Changeset cc6e5c for src/Python


Ignore:
Timestamp:
May 20, 2014, 8:47:10 AM (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:
975b83
Parents:
0d4168
git-author:
Frederik Heber <heber@…> (09/28/13 00:59:47)
git-committer:
Frederik Heber <heber@…> (05/20/14 08:47:10)
Message:

Replaced Reactions by simple function exported to pyMoleCuilder.

  • Reactions are a bad idea from the start, calculations do not need to be undone. Hence, why make them into an Action that is specifically undoable?
  • removed all Reaction..-related files.
  • removed ActinQueue::getLastAction().
  • removed CalculateBoundingBoxAction, CalculateCellVolumeAction, and CalculateMolarMassAction, replaced by small function in Python folder.
  • TESTFIX: removed associated regression tests in Analysis.
  • modified boxmaker.py.in as names of functions changed.
  • removed Actions/pyMoleCuilder.cpp, is redunant with PythonScripting_impl.hpp.
Location:
src/Python
Files:
3 added
2 edited
3 moved

Legend:

Unmodified
Added
Removed

  • src/Python/Makefile.am

    r0d4168 rcc6e5c  
    33
    44PYTHONSOURCE = \
    5         Python/PythonScripting.cpp
     5        Python/exit.cpp \
     6        Python/getBoundingBox.cpp \
     7        Python/getDomainVolume.cpp \
     8        Python/getSelectedMolarMass.cpp \
     9        Python/PythonScripting.cpp \
     10        Python/reinit.cpp
    611                                 
    712PYTHONHEADER = \
     13        Python/modules.hpp \
    814        Python/PythonScripting_impl.hpp \
    915        Python/PythonScripting.hpp

  • src/Python/PythonScripting_impl.hpp

    r0d4168 rcc6e5c  
    2121
    2222#include "CodePatterns/toString.hpp"
     23
     24// all "getter" functions
     25#include "modules.hpp"
    2326
    2427//!> define all present actions
    … …  
    6467
    6568} /* namespace PythonTypes */
     69
    6670} /* namespace MoleCuilder */
     71
    6772
    6873BOOST_PYTHON_MODULE(pyMoleCuilder)
    6974{
     75  // from this moment on, we need to be sure to deeinitialize in the correct or
     76  // this is handled by the cleanup function
     77  atexit(MoleCuilder::detail::module_exit);
     78
    7079  // set the docstring of the current module scope
    7180  boost::python::scope().attr("__doc__") = "pyMolecuilder are the python bindings to all Actions of the program suite MoleCuilder.\n\nMoleCuilder is a program to build molecular (dynamics) worlds, allowing you indefinite manipulation, control and analysis over the atoms and molecules within a simulation domain.";
     81
     82  boost::python::def(
     83      "reinit",
     84      MoleCuilder::detail::module_reinit,
     85      "Reinitializes the internal state of the python module as if it had been freshly imported,saves all input files beforehand."
     86  );
     87  boost::python::def< MoleCuilder::detail::doubleVec() >(
     88      "getBoundingBox",
     89      MoleCuilder::detail::module_getBoundingBox,
     90      "returns the cuboid bounding box of the current domain."
     91  );
     92  boost::python::def< double() >(
     93      "getDomainVolume",
     94      MoleCuilder::detail::module_getDomainVolume,
     95      "returns the volume of the simulation domain."
     96  );
     97  boost::python::def< double() >(
     98      "getSelectedMolarMass",
     99      MoleCuilder::detail::module_getSelectedMolarMass,
     100      "returns the molar mass of all selected atoms."
     101  );
    72102
    73103  // STL Vectors:
    … …  
    86116  ;
    87117
    88 
     118  // access to all Actions
    89119#define export_print(z,n,list) \
    90120  BOOST_PP_CAT(export_, BOOST_PP_SEQ_ELEM(n, list))();

  • src/Python/getBoundingBox.cpp

    r0d4168 rcc6e5c  
    22 * Project: MoleCuilder
    33 * Description: creates and alters molecular systems
    4  * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
     4 * Copyright (C)  2013 Frederik Heber. All rights reserved.
    55 *
    66 *
    … …  
    2222
    2323/*
    24  * CalculateBoundingBoxAction.cpp
     24 * getBoundingBox.cpp
    2525 *
    26  *  Created on: Nov 02, 2011
     26 *  Created on: Sep 28, 2013
    2727 *      Author: heber
    2828 */
    … …  
    3535#include "CodePatterns/MemDebug.hpp"
    3636
    37 #include "CodePatterns/Log.hpp"
     37#include "modules.hpp"
    3838
    3939#include "Box.hpp"
    4040#include "CodePatterns/Assert.hpp"
     41#include "CodePatterns/Log.hpp"
    4142#include "LinearAlgebra/Plane.hpp"
    4243#include <vector>
    … …  
    4445#include "World.hpp"
    4546
    46 #include <iostream>
    4747#include <string>
    4848
    49 #include "CalculateBoundingBoxAction.hpp"
    50 
    51 using namespace MoleCuilder;
    52 
    53 // and construct the stuff
    54 #include "CalculateBoundingBoxAction.def"
    55 #include "Reaction_impl_pre.hpp"
    56 
    57 #include "Reaction_impl.hpp"
    58 
    5949/** =========== define the function ====================== */
    60 doubleVec * AnalysisCalculateBoundingBoxAction::doCalc() {
     50MoleCuilder::detail::doubleVec MoleCuilder::detail::module_getBoundingBox()
     51{
    6152  typedef std::pair<Plane,Plane> PairOfPlanes;
    6253  typedef std::vector<PairOfPlanes> PairOfPlanesVector;
    … …  
    7465  LOG(0, "RESULT: The current bounding box is " << returnvalues << ".");
    7566
    76   return (new doubleVec(returnvalues));
     67  return returnvalues;
    7768}
    78 /** =========== end of function ====================== */

  • src/Python/getDomainVolume.cpp

    r0d4168 rcc6e5c  
    22 * Project: MoleCuilder
    33 * Description: creates and alters molecular systems
    4  * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
     4 * Copyright (C)  2013 Frederik Heber. All rights reserved.
    55 *
    66 *
    … …  
    2222
    2323/*
    24  * CalculateCellVolumeAction.cpp
     24 * getDomainVolume.cpp
    2525 *
    26  *  Created on: Oct 12, 2011
     26 *  Created on: Sep 28, 2013
    2727 *      Author: heber
    2828 */
    … …  
    3535#include "CodePatterns/MemDebug.hpp"
    3636
     37#include "modules.hpp"
     38
    3739#include "CodePatterns/Log.hpp"
    3840
    … …  
    4143#include "World.hpp"
    4244
    43 #include <iostream>
    4445#include <string>
    4546
    46 #include "CalculateCellVolumeAction.hpp"
    47 
    48 using namespace MoleCuilder;
    49 
    50 // and construct the stuff
    51 #include "CalculateCellVolumeAction.def"
    52 #include "Reaction_impl_pre.hpp"
    53 
    54 #include "Reaction_impl.hpp"
    55 
    56 /** =========== define the function ====================== */
    57 double * AnalysisCalculateCellVolumeAction::doCalc() {
     47double MoleCuilder::detail::module_getDomainVolume() {
    5848  // calculate volume from Box
    5949  Box &B = World::getInstance().getDomain();
    … …  
    6353  LOG(0, "RESULT: The current box volume is " << volume << ".");
    6454
    65   return (new double(volume));
     55  return volume;
    6656}
    67 /** =========== end of function ====================== */

  • src/Python/getSelectedMolarMass.cpp

    r0d4168 rcc6e5c  
    22 * Project: MoleCuilder
    33 * Description: creates and alters molecular systems
    4  * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
     4 * Copyright (C)  2013 Frederik Heber. All rights reserved.
    55 *
    66 *
    … …  
    2222
    2323/*
    24  * CalculateMolarMassAction.cpp
     24 * getSelectedMolarMass.cpp
    2525 *
    26  *  Created on: Nov 02, 2011
     26 *  Created on: Sep 28, 2013
    2727 *      Author: heber
    2828 */
    … …  
    3535#include "CodePatterns/MemDebug.hpp"
    3636
     37#include "modules.hpp"
     38
    3739#include "CodePatterns/Log.hpp"
    3840
    … …  
    4143#include "World.hpp"
    4244
    43 #include <iostream>
    4445#include <string>
    4546
    46 #include "CalculateMolarMassAction.hpp"
    47 
    48 using namespace MoleCuilder;
    49 
    50 // and construct the stuff
    51 #include "CalculateMolarMassAction.def"
    52 #include "Reaction_impl_pre.hpp"
    53 
    54 #include "Reaction_impl.hpp"
    55 
    56 /** =========== define the function ====================== */
    57 double * AnalysisCalculateMolarMassAction::doCalc() {
     47double MoleCuilder::detail::module_getSelectedMolarMass() {
    5848  double mass = 0.;
    5949  size_t totalnumber = 0;
    … …  
    6757  LOG(0, "RESULT: The mass of " << totalnumber << " selected atoms is " << mass << " atomicmassunit.");
    6858
    69   return (new double(mass));
     59  return mass;
    7060}
    71 /** =========== end of function ====================== */
     61
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