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root/OpenMD/trunk/src/io/StatWriter.cpp

Comparing trunk/src/io/StatWriter.cpp (file contents):
Revision 1436 by chuckv, Tue Apr 20 19:59:45 2010 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 35 | Line 35
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).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#define _LARGEFILE_SOURCE64
44		#define _FILE_OFFSET_BITS 64
45	+	#ifdef _MSC_VER
46	+	#define isnan(x) _isnan((x))
47	+	#define isinf(x) (!_finite(x) && !_isnan(x))
48	+	#endif
49
50		#include "io/StatWriter.hpp"
51	+	#include "brains/Stats.hpp"
52		#include "utils/simError.h"
53
54	+	using namespace std;
55	+
56		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	–	}
57
58	<	StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
59	<
58	>	StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){
59	>
60		#ifdef IS_MPI
61		if(worldRank == 0 ){
62		#endif // is_mpi
63	<
63	>
64		statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
65
66		if( !statfile_ ){
#	Line 109 | Line 97 | namespace OpenMD {
97		#endif // is_mpi
98		}
99
100	+
101		void StatWriter::writeTitle() {
102
103	+	Stats::StatsBitSet mask = stats_->getStatsMask();
104
105		#ifdef IS_MPI
106		if(worldRank == 0 ){
#	Line 118 | Line 108 | namespace OpenMD {
108
109		//write title
110		statfile_ << "#";
111	<	for (int i =0; i < mask_.size(); ++i) {
112	<	if (mask_[i]) {
113	<	statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
111	>	for (unsigned int i = 0; i <mask.size(); ++i) {
112	>	if (mask[i]) {
113	>	statfile_ << "\t" << stats_->getTitle(i) <<
114	>	"(" << stats_->getUnits(i) << ")";
115		}
116		}
117		statfile_ << std::endl;
#	Line 130 | Line 121 | namespace OpenMD {
121		#endif // is_mpi
122		}
123
124	<	void StatWriter::writeStat(const Stats& s){
125	<
124	>	void StatWriter::writeStat() {
125	>
126		#ifdef IS_MPI
127		if(worldRank == 0 ){
128		#endif // is_mpi
129
130	+	Stats::StatsBitSet mask = stats_->getStatsMask();
131		statfile_.precision(8);
132	<	for (int i =0; i < mask_.size(); ++i) {
133	<	if (mask_[i]) {
134	<	if (! std::isinf(s[i]) && ! std::isnan(s[i])){
135	<	statfile_ << "\t" << s[i];
136	<	}
137	<	else{
132	>	for (unsigned int i = 0; i < mask.size(); ++i) {
133	>	if (mask[i]) {
134	>	if (stats_->getDataType(i) == "RealType")
135	>	writeReal(i);
136	>	else if (stats_->getDataType(i) == "Vector3d")
137	>	writeVector(i);
138	>	else if (stats_->getDataType(i) == "Mat3x3d")
139	>	writeMatrix(i);
140	>	else {
141		sprintf( painCave.errMsg,
142	<	"Statwriter detected a numerical error writing: %s ",
143	<	Stats::getTitle(i).c_str());
142	>	"StatWriter found an unknown data type for: %s ",
143	>	stats_->getTitle(i).c_str());
144		painCave.isFatal = 1;
145		simError();
146		}
147	<
153	<	}
147	>	}
148		}
149	+
150		statfile_ << std::endl;
156	–
151		statfile_.flush();
152
153		#ifdef IS_MPI
#	Line 162 | Line 156 | namespace OpenMD {
156		#endif // is_mpi
157		}
158
159	+	void StatWriter::writeReal(int i) {
160	+
161	+	RealType s = stats_->getRealData(i);
162	+
163	+	if (! isinf(s) && ! isnan(s)) {
164	+	statfile_ << "\t" << s;
165	+	} else{
166	+	sprintf( painCave.errMsg,
167	+	"StatWriter detected a numerical error writing: %s ",
168	+	stats_->getTitle(i).c_str());
169	+	painCave.isFatal = 1;
170	+	simError();
171	+	}
172	+	}
173	+
174	+	void StatWriter::writeVector(int i) {
175	+
176	+	Vector3d s = stats_->getVectorData(i);
177	+	if (isinf(s[0]) || isnan(s[0]) ||
178	+	isinf(s[1]) || isnan(s[1]) ||
179	+	isinf(s[2]) || isnan(s[2]) ) {
180	+	sprintf( painCave.errMsg,
181	+	"StatWriter detected a numerical error writing: %s",
182	+	stats_->getTitle(i).c_str());
183	+	painCave.isFatal = 1;
184	+	simError();
185	+	} else {
186	+	statfile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
187	+	}
188	+	}
189	+
190	+	void StatWriter::writeMatrix(int i) {
191	+
192	+	Mat3x3d s = stats_->getMatrixData(i);
193	+
194	+	for (unsigned int i = 0; i < 3; i++) {
195	+	for (unsigned int j = 0; j < 3; j++) {
196	+	if (isinf(s(i,j)) || isnan(s(i,j))) {
197	+	sprintf( painCave.errMsg,
198	+	"StatWriter detected a numerical error writing: %s",
199	+	stats_->getTitle(i).c_str());
200	+	painCave.isFatal = 1;
201	+	simError();
202	+	} else {
203	+	statfile_ << "\t" << s(i,j);
204	+	}
205	+	}
206	+	}
207	+	}
208		}

Comparing trunk/src/io/StatWriter.cpp (property svn:keywords):
Revision 1436 by chuckv, Tue Apr 20 19:59:45 2010 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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