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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 1764 by gezelter, Tue Jul 3 18:32:27 2012 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, 24107 (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
46	<	#include <string.h>
47	<	#include <iostream>
48	<	#include <fstream>
46	>	#include "io/StatWriter.hpp"
47	>	#include "brains/Stats.hpp"
48	>	#include "utils/simError.h"
49
50	<	#include "ReadWrite.hpp"
9	<	#include "simError.h"
50	>	using namespace std;
51
52	<
53	<	StatWriter::StatWriter( SimInfo* the_entry_plug ){
54	<
55	<	entry_plug = the_entry_plug;
15	<
52	>	namespace OpenMD {
53	>
54	>	StatWriter::StatWriter( const std::string& filename, Stats* stats) : stats_(stats){
55	>
56		#ifdef IS_MPI
57	<	if(worldRank == 0 ){
57	>	if(worldRank == 0 ){
58		#endif // is_mpi
59	<
60	<	outName =  entry_plug->statusName;
21	<
22	<	//std::cerr << "Opening " << outName << " for stat\n";
23	<
24	<	outFile.open(outName.c_str(), ios::out | ios::trunc );
59	>
60	>	statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
61
62	<	if( !outFile ){
62	>	if( !statfile_ ){
63
64	<	sprintf( painCave.errMsg,
65	<	"Could not open \"%s\" for stat output.\n",
66	<	outName.c_str());
67	<	painCave.isFatal = 1;
68	<	simError();
64	>	sprintf( painCave.errMsg,
65	>	"Could not open \"%s\" for stat output.\n",
66	>	filename.c_str());
67	>	painCave.isFatal = 1;
68	>	simError();
69	>	}
70	>
71	>	writeTitle();
72	>
73	>	#ifdef IS_MPI
74		}
75
76	<	//outFile.setf( ios::scientific );
77	<	outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved";
76	>	sprintf( checkPointMsg,
77	>	"Sucessfully opened output file for stating.\n");
78	>	errorCheckPoint();
79	>	#endif // is_mpi
80
81	<	if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
39	<	outFile << "\tV_raw";
40	<
41	<	if (entry_plug->useSolidThermInt)
42	<	outFile << "\tV_harm";
81	>	}
82
83	<	outFile << "\n";
83	>	StatWriter::~StatWriter( ){
84
46	–
85		#ifdef IS_MPI
86	<	}
86	>	if(worldRank == 0 ){
87	>	#endif // is_mpi
88
89	<	sprintf( checkPointMsg,
90	<	"Sucessfully opened output file for stating.\n");
91	<	MPIcheckPoint();
89	>	statfile_.close();
90	>
91	>	#ifdef IS_MPI
92	>	}
93		#endif // is_mpi
94	+	}
95
55	–	tStats = new Thermo( entry_plug );
56	–	}
96
97	<	StatWriter::~StatWriter( ){
97	>	void StatWriter::writeTitle() {
98
99	+	Stats::StatsBitSet mask = stats_->getStatsMask();
100	+
101		#ifdef IS_MPI
102	<	if(worldRank == 0 ){
102	>	if(worldRank == 0 ){
103		#endif // is_mpi
104
105	<	outFile.close();
106	<	delete tStats;
105	>	//write title
106	>	statfile_ << "#";
107	>	for (int i = 0; i <mask.size(); ++i) {
108	>	if (mask[i]) {
109	>	statfile_ << "\t" << stats_->getTitle(i) <<
110	>	"(" << stats_->getUnits(i) << ")";
111	>	}
112	>	}
113	>	statfile_ << std::endl;
114
115		#ifdef IS_MPI
116	+	}
117	+	#endif // is_mpi
118		}
119	+
120	+	void StatWriter::writeStat() {
121	+
122	+	#ifdef IS_MPI
123	+	if(worldRank == 0 ){
124		#endif // is_mpi
70	–	}
125
126	<	void StatWriter::writeStat( double currentTime ){
126	>	Stats::StatsBitSet mask = stats_->getStatsMask();
127	>	statfile_.precision(8);
128	>	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	>	sprintf( painCave.errMsg,
138	>	"StatWriter found an unknown data type for: %s ",
139	>	stats_->getTitle(i).c_str());
140	>	painCave.isFatal = 1;
141	>	simError();
142	>	}
143	>	}
144	>	}
145	>
146	>	statfile_ << std::endl;
147	>	statfile_.flush();
148
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	–
149		#ifdef IS_MPI
150	<	if(worldRank == 0 ){
150	>	}
151	>	errorCheckPoint();
152		#endif // is_mpi
153	+	}
154
155	<	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;
155	>	void StatWriter::writeReal(int i) {
156
157	<	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;
157	>	RealType s = stats_->getRealData(i);
158
159	<	outFile << "\n";
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	<	outFile.flush();
170	>	void StatWriter::writeVector(int i) {
171
172	<	#ifdef IS_MPI
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		}
112	–	#endif // is_mpi
113	–	}
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	+	}

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 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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