Changeset 4f7f34e

Timestamp:

Jun 25, 2010, 8:11:20 AM (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:

a356f2

Parents:

d0fbec

Message:

ParseCommandLineOptions() is not used anymore.

• new Actions InputAction and OutputAction.
• ParseCommandLineOptions() is not called anymore in main(), instead all is handled by CommandLineUI
• Creating first molecule and loading Bondgraph is done in main()

• TESTFIX: boost::program_options returns 134 in case of missing argument, not 255 and also no more CRITICAL message is given: testsuite-standard_options and testsuite-simple_configurations

Files:

• src/Actions/Makefile.am (modified) (2 diffs)
• src/Actions/MapOfActions.cpp (modified) (3 diffs)
• src/Actions/WorldAction/InputAction.cpp (added)
• src/Actions/WorldAction/InputAction.hpp (added)
• src/Actions/WorldAction/OutputAction.cpp (added)
• src/Actions/WorldAction/OutputAction.hpp (added)
• src/CommandLineParser.cpp (modified) (1 diff)
• src/Makefile.am (modified) (1 diff)
• src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) (3 diffs)
• src/builder.cpp (modified) (4 diffs)
• tests/regression/testsuite-simple_configuration.at (modified) (2 diffs)
• tests/regression/testsuite-standard_options.at (modified) (1 diff)

src/Actions/Makefile.am

@@ -120 +120 @@
   WorldAction/CenterOnEdgeAction.cpp \
   WorldAction/ChangeBoxAction.cpp \
+  WorldAction/InputAction.cpp \
+  WorldAction/OutputAction.cpp \
   WorldAction/RemoveSphereOfAtomsAction.cpp \
   WorldAction/RepeatBoxAction.cpp \
@@ -131 +133 @@
   WorldAction/CenterOnEdgeAction.hpp \
   WorldAction/ChangeBoxAction.hpp \
+  WorldAction/InputAction.hpp \
+  WorldAction/OutputAction.hpp \
   WorldAction/RemoveSphereOfAtomsAction.hpp \
   WorldAction/RepeatBoxAction.hpp \

src/Actions/MapOfActions.cpp

@@ -83 +83 @@
   DescriptionMap["fragment-mol"] = "create for a given molecule into fragments up to given order";
   DescriptionMap["help"] = "Give this help screen";
+  DescriptionMap["input"] = "specify input files";
   DescriptionMap["linear-interpolate"] = "linear interpolation in discrete steps between start and end position of a 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["pair-correlation"] = "pair correlation analysis between two elements, element and point or element and surface";
   DescriptionMap["parse-xyz"] = "parse xyz file into World";
@@ -190 +192 @@
   TypeMap["molecular-volume"] = Molecule;
   TypeMap["nonconvex-envelope"] = Molecule;
+  TypeMap["output"] = String;
   TypeMap["parse-xyz"] = String;
   TypeMap["pair-correlation"] = String;
@@ -262 +265 @@
   generic.insert("fragment-mol");
   generic.insert("help");
-        generic.insert("linear-interpolate");
+  generic.insert("input");
+  generic.insert("linear-interpolate");
 //  generic.insert("molecular-volume");
   generic.insert("nonconvex-envelope");
+  generic.insert("output");
         generic.insert("pair-correlation");
         generic.insert("parse-xyz");

src/CommandLineParser.cpp

@@ -56 +56 @@
 {
   // go through all arguments
+  cout << Verbose(1) << "By default putting input into the sequence." << endl;
+  // TODO: This may be bad, because const string "input" is destroyed at end of function
+  SequenceOfActions.push_back("input");
   for (int i=1;i<argc;i++) {
     (cout << Verbose(1) << "Checking on " << argv[i] << endl);

src/Makefile.am

@@ -63 +63 @@
 
 ACTIONSHEADER = \
-  ${ANALYSISACTIONHEADER} \
-  ${ATOMACTIONHEADER} \
-  ${CMDACTIONHEADER} \
-  ${FRAGMENTATIONACTIONHEADER} \
-  ${MOLECULEACTIONHEADER} \
-  ${PARSERACTIONHEADER} \
-  ${TESSELATIONACTIONHEADER} \
-  ${WORLDACTIONHEADER} \
   Actions/Action.hpp \
   Actions/ActionHistory.hpp \

src/UIElements/CommandLineUI/CommandLineWindow.cpp

@@ -47 +47 @@
 #include "Actions/WorldAction/CenterOnEdgeAction.hpp"
 #include "Actions/WorldAction/ChangeBoxAction.hpp"
+#include "Actions/WorldAction/InputAction.hpp"
+#include "Actions/WorldAction/OutputAction.hpp"
 #include "Actions/WorldAction/RemoveSphereOfAtomsAction.hpp"
 #include "Actions/WorldAction/RepeatBoxAction.hpp"
@@ -81 +83 @@
 
 void CommandLineWindow::display() {
+  //cout << ActionRegistry::getInstance();
+
   // go through all possible actions
   for (std::list<std::string>::iterator CommandRunner = CommandLineParser::getInstance().SequenceOfActions.begin(); CommandRunner != CommandLineParser::getInstance().SequenceOfActions.end(); ++CommandRunner) {
@@ -156 +160 @@
   new WorldCenterOnEdgeAction();
   new WorldChangeBoxAction();
+  new WorldInputAction();
+  new WorldOutputAction();
   new WorldRemoveSphereOfAtomsAction();
   new WorldRepeatBoxAction();

src/builder.cpp

@@ -2181 +2181 @@
     int ExitFlag = 0;
     bool ArgumentsCopied = false;
-    char *ConfigFileName = new char[MAXSTRINGSIZE];
+    //char *ConfigFileName = new char[MAXSTRINGSIZE];
     std::string BondGraphFileName("\n");
     FormatParserStorage::getInstance().addMpqc();
@@ -2210 +2210 @@
     // Parse command line options and if present create respective UI
     {
-      set<int> ArgcList;
-      ArgcList.insert(0); // push back program!
-      ArgcList.insert(1); // push back config file name
+      //set<int> ArgcList;
+      //ArgcList.insert(0); // push back program!
+      //ArgcList.insert(1); // push back config file name
       // handle arguments by ParseCommandLineOptions()
-      ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), &ConfigFileName, BondGraphFileName, ArgcList);
-      World::getInstance().setExitFlag(ExitFlag);
+      //ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), &ConfigFileName, BondGraphFileName, ArgcList);
+      //World::getInstance().setExitFlag(ExitFlag);
       // copy all remaining arguments to a new argv
-      Arguments = new char *[ArgcList.size()];
+      Arguments = new char *[argc];
       cout << "The following arguments are handled by CommandLineParser: ";
-      for (set<int>::iterator ArgcRunner = ArgcList.begin(); ArgcRunner != ArgcList.end(); ++ArgcRunner) {
-        Arguments[ArgcSize] = new char[strlen(argv[*ArgcRunner])+2];
-        strcpy(Arguments[ArgcSize], argv[*ArgcRunner]);
-        cout << " " << argv[*ArgcRunner];
+      for (int ArgcRunner=0;ArgcRunner<argc;ArgcRunner++) {
+      //for (set<int>::iterator ArgcRunner = ArgcList.begin(); ArgcRunner != ArgcList.end(); ++ArgcRunner) {
+        Arguments[ArgcSize] = new char[strlen(argv[ArgcRunner])+2];
+        strcpy(Arguments[ArgcSize], argv[ArgcRunner]);
+        cout << " " << argv[ArgcRunner];
         ArgcSize++;
       }
@@ -2258 +2259 @@
     }
 
-    std::string FilenamePrefix(ConfigFileName);
-    FormatParserStorage::getInstance().SetOutputPrefixForAll(FilenamePrefix);
     FormatParserStorage::getInstance().SaveAll();
     ChangeTracker::getInstance().saveStatus();
@@ -2269 +2268 @@
     delete[](Arguments);
   }
-  delete[](ConfigFileName);
+  //delete[](ConfigFileName);
 
   ExitFlag = World::getInstance().getExitFlag();

tests/regression/testsuite-simple_configuration.at

@@ -52 +52 @@
 AT_SETUP([Simple configuration - invalid commands on empty configs])
 AT_KEYWORDS([configuration])
-AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "Not enough" stderr], 0, [1
-], [ignore])
+AT_CHECK([../../molecuilder empty.conf -e ${abs_top_srcdir}/src/ -t -s -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
 AT_CLEANUP
 
@@ -61 +59 @@
 AT_KEYWORDS([configuration])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/7/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 255, [ignore], [stderr])
-AT_CHECK([fgrep -c "CRITICAL: Not enough" stderr], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -t], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -s -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -E -c -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -E -c -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -c -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -b -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -U -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -T -u], 134, [ignore], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -u], 134, [ignore], [stderr])
 AT_CLEANUP
 

tests/regression/testsuite-standard_options.at

@@ -18 +18 @@
 AT_SETUP([Standard Options - no element database])
 AT_KEYWORDS([options])
-AT_CHECK([../../molecuilder -e], 255, [ignore], [stderr])
-AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -e], 134, [ignore], [stderr])
 AT_CLEANUP