Changeset 064178

Timestamp:

Oct 6, 2011, 9:16:19 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:

29daad

Parents:

81c980b

git-author:

Frederik Heber <heber@…> (08/11/11 14:20:59)

git-committer:

Frederik Heber <heber@…> (10/06/11 09:16:19)

Message:

Added color database to periodentafel.

• periodentafel::LoadColorDatabase() added and added to cstor.
• element::color as unsigned char[3] added.
• element::getColor() added.
• ColorDB const string in elements_db.[ch]pp added.
• added LoadColorDatabase() to periodentafelTest::LoadStoreTest().

Location:

src

Files:

• Helpers/defs.cpp (modified) (1 diff)
• Helpers/defs.hpp (modified) (1 diff)
• element.cpp (modified) (1 diff)
• element.hpp (modified) (2 diffs)
• elements_db.cpp (modified) (1 diff)
• elements_db.hpp (modified) (1 diff)
• periodentafel.cpp (modified) (2 diffs)
• periodentafel.hpp (modified) (1 diff)
• unittests/PeriodentafelUnitTest.cpp (modified) (2 diffs)

src/Helpers/defs.cpp ¶

@@ -59 +59 @@
 const char *STANDARDHBONDDISTANCEDB = "Hbonddistance.db";    //!< default filename of typial bond distance to hydrogen database
 const char *STANDARDHBONDANGLEDB = "Hbondangle.db";    //!< default filename of typial bond angle to hydrogen database
+const char *STANDARDCOLORDB = "color.db";    //!< default filename of typial bond angle to hydrogen database
 
 // some values

src/Helpers/defs.hpp ¶

@@ -69 +69 @@
 extern "C" const char *STANDARDVALENCEDB;    //!< default filename of valence number per element database
 extern "C" const char *STANDARDORBITALDB;    //!< default filename of orbitals per element database
-extern "C" const char *STANDARDHBONDDISTANCEDB;    //!< default filename of typial bond distance to hydrogen database
-extern "C" const char *STANDARDHBONDANGLEDB;    //!< default filename of typial bond angle to hydrogen database
+extern "C" const char *STANDARDHBONDDISTANCEDB;    //!< default filename of typical bond distance to hydrogen database
+extern "C" const char *STANDARDHBONDANGLEDB;    //!< default filename of typical bond angle to hydrogen database
+extern "C" const char *STANDARDCOLORDB;    //!< default filename of color database
 
 // some values

src/element.cpp ¶

@@ -118 +118 @@
 }
 
+const unsigned char * element::getColor() const
+{
+  return color;
+}
+
 double element::getElectronegativity() const
 {

src/element.hpp ¶

@@ -41 +41 @@
     atomicNumber_t getNumber() const;
     double getMass() const;
+    const unsigned char *getColor() const;
     double getCovalentRadius() const;
     double getElectronegativity() const;
@@ -75 +76 @@
     double HBondDistance[NDIM]; //!< distance in Angstrom of this element to hydrogen  (for single, double and triple bonds)
     double HBondAngle[NDIM];     //!< typical angle for one, two, three bonded hydrogen (in degrees)
+    unsigned char color[3];   //!< typical color for this element (from Jmol)
 
     std::string name;  //!< atom name, i.e. "Hydrogen"

src/elements_db.cpp ¶

@@ -436 +436 @@
 80      0.12000000000000E+02\n\
 ";
+
+const char *ColorDB =\
+"# AtomicNumber, symbol, [red, green, blue] component, hex value\n\
+1\tH\t255\t255\t255\n\
+2\tHe\t217\t255\t255\n\
+3\tLi\t204\t128\t255\n\
+4\tBe\t194\t255\t0\n\
+5\tB\t255\t181\t181\n\
+6\tC\t144\t144\t144\n\
+7\tN\t48\t80\t248\n\
+8\tO\t255\t13\t13\n\
+9\tF\t144\t224\t80\n\
+10\tNe\t179\t227\t245\n\
+11\tNa\t171\t92\t242\n\
+12\tMg\t138\t255\t0\n\
+13\tAl\t191\t166\t166\n\
+14\tSi\t240\t200\t160\n\
+15\tP\t255\t128\t0\n\
+16\tS\t255\t255\t48\n\
+17\tCl\t31\t240\t31\n\
+18\tAr\t128\t209\t227\n\
+19\tK\t143\t64\t212\n\
+20\tCa\t61\t255\t0\n\
+21\tSc\t230\t230\t230\n\
+22\tTi\t191\t194\t199\n\
+23\tV\t166\t166\t171\n\
+24\tCr\t138\t153\t199\n\
+25\tMn\t156\t122\t199\n\
+26\tFe\t224\t102\t51\n\
+27\tCo\t240\t144\t160\n\
+28\tNi\t80\t208\t80\n\
+29\tCu\t200\t128\t51\n\
+30\tZn\t125\t128\t176\n\
+31\tGa\t194\t143\t143\n\
+32\tGe\t102\t143\t143\n\
+33\tAs\t189\t128\t227\n\
+34\tSe\t255\t161\t0\n\
+35\tBr\t166\t41\t41\n\
+36\tKr\t92\t184\t209\n\
+37\tRb\t112\t46\t176\n\
+38\tSr\t0\t255\t0\n\
+39\tY\t148\t255\t255\n\
+40\tZr\t148\t224\t224\n\
+41\tNb\t115\t194\t201\n\
+42\tMo\t84\t181\t181\n\
+43\tTc\t59\t158\t158\n\
+44\tRu\t36\t143\t143\n\
+45\tRh\t10\t125\t140\n\
+46\tPd\t0\t105\t133\n\
+47\tAg\t192\t192\t192\n\
+48\tCd\t255\t217\t143\n\
+49\tIn\t166\t117\t115\n\
+50\tSn\t102\t128\t128\n\
+51\tSb\t158\t99\t181\n\
+52\tTe\t212\t122\t0\n\
+53\tI\t148\t0\t148\n\
+54\tXe\t66\t158\t176\n\
+55\tCs\t87\t23\t143\n\
+56\tBa\t0\t201\t0\n\
+57\tLa\t112\t212\t255\n\
+58\tCe\t255\t255\t199\n\
+59\tPr\t217\t255\t199\n\
+60\tNd\t199\t255\t199\n\
+61\tPm\t163\t255\t199\n\
+62\tSm\t143\t255\t199\n\
+63\tEu\t97\t255\t199\n\
+64\tGd\t69\t255\t199\n\
+65\tTb\t48\t255\t199\n\
+66\tDy\t31\t255\t199\n\
+67\tHo\t0\t255\t156\n\
+68\tEr\t0\t230\t117\n\
+69\tTm\t0\t212\t82\n\
+70\tYb\t0\t191\t56\n\
+71\tLu\t0\t171\t36\n\
+72\tHf\t77\t194\t255\n\
+73\tTa\t77\t166\t255\n\
+74\tW\t33\t148\t214\n\
+75\tRe\t38\t125\t171\n\
+76\tOs\t38\t102\t150\n\
+77\tIr\t23\t84\t135\n\
+78\tPt\t208\t208\t224\n\
+79\tAu\t255\t209\t35\n\
+80\tHg\t184\t184\t208\n\
+81\tTl\t166\t84\t77\n\
+82\tPb\t87\t89\t97\n\
+83\tBi\t158\t79\t181\n\
+84\tPo\t171\t92\t0\n\
+85\tAt\t117\t79\t69\n\
+86\tRn\t66\t130\t150\n\
+87\tFr\t66\t0\t102\n\
+88\tRa\t0\t125\t0\n\
+89\tAc\t112\t171\t250\n\
+90\tTh\t0\t186\t255\n\
+91\tPa\t0\t161\t255\n\
+92\tU\t0\t143\t255\n\
+93\tNp\t0\t128\t255\n\
+94\tPu\t0\t107\t255\n\
+95\tAm\t84\t92\t242\n\
+96\tCm\t120\t92\t227\n\
+97\tBk\t138\t79\t227\n\
+98\tCf\t161\t54\t212\n\
+99\tEs\t179\t31\t212\n\
+100\tFm\t179\t31\t186\n\
+101\tMd\t179\t13\t166\n\
+102\tNo\t189\t13\t135\n\
+103\tLr\t199\t0\t102\n\
+104\tRf\t204\t0\t89\n\
+105\tDb\t209\t0\t79\n\
+106\tSg\t217\t0\t69\n\
+107\tBh\t224\t0\t56\n\
+108\tHs\t230\t0\t46\n\
+";

src/elements_db.hpp ¶

@@ -15 +15 @@
 
 
+extern const char *ColorDB;
 extern const char *elementsDB;
 extern const char *ElectronegativitiesDB;

src/periodentafel.cpp ¶

@@ -87 +87 @@
         LoadHBondLengthsDatabase(input);
     ASSERT(status, "HBond distance entry of element initialization failed");
+  }
+  {
+    stringstream input(ColorDB,ios_base::in);
+#ifndef NDEBUG
+    bool status =
+#endif
+        LoadColorDatabase(input);
+    ASSERT(status, "color entry of element initialization failed");
   }
 };
@@ -531 +539 @@
 }
 
+/** load the color info.
+ * \param *input stream to parse from
+ * \return true - parsing successful, false - something went wrong
+ */
+bool periodentafel::LoadColorDatabase(istream &input)
+{
+  char dummy[MAXSTRINGSIZE];
+  if (!input.fail()) {
+    input.getline(dummy, MAXSTRINGSIZE);
+    while (!input.eof()) {
+      atomicNumber_t Z;
+      input >> Z;
+      ASSERT(elements.count(Z), "Element not present");
+      input >> ws;
+      input >> dummy;
+      {
+        int tmpcolor;   // char here will only parse a single char (i.e. only "2" out of "255")
+        for (int i=0;i<3;++i) {
+          input >> ws;
+          input >> tmpcolor;
+          elements[Z]->color[i] = (unsigned char)tmpcolor;
+        }
+      }
+      input >> ws;
+      {
+        const element * tmp = FindElement(Z);
+//        DoLog(0) && (Log() << Verbose(0) << "Element " << tmp->getName() << " has ("
+//            << (int)tmp->color[0] << "," << (int)tmp->color[1] << "," << (int)tmp->color[2]
+//            << ") colors." << std::endl);
+      }
+    }
+    return true;
+  } else
+    return false;
+}
+
 /** Stores element list to file.
  */

src/periodentafel.hpp ¶

@@ -62 +62 @@
   private:
 
+  bool LoadColorDatabase(istream &input);
   bool LoadElementsDatabase(std::istream &input);
   bool LoadElectronegativityDatabase(std::istream &input);

src/unittests/PeriodentafelUnitTest.cpp ¶

@@ -89 +89 @@
   stringstream HbondangleDBstream(HbondangleDB,ios_base::in);
   stringstream HbonddistanceDBstream(HbonddistanceDB,ios_base::in);
+  stringstream ColorDBstream(ColorDB,ios_base::in);
   CPPUNIT_ASSERT(tafel->LoadElementsDatabase(elementsDBstream) && "General element initialization failed");
   CPPUNIT_ASSERT(tafel->LoadElectronegativityDatabase(ElectronegativityDBstream) && "Electronegativity entry of element initialization failed");
@@ -95 +96 @@
   CPPUNIT_ASSERT(tafel->LoadHBondAngleDatabase(HbondangleDBstream) && "HBond angle entry of element initialization failed");
   CPPUNIT_ASSERT(tafel->LoadHBondLengthsDatabase(HbonddistanceDBstream) && "HBond distance entry of element initialization failed");
+  CPPUNIT_ASSERT(tafel->LoadColorDatabase(ColorDBstream) && "color entry of element initialization failed");
   // check presence of elements
   atomicNumber_t Z = 1;