Changeset 4e10f5 for src/Actions/MapOfActions.cpp

Timestamp:

Jul 7, 2010, 4:08:32 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

77a570

Parents:

5630bd (diff), 192f6e (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'stable' into StructureRefactoring

Conflicts:

src/Actions/WorldAction/CenterOnEdgeAction.cpp
src/Actions/WorldAction/ChangeBoxAction.cpp
src/Actions/WorldAction/RepeatBoxAction.cpp
src/Actions/WorldAction/ScaleBoxAction.cpp
src/World.cpp
src/boundary.cpp

File:

• src/Actions/MapOfActions.cpp (modified) (16 diffs)

src/Actions/MapOfActions.cpp

@@ -67 +67 @@
 #include "Actions/WorldAction/SetDefaultNameAction.hpp"
 #include "Actions/WorldAction/SetGaussianBasisAction.hpp"
+#include "Actions/WorldAction/SetOutputFormatsAction.hpp"
 #include "Actions/Values.hpp"
 
@@ -72 +73 @@
 {
   VectorValue VV;
-  if (values.size() != 3) {
-    cerr <<  "Specified vector does not have three components but " << values.size() << endl;
+  std::vector<std::string> components;
+
+  // split comma-separated values
+  if (values.size() != 1) {
+    cerr <<  "Not one vector but " << components.size() << " given " << endl;
+    throw boost::program_options::validation_error("Unequal to one vector given");
+  }
+  std::string argument(values.at(0));
+  std::string::iterator Aiter = argument.begin();
+  std::string::iterator Biter = argument.begin();
+  for (; Aiter != argument.end(); ++Aiter) {
+    if (*Aiter == ',') {
+      components.push_back(string(Biter,Aiter));
+      do {
+        Aiter++;
+      } while (*Aiter == ' ' || *Aiter == '\t');
+      Biter = Aiter;
+    }
+  }
+  components.push_back(string(Biter,argument.end()));
+
+  if (components.size() != 3) {
+    cerr <<  "Specified vector does not have three components but " << components.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));
+  VV.x = boost::lexical_cast<double>(components.at(0));
+  VV.y = boost::lexical_cast<double>(components.at(1));
+  VV.z = boost::lexical_cast<double>(components.at(2));
   v = boost::any(VectorValue(VV));
 }
@@ -85 +107 @@
 {
   BoxValue BV;
-  if (values.size() != 6) {
-    cerr <<  "Specified vector does not have three components but " << values.size() << endl;
+  std::vector<std::string> components;
+
+  // split comma-separated values
+  if (values.size() != 1) {
+    cerr <<  "Not one vector but " << components.size() << " given " << endl;
+    throw boost::program_options::validation_error("Unequal to one vector given");
+  }
+  std::string argument(values.at(0));
+  std::string::iterator Aiter = argument.begin();
+  std::string::iterator Biter = argument.begin();
+  for (; Aiter != argument.end(); ++Aiter) {
+    if (*Aiter == ',') {
+      components.push_back(string(Biter,Aiter));
+      do {
+        Aiter++;
+      } while (*Aiter == ' ' || *Aiter == '\t');
+      Biter = Aiter;
+    }
+  }
+  components.push_back(string(Biter,argument.end()));
+
+  if (components.size() != 6) {
+    cerr <<  "Specified vector does not have three components but " << components.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));
+  BV.xx = boost::lexical_cast<double>(components.at(0));
+  BV.xy = boost::lexical_cast<double>(components.at(1));
+  BV.xz = boost::lexical_cast<double>(components.at(2));
+  BV.yy = boost::lexical_cast<double>(components.at(3));
+  BV.yz = boost::lexical_cast<double>(components.at(4));
+  BV.zz = boost::lexical_cast<double>(components.at(5));
   v = boost::any(BoxValue(BV));
 }
@@ -130 +173 @@
   DescriptionMap["input"] = "specify input files";
   DescriptionMap["linear-interpolate"] = "linear interpolation in discrete steps between start and end position of a molecule";
+  DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
   DescriptionMap["nonconvex-envelope"] = "create the non-convex envelope for a molecule";
-  DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
-  DescriptionMap["output"] = "specify output formats";
+  DescriptionMap["output"] = "write output files";
+  DescriptionMap["set-output"] = "specify output formats";
   DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements, element and point or element and surface";
   DescriptionMap["parse-xyz"] = "parse xyz file into World";
@@ -140 +184 @@
   DescriptionMap["repeat-box"] = "create periodic copies of the simulation box per axis";
   DescriptionMap["rotate-to-pas"] = "calculate the principal axis system of the specified molecule and rotate specified axis to align with main axis";
-  DescriptionMap["set-basis"] = "set the name of the gaussian basis set for MPQC";
   DescriptionMap["save-adjacency"] = "name of the adjacency file to write to";
   DescriptionMap["save-bonds"] = "name of the bonds file to write to";
@@ -146 +189 @@
   DescriptionMap["SaveXyz"] = "save world as xyz file";
   DescriptionMap["scale-box"] = "scale box and atomic positions inside";
+  DescriptionMap["set-basis"] = "set the name of the gaussian basis set for MPQC";
+  DescriptionMap["set-output"] = "specify output formats";
   DescriptionMap["subgraph-dissect"] = "dissect the molecular system into molecules representing disconnected subgraphs";
   DescriptionMap["suspend-in-water"] = "suspend the given molecule in water such that in the domain the mean density is as specified";
@@ -189 +234 @@
   ShortFormMap["center-in-box"] = "b";
   ShortFormMap["change-element"] = "E";
-  ShortFormMap["convex-envelope"] = "o";
+//  ShortFormMap["convex-envelope"] = "x";
   ShortFormMap["default-molname"] = "X";
   ShortFormMap["depth-first-search"] = "D";
@@ -200 +245 @@
   ShortFormMap["linear-interpolate"] = "L";
   ShortFormMap["nonconvex-envelope"] = "N";
+//  ShortFormMap["output"] = "o";
   ShortFormMap["pair-correlation"] = "C";
   ShortFormMap["parse-xyz"] = "p";
@@ -211 +257 @@
   ShortFormMap["scale-box"] = "s";
   ShortFormMap["set-basis"] = "M";
+  ShortFormMap["set-output"] = "o";
   ShortFormMap["subgraph-dissect"] = "I";
   ShortFormMap["suspend-in-water"] = "u";
@@ -238 +285 @@
   TypeMap["molecular-volume"] = Molecule;
   TypeMap["nonconvex-envelope"] = Molecule;
-  TypeMap["output"] = String;
+  TypeMap["output"] = None;
   TypeMap["parse-xyz"] = String;
   TypeMap["pair-correlation"] = String;
@@ -251 +298 @@
   TypeMap["scale-box"] = Vector;
   TypeMap["set-basis"] = String;
+  TypeMap["set-output"] = ListOfString;
   TypeMap["subgraph-dissect"] = None;
   TypeMap["suspend-in-water"] = Double;
@@ -349 +397 @@
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "default-molname") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "set-basis") );
+  MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "set-output") );
 
   // put actions into command line category
@@ -386 +435 @@
   generic.insert("scale-box");
   generic.insert("set-basis");
+  generic.insert("set-output");
         generic.insert("subgraph-dissect");
   generic.insert("suspend-in-water");
@@ -484 +534 @@
   new WorldSetDefaultNameAction();
   new WorldSetGaussianBasisAction();
+  new WorldSetOutputFormatsAction();
 }
 
@@ -561 +612 @@
               ;
             break;
+          case ListOfString:
+            ListRunner->second->add_options()
+              (getKeyAndShortForm(*OptionRunner).c_str(),
+                  po::value< vector<std::string> >()->multitoken(),
+                  getDescription(*OptionRunner).c_str())
+              ;
+            break;
           case Axis:
             ListRunner->second->add_options()
@@ -573 +631 @@
             ListRunner->second->add_options()
               (getKeyAndShortForm(*OptionRunner).c_str(),
-                  po::value<VectorValue>()->multitoken(),
+                  po::value<VectorValue>(),
                   getDescription(*OptionRunner).c_str())
               ;