Changeset 37f9d4 for src

Timestamp:

Oct 5, 2011, 9:18:21 AM (13 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:

c88597

Parents:

2e352f

git-author:

Frederik Heber <heber@…> (05/10/11 17:30:45)

git-committer:

Frederik Heber <heber@…> (10/05/11 09:18:21)

Message:

Changed some non-standard stuff with CreateMicelleAction.

• renamed files CreateMicelle -> CreateMicelleAction.
• rewrote german comments in english.
• removed #define, replaced by typedefs.
• removed commented-out code pieces.

• TESTFIX: regression test 93 failed due to ATOMDATA line being different for tensid.data and water.data. I use the one from tensid.data and re-created the water.data with this line.

Changed due to rebase onto v1.1.3:

• renaming done before already.

Location:

src/Actions/MoleculeAction

Files:

• CreateMicelleAction.cpp (modified) (11 diffs)
• CreateMicelleAction.def (modified) (3 diffs)

src/Actions/MoleculeAction/CreateMicelleAction.cpp

@@ -37 +37 @@
 #include <iostream>
 #include <string>
+#include <vector>
 
 #include "Parser/PdbParser.hpp"
@@ -56 +57 @@
 #include "Actions/ValueStorage.hpp"
 
-//#define PATH "/home/dueck/workspace/tenside/tmp/"
-#define AtomVector std::vector <atom *>
-#define MoleculeVector std::vector <molecule *>
-#define AtomList list <atom *>
-
-int Delta2(int x1, int x2);
-double Sqlength (Vector x);
 
 /** =========== define the function ====================== */
 Action::state_ptr MoleculeCreateMicelleAction::performCall()
 {
+  typedef std::vector <atom *> AtomVector;
+  typedef std::vector <molecule *> MoleculeVector;
+
   getParametersfromValueStorage();
         
@@ -77 +74 @@
   molecule *stick = *(all.begin());
 
-  //3.Molekuel zentrieren
+  // center molecule
 
   stick->CenterOrigin();
 
-  //4.Haupttraegheitsachse bestimmen
+  // determine principal axis system and rotate such that greatest extension is along z axis
   Vector den(0.0,0.0,1.0);
 
@@ -90 +87 @@
   */
   string path;
-  /**/
-  /*XyzParser *parserx = new XyzParser;
-  {
-    std::ofstream file;
-    path = PATH;
-    path += "/tensidrot.xyz";
-    file.open(path.c_str());
-    FormatParserStorage::getInstance().getXyz().save(&file, World::getInstance().getAllAtoms());
-    file.close();
-  }*/
-  //5.b: Molekuel um 180 Grad drehen
 
   Line RotationAxis(Vector(0.0,0.0,0.0), Vector(1.0,0.0,0.0)); // pt is the current Vector of point on surface
@@ -107 +93 @@
     (*it)->setPosition(RotationAxis.rotateVector((*it)->getPosition(),M_PI));
 
+  /// Align molecule with its PAS multiple times with the some surface
 
-  /*{
-    std::ofstream file;
-    path = PATH;
-    path += "/tensid2rot.xyz";
-    file.open(path.c_str());
-    FormatParserStorage::getInstance().getXyz().save(&file, World::getInstance().getAllAtoms());
-    file.close();
-  }*/
-
-  //6.Molekuel mehrfach strukturiert mit der Haupttraegheitsachse senkrecht zu einer parametrisierten Oberflaeche anordnen
-
-  //6.1. Punkte auf der Oberflaeche bestimmen
-  //Algorithmus entnommen aus "http://www.cgafaq.info/wiki/Evenly_distributed_points_on_sphere"
+  // get points on surface
 
   int ka =0;
@@ -128 +103 @@
   std::vector<Vector> pt = s.getHomogeneousPointsOnSurface(params.N);
 
-  //6.2.a. "stick" 180 Grad an x-y-Ebene spiegeln
+  // mirror along x-y plane
 
   for (molecule::iterator it2=stick->begin();it2 !=stick->end();++it2)
@@ -137 +112 @@
   }
 
-
-  //6.2.b. "stick" um Radius und Molekuelausdehnung in z-Richtung verschieben.
+  // shift molecule by its extension along z axis
 
   for (molecule::iterator it2=stick->begin();it2 !=stick->end();++it2)
@@ -147 +121 @@
   }
 
-
-
-
-  /*{
-    std::ofstream file;
-    path = PATH;
-    path += "/tensid3rot.xyz";
-    file.open(path.c_str());
-    FormatParserStorage::getInstance().getXyz().save(&file, World::getInstance().getAllAtoms());
-    file.close();
-  }*/
-
-//6.3.Erzeugen einer Molekuelliste, die das Molekuel "stick" "N" mal kopiert und um eine Sphaere herum verteilt 
+  // copy molecule N times and rotate it to point radially away from surface
 
   //double MYEPSILON=1e-10;
@@ -165 +127 @@
   for (ka = 0; ka<pt.size()-1; ka++)
   {
-    cout << "Creating " << ka+1 << " copy of tenside molecule 'stick' with " << stick->getAtomCount() << " atoms, ";
+    LOG(1, "STATUS: Creating " << ka+1 << " copy of tenside molecule 'stick' with " << stick->getAtomCount() << " atoms, ");
           molecule *Tensid=stick->CopyMolecule();
 
-          cout << "rotating ...";
+          LOG(2, "INFO: Rotating ... ");
     Vector ZAxis(Vector(0.0,0.0,1.0));
     Vector Axis(pt[ka]);
@@ -180 +142 @@
       *(*it2)+=params.center;
     }
-    cout << "done." << endl;
+    LOG(2, "INFO: \tdone.");
 
     Tensid=NULL;
   }
 
-  cout << "shifting " << ka+1 << " copy of tenside molecule, ";
+  // shift molecule at given position on surface
+
+  LOG(1, "STATUS: Shifting " << ka+1 << " copy of tenside molecule, ");
   molecule *Tensid=stick;
-  cout << "rotating ...";
+  LOG(2, "INFO: Rotating ...");
   Vector ZAxis(Vector(0.0,0.0,1.0));
   Vector Axis(pt[pt.size()-1]);
@@ -199 +163 @@
     *(*it2)+=params.center;
   }
-  cout << "done." << endl;
+  LOG(2, "INFO: \tdone.");
 
   Tensid=NULL;
 
-  //GraphSubgraphDissection();
   return Action::success;
 }

src/Actions/MoleculeAction/CreateMicelleAction.def

@@ -1 +1 @@
 /*
- * CreateMicelleAction.def
+ * CreateMicelle.def
  *
  *  Created on: Sept 29, 2010
@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include <vector>
 #include "LinearAlgebra/Vector.hpp"
 class CreateMicelle;
 
-// i.e. there is an integer with variable name Z that can be found in
-// ValueStorage by the token "Z" -> first column: int, Z, "Z"
-// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (int)(Vector)(double)
-#define paramtokens ("create-micelle")("position")("radius")
-#define paramdescriptions ("molecule to copy")("position in R^3 space")("radius of sphere")
+
+// "undefine" if no parameters are required
+#define paramtypes (int) (Vector) (double)
+#define paramtokens ("create-micelle") ("position") ("radius")
+#define paramdescriptions ("number of molecules")("center of micelle in R^3 space")("radius of mcielle")
 #undef paramdefaults
-#define paramreferences (N)(center)(radius)
+#define paramreferences (N) (center) (radius)
 
 #undef statetypes
@@ -24 +24 @@
 // some defines for all the names, you may use ACTION, STATE and PARAMS
 #define CATEGORY Molecule
+#define ACTIONNAME CreateMicelle
 #define MENUNAME "molecule"
-#define MENUPOSITION 10
-#define ACTIONNAME CreateMicelle
+#define MENUPOSITION 2
 #define TOKEN "create-micelle"
 
 // finally the information stored in the ActionTrait specialization
-#define DESCRIPTION "creates a micelle structure out of a single given molecule"
+#define DESCRIPTION "creates a micelle of molecules"
 #undef SHORTFORM