ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/io/StatWriter.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/io/StatWriter.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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>
5	<	#include <iostream>
6	<	#include <fstream>
7	<
8	<	#include "io/ReadWrite.hpp"
46	>	#include "io/StatWriter.hpp"
47		#include "utils/simError.h"
48
49	+	using namespace std;
50
51	<	StatWriter::StatWriter( SimInfo* the_entry_plug ){
51	>	namespace OpenMD {
52	>	StatsBitSet parseStatFileFormat(const std::string& format) {
53	>	StringTokenizer tokenizer(format, " ,;|\t\n\r");
54	>	StatsBitSet mask;
55	>	while(tokenizer.hasMoreTokens()) {
56	>	std::string token(tokenizer.nextToken());
57	>	toUpper(token);
58	>	Stats::StatsMapType::iterator i = Stats::statsMap.find(token);
59	>	if (i != Stats::statsMap.end()) {
60	>	mask.set(i->second);
61	>	} else {
62	>	sprintf( painCave.errMsg,
63	>	"%s is not a valid statFileFormat keyword.\n", token.c_str() );
64	>	painCave.isFatal = 0;
65	>	painCave.severity = OPENMD_ERROR;
66	>	simError();
67	>	}
68	>	}
69	>
70	>	return mask;
71	>	}
72	>
73	>	StatWriter::StatWriter( const std::string& filename, const StatsBitSet& mask) : mask_(mask){
74
14	–	entry_plug = the_entry_plug;
15	–
75		#ifdef IS_MPI
76	<	if(worldRank == 0 ){
76	>	if(worldRank == 0 ){
77		#endif // is_mpi
78
79	<	outName =  entry_plug->statusName;
21	<
22	<	//std::cerr << "Opening " << outName << " for stat\n";
23	<
24	<	outFile.open(outName.c_str(), ios::out | ios::trunc );
79	>	statfile_.open(filename.c_str(), std::ios::out | std::ios::trunc );
80
81	<	if( !outFile ){
81	>	if( !statfile_ ){
82
83	<	sprintf( painCave.errMsg,
84	<	"Could not open \"%s\" for stat output.\n",
85	<	outName.c_str());
86	<	painCave.isFatal = 1;
87	<	simError();
88	<	}
83	>	sprintf( painCave.errMsg,
84	>	"Could not open \"%s\" for stat output.\n",
85	>	filename.c_str());
86	>	painCave.isFatal = 1;
87	>	simError();
88	>	}
89
90	<	//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";
90	>	writeTitle();
91
41	–	if (entry_plug->useSolidThermInt)
42	–	outFile << "\tV_harm";
43	–
44	–	outFile << "\n";
45	–
46	–
92		#ifdef IS_MPI
93	<	}
93	>	}
94
95	<	sprintf( checkPointMsg,
96	<	"Sucessfully opened output file for stating.\n");
97	<	MPIcheckPoint();
95	>	sprintf( checkPointMsg,
96	>	"Sucessfully opened output file for stating.\n");
97	>	errorCheckPoint();
98		#endif // is_mpi
99
100	<	tStats = new Thermo( entry_plug );
56	<	}
100	>	}
101
102	<	StatWriter::~StatWriter( ){
102	>	StatWriter::~StatWriter( ){
103
104		#ifdef IS_MPI
105	<	if(worldRank == 0 ){
105	>	if(worldRank == 0 ){
106		#endif // is_mpi
107
108	<	outFile.close();
65	<	delete tStats;
108	>	statfile_.close();
109
110		#ifdef IS_MPI
111	<	}
111	>	}
112		#endif // is_mpi
113	<	}
113	>	}
114
115	<	void StatWriter::writeStat( double currentTime ){
115	>	void StatWriter::writeTitle() {
116
74	–	double totE, potE, kinE, temp, press, vol;
75	–	double conservedQuantity;
117
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	–
118		#ifdef IS_MPI
119	<	if(worldRank == 0 ){
119	>	if(worldRank == 0 ){
120		#endif // is_mpi
121
122	<	outFile.precision(8);
123	<	outFile
124	<	<< currentTime << "\t"
125	<	<< totE << "\t"
126	<	<< potE << "\t"
127	<	<< kinE << "\t"
128	<	<< temp << "\t"
129	<	<< press << "\t"
97	<	<< vol << "\t"
98	<	<< conservedQuantity;
122	>	//write title
123	>	statfile_ << "#";
124	>	for (int i =0; i < mask_.size(); ++i) {
125	>	if (mask_[i]) {
126	>	statfile_ << "\t" << Stats::getTitle(i) << "(" << Stats::getUnits(i) << ")";
127	>	}
128	>	}
129	>	statfile_ << std::endl;
130
131	<	if (entry_plug->useSolidThermInt || entry_plug->useLiquidThermInt)
132	<	outFile << "\t" << entry_plug->vRaw;
133	<
134	<	if (entry_plug->useSolidThermInt)
104	<	outFile << "\t" << entry_plug->vHarm;
131	>	#ifdef IS_MPI
132	>	}
133	>	#endif // is_mpi
134	>	}
135
136	<	outFile << "\n";
136	>	void StatWriter::writeStat(const Stats& s){
137
138	<	outFile.flush();
138	>	#ifdef IS_MPI
139	>	if(worldRank == 0 ){
140	>	#endif // is_mpi
141
142	+	statfile_.precision(8);
143	+	for (int i =0; i < mask_.size(); ++i) {
144	+	if (mask_[i]) {
145	+	if (! isinf(s[i]) && ! isnan(s[i])){
146	+	statfile_ << "\t" << s[i];
147	+	}
148	+	else{
149	+	sprintf( painCave.errMsg,
150	+	"StatWriter detected a numerical error writing: %s ",
151	+	Stats::getTitle(i).c_str());
152	+	painCave.isFatal = 1;
153	+	simError();
154	+	}
155	+	}
156	+	}
157	+	statfile_ << std::endl;
158	+
159	+	statfile_.flush();
160	+
161		#ifdef IS_MPI
162	<	}
162	>	}
163	>	errorCheckPoint();
164		#endif // is_mpi
165	<	}
165	>	}
166
167	+	}

Comparing:
trunk/src/io/StatWriter.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/io/StatWriter.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines