Changeset a9d254

Timestamp:

May 21, 2008, 11:14:06 AM (17 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:

ca2b83

Parents:

3b67a1

Message:

new function CenterInBox, some char* converted to string

CenterInBox centers the given geometry in a rectangular box of given edge lengths
new g++ that came with ubuntu hardy complained about deprecated use of char* instead of string (for constant char arrays such: "test")

File:

• src/molecules.cpp (modified) (5 diffs)

src/molecules.cpp

@@ -461 +461 @@
     istringstream *item = new istringstream(line);
     //istringstream input(line);
-    cout << Verbose(1) << "Reading: " << line << endl;
+    //cout << Verbose(1) << "Reading: " << line << endl;
     *item >> shorthand;
     *item >> x[0];
@@ -596 +596 @@
   cell_size[4] = 0.;
   cell_size[5] = dim->x[2];
+};
+
+/** Centers the molecule in the box whose lengths are defined by vector \a *BoxLengths.
+ * \param *out output stream for debugging
+ * \param *BoxLengths box lengths
+ */
+bool molecule::CenterInBox(ofstream *out, vector *BoxLengths)
+{
+  bool status = true;
+  atom *ptr = NULL;
+  vector *min = new vector;
+  vector *max = new vector;
+  
+  // gather min and max for each axis
+  ptr = start->next;  // start at first in list
+  if (ptr != end) {   //list not empty?
+    for (int i=0;i<NDIM;i++) {
+      max->x[i] = ptr->x.x[i];
+      min->x[i] = ptr->x.x[i];
+    }
+    while (ptr->next != end) {  // continue with second if present
+      ptr = ptr->next;
+      //ptr->Output(1,1,out);
+      for (int i=0;i<NDIM;i++) {
+        max->x[i] = (max->x[i] < ptr->x.x[i]) ? ptr->x.x[i] : max->x[i];
+        min->x[i] = (min->x[i] > ptr->x.x[i]) ? ptr->x.x[i] : min->x[i];
+      }
+    }
+  }
+  // sanity check
+  for(int i=0;i<NDIM;i++) {
+    if (max->x[i] - min->x[i] > BoxLengths->x[i])
+      status = false;
+  }
+  // warn if check failed
+  if (!status)
+    *out << "WARNING: molecule is bigger than defined box!" << endl;
+  else {  // else center in box 
+    ptr = start;
+    while (ptr->next != end) {
+      ptr = ptr->next;
+      for (int i=0;i<NDIM;i++)
+        ptr->x.x[i] += -(max->x[i] + min->x[i])/2. + BoxLengths->x[i]/2.; // first term centers molecule at (0,0,0), second shifts to center of new box
+    }
+  }
+
+  // free and exit
+  delete(min);
+  delete(max);
+  return status;
 };
 
@@ -884 +934 @@
  * \param *text question before entering
  */
-atom * molecule::AskAtom(char *text)
+atom * molecule::AskAtom(string text)
 {
   int No;
@@ -1204 +1254 @@
  * \return string of the flag
  */
-char * molecule::GetColor(enum Shading color)
+string molecule::GetColor(enum Shading color)
 {
   switch(color) {
@@ -3240 +3290 @@
   
   // Hier muessen von 1 bis NumberOfBondsPerAtom[Walker->nr] alle Kombinationen
-  // von Endstuecken (aus den Bonds) hinzugefÃŒgt werden und fÃŒr verbleibende ANOVAOrder
-  // rekursiv GraphCrawler in der nÀchsten Ebene aufgerufen werden
+  // von Endstuecken (aus den Bonds) hinzugefￜￜgt werden und fￜￜr verbleibende ANOVAOrder
+  // rekursiv GraphCrawler in der nￜￜchsten Ebene aufgerufen werden
   
   *out << Verbose(1+verbosity) << "Begin of SPFragmentGenerator." << endl;