Changeset f1eabd

Timestamp:

Oct 19, 2014, 5:08:50 PM (11 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:

0ea063

Parents:

98d166

git-author:

Frederik Heber <heber@…> (09/12/14 07:39:58)

git-committer:

Frederik Heber <heber@…> (10/19/14 17:08:50)

Message:

Extracted ParsePotentialsAction from FitCompoundPotentialAction.

Files:

• doc/userguide/userguide.xml (modified) (2 diffs)
• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (1 diff)
• src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) (4 diffs)
• src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) (2 diffs)
• src/Actions/PotentialAction/ParsePotentialsAction.cpp (added)
• src/Actions/PotentialAction/ParsePotentialsAction.def (added)
• src/Actions/PotentialAction/ParsePotentialsAction.hpp (added)
• tests/Python/AllActions/options.dat (modified) (1 diff)

doc/userguide/userguide.xml

@@ -2109 +2109 @@
             a fragment of order 1, e.g. a single hydrogen atom.</para>
           </note>
+        </section>
+
+        <section xml:id='potentials.fit-compound-potential'>
+          <title xml:id='potentials.fit-compound-potential.title'>Fitting
+          many empirical potentials simultaneously</title>
+
 
           <para>Another way is using a file containing a specific set of
@@ -2143 +2149 @@
           with this file.</para>
         </section>
+
+        
+        <section xml:id='potentials.parse-potential'>
+          <title xml:id='potentials.parse-potential.title'>Parsing an
+          empirical potentials file</title>
+
+          <para>Responsible for the compound potential is every potential
+          function whose signature matches with the designated fragment-charges
+          and who is currently known to an internal instance called the
+          PotentialRegistry.</para>
+
+          <para>More potentials can be registered (fit-potential will also
+          register the potential it fits) by parsing them from a file.</para>
+
+          <programlisting>
+                ... --parse-potentials water.potentials
+          </programlisting>
+
+          <note>Currently, only <productname>TREMOLO</productname> potential
+          files are understood and can be parsed.</note>
+        </section>
+
 
         <section xml:id='potentials.fit-particle-charges'>

src/Actions/GlobalListOfActions.hpp

@@ -83 +83 @@
   (PotentialFitParticleCharges) \
   (PotentialParseHomologies) \
+  (PotentialParsePotentials) \
   (PotentialSaveHomologies) \
   (ParserParseTremoloPotentials) \

src/Actions/Makefile.am

@@ -351 +351 @@
   Actions/PotentialAction/FitParticleChargesAction.cpp \
   Actions/PotentialAction/ParseHomologiesAction.cpp \
+  Actions/PotentialAction/ParsePotentialsAction.cpp \
   Actions/PotentialAction/SaveHomologiesAction.cpp
 POTENTIALACTIONHEADER = \
   Actions/PotentialAction/FitParticleChargesAction.hpp \
   Actions/PotentialAction/ParseHomologiesAction.hpp \
+  Actions/PotentialAction/ParsePotentialsAction.hpp \
   Actions/PotentialAction/SaveHomologiesAction.hpp
 POTENTIALACTIONDEFS = \
   Actions/PotentialAction/FitParticleChargesAction.def  \
   Actions/PotentialAction/ParseHomologiesAction.def \
+  Actions/PotentialAction/ParsePotentialsAction.def \
   Actions/PotentialAction/SaveHomologiesAction.def
 

src/Actions/PotentialAction/FitCompoundPotentialAction.cpp

@@ -49 +49 @@
 #include "Fragmentation/Homology/HomologyGraph.hpp"
 #include "Fragmentation/Summation/SetValues/Fragment.hpp"
-#include "Potentials/Exceptions.hpp"
-#include "Potentials/PotentialDeserializer.hpp"
-#include "Potentials/PotentialFactory.hpp"
-#include "Potentials/PotentialRegistry.hpp"
 #include "Potentials/PotentialTrainer.hpp"
 #include "Potentials/SerializablePotential.hpp"
@@ -65 +61 @@
 
 ActionState::ptr PotentialFitCompoundPotentialAction::performCall() {
-  // fragment specifies the homology fragment to use
-  SerializablePotential::ParticleTypes_t fragmentnumbers =
-      PotentialTrainer::getNumbersFromElements(params.fragment.get());
-
-  // either charges and a potential is specified or a file
-  if (boost::filesystem::exists(params.potential_file.get())) {
-    std::ifstream returnstream(params.potential_file.get().string().c_str());
-    if (returnstream.good()) {
-      try {
-        PotentialDeserializer deserialize(returnstream);
-        deserialize();
-      } catch (SerializablePotentialMissingValueException &e) {
-        if (const std::string *key = boost::get_error_info<SerializablePotentialKey>(e))
-          STATUS("Missing value when parsing information for potential "+*key+".");
-        else
-          STATUS("Missing value parsing information for potential with unknown key.");
-        return Action::failure;
-      } catch (SerializablePotentialIllegalKeyException &e) {
-        if (const std::string *key = boost::get_error_info<SerializablePotentialKey>(e))
-          STATUS("Illegal key parsing information for potential "+*key+".");
-        else
-          STATUS("Illegal key parsing information for potential with unknown key.");
-        return Action::failure;
-      }
-    } else {
-      STATUS("Failed to parse from "+params.potential_file.get().string()+".");
-      return Action::failure;
-    }
-    returnstream.close();
-
-    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 World's homologies.");
-
-  } else {
-      STATUS("No existing potential file given!");
-      return Action::failure;
-  }
-
-  // parse homologies into container
+  // get homologies container
   HomologyContainer &homologies = World::getInstance().getHomologies();
 
@@ -118 +75 @@
   }
 
+  // fragment specifies the homology fragment to use
+  SerializablePotential::ParticleTypes_t fragmentnumbers =
+      PotentialTrainer::getNumbersFromElements(params.fragment.get());
+
   // then we ought to pick the right HomologyGraph ...
   const HomologyGraph graph =
@@ -129 +90 @@
   }
 
-  // training
+  // next we use the set of homologous fragments for training from the present potentials
   PotentialTrainer trainer;
   const bool status = trainer(

src/Actions/PotentialAction/FitCompoundPotentialAction.def

@@ -17 +17 @@
 #include "Parameters/Validators/STLVectorValidator.hpp"
 #include "Parameters/Validators/Specific/ElementValidator.hpp"
-#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
 #include "Parameters/Validators/Specific/FileSuffixValidator.hpp"
 #include "Parameters/Validators/Specific/PotentialTypeValidator.hpp"
@@ -31 +30 @@
 #define paramvalids \
 (DummyValidator<boost::filesystem::path>()) \
-(FilePresentValidator() && FileSuffixValidator("potentials")) \
+(FileSuffixValidator("potentials")) \
 (STLVectorValidator< std::vector<const element *> >(1,99, ElementValidator())) \
 (PositiveValidator<unsigned int>()) \

tests/Python/AllActions/options.dat

@@ -124 +124 @@
 output-types    "xyz mpqc"
 parse-homologies        "homology.dat"
+parse-potentials        "water.potentials"
 parse-tremolo-potentials        "argon.potentials"
 parse-tremolo-potentials        "tensid.potentials"