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Comparing trunk/src/io/ZConsWriter.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

# Line 1 | Line 1
1 + /*
2 + * Copyright (c) 2005 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
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
40 + */
41 +
42   #include <algorithm>
43   #include <iostream>
44   #include <vector>
4 – //#include <pair>
5 – #include "ZConsWriter.hpp"
6 – #include "simError.h"
45  
8 – using namespace std;
46  
47 < ZConsWriter::ZConsWriter(const char* filename, vector<ZConsParaItem>* thePara)
48 < {
49 <  //use master - slave mode, only master node writes to disk
47 > #include "io/ZConsWriter.hpp"
48 > #include "utils/simError.h"
49 >
50 >
51 > namespace oopse {
52 >  ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
53 >    //use master - slave mode, only master node writes to disk
54   #ifdef IS_MPI
55 <  if(worldRank == 0){
55 >    if(worldRank == 0){
56   #endif
57  
58 <   output.open(filename);
18 <  
19 <   if(!output){
20 <     sprintf( painCave.errMsg,
21 <              "Could not open %s for z constrain output \n",
22 <         filename);
23 <     painCave.isFatal = 1;
24 <     simError();
25 <   }
26 <   output << "#number of z constrain molecules" << endl;
27 <   output << "#global Index of molecule\tzPos" << endl;
28 <   output << "#every frame will contain below data" <<endl;
29 <   output << "#time(fs)" << endl;
30 <   output << "#number of fixed z-constrain molecules" << endl;
31 <   output << "#global Index of molecule\tzconstrain force\tcurrentZPos" << endl;
58 >      output_.open(filename.c_str());
59  
60 <   parameters = thePara;
61 <   writeZPos();
60 >      if(!output_){
61 >        sprintf( painCave.errMsg,
62 >                 "Could not open %s for z constrain output_ \n", filename.c_str());
63 >        painCave.isFatal = 1;
64 >        simError();
65 >      }
66  
67 +      output_ << "//time(fs)" << std::endl;
68 +      output_ << "//number of fixed z-constrain molecules" << std::endl;
69 +      output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;
70 +
71   #ifdef IS_MPI
72 <  }
72 >    }
73   #endif  
74  
75 < }
75 >  }
76  
77 < ZConsWriter::~ZConsWriter()
78 < {
77 >  ZConsWriter::~ZConsWriter()
78 >  {
79  
80   #ifdef IS_MPI
81 <  if(worldRank == 0 ){
81 >    if(worldRank == 0 ){
82   #endif  
83 <  output.close();  
83 >      output_.close();  
84   #ifdef IS_MPI  
85 <  }
85 >    }
86   #endif
87 < }
87 >  }
88  
89 < /**
55 < *
56 < */
57 < void ZConsWriter::writeFZ(double time, int num, int* index, double* fz, double* curZPos, double* zpos){
58 <
89 >  void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
90   #ifndef IS_MPI
91 <  output << time << endl;
92 <  output << num << endl;
62 <  
63 <  for(int i = 0; i < num; i++)
64 <    output << index[i] <<"\t" << fz[i] << "\t" << curZPos[i] << "\t" << zpos[i] <<endl;
91 >    output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
92 >    output_ << fixedZmols.size() << std::endl;
93  
94 +    std::list<ZconstraintMol>::const_iterator i;
95 +    for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
96 +      output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
97 +    }
98   #else
99 <  int totalNum;
100 <  MPI_Allreduce(&num, &totalNum, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
101 <  
102 <  if(worldRank == 0){
103 <    output << time << endl;
104 <    output << totalNum << endl;
105 <  }
74 <  
75 <  int whichNode;
76 <  enum CommType { RequesPosAndForce, EndOfRequest} status;
77 <  double pos;
78 <  double force;
79 <  double zconsPos;
80 <  int localIndex;
81 <  MPI_Status ierr;
82 <  int tag = 0;
83 <  
84 <  if(worldRank == 0){
99 >    int nproc;
100 >    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
101 >    const int masterNode = 0;
102 >    int myNode = worldRank;
103 >    std::vector<int> tmpNFixedZmols(nproc, 0);
104 >    std::vector<int> nFixedZmolsInProc(nproc, 0);
105 >    tmpNFixedZmols[myNode] = fixedZmols.size();
106      
107 <    int globalIndexOfCurMol;
108 <    int *MolToProcMap;
109 <    MolToProcMap = mpiSim->getMolToProcMap();
89 <    
90 <    for(int i = 0; i < (int)(parameters->size()); i++){
91 <      
92 <      globalIndexOfCurMol = (*parameters)[i].zconsIndex;
93 <      whichNode = MolToProcMap[globalIndexOfCurMol];
94 <      
95 <      if(whichNode == 0){
96 <        
97 <       for(int j = 0; j < num; j++)
98 <        if(index[j] == globalIndexOfCurMol){
99 <          localIndex = j;
100 <          break;
101 <        }
107 >    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
108 >    MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT,
109 >                  MPI_SUM, MPI_COMM_WORLD);
110  
111 <      force = fz[localIndex];
112 <      pos = curZPos[localIndex];
113 <      
106 <      }
107 <      else{
108 <        status = RequesPosAndForce;
109 <        MPI_Send(&status, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD);
110 <        MPI_Send(&globalIndexOfCurMol, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD);
111 <        MPI_Recv(&force, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr);
112 <        MPI_Recv(&pos, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr);
113 <        MPI_Recv(&zconsPos, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr);
114 <      }
115 <
116 <     output << globalIndexOfCurMol << "\t" << force << "\t" << pos << "\t"<<  zconsPos << endl;
117 <              
118 <    } //End of Request Loop
111 >    MPI_Status ierr;
112 >    int zmolIndex;
113 >    RealType data[3];
114      
115 <    //Send ending request message to slave nodes    
121 <    status = EndOfRequest;
122 <    for(int i =1; i < mpiSim->getNProcessors(); i++)
123 <      MPI_Send(&status, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
124 <    
125 <  }
126 <  else{
127 <  
128 <    int whichMol;
129 <    bool done = false;
115 >    if (masterNode == 0) {
116  
117 <    while (!done){  
118 <      
119 <      MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr);
120 <    
121 <      switch (status){
122 <          
123 <         case RequesPosAndForce :
124 <          
125 <           MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr);
126 <    
127 <           for(int i = 0; i < num; i++)
128 <           if(index[i] == whichMol){
129 <             localIndex = i;
130 <             break;
131 <           }
132 <    
133 <           MPI_Send(&fz[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);    
134 <           MPI_Send(&curZPos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);    
135 <           MPI_Send(&zpos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);    
136 <           break;
137 <      
138 <        case EndOfRequest :
139 <        
140 <         done = true;
141 <         break;
117 >      std::vector<ZconsData> zconsData;
118 >      ZconsData tmpData;      
119 >      for(int i =0 ; i < nproc; ++i) {
120 >        if (i == masterNode) {
121 >          std::list<ZconstraintMol>::const_iterator j;
122 >          for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
123 >            tmpData.zmolIndex = j->mol->getGlobalIndex() ;
124 >            tmpData.zforce= j->fz;
125 >            tmpData.zpos = j->zpos;
126 >            tmpData.zconsPos = j->param.zTargetPos;
127 >            zconsData.push_back(tmpData);
128 >          }                
129 >
130 >        } else {
131 >          for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
132 >            MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
133 >            MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
134 >            tmpData.zmolIndex = zmolIndex;
135 >            tmpData.zforce= data[0];
136 >            tmpData.zpos = data[1];
137 >            tmpData.zconsPos = data[2];
138 >            zconsData.push_back(tmpData);                                        
139 >          }
140 >        }
141 >            
142        }
157 –      
158 –    }
159 –          
160 –  }
143  
162 – #endif
144  
145 < }
145 >      output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
146 >      output_ << zconsData.size() << std::endl;
147  
148 < /*
149 < *
150 < */
151 < void ZConsWriter::writeZPos(){
148 >      std::vector<ZconsData>::iterator l;
149 >      for (l = zconsData.begin(); l != zconsData.end(); ++l) {
150 >        output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" <<  l->zconsPos << std::endl;
151 >      }
152 >        
153 >    } else {
154  
155 < #ifdef IS_MPI
156 <  if(worldRank == 0){
155 >      std::list<ZconstraintMol>::const_iterator j;
156 >      for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
157 >        zmolIndex = j->mol->getGlobalIndex();            
158 >        data[0] = j->fz;
159 >        data[1] = j->zpos;
160 >        data[2] = j->param.zTargetPos;
161 >        MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
162 >        MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
163 >            
164 >      }
165 >    }
166   #endif
174 –    
175 –    output << parameters->size() << endl;    
176 –    
177 –    for(int i =0 ; i < (int)(parameters->size()); i++)
178 –      output << (*parameters)[i].zconsIndex << "\t" <<  (*parameters)[i].zPos << endl;
179 –
180 – #ifdef IS_MPI
167    }
168 < #endif
168 >
169   }

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