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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#define _LARGEFILE_SOURCE64
#define _FILE_OFFSET_BITS 64

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

using namespace std;

namespace OpenMD {
  
  StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){
    
#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() {

    Stats::StatsBitSet mask = stats_->getStatsMask();    

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

      Stats::StatsBitSet mask = stats_->getStatsMask();
      statfile_.precision(8);
      for (int i = 0; i < mask.size(); ++i) {
        if (mask[i]) {
          if (stats_->getDataType(i) == "RealType")
            writeReal(i);
          else if (stats_->getDataType(i) == "Vector3d")
            writeVector(i);
          else if (stats_->getDataType(i) == "Mat3x3d")
            writeMatrix(i);
          else {
            sprintf( painCave.errMsg,
                     "StatWriter found an unknown data type for: %s ",
                     stats_->getTitle(i).c_str());
            painCave.isFatal = 1;
            simError();
          }
        }
      }
            
      statfile_ << std::endl;
      statfile_.flush();

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

  void StatWriter::writeReal(int i) {

    RealType s = stats_->getRealData(i);

    if (! isinf(s) && ! isnan(s)) {
      statfile_ << "\t" << s;
    } else{
      sprintf( painCave.errMsg,
               "StatWriter detected a numerical error writing: %s ",
               stats_->getTitle(i).c_str());
      painCave.isFatal = 1;
      simError();
    }    
  }

  void StatWriter::writeVector(int i) {

    Vector3d s = stats_->getVectorData(i);
    if (isinf(s[0]) || isnan(s[0]) || 
        isinf(s[1]) || isnan(s[1]) || 
        isinf(s[2]) || isnan(s[2]) ) {      
      sprintf( painCave.errMsg,
               "StatWriter detected a numerical error writing: %s",
               stats_->getTitle(i).c_str());
      painCave.isFatal = 1;
      simError();
    } else {
      statfile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
    }
  }

  void StatWriter::writeMatrix(int i) {

    Mat3x3d s = stats_->getMatrixData(i);

    for (unsigned int i = 0; i < 3; i++) {
      for (unsigned int j = 0; j < 3; j++) {
        if (isinf(s(i,j)) || isnan(s(i,j))) {      
          sprintf( painCave.errMsg,
                   "StatWriter detected a numerical error writing: %s",
                   stats_->getTitle(i).c_str());
          painCave.isFatal = 1;
          simError();
        } else {
          statfile_ << "\t" << s(i,j);
        }
      }
    }
  }    
}
Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 10 months ago) by gezelter
File size:	5821 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	2	#define _LARGEFILE_SOURCE64
44			#define _FILE_OFFSET_BITS 64
45
46	gezelter	246	#include "io/StatWriter.hpp"
47	gezelter	1764	#include "brains/Stats.hpp"
48	tim	3	#include "utils/simError.h"
49	gezelter	2
50	gezelter	1437	using namespace std;
51
52	gezelter	1390	namespace OpenMD {
53	gezelter	1764
54			StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){
55	tim	681
56	gezelter	2	#ifdef IS_MPI
57	gezelter	507	if(worldRank == 0 ){
58	gezelter	2	#endif // is_mpi
59	gezelter	1764
60	gezelter	507	statfile_.open(filename.c_str(), std::ios::out \| std::ios::trunc );
61	gezelter	2
62	gezelter	507	if( !statfile_ ){
63	gezelter	2
64	gezelter	507	sprintf( painCave.errMsg,
65			"Could not open \"%s\" for stat output.\n",
66			filename.c_str());
67			painCave.isFatal = 1;
68			simError();
69			}
70	gezelter	2
71	gezelter	507	writeTitle();
72	gezelter	2
73			#ifdef IS_MPI
74	gezelter	507	}
75	gezelter	2
76	gezelter	507	sprintf( checkPointMsg,
77			"Sucessfully opened output file for stating.\n");
78	gezelter	1241	errorCheckPoint();
79	gezelter	2	#endif // is_mpi
80
81	gezelter	507	}
82	gezelter	2
83	gezelter	507	StatWriter::~StatWriter( ){
84	gezelter	2
85			#ifdef IS_MPI
86	gezelter	507	if(worldRank == 0 ){
87	gezelter	2	#endif // is_mpi
88
89	gezelter	507	statfile_.close();
90	gezelter	2
91			#ifdef IS_MPI
92	gezelter	507	}
93			#endif // is_mpi
94	gezelter	2	}
95
96	gezelter	1764
97	gezelter	507	void StatWriter::writeTitle() {
98	gezelter	2
99	gezelter	1764	Stats::StatsBitSet mask = stats_->getStatsMask();
100	gezelter	2
101	gezelter	246	#ifdef IS_MPI
102			if(worldRank == 0 ){
103			#endif // is_mpi
104	gezelter	2
105	gezelter	507	//write title
106			statfile_ << "#";
107	gezelter	1764	for (int i = 0; i <mask.size(); ++i) {
108			if (mask[i]) {
109			statfile_ << "\t" << stats_->getTitle(i) <<
110			"(" << stats_->getUnits(i) << ")";
111	gezelter	507	}
112			}
113			statfile_ << std::endl;
114	gezelter	246
115	gezelter	2	#ifdef IS_MPI
116	gezelter	507	}
117			#endif // is_mpi
118	gezelter	246	}
119
120	gezelter	1764	void StatWriter::writeStat() {
121
122	gezelter	246	#ifdef IS_MPI
123			if(worldRank == 0 ){
124	gezelter	2	#endif // is_mpi
125
126	gezelter	1764	Stats::StatsBitSet mask = stats_->getStatsMask();
127	gezelter	507	statfile_.precision(8);
128	gezelter	1764	for (int i = 0; i < mask.size(); ++i) {
129			if (mask[i]) {
130			if (stats_->getDataType(i) == "RealType")
131			writeReal(i);
132			else if (stats_->getDataType(i) == "Vector3d")
133			writeVector(i);
134			else if (stats_->getDataType(i) == "Mat3x3d")
135			writeMatrix(i);
136			else {
137	chuckv	1436	sprintf( painCave.errMsg,
138	gezelter	1764	"StatWriter found an unknown data type for: %s ",
139			stats_->getTitle(i).c_str());
140	chuckv	1436	painCave.isFatal = 1;
141			simError();
142	gezelter	1764	}
143			}
144	gezelter	507	}
145	gezelter	1764
146	gezelter	507	statfile_ << std::endl;
147			statfile_.flush();
148	gezelter	2
149			#ifdef IS_MPI
150	gezelter	246	}
151	chuckv	1436	errorCheckPoint();
152	gezelter	2	#endif // is_mpi
153	gezelter	507	}
154	gezelter	2
155	gezelter	1764	void StatWriter::writeReal(int i) {
156
157			RealType s = stats_->getRealData(i);
158
159			if (! isinf(s) && ! isnan(s)) {
160			statfile_ << "\t" << s;
161			} else{
162			sprintf( painCave.errMsg,
163			"StatWriter detected a numerical error writing: %s ",
164			stats_->getTitle(i).c_str());
165			painCave.isFatal = 1;
166			simError();
167			}
168			}
169
170			void StatWriter::writeVector(int i) {
171
172			Vector3d s = stats_->getVectorData(i);
173			if (isinf(s[0]) \|\| isnan(s[0]) \|\|
174			isinf(s[1]) \|\| isnan(s[1]) \|\|
175			isinf(s[2]) \|\| isnan(s[2]) ) {
176			sprintf( painCave.errMsg,
177			"StatWriter detected a numerical error writing: %s",
178			stats_->getTitle(i).c_str());
179			painCave.isFatal = 1;
180			simError();
181			} else {
182			statfile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
183			}
184			}
185
186			void StatWriter::writeMatrix(int i) {
187
188			Mat3x3d s = stats_->getMatrixData(i);
189
190			for (unsigned int i = 0; i < 3; i++) {
191			for (unsigned int j = 0; j < 3; j++) {
192			if (isinf(s(i,j)) \|\| isnan(s(i,j))) {
193			sprintf( painCave.errMsg,
194			"StatWriter detected a numerical error writing: %s",
195			stats_->getTitle(i).c_str());
196			painCave.isFatal = 1;
197			simError();
198			} else {
199			statfile_ << "\t" << s(i,j);
200			}
201			}
202			}
203			}
204	gezelter	246	}