source: src/atom.hpp@ d6c485

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 d6c485 was e138de, checked in by Frederik Heber <heber@…>, 15 years ago

Huge change from ofstream * (const) out --> Log().

  • first shift was done via regular expressions
  • then via error messages from the code
  • note that class atom, class element and class molecule kept in parts their output stream, was they print to file.
  • make check runs fine
  • MISSING: Verbosity is not fixed for everything (i.e. if no endl; is present and next has Verbose(0) ...)

Signed-off-by: Frederik Heber <heber@…>
  • Property mode set to 100644
File size: 2.2 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
31/****************************************** forward declarations *****************************/
32
33class Vector;
34
35/********************************************** declarations *******************************/
36
37/** Single atom.
38 * Class incorporates position, type
39 */
40class atom : public TesselPoint, public TrajectoryParticle, public GraphNode, public BondedParticle, public virtual ParticleInfo, public virtual AtomInfo {
41 public:
42 atom *previous; //!< previous atom in molecule list
43 atom *next; //!< next atom in molecule list
44 atom *father; //!< In many-body bond order fragmentations points to originating atom
45 int *sort; //!< sort criteria
46
47 atom();
48 atom(class atom *pointer);
49 virtual ~atom();
50
51 bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
52 bool OutputArrayIndexed(ofstream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
53 bool OutputXYZLine(ofstream *out) const;
54 bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;
55 bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
56 void OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo) const;
57
58 void InitComponentNr();
59
60 void EqualsFather ( const atom *ptr, const atom **res ) const;
61 void CorrectFather();
62 atom *GetTrueFather();
63 bool Compare(const atom &ptr) const;
64
65 double DistanceToVector(const Vector &origin) const;
66 double DistanceSquaredToVector(const Vector &origin) const;
67 bool IsInParallelepiped(const Vector offset, const double *parallelepiped) const;
68
69 private:
70};
71
72#endif /* ATOM_HPP_ */
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