source: src/atom.hpp@ 1b2d30

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 Candidate_v1.7.0 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 1b2d30 was 1b2d30, checked in by Frederik Heber <heber@…>, 15 years ago

Extended PcpParser, completed MpqcParser.

  • BUGFIX: ConfigFileBuffer::InitFileBuffer() did not clear istream before re-use.
  • class PcpParser
    • operator== - compares every variable by ASSERTs.
    • constructor initializes variables all to sensible values.
  • class MpqcParser
    • new function save() - calls either SaveHessian() or Save() according to flag HessianPresent.
    • new functions SaveHessian() and Save() which contain both parts of config::SaveMPQC().
    • no function load() - this functionality has not been present and is not needed right away.
  • Extended ParserUnitTest
    • new test case readwritePcpTest() - load from static string, store, load again and compare both.
    • new test case writeMpqcTest() - write a state of the world and compare to one from static string.
    • all static strings have been made static and set before all functions.
    • new string containing an example pcp config file.
    • we check whether hydrogen and oxygen are known to the world as we test with these two elements.
  • atom::OutputMPQCLine() - now takes ostream instead of ofstream.
  • config::SaveMPQC() - adapted accordingly (cast is necessary)
  • Property mode set to 100644
File size: 3.6 KB
Line 
1/*
2 * atom.hpp
3 *
4 * Created on: Aug 3, 2009
5 * Author: heber
6 */
7
8#ifndef ATOM_HPP_
9#define ATOM_HPP_
10
11using namespace std;
12
13/*********************************************** includes ***********************************/
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include <iostream>
21#include <list>
22#include <vector>
23
24#include "atom_atominfo.hpp"
25#include "atom_bondedparticle.hpp"
26#include "atom_graphnode.hpp"
27#include "atom_particleinfo.hpp"
28#include "atom_trajectoryparticle.hpp"
29#include "tesselation.hpp"
30#include "types.hpp"
31
32/****************************************** forward declarations *****************************/
33
34class Vector;
35class World;
36
37/********************************************** declarations *******************************/
38
39/** Single atom.
40 * Class incorporates position, type
41 */
42class atom : public TesselPoint, public TrajectoryParticle, public GraphNode, public BondedParticle, public virtual ParticleInfo, public virtual AtomInfo {
43 friend atom* NewAtom(atomId_t);
44 friend void DeleteAtom(atom*);
45 public:
46 atom *previous; //!< previous atom in molecule list
47 atom *next; //!< next atom in molecule list
48 atom *father; //!< In many-body bond order fragmentations points to originating atom
49 int *sort; //!< sort criteria
50
51 virtual atom *clone();
52
53 bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
54 bool OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
55 bool OutputXYZLine(ofstream *out) const;
56 bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;
57 bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
58 void OutputMPQCLine(ostream * const out, const Vector *center, int *AtomNo) const;
59
60 void InitComponentNr();
61
62 void EqualsFather ( const atom *ptr, const atom **res ) const;
63 void CorrectFather();
64 atom *GetTrueFather();
65 bool Compare(const atom &ptr) const;
66
67 double DistanceToVector(const Vector &origin) const;
68 double DistanceSquaredToVector(const Vector &origin) const;
69 bool IsInParallelepiped(const Vector offset, const double *parallelepiped) const;
70
71 // getter and setter
72
73 /**
74 * returns the World that contains this atom.
75 * Use this if you need to get the world without locking
76 * the singleton for example.
77 *
78 */
79 World *getWorld();
80 void setWorld(World*);
81
82 virtual atomId_t getId();
83 virtual bool changeId(atomId_t newId);
84
85 /**
86 * this function sets the Id without notifying the world. Only use it, if the world has already
87 * gotten an ID for this Atom.
88 */
89 virtual void setId(atomId_t);
90
91 protected:
92 /**
93 * Protected constructor to ensure construction of atoms through the world.
94 * see World::createAtom()
95 */
96 atom();
97
98 /**
99 * Protected copy-constructor to ensure construction of atoms by cloning.
100 * see atom::clone()
101 */
102 atom(class atom *pointer);
103
104 /**
105 * Protected destructor to ensure destruction of atoms through the world.
106 * see World::destroyAtom()
107 */
108 virtual ~atom();
109 private:
110 World* world;
111 atomId_t id;
112};
113
114/**
115 * internal method used by the world. Do not use if you don't know what you are doing.
116 * You might get burned...
117 * Use World::createAtom() instead.
118 */
119atom* NewAtom(atomId_t _id);
120
121/**
122* internal method used by the world. Do not use if you don't know what you are doing.
123 * You might get burned...
124 * Use World::destroyAtom() instead.
125 */
126void DeleteAtom(atom*);
127
128
129#endif /* ATOM_HPP_ */
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