Changeset d449a9

Timestamp:

Aug 9, 2013, 2:20:35 PM (12 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:

f0025d

Parents:

1e1098

git-author:

Frederik Heber <heber@…> (06/24/13 09:08:12)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:35)

Message:

Split off parsing and saving of homologies into new Actions.

Files:

• src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (3 diffs)
• src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) (1 diff)
• src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) (3 diffs)
• src/Actions/FragmentationAction/FitPotentialAction.def (modified) (1 diff)
• src/Actions/FragmentationAction/ParseHomologiesAction.cpp (added)
• src/Actions/FragmentationAction/ParseHomologiesAction.def (added)
• src/Actions/FragmentationAction/ParseHomologiesAction.hpp (added)
• src/Actions/FragmentationAction/SaveHomologiesAction.cpp (added)
• src/Actions/FragmentationAction/SaveHomologiesAction.def (added)
• src/Actions/FragmentationAction/SaveHomologiesAction.hpp (added)
• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (1 diff)
• tests/Python/AllActions/options.dat (modified) (3 diffs)
• tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) (4 diffs)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -220 +220 @@
 }
 
-void parseHomologiesFromFile(
-    const boost::filesystem::path &homology_file
-    )
-{
-  HomologyContainer &homology_container = World::getInstance().getHomologies();
-  if (boost::filesystem::exists(homology_file)) {
-    std::ifstream returnstream(homology_file.string().c_str());
-    if (returnstream.good()) {
-      boost::archive::text_iarchive ia(returnstream);
-      ia >> homology_container;
-    } else {
-      ELOG(2, "Failed to parse from " << homology_file.string() << ".");
-    }
-    returnstream.close();
-  } else {
-    LOG(2, "Could not open " << homology_file.string()
-        << ", creating empty container.");
-  }
-}
-
 void appendToHomologies(
     const FragmentationShortRangeResults &shortrangeresults,
@@ -306 +286 @@
     }
   }
-}
-
-bool writeHomologiesToFile(
-    const boost::filesystem::path &homology_file
-    )
-{
-  /// store homology container again
-  HomologyContainer &homology_container = World::getInstance().getHomologies();
-  std::ofstream outputstream(homology_file.string().c_str());
-  if (outputstream.good()) { // check if opened
-    boost::archive::text_oarchive oa(outputstream);
-    oa << homology_container;
-    if (outputstream.fail()) { // check if correctly written
-      LOG(1, "Failed to write to file " << homology_file.string() << ".");
-      return false;
-    } else
-      outputstream.close();
-  } else {
-    LOG(1, "Failed to open file " << homology_file.string()
-        << " for writing.");
-    return false;
-  }
-  return true;
 }
 
@@ -427 +384 @@
     // append all keysets to homology file
     appendToHomologies(shortrangeresults, longrangeresults);
-    if (!params.homology_file.get().empty()) {
-      const boost::filesystem::path &homology_file = params.homology_file.get();
-      if (homology_file.string() != "") {
-        LOG(1, "INFO: Parsing HomologyGraphs from file " << homology_file.string() << ".");
-        parseHomologiesFromFile(homology_file);
-        LOG(1, "INFO: Appending HomologyGraphs to file " << homology_file.string() << ".");
-        if (!writeHomologiesToFile(homology_file))
-          return Action::failure;
-      }
-    }
   }
 #else

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def

@@ -10 +10 @@
 
 #include "Parameters/Validators/DummyValidator.hpp"
-#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (boost::filesystem::path)(boost::filesystem::path)
-#define paramtokens ("homology-file")("fragment-resultfile")
-#define paramdescriptions ("path to file containing homology container to append to")("parse fragment results from the given file")
-#define paramdefaults (PARAM_DEFAULT(""))(PARAM_DEFAULT(""))
-#define paramreferences (homology_file)(resultsfile)
+#define paramtypes (boost::filesystem::path)
+#define paramtokens ("fragment-resultfile")
+#define paramdescriptions ("parse fragment results from the given file")
+#define paramdefaults (PARAM_DEFAULT(""))
+#define paramreferences (resultsfile)
 #define paramvalids \
-(DummyValidator< boost::filesystem::path >()) \
 (DummyValidator< boost::filesystem::path >())
 

src/Actions/FragmentationAction/FitPotentialAction.cpp

@@ -152 +152 @@
     LOG(0, "STATUS: I'm training now a set of potentials parsed from "
         << params.potential_file.get().string() << " on a fragment "
-        << fragmentnumbers << " on data from " << params.homology_file.get() << ".");
+        << fragmentnumbers << " on data from World's homologies.");
 
   } else {
@@ -168 +168 @@
 
       LOG(0, "STATUS: I'm training now a " << params.potentialtype.get()
-          << " potential on charges " << chargenumbers << " on data from "
-          << params.homology_file.get() << ".");
+          << " potential on charges " << chargenumbers << " on data from World's homologies.");
 
       // register desired potential and an additional constant one
@@ -186 +185 @@
 
   // parse homologies into container
-  HomologyContainer homologies;
-  if (boost::filesystem::exists(params.homology_file.get())) {
-    std::ifstream returnstream(params.homology_file.get().string().c_str());
-    if (returnstream.good()) {
-      boost::archive::text_iarchive ia(returnstream);
-      ia >> homologies;
-    } else {
-      ELOG(0, "Failed to parse from " << params.homology_file.get().string() << ".");
-      return Action::failure;
-    }
-    returnstream.close();
-  } else {
-    ELOG(0, params.homology_file.get() << " does not exist.");
-    return Action::failure;
-  }
+  HomologyContainer &homologies = World::getInstance().getHomologies();
 
   // first we try to look into the HomologyContainer

src/Actions/FragmentationAction/FitPotentialAction.def

@@ -23 +23 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (boost::filesystem::path)(boost::filesystem::path)(std::string)(boost::filesystem::path)(std::vector<const element *>)(std::vector<const element *>)(unsigned int)
-#define paramtokens ("homology-file")("training-file")("potential-type")("potential-file")("potential-charges")("fragment-charges")("take-best-of")
-#define paramdescriptions ("homology file to parse")("optional file to write training data to")("potential type to fit")("potential file specifying multiple potentials to fit")("charges specifying the potential")("charges specifying the fragment")("take the best among this many approximations")
-#define paramdefaults (NOPARAM_DEFAULT)(PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))
-#define paramreferences (homology_file)(training_file)(potentialtype)(potential_file)(charges)(fragment)(best_of_howmany)
+#define paramtypes (boost::filesystem::path)(std::string)(boost::filesystem::path)(std::vector<const element *>)(std::vector<const element *>)(unsigned int)
+#define paramtokens ("training-file")("potential-type")("potential-file")("potential-charges")("fragment-charges")("take-best-of")
+#define paramdescriptions ("optional file to write training data to")("potential type to fit")("potential file specifying multiple potentials to fit")("charges specifying the potential")("charges specifying the fragment")("take the best among this many approximations")
+#define paramdefaults (PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))
+#define paramreferences (training_file)(potentialtype)(potential_file)(charges)(fragment)(best_of_howmany)
 #define paramvalids \
-(FilePresentValidator()) \
 (DummyValidator<boost::filesystem::path>()) \
 (EmptyStringValidator() || PotentialTypeValidator()) \

src/Actions/GlobalListOfActions.hpp

@@ -124 +124 @@
   (FragmentationAnalyseFragmentationResults) \
   (FragmentationFragmentation) \
+  (FragmentationParseHomologies) \
+  (FragmentationSaveHomologies) \
   (FragmentationStoreSaturatedFragment) \
   (FillRegularGrid) \

src/Actions/Makefile.am

@@ -213 +213 @@
 
 FRAGMENTATIONACTIONSOURCE = \
+  Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp \
   Actions/FragmentationAction/FragmentationAction.cpp \
-  Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp \
+  Actions/FragmentationAction/ParseHomologiesAction.cpp \
+  Actions/FragmentationAction/SaveHomologiesAction.cpp \
   Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp
 FRAGMENTATIONACTIONHEADER = \
+  Actions/FragmentationAction/AnalyseFragmentationResultsAction.hpp \
   Actions/FragmentationAction/FragmentationAction.hpp \
-  Actions/FragmentationAction/AnalyseFragmentationResultsAction.hpp \
+  Actions/FragmentationAction/ParseHomologiesAction.hpp \
+  Actions/FragmentationAction/SaveHomologiesAction.hpp \
   Actions/FragmentationAction/StoreSaturatedFragmentAction.hpp
 FRAGMENTATIONACTIONDEFS = \
+  Actions/FragmentationAction/AnalyseFragmentationResultsAction.def \
   Actions/FragmentationAction/FragmentationAction.def \
-  Actions/FragmentationAction/AnalyseFragmentationResultsAction.def \
+  Actions/FragmentationAction/ParseHomologiesAction.def \
+  Actions/FragmentationAction/SaveHomologiesAction.def \
   Actions/FragmentationAction/StoreSaturatedFragmentAction.def
 

tests/Python/AllActions/options.dat

@@ -83 +83 @@
 fragment-resultfile     "results.dat"
 grid-level      "5"
-homology-file   "homology.dat"
 id-mapping      "1"
 input   "test.data"
@@ -118 +117 @@
 output-types    "xyz"
 output-types    "xyz mpqc"
+parse-homologies        "homology.dat"
 parse-tremolo-potentials        "argon.potentials"
 parse-tremolo-potentials        "tensid.potentials"
@@ -154 +154 @@
 save-adjacency  "test.adj"
 save-bonds      "test.bond"
+save-homologies "homology.dat"
 save-selected-atoms     "testsave.xyz"
 save-selected-atoms-as-exttypes "test.exttypes"

tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at

@@ -20 +20 @@
 
 AT_SETUP([Fragmentation - Fit morse potential to water])
-AT_KEYWORDS([fragmentation fit-potential morse])
+AT_KEYWORDS([fragmentation parse-homologies fit-potential morse])
 AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
@@ -26 +26 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder --fit-potential --potential-type "morse" --homology-file $file --potential-charges 8 1 --fragment-charges 1 8 1 --take-best-of 5], 0, [stdout], [ignore])
+AT_CHECK([../../molecuilder --parse-homologies $file --fit-potential --potential-type "morse" --potential-charges 8 1 --fragment-charges 1 8 1 --take-best-of 5], 0, [stdout], [ignore])
 # check that L_2 error is below 1e-6
 AT_CHECK([grep "Best parameters with L2 error" stdout | awk '{if ($8 > 1e-6) exit 1}'], 0, [ignore], [ignore])
@@ -35 +35 @@
 
 AT_SETUP([Fragmentation - Fit harmonic_angle potential to water])
-AT_KEYWORDS([fragmentation fit-potential harmonic_angle])
+AT_KEYWORDS([fragmentation parse-homologies fit-potential harmonic_angle])
 AT_SKIP_IF([../../molecuilder --help --actionname fit-potential; if test $? -eq 5; then /bin/true; else /bin/false; fi])
 
@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitPotential/pre/$file $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder --fit-potential --potential-type "harmonic_angle" --homology-file $file --potential-charges 1 8 1 --fragment-charges 1 8 1 --take-best-of 5], 0, [stdout], [ignore])
+AT_CHECK([../../molecuilder --parse-homologies $file --fit-potential --potential-type "harmonic_angle" --potential-charges 1 8 1 --fragment-charges 1 8 1 --take-best-of 5], 0, [stdout], [ignore])
 # check that L_2 error is below 1e-6
 AT_CHECK([grep "||e||_2:" stdout | awk '{if ($7 > 1e-6) exit 1}'], 0, [ignore], [ignore])