Changeset b81f1c for src

Timestamp:

Apr 6, 2011, 1:50:41 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

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

Children:

8766e72

Parents:

819cbe

git-author:

Frederik Heber <heber@…> (04/01/11 15:14:39)

git-committer:

Frederik Heber <heber@…> (04/06/11 13:50:41)

Message:

Removed libMolecuilderRandomNumbers from LinearAlgebra.

• added RealSpaceMatrix::setRotation() that accepts phi[NDIM].
• moved RealSpaceMatrix::setRandomRotation() to boundary.cpp where it is solely used.

Location:

src

Files:

• LinearAlgebra/Makefile.am (modified) (1 diff)
• LinearAlgebra/RealSpaceMatrix.cpp (modified) (2 diffs)
• LinearAlgebra/RealSpaceMatrix.hpp (modified) (1 diff)
• boundary.cpp (modified) (3 diffs)

src/LinearAlgebra/Makefile.am

@@ -48 +48 @@
 libMolecuilderLinearAlgebra_la_LIBADD = \
         ../Exceptions/libMolecuilderExceptions.la \
-        ../RandomNumbers/libMolecuilderRandomNumbers.la \
         $(GSL_LIBS)
 nobase_libMolecuilderLinearAlgebra_la_include_HEADERS = ${LINALGHEADER}

src/LinearAlgebra/RealSpaceMatrix.cpp

@@ -28 +28 @@
 #include "LinearAlgebra/Vector.hpp"
 #include "LinearAlgebra/VectorContent.hpp"
-#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
-#include "RandomNumbers/RandomNumberGenerator.hpp"
 
 #include <gsl/gsl_blas.h>
@@ -123 +121 @@
   set(2,1, cos(y)*sin(x));
   set(2,2, cos(x)*cos(y));
-}
-
-void RealSpaceMatrix::setRandomRotation()
-{
-  double phi[NDIM];
-  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
-  const double rng_min = random.min();
-  const double rng_max = random.max();
-
-
-  for (int i=0;i<NDIM;i++) {
-    phi[i] = (random()/(rng_max-rng_min))*(2.*M_PI);
-    std::cout << "Random angle is " << phi[i] << std::endl;
-  }
-
-  set(0,0,  cos(phi[0])            *cos(phi[2]) + (sin(phi[0])*sin(phi[1])*sin(phi[2])));
-  set(0,1,  sin(phi[0])            *cos(phi[2]) - (cos(phi[0])*sin(phi[1])*sin(phi[2])));
-  set(0,2,              cos(phi[1])*sin(phi[2])                                        );
-  set(1,0, -sin(phi[0])*cos(phi[1])                                                    );
-  set(1,1,  cos(phi[0])*cos(phi[1])                                                    );
-  set(1,2,              sin(phi[1])                                                    );
-  set(2,0, -cos(phi[0])            *sin(phi[2]) + (sin(phi[0])*sin(phi[1])*cos(phi[2])));
-  set(2,1, -sin(phi[0])            *sin(phi[2]) - (cos(phi[0])*sin(phi[1])*cos(phi[2])));
-  set(2,2,              cos(phi[1])*cos(phi[2])                                        );
-}
-
+//  double phi[NDIM];
+//  phi[0] = x;
+//  phi[0] = y;
+//  phi[0] = z;
+//  setRotation(phi);
+}
+
+void RealSpaceMatrix::setRotation(const double phi[NDIM])
+{
+  setRotation(phi[0], phi[1], phi[2]);
+//  set(0,0,  cos(phi[0])            *cos(phi[2]) + (sin(phi[0])*sin(phi[1])*sin(phi[2])));
+//  set(0,1,  sin(phi[0])            *cos(phi[2]) - (cos(phi[0])*sin(phi[1])*sin(phi[2])));
+//  set(0,2,              cos(phi[1])*sin(phi[2])                                        );
+//  set(1,0, -sin(phi[0])*cos(phi[1])                                                    );
+//  set(1,1,  cos(phi[0])*cos(phi[1])                                                    );
+//  set(1,2,              sin(phi[1])                                                    );
+//  set(2,0, -cos(phi[0])            *sin(phi[2]) + (sin(phi[0])*sin(phi[1])*cos(phi[2])));
+//  set(2,1, -sin(phi[0])            *sin(phi[2]) - (cos(phi[0])*sin(phi[1])*cos(phi[2])));
+//  set(2,2,              cos(phi[1])*cos(phi[2])                                        );
+}
 
 RealSpaceMatrix &RealSpaceMatrix::operator=(const RealSpaceMatrix &src)

src/LinearAlgebra/RealSpaceMatrix.hpp

@@ -74 +74 @@
    */
   void setRotation(const double x, const double y, const double z);
-  void setRandomRotation();
 
+  /**
+   * Sets all matrix corresponding to a rotation matrix,
+   * first around the x-, then the y-, finally the z-axis
+   * with given angles.
+   */
+  void setRotation(const double phi[NDIM]);
   /**
    * Access the matrix at index (i,j)

src/boundary.cpp

@@ -1044 +1044 @@
 }
 
+/** Sets given 3x3 matrix to a random rotation matrix.
+ *
+ * @param a matrix to set
+ */
+inline void setRandomRotation(RealSpaceMatrix &a)
+{
+  double phi[NDIM];
+  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
+  const double rng_min = random.min();
+  const double rng_max = random.max();
+
+  for (int i=0;i<NDIM;i++) {
+    phi[i] = (random()/(rng_max-rng_min))*(2.*M_PI);
+    std::cout << "Random angle is " << phi[i] << std::endl;
+  }
+
+  a.set(0,0,  cos(phi[0])            *cos(phi[2]) + (sin(phi[0])*sin(phi[1])*sin(phi[2])));
+  a.set(0,1,  sin(phi[0])            *cos(phi[2]) - (cos(phi[0])*sin(phi[1])*sin(phi[2])));
+  a.set(0,2,              cos(phi[1])*sin(phi[2])                                        );
+  a.set(1,0, -sin(phi[0])*cos(phi[1])                                                    );
+  a.set(1,1,  cos(phi[0])*cos(phi[1])                                                    );
+  a.set(1,2,              sin(phi[1])                                                    );
+  a.set(2,0, -cos(phi[0])            *sin(phi[2]) + (sin(phi[0])*sin(phi[1])*cos(phi[2])));
+  a.set(2,1, -sin(phi[0])            *sin(phi[2]) - (cos(phi[0])*sin(phi[1])*cos(phi[2])));
+  a.set(2,2,              cos(phi[1])*cos(phi[2])                                        );
+}
+
 /** Fills the empty space of the simulation box with water.
  * \param *filler molecule which the box is to be filled with
@@ -1131 +1158 @@
         // ... and rotation matrix
         if (DoRandomRotation)
-          Rotations.setRandomRotation();
+          setRandomRotation(Rotations);
         else
           Rotations.setIdentity();
@@ -1191 +1218 @@
     // otherwise translate and randomize to final position
     if (DoRandomRotation)
-      Rotations.setRandomRotation();
+      setRandomRotation(Rotations);
     else
       Rotations.setIdentity();