Changeset 50d49d


Ignore:
Timestamp:
Feb 28, 2016, 5:59:42 PM (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_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:
b9d387
Parents:
0824dd
git-author:
Frederik Heber <heber@…> (02/13/16 10:59:21)
git-committer:
Frederik Heber <heber@…> (02/28/16 17:59:42)
Message:

FIX: Renamed FitParticleCharges -> FitPartialCharges.

  • fitting partial charges is much clearer and the proper word for the action, also the class that does all the work is called PartialNucleiChargeFitter.
  • all files, all classes.
  • also renamed fit-particle-charges -> fit-partial-charges, also all files, within all tests and the command itself.
Files:
7 edited
7 moved

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    r0824dd r50d49d  
    18141814          <note>Again, only the <productname>TREMOLO</productname>potential format is understood currently and is written.</note>
    18151815        </section>
    1816         <section xml:id="potentials.fit-particle-charges">
    1817           <title xml:id="potentials.fit-particle-charges.title">Fitting particle charges</title>
     1816        <section xml:id="potentials.fit-partial-charges">
     1817          <title xml:id="potentials.fit-partial-charges.title">Fitting partial particle charges</title>
    18181818          <para>The above empirical potential just model the short-range
    18191819          behavior in the molecular fragment, namely the (covalently) bonded interaction.
    … …  
    18291829          action as follows.</para>
    18301830          <programlisting>
    1831   ... --fit-particle-charges \
     1831  ... --fit-partial-charges \
    18321832      --fragment-charges 8 1 1 \
    18331833      --potential-file water.potentials \

  • src/Actions/GlobalListOfActions.hpp

    r0824dd r50d49d  
    8989  (MoleculeTranslate) \
    9090  (MoleculeVerletIntegration) \
    91   (PotentialFitParticleCharges) \
     91  (PotentialFitPartialCharges) \
    9292  (PotentialParseHomologies) \
    9393  (PotentialParsePotentials) \

  • src/Actions/Makefile.am

    r0824dd r50d49d  
    374374
    375375POTENTIALACTIONSOURCE = \
    376   Actions/PotentialAction/FitParticleChargesAction.cpp \
     376  Actions/PotentialAction/FitPartialChargesAction.cpp \
    377377  Actions/PotentialAction/ParseHomologiesAction.cpp \
    378378  Actions/PotentialAction/ParsePotentialsAction.cpp \
    … …  
    380380  Actions/PotentialAction/SavePotentialsAction.cpp
    381381POTENTIALACTIONHEADER = \
    382   Actions/PotentialAction/FitParticleChargesAction.hpp \
     382  Actions/PotentialAction/FitPartialChargesAction.hpp \
    383383  Actions/PotentialAction/ParseHomologiesAction.hpp \
    384384  Actions/PotentialAction/ParsePotentialsAction.hpp \
    … …  
    386386  Actions/PotentialAction/SavePotentialsAction.hpp
    387387POTENTIALACTIONDEFS = \
    388   Actions/PotentialAction/FitParticleChargesAction.def  \
     388  Actions/PotentialAction/FitPartialChargesAction.def  \
    389389  Actions/PotentialAction/ParseHomologiesAction.def \
    390390  Actions/PotentialAction/ParsePotentialsAction.def \

  • src/Actions/PotentialAction/FitPartialChargesAction.cpp

    r0824dd r50d49d  
    2222
    2323/*
    24  * FitParticleChargesAction.cpp
     24 * FitPartialChargesAction.cpp
    2525 *
    2626 *  Created on: Jul 03, 2013
    … …  
    5151#include <string>
    5252
    53 #include "Actions/PotentialAction/FitParticleChargesAction.hpp"
     53#include "Actions/PotentialAction/FitPartialChargesAction.hpp"
    5454
    5555#include "Potentials/PartialNucleiChargeFitter.hpp"
    … …  
    6767
    6868// and construct the stuff
    69 #include "FitParticleChargesAction.def"
     69#include "FitPartialChargesAction.def"
    7070#include "Action_impl_pre.hpp"
    7171/** =========== define the function ====================== */
    … …  
    113113}
    114114
    115 ActionState::ptr PotentialFitParticleChargesAction::performCall() {
     115ActionState::ptr PotentialFitPartialChargesAction::performCall() {
    116116
    117117  // fragment specifies the homology fragment to use
    … …  
    189189}
    190190
    191 ActionState::ptr PotentialFitParticleChargesAction::performUndo(ActionState::ptr _state) {
     191ActionState::ptr PotentialFitPartialChargesAction::performUndo(ActionState::ptr _state) {
    192192  return Action::success;
    193193}
    194194
    195 ActionState::ptr PotentialFitParticleChargesAction::performRedo(ActionState::ptr _state){
     195ActionState::ptr PotentialFitPartialChargesAction::performRedo(ActionState::ptr _state){
    196196  return Action::success;
    197197}
    198198
    199 bool PotentialFitParticleChargesAction::canUndo() {
     199bool PotentialFitPartialChargesAction::canUndo() {
    200200  return false;
    201201}
    202202
    203 bool PotentialFitParticleChargesAction::shouldUndo() {
     203bool PotentialFitPartialChargesAction::shouldUndo() {
    204204  return false;
    205205}

  • src/Actions/PotentialAction/FitPartialChargesAction.def

    r0824dd r50d49d  
    11/*
    2  * FitParticleChargesAction.def
     2 * FitPartialChargesAction.def
    33 *
    44 *  Created on: Jul 03, 2013
    … …  
    3636#define MENUNAME "potential"
    3737#define MENUPOSITION 4
    38 #define ACTIONNAME FitParticleCharges
    39 #define TOKEN "fit-particle-charges"
     38#define ACTIONNAME FitPartialCharges
     39#define TOKEN "fit-partial-charges"
    4040
    4141
    4242// finally the information stored in the ActionTrait specialization
    43 #define DESCRIPTION "fits partial nuclear charges to present particle types from long-range fragmentation results"
     43#define DESCRIPTION "fits partial nuclear charges to present particle types from loaded homologies containing sampled grids."
    4444#undef SHORTFORM

  • src/Actions/PotentialAction/FitPartialChargesAction.hpp

    r0824dd r50d49d  
    11/*
    2  * FitParticleChargesAction.hpp
     2 * FitPartialChargesAction.hpp
    33 *
    44 *  Created on: Jul 03, 2013
    … …  
    1717#include "Actions/Action.hpp"
    1818
    19 #include "FitParticleChargesAction.def"
     19#include "FitPartialChargesAction.def"
    2020#include "Action_impl_header.hpp"
    2121

  • tests/GuiChecks/Makefile.am

    r0824dd r50d49d  
    150150        $(srcdir)/./RandomNumbers/Distribution/testsuite-set-random-number-distribution.at \
    151151        $(srcdir)/./Potential/testsuite-potential.at \
    152         $(srcdir)/./Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at \
     152        $(srcdir)/./Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at \
    153153        $(srcdir)/./Potential/FitPotential/testsuite-potential-fit-potential.at \
    154154        $(srcdir)/./Bond/Add/testsuite-bond-add.at \

  • tests/GuiChecks/Potential/FitParticleCharges/testsuite-potential-fit-partial-charges.at

    r0824dd r50d49d  
    2222
    2323AT_SETUP([Potential - Fit particle charges to water])
    24 AT_KEYWORDS([potential parse-homologies fit-particle-charges])
    25 AT_SKIP_IF([../../molecuilder --help fit-particle-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
     24AT_KEYWORDS([potential parse-homologies fit-partial-charges])
     25AT_SKIP_IF([../../molecuilder --help fit-partial-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
    2626
    2727# homology file created with water.pdb and as follows:
    2828# molecuilder -i water.pdb --select-all-atoms --fragment-molecule --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 5 --store-grids 1 --analyse-fragment-results --save-homologies homology_grid.dat
    2929file=homology_grid.dat
    30 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitParticleCharges/pre/$file $file], 0)
     30AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$file $file], 0)
    3131AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    32 AT_CHECK([../../molecuilder --dry-run --parse-homologies $file --fit-particle-charges --potential-file water.particles --fragment-charges 8 1 1 --radius 1.5 --no-dry-run --store-session session-potential-fit-particle-charges.py --session-type python], 0, [stdout], [ignore])
    33 AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-particle-charges.py >session-potential-fit-particle-charges_new.py], 0, [ignore], [ignore])
    34 AT_CHECK([../../molecuilderguitest session-potential-fit-particle-charges_new.py], 0, [stdout], [ignore])
     32AT_CHECK([../../molecuilder --dry-run --parse-homologies $file --fit-partial-charges --potential-file water.particles --fragment-charges 8 1 1 --radius 1.5 --no-dry-run --store-session session-potential-fit-partial-charges.py --session-type python], 0, [stdout], [ignore])
     33AT_CHECK([grep -v "Command.*DryRun" session-potential-fit-partial-charges.py >session-potential-fit-partial-charges_new.py], 0, [ignore], [ignore])
     34AT_CHECK([../../molecuilderguitest session-potential-fit-partial-charges_new.py], 0, [stdout], [ignore])
    3535# check that L_2 error is below 1e-6
    3636

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

    r0824dd r50d49d  
    2323
    2424# fitting particle charges to fragment results
    25 m4_include([Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at])
     25m4_include([Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at])

  • tests/regression/Makefile.am

    r0824dd r50d49d  
    183183        $(srcdir)/Parser/Xyz/testsuite-parser-xyz-save.at \
    184184        $(srcdir)/Potential/testsuite-potential.at \
    185         $(srcdir)/Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at \
     185        $(srcdir)/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at \
    186186        $(srcdir)/Potential/FitPotential/testsuite-potential-fit-potential.at \
    187187        $(srcdir)/RandomNumbers/testsuite-randomnumbers.at \

  • tests/regression/Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at

    r0824dd r50d49d  
    1616#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
    1717#
    18 ### fit particle charges
     18### fit partial particle charges
    1919
    2020# the potential has been generated by:
    2121# ./molecuilder -i pre/water.pdb --center-in-box "8,0,8,0,0,8" --select-all-atoms --fragment-molecule BondFragment --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 4 --DoPrintDebug 1 --DoValenceOnly 0 --analyse-fragment-results --store-grids 1 --save-homologies homology_grid_4_full.dat
    2222
    23 AT_SETUP([Potential - Fit particle charges to water])
    24 AT_KEYWORDS([potential parse-homologies fit-particle-charges])
    25 AT_SKIP_IF([../../molecuilder --help fit-particle-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
     23AT_SETUP([Potential - Fit partial charges to water])
     24AT_KEYWORDS([potential parse-homologies fit-partial-charges])
     25AT_SKIP_IF([../../molecuilder --help fit-partial-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
    2626
    2727# homology file created with water.pdb and as follows:
    2828# molecuilder -i water.pdb --select-all-atoms --fragment-molecule --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 5 --store-grids 1 --analyse-fragment-results --save-homologies homology_grid.dat
    2929file=homology_grid.dat
    30 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitParticleCharges/pre/$file $file], 0)
     30AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Potential/FitPartialCharges/pre/$file $file], 0)
    3131AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
    32 AT_CHECK([../../molecuilder --parse-homologies $file --fit-particle-charges --potential-file water.particles --fragment-charges 8 1 1 --radius 1.5], 0, [stdout], [ignore])
     32AT_CHECK([../../molecuilder --parse-homologies $file --fit-partial-charges --fragment-charges 8 1 1 --radius 1.5], 0, [stdout], [ignore])
    3333# check that L_2 error is below 1e-6
    3434AT_CHECK([grep "L2-Norm" stdout | awk '{if ($6 > 1e1) exit 1}'], 0, [ignore], [ignore])

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

    r0824dd r50d49d  
    2323
    2424# fitting particle charges to fragment results
    25 m4_include([Potential/FitParticleCharges/testsuite-potential-fit-particle-charges.at])
     25m4_include([Potential/FitPartialCharges/testsuite-potential-fit-partial-charges.at])
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