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root/OpenMD/branches/development/src/io/StatWriter.cpp

Comparing:
trunk/src/io/StatWriter.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/io/StatWriter.cpp (file contents), Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

#	Line 1 | Line 1
1	+	/*
2	+	* Copyright (c) 2005, 2010 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, 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 <string.h>
51	<	#include <iostream>
52	<	#include <fstream>
50	>	#include "io/StatWriter.hpp"
51	>	#include "brains/Stats.hpp"
52	>	#include "utils/simError.h"
53
54	<	#include "ReadWrite.hpp"
9	<	#include "simError.h"
54	>	using namespace std;
55
56	<
57	<	StatWriter::StatWriter( SimInfo* the_entry_plug ){
58	<
59	<	entry_plug = the_entry_plug;
15	<
56	>	namespace OpenMD {
57	>
58	>	StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){
59	>
60		#ifdef IS_MPI
61	<	if(worldRank == 0 ){
61	>	if(worldRank == 0 ){
62		#endif // is_mpi
63	<
64	<	outName =  entry_plug->statusName;
21	<
22	<	//std::cerr << "Opening " << outName << " for stat\n";
23	<
24	<	outFile.open(outName.c_str(), ios::out | ios::trunc );
63	>
64	>	statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
65
66	<	if( !outFile ){
66	>	if( !statfile_ ){
67
68	<	sprintf( painCave.errMsg,
69	<	"Could not open \"%s\" for stat output.\n",
70	<	outName.c_str());
71	<	painCave.isFatal = 1;
72	<	simError();
68	>	sprintf( painCave.errMsg,
69	>	"Could not open \"%s\" for stat output.\n",
70	>	filename.c_str());
71	>	painCave.isFatal = 1;
72	>	simError();
73	>	}
74	>
75	>	writeTitle();
76	>
77	>	#ifdef IS_MPI
78		}
79
80	<	//outFile.setf( ios::scientific );
81	<	outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved";
80	>	sprintf( checkPointMsg,
81	>	"Sucessfully opened output file for stating.\n");
82	>	errorCheckPoint();
83	>	#endif // is_mpi
84
85	<	if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
39	<	outFile << "\tV_raw";
40	<
41	<	if (entry_plug->useSolidThermInt)
42	<	outFile << "\tV_harm";
85	>	}
86
87	<	outFile << "\n";
87	>	StatWriter::~StatWriter( ){
88
46	–
89		#ifdef IS_MPI
90	<	}
90	>	if(worldRank == 0 ){
91	>	#endif // is_mpi
92
93	<	sprintf( checkPointMsg,
94	<	"Sucessfully opened output file for stating.\n");
95	<	MPIcheckPoint();
93	>	statfile_.close();
94	>
95	>	#ifdef IS_MPI
96	>	}
97		#endif // is_mpi
98	+	}
99
55	–	tStats = new Thermo( entry_plug );
56	–	}
100
101	<	StatWriter::~StatWriter( ){
101	>	void StatWriter::writeTitle() {
102
103	+	Stats::StatsBitSet mask = stats_->getStatsMask();
104	+
105		#ifdef IS_MPI
106	<	if(worldRank == 0 ){
106	>	if(worldRank == 0 ){
107		#endif // is_mpi
108
109	<	outFile.close();
110	<	delete tStats;
109	>	//write title
110	>	statfile_ << "#";
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;
118
119		#ifdef IS_MPI
120	+	}
121	+	#endif // is_mpi
122		}
123	+
124	+	void StatWriter::writeStat() {
125	+
126	+	#ifdef IS_MPI
127	+	if(worldRank == 0 ){
128		#endif // is_mpi
70	–	}
129
130	<	void StatWriter::writeStat( double currentTime ){
130	>	Stats::StatsBitSet mask = stats_->getStatsMask();
131	>	statfile_.precision(8);
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 found an unknown data type for: %s ",
143	>	stats_->getTitle(i).c_str());
144	>	painCave.isFatal = 1;
145	>	simError();
146	>	}
147	>	}
148	>	}
149	>
150	>	statfile_ << std::endl;
151	>	statfile_.flush();
152
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	–
153		#ifdef IS_MPI
154	<	if(worldRank == 0 ){
154	>	}
155	>	errorCheckPoint();
156		#endif // is_mpi
157	+	}
158
159	<	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;
159	>	void StatWriter::writeReal(int i) {
160
161	<	if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
101	<	outFile << "\t" << entry_plug->vRaw;
102	<
103	<	if (entry_plug->useSolidThermInt)
104	<	outFile << "\t" << entry_plug->vHarm;
161	>	RealType s = stats_->getRealData(i);
162
163	<	outFile << "\n";
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	<	outFile.flush();
174	>	void StatWriter::writeVector(int i) {
175
176	<	#ifdef IS_MPI
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		}
112	–	#endif // is_mpi
113	–	}
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 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/io/StatWriter.cpp (property svn:keywords), Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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