src/io/StatWriter.cpp

/*
 * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#define _LARGEFILE_SOURCE64
#define _FILE_OFFSET_BITS 64

#include "io/StatWriter.hpp"
#include "utils/simError.h"

using namespace std;

namespace OpenMD {
  StatsBitSet parseStatFileFormat(const std::string& format) {
    StringTokenizer tokenizer(format, " ,;|\t\n\r");
    StatsBitSet mask;
    while(tokenizer.hasMoreTokens()) {
        std::string token(tokenizer.nextToken());
        toUpper(token);
        Stats::StatsMapType::iterator i = Stats::statsMap.find(token);
        if (i != Stats::statsMap.end()) {
            mask.set(i->second);
        } else {
          sprintf( painCave.errMsg,
                       "%s is not a valid statFileFormat keyword.\n", token.c_str() );
          painCave.isFatal = 0;
          painCave.severity = OPENMD_ERROR;
          simError();            
        }
    }
    
    return mask;
  }
  
  StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){

#ifdef IS_MPI
    if(worldRank == 0 ){
#endif // is_mpi

      statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
    
      if( !statfile_ ){
      
        sprintf( painCave.errMsg,
                 "Could not open \"%s\" for stat output.\n",
                 filename.c_str());
        painCave.isFatal = 1;
        simError();
      }

      writeTitle();
    
#ifdef IS_MPI
    }

    sprintf( checkPointMsg,
             "Sucessfully opened output file for stating.\n");
    errorCheckPoint();
#endif // is_mpi

  }

  StatWriter::~StatWriter( ){

#ifdef IS_MPI
    if(worldRank == 0 ){
#endif // is_mpi

      statfile_.close();

#ifdef IS_MPI
    }
#endif // is_mpi
  }

  void StatWriter::writeTitle() {


#ifdef IS_MPI
    if(worldRank == 0 ){
#endif // is_mpi

      //write title
      statfile_ << "#";
      for (int i =0; i < mask_.size(); ++i) {
        if (mask_[i]) {
          statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
        }
      }
      statfile_ << std::endl;

#ifdef IS_MPI
    }
#endif // is_mpi    
  }

  void StatWriter::writeStat(const Stats& s){

#ifdef IS_MPI
    if(worldRank == 0 ){
#endif // is_mpi

      statfile_.precision(8);
      for (int i =0; i < mask_.size(); ++i) {
        if (mask_[i]) {
          if (! isinf(s[i]) && ! isnan(s[i])){
            statfile_ << "\t" << s[i];
          }
          else{
            sprintf( painCave.errMsg,
                     "StatWriter detected a numerical error writing: %s ",
                     Stats::getTitle(i).c_str());
            painCave.isFatal = 1;
            simError();
          }          
        }
      }
      statfile_ << std::endl;

      statfile_.flush();

#ifdef IS_MPI
    }
    errorCheckPoint();
#endif // is_mpi
  }

}
Revision:	1437
Committed:	Wed Apr 21 14:59:18 2010 UTC (15 years ago) by gezelter
File size:	4758 byte(s)
Log Message:	Adding nan/inf detection to DumpWriter, fixing one message
#	User	Rev	Content
1	gezelter	507	/*
2	chuckv	1436	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3	gezelter	246	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	246	*/
41
42	gezelter	2	#define _LARGEFILE_SOURCE64
43			#define _FILE_OFFSET_BITS 64
44
45	gezelter	246	#include "io/StatWriter.hpp"
46	tim	3	#include "utils/simError.h"
47	gezelter	2
48	gezelter	1437	using namespace std;
49
50	gezelter	1390	namespace OpenMD {
51	tim	681	StatsBitSet parseStatFileFormat(const std::string& format) {
52			StringTokenizer tokenizer(format, " ,;\|\t\n\r");
53			StatsBitSet mask;
54			while(tokenizer.hasMoreTokens()) {
55			std::string token(tokenizer.nextToken());
56			toUpper(token);
57			Stats::StatsMapType::iterator i = Stats::statsMap.find(token);
58			if (i != Stats::statsMap.end()) {
59			mask.set(i->second);
60			} else {
61			sprintf( painCave.errMsg,
62			"%s is not a valid statFileFormat keyword.\n", token.c_str() );
63			painCave.isFatal = 0;
64	gezelter	1390	painCave.severity = OPENMD_ERROR;
65	tim	681	simError();
66			}
67			}
68
69			return mask;
70			}
71
72	gezelter	507	StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
73	gezelter	2
74			#ifdef IS_MPI
75	gezelter	507	if(worldRank == 0 ){
76	gezelter	2	#endif // is_mpi
77
78	gezelter	507	statfile_.open(filename.c_str(), std::ios::out \| std::ios::trunc );
79	gezelter	2
80	gezelter	507	if( !statfile_ ){
81	gezelter	2
82	gezelter	507	sprintf( painCave.errMsg,
83			"Could not open \"%s\" for stat output.\n",
84			filename.c_str());
85			painCave.isFatal = 1;
86			simError();
87			}
88	gezelter	2
89	gezelter	507	writeTitle();
90	gezelter	2
91			#ifdef IS_MPI
92	gezelter	507	}
93	gezelter	2
94	gezelter	507	sprintf( checkPointMsg,
95			"Sucessfully opened output file for stating.\n");
96	gezelter	1241	errorCheckPoint();
97	gezelter	2	#endif // is_mpi
98
99	gezelter	507	}
100	gezelter	2
101	gezelter	507	StatWriter::~StatWriter( ){
102	gezelter	2
103			#ifdef IS_MPI
104	gezelter	507	if(worldRank == 0 ){
105	gezelter	2	#endif // is_mpi
106
107	gezelter	507	statfile_.close();
108	gezelter	2
109			#ifdef IS_MPI
110	gezelter	507	}
111			#endif // is_mpi
112	gezelter	2	}
113
114	gezelter	507	void StatWriter::writeTitle() {
115	gezelter	2
116
117	gezelter	246	#ifdef IS_MPI
118			if(worldRank == 0 ){
119			#endif // is_mpi
120	gezelter	2
121	gezelter	507	//write title
122			statfile_ << "#";
123			for (int i =0; i < mask_.size(); ++i) {
124			if (mask_[i]) {
125			statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
126			}
127			}
128			statfile_ << std::endl;
129	gezelter	246
130	gezelter	2	#ifdef IS_MPI
131	gezelter	507	}
132			#endif // is_mpi
133	gezelter	246	}
134
135	gezelter	507	void StatWriter::writeStat(const Stats& s){
136	gezelter	246
137			#ifdef IS_MPI
138			if(worldRank == 0 ){
139	gezelter	2	#endif // is_mpi
140
141	gezelter	507	statfile_.precision(8);
142			for (int i =0; i < mask_.size(); ++i) {
143			if (mask_[i]) {
144	gezelter	1437	if (! isinf(s[i]) && ! isnan(s[i])){
145			statfile_ << "\t" << s[i];
146	chuckv	1436	}
147			else{
148			sprintf( painCave.errMsg,
149	gezelter	1437	"StatWriter detected a numerical error writing: %s ",
150	chuckv	1436	Stats::getTitle(i).c_str());
151			painCave.isFatal = 1;
152			simError();
153	gezelter	1437	}
154	gezelter	507	}
155			}
156			statfile_ << std::endl;
157	gezelter	2
158	gezelter	507	statfile_.flush();
159	gezelter	2
160			#ifdef IS_MPI
161	gezelter	246	}
162	chuckv	1436	errorCheckPoint();
163	gezelter	2	#endif // is_mpi
164	gezelter	507	}
165	gezelter	2
166	gezelter	246	}