source: src/World.cpp@ 2f40c0e

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 2f40c0e was 55240c4, checked in by Frederik Heber <heber@…>, 15 years ago

Merge branch 'stable' into PcpAndMpqcParser

Conflicts:

molecuilder/src/Makefile.am

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File size: 7.3 KB
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1/*
2 * World.cpp
3 *
4 * Created on: Feb 3, 2010
5 * Author: crueger
6 */
7
8#include "Helpers/MemDebug.hpp"
9
10#include "World.hpp"
11
12#include "atom.hpp"
13#include "config.hpp"
14#include "molecule.hpp"
15#include "periodentafel.hpp"
16#include "ThermoStatContainer.hpp"
17#include "Descriptors/AtomDescriptor.hpp"
18#include "Descriptors/AtomDescriptor_impl.hpp"
19#include "Descriptors/MoleculeDescriptor.hpp"
20#include "Descriptors/MoleculeDescriptor_impl.hpp"
21#include "Descriptors/SelectiveIterator_impl.hpp"
22#include "Actions/ManipulateAtomsProcess.hpp"
23
24#include "Patterns/Singleton_impl.hpp"
25
26using namespace std;
27
28/******************************* getter and setter ************************/
29periodentafel *&World::getPeriode(){
30 return periode;
31}
32
33config *&World::getConfig(){
34 return configuration;
35}
36
37// Atoms
38
39atom* World::getAtom(AtomDescriptor descriptor){
40 return descriptor.find();
41}
42
43vector<atom*> World::getAllAtoms(AtomDescriptor descriptor){
44 return descriptor.findAll();
45}
46
47vector<atom*> World::getAllAtoms(){
48 return getAllAtoms(AllAtoms());
49}
50
51int World::numAtoms(){
52 return atoms.size();
53}
54
55// Molecules
56
57molecule *World::getMolecule(MoleculeDescriptor descriptor){
58 return descriptor.find();
59}
60
61std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
62 return descriptor.findAll();
63}
64
65std::vector<molecule*> World::getAllMolecules(){
66 return getAllMolecules(AllMolecules());
67}
68
69int World::numMolecules(){
70 return molecules_deprecated->ListOfMolecules.size();
71}
72
73// system
74
75double * World::getDomain() {
76 return cell_size;
77}
78
79void World::setDomain(double * matrix)
80{
81
82}
83
84std::string World::getDefaultName() {
85 return defaultName;
86}
87
88void World::setDefaultName(std::string name)
89{
90 defaultName = name;
91};
92
93class ThermoStatContainer * World::getThermostats()
94{
95 return Thermostats;
96}
97
98
99int World::getExitFlag() {
100 return ExitFlag;
101}
102
103void World::setExitFlag(int flag) {
104 if (ExitFlag < flag)
105 ExitFlag = flag;
106}
107
108/******************** Methods to change World state *********************/
109
110molecule* World::createMolecule(){
111 OBSERVE;
112 molecule *mol = NULL;
113 mol = NewMolecule();
114 assert(!molecules.count(currMoleculeId));
115 mol->setId(currMoleculeId++);
116 // store the molecule by ID
117 molecules[mol->getId()] = mol;
118 mol->signOn(this);
119 return mol;
120}
121
122void World::destroyMolecule(molecule* mol){
123 OBSERVE;
124 destroyMolecule(mol->getId());
125}
126
127void World::destroyMolecule(moleculeId_t id){
128 OBSERVE;
129 molecule *mol = molecules[id];
130 assert(mol);
131 DeleteMolecule(mol);
132 molecules.erase(id);
133}
134
135double *World::cell_size = NULL;
136
137atom *World::createAtom(){
138 OBSERVE;
139 atomId_t id = getNextAtomId();
140 atom *res = NewAtom(id);
141 res->setWorld(this);
142 // store the atom by ID
143 atoms[res->getId()] = res;
144 return res;
145}
146
147
148int World::registerAtom(atom *atom){
149 OBSERVE;
150 atomId_t id = getNextAtomId();
151 atom->setId(id);
152 atom->setWorld(this);
153 atoms[atom->getId()] = atom;
154 return atom->getId();
155}
156
157void World::destroyAtom(atom* atom){
158 OBSERVE;
159 int id = atom->getId();
160 destroyAtom(id);
161}
162
163void World::destroyAtom(atomId_t id) {
164 OBSERVE;
165 atom *atom = atoms[id];
166 assert(atom);
167 DeleteAtom(atom);
168 atoms.erase(id);
169 releaseAtomId(id);
170}
171
172bool World::changeAtomId(atomId_t oldId, atomId_t newId, atom* target){
173 OBSERVE;
174 // in case this call did not originate from inside the atom, we redirect it,
175 // to also let it know that it has changed
176 if(!target){
177 target = atoms[oldId];
178 assert(target && "Atom with that ID not found");
179 return target->changeId(newId);
180 }
181 else{
182 if(reserveAtomId(newId)){
183 atoms.erase(oldId);
184 atoms.insert(pair<atomId_t,atom*>(newId,target));
185 return true;
186 }
187 else{
188 return false;
189 }
190 }
191}
192
193ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name,AtomDescriptor descr){
194 return new ManipulateAtomsProcess(op, descr,name,true);
195}
196
197ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name){
198 return manipulateAtoms(op,name,AllAtoms());
199}
200
201/********************* Internal Change methods for double Callback and Observer mechanism ********/
202
203void World::doManipulate(ManipulateAtomsProcess *proc){
204 proc->signOn(this);
205 {
206 OBSERVE;
207 proc->doManipulate(this);
208 }
209 proc->signOff(this);
210}
211/******************************* IDManagement *****************************/
212
213// Atoms
214
215atomId_t World::getNextAtomId(){
216 // see if we can reuse some Id
217 if(atomIdPool.empty()){
218 return currAtomId++;
219 }
220 else{
221 // we give out the first ID from the pool
222 atomId_t id = *(atomIdPool.begin());
223 atomIdPool.erase(id);
224 return id;
225 }
226}
227
228void World::releaseAtomId(atomId_t id){
229 atomIdPool.insert(id);
230 // defragmentation of the pool
231 set<atomId_t>::reverse_iterator iter;
232 // go through all Ids in the pool that lie immediately below the border
233 while(!atomIdPool.empty() && *(atomIdPool.rbegin())==(currAtomId-1)){
234 atomIdPool.erase(--currAtomId);
235 }
236}
237
238bool World::reserveAtomId(atomId_t id){
239 if(id>=currAtomId ){
240 // add all ids between the new one and current border as available
241 for(atomId_t pos=currAtomId; pos<id; ++pos){
242 atomIdPool.insert(pos);
243 }
244 currAtomId=id+1;
245 return true;
246 }
247 else if(atomIdPool.count(id)){
248 atomIdPool.erase(id);
249 return true;
250 }
251 else{
252 // this ID could not be reserved
253 return false;
254 }
255}
256
257// Molecules
258
259/******************************* Iterators ********************************/
260
261// Build the AtomIterator from template
262CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor);
263
264
265World::AtomIterator World::getAtomIter(AtomDescriptor descr){
266 return AtomIterator(descr,atoms);
267}
268
269World::AtomIterator World::atomEnd(){
270 return AtomIterator(AllAtoms(),atoms,atoms.end());
271}
272
273// build the MoleculeIterator from template
274CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet,MoleculeDescriptor);
275
276World::MoleculeIterator World::getMoleculeIter(MoleculeDescriptor descr){
277 return MoleculeIterator(descr,molecules);
278}
279
280World::MoleculeIterator World::moleculeEnd(){
281 return MoleculeIterator(AllMolecules(),molecules,molecules.end());
282}
283
284/******************************* Singleton Stuff **************************/
285
286World::World() :
287 Observable("World"),
288 periode(new periodentafel),
289 configuration(new config),
290 Thermostats(new ThermoStatContainer),
291 ExitFlag(0),
292 atoms(),
293 currAtomId(0),
294 molecules(),
295 currMoleculeId(0),
296 molecules_deprecated(new MoleculeListClass(this))
297{
298 cell_size = new double[6];
299 cell_size[0] = 20.;
300 cell_size[1] = 0.;
301 cell_size[2] = 20.;
302 cell_size[3] = 0.;
303 cell_size[4] = 0.;
304 cell_size[5] = 20.;
305 defaultName = "none";
306 molecules_deprecated->signOn(this);
307}
308
309World::~World()
310{
311 molecules_deprecated->signOff(this);
312 delete[] cell_size;
313 delete molecules_deprecated;
314 delete periode;
315 delete configuration;
316 delete Thermostats;
317 MoleculeSet::iterator molIter;
318 for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
319 DeleteMolecule((*molIter).second);
320 }
321 molecules.clear();
322 AtomSet::iterator atIter;
323 for(atIter=atoms.begin();atIter!=atoms.end();++atIter){
324 DeleteAtom((*atIter).second);
325 }
326 atoms.clear();
327}
328
329// Explicit instantiation of the singleton mechanism at this point
330
331CONSTRUCT_SINGLETON(World)
332
333/******************************* deprecated Legacy Stuff ***********************/
334
335MoleculeListClass *&World::getMolecules() {
336 return molecules_deprecated;
337}
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