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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 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   #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 OpenMD {
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 = OPENMD_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();
85 <    }
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 <    //outFile.setf( ios::scientific );
36 <    outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved";
37 <
38 <    if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
39 <      outFile << "\tV_raw";
87 >      writeTitle();
88      
41 –    if (entry_plug->useSolidThermInt)
42 –      outFile << "\tV_harm";
43 –
44 –    outFile << "\n";
45 –
46 –    
89   #ifdef IS_MPI
90 <  }
90 >    }
91  
92 <  sprintf( checkPointMsg,
93 <           "Sucessfully opened output file for stating.\n");
94 <  MPIcheckPoint();
92 >    sprintf( checkPointMsg,
93 >             "Sucessfully opened output file for stating.\n");
94 >    errorCheckPoint();
95   #endif // is_mpi
96  
97 <  tStats = new Thermo( entry_plug );
56 < }
97 >  }
98  
99 < StatWriter::~StatWriter( ){
99 >  StatWriter::~StatWriter( ){
100  
101   #ifdef IS_MPI
102 <  if(worldRank == 0 ){
102 >    if(worldRank == 0 ){
103   #endif // is_mpi
104  
105 <    outFile.close();
65 <    delete tStats;
105 >      statfile_.close();
106  
107   #ifdef IS_MPI
108 <  }
108 >    }
109   #endif // is_mpi
110 < }
110 >  }
111  
112 < void StatWriter::writeStat( double currentTime ){
112 >  void StatWriter::writeTitle() {
113  
74 –  double totE, potE, kinE, temp, press, vol;
75 –  double conservedQuantity;
114  
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 –
115   #ifdef IS_MPI
116 <  if(worldRank == 0 ){
116 >    if(worldRank == 0 ){
117   #endif // is_mpi
118  
119 <    outFile.precision(8);
120 <    outFile
121 <      << currentTime << "\t"
122 <      << totE << "\t"
123 <      << potE << "\t"
124 <      << kinE << "\t"
125 <      << temp << "\t"
126 <      << press << "\t"
97 <      << vol << "\t"
98 <      << conservedQuantity;
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 <    if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
129 <      outFile << "\t" << entry_plug->vRaw;
130 <    
131 <    if (entry_plug->useSolidThermInt)
104 <      outFile << "\t" << entry_plug->vHarm;
128 > #ifdef IS_MPI
129 >    }
130 > #endif // is_mpi    
131 >  }
132  
133 <    outFile << "\n";
133 >  void StatWriter::writeStat(const Stats& s){
134  
135 <    outFile.flush();
135 > #ifdef IS_MPI
136 >    if(worldRank == 0 ){
137 > #endif // is_mpi
138  
139 +      statfile_.precision(8);
140 +      for (int i =0; i < mask_.size(); ++i) {
141 +        if (mask_[i]) {
142 +          statfile_ << "\t" << s[i];
143 +        }
144 +      }
145 +      statfile_ << std::endl;
146 +
147 +      statfile_.flush();
148 +
149   #ifdef IS_MPI
150 <  }
150 >    }
151   #endif // is_mpi
152 < }
152 >  }
153  
154 + }

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