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Changeset 505d05

Timestamp:

Oct 31, 2011, 11:48:46 AM (14 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:

e65878

Parents:

72105a

git-author:

Frederik Heber <heber@…> (05/11/11 16:14:56)

git-committer:

Frederik Heber <heber@…> (10/31/11 11:48:46)

Message:

DipoleAngularCorrelation: output now contains name _and position_ of first atom of dipole molecule.

TESTFIX: Had to change _values...dat files accordingly.

Files:

: 39 edited

src/Analysis/analysis_correlation.cpp (modified) (5 diffs)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_X.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0000.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0002.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0004.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0005.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0006.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0009.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0010.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0011.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0012.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0014.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0015.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0016.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0017.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0019.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0020.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0021.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0022.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0023.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0024.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0025.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0026.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0029.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0031.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0032.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0034.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat (modified) (1 diff)
tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) (4 diffs)

Legend:

: Unmodified
: Added
: Removed

src/Analysis/analysis_correlation.cpp

-              r72105a
+              r505d05
 #include <iostream>
 #include <iomanip>
+#include <limits>
 #include "atom.hpp"
 …
   // get highest trajectory size
   LOG(0,"STATUS: Retrieving maximum amount of time steps ...");
+  size_t max_timesteps = 0;
+  size_t min_timesteps = -1;
+  if (atoms.size() == 0)
+    return range<size_t>(0,0);
+  size_t max_timesteps = std::numeric_limits<size_t>::min();
+  size_t min_timesteps = std::numeric_limits<size_t>::max();
   BOOST_FOREACH(atom *_atom, atoms) {
     if (_atom->getTrajectorySize() > max_timesteps)
       max_timesteps  = _atom->getTrajectorySize();
     if ((_atom->getTrajectorySize() <= max_timesteps) && (min_timesteps == (size_t)-1))
+    if (_atom->getTrajectorySize() < min_timesteps)
       min_timesteps = _atom->getTrajectorySize();
+  }
 …
   // set time step
+  LOG(0,"STATUS: Stepping onto to time step " << timestep << ".");
   World::getInstance().setTime(timestep);
   // get all molecules for this time step
   LOG(0,"STATUS: Gathering molecules for time step " << timestep << " ...");
+  LOG(0,"STATUS: Gathering molecules from " << atoms.size() << " atoms for time step " << timestep << " ...");
   std::set<molecule *> molecules;
   BOOST_FOREACH(atom *_atom, atoms)
 …
   // calculate dipoles for each
   LOG(0,"STATUS: Calculating dipoles for time step " << timestep << " ...");
+  LOG(0,"STATUS: Calculating dipoles for " << molecules.size() << " molecules for time step " << timestep << " ...");
   size_t i=0;
   BOOST_FOREACH(molecule *_mol, molecules) {
     const Vector Dipole = getDipole(_mol->begin(), _mol->end());
     LOG(2,"INFO: Dipole vector at time step " << timestep << " for for molecule "
+    LOG(2,"INFO: Dipole vector at time step " << timestep << " for molecule "
         << _mol->getId() << " is " << Dipole);
     molecule::const_iterator iter = _mol->begin();
 …
 void OutputDipoleAngularCorrelation_Value( ofstream * const file, DipoleAngularCorrelationMap::const_iterator &runner )
+{
   *file << runner->second->getName();
+  *file << *(runner->second);
 };

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_X.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		0 0 0 O1
	2	0 0 0 O1,(0,0,0)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0000.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		0 0 0 O1
	2	0 0 0 O1,(0,0,0)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0001.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		19.988355 0 0 O1
	2	19.988355 0 0 O1,(0.005,0,-0.029)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0002.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		29.965633 0 0 O1
	2	29.965633 0 0 O1,(0.011,0,-0.042)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0003.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		39.9495 0 0 O1
	2	39.9495 0 0 O1,(0.019,0,-0.054)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0004.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		49.902784 0 0 O1
	2	49.902784 0 0 O1,(0.029,0,-0.064)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0005.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		59.912167 0 0 O1
	2	59.912167 0 0 O1,(0.041,0,-0.073)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0006.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		69.875251 0 0 O1
	2	69.875251 0 0 O1,(0.054,0,-0.079)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0007.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		79.865555 0 0 O1
	2	79.865555 0 0 O1,(0.068,0,-0.083)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0008.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		89.89515 0 0 O1
	2	89.89515 0 0 O1,(0.083,0,-0.084)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0009.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		99.906381 0 0 O1
	2	99.906381 0 0 O1,(0.098,0,-0.083)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0010.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		109.87721 0 0 O1
	2	109.87721 0 0 O1,(0.112,0,-0.079)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0011.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		119.86589 0 0 O1
	2	119.86589 0 0 O1,(0.125,0,-0.073)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0012.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		129.84549 0 0 O1
	2	129.84549 0 0 O1,(0.137,0,-0.065)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0013.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		139.83507 0 0 O1
	2	139.83507 0 0 O1,(0.148,0,-0.055)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0014.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		149.86497 0 0 O1
	2	149.86497 0 0 O1,(0.157,0,-0.043)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0015.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		159.84406 0 0 O1
	2	159.84406 0 0 O1,(0.163,0,-0.03)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0016.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		169.85203 0 0 O1
	2	169.85203 0 0 O1,(0.167,0,-0.016)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0017.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		179.86908 0 0 O1
	2	179.86908 0 0 O1,(0.168,0,-0.001)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0018.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		170.11885 0 0 O1
	2	170.11885 0 0 O1,(0.167,0,0.014)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0019.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		160.12587 0 0 O1
	2	160.12587 0 0 O1,(0.163,0,0.028)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0020.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		150.15625 0 0 O1
	2	150.15625 0 0 O1,(0.157,0,0.041)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0021.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		140.19504 0 0 O1
	2	140.19504 0 0 O1,(0.149,0,0.053)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0022.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		130.19256 0 0 O1
	2	130.19256 0 0 O1,(0.139,0,0.064)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0023.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		120.1801 0 0 O1
	2	120.1801 0 0 O1,(0.127,0,0.073)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0024.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		110.19844 0 0 O1
	2	110.19844 0 0 O1,(0.114,0,0.079)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0025.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		100.20052 0 0 O1
	2	100.20052 0 0 O1,(0.1,0,0.083)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0026.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		90.191972 0 0 O1
	2	90.191972 0 0 O1,(0.085,0,0.084)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0027.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		80.186503 0 0 O1
	2	80.186503 0 0 O1,(0.07,0,0.083)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0028.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		70.198098 0 0 O1
	2	70.198098 0 0 O1,(0.056,0,0.079)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0029.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		60.230824 0 0 O1
	2	60.230824 0 0 O1,(0.043,0,0.073)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0030.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		50.269692 0 0 O1
	2	50.269692 0 0 O1,(0.031,0,0.065)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0031.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		40.265045 0 0 O1
	2	40.265045 0 0 O1,(0.02,0,0.055)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0032.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		30.279625 0 0 O1
	2	30.279625 0 0 O1,(0.011,0,0.043)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0033.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		20.309244 0 0 O1
	2	20.309244 0 0 O1,(0.005,0,0.03)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0034.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		10.334328 0 0 O1
	2	10.334328 0 0 O1,(0.001,0,0.016)

tests/regression/Analysis/DipoleAngularCorrelation/post/water_values_Y.0035.dat

r72105a	r505d05
1	1	BinStart BinCenter BinEnd FirstAtomOfMolecule
2		0.31401001 0 0 O1
	2	0.31401001 0 0 O1,(-0,0,0.001)

tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at

-              r72105a
+              r505d05
 AT_KEYWORDS([analysis dipole correlation pdb dipole-angular-correlation])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.pdb .], 0)
 AT_CHECK([../../molecuilder -v 4 -i watermulti_X.pdb -o pdb --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values --bin-output-file water_histogram], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -v 4 -i watermulti_X.pdb -o pdb -I --select-all-atoms --dipole-angular-correlation H2O --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values --bin-output-file water_histogram], 0, [stdout], [stderr])
 i=0; while test $i -ne 36; do
         step=`printf %04d $i`
 …
 AT_KEYWORDS([analysis dipole correlation pdb dipole-angular-correlation])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.pdb .], 0)
 AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.pdb -o pdb --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values --bin-output-file water_histogram], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.pdb -o pdb -I --select-all-atoms --dipole-angular-correlation H2O --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values --bin-output-file water_histogram], 0, [stdout], [stderr])
 i=0; while test $i -ne 36; do
         step=`printf %04d $i`
 …
 AT_KEYWORDS([analysis dipole correlation xyz dipole-angular-correlation])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz .], 0)
 AT_CHECK([../../molecuilder -v 4 -i watermulti_X.xyz -o xyz -I --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values --bin-output-file water_histogram], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -v 4 -i watermulti_X.xyz -o xyz -I --select-all-atoms --dipole-angular-correlation H2O --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values --bin-output-file water_histogram], 0, [stdout], [stderr])
 i=0; while test $i -ne 36; do
         step=`printf %04d $i`
 …
 AT_KEYWORDS([analysis dipole correlation xyz dipole-angular-correlation])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz .], 0)
 AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.xyz -o xyz -I --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values --bin-output-file water_histogram], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.xyz -o xyz -I --select-all-atoms --dipole-angular-correlation H2O --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values --bin-output-file water_histogram], 0, [stdout], [stderr])
 i=0; while test $i -ne 36; do
         step=`printf %04d $i`

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