Changeset b9c847

Timestamp:

Jul 2, 2010, 1:44:23 PM (14 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:

c27778

Parents:

4a611e

Message:

New SetOutputFormatsAction introduced.

Fixes:

• World::setDomain() is now OBSERVE'd and used to the set the domain.
• FIX: CenterInBoxAction, CenterOnEdgeAction, ChangeBoxAction, RepeatBoxAction, ScaleBoxAction did not tell the World that is cell_size has been changed, now they call setDomain()

new SetOutputFormatsAction:

• new action SetOutputFormatsAction which instantiates various specializations of FormatParser in FormatParserStorage.
• main(): mpqc, pcp and xyz and no more added by default to FormatParserStorage, this now has to be done by specifying them (e.g. on the command line as -o pcp mpqc xyz)
• TESTFIXES: case 10,11,13,16,17,22 all failed due to the missing -o specification which has been added (this has been intended in this way from the very beginning of the ParseCommandLineOptions() refactoring)
• action "convex-envelope" now more has ShortForm "-o" due to obvious reasons.

Files:

• src/Actions/Makefile.am (modified) (2 diffs)
• src/Actions/MapOfActions.cpp (modified) (11 diffs)
• src/Actions/WorldAction/CenterInBoxAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/ChangeBoxAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/RepeatBoxAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/ScaleBoxAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/SetOutputFormatsAction.cpp (added)
• src/Actions/WorldAction/SetOutputFormatsAction.hpp (added)
• src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) (1 diff)
• src/World.cpp (modified) (1 diff)
• src/builder.cpp (modified) (1 diff)
• tests/regression/testsuite-domain.at (modified) (2 diffs)
• tests/regression/testsuite-simple_configuration.at (modified) (4 diffs)
• tests/regression/testsuite-tesselation.at (modified) (2 diffs)

src/Actions/Makefile.am

@@ -126 +126 @@
   WorldAction/ScaleBoxAction.cpp \
   WorldAction/SetDefaultNameAction.cpp \
-  WorldAction/SetGaussianBasisAction.cpp               
+  WorldAction/SetGaussianBasisAction.cpp \               
+  WorldAction/SetOutputFormatsAction.cpp
 WORLDACTIONHEADER = \
   WorldAction/AddEmptyBoundaryAction.hpp \
@@ -139 +140 @@
   WorldAction/ScaleBoxAction.hpp \
   WorldAction/SetDefaultNameAction.hpp \
-  WorldAction/SetGaussianBasisAction.hpp
+  WorldAction/SetGaussianBasisAction.hpp \
+  WorldAction/SetOutputFormatsAction.hpp               
 

src/Actions/MapOfActions.cpp

@@ -65 +65 @@
 #include "Actions/WorldAction/SetDefaultNameAction.hpp"
 #include "Actions/WorldAction/SetGaussianBasisAction.hpp"
+#include "Actions/WorldAction/SetOutputFormatsAction.hpp"
 #include "Actions/Values.hpp"
 
@@ -128 +129 @@
   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";
@@ -138 +140 @@
   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";
@@ -144 +145 @@
   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";
@@ -187 +190 @@
   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";
@@ -210 +213 @@
   ShortFormMap["scale-box"] = "s";
   ShortFormMap["set-basis"] = "M";
+  ShortFormMap["set-output"] = "o";
   ShortFormMap["subgraph-dissect"] = "I";
   ShortFormMap["suspend-in-water"] = "u";
@@ -237 +241 @@
   TypeMap["molecular-volume"] = Molecule;
   TypeMap["nonconvex-envelope"] = Molecule;
-  TypeMap["output"] = ListOfString;
+  TypeMap["output"] = None;
   TypeMap["parse-xyz"] = String;
   TypeMap["pair-correlation"] = String;
@@ -250 +254 @@
   TypeMap["scale-box"] = Vector;
   TypeMap["set-basis"] = String;
+  TypeMap["set-output"] = ListOfString;
   TypeMap["subgraph-dissect"] = None;
   TypeMap["suspend-in-water"] = Double;
@@ -348 +353 @@
   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
@@ -385 +391 @@
   generic.insert("scale-box");
   generic.insert("set-basis");
+  generic.insert("set-output");
         generic.insert("subgraph-dissect");
   generic.insert("suspend-in-water");
@@ -483 +490 @@
   new WorldSetDefaultNameAction();
   new WorldSetGaussianBasisAction();
+  new WorldSetOutputFormatsAction();
 }
 

src/Actions/WorldAction/CenterInBoxAction.cpp

@@ -38 +38 @@
 
   if(dialog->display()) {
+    World::getInstance().setDomain(cell_size);
     // center
     vector<molecule *> AllMolecules = World::getInstance().getAllMolecules();

src/Actions/WorldAction/CenterOnEdgeAction.cpp

@@ -65 +65 @@
       cell_size[j] = (Max[i]-Min[i]);
     }
+    World::getInstance().setDomain(cell_size);
     // translate all atoms, such that Min is aty (0,0,0)
     for (vector<atom*>::iterator AtomRunner = AllAtoms.begin(); AtomRunner != AllAtoms.end(); ++AtomRunner)

src/Actions/WorldAction/ChangeBoxAction.cpp

@@ -39 +39 @@
   if(dialog->display()) {
     DoLog(0) && (Log() << Verbose(0) << "Setting box domain to " << cell_size[0] << "," << cell_size[1] << "," << cell_size[2] << "," << cell_size[3] << "," << cell_size[4] << "," << cell_size[5] << "," << endl);
+    World::getInstance().setDomain(cell_size);
     delete dialog;
     return Action::success;

src/Actions/WorldAction/RepeatBoxAction.cpp

@@ -72 +72 @@
     }
 
+    World::getInstance().setDomain(cell_size);
     molecule *newmol = NULL;
     Vector ** vectors = NULL;

src/Actions/WorldAction/ScaleBoxAction.cpp

@@ -55 +55 @@
       cell_size[j]*=x[i];
     }
+    World::getInstance().setDomain(cell_size);
 
     delete dialog;

src/UIElements/CommandLineUI/CommandLineDialog.cpp

@@ -158 +158 @@
 bool CommandLineDialog::StringsCommandLineQuery::handle() {
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    temp = CommandLineParser::getInstance().vm[getTitle()].as<string>();
-    // dissect by ","
-    string::iterator olditer = temp.begin();
-    for(string::iterator iter = temp.begin(); iter != temp.end(); ++iter) {
-      if (*iter == ' ') {
-        tmp.push_back(string(iter, olditer));
-        olditer = iter;
-      }
-    }
-    if (olditer != temp.begin())  // insert last part also
-      tmp.push_back(string(olditer, temp.end()));
+    tmp = CommandLineParser::getInstance().vm[getTitle()].as< vector<string> >();
     return true;
   } else {

src/World.cpp

@@ -80 +80 @@
 void World::setDomain(double * matrix)
 {
-
+  OBSERVE;
+  cell_size[0] = matrix[0];
+  cell_size[1] = matrix[1];
+  cell_size[2] = matrix[2];
+  cell_size[3] = matrix[3];
+  cell_size[4] = matrix[4];
+  cell_size[5] = matrix[5];
 }
 

src/builder.cpp

@@ -121 +121 @@
   bool ArgumentsCopied = false;
   std::string BondGraphFileName("\n");
-  FormatParserStorage::getInstance().addMpqc();
-  FormatParserStorage::getInstance().addPcp();
-  FormatParserStorage::getInstance().addXyz();
 
   // print version check whether arguments are present at all

tests/regression/testsuite-domain.at

@@ -3 +3 @@
 AT_SETUP([Domain - defining simulation domain])
 AT_KEYWORDS([domain])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -B 10 0 10 0 0 10], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o pcp -B 10 0 10 0 0 10], 0, [stdout], [stderr])
 AT_CHECK([fgrep "BoxLength" test.conf], 0, [stdout], [stderr])
 AT_CHECK([diff test.conf ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/1/post/test.conf], 0, [stdout], [stderr])
@@ -44 +44 @@
 AT_KEYWORDS([domain])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -d 1 1 1], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o xyz -d 1 1 1], 0, [stdout], [stderr])
 AT_CHECK([file=test.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-x.conf], 0)
-AT_CHECK([../../molecuilder test-x.conf -e ${abs_top_srcdir}/src/ -d 2 1 1], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test-x.conf -e ${abs_top_srcdir}/src/ -o xyz -d 2 1 1], 0, [stdout], [stderr])
 AT_CHECK([file=test-x.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-x.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([file=test-x.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-y.conf], 0)
-AT_CHECK([../../molecuilder test-y.conf -e ${abs_top_srcdir}/src/ -d 1 2 1], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test-y.conf -e ${abs_top_srcdir}/src/ -o xyz -d 1 2 1], 0, [stdout], [stderr])
 AT_CHECK([file=test-y.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-y.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([file=test-y.conf.xyz; diff $file-sorted $file-sorted2], 0, [ignore], [ignore])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/pre/test.conf test-z.conf], 0)
-AT_CHECK([../../molecuilder test-z.conf -e ${abs_top_srcdir}/src/ -d 1 1 2], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test-z.conf -e ${abs_top_srcdir}/src/ -o xyz -d 1 1 2], 0, [stdout], [stderr])
 AT_CHECK([file=test-z.conf.xyz;sort -n $file | grep -v "Created by" >$file-sorted], 0, [ignore], [ignore])
 AT_CHECK([file=test-z.conf.xyz;sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Domain/6/post/$file  | grep -v "Created by" >$file-sorted2], 0, [ignore], [ignore])

tests/regression/testsuite-simple_configuration.at

@@ -14 +14 @@
 AT_KEYWORDS([configuration])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/2/pre/test.xyz .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -p test.xyz], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -p test.xyz], 0, [ignore], [ignore])
 AT_CHECK([fgrep "Ion_Type1_1" test.conf], 0, [Ion_Type1_1       10.000000000    10.000000000    10.000000000    0 # molecule nr 0
 ], [ignore])
@@ -25 +25 @@
 AT_SETUP([Simple configuration - adding atom])
 AT_KEYWORDS([configuration])
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -a 1 --position 10. 10. 10.], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -a 1 --position 10. 10. 10.], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/3/post/$file], 0, [ignore], [ignore])
@@ -43 +43 @@
 AT_KEYWORDS([configuration])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/pre/test.conf .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -r 0], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o mpqc pcp xyz -r 0], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
 AT_CHECK([file=test.conf.in; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/5/post/$file], 0, [ignore], [ignore])
@@ -75 +75 @@
 AT_KEYWORDS([configuration])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/pre/test.* .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -R 7. --position 7.283585982 3.275186040 3.535886037], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o xyz -R 7. --position 7.283585982 3.275186040 3.535886037], 0, [stdout], [stderr])
 AT_CHECK([sort -n test.conf.xyz | grep -v "Created by" >test.conf.xyz-sorted], 0, [ignore], [ignore])
 AT_CHECK([sort -n ${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.conf.xyz  | grep -v "Created by" >${abs_top_srcdir}/${AUTOTEST_PATH}/Simple_configuration/8/post/test.conf.xyz-sorted], 0, [ignore], [ignore])

tests/regression/testsuite-tesselation.at

@@ -12 +12 @@
 AT_SETUP([Tesselation - Convex Envelope])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/pre/* .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o 0 --convex-file ConvexEnvelope --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ --convex-envelope 0 --convex-file ConvexEnvelope --nonconvex-file NonConvexEnvelope], 0, [stdout], [stderr])
 AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
 #AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/2/post/$file], 0, [ignore], [ignore])
@@ -30 +30 @@
 #AT_SETUP([Tesselation - big convex Envelope])
 #AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/pre/* .], 0)
-#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -o ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
+#AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ --convex-envelope ConvexEnvelope NonConvexEnvelope], 0, [stdout], [stderr])
 #AT_CHECK([file=ConvexEnvelope.dat; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])
 #AT_CHECK([file=ConvexEnvelope.r3d; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Tesselation/4/post/$file], 0, [ignore], [ignore])