Changeset e9dc19

Timestamp:

Sep 26, 2012, 5:24:47 PM (13 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:

52cac0

Parents:

43f2278

git-author:

Frederik Heber <heber@…> (08/06/12 17:20:15)

git-committer:

Frederik Heber <heber@…> (09/26/12 17:24:47)

Message:

FIX: MpqcParser now does not center the written set of atoms anymore.

• This allows placing the molecule within the grid of the simulation domain.
• TESTFIX: adapted ParserMpqcUnitTest due to changed coordinates.
• TESTFIX: regression tests Parser/Mpqc and Atoms/Add due to changed coordinates.

Files:

• src/Parser/MpqcParser.cpp (modified) (1 diff)
• src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) (4 diffs)
• tests/regression/Atoms/Add/post/test.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/doublewater.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/test.in (modified) (1 diff)

src/Parser/MpqcParser.cpp

@@ -235 +235 @@
 
   // calculate center
-  for (std::vector<atom *>::const_iterator runner = atoms.begin();runner != atoms.end(); ++runner)
-    center += (*runner)->getPosition();
-  center.Scale(1./(double)atoms.size());
+//  for (std::vector<atom *>::const_iterator runner = atoms.begin();runner != atoms.end(); ++runner)
+//    center += (*runner)->getPosition();
+//  center.Scale(1./(double)atoms.size());
+  center.Zero();
 
   // first without hessian

src/Parser/unittests/ParserMpqcUnitTest.cpp

@@ -59 +59 @@
 \tunit = angstrom\n\
 \t{ atoms geometry } = {\n\
-\t\tO [ -0.505735\t0\t0 ]\n\
-\t\tH [ 0.252867\t0\t0.504284 ]\n\
-\t\tH [ 0.252867\t0\t-0.504284 ]\n\
+\t\tO [ 0\t0\t0 ]\n\
+\t\tH [ 0.758602\t0\t0.504284 ]\n\
+\t\tH [ 0.758602\t0\t-0.504284 ]\n\
 \t}\n\
 )\n\
@@ -83 +83 @@
 \tunit = angstrom\n\
 \t{ atoms geometry } = {\n\
-\t\tO [ -0.505735\t0\t0 ]\n\
-\t\tH [ 0.252867\t0\t0.504284 ]\n\
-\t\tH [ 0.252867\t0\t-0.504284 ]\n\
+\t\tO [ 0\t0\t0 ]\n\
+\t\tH [ 0.758602\t0\t0.504284 ]\n\
+\t\tH [ 0.758602\t0\t-0.504284 ]\n\
 \t}\n\
 )\n\
@@ -111 +111 @@
 \tunit = angstrom\n\
 \t{ atoms geometry } = {\n\
-\t\tO [ -0.505735\t0\t0 ]\n\
-\t\tH [ 0.252867\t0\t0.504284 ]\n\
-\t\tH [ 0.252867\t0\t-0.504284 ]\n\
+\t\tO [ 0\t0\t0 ]\n\
+\t\tH [ 0.758602\t0\t0.504284 ]\n\
+\t\tH [ 0.758602\t0\t-0.504284 ]\n\
 \t}\n\
 )\n\
@@ -144 +144 @@
 \tunit = angstrom\n\
 \t{ atoms geometry } = {\n\
-\t\tO [ -0.505735\t0\t0 ]\n\
-\t\tH [ 0.252867\t0\t0.504284 ]\n\
-\t\tH [ 0.252867\t0\t-0.504284 ]\n\
+\t\tO [ 0\t0\t0 ]\n\
+\t\tH [ 0.758602\t0\t0.504284 ]\n\
+\t\tH [ 0.758602\t0\t-0.504284 ]\n\
 \t}\n\
 )\n\

tests/regression/Atoms/Add/post/test.in

@@ -18 +18 @@
         unit = angstrom
         { atoms geometry } = {
-                H [ 0   0       0 ]
+                H [ 10  10      10 ]
         }
 )

tests/regression/Parser/Mpqc/post/doublewater.in

@@ -18 +18 @@
         unit = angstrom
         { atoms geometry } = {
-                O [ -1.506      0       0 ]
-                H [ -0.747      0       0.504 ]
-                H [ -0.747      0       -0.504 ]
-                O [ 0.494       0       0 ]
-                H [ 1.253       0       0.504 ]
-                H [ 1.253       0       -0.504 ]
+                O [ -0.506      0       0 ]
+                H [ 0.253       0       0.504 ]
+                H [ 0.253       0       -0.504 ]
+                O [ 1.494       0       0 ]
+                H [ 2.253       0       0.504 ]
+                H [ 2.253       0       -0.504 ]
         }
 )

tests/regression/Parser/Mpqc/post/test.in

@@ -18 +18 @@
         unit = angstrom
         { atoms geometry } = {
-                H [ 0   0       0 ]
+                H [ 10  10      10 ]
         }
 )