –    int myNode = worldRank;
116 –    std::vector<int> tmpNIntObjects(nproc, 0);
117 –    std::vector<int> nIntObjectsInProc(nproc, 0);
118 –    tmpNIntObjects[myNode] = info_->getNGlobalIntegrableObjects();
115      
116 <    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
117 <    MPI_Allreduce(&tmpNIntObjects[0], &nIntObjectsInProc[0], nproc, MPI_INT,
118 <                  MPI_SUM, MPI_COMM_WORLD);
116 >    std::string buffer;
117 >
118 >    std::vector<Restraint*>::const_iterator resti;
119 >
120 >    for(resti=restraints.begin(); resti != restraints.end(); ++resti){
121 >      if ((*resti)->getPrintRestraint()) {
122 >        
123 >        std::string myName = (*resti)->getRestraintName();
124 >        int myType = (*resti)->getRestraintType();
125 >
126 >        buffer += (myName + ":");
127 >        
128 >        if (myType & Restraint::rtDisplacement)
129 >          buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
130 >        
131 >        if (myType & Restraint::rtTwist)
132 >          buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)";
133 >        
134 >        if (myType & Restraint::rtSwingX)
135 >          buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
136 >        
137 >        if (myType & Restraint::rtSwingY)
138 >          buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
139 >        
140 >        buffer += "\n";
141 >      }
142 >    }
143      
144 <    MPI_Status ierr;
125 <    int intObIndex;
126 <    double zAngle;
144 >    const int masterNode = 0;
145      
146 <    if (masterNode == 0) {
147 <      std::map<int, double> zAngData;
148 <      for(int i = 0 ; i < nproc; ++i) {
149 <        if (i == masterNode) {
150 <          for (mol = info_->beginMolecule(mi); mol != NULL;
151 <               mol = info_->nextMolecule(mi)) {
152 <            
153 <            for (integrableObject = mol->beginIntegrableObject(ii);
154 <                 integrableObject != NULL;
155 <                 integrableObject = mol->nextIntegrableObject(ii)) {
156 <              
157 <              intObIndex = integrableObject->getGlobalIndex() ;
158 <              zAngle = integrableObject->getZangle();
159 <              zAngData.insert(pair<int, double>(intObIndex, zAngle));
160 <            }      
143 <          }
144 <          
146 >    if (worldRank == masterNode) {
147 >      (*output_) << "#time\t";
148 >      (*output_) << buffer;
149 >      
150 >      int nProc;
151 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
152 >      for (int i = 1; i < nProc; ++i) {
153 >        
154 >        // receive the length of the string buffer that was
155 >        // prepared by processor i
156 >        
157 >        int recvLength;
158 >        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
159 >        char* recvBuffer = new char[recvLength];
160 >        if (recvBuffer == NULL) {
161          } else {
162 <          for(int k = 0; k < nIntObjectsInProc[i]; ++k) {
163 <            MPI_Recv(&intObIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
164 <            MPI_Recv(&zAngle, 1, MPI_DOUBLE, i, 0, MPI_COMM_WORLD,&ierr);
165 <            zAngData.insert(pair<int, double>(intObIndex, zAngle));
150 <          }
162 >          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
163 >                   &istatus);
164 >          (*output_) << recvBuffer;
165 >          delete [] recvBuffer;
166          }
167 <        
167 >      }
168 >      (*output_).flush();
169 >    } else {
170 >      int sendBufferLength = buffer.size() + 1;
171 >      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
172 >      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
173 >               0, MPI_COMM_WORLD);
174 >    }
175 >    
176 > #endif // is_mpi    
177 >    
178 >  }    
179 >  
180 >  void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
181 >    
182 > #ifdef IS_MPI
183 >    MPI_Status istatus;
184 > #endif
185 >    
186 > #ifndef IS_MPI
187 >    (*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
188 >    
189 >    // output some information about the molecules
190 >    std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
191 >    std::map<int, Restraint::RealPair>::const_iterator j;
192 >    
193 >    for( i = restInfo.begin(); i != restInfo.end(); ++i){
194 >      for(j = (*i).begin(); j != (*i).end(); ++j){                
195 >        (*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
196        }
197 <      
198 <      finalOut
199 <        << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
200 <        << " : omega values at this time\n";
201 <      
202 <      std::map<int, double>::iterator l;
203 <      for (l = zAngData.begin(); l != zAngData.end(); ++l) {
204 <        finalOut << l->second << "\n";
197 >      (*output_) << std::endl;
198 >    }
199 >    (*output_).flush();
200 > #else
201 >    std::string buffer, first, second;
202 >    std::stringstream ss;
203 >    
204 >    std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
205 >    std::map<int, Restraint::RealPair>::const_iterator j;
206 >    
207 >    for( i = restInfo.begin(); i != restInfo.end(); ++i){
208 >      for(j = (*i).begin(); j != (*i).end(); ++j){
209 >        ss.clear();
210 >        ss << (j->second).first;
211 >        ss >> first;
212 >        ss.clear();
213 >        ss << (j->second).second;
214 >        ss >> second;
215 >        buffer += ("\t" + first + "\t" + second);      
216        }
217 +      buffer += "\n";    
218 +    }
219 +    
220 +    const int masterNode = 0;
221 +    
222 +    if (worldRank == masterNode) {
223 +      (*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
224 +      (*output_) << buffer;
225        
226 <    } else {
227 <      
228 <      for (mol = info_->beginMolecule(mi); mol != NULL;
167 <           mol = info_->nextMolecule(mi)) {
226 >      int nProc;
227 >      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
228 >      for (int i = 1; i < nProc; ++i) {
229          
230 <        for (integrableObject = mol->beginIntegrableObject(ii);
231 <             integrableObject != NULL;
232 <             integrableObject = mol->nextIntegrableObject(ii)) {
233 <          intObIndex = integrableObject->getGlobalIndex();            
234 <          zAngle = integrableObject->getZangle();
235 <          MPI_Send(&intObIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
236 <          MPI_Send(&zAngle, 1, MPI_DOUBLE, masterNode, 0, MPI_COMM_WORLD);
230 >        // receive the length of the string buffer that was
231 >        // prepared by processor i
232 >        
233 >        int recvLength;
234 >        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
235 >        char* recvBuffer = new char[recvLength];
236 >        if (recvBuffer == NULL) {
237 >        } else {
238 >          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
239 >                   &istatus);
240 >          (*output_) << recvBuffer;
241 >          
242 >          delete [] recvBuffer;
243          }
244 <      }
244 >      }
245 >      (*output_).flush();
246 >    } else {
247 >      int sendBufferLength = buffer.size() + 1;
248 >      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
249 >      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
250 >               0, MPI_COMM_WORLD);
251      }
252 < #endif
252 > #endif // is_mpi
253 >  }
254 >  
255 >  
256 >  RestWriter::~RestWriter() {
257      
258   #ifdef IS_MPI
182 –    finalOut.close();
183 – #endif
259      
260 +    if (worldRank == 0) {
261 + #endif // is_mpi
262 +      if (createRestFile_){
263 +        writeClosing(*output_);
264 +        delete output_;
265 +      }
266 + #ifdef IS_MPI
267 +    }
268 + #endif // is_mpi
269    }
270    
271 < }
271 >  void RestWriter::writeClosing(std::ostream& os) {
272 >    os.flush();
273 >  }
274 >  
275 > }// end namespace OpenMD
276 >

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines