Changeset 69c733 for src

Timestamp:

Nov 14, 2012, 10:01:46 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:

88c2c1

Parents:

8a8c8c

git-author:

Frederik Heber <heber@…> (07/15/12 12:54:01)

git-committer:

Frederik Heber <heber@…> (11/14/12 10:01:46)

Message:

Added second part to FragmentationAutomationAction that calculates long-range part.

• we create VMGJobs, as of now with a lot of 0 as sampled_grid.
• added HAVE_VMG to compile on VMGJob only if vmg is available.
• new option DoLongrange to FragmentationAutomationAction to deactivate long-range calculations by default.

Location:

src/Actions/FragmentationAction

Files:

• FragmentationAutomationAction.cpp (modified) (3 diffs)
• FragmentationAutomationAction.def (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -61 +61 @@
 #include "Jobs/MPQCData.hpp"
 #include "Jobs/MPQCData_printKeyNames.hpp"
+#ifdef HAVE_VMG
+#include "Jobs/VMGJob.hpp"
+#endif
 #include "molecule.hpp"
 #include "World.hpp"
@@ -448 +451 @@
 }
 
+#ifdef HAVE_VMG
+bool createLongRangeJobs(
+    FragmentController &controller,
+    const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters &params,
+    const size_t NoJobs)
+{
+  const int GRID = pow(2,5);
+  std::vector<FragmentJob::ptr> jobs;
+  std::vector< double > sampled_input (GRID*GRID*GRID, 0.);
+  for (size_t i=0; i< NoJobs; ++i) {
+    const JobId_t next_id = controller.getAvailableId();
+    LOG(1, "INFO: Creating VMGJob.");
+    FragmentJob::ptr testJob( new VMGJob(next_id, sampled_input) );
+    jobs.push_back(testJob);
+  }
+  controller.addJobs(jobs);
+  controller.sendJobs(params.host.get(), params.port.get());
+  return true;
+}
+#endif
+
 void WaitforResults(
     boost::asio::io_service &io_service,
@@ -483 +507 @@
   RunService(io_service, "Requesting ids");
 
-  // Phase Two: create and add jobs
+  // Phase Two: create and add MPQCJobs
   if (!createJobsFromFiles(controller, params, jobfiles))
     return Action::failure;
-  RunService(io_service, "Adding jobs");
+  RunService(io_service, "Adding MPQCJobs");
 
   // Phase Three: calculate result
   WaitforResults(io_service, controller, params, jobfiles.size());
-
-  // Phase Three: get result
   controller.receiveResults(params.host.get(), params.port.get());
-  RunService(io_service, "Phase Four");
-
-  // Final phase: print result
+  RunService(io_service, "Requesting short-range results");
+
+  // print intermediate short-range results
   {
     LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
-    std::vector<FragmentResult::ptr> results = controller.getReceivedResults();
+    std::vector<FragmentResult::ptr> MPQCresults = controller.getReceivedResults();
     printReceivedMPQCResults(
-        results,
+        MPQCresults,
         params.path.get(),
         getNoAtomsFromAdjacencyFile(params.path.get()));
   }
+
+#ifdef HAVE_VMG
+  if (params.DoLongrange.get()) {
+  // Phase Four: obtain more ids
+  requestIds(controller, params, jobfiles.size()+1); // one more for the big job
+  RunService(io_service, "Requesting ids");
+
+  // Phase Five: create VMGJobs
+  if (!createLongRangeJobs(controller, params, jobfiles.size()+1))
+    return Action::failure;
+  RunService(io_service, "Adding VMGJobs");
+
+  // Phase Six: calculate result
+  WaitforResults(io_service, controller, params, jobfiles.size()+1);
+  controller.receiveResults(params.host.get(), params.port.get());
+  RunService(io_service, "Requesting long-range results");
+  std::vector<FragmentResult::ptr> VMGresults = controller.getReceivedResults();
+  }
+#endif
   size_t Exitflag = controller.getExitflag();
 

src/Actions/FragmentationAction/FragmentationAutomationAction.def

@@ -20 +20 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::vector< boost::filesystem::path >)(std::string)(std::string)(std::string)(boost::filesystem::path)
-#define paramtokens ("fragment-jobs")("fragment-path")("server-address")("server-port")("fragment-executable")
-#define paramdescriptions ("vector of fragment files")("prefix of each fragment file")("hostname of server")("controller port of server")("executable to launch on clients")
-#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT("127.0.0.1"))(PARAM_DEFAULT("1026"))(NOPARAM_DEFAULT)
-#define paramreferences (jobfiles)(path)(host)(port)(executable)
+#define paramtypes (std::vector< boost::filesystem::path >)(std::string)(std::string)(std::string)(boost::filesystem::path)(bool)
+#define paramtokens ("fragment-jobs")("fragment-path")("server-address")("server-port")("fragment-executable")("DoLongrange")
+#define paramdescriptions ("vector of fragment files")("prefix of each fragment file")("hostname of server")("controller port of server")("executable to launch on clients")("whether to calculate long-range contributions")
+#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT("127.0.0.1"))(PARAM_DEFAULT("1026"))(NOPARAM_DEFAULT)(PARAM_DEFAULT("0"))
+#define paramreferences (jobfiles)(path)(host)(port)(executable)(DoLongrange)
 #define paramvalids \
 (STLVectorValidator< std::vector< boost::filesystem::path > >(ParserFileValidator() && FilePresentValidator())) \
@@ -30 +30 @@
 (DummyValidator< std::string >()) \
 (DummyValidator< std::string >()) \
-(DummyValidator< boost::filesystem::path >())
+(DummyValidator< boost::filesystem::path >()) \
+(DummyValidator< bool >())
 
 #undef statetypes