Changeset 0ea063 for src

Timestamp:

Oct 19, 2014, 5:08:51 PM (10 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:

9e1bfb

Parents:

f1eabd

git-author:

Frederik Heber <heber@…> (09/12/14 07:54:12)

git-committer:

Frederik Heber <heber@…> (10/19/14 17:08:51)

Message:

Extracted SavePotentialsAction.

• PotentialTrainer::StorePotentials removed.
• Fit...Actions do not store anymore.
• TESTFIX: potential regression tests now use save-potentials and compare against stored file.

Location:

src

Files:

• Actions/GlobalListOfActions.hpp (modified) (1 diff)
• Actions/Makefile.am (modified) (1 diff)
• Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) (1 diff)
• Actions/PotentialAction/FitCompoundPotentialAction.def (modified) (1 diff)
• Actions/PotentialAction/FitPotentialAction.cpp (modified) (1 diff)
• Actions/PotentialAction/FitPotentialAction.def (modified) (2 diffs)
• Actions/PotentialAction/SavePotentialsAction.cpp (added)
• Actions/PotentialAction/SavePotentialsAction.def (added)
• Actions/PotentialAction/SavePotentialsAction.hpp (added)
• Potentials/PotentialTrainer.cpp (modified) (1 diff)
• Potentials/PotentialTrainer.hpp (modified) (1 diff)

src/Actions/GlobalListOfActions.hpp ¶

@@ -85 +85 @@
   (PotentialParsePotentials) \
   (PotentialSaveHomologies) \
+  (PotentialSavePotentials) \
   (ParserParseTremoloPotentials) \
   (ParserSaveSelectedAtomsAsExtTypes) \

src/Actions/Makefile.am ¶

@@ -352 +352 @@
   Actions/PotentialAction/ParseHomologiesAction.cpp \
   Actions/PotentialAction/ParsePotentialsAction.cpp \
-  Actions/PotentialAction/SaveHomologiesAction.cpp
+  Actions/PotentialAction/SaveHomologiesAction.cpp \
+  Actions/PotentialAction/SavePotentialsAction.cpp
 POTENTIALACTIONHEADER = \
   Actions/PotentialAction/FitParticleChargesAction.hpp \
   Actions/PotentialAction/ParseHomologiesAction.hpp \
   Actions/PotentialAction/ParsePotentialsAction.hpp \
-  Actions/PotentialAction/SaveHomologiesAction.hpp
+  Actions/PotentialAction/SaveHomologiesAction.hpp \
+  Actions/PotentialAction/SavePotentialsAction.hpp
 POTENTIALACTIONDEFS = \
   Actions/PotentialAction/FitParticleChargesAction.def  \
   Actions/PotentialAction/ParseHomologiesAction.def \
   Actions/PotentialAction/ParsePotentialsAction.def \
-  Actions/PotentialAction/SaveHomologiesAction.def
+  Actions/PotentialAction/SaveHomologiesAction.def \
+  Actions/PotentialAction/SavePotentialsAction.def
 
 if CONDLEVMAR

src/Actions/PotentialAction/FitCompoundPotentialAction.cpp ¶

@@ -103 +103 @@
   }
 
-  // store the potentials
-  if (!params.potential_file.get().string().empty()) {
-    PotentialTrainer::storePotentials(params.potential_file.get());
-  }
-
   return Action::success;
 }

src/Actions/PotentialAction/FitCompoundPotentialAction.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::vector<const element *>)(unsigned int)(double)
-#define paramtokens ("training-file")("potential-file")("fragment-charges")("take-best-of")("set-threshold")
-#define paramdescriptions ("optional file to write training data to")("potential file specifying multiple potentials to fit")("charges specifying the fragment")("take the best among this many approximations")("Require L2 error to be smaller than threshold, overrides number of attempts")
-#define paramdefaults (PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))(PARAM_DEFAULT(1.))
-#define paramreferences (training_file)(potential_file)(fragment)(best_of_howmany)(threshold)
+#define paramtypes (boost::filesystem::path)(std::vector<const element *>)(unsigned int)(double)
+#define paramtokens ("training-file")("fragment-charges")("take-best-of")("set-threshold")
+#define paramdescriptions ("optional file to write training data to")("charges specifying the fragment")("take the best among this many approximations")("Require L2 error to be smaller than threshold, overrides number of attempts")
+#define paramdefaults (PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))(PARAM_DEFAULT(1.))
+#define paramreferences (training_file)(fragment)(best_of_howmany)(threshold)
 #define paramvalids \
 (DummyValidator<boost::filesystem::path>()) \
-(FileSuffixValidator("potentials")) \
 (STLVectorValidator< std::vector<const element *> >(1,99, ElementValidator())) \
 (PositiveValidator<unsigned int>()) \

src/Actions/PotentialAction/FitPotentialAction.cpp ¶

@@ -154 +154 @@
   }
 
-  // store the potentials
-  // print fitted potentials
-  std::stringstream potentials;
-  PotentialSerializer serialize(potentials);
-  serialize();
-  LOG(1, "STATUS: Resulting parameters are " << std::endl << potentials.str());
-  if (!params.potential_file.get().string().empty()) {
-    PotentialTrainer::storePotentials(params.potential_file.get());
-  }
-
   return Action::success;
 }

src/Actions/PotentialAction/FitPotentialAction.def ¶

@@ -18 +18 @@
 #include "Parameters/Validators/Specific/ElementValidator.hpp"
 #include "Parameters/Validators/Specific/EmptyStringValidator.hpp"
-#include "Parameters/Validators/Specific/FileSuffixValidator.hpp"
-#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
-#include "Parameters/Validators/Specific/FileSuffixValidator.hpp"
 #include "Parameters/Validators/Specific/PotentialTypeValidator.hpp"
 
@@ -26 +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)(std::vector<const element *>)(std::vector<const element *>)(unsigned int)(double)
-#define paramtokens ("training-file")("potential-file")("potential-type")("potential-charges")("fragment-charges")("take-best-of")("set-threshold")
-#define paramdescriptions ("optional file to write training data to")("optional potential file to wrote resulting potentials to")("potential type to fit")("charges specifying the potential")("charges specifying the fragment")("take the best among this many approximations")("Require L2 error to be smaller than threshold, overrides number of attempts")
-#define paramdefaults (PARAM_DEFAULT(""))(PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))(PARAM_DEFAULT(1.))
-#define paramreferences (training_file)(potential_file)(potentialtype)(charges)(fragment)(best_of_howmany)(threshold)
+#define paramtypes (boost::filesystem::path)(std::string)(std::vector<const element *>)(std::vector<const element *>)(unsigned int)(double)
+#define paramtokens ("training-file")("potential-type")("potential-charges")("fragment-charges")("take-best-of")("set-threshold")
+#define paramdescriptions ("optional file to write training data to")("potential type to fit")("charges specifying the potential")("charges specifying the fragment")("take the best among this many approximations")("Require L2 error to be smaller than threshold, overrides number of attempts")
+#define paramdefaults (PARAM_DEFAULT(""))(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))(PARAM_DEFAULT(1.))
+#define paramreferences (training_file)(potentialtype)(charges)(fragment)(best_of_howmany)(threshold)
 #define paramvalids \
 (DummyValidator<boost::filesystem::path>()) \
-(!FilePresentValidator() || FileSuffixValidator("potentials")) \
 (PotentialTypeValidator()) \
 (STLVectorValidator< std::vector<const element *> >(0,99, ElementValidator())) \

src/Potentials/PotentialTrainer.cpp ¶

@@ -167 +167 @@
 }
 
-void PotentialTrainer::storePotentials(
-    const boost::filesystem::path &_potentialfile
-    )
-{
-  // print fitted potentials
-  std::stringstream potentials;
-  PotentialSerializer serialize(potentials);
-  serialize();
-  std::ofstream returnstream(_potentialfile.string().c_str());
-  if (returnstream.good()) {
-    returnstream << potentials.str();
-  }
-}
-
 HomologyGraph PotentialTrainer::getFirstGraphwithSpecifiedElements(
     const HomologyContainer &homologies,

src/Potentials/PotentialTrainer.hpp ¶

@@ -39 +39 @@
         const unsigned int _best_of_howmany) const;
 
-  static void storePotentials(
-      const boost::filesystem::path &_potentialfile
-      );
-
   static
   HomologyGraph getFirstGraphwithSpecifiedElements(