Changeset 2082637


Ignore:
Timestamp:
May 7, 2016, 7:03:56 AM (9 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_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:
708ec1
Parents:
fde8e7
git-author:
Frederik Heber <heber@…> (02/29/16 17:14:58)
git-committer:
Frederik Heber <heber@…> (05/07/16 07:03:56)
Message:

Added Parse- and SaveParticleParametersAction to parse/save ParticleRegistry.

  • added regression test for parsing and saving particles file.
Files:
8 added
7 edited

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    rfde8e7 r2082637  
    18431843          to give the range of the excluded zone.</para>
    18441844        </section>
     1845        <section xml:id="potentials.parse-particle-parameters">
     1846          <title xml:id="potentials.parse-particle-parameters.title">Parsing a particles file</title>
     1847          <para>Empirical Potential contain parameters for function that model
     1848          interactions between two or more specific particles. However,
     1849          interactions can also be more general, such as a Coulomb
     1850          potential, that interacts with any other particle with non-zero
     1851          charge, or Lennard-Jones potential that interacts with any other
     1852          particle close enough.
     1853          Parameters for these particles are encoded in the internal Particle
     1854          class and are parsed from and stored to a special particles file.
     1855          This parse particle parameters function loads the parameters from
     1856          a file, instantiates them in a new particle, and registers them
     1857          such that they are known within molecuilder.</para>
     1858          <para>More particles can be registered (<emphasis role="bold">fit-partial-charges</emphasis> will also
     1859          register the particles it fits) by parsing them from a file.</para>
     1860          <programlisting>
     1861  ... --parse-particle-parameters water.particles
     1862   </programlisting>
     1863          <note>Currently, only <productname>TREMOLO</productname>particles files are understood and can be parsed.</note>
     1864        </section>
     1865        <section xml:id="potentials.save-particle-parameters">
     1866          <title xml:id="potentials.save-particle-parameters.title">Saving a particles file</title>
     1867          <para>The opposite to <emphasis role="bold">parse-particle-parameters</emphasis>
     1868          is to save all currently registered particle and their parameters to
     1869          the given file.</para>
     1870          <programlisting>
     1871  ... --save-particle-parameters water.particles
     1872   </programlisting>
     1873          <note>Again, only the <productname>TREMOLO</productname>particles format is understood currently and is written.</note>
     1874        </section>
    18451875      </section>
    18461876      <section xml:id="dynamics">

  • src/Actions/GlobalListOfActions.hpp

    rfde8e7 r2082637  
    9191  (PotentialFitPartialCharges) \
    9292  (PotentialParseHomologies) \
     93  (PotentialParseParticleParameters) \
    9394  (PotentialParsePotentials) \
    9495  (PotentialSaveHomologies) \
     96  (PotentialSaveParticleParameters) \
    9597  (PotentialSavePotentials) \
    9698  (ParserParseTremoloPotentials) \

  • src/Actions/Makefile.am

    rfde8e7 r2082637  
    376376  Actions/PotentialAction/FitPartialChargesAction.cpp \
    377377  Actions/PotentialAction/ParseHomologiesAction.cpp \
     378  Actions/PotentialAction/ParseParticleParametersAction.cpp \
    378379  Actions/PotentialAction/ParsePotentialsAction.cpp \
    379380  Actions/PotentialAction/SaveHomologiesAction.cpp \
     381  Actions/PotentialAction/SaveParticleParametersAction.cpp \
    380382  Actions/PotentialAction/SavePotentialsAction.cpp
    381383POTENTIALACTIONHEADER = \
    382384  Actions/PotentialAction/FitPartialChargesAction.hpp \
    383385  Actions/PotentialAction/ParseHomologiesAction.hpp \
     386  Actions/PotentialAction/ParseParticleParametersAction.hpp \
    384387  Actions/PotentialAction/ParsePotentialsAction.hpp \
    385388  Actions/PotentialAction/SaveHomologiesAction.hpp \
     389  Actions/PotentialAction/SaveParticleParametersAction.hpp \
    386390  Actions/PotentialAction/SavePotentialsAction.hpp
    387391POTENTIALACTIONDEFS = \
    388392  Actions/PotentialAction/FitPartialChargesAction.def  \
    389393  Actions/PotentialAction/ParseHomologiesAction.def \
     394  Actions/PotentialAction/ParseParticleParametersAction.def \
    390395  Actions/PotentialAction/ParsePotentialsAction.def \
    391396  Actions/PotentialAction/SaveHomologiesAction.def \
     397  Actions/PotentialAction/SaveParticleParametersAction.def \
    392398  Actions/PotentialAction/SavePotentialsAction.def
    393399

  • src/Actions/PotentialAction/FitPartialChargesAction.cpp

    rfde8e7 r2082637  
    5656
    5757#include "Element/element.hpp"
     58#include "Element/periodentafel.hpp"
    5859#include "Fragmentation/Homology/HomologyContainer.hpp"
    5960#include "Fragmentation/Homology/HomologyGraph.hpp"

  • tests/Python/AllActions/options.dat

    rfde8e7 r2082637  
    128128output-types    "xyz mpqc"
    129129parse-homologies        "homology.dat"
     130parse-particle-parameters       "water.particles"
    130131parse-potentials        "water.potentials"
    131132parse-tremolo-potentials        "argon.potentials"
    … …  
    167168save-bonds      "test.bond"
    168169save-homologies "homology.dat"
     170save-particle-parameters        "water.particles"
    169171save-potentials "water.potentials"
    170172save-selected-atoms     "testsave.xyz"

  • tests/regression/Makefile.am

    rfde8e7 r2082637  
    186186        $(srcdir)/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at \
    187187        $(srcdir)/Potential/FitPotential/testsuite-potential-fit-potential.at \
     188        $(srcdir)/Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at \
    188189        $(srcdir)/Potential/SaveParsePotentials/testsuite-potential-save-parse-potentials.at \
    189190        $(srcdir)/RandomNumbers/testsuite-randomnumbers.at \

  • tests/regression/Potential/testsuite-potential.at

    rfde8e7 r2082637  
    2525m4_include([Potential/FitPotential/testsuite-potential-fit-potential.at])
    2626
     27# parsing and saving particles file
     28m4_include([Potential/SaveParseParticleParameters/testsuite-potential-save-parse-particle-parameters.at])
     29
    2730# fitting particle charges to fragment results
    2831m4_include([Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at])
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