source: src/World.cpp@ 192f6e

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 192f6e was b9c847, checked in by Frederik Heber <heber@…>, 15 years ago

New SetOutputFormatsAction introduced.

Fixes:

new SetOutputFormatsAction:

  • new action SetOutputFormatsAction which instantiates various specializations of FormatParser in FormatParserStorage.
  • main(): mpqc, pcp and xyz and no more added by default to FormatParserStorage, this now has to be done by specifying them (e.g. on the command line as -o pcp mpqc xyz)
  • TESTFIXES: case 10,11,13,16,17,22 all failed due to the missing -o specification which has been added (this has been intended in this way from the very beginning of the ParseCommandLineOptions() refactoring)
  • action "convex-envelope" now more has ShortForm "-o" due to obvious reasons.
  • Property mode set to 100644
File size: 7.7 KB
RevLine 
[5d1611]1/*
2 * World.cpp
3 *
4 * Created on: Feb 3, 2010
5 * Author: crueger
6 */
7
[112b09]8#include "Helpers/MemDebug.hpp"
9
[5d1611]10#include "World.hpp"
11
[d346b6]12#include "atom.hpp"
[8e1f7af]13#include "config.hpp"
[354859]14#include "molecule.hpp"
15#include "periodentafel.hpp"
[43dad6]16#include "ThermoStatContainer.hpp"
[fc1b24]17#include "Descriptors/AtomDescriptor.hpp"
[865a945]18#include "Descriptors/AtomDescriptor_impl.hpp"
[1c51c8]19#include "Descriptors/MoleculeDescriptor.hpp"
20#include "Descriptors/MoleculeDescriptor_impl.hpp"
[6e97e5]21#include "Descriptors/SelectiveIterator_impl.hpp"
[7c4e29]22#include "Actions/ManipulateAtomsProcess.hpp"
[6d574a]23#include "Helpers/Assert.hpp"
[d346b6]24
[23b547]25#include "Patterns/Singleton_impl.hpp"
26
[d346b6]27using namespace std;
[4d9c01]28
[5d1611]29/******************************* getter and setter ************************/
[354859]30periodentafel *&World::getPeriode(){
[5d1611]31 return periode;
32}
33
[8e1f7af]34config *&World::getConfig(){
35 return configuration;
36}
37
[1c51c8]38// Atoms
39
[7a1ce5]40atom* World::getAtom(AtomDescriptor descriptor){
[fc1b24]41 return descriptor.find();
42}
43
[7a1ce5]44vector<atom*> World::getAllAtoms(AtomDescriptor descriptor){
[fc1b24]45 return descriptor.findAll();
46}
47
[0e2a47]48vector<atom*> World::getAllAtoms(){
49 return getAllAtoms(AllAtoms());
50}
51
[354859]52int World::numAtoms(){
53 return atoms.size();
54}
55
[1c51c8]56// Molecules
57
58molecule *World::getMolecule(MoleculeDescriptor descriptor){
59 return descriptor.find();
60}
61
62std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
63 return descriptor.findAll();
64}
65
[97ebf8]66std::vector<molecule*> World::getAllMolecules(){
67 return getAllMolecules(AllMolecules());
68}
69
[354859]70int World::numMolecules(){
71 return molecules_deprecated->ListOfMolecules.size();
72}
73
[5f612ee]74// system
75
76double * World::getDomain() {
77 return cell_size;
78}
79
80void World::setDomain(double * matrix)
81{
[b9c847]82 OBSERVE;
83 cell_size[0] = matrix[0];
84 cell_size[1] = matrix[1];
85 cell_size[2] = matrix[2];
86 cell_size[3] = matrix[3];
87 cell_size[4] = matrix[4];
88 cell_size[5] = matrix[5];
[5f612ee]89}
90
[387b36]91std::string World::getDefaultName() {
[5f612ee]92 return defaultName;
93}
94
[387b36]95void World::setDefaultName(std::string name)
[5f612ee]96{
[387b36]97 defaultName = name;
[5f612ee]98};
99
[43dad6]100class ThermoStatContainer * World::getThermostats()
101{
102 return Thermostats;
103}
104
105
[e4b5de]106int World::getExitFlag() {
107 return ExitFlag;
108}
109
110void World::setExitFlag(int flag) {
111 if (ExitFlag < flag)
112 ExitFlag = flag;
113}
[5f612ee]114
[afb47f]115/******************** Methods to change World state *********************/
116
[354859]117molecule* World::createMolecule(){
118 OBSERVE;
119 molecule *mol = NULL;
[cbc5fb]120 mol = NewMolecule();
[6d574a]121 ASSERT(!molecules.count(currMoleculeId),"currMoleculeId did not specify an unused ID");
[cbc5fb]122 mol->setId(currMoleculeId++);
[244d26]123 // store the molecule by ID
[cbc5fb]124 molecules[mol->getId()] = mol;
[354859]125 mol->signOn(this);
126 return mol;
127}
128
[cbc5fb]129void World::destroyMolecule(molecule* mol){
130 OBSERVE;
131 destroyMolecule(mol->getId());
132}
133
134void World::destroyMolecule(moleculeId_t id){
135 OBSERVE;
136 molecule *mol = molecules[id];
[6d574a]137 ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
[cbc5fb]138 DeleteMolecule(mol);
139 molecules.erase(id);
140}
141
[5f612ee]142double *World::cell_size = NULL;
[7c4e29]143
[46d958]144atom *World::createAtom(){
145 OBSERVE;
[88d586]146 atomId_t id = getNextAtomId();
147 atom *res = NewAtom(id);
[46d958]148 res->setWorld(this);
[244d26]149 // store the atom by ID
[46d958]150 atoms[res->getId()] = res;
151 return res;
152}
153
[5f612ee]154
[46d958]155int World::registerAtom(atom *atom){
156 OBSERVE;
[88d586]157 atomId_t id = getNextAtomId();
158 atom->setId(id);
[46d958]159 atom->setWorld(this);
160 atoms[atom->getId()] = atom;
161 return atom->getId();
162}
163
164void World::destroyAtom(atom* atom){
165 OBSERVE;
166 int id = atom->getId();
167 destroyAtom(id);
168}
169
[cbc5fb]170void World::destroyAtom(atomId_t id) {
[46d958]171 OBSERVE;
172 atom *atom = atoms[id];
[6d574a]173 ASSERT(atom,"Atom ID that was meant to be destroyed did not exist");
[46d958]174 DeleteAtom(atom);
175 atoms.erase(id);
[88d586]176 releaseAtomId(id);
177}
178
179bool World::changeAtomId(atomId_t oldId, atomId_t newId, atom* target){
180 OBSERVE;
181 // in case this call did not originate from inside the atom, we redirect it,
182 // to also let it know that it has changed
183 if(!target){
184 target = atoms[oldId];
[6d574a]185 ASSERT(target,"Atom with that ID not found");
[88d586]186 return target->changeId(newId);
187 }
188 else{
189 if(reserveAtomId(newId)){
190 atoms.erase(oldId);
191 atoms.insert(pair<atomId_t,atom*>(newId,target));
192 return true;
193 }
194 else{
195 return false;
196 }
197 }
[46d958]198}
199
[7c4e29]200ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name,AtomDescriptor descr){
201 return new ManipulateAtomsProcess(op, descr,name,true);
202}
203
[0e2a47]204ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name){
205 return manipulateAtoms(op,name,AllAtoms());
206}
207
[afb47f]208/********************* Internal Change methods for double Callback and Observer mechanism ********/
209
210void World::doManipulate(ManipulateAtomsProcess *proc){
211 proc->signOn(this);
212 {
213 OBSERVE;
214 proc->doManipulate(this);
215 }
216 proc->signOff(this);
217}
[88d586]218/******************************* IDManagement *****************************/
219
[57adc7]220// Atoms
221
[88d586]222atomId_t World::getNextAtomId(){
223 // see if we can reuse some Id
224 if(atomIdPool.empty()){
225 return currAtomId++;
226 }
227 else{
228 // we give out the first ID from the pool
229 atomId_t id = *(atomIdPool.begin());
230 atomIdPool.erase(id);
[23b547]231 return id;
[88d586]232 }
233}
234
235void World::releaseAtomId(atomId_t id){
236 atomIdPool.insert(id);
237 // defragmentation of the pool
238 set<atomId_t>::reverse_iterator iter;
239 // go through all Ids in the pool that lie immediately below the border
240 while(!atomIdPool.empty() && *(atomIdPool.rbegin())==(currAtomId-1)){
241 atomIdPool.erase(--currAtomId);
242 }
243}
[afb47f]244
[88d586]245bool World::reserveAtomId(atomId_t id){
246 if(id>=currAtomId ){
247 // add all ids between the new one and current border as available
248 for(atomId_t pos=currAtomId; pos<id; ++pos){
249 atomIdPool.insert(pos);
250 }
251 currAtomId=id+1;
252 return true;
253 }
254 else if(atomIdPool.count(id)){
255 atomIdPool.erase(id);
256 return true;
257 }
258 else{
259 // this ID could not be reserved
260 return false;
261 }
262}
[57adc7]263
264// Molecules
265
[865a945]266/******************************* Iterators ********************************/
267
[6e97e5]268// Build the AtomIterator from template
269CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor);
270
[865a945]271
272World::AtomIterator World::getAtomIter(AtomDescriptor descr){
[6e97e5]273 return AtomIterator(descr,atoms);
[865a945]274}
[354859]275
[6e97e5]276World::AtomIterator World::atomEnd(){
277 return AtomIterator(AllAtoms(),atoms,atoms.end());
[7c4e29]278}
279
[6e97e5]280// build the MoleculeIterator from template
281CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet,MoleculeDescriptor);
282
[1c51c8]283World::MoleculeIterator World::getMoleculeIter(MoleculeDescriptor descr){
[6e97e5]284 return MoleculeIterator(descr,molecules);
[1c51c8]285}
286
[6e97e5]287World::MoleculeIterator World::moleculeEnd(){
288 return MoleculeIterator(AllMolecules(),molecules,molecules.end());
[1c51c8]289}
290
[5d1611]291/******************************* Singleton Stuff **************************/
292
[7a1ce5]293World::World() :
[cd5047]294 Observable("World"),
[354859]295 periode(new periodentafel),
[8e1f7af]296 configuration(new config),
[43dad6]297 Thermostats(new ThermoStatContainer),
[e4b5de]298 ExitFlag(0),
[d2dbac0]299 atoms(),
[24a5e0]300 currAtomId(0),
301 molecules(),
302 currMoleculeId(0),
303 molecules_deprecated(new MoleculeListClass(this))
[7dad10]304{
[b34306]305 cell_size = new double[6];
[fd179f]306 cell_size[0] = 20.;
307 cell_size[1] = 0.;
308 cell_size[2] = 20.;
309 cell_size[3] = 0.;
310 cell_size[4] = 0.;
311 cell_size[5] = 20.;
[387b36]312 defaultName = "none";
[7dad10]313 molecules_deprecated->signOn(this);
314}
[5d1611]315
316World::~World()
[354859]317{
[028c2e]318 molecules_deprecated->signOff(this);
[5f612ee]319 delete[] cell_size;
[46d958]320 delete molecules_deprecated;
[354859]321 delete periode;
[8e1f7af]322 delete configuration;
[43dad6]323 delete Thermostats;
[cbc5fb]324 MoleculeSet::iterator molIter;
325 for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
326 DeleteMolecule((*molIter).second);
327 }
328 molecules.clear();
329 AtomSet::iterator atIter;
330 for(atIter=atoms.begin();atIter!=atoms.end();++atIter){
331 DeleteAtom((*atIter).second);
[46d958]332 }
333 atoms.clear();
[354859]334}
[5d1611]335
[23b547]336// Explicit instantiation of the singleton mechanism at this point
[5d1611]337
[23b547]338CONSTRUCT_SINGLETON(World)
[5d1611]339
340/******************************* deprecated Legacy Stuff ***********************/
341
[354859]342MoleculeListClass *&World::getMolecules() {
343 return molecules_deprecated;
[5d1611]344}
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