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root/OpenMD/branches/development/src/io/RestWriter.cpp
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Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 423 by chrisfen, Thu Mar 10 19:11:02 2005 UTC vs.
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 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
# Line 38 | Line 38
38   * University of Notre Dame has been advised of the possibility of
39   * such damages.
40   */
41 <
42 < #include <algorithm>
41 >
42 >
43   #include <iostream>
44 #include <map>
44  
46 #include "primitives/Molecule.hpp"
45   #include "io/RestWriter.hpp"
46   #include "utils/simError.h"
47 + #include "brains/SnapshotManager.hpp"
48 + #ifdef IS_MPI
49 + #include <mpi.h>
50 + #endif
51  
50
52   namespace oopse {
53 <  RestWriter::RestWriter(SimInfo* info) :
54 <  info_(info) {
55 <    
56 <    //we use master - slave mode, only master node writes to disk
57 <    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 <    
53 >  RestWriter::RestWriter(SimInfo* info, const std::string& filename,
54 >                         std::vector<Restraint*> restraints ) :
55 >    info_(info){
56 >
57 >    //use master - slave mode, only master node writes to disk
58   #ifdef IS_MPI
59 <    if(worldRank == 0 ){
60 < #endif    
61 <      finalOut.open( outName.c_str(), std::ios::out | std::ios::trunc );
62 <      if( !finalOut ){
59 >    if(worldRank == 0){
60 > #endif
61 >      
62 >      output_.open(filename.c_str());
63 >      
64 >      if(!output_){
65          sprintf( painCave.errMsg,
66 <                 "Could not open \"%s\" for zAngle output.\n",
67 <                 outName.c_str() );
66 >                 "Could not open %s for restraint output.\n",
67 >                 filename.c_str());
68          painCave.isFatal = 1;
69          simError();
70        }
71 < #ifdef IS_MPI
72 <    }
86 < #endif // is_mpi
87 <    
88 < #ifndef IS_MPI
89 <    // first we do output for the single processor version
90 <    finalOut
91 <      << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
92 <      << " : omega values at this time\n";
93 <    
94 <    for (mol = info_->beginMolecule(mi); mol != NULL;
95 <         mol = info_->nextMolecule(mi)) {
71 >
72 >      output_ << "#time\t";
73        
74 <      for (integrableObject = mol->beginIntegrableObject(ii);
75 <           integrableObject != NULL;
76 <           integrableObject = mol->nextIntegrableObject(ii)) {    
74 >      // TODO:  get Restraint info from slave nodes:
75 >      std::vector<Restraint*>::const_iterator resti;
76 >      for(resti=restraints.begin(); resti != restraints.end(); ++resti){
77 >        std::string myName = (*resti)->getRestraintName();
78 >        int myType = (*resti)->getRestraintType();
79          
80 <        sprintf( tempBuffer,
102 <                 "%14.10lf\n",
103 <                 integrableObject->getZangle());
104 <        strcpy( writeLine, tempBuffer );
80 >        output_ << myName << ":";
81          
82 <        finalOut << writeLine;      
83 <      }
108 <      
109 <    }
110 <    
111 < #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();
119 <    
120 <    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
121 <    MPI_Allreduce(&tmpNIntObjects[0], &nIntObjectsInProc[0], nproc, MPI_INT,
122 <                  MPI_SUM, MPI_COMM_WORLD);
123 <    
124 <    MPI_Status ierr;
125 <    int intObIndex;
126 <    double zAngle;
127 <  
128 <    if (masterNode == 0) {
129 <      std::map<int, double> zAngData;
130 <      for(int i = 0 ; i < nproc; ++i) {
131 <        if (i == masterNode) {
132 <          for (mol = info_->beginMolecule(mi); mol != NULL;
133 <               mol = info_->nextMolecule(mi)) {
134 <            
135 <            for (integrableObject = mol->beginIntegrableObject(ii);
136 <                 integrableObject != NULL;
137 <                 integrableObject = mol->nextIntegrableObject(ii)) {
138 <              
139 <              intObIndex = integrableObject->getGlobalIndex() ;
140 <              zAngle = integrableObject->getZangle();
141 <              zAngData.insert(std::pair<int, double>(intObIndex, zAngle));
142 <            }      
143 <          }
144 <          
145 <        } else {
146 <          for(int k = 0; k < nIntObjectsInProc[i]; ++k) {
147 <            MPI_Recv(&intObIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
148 <            MPI_Recv(&zAngle, 1, MPI_DOUBLE, i, 0, MPI_COMM_WORLD,&ierr);
149 <            zAngData.insert(std::pair<int, double>(intObIndex, zAngle));
150 <          }
151 <        }
82 >        if (myType & Restraint::rtDisplacement)
83 >          output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)";
84          
85 <      }
86 <      
155 <      finalOut
156 <        << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
157 <        << " : omega values at this time\n";
158 <      
159 <      std::map<int, double>::iterator l;
160 <      for (l = zAngData.begin(); l != zAngData.end(); ++l) {
161 <        finalOut << l->second << "\n";
162 <      }
163 <      
164 <    } else {
165 <      
166 <      for (mol = info_->beginMolecule(mi); mol != NULL;
167 <           mol = info_->nextMolecule(mi)) {
85 >        if (myType & Restraint::rtTwist)
86 >          output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
87          
88 <        for (integrableObject = mol->beginIntegrableObject(ii);
89 <             integrableObject != NULL;
90 <             integrableObject = mol->nextIntegrableObject(ii)) {
91 <          intObIndex = integrableObject->getGlobalIndex();            
92 <          zAngle = integrableObject->getZangle();
93 <          MPI_Send(&intObIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
175 <          MPI_Send(&zAngle, 1, MPI_DOUBLE, masterNode, 0, MPI_COMM_WORLD);
176 <        }
88 >        if (myType & Restraint::rtSwingX)
89 >          output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
90 >        
91 >        if (myType & Restraint::rtSwingY)
92 >          output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
93 >        
94        }
95 +      output_ << "\n";
96 + #ifdef IS_MPI
97      }
98 < #endif
99 <    
98 > #endif      
99 >  }
100 >  
101 >  RestWriter::~RestWriter() {
102   #ifdef IS_MPI
103 <    finalOut.close();
103 >    if(worldRank == 0 ){
104 > #endif  
105 >      output_.close();  
106 > #ifdef IS_MPI  
107 >    }
108   #endif
109 +  }
110 +  
111 +  void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
112 +      
113      
114 +    output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
115 +        
116 +    // output some information about the molecules
117 +    std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
118 +    std::map<int, Restraint::RealPair>::const_iterator j;
119 +    for( i = restInfo.begin(); i != restInfo.end(); ++i){
120 +      for(j = (*i).begin(); j != (*i).end(); ++j){                
121 +        output_ << "\t" << (j->second).first << "\t" << (j->second).second;
122 +      }
123 +      output_ << std::endl;
124 +    }
125    }
126    
127 < }
127 > }// end oopse
128 >  

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