source: src/cleanUp.cpp@ 0716eac

Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
Last change on this file since 0716eac was d8c6c7, checked in by Frederik Heber <frederik.heber@…>, 8 years ago

Added GeometryObject and GeometryRegistry.

  • Property mode set to 100644
File size: 7.5 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 * Copyright (C) 2013 Frederik Heber. All rights reserved.
6 *
7 *
8 * This file is part of MoleCuilder.
9 *
10 * MoleCuilder is free software: you can redistribute it and/or modify
11 * it under the terms of the GNU General Public License as published by
12 * the Free Software Foundation, either version 2 of the License, or
13 * (at your option) any later version.
14 *
15 * MoleCuilder is distributed in the hope that it will be useful,
16 * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 * GNU General Public License for more details.
19 *
20 * You should have received a copy of the GNU General Public License
21 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
22 */
23
24/*
25 * cleanUp.cpp
26 *
27 * Created on: Oct 28, 2011
28 * Author: heber
29 */
30
31// include config.h
32#ifdef HAVE_CONFIG_H
33#include <config.h>
34#endif
35
36#include <iostream>
37#include <iomanip>
38
39//#include "CodePatterns/MemDebug.hpp"
40
41#include "cleanUp.hpp"
42
43#include "Atom/AtomObserver.hpp"
44
45#include "CodePatterns/Chronos.hpp"
46#include "CodePatterns/errorlogger.hpp"
47#include "CodePatterns/logger.hpp"
48#include "CodePatterns/Observer/ObserverLog.hpp"
49#include "CodePatterns/Observer/GlobalObservableInfo.hpp"
50
51#include "Actions/ActionQueue.hpp"
52#include "Actions/OptionRegistry.hpp"
53
54#include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
55
56#include "Geometry/GeometryRegistry.hpp"
57
58#include "MoleculeObserver.hpp"
59
60#include "Potentials/PotentialFactory.hpp"
61#include "Potentials/PotentialRegistry.hpp"
62
63#include "RandomNumbers/RandomNumberDistributionFactory.hpp"
64#include "RandomNumbers/RandomNumberEngineFactory.hpp"
65#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
66
67#include "Parser/ChangeTracker.hpp"
68#include "Parser/FormatParserStorage.hpp"
69#include "Parser/XmlParser.hpp"
70
71#include "Shapes/ShapeFactory.hpp"
72#include "Shapes/ShapeRegistry.hpp"
73
74#include "UIElements/CommandLineUI/CommandLineParser.hpp"
75#include "UIElements/Menu/MenuDescription.hpp"
76#include "UIElements/UIFactory.hpp"
77#include "World.hpp"
78#include "WorldTime.hpp"
79
80/** In this function all dynamicly allocated member variables to static/global
81 * variables are added to the ignore list of Memory/MemDebug.
82 *
83 * Use this to prevent their listing in the Memory::getState() at the end of the
84 * program. Check with valgrind that truely no memory leak occurs!
85 */
86void AddStaticEntitiestoIgnoreList()
87{
88 // XmlParser has static instance that uses vectorContent as well
89 //Memory::ignore(FormatParser< xml >::defaultAtomInfo.field.get());
90}
91
92/** purges all static (singleton) instances in correct order of dependency.
93 *
94 */
95void purgeStaticInstances()
96{
97 // make sure that ActionQueue is already purged!
98 FragmentationResultContainer::purgeInstance();
99 GeometryRegistry::purgeInstance();
100 Chronos::purgeInstance();
101 PotentialFactory::purgeInstance();
102 PotentialRegistry::purgeInstance();
103 RandomNumberDistributionFactory::purgeInstance();
104 RandomNumberEngineFactory::purgeInstance();
105 RandomNumberGeneratorFactory::purgeInstance();
106 ShapeFactory::purgeInstance();
107 ShapeRegistry::purgeInstance();
108 FormatParserStorage::purgeInstance();
109 ChangeTracker::purgeInstance();
110 World::purgeInstance();
111 AtomObserver::purgeInstance();
112 MoleculeObserver::purgeInstance();
113 MenuDescription::purgeInstance();
114 UIFactory::purgeInstance();
115 CommandLineParser::purgeInstance();
116 logger::purgeInstance();
117 errorLogger::purgeInstance();
118 WorldTime::purgeInstance();
119}
120
121void stopAndPurgeQueue()
122{
123#ifdef HAVE_ACTION_THREAD
124 // adding a wait here such that ActionQueue's run_thread is done any may stop
125 waitQueue();
126#endif
127 MoleCuilder::ActionQueue::purgeInstance();
128 MoleCuilder::OptionRegistry::purgeInstance();
129}
130
131void printTimings(const MoleCuilder::ActionQueue::ActionTokens_t &tokens);
132
133/** Cleans all singleton instances in an orderly fashion.
134 * C++ does not guarantee any specific sequence of removal of single instances
135 * which have static/global variables. Some singletons depend on others hence we
136 * ascertain a specific ordering here, which is is used via the atexit() hook.
137 */
138void cleanUp()
139{
140 // stop queue
141 const MoleCuilder::ActionQueue::ActionTokens_t tokens = MoleCuilder::ActionQueue::getInstance().getListOfActions();
142 stopAndPurgeQueue();
143 // give timings per Action, requires still present Chronos
144 printTimings(tokens);
145
146 // purge static instances from memory
147 purgeStaticInstances();
148 // put some static variables' dynamic contents on the Memory::ignore map to avoid their
149 // admonishing lateron
150 AddStaticEntitiestoIgnoreList();
151#ifdef LOG_OBSERVER
152 cout << observerLog().getLog();
153#endif
154#ifndef NDEBUG
155 // CodePatterns always initializes observerLog except with NDEBUG
156 ObserverLog::purgeInstance();
157 GlobalObservableInfo::purgeInstance();
158#endif
159 //Memory::getState();
160}
161
162/** We give a list of all times per action and a total time.
163 *
164 * We require a list of Action tokens such that we do not access the ActionQueue.
165 * Timings are printed when Actions have all been performed, hence the queue should
166 * already be purged and we cannot access it anymore.
167 *
168 * \param tokens
169 */
170void printTimings(const MoleCuilder::ActionQueue::ActionTokens_t &tokens)
171{
172// const MoleCuilder::ActionQueue::ActionTokens_t tokens = MoleCuilder::ActionQueue::getInstance().getListOfActions();
173 const Chronos &Chron = Chronos::getInstance();
174 if (!DoLog(2)) {
175 std::cout << "(Non-zero) Times used per Action [seconds]:" << std::endl;
176 for (MoleCuilder::ActionQueue::ActionTokens_t::const_iterator iter = tokens.begin();
177 iter != tokens.end(); ++iter)
178 if (Chron.getTime(*iter) != 0.) { // dont give if action has not been used
179 std::cout << " " << setiosflags(ios::left) << setw(24) << setfill('.') << *iter;
180 std::cout << setiosflags(ios::left)
181#ifdef HAVE_SYS_TIMES_H
182 << setprecision(3)
183#else
184 << setprecision(9)
185#endif
186 << fixed << Chron.getTime(*iter) << std::endl;
187 }
188 } else {
189 std::cout << "Measured times [seconds]:" << std::endl;
190 const Chronos::TimekeepingMap &timemap = Chron.getTimekeepingMap();
191 for (Chronos::TimekeepingMap::const_iterator iter = timemap.begin();
192 iter != timemap.end();
193 ++iter) {
194 std::cout << " " << setiosflags(ios::left) << setw(24) << setfill('.') << iter->first;
195 std::cout << setiosflags(ios::left)
196#ifdef HAVE_SYS_TIMES_H
197 << setprecision(3)
198#else
199 << setprecision(9)
200#endif
201 << fixed << iter->second << std::endl;
202 }
203 }
204 std::cout << "Total Time: " << Chron.SumUpTotalTime() << " seconds" << std::endl;
205 std::cout << "Total Actions called: " << Chron.SumUpTotalFunctions() << std::endl;
206}
207
208/** Dump current memory chunks.
209 *
210 */
211void dumpMemory()
212{
213 //ofstream ost("molecuilder.memdump");
214 //Memory::dumpMemory(ost);
215}
216
217/** Save the current World to output files and exit.
218 *
219 * @return retrieved from World::getExitFlag()
220 */
221int saveAll()
222{
223 FormatParserStorage::getInstance().SaveAll();
224 ChangeTracker::getInstance().saveStatus();
225
226 int ExitFlag = World::getInstance().getExitFlag();
227 return (ExitFlag == 1 ? 0 : ExitFlag);
228}
229
230#ifdef HAVE_ACTION_THREAD
231/** Stops the queue such that all Actions are done.
232 *
233 */
234void stopQueue()
235{
236 MoleCuilder::ActionQueue::getInstance().stop();
237}
238
239/** Waits for the queue to idle.
240 *
241 */
242void waitQueue()
243{
244 MoleCuilder::ActionQueue::getInstance().wait();
245}
246#endif
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