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Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC vs.
Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 UTC

# Line 6 | Line 6
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  
43 + #include <string>
44 + #include <sstream>
45   #include <iostream>
46  
47   #include "io/RestWriter.hpp"
# Line 49 | Line 51
51   #include <mpi.h>
52   #endif
53  
54 < namespace oopse {
54 > namespace OpenMD {
55    RestWriter::RestWriter(SimInfo* info, const std::string& filename,
56                           std::vector<Restraint*> restraints ) :
57      info_(info){
58 <
59 <    //use master - slave mode, only master node writes to disk
58 >    createRestFile_ = true;
59 >    
60   #ifdef IS_MPI
61      if(worldRank == 0){
62   #endif
63 <      
64 <      output_.open(filename.c_str());
65 <      
63 >  
64 >      output_ = new std::ofstream(filename.c_str());
65 >
66        if(!output_){
67          sprintf( painCave.errMsg,
68                   "Could not open %s for restraint output.\n",
# Line 69 | Line 71 | namespace oopse {
71          simError();
72        }
73  
74 <      output_ << "#time\t";
75 <      
76 <      // TODO:  get Restraint info from slave nodes:
75 <      std::vector<Restraint*>::const_iterator resti;
76 <      for(resti=restraints.begin(); resti != restraints.end(); ++resti){
74 > #ifdef IS_MPI
75 >    }
76 > #endif // is_mpi
77  
78 <        if ((*resti)->getPrintRestraint()) {
79 <          std::string myName = (*resti)->getRestraintName();
80 <          int myType = (*resti)->getRestraintType();
78 >
79 > #ifdef IS_MPI
80 >    MPI_Status istatus;
81 > #endif
82 >    
83 > #ifndef IS_MPI
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 >        std::string myName = (*resti)->getRestraintName();
93 >        int myType = (*resti)->getRestraintType();
94 >        
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 <          output_ << myName << ":";
107 <          
84 <          if (myType & Restraint::rtDisplacement)
85 <            output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)";
86 <          
87 <          if (myType & Restraint::rtTwist)
88 <            output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
89 <          
90 <          if (myType & Restraint::rtSwingX)
91 <            output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
92 <          
93 <          if (myType & Restraint::rtSwingY)
94 <            output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
95 <          
96 <        }
106 >        if (myType & Restraint::rtSwingY)
107 >          (*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
108        }
98 –      output_ << "\n";
99 – #ifdef IS_MPI
109      }
110 < #endif      
111 <  }
110 >
111 >    (*output_) << "\n";
112 >    (*output_).flush();
113 >    
114 > #else
115 >    
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 >    const int masterNode = 0;
145 >    
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 >          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
163 >                   &istatus);
164 >          (*output_) << recvBuffer;
165 >          delete [] recvBuffer;
166 >        }
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 <  RestWriter::~RestWriter() {
180 >  void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
181 >    
182   #ifdef IS_MPI
183 <    if(worldRank == 0 ){
107 < #endif  
108 <      output_.close();  
109 < #ifdef IS_MPI  
110 <    }
183 >    MPI_Status istatus;
184   #endif
112 –  }
113 –  
114 –  void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
115 –      
185      
186 <    output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
187 <        
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;
195 >        (*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
196        }
197 <      output_ << std::endl;
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 +      int nProc;
227 +      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
228 +      for (int i = 1; i < nProc; ++i) {
229 +        
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 +      }
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 // is_mpi
253    }
254    
130 – }// end oopse
255    
256 +  RestWriter::~RestWriter() {
257 +    
258 + #ifdef IS_MPI
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 +  void RestWriter::writeClosing(std::ostream& os) {
272 +    os.flush();
273 +  }
274 +  
275 + }// end namespace OpenMD
276 +

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