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root/OpenMD/trunk/src/io/StatWriter.cpp
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Comparing trunk/src/io/StatWriter.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 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   #define _LARGEFILE_SOURCE64
43   #define _FILE_OFFSET_BITS 64
44  
45 < #include <string.h>
46 < #include <iostream>
6 < #include <fstream>
45 > #include "io/StatWriter.hpp"
46 > #include "utils/simError.h"
47  
48 < #include "ReadWrite.hpp"
49 < #include "simError.h"
48 > namespace oopse {
49 >  StatsBitSet parseStatFileFormat(const std::string& format) {
50 >    StringTokenizer tokenizer(format, " ,;|\t\n\r");
51 >    StatsBitSet mask;
52 >    while(tokenizer.hasMoreTokens()) {
53 >        std::string token(tokenizer.nextToken());
54 >        toUpper(token);
55 >        Stats::StatsMapType::iterator i = Stats::statsMap.find(token);
56 >        if (i != Stats::statsMap.end()) {
57 >            mask.set(i->second);
58 >        } else {
59 >          sprintf( painCave.errMsg,
60 >                       "%s is not a valid statFileFormat keyword.\n", token.c_str() );
61 >          painCave.isFatal = 0;
62 >          painCave.severity = OOPSE_ERROR;
63 >          simError();            
64 >        }
65 >    }
66 >    
67 >    return mask;
68 >  }
69 >  
70 >  StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
71  
11 –
12 – StatWriter::StatWriter( SimInfo* the_entry_plug ){
13 –
14 –  entry_plug = the_entry_plug;
15 –
72   #ifdef IS_MPI
73 <  if(worldRank == 0 ){
73 >    if(worldRank == 0 ){
74   #endif // is_mpi
75  
76 <    outName =  entry_plug->statusName;
21 <
22 <    //std::cerr << "Opening " << outName << " for stat\n";
23 <
24 <    outFile.open(outName.c_str(), ios::out | ios::trunc );
76 >      statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
77      
78 <    if( !outFile ){
78 >      if( !statfile_ ){
79        
80 <      sprintf( painCave.errMsg,
81 <               "Could not open \"%s\" for stat output.\n",
82 <               outName.c_str());
83 <      painCave.isFatal = 1;
84 <      simError();
80 >        sprintf( painCave.errMsg,
81 >                 "Could not open \"%s\" for stat output.\n",
82 >                 filename.c_str());
83 >        painCave.isFatal = 1;
84 >        simError();
85 >      }
86 >
87 >      writeTitle();
88 >    
89 > #ifdef IS_MPI
90      }
91  
92 <    //outFile.setf( ios::scientific );
93 <    outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved";
92 >    sprintf( checkPointMsg,
93 >             "Sucessfully opened output file for stating.\n");
94 >    errorCheckPoint();
95 > #endif // is_mpi
96  
97 <    if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
39 <      outFile << "\tV_raw";
40 <    
41 <    if (entry_plug->useSolidThermInt)
42 <      outFile << "\tV_harm";
97 >  }
98  
99 <    outFile << "\n";
99 >  StatWriter::~StatWriter( ){
100  
46 –    
101   #ifdef IS_MPI
102 <  }
102 >    if(worldRank == 0 ){
103 > #endif // is_mpi
104  
105 <  sprintf( checkPointMsg,
106 <           "Sucessfully opened output file for stating.\n");
107 <  MPIcheckPoint();
105 >      statfile_.close();
106 >
107 > #ifdef IS_MPI
108 >    }
109   #endif // is_mpi
110 +  }
111  
112 <  tStats = new Thermo( entry_plug );
56 < }
112 >  void StatWriter::writeTitle() {
113  
58 – StatWriter::~StatWriter( ){
114  
115   #ifdef IS_MPI
116 <  if(worldRank == 0 ){
116 >    if(worldRank == 0 ){
117   #endif // is_mpi
118  
119 <    outFile.close();
120 <    delete tStats;
119 >      //write title
120 >      statfile_ << "#";
121 >      for (int i =0; i < mask_.size(); ++i) {
122 >        if (mask_[i]) {
123 >          statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
124 >        }
125 >      }
126 >      statfile_ << std::endl;
127  
128   #ifdef IS_MPI
129 +    }
130 + #endif // is_mpi    
131    }
69 – #endif // is_mpi
70 – }
132  
133 < void StatWriter::writeStat( double currentTime ){
133 >  void StatWriter::writeStat(const Stats& s){
134  
74 –  double totE, potE, kinE, temp, press, vol;
75 –  double conservedQuantity;
76 –
77 –  totE = tStats->getTotalE();
78 –  potE = tStats->getPotential();
79 –  kinE = tStats->getKinetic();
80 –  temp = tStats->getTemperature();
81 –  press = tStats->getPressure();
82 –  vol = tStats->getVolume();
83 –  conservedQuantity = entry_plug->the_integrator->getConservedQuantity();
84 –
135   #ifdef IS_MPI
136 <  if(worldRank == 0 ){
136 >    if(worldRank == 0 ){
137   #endif // is_mpi
138  
139 <    outFile.precision(8);
90 <    outFile
91 <      << currentTime << "\t"
92 <      << totE << "\t"
93 <      << potE << "\t"
94 <      << kinE << "\t"
95 <      << temp << "\t"
96 <      << press << "\t"
97 <      << vol << "\t"
98 <      << conservedQuantity;
139 >      statfile_.precision(8);
140  
141 <    if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
142 <      outFile << "\t" << entry_plug->vRaw;
143 <    
144 <    if (entry_plug->useSolidThermInt)
145 <      outFile << "\t" << entry_plug->vHarm;
141 >      for (int i =0; i < mask_.size(); ++i) {
142 >        if (mask_[i]) {
143 >          statfile_ << "\t" << s[i];
144 >        }
145 >      }
146 >      statfile_ << std::endl;
147  
148 <    outFile << "\n";
148 >      statfile_.flush();
149  
108 –    outFile.flush();
109 –
150   #ifdef IS_MPI
151 <  }
151 >    }
152   #endif // is_mpi
153 < }
153 >  }
154  
155 + }

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