Changeset 0286bc for src

Timestamp:

Jun 7, 2010, 11:53:44 PM (15 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:

19c0e3

Parents:

3610bb

git-author:

Frederik Heber <heber@…> (06/07/10 23:48:31)

git-committer:

Frederik Heber <heber@…> (06/07/10 23:53:44)

Message:

BUGFIX: ListOfDoubles changed to Box and Vector.

• ListOfDoubles is now Box/Vector at appropriate places thanks to new validators and types
• new types BoxValue and VectorValue, being structures for symmetric 3x3 matrices and 3-dim vectors
• new file Values.hpp, containing the definitions added to Makefile.am
• new overloaded validate functions for boost::program_options
• CommandLineUI
  • adapted VectorCommandLineQuery and BoxCommandLineQuery to expect VectorValue and BoxValue
  • BUGFIX: CommandLineDialog::BooleanCommandLineQuery::handle() had copy&paste from Menu instead of program_options
• MapOfActions
  • center-in-box and change-box expect Box not ListOfDoubles
  • distances and lengths expect Vector not ListOfDoubles
  • new DoRotate option
  • inserted fill-molecule action

Location:

src

Files:

• Actions/Makefile.am (modified) (1 diff)
• Actions/MapOfActions.cpp (modified) (10 diffs)
• Actions/Values.hpp (added)
• UIElements/CommandLineUI/CommandLineDialog.cpp (modified) (4 diffs)

src/Actions/Makefile.am

@@ -30 +30 @@
   ${TESSELATIONACTIONHEADER} \
   ${WORLDACTIONHEADER} \
-  MapOfActions.hpp
+  MapOfActions.hpp \
+  Values.hpp
   
 ANALYSISACTIONSOURCE = \

src/Actions/MapOfActions.cpp

@@ -12 +12 @@
 #include "Helpers/Assert.hpp"
 
+#include <boost/lexical_cast.hpp>
+#include <boost/optional.hpp>
+#include <boost/program_options.hpp>
+
 #include "CommandLineParser.hpp"
 #include "log.hpp"
 #include "verbose.hpp"
+
+#include "Actions/Values.hpp"
+
+void validate(boost::any& v, const std::vector<std::string>& values, VectorValue *, int)
+{
+  VectorValue VV;
+  if (values.size() != 3) {
+    cerr <<  "Specified vector does not have three components but " << values.size() << endl;
+    throw boost::program_options::validation_error("Specified vector does not have three components");
+  }
+  VV.x = boost::lexical_cast<double>(values.at(0));
+  VV.y = boost::lexical_cast<double>(values.at(1));
+  VV.z = boost::lexical_cast<double>(values.at(2));
+  v = boost::any(VectorValue(VV));
+}
+
+void validate(boost::any& v, const std::vector<std::string>& values, BoxValue *, int)
+{
+  BoxValue BV;
+  if (values.size() != 6) {
+    cerr <<  "Specified vector does not have three components but " << values.size() << endl;
+    throw boost::program_options::validation_error("Specified symmetric box matrix does not have six components");
+  }
+  BV.xx = boost::lexical_cast<double>(values.at(0));
+  BV.xy = boost::lexical_cast<double>(values.at(1));
+  BV.xz = boost::lexical_cast<double>(values.at(2));
+  BV.yy = boost::lexical_cast<double>(values.at(3));
+  BV.yz = boost::lexical_cast<double>(values.at(4));
+  BV.zz = boost::lexical_cast<double>(values.at(5));
+  v = boost::any(BoxValue(BV));
+}
+
 
 /** Constructor of class MapOfActions.
@@ -76 +112 @@
   DescriptionMap["distance"] = "distance in space";
   DescriptionMap["distances"] = "list of three of distances in space, one for each axis direction";
+  DescriptionMap["DoRotate"] = "whether to rotate or just report angles";
   DescriptionMap["element"] = "set of elements";
   DescriptionMap["end-mol"] = "last or end step";
@@ -133 +170 @@
   TypeMap["bond-table"] = String;
   TypeMap["boundary"] = Vector;
-  TypeMap["center-in-box"] = ListOfDoubles;
-  TypeMap["change-box"] = ListOfDoubles;
+  TypeMap["center-in-box"] = Box;
+  TypeMap["change-box"] = Box;
   TypeMap["change-element"] = Element;
   TypeMap["change-molname"] = String;
@@ -171 +208 @@
   TypeMap["bin-start"] = Double;
   TypeMap["distance"] = Double;
-  TypeMap["distances"] = ListOfDoubles;
+  TypeMap["distances"] = Vector;
+  TypeMap["DoRotate"] = Boolean;
   TypeMap["elements"] = Element;
   TypeMap["elements"] = ListOfElements;
   TypeMap["length"] = Double;
-  TypeMap["lengths"] = ListOfDoubles;
+  TypeMap["lengths"] = Vector;
   TypeMap["MaxDistance"] = Double;
   TypeMap["molecule-by-id"] = Molecule;
@@ -202 +240 @@
 //      generic.insert("element-db");
 //      generic.insert("fastparsing");
-//  generic.insert("fill-molecule");
+  generic.insert("fill-molecule");
 //  generic.insert("fragment-mol");
   generic.insert("help");
@@ -215 +253 @@
 //  generic.insert("remove-atom");
 //  generic.insert("remove-sphere");
-    generic.insert("repeat-box");
+  generic.insert("repeat-box");
 //  generic.insert("rotate-to-pas");
 //      generic.insert("save-adjacency");
@@ -238 +276 @@
     generic.insert("input");
 //  generic.insert("length");
-//  generic.insert("lengths");
-//  generic.insert("MaxDistance");
-//  generic.insert("molecule-by-id");
 //  generic.insert("output-file");
 //  generic.insert("periodic");
@@ -248 +283 @@
     // positional arguments
     inputfile.insert("input");
+
+    // hidden arguments
+//  generic.insert("distance");
+    generic.insert("DoRotate");
+    generic.insert("distances");
+    generic.insert("lengths");
+    generic.insert("MaxDistance");
+    generic.insert("molecule-by-id");
 }
 
@@ -284 +327 @@
               ;
             break;
+          case Box:
+            ListRunner->second->add_options()
+              (getKeyAndShortForm(*OptionRunner).c_str(),
+                  po::value<BoxValue>()->multitoken(),
+                  getDescription(*OptionRunner).c_str())
+              ;
+            break;
           case Integer:
             ListRunner->second->add_options()
@@ -337 +387 @@
             ListRunner->second->add_options()
               (getKeyAndShortForm(*OptionRunner).c_str(),
-                  po::value< vector<double> >()->multitoken(),
-                  getDescription(*OptionRunner).c_str())
-              ;
-            break;
-          case Box:
-            ListRunner->second->add_options()
-              (getKeyAndShortForm(*OptionRunner).c_str(),
-                  po::value< vector<double> >(),
+                  po::value<VectorValue>()->multitoken(),
                   getDescription(*OptionRunner).c_str())
               ;

src/UIElements/CommandLineUI/CommandLineDialog.cpp

@@ -15 +15 @@
 #include <Descriptors/MoleculeIdDescriptor.hpp>
 #include "CommandLineUI/CommandLineDialog.hpp"
+
+#include "Actions/Values.hpp"
 
 #include "element.hpp"
@@ -116 +118 @@
 
 bool CommandLineDialog::BooleanCommandLineQuery::handle() {
-  bool badInput = false;
-  char input = ' ';
-  do{
-    badInput = false;
-    Log() << Verbose(0) << getTitle();
-    cin >> input;
-    if ((input == 'y' ) || (input == 'Y')) {
-      tmp = true;
-    } else if ((input == 'n' ) || (input == 'N')) {
-      tmp = false;
-    } else {
-      badInput=true;
-      cin.clear();
-      cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
-      Log() << Verbose(0) << "Input was not of [yYnN]!" << endl;
-    }
-  } while(badInput);
-  // clear the input buffer of anything still in the line
-  cin.ignore(std::numeric_limits<streamsize>::max(),'\n');
-  return true;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    tmp = CommandLineParser::getInstance().vm[getTitle()].as<bool>();
+    return true;
+  } else
+    return false;
 }
 
@@ -210 +197 @@
 
 bool CommandLineDialog::VectorCommandLineQuery::handle() {
-  vector<double> temp;
-  if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    temp = CommandLineParser::getInstance().vm[getTitle()].as<vector<double> >();
-    assert((temp.size() == 3) && "Vector from command line does not have three components.");
-    for (int i=0;i<NDIM;i++)
-      tmp->at(i) = temp[i];
+  VectorValue temp;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    temp = CommandLineParser::getInstance().vm[getTitle()].as< VectorValue >();
+    tmp->at(0) = temp.x;
+    tmp->at(1) = temp.y;
+    tmp->at(2) = temp.z;
     return true;
   } else
@@ -230 +217 @@
 
 bool CommandLineDialog::BoxCommandLineQuery::handle() {
-  vector<double> temp;
-  if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    temp = CommandLineParser::getInstance().vm[getTitle()].as<vector<double> >();
-    assert((temp.size() == 6) && "Symmetric box matrix from command line does not have six components.");
-    for (int i=0;i<6;i++) {
-      tmp[i] = temp[i];
-    }
+  BoxValue temp;
+  if (CommandLineParser::getInstance().vm.count(getTitle())) {
+    temp = CommandLineParser::getInstance().vm[getTitle()].as< BoxValue >();
+    tmp[0] = temp.xx;
+    tmp[1] = temp.xy;
+    tmp[2] = temp.xz;
+    tmp[3] = temp.yy;
+    tmp[4] = temp.yz;
+    tmp[5] = temp.zz;
     return true;
   } else