source: src/molecule_pointcloud.cpp@ ba9f5b

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Last change on this file since ba9f5b was 274d45, checked in by Frederik Heber <heber@…>, 15 years ago

FIX: Atoms were stored not in the sequence they were loaded.

  1. The main problem is molecule::atomSet which is a set<atom *>, i.e. atoms are sorted by their appearance in memory. As memory need not be allocated sequentially, this gives rise to extreme arbitririty which is not desired. Instead the atoms should be stored in the sequence they were loaded/created. The solution is as follows:
  • config::SaveAll()
  • molecule::atomSet is now a list<atom *>
  • molecule::atomIds is a new set<atomId_t> (atomIdSet) which controls that (global) ids remain unique in the no more Atomset's set (but list)
  • molecule::erase() erases also in atomIds
  • molecule::insert() checks whether id is present by atomIds
  • molecule::find() as std::list does not have a find, we just go through the list until the object is found (or not), this may be speeded up by another internal list.
  • molecule::InternalPointer made lots of confusion as virtual function GoToFirst() is const, hence begin() (needed therein) returns const_iterator, which then cannot be simply re-cast into an iterator: We make it a pointer, reinterpret_cast the pointer and reference it back. Although InternalPointer is mutable, the compiler cannot use the non-const function begin() (it cannot be made const, as overloading is not allowed). (this is noted in the code also extensively.)
  • molecule::containsAtom() does not use count but the new find, as it returns only boolean anyway.
  • rewrote MoleculeListClass::SimpleMerge() to get rid of the extra iterator, as we remove all atoms in the end anyway.
  • FIX: MoleculeListClass::SimpleMultiMerge() - the created mol was not inserted into the moleculelist in the end, although it is the only one to remain.
  1. All other databases had missing headers with respect to those stored in elements_db.cpp. Hence, valence of hydrogen was not parsed and this caused several failures in CalculateOrbitals() (Psi numbers and MaxMinSetp in pcp conf file).
  1. Subsequenytly, various test cases (12, 21, 30, 31, 36-38, 39) were broken. This had two reasons:
  • Seemingly, CalculateOrbitals() was broken before hence MaxMinStep (pcp config) and MaxPsiDouble/PsiMaxNn[Up|Down] were always 0. (10-21,30-31,39)
  • As the order is now correct, fixes from commits c9217161ec2a5d5db508557fe98a32068461f45b and 22a6da8380911571debebd69444d2615450bbbd8 were obselete and have been reverted (order of the Ion?_Type...): Molecules/6 (30), Molecules/7 (31), Filling/1 (39)
  • Due to different ordering, Tesselation/3 (38) had completely different .dat file (though same tesselation)
  • r3d had small differences, mostly order or epsilon (0 not being 0 but ..-e16), hence diffing was deactivated, as r3d is deprecated anyway (since vmd can render triangles as well and better).

Signed-off-by: Frederik Heber <heber@…>
  • Property mode set to 100644
File size: 1.8 KB
Line 
1/*
2 * molecule_pointcloud.cpp
3 *
4 * Created on: Oct 5, 2009
5 * Author: heber
6 */
7
8#include "Helpers/MemDebug.hpp"
9
10#include "atom.hpp"
11#include "config.hpp"
12#include "info.hpp"
13#include "memoryallocator.hpp"
14#include "molecule.hpp"
15
16/************************************* Functions for class molecule *********************************/
17
18/** Returns a name for this point cloud, here the molecule's name.
19 * \return name of point cloud
20 */
21const char * const molecule::GetName() const
22{
23 return name;
24};
25
26/** Determine center of all atoms.
27 * \param *out output stream for debugging
28 * \return pointer to allocated with central coordinates
29 */
30Vector *molecule::GetCenter() const
31{
32 Vector *center = DetermineCenterOfAll();
33 return center;
34};
35
36
37/** PointCloud implementation of GoPoint
38 * Uses atoms and STL stuff.
39 */
40TesselPoint* molecule::GetPoint() const
41{
42 return (*InternalPointer);
43};
44
45/** PointCloud implementation of GoToNext.
46 * Uses atoms and STL stuff.
47 */
48void molecule::GoToNext() const
49{
50 if (InternalPointer != atoms.end())
51 InternalPointer++;
52};
53
54/** PointCloud implementation of GoToFirst.
55 * Uses atoms and STL stuff.
56 */
57void molecule::GoToFirst() const
58{
59 // evil hack necessary because
60 // -# although InternalPointer is mutable
61 // -# only const_iterator begin() is called due to const in the function declaration above
62 // -# and there is no cast from const_iterator to const iterator
63 atomSet::const_iterator test = begin();
64 InternalPointer = *(reinterpret_cast<atomSet::iterator *>(&test));
65};
66
67/** PointCloud implementation of IsEmpty.
68 * Uses atoms and STL stuff.
69 */
70bool molecule::IsEmpty() const
71{
72 return (empty());
73};
74
75/** PointCloud implementation of IsLast.
76 * Uses atoms and STL stuff.
77 */
78bool molecule::IsEnd() const
79{
80 return (InternalPointer == atoms.end());
81};
82
83int molecule::GetMaxId() const {
84 return getAtomCount();
85}
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