Changeset e3c4c5 for src

Timestamp:

Oct 11, 2015, 7:11:38 AM (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:

4f8079

Parents:

6c30ab

git-author:

Frederik Heber <heber@…> (09/10/15 14:41:24)

git-committer:

Frederik Heber <heber@…> (10/11/15 07:11:38)

Message:

MpqcParser additionally allows to save optimization jobs.

• this is enabled via a new flag "jobtype" that can be either Default or Optimization.
• also storing "checkpoint = no" per default for all mpqc input files. This is a safety measures such that no old checkpoint files are used that reside in the same folder accidentally. This is especially important for fragment files.
• TESTFIX: changed all regression tests comparing against .in files, added new checkpoint statement.
• TESTFIX: changed unit test ParserMpqcUnitTest in the same manner.

Location:

src/Parser

Files:

• MpqcParser.cpp (modified) (2 diffs)
• MpqcParser_Parameters.cpp (modified) (3 diffs)
• MpqcParser_Parameters.hpp (modified) (4 diffs)
• unittests/ParserMpqcUnitTest.cpp (modified) (4 diffs)

src/Parser/MpqcParser.cpp

@@ -309 +309 @@
     *file << "% Created by MoleCuilder" << endl;
     *file << "mpqc: (" << endl;
+    *file << "\tcheckpoint = no" << endl;
     *file << "\tsavestate = " << getParams().getParameter(MpqcParser_Parameters::savestateParam) << endl;
     *file << "\tdo_gradient = " << getParams().getParameter(MpqcParser_Parameters::do_gradientParam) << endl;
@@ -374 +375 @@
       ELOG(0, "Unknown level of theory requested for MPQC output file.");
     }
+    const std::string jobtype = getParams().getParameter(MpqcParser_Parameters::jobtypeParam);
+    if (jobtype == getParams().getJobtypeName(MpqcParser_Parameters::Optimization)) {
+      *file << "\t% optimizer object for the molecular geometry" << endl;
+      *file << "\topt<QNewtonOpt>: (" << endl;
+      *file << "\t\tfunction = $..:mole" << endl;
+      *file << "\t\tupdate<BFGSUpdate>: ()" << endl;
+      *file << "\t\tconvergence<MolEnergyConvergence>: (" << endl;
+      *file << "\t\t\tcartesian = yes" << endl;
+      *file << "\t\t\tenergy = $..:..:mole" << endl;
+      *file << "\t\t)" << endl;
+      *file << "\t)" << endl;
+    }
     *file << ")" << endl;
     *file << "molecule<Molecule>: (" << endl;

src/Parser/MpqcParser_Parameters.cpp

@@ -69 +69 @@
     ParamNames[integrationParam] = "integration";
     ParamNames[theoryParam] = "theory";
+    ParamNames[jobtypeParam] = "jobtype";
   }
 
@@ -87 +88 @@
   //InvertMap<TheoryNamesType,TheoryLookupType>(TheoryNames,TheoryLookup);
 
+  // create Jobs parameter
+  {
+    ValidJobtypes.clear();
+    ValidJobtypes.resize(unknownJob);
+    ValidJobtypes[Default]="Default";
+    ValidJobtypes[Optimization]="Optimization";
+    appendParameter(
+        new Parameter<std::string>(
+            ParamNames[jobtypeParam],
+            ValidJobtypes,
+            ValidJobtypes[Default]));
+  }
+
   // create integration parameter
   {
@@ -177 +191 @@
 }
 
+/** Getter for name of a specific Parameter.
+ *
+ * @param param index among enum Jobtype
+ * @return name of the desired Jobtype
+ */
+const std::string &MpqcParser_Parameters::getJobtypeName(const enum Jobtype jobtype) const
+{
+  return ValidJobtypes[jobtype];
+}
+
 /** Getter for the name of specific of IntegrationMethod.
  *

src/Parser/MpqcParser_Parameters.hpp

@@ -58 +58 @@
     integrationParam,//!< integrationParam, integration method to use in MBPT2 R12
     theoryParam,     //!< theoryParam, level of theory to use
+    jobtypeParam,    //!< jobtypeParam, job type to use
     unknownParam};   //!< unknownParam, designates an unknown parameter
 
@@ -69 +70 @@
     MBPT2_R12,  //!< Moeller Plesset Perturbation Theory second order with R12 integral
     unknownTheory //!< designates an unknown theory
+  };
+
+  /** Enumeration of all known jobtypes.
+   *
+   */
+  enum Jobtype {
+    Default,       //!< standard energy and force calculation
+    Optimization,       //!< additional optimization of geometry
+    unknownJob //!< designates an unknown job
   };
 
@@ -93 +103 @@
   const std::string &getParameterName(const enum Parameters param) const;
   const std::string &getTheoryName(const enum Theory theory) const;
+  const std::string &getJobtypeName(const enum Jobtype jobtype) const;
   const std::string &getIntegrationMethodName(const enum IntegrationMethod integration) const;
 
@@ -99 +110 @@
   //!> vector with all available theories in same order as enum Theory.
   std::vector<std::string> ValidTheories;
+
+  //!> vector with all available jobtypes in same order as enum Jobs.
+  std::vector<std::string> ValidJobtypes;
 
   //!> vector with all available integration methods in same order as enum IntegrationMethod.

src/Parser/unittests/ParserMpqcUnitTest.cpp

@@ -63 +63 @@
 static string waterMpqc_CLHF ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -86 +87 @@
 static string waterMpqc_CLKS ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -110 +112 @@
 static string waterMpqc_MBPT2 ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -138 +141 @@
 static string waterMpqc_MBPT2_R12 ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\