source: src/helpers.hpp@ 05a97c

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 05a97c was 9879f6, checked in by Frederik Heber <heber@…>, 15 years ago

Huge Refactoring due to class molecule now being an STL container.

  • molecule::start and molecule::end were dropped. Hence, the usual construct Walker = start while (Walker->next != end) {

Walker = walker->next
...

}
was changed to
for (molecule::iterator iter = begin(); iter != end(); ++iter) {

...

}
and (*iter) used instead of Walker.

  • Two build errors remain (beside some more in folder Actions, Patterns and unittest) in molecule_pointcloud.cpp and molecule.cpp
  • lists.cpp was deleted as specialization of atom* was not needed anymore
  • link, unlink, add, remove, removewithoutcheck all are not needed for atoms anymore, just for bonds (where first, last entries remain in molecule)
  • CreateFatherLookupTable() was put back into class molecule.
  • molecule::InternalPointer is now an iterator
  • class PointCloud: GoToPrevious() and GetTerminalPoint() were dropped as not needed.
  • some new STL functions in class molecule: size(), empty(), erase(), find() and insert()
  • Property mode set to 100644
File size: 3.2 KB
RevLine 
[14de469]1/** \file helpers.hpp
2 *
[6ac7ee]3 * Declaration of some auxiliary functions for memory dis-/allocation and so on
[14de469]4 */
5
6#ifndef HELPERS_HPP_
7#define HELPERS_HPP_
8
9using namespace std;
10
[f66195]11/*********************************************** includes ***********************************/
12
[cd4ccc]13// include config.h
14#ifdef HAVE_CONFIG_H
15#include <config.h>
16#endif
17
[14de469]18#include <fstream>
19
[99593f]20#include "defs.hpp"
[e138de]21#include "log.hpp"
[29812d]22#include "memoryallocator.hpp"
[6dea43]23
[99593f]24/********************************************** definitions *********************************/
25
26// some algebraic matrix stuff
27double RDET3(const double a[NDIM*NDIM]);
28double RDET2(const double a[4]);
29double RDET2(const double a0, const double a1, const double a2, const double a3);
30
[14de469]31/********************************************** helpful functions *********************************/
32
[d3a46d]33// taken out of TREMOLO
34/*@-namechecks@*/
35#ifndef __GNUC__
36# undef __attribute__
37# define __attribute__(x)
38#endif
39/*@=namechecks@*/
40
41/* Behandelt aufgetretene Fehler. error ist der Fehlertyp(enum Errors)
[042f82]42 void *SpecialData ist ein untypisierter Zeiger auf Spezielle Daten zur Fehlerbehandlung.
43 Man koennte auch noch einen Zeiger auf eine Funktion uebergeben */
[d3a46d]44extern void /*@exits@*/ debug(const char *output);
[042f82]45 //__attribute__ ((__return__));
[d3a46d]46#define debug(data) debug_in((data), __FILE__, __LINE__)
47
48extern void /*@exits@*/ debug_in(const char *output,
[042f82]49 const char *file, const int line);
50 //__attribute__ ((__return__));
[d3a46d]51
[14de469]52double ask_value(const char *text);
53bool check_bounds(double *x, double *cell_size);
54void bound(double *b, double lower_bound, double upper_bound);
55int pot(int base, int n);
[5034e1]56int CountLinesinFile(ifstream &InputFile);
[14de469]57char *FixedDigitNumber(const int FragmentNumber, const int digits);
[e198c7]58bool IsValidNumber( const char *string);
[f66195]59int CompareDoubles (const void * a, const void * b);
[99593f]60double * ReturnFullMatrixforSymmetric(const double * const cell_size);
61double * InverseMatrix(const double * const A);
[6cd79d]62void performCriticalExit();
[14de469]63
[6d35e4]64/********************************************** helpful template functions *********************************/
65
[c144ed2]66/** Flips two values.
[ad8b0d]67 * \param x first value
68 * \param y second value
[c144ed2]69 */
[ad8b0d]70template <typename T> void flip(T &x, T &y)
[c144ed2]71{
72 T tmp;
[ad8b0d]73 tmp = x;
74 x = y;
75 y = tmp;
[c144ed2]76};
77
[9dbea5]78/** returns greater of the two values.
79 * \param x first value
80 * \param y second value
81 * \return greater of the two (by operator>())
82 */
[76102e]83template <typename T> T Max(T x, T y)
[9dbea5]84{
85 if (x > y)
86 return x;
87 else return y;
88};
89
90/** returns smaller of the two values.
91 * \param x first value
92 * \param y second value
93 * \return smaller of the two (by operator<())
94 */
[76102e]95template <typename T> T Min(T x, T y)
[9dbea5]96{
97 if (x < y)
98 return x;
99 else return y;
100};
101
[6d35e4]102/** Frees a two-dimensional array.
103 * \param *ptr pointer to array
104 * \param dim first dim of array
105 */
106template <typename X> void Free2DArray(X **ptr, int dim)
107{
[042f82]108 int i;
109 if (ptr != NULL) {
110 for(i=dim;i--;)
111 if (ptr[i] != NULL)
112 free(ptr[i]);
113 free(ptr);
114 }
[6d35e4]115};
[14de469]116
[5034e1]117template <typename T> void Increment(T *value, T *inc)
[e9f8f9]118{
[5034e1]119 *value += *inc;
[e9f8f9]120};
121
[5034e1]122template <typename T> void AbsoluteValue(T *value, T *abs)
[e9f8f9]123{
[5034e1]124 *value = *abs;
[e9f8f9]125};
126
[5034e1]127template <typename T> void IncrementalAbsoluteValue(T *value, T *abs)
128{
129 *value = *abs;
130 (*abs) += 1;
131};
[14de469]132
[7dad10]133#define PLURAL_S(v) (((v)==1)?"":"s")
[f66195]134
[14de469]135#endif /*HELPERS_HPP_*/
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