Changeset 4e855e for src/molecule_dynamics.cpp

Timestamp:

Feb 4, 2011, 6:56:38 PM (15 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:

febef3

Parents:

fd3788

git-author:

Frederik Heber <heber@…> (02/04/11 18:54:12)

git-committer:

Frederik Heber <heber@…> (02/04/11 18:56:38)

Message:

BondGraph::LoadBondLengthTable() now accepts istream instead of const char *.

• This has been quite a lot of work because the matrix parsing is involved.
• Hence, the fix is not really clean, this should get fixed as soon as we deal with the BondGraph implementation.
• This fixes ticket #130.

File:

• src/molecule_dynamics.cpp (modified) (2 diffs)

src/molecule_dynamics.cpp

@@ -574 +574 @@
 {
   Info FunctionInfo(__func__);
-  ifstream input(file);
   string token;
   stringstream item;
@@ -582 +581 @@
 
   const int AtomCount = getAtomCount();
-  // check file
-  if (input == NULL) {
+  // parse file into ForceMatrix
+  std::ifstream input(file);
+  if ((input.good()) && (!Force.ParseMatrix(input, 0,0,0))) {
+    DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse Force Matrix file " << file << "." << endl);
+    performCriticalExit();
     return false;
-  } else {
-    // parse file into ForceMatrix
-    if (!Force.ParseMatrix(file, 0,0,0)) {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse Force Matrix file " << file << "." << endl);
-      performCriticalExit();
-      return false;
-    }
-    if (Force.RowCounter[0] != AtomCount) {
-      DoeLog(0) && (eLog()<< Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << getAtomCount() << "." << endl);
-      performCriticalExit();
-      return false;
-    }
-    // correct Forces
-    Velocity.Zero();
-    for(int i=0;i<AtomCount;i++)
-      for(int d=0;d<NDIM;d++) {
-        Velocity[d] += Force.Matrix[0][i][d+offset];
-      }
-    for(int i=0;i<AtomCount;i++)
-      for(int d=0;d<NDIM;d++) {
-        Force.Matrix[0][i][d+offset] -= Velocity[d]/static_cast<double>(AtomCount);
-      }
-    // solve a constrained potential if we are meant to
-    if (configuration.DoConstrainedMD) {
-      // calculate forces and potential
-      atom **PermutationMap = NULL;
-      ConstrainedPotentialEnergy = MinimiseConstrainedPotential(PermutationMap,configuration.DoConstrainedMD, 0, configuration.GetIsAngstroem());
-      EvaluateConstrainedForces(configuration.DoConstrainedMD, 0, PermutationMap, &Force);
-      delete[](PermutationMap);
-    }
-
-    // and perform Verlet integration for each atom with position, velocity and force vector
-    // check size of vectors
-    for_each(atoms.begin(),
-             atoms.end(),
-             boost::bind(&atom::VelocityVerletUpdate,_1,MDSteps+1, &configuration, &Force, (const size_t) 0));
-  }
+  }
+  input.close();
+  if (Force.RowCounter[0] != AtomCount) {
+    DoeLog(0) && (eLog()<< Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << getAtomCount() << "." << endl);
+    performCriticalExit();
+    return false;
+  }
+  // correct Forces
+  Velocity.Zero();
+  for(int i=0;i<AtomCount;i++)
+    for(int d=0;d<NDIM;d++) {
+      Velocity[d] += Force.Matrix[0][i][d+offset];
+    }
+  for(int i=0;i<AtomCount;i++)
+    for(int d=0;d<NDIM;d++) {
+      Force.Matrix[0][i][d+offset] -= Velocity[d]/static_cast<double>(AtomCount);
+    }
+  // solve a constrained potential if we are meant to
+  if (configuration.DoConstrainedMD) {
+    // calculate forces and potential
+    atom **PermutationMap = NULL;
+    ConstrainedPotentialEnergy = MinimiseConstrainedPotential(PermutationMap,configuration.DoConstrainedMD, 0, configuration.GetIsAngstroem());
+    EvaluateConstrainedForces(configuration.DoConstrainedMD, 0, PermutationMap, &Force);
+    delete[](PermutationMap);
+  }
+
+  // and perform Verlet integration for each atom with position, velocity and force vector
+  // check size of vectors
+  for_each(atoms.begin(),
+           atoms.end(),
+           boost::bind(&atom::VelocityVerletUpdate,_1,MDSteps+1, &configuration, &Force, (const size_t) 0));
+
   // correct velocities (rather momenta) so that center of mass remains motionless
   Velocity = atoms.totalMomentumAtStep(MDSteps+1);