Changeset 78202b

Timestamp:

May 18, 2016, 10:02:06 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, 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_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, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, 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:

2fd88d1

Parents:

16d67a

git-author:

Frederik Heber <heber@…> (03/07/16 14:22:05)

git-committer:

Frederik Heber <heber@…> (05/18/16 22:02:06)

Message:

Adding potential action to parse and save atom fragment associations.

• Made KeySet serializable.
• added documentation on save and parse atom fragments.

Files:

• doc/userguide/userguide.xml (modified) (1 diff)
• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (3 diffs)
• src/Actions/PotentialAction/ParseAtomFragmentsAction.cpp (added)
• src/Actions/PotentialAction/ParseAtomFragmentsAction.def (added)
• src/Actions/PotentialAction/ParseAtomFragmentsAction.hpp (added)
• src/Actions/PotentialAction/SaveAtomFragmentsAction.cpp (added)
• src/Actions/PotentialAction/SaveAtomFragmentsAction.def (added)
• src/Actions/PotentialAction/SaveAtomFragmentsAction.hpp (added)
• src/Fragmentation/Homology/AtomFragmentsMap.hpp (modified) (1 diff)
• src/Fragmentation/KeySet.hpp (modified) (2 diffs)
• tests/Python/AllActions/options.dat (modified) (2 diffs)

doc/userguide/userguide.xml

@@ -1713 +1713 @@
         <filename>homologies.dat</filename>.</para>
       </section>
+      <section xml:id="atomfragments">
+        <title xml:id="atomfragments.title">AtomFragments</title>
+        <para>Similarly, to <link linkend="homology">Homologies</link> also
+        the associations between atoms and the respective fragments they take
+        part in can be stored to a file and parse again at a later time.</para>
+       <programlisting>... --parse-atom-fragments atomfragments.dat</programlisting>
+        <para>This parses the all atom fragment associattions contained in the file
+        <filename>atomfragments.dat</filename> and <emphasis role="italic">appends</emphasis> 
+        them to the atom fragments associations container.</para>
+        <programlisting>... --save-atom-fragments atomfragments.dat</programlisting>
+        <para>Complementary, this stores the current contents of the atom fragments 
+        associations container, <emphasis role="italic">overwriting</emphasis> the file
+        <filename>atomfragments.dat</filename>.</para>
+      </section>
       <section xml:id="potentials">
         <title xml:id="potentials.title">Potentials</title>

src/Actions/GlobalListOfActions.hpp

@@ -90 +90 @@
   (MoleculeVerletIntegration) \
   (PotentialFitPartialCharges) \
+  (PotentialParseAtomFragments) \
   (PotentialParseHomologies) \
   (PotentialParseParticleParameters) \
   (PotentialParsePotentials) \
+  (PotentialSaveAtomFragments) \
   (PotentialSaveHomologies) \
   (PotentialSaveParticleParameters) \

src/Actions/Makefile.am

@@ -375 +375 @@
 POTENTIALACTIONSOURCE = \
   Actions/PotentialAction/FitPartialChargesAction.cpp \
+  Actions/PotentialAction/ParseAtomFragmentsAction.cpp \
   Actions/PotentialAction/ParseHomologiesAction.cpp \
   Actions/PotentialAction/ParseParticleParametersAction.cpp \
   Actions/PotentialAction/ParsePotentialsAction.cpp \
+  Actions/PotentialAction/SaveAtomFragmentsAction.cpp \
   Actions/PotentialAction/SaveHomologiesAction.cpp \
   Actions/PotentialAction/SaveParticleParametersAction.cpp \
@@ -383 +385 @@
 POTENTIALACTIONHEADER = \
   Actions/PotentialAction/FitPartialChargesAction.hpp \
+  Actions/PotentialAction/ParseAtomFragmentsAction.hpp \
   Actions/PotentialAction/ParseHomologiesAction.hpp \
   Actions/PotentialAction/ParseParticleParametersAction.hpp \
   Actions/PotentialAction/ParsePotentialsAction.hpp \
+  Actions/PotentialAction/SaveAtomFragmentsAction.hpp \
   Actions/PotentialAction/SaveHomologiesAction.hpp \
   Actions/PotentialAction/SaveParticleParametersAction.hpp \
@@ -391 +395 @@
 POTENTIALACTIONDEFS = \
   Actions/PotentialAction/FitPartialChargesAction.def  \
+  Actions/PotentialAction/ParseAtomFragmentsAction.def \
   Actions/PotentialAction/ParseHomologiesAction.def \
   Actions/PotentialAction/ParseParticleParametersAction.def \
   Actions/PotentialAction/ParsePotentialsAction.def \
+  Actions/PotentialAction/SaveAtomFragmentsAction.def \
   Actions/PotentialAction/SaveHomologiesAction.def \
   Actions/PotentialAction/SaveParticleParametersAction.def \

src/Fragmentation/Homology/AtomFragmentsMap.hpp

@@ -21 +21 @@
 
 #include <boost/serialization/export.hpp>
+#include <boost/serialization/set.hpp>
+#include <boost/serialization/list.hpp>
 #include <boost/serialization/map.hpp>
 #include <boost/serialization/version.hpp>

src/Fragmentation/KeySet.hpp

@@ -15 +15 @@
 #include <set>
 
+#include <boost/serialization/base_object.hpp>
+#include <boost/serialization/set.hpp>
 
 class KeySet : public std::set<int>
@@ -25 +27 @@
 
   bool ScanBufferIntoKeySet(char *buffer);
+
+private:
+  friend class boost::serialization::access;
+  // serialization
+  template <typename Archive>
+  void serialize(Archive& ar, const unsigned int version)
+  {
+    ar & boost::serialization::base_object< std::set<int> >(*this);
+  }
 };
 

tests/Python/AllActions/options.dat

@@ -128 +128 @@
 output-types    "xyz"
 output-types    "xyz mpqc"
+parse-atom-fragments    "atomfragments.dat"
 parse-homologies        "homology.dat"
 parse-particle-parameters       "water.particles"
@@ -167 +168 @@
 save-adjacency  "test.adj"
 save-bonds      "test.bond"
+save-atom-fragments     "atomfragments.dat"
 save-homologies "homology.dat"
 save-particle-parameters        "water.particles"