Changeset 2f429e

Timestamp:

Oct 11, 2015, 7:11:38 AM (9 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:

d26fb7

Parents:

3b1c36

git-author:

Frederik Heber <heber@…> (09/22/15 18:02:47)

git-committer:

Frederik Heber <heber@…> (10/11/15 07:11:38)

Message:

Elements are now parsed as string (and tried for being int).

• this allows to parse both "He" and "2", i.e. both symbol and atomic number.
• this works for both command-line and Python.

Location:

src

Files:

• Parameters/Specifics/Value_element.cpp (modified) (2 diffs)
• Parameters/Specifics/Value_elements.cpp (modified) (1 diff)
• UIElements/CommandLineUI/CommandLineParser.cpp (modified) (2 diffs)
• UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) (2 diffs)
• UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) (2 diffs)

src/Parameters/Specifics/Value_element.cpp

@@ -35 +35 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <boost/lexical_cast.hpp>
+
 #include "Value_element.hpp"
 
@@ -45 +47 @@
 static const element * FindElementByString(const std::string &_value)
 {
-  static ConvertTo<atomicNumber_t> converter;
-  const element * _element =
-      World::getInstance().getPeriode()->FindElement(converter(_value));
-  return _element;
+  const element * elem = NULL;
+  try {
+    const int tempvalue = boost::lexical_cast<atomicNumber_t>(_value);
+    elem = World::getInstance().getPeriode()->FindElement(tempvalue);
+  } catch( boost::bad_lexical_cast &e) {
+    elem = World::getInstance().getPeriode()->FindElement(_value);
+  }
+  return elem;
 }
 

src/Parameters/Specifics/Value_elements.cpp

@@ -57 +57 @@
   for(tokenizer::iterator beg=tok.begin();
       beg != tok.end();++beg) {
-    const int tempvalue = boost::lexical_cast<atomicNumber_t>(*beg);
-    const element * _element =
-        World::getInstance().getPeriode()->FindElement(tempvalue);
-    ASSERT( _element != NULL,
+    const element * elem = NULL;
+    try {
+      const int tempvalue = boost::lexical_cast<atomicNumber_t>(*beg);
+      elem = World::getInstance().getPeriode()->FindElement(tempvalue);
+    } catch( boost::bad_lexical_cast &e) {
+      elem = World::getInstance().getPeriode()->FindElement(*beg);
+    }
+    ASSERT( elem != NULL,
         "FindElementsByString() - cannnot find element "
-        +toString(tempvalue)+" in periodentafel.");
-    elements.push_back(_element);
+        +toString(*beg)+" in periodentafel.");
+    elements.push_back(elem);
   }
   return elements;

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -390 +390 @@
 //            currentOption->hasDefaultValue() ?
 //                  po::value < const element * >()->default_value(boost::lexical_cast<const element *>(currentOption->getDefaultValue().c_str())) :
-                  po::value < int >(),
+                  po::value < std::string >(),
                   currentOption->getDescription().c_str())
         ;
@@ -399 +399 @@
 //            currentOption->hasDefaultValue() ?
 //                  po::value < std::vector<const element *> >()->default_value(boost::lexical_cast< std::vector<const element *> >(currentOption->getDefaultValue().c_str())) :
-                  po::value < std::vector<int> >()->multitoken(),
+                  po::value < std::vector<std::string> >()->multitoken(),
                   currentOption->getDescription().c_str())
         ;

src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp

@@ -36 +36 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <string>
+
 #include "CommandLineUI/Query/CommandLineQuery.hpp"
 #include "CommandLineUI/CommandLineParser.hpp"
@@ -54 +56 @@
   // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
   periodentafel *periode = World::getInstance().getPeriode();
-  int Z = -1;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    std::string argument("none");
     try {
-      Z = CommandLineParser::getInstance().vm[getTitle()].as< int >();
+      argument = CommandLineParser::getInstance().vm[getTitle()].as< std::string >();
+      try {
+        int Z = -1;
+        Z = boost::lexical_cast<int>(argument);
+        temp = periode->FindElement(Z);
+      } catch(boost::bad_lexical_cast &e) {
+        temp = periode->FindElement(argument);
+      }
     } catch(boost::bad_any_cast &e) {
-      Z = -1;
       return false;
     }
-    temp = periode->FindElement(Z);
     ASSERT(temp != NULL, "Invalid element specified in ElementCommandLineQuery");
     return true;

src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp

@@ -36 +36 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include <string>
+
 #include "CommandLineUI/Query/CommandLineQuery.hpp"
 #include "CommandLineUI/CommandLineParser.hpp"
@@ -51 +53 @@
 {}
 
+template <typename T>
+std::vector<const element *> getElementsFromInput(const std::vector<std::string> &_input)
+{
+  periodentafel *periode = World::getInstance().getPeriode();
+  std::vector<const element *> result;
+  const element *temp_element;
+  for (typename std::vector<std::string>::const_iterator ZRunner = _input.begin(); ZRunner != _input.end(); ++ZRunner) {
+    const T argument = boost::lexical_cast<T>(*ZRunner);
+    temp_element = periode->FindElement(argument);
+    ASSERT(temp_element != NULL, "Invalid element specified in ElementCommandLineQuery");
+    result.push_back(temp_element);
+  }
+  return result;
+}
+
 bool CommandLineDialog::ElementsCommandLineQuery::handle() {
   // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
-  periodentafel *periode = World::getInstance().getPeriode();
-  std::vector<int> AllElements;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
     try {
-      AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
+      std::vector<std::string> AllArguments;
+      AllArguments = CommandLineParser::getInstance().vm[getTitle()].as< vector<std::string> >();
+      try {
+        temp = getElementsFromInput<int>(AllArguments);
+      } catch(boost::bad_lexical_cast &e) {
+        try {
+        temp = getElementsFromInput<std::string>(AllArguments);
+        } catch(boost::bad_lexical_cast &e) {
+          return false;
+        }
+      }
     } catch(boost::bad_any_cast &e) {
-      AllElements.clear();
       return false;
     }
-    const element *temp_element;
-    for (vector<int>::iterator ZRunner = AllElements.begin(); ZRunner != AllElements.end(); ++ZRunner) {
-      temp_element = periode->FindElement(*ZRunner);
-      ASSERT(temp_element != NULL, "Invalid element specified in ElementCommandLineQuery");
-      temp.push_back(temp_element);
-    }
-    return true;
+    if (temp.empty())
+      return false;
+    else
+      return true;
   }
   return false;