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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 1465 by chuckv, Fri Jul 9 23:08:25 2010 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]  Vardeman & Gezelter, in progress (2009).
40	+	*/
41	+
42		#define _LARGEFILE_SOURCE64
43		#define _FILE_OFFSET_BITS 64
44
45	<	#include <string.h>
46	<	#include <iostream>
6	<	#include <fstream>
45	>	#include "io/StatWriter.hpp"
46	>	#include "utils/simError.h"
47
48	<	#include "ReadWrite.hpp"
9	<	#include "simError.h"
48	>	using namespace std;
49
50	+	namespace OpenMD {
51	+	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	+	painCave.severity = OPENMD_ERROR;
65	+	simError();
66	+	}
67	+	}
68	+
69	+	return mask;
70	+	}
71	+
72	+	StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
73
12	–	StatWriter::StatWriter( SimInfo* the_entry_plug ){
13	–
14	–	entry_plug = the_entry_plug;
15	–
74		#ifdef IS_MPI
75	<	if(worldRank == 0 ){
75	>	if(worldRank == 0 ){
76		#endif // is_mpi
77
78	<	outName =  entry_plug->statusName;
21	<
22	<	//std::cerr << "Opening " << outName << " for stat\n";
23	<
24	<	outFile.open(outName.c_str(), ios::out | ios::trunc );
78	>	statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
79
80	<	if( !outFile ){
80	>	if( !statfile_ ){
81
82	<	sprintf( painCave.errMsg,
83	<	"Could not open \"%s\" for stat output.\n",
84	<	outName.c_str());
85	<	painCave.isFatal = 1;
86	<	simError();
87	<	}
82	>	sprintf( painCave.errMsg,
83	>	"Could not open \"%s\" for stat output.\n",
84	>	filename.c_str());
85	>	painCave.isFatal = 1;
86	>	simError();
87	>	}
88
89	<	//outFile.setf( ios::scientific );
36	<	outFile << "#time(fs)\tE_tot\tV\tKE\tT(K)\tP(atm)\tVol(A^3)\tH_conserved";
37	<
38	<	if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
39	<	outFile << "\tV_raw";
89	>	writeTitle();
90
41	–	if (entry_plug->useSolidThermInt)
42	–	outFile << "\tV_harm";
43	–
44	–	outFile << "\n";
45	–
46	–
91		#ifdef IS_MPI
92	<	}
92	>	}
93
94	<	sprintf( checkPointMsg,
95	<	"Sucessfully opened output file for stating.\n");
96	<	MPIcheckPoint();
94	>	sprintf( checkPointMsg,
95	>	"Sucessfully opened output file for stating.\n");
96	>	errorCheckPoint();
97		#endif // is_mpi
98
99	<	tStats = new Thermo( entry_plug );
56	<	}
99	>	}
100
101	<	StatWriter::~StatWriter( ){
101	>	StatWriter::~StatWriter( ){
102
103		#ifdef IS_MPI
104	<	if(worldRank == 0 ){
104	>	if(worldRank == 0 ){
105		#endif // is_mpi
106
107	<	outFile.close();
65	<	delete tStats;
107	>	statfile_.close();
108
109		#ifdef IS_MPI
110	<	}
110	>	}
111		#endif // is_mpi
112	<	}
112	>	}
113
114	<	void StatWriter::writeStat( double currentTime ){
114	>	void StatWriter::writeTitle() {
115
74	–	double totE, potE, kinE, temp, press, vol;
75	–	double conservedQuantity;
116
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	–
117		#ifdef IS_MPI
118	<	if(worldRank == 0 ){
118	>	if(worldRank == 0 ){
119		#endif // is_mpi
120
121	<	outFile.precision(8);
122	<	outFile
123	<	<< currentTime << "\t"
124	<	<< totE << "\t"
125	<	<< potE << "\t"
126	<	<< kinE << "\t"
127	<	<< temp << "\t"
128	<	<< press << "\t"
97	<	<< vol << "\t"
98	<	<< conservedQuantity;
121	>	//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
130	<	if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
131	<	outFile << "\t" << entry_plug->vRaw;
132	<
133	<	if (entry_plug->useSolidThermInt)
104	<	outFile << "\t" << entry_plug->vHarm;
130	>	#ifdef IS_MPI
131	>	}
132	>	#endif // is_mpi
133	>	}
134
135	<	outFile << "\n";
135	>	void StatWriter::writeStat(const Stats& s){
136
137	<	outFile.flush();
137	>	#ifdef IS_MPI
138	>	if(worldRank == 0 ){
139	>	#endif // is_mpi
140
141	+	statfile_.precision(8);
142	+	for (int i =0; i < mask_.size(); ++i) {
143	+	if (mask_[i]) {
144	+	if (! isinf(s[i]) && ! isnan(s[i])){
145	+	statfile_ << "\t" << s[i];
146	+	}
147	+	else{
148	+	sprintf( painCave.errMsg,
149	+	"StatWriter detected a numerical error writing: %s ",
150	+	Stats::getTitle(i).c_str());
151	+	painCave.isFatal = 1;
152	+	simError();
153	+	}
154	+	}
155	+	}
156	+	statfile_ << std::endl;
157	+
158	+	statfile_.flush();
159	+
160		#ifdef IS_MPI
161	<	}
161	>	}
162	>	errorCheckPoint();
163		#endif // is_mpi
164	<	}
164	>	}
165
166	+	}

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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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