Changeset a9558f for src/Jobs

Timestamp:

Oct 26, 2012, 3:54:07 PM (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:

4bc75d

Parents:

28e894

git-author:

Frederik Heber <heber@…> (07/12/12 10:40:29)

git-committer:

Frederik Heber <heber@…> (10/26/12 15:54:07)

Message:

Restructured MPQCData, added times, and nuclear repulsion energy.

• constructors for MPQCData's energy_t and times_t, setting all to zero.

Location:

src/Jobs

Files:

• MPQCCommandJob.cpp (modified) (1 diff)
• MPQCCommandJob_MPQCData.cpp (modified) (3 diffs)
• MPQCCommandJob_MPQCData.hpp (modified) (3 diffs)
• MPQCJob.cpp (modified) (1 diff)
• MPQCJob.hpp (modified) (2 diffs)
• unittests/MPQCCommandJobUnitTest.cpp (modified) (1 diff)
• unittests/MPQCDataUnitTest.cpp (modified) (4 diffs)

src/Jobs/MPQCCommandJob.cpp

@@ -134 +134 @@
       tok_iter++;
       std::stringstream energystring(*tok_iter);
-      energystring >> data.energy;
+      energystring >> data.energies.total;
     }
     // ... and forces ("Total Gradient") from resultstring

src/Jobs/MPQCCommandJob_MPQCData.cpp

@@ -43 +43 @@
 #include "LinearAlgebra/defs.hpp"
 
-
-/** Constructor for class MPQCData.
- *
- */
-MPQCData::MPQCData() :
-    energy(0.)
+MPQCData::energy_t::energy_t() :
+  total(0.),
+  nuclear_repulsion(0.),
+  electron_repulsion(0.),
+  correlation(0.),
+  overlap(0.),
+  kinetic(0.),
+  hcore(0.)
 {}
 
-/** Destructor for class MPQCData.
- *
- */
-MPQCData::~MPQCData()
+MPQCData::times_t::times_t() :
+  walltime(0.),
+  cputime(0.),
+  flops(0.)
 {}
 
@@ -62 +64 @@
 bool MPQCData::operator==(const MPQCData &other) const
 {
-  if (fabs(energy - other.energy) > std::numeric_limits<double>::epsilon()) {
+  if (fabs(energies.total - other.energies.total) > std::numeric_limits<double>::epsilon()) {
     LOG(1, "INFO: Energy's in MPQCData differ: "
-        << energy << " != " << other.energy << ".");
+        << energies.total << " != " << other.energies.total << ".");
     return false;
   }
@@ -85 +87 @@
 std::ostream & operator<<(std::ostream &ost, const MPQCData &data)
 {
-  ost << "Energy: " << data.energy << "\t";
-  ost << "Forces: " << data.forces;
+  ost << "Energy: " << data.energies.total << "\t";
+  ost << "Forces: " << data.forces << "\t";
+  ost << "Times: " << data.times.walltime << ", " << data.times.cputime << ", " << data.times.flops;
   return ost;
 }

src/Jobs/MPQCCommandJob_MPQCData.hpp

@@ -37 +37 @@
   friend std::ostream & operator<<(std::ostream &ost, const MPQCData &data);
 public:
-  MPQCData();
-  ~MPQCData();
-
   bool operator==(const MPQCData &other) const;
 
@@ -46 +43 @@
   }
 
+  /// Energie structure
+  struct energy_t {
+    /** Constructor for struct energy_t, sets all to zero.
+     *
+     */
+    energy_t();
+
+    double total;
+    double nuclear_repulsion;
+    double electron_repulsion;
+    double correlation;
+    double overlap;
+    double kinetic;
+    double hcore;
+  } energies;
+
+  /// Forces
   typedef std::vector<double> vector_type;
+  std::vector< vector_type  > forces;
 
-  double energy;
-  std::vector< vector_type  > forces;
+  /// Timing structure
+  struct times_t {
+    /** Constructor for struct times_t, sets all to zero.
+     *
+     */
+    times_t();
+
+    double walltime;
+    double cputime;
+    double flops;
+  } times;
 
 private:
@@ -57 +81 @@
   void serialize(Archive& ar, const unsigned int version)
   {
-    ar & energy;
+    ar & energies.total;
+    ar & energies.nuclear_repulsion;
+    ar & energies.electron_repulsion;
+    ar & energies.correlation;
+    ar & energies.overlap;
+    ar & energies.kinetic;
+    ar & energies.hcore;
     ar & forces;
+    ar & times.walltime;
+    ar & times.cputime;
+    ar & times.flops;
   }
 };

src/Jobs/MPQCJob.cpp

@@ -46 +46 @@
 #include <sstream>
 
+MPQCJob::MPQCJob(const JobId_t _JobId, const std::string &_inputfile) :
+  FragmentJob(_JobId),
+  inputfile(_inputfile)
+{}
+
+MPQCJob::MPQCJob() :
+  FragmentJob(JobId::IllegalJob)
+{}
+
+MPQCJob::~MPQCJob()
+{}
+
 FragmentResult::ptr MPQCJob::Work()
 {

src/Jobs/MPQCJob.hpp

@@ -27 +27 @@
 {
 public:
-  MPQCJob(const JobId_t _JobId, const std::string &_inputfile) :
-    FragmentJob(_JobId),
-    inputfile(_inputfile)
-  {}
-  virtual ~MPQCJob() {}
+  MPQCJob(const JobId_t _JobId, const std::string &_inputfile);
+  virtual ~MPQCJob();
 
   FragmentResult::ptr Work();
@@ -42 +39 @@
   /** private default cstor for serialization only
    */
-  MPQCJob() :
-    FragmentJob(JobId::IllegalJob)
-  {}
+  MPQCJob();
 
   friend class boost::serialization::access;

src/Jobs/unittests/MPQCCommandJobUnitTest.cpp

@@ -110 +110 @@
   // prepare result container
   MPQCData data;
-  data.energy = -75.637499283020;
+  data.energies.total = -75.637499283020;
   std::vector<double> force;
   std::vector< std::vector<double> > forces;

src/Jobs/unittests/MPQCDataUnitTest.cpp

@@ -67 +67 @@
   data = new MPQCData;
 
-  data->energy = -37.3479855;
+  data->energies.total = -37.3479855;
   std::vector<double> force;
   std::vector< std::vector<double> > forces;
@@ -100 +100 @@
 
   // construct closer and closer pendant
-  otherData.energy = -37.3479855;
+  otherData.energies.total = -37.3479855;
   CPPUNIT_ASSERT( *data != otherData );
   std::vector<double> force;
@@ -117 +117 @@
 
   // change energy
-  otherData.energy = -4;
+  otherData.energies.total = -4;
   CPPUNIT_ASSERT( *data != otherData );
-  otherData.energy = -37.3479855;
+  otherData.energies.total = -37.3479855;
   CPPUNIT_ASSERT( *data == otherData );
 
@@ -129 +129 @@
 
   // check sensibility
-  otherData.energy -= 1e-1*std::numeric_limits<double>::epsilon();
+  otherData.energies.total -= 1e-1*std::numeric_limits<double>::epsilon();
   CPPUNIT_ASSERT( *data == otherData );
   otherData.forces[1][0] -= 1e-1*std::numeric_limits<double>::epsilon();