Changeset 36bb2d for src/Jobs

Timestamp:

Nov 20, 2012, 11:04:12 AM (12 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:

a22e05

Parents:

cebac0 (diff), a1436b (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'VMGJob_SamplingNucleiCharges' into Candidate_v1.3.5

Location:

src/Jobs

Files:

• Grid/Makefile.am (added)
• Grid/SamplingGrid.cpp (added)
• Grid/SamplingGrid.hpp (added)
• Grid/SamplingGridProperties.cpp (added)
• Grid/SamplingGridProperties.hpp (added)
• Grid/unittests/Makefile.am (added)
• Grid/unittests/SamplingGridPropertiesUnitTest.cpp (added)
• Grid/unittests/SamplingGridPropertiesUnitTest.hpp (added)
• Grid/unittests/SamplingGridUnitTest.cpp (added)
• Grid/unittests/SamplingGridUnitTest.hpp (added)
• InterfaceVMGJob.cpp (added)
• InterfaceVMGJob.hpp (added)
• MPQCData.cpp (modified) (1 diff)
• MPQCData.hpp (modified) (4 diffs)
• MPQCDataFused.hpp (modified) (1 diff)
• MPQCDataMap.hpp (modified) (2 diffs)
• MPQCData_printKeyNames.hpp (modified) (1 diff)
• MPQCJob.cpp (modified) (1 diff)
• MPQCJob.hpp (modified) (4 diffs)
• Makefile.am (modified) (2 diffs)
• VMGData.cpp (added)
• VMGData.hpp (added)
• VMGJob.cpp (added)
• VMGJob.hpp (added)

src/Jobs/MPQCData.cpp

@@ -42 +42 @@
 #include "CodePatterns/Log.hpp"
 #include "LinearAlgebra/defs.hpp"
+
+MPQCData::MPQCData(const SamplingGridProperties &_props) :
+  sampled_grid(_props)
+{}
+
+MPQCData::MPQCData()
+{}
 
 MPQCData::energy_t::energy_t() :

src/Jobs/MPQCData.hpp

@@ -20 +20 @@
 #include <vector>
 
+#include "Jobs/Grid/SamplingGrid.hpp"
+
 class MPQCCommandJob;
 class MPQCCommandJobTest;
@@ -37 +39 @@
   friend std::ostream & operator<<(std::ostream &ost, const MPQCData &data);
 public:
+  /** Constructor for class MPQCData with full sampling information.
+   *
+   * \param _props properties of the grid
+   */
+  MPQCData(const SamplingGridProperties &_props);
+
+  /** Default Constructor for class MPQCData.
+   *
+   */
+  MPQCData();
+
   bool operator==(const MPQCData &other) const;
 
@@ -66 +79 @@
   std::vector< vector_type  > forces;
 
+  /// Density
+  SamplingGrid sampled_grid;
+
+  // nuclei positions and charges
+  std::vector< std::vector<double> > positions;
+  std::vector<double> charges;
+
   /// Timing structure
   struct times_t {
@@ -94 +114 @@
     ar & energies.eigenvalues;
     ar & forces;
+    ar & sampled_grid;
+    ar & positions;
+    ar & charges;
     ar & times.walltime;
     ar & times.cputime;

src/Jobs/MPQCDataFused.hpp

@@ -37 +37 @@
   struct forces {};
 
+  // keys for sampled_grid
+  struct sampled_grid {};
+
   // keys for times_t
   struct times_walltime {};

src/Jobs/MPQCDataMap.hpp

@@ -21 +21 @@
 class Histogram;
 class IndexedVectors;
+class SamplingGrid;
 
 /// \note: We had to split up the map because boost::fusion only allows for
@@ -72 +73 @@
 
 /** This boost::fusion map defines key-value or rather key-type pairs with
+ * which we associate all sampled_grid data members in MPQCData and their type.
+ *
+ * This lets us resolves any ambiguitites of types in MPQCData, e.g.
+ * to know vector<double> is forces or energy_eigenvalues.
+ *
+ */
+typedef boost::fusion::map<
+    boost::fusion::pair<MPQCDataFused::sampled_grid, SamplingGrid >
+> MPQCDataGridMap_t;
+
+typedef boost::mpl::list<
+    MPQCDataFused::sampled_grid
+> MPQCDataGridVector_t;
+
+/** This boost::fusion map defines key-value or rather key-type pairs with
  * which we associate all times_t data members in MPQCData and their type.
  *

src/Jobs/MPQCData_printKeyNames.hpp

@@ -40 +40 @@
         (energy_eigenvalues) \
         (forces) \
+        (sampled_grid) \
         (times_walltime) \
         (times_cputime) \

src/Jobs/MPQCJob.cpp

@@ -46 +46 @@
 #include <sstream>
 
-MPQCJob::MPQCJob(const JobId_t _JobId, const std::string &_inputfile) :
+MPQCJob::MPQCJob(
+    const JobId_t _JobId,
+    const std::string &_inputfile,
+    const double _begin[3],
+    const double _size,
+    const int _level) :
   FragmentJob(_JobId),
-  inputfile(_inputfile)
+  inputfile(_inputfile),
+  grid(_begin, _size, _level)
 {}
 

src/Jobs/MPQCJob.hpp

@@ -19 +19 @@
 #include "JobMarket/Jobs/FragmentJob.hpp"
 
+#include "Jobs/Grid/SamplingGridProperties.hpp"
+
 #include <string>
 
@@ -27 +29 @@
 {
 public:
-  MPQCJob(const JobId_t _JobId, const std::string &_inputfile);
+  MPQCJob(
+      const JobId_t _JobId,
+      const std::string &_inputfile,
+      const double _begin[3],
+      const double _size,
+      const int _level);
   virtual ~MPQCJob();
 
@@ -33 +40 @@
 
 private:
-  //!> contents of the input file
+  //!> contents of inputfile
   const std::string inputfile;
+  //!> information for how to sample the density
+  const SamplingGridProperties grid;
 
 private:
@@ -48 +57 @@
     ar & boost::serialization::base_object<FragmentJob>(*this);
     ar & const_cast<std::string &>(inputfile);
+    ar & const_cast<SamplingGridProperties &>(grid);
   }
 };

src/Jobs/Makefile.am

@@ -6 +6 @@
         Jobs/MPQCData.cpp \
         Jobs/MPQCJob.cpp
+if CONDVMG
+JOBSSOURCE += \
+        Jobs/InterfaceVMGJob.cpp \
+        Jobs/VMGData.cpp \
+        Jobs/VMGJob.cpp
+endif
 
 JOBSHEADER = \
@@ -14 +20 @@
         Jobs/MPQCData_printKeyNames.hpp \
         Jobs/MPQCJob.hpp 
+if CONDVMG
+JOBSHEADER += \
+        Jobs/InterfaceVMGJob.hpp \
+        Jobs/VMGData.hpp \
+        Jobs/VMGJob.hpp
+endif
 
 lib_LTLIBRARIES += libMolecuilderJobs.la
 libMolecuilderJobs_la_includedir = $(includedir)/MoleCuilder/
 nobase_libMolecuilderJobs_la_include_HEADERS = $(JOBSHEADER)
-libMolecuilderJobs_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS}
+libMolecuilderJobs_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS)
 libMolecuilderJobs_la_LDFLAGS = $(AM_LDFLAGS) \
   $(BOOST_SERIALIZATION_LDFLAGS) \
+  $(BOOST_SYSTEM_LDFLAGS) \
   $(JobMarket_LDFLAGS) \
   $(CodePatterns_LDFLAGS)
 libMolecuilderJobs_la_SOURCES = $(JOBSSOURCE)
 libMolecuilderJobs_la_LIBADD = \
-        $(JobMarket_LIBS) \
+  libMolecuilderJobsGrid.la \
+  $(VMG_LIBS) \
+  $(JobMarket_LIBS) \
   $(BOOST_SERIALIZATION_LIBS) \
-        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
+  $(BOOST_SYSTEM_LIBS) \
+  $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
   $(CodePatterns_LIBS)
-
+if CONDVMGMPI
+libMolecuilderJobs_la_CPPFLAGS += $(MPI_CXXFLAGS)
+libMolecuilderJobs_la_LDFLAGS += $(MPI_CXXLDFLAGS)
+endif
+