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root/OpenMD/trunk/src/io/ZConsWriter.cpp
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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 1390 by gezelter, Wed Nov 25 20:02:06 2009 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. Redistributions of source code must retain the above copyright
10 + *    notice, this list of conditions and the following disclaimer.
11 + *
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.
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 + *
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>
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 < {
12 <  //use master - slave mode, only master node writes to disk
47 > #include "io/ZConsWriter.hpp"
48 > #include "utils/simError.h"
49   #ifdef IS_MPI
50 <  if(worldRank == 0){
50 > #include <mpi.h>
51   #endif
52  
53 <   output.open(filename);
54 <  
55 <   if(!output){
56 <     sprintf( painCave.errMsg,
57 <              "Could not open %s for z constrain output \n",
58 <         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;
53 > namespace OpenMD {
54 >  ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
55 >    //use master - slave mode, only master node writes to disk
56 > #ifdef IS_MPI
57 >    if(worldRank == 0){
58 > #endif
59  
60 <   parameters = thePara;
34 <   writeZPos();
60 >      output_.open(filename.c_str());
61  
62 +      if(!output_){
63 +        sprintf( painCave.errMsg,
64 +                 "Could not open %s for z constrain output_ \n", filename.c_str());
65 +        painCave.isFatal = 1;
66 +        simError();
67 +      }
68 +
69 +      output_ << "//time(fs)" << std::endl;
70 +      output_ << "//number of fixed z-constrain molecules" << std::endl;
71 +      output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;
72 +
73   #ifdef IS_MPI
74 <  }
74 >    }
75   #endif  
76  
77 < }
77 >  }
78  
79 < ZConsWriter::~ZConsWriter()
80 < {
79 >  ZConsWriter::~ZConsWriter()
80 >  {
81  
82   #ifdef IS_MPI
83 <  if(worldRank == 0 ){
83 >    if(worldRank == 0 ){
84   #endif  
85 <  output.close();  
85 >      output_.close();  
86   #ifdef IS_MPI  
87 <  }
87 >    }
88   #endif
89 < }
89 >  }
90  
91 < /**
55 < *
56 < */
57 < void ZConsWriter::writeFZ(double time, int num, int* index, double* fz, double* curZPos, double* zpos){
58 <
91 >  void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
92   #ifndef IS_MPI
93 <  output << time << endl;
94 <  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;
93 >    output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
94 >    output_ << fixedZmols.size() << std::endl;
95  
96 +    std::list<ZconstraintMol>::const_iterator i;
97 +    for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
98 +      output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
99 +    }
100   #else
101 <  int totalNum;
102 <  MPI_Allreduce(&num, &totalNum, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
103 <  
104 <  if(worldRank == 0){
105 <    output << time << endl;
106 <    output << totalNum << endl;
107 <  }
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){
101 >    int nproc;
102 >    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
103 >    const int masterNode = 0;
104 >    int myNode = worldRank;
105 >    std::vector<int> tmpNFixedZmols(nproc, 0);
106 >    std::vector<int> nFixedZmolsInProc(nproc, 0);
107 >    tmpNFixedZmols[myNode] = fixedZmols.size();
108      
109 <    int globalIndexOfCurMol;
110 <    int *MolToProcMap;
111 <    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 <        }
109 >    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
110 >    MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT,
111 >                  MPI_SUM, MPI_COMM_WORLD);
112  
113 <      force = fz[localIndex];
114 <      pos = curZPos[localIndex];
115 <      
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
113 >    MPI_Status ierr;
114 >    int zmolIndex;
115 >    RealType data[3];
116      
117 <    //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;
117 >    if (masterNode == 0) {
118  
119 <    while (!done){  
120 <      
121 <      MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr);
122 <    
123 <      switch (status){
124 <          
125 <         case RequesPosAndForce :
126 <          
127 <           MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr);
128 <    
129 <           for(int i = 0; i < num; i++)
130 <           if(index[i] == whichMol){
131 <             localIndex = i;
132 <             break;
133 <           }
134 <    
135 <           MPI_Send(&fz[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);    
136 <           MPI_Send(&curZPos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);    
137 <           MPI_Send(&zpos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);    
138 <           break;
139 <      
140 <        case EndOfRequest :
141 <        
142 <         done = true;
143 <         break;
119 >      std::vector<ZconsData> zconsData;
120 >      ZconsData tmpData;      
121 >      for(int i =0 ; i < nproc; ++i) {
122 >        if (i == masterNode) {
123 >          std::list<ZconstraintMol>::const_iterator j;
124 >          for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
125 >            tmpData.zmolIndex = j->mol->getGlobalIndex() ;
126 >            tmpData.zforce= j->fz;
127 >            tmpData.zpos = j->zpos;
128 >            tmpData.zconsPos = j->param.zTargetPos;
129 >            zconsData.push_back(tmpData);
130 >          }                
131 >
132 >        } else {
133 >          for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
134 >            MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
135 >            MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
136 >            tmpData.zmolIndex = zmolIndex;
137 >            tmpData.zforce= data[0];
138 >            tmpData.zpos = data[1];
139 >            tmpData.zconsPos = data[2];
140 >            zconsData.push_back(tmpData);                                        
141 >          }
142 >        }
143 >            
144        }
157 –      
158 –    }
159 –          
160 –  }
145  
162 – #endif
146  
147 < }
147 >      output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
148 >      output_ << zconsData.size() << std::endl;
149  
150 < /*
151 < *
152 < */
153 < void ZConsWriter::writeZPos(){
150 >      std::vector<ZconsData>::iterator l;
151 >      for (l = zconsData.begin(); l != zconsData.end(); ++l) {
152 >        output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" <<  l->zconsPos << std::endl;
153 >      }
154 >        
155 >    } else {
156  
157 < #ifdef IS_MPI
158 <  if(worldRank == 0){
157 >      std::list<ZconstraintMol>::const_iterator j;
158 >      for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
159 >        zmolIndex = j->mol->getGlobalIndex();            
160 >        data[0] = j->fz;
161 >        data[1] = j->zpos;
162 >        data[2] = j->param.zTargetPos;
163 >        MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
164 >        MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
165 >            
166 >      }
167 >    }
168   #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
169    }
170 < #endif
170 >
171   }

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