Changeset 531f27

Timestamp:

Apr 6, 2012, 11:45:30 AM (13 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:

23fd43

Parents:

80ca29

git-author:

Frederik Heber <heber@…> (04/05/12 08:53:23)

git-committer:

Frederik Heber <heber@…> (04/06/12 11:45:30)

Message:

Added SaveSelectedAtomsAsExtTypesAction that creates a tremolo-specific .exttypes file.

• the functionality is implemented in TremoloParser.
• it is required to perform a save on the atoms before such that ids are correct.
• the actions tells whether ids are valid or not.
• also added regression test Parser/Tremolo-Exttypes.

Files:

• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (3 diffs)
• src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (added)
• src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.def (added)
• src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.hpp (added)
• src/Parser/TremoloParser.cpp (modified) (1 diff)
• src/Parser/TremoloParser.hpp (modified) (1 diff)
• tests/Python/AllActions/options.dat (modified) (2 diffs)
• tests/regression/Makefile.am (modified) (1 diff)
• tests/regression/Parser/Tremolo-Exttypes/post/test-right.exttypes (added)
• tests/regression/Parser/Tremolo-Exttypes/post/test-wrong.exttypes (added)
• tests/regression/Parser/Tremolo-Exttypes/pre/test.xyz (added)
• tests/regression/Parser/Tremolo-Exttypes/testsuite-parser-tremolo-save-selected-atoms-as-exttypes.at (added)
• tests/regression/Parser/testsuite-parser.at (modified) (1 diff)

src/Actions/GlobalListOfActions.hpp

@@ -45 +45 @@
         (ParserSetTremoloAtomdata) \
         (ParserParseTremoloPotentials) \
+        (ParserSaveSelectedAtomsAsExtTypes) \
         (ParserSetParserParameters) \
         (ParserSetOutputFormats) \

src/Actions/Makefile.am

@@ -261 +261 @@
 PARSERACTIONSOURCE = \
   Actions/ParserAction/ParseTremoloPotentialsAction.cpp \
+  Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp \
   Actions/ParserAction/SetParserParametersAction.cpp \
   Actions/ParserAction/SetOutputFormatsAction.cpp \
@@ -266 +267 @@
 PARSERACTIONHEADER = \
   Actions/ParserAction/ParseTremoloPotentialsAction.hpp \
+  Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.hpp \
   Actions/ParserAction/SetParserParametersAction.hpp \
   Actions/ParserAction/SetOutputFormatsAction.hpp \
@@ -271 +273 @@
 PARSERACTIONDEFS = \
   Actions/ParserAction/ParseTremoloPotentialsAction.def \
+  Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.def \
   Actions/ParserAction/SetParserParametersAction.def \
   Actions/ParserAction/SetOutputFormatsAction.def \

src/Parser/TremoloParser.cpp

@@ -521 +521 @@
 }
 
+bool FormatParser< tremolo >::saveAtomsInExttypes(std::ostream &output, const std::vector<atom*> &atoms, const int id) const
+{
+  bool status = true;
+  // parse the file
+  for (std::vector<atom *>::const_iterator iter = atoms.begin();
+      iter != atoms.end(); ++iter) {
+    const int atomicid = getLocalId((*iter)->getId());
+    if (atomicid == -1)
+      status = false;
+    output << atomicid << "\t" << id << std::endl;
+  }
+
+  return status;
+}
+
 /**
  * Reads neighbor information for one atom from the input.

src/Parser/TremoloParser.hpp

@@ -71 +71 @@
   }
 
+  /** Save given \a atoms in tremolo's exttypes file
+   *
+   * \note You should have stored the atoms beforehand to give them unique
+   * and sensible ids.
+   *
+   * @param output output stream
+   * @param atoms vector of atoms whose ids to store
+   * @param id id to given this exttypes group
+   * @return true - all atomic ids are valid, false - one id was not set (-1)
+   */
+  bool saveAtomsInExttypes(std::ostream &output, const std::vector<atom*> &atoms, const int id) const;
+
 protected:
   void AtomInserted(atomId_t);

tests/Python/AllActions/options.dat

@@ -65 +65 @@
 end-step        "1"
 fastparsing     "1"
+filename        "test.exttypes"
 fill-molecule   "filler.xyz"
 fill-void       "hydrogen.xyz"
@@ -135 +136 @@
 save-bonds      "test.bond"
 save-selected-atoms     "testsave.xyz"
+save-selected-atoms-as-exttypes "test.exttypes"
 save-selected-molecules "testsave.xyz"
 save-temperature        "test.ekin"

tests/regression/Makefile.am

@@ -134 +134 @@
         $(srcdir)/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at \
         $(srcdir)/Parser/Tremolo/testsuite-parser-tremolo-save.at \
+        $(srcdir)/Parser/Tremolo-Exttypes/testsuite-parser-tremolo-save-selected-atoms-as-exttypes.at \
         $(srcdir)/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials.at \
         $(srcdir)/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at \

tests/regression/Parser/testsuite-parser.at

@@ -58 +58 @@
 m4_include([Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at])
 
+# writing and exttypes file
+m4_include([Parser/Tremolo-Exttypes/testsuite-parser-tremolo-save-selected-atoms-as-exttypes.at])
+
 # parsing xyz
 m4_include([Parser/Xyz/testsuite-parser-xyz-empty.at])